Daily Papers

Continual learning (CL) has remained a significant challenge for deep neural networks as learning new tasks erases previously acquired knowledge, either partially or completely. Existing solutions often rely on experience rehearsal or full model surrogates to mitigate CF. While effective, these approaches introduce substantial memory and computational overhead, limiting their scalability and applicability in real-world scenarios. To address this, we propose SPARC, a scalable CL approach that eliminates the need for experience rehearsal and full-model surrogates. By effectively combining task-specific working memories and task-agnostic semantic memory for cross-task knowledge consolidation, SPARC results in a remarkable parameter efficiency, using only 6% of the parameters required by full-model surrogates. Despite its lightweight design, SPARC achieves superior performance on Seq-TinyImageNet and matches rehearsal-based methods on various CL benchmarks. Additionally, weight re-normalization in the classification layer mitigates task-specific biases, establishing SPARC as a practical and scalable solution for CL under stringent efficiency constraints.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

In text-to-SQL task, seq-to-seq models often lead to sub-optimal performance due to limitations in their architecture. In this paper, we present a simple yet effective approach that adapts transformer-based seq-to-seq model to robust text-to-SQL generation. Instead of inducing constraint to decoder or reformat the task as slot-filling, we propose to train seq-to-seq model with Schema aware Denoising (SeaD), which consists of two denoising objectives that train model to either recover input or predict output from two novel erosion and shuffle noises. These denoising objectives acts as the auxiliary tasks for better modeling the structural data in S2S generation. In addition, we improve and propose a clause-sensitive execution guided (EG) decoding strategy to overcome the limitation of EG decoding for generative model. The experiments show that the proposed method improves the performance of seq-to-seq model in both schema linking and grammar correctness and establishes new state-of-the-art on WikiSQL benchmark. The results indicate that the capacity of vanilla seq-to-seq architecture for text-to-SQL may have been under-estimated.

Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the high variability caused by disease heterogeneity, makes it challenging to integrate snRNA-seq data from multiple sources for precise analyses. To address these challenges, we present scMamba, a pre-trained model designed to improve the quality and utility of snRNA-seq analysis, with a particular focus on neurodegenerative diseases. Inspired by the recent Mamba model, scMamba introduces a novel architecture that incorporates a linear adapter layer, gene embeddings, and bidirectional Mamba blocks, enabling efficient processing of snRNA-seq data while preserving information from the raw input. Notably, scMamba learns generalizable features of cells and genes through pre-training on snRNA-seq data, without relying on dimension reduction or selection of highly variable genes. We demonstrate that scMamba outperforms benchmark methods in various downstream tasks, including cell type annotation, doublet detection, imputation, and the identification of differentially expressed genes.

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

We introduce xGen-small, a family of 4B and 9B Transformer decoder models optimized for long-context applications. Our vertically integrated pipeline unites domain-balanced, frequency-aware data curation; multi-stage pre-training with quality annealing and length extension to 128k tokens; and targeted post-training via supervised fine-tuning, preference learning, and online reinforcement learning. xGen-small delivers strong performance across various tasks, especially in math and coding domains, while excelling at long context benchmarks.

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

MIDOG 2025 Track 1 requires mitosis detection in whole-slideimages (WSIs) containing non-tumor, inflamed, and necrotic re-gions. Due to the complicated and heterogeneous context, aswell as possible artifacts, there are often false positives and falsenegatives, thus degrading the detection F1-score. To addressthis problem, we propose a two-stage framework. Firstly, an im-proved YOLO11x, integrated with EMA attention and LSConv,is employed to generate mitosis candidates. We use a low confi-dence threshold to generate as many proposals as possible, en-suring the detection recall. Then, a ConvNeXt-Tiny classifieris employed to filter out the false positives, ensuring the detec-tion precision. Consequently, the proposed two-stage frame-work can generate a high detection F1-score. Evaluated on afused dataset comprising MIDOG++, MITOS_WSI_CCMCT,and MITOS_WSI_CMC, our framework achieves an F1-scoreof 0.882, which is 0.035 higher than the single-stage YOLO11xbaseline. This performance gain is produced by a significantprecision improvement, from 0.762 to 0.839, and a comparablerecall. On the MIDOG 2025 Track 1 preliminary test set, thealgorithm scores an F1 score of 0.7587. The code is available athttps://github.com/xxiao0304/MIDOG-2025-Track-1-of-SZTU.

In this paper, we present a simple and efficient GEC sequence tagger using a Transformer encoder. Our system is pre-trained on synthetic data and then fine-tuned in two stages: first on errorful corpora, and second on a combination of errorful and error-free parallel corpora. We design custom token-level transformations to map input tokens to target corrections. Our best single-model/ensemble GEC tagger achieves an F_{0.5} of 65.3/66.5 on CoNLL-2014 (test) and F_{0.5} of 72.4/73.6 on BEA-2019 (test). Its inference speed is up to 10 times as fast as a Transformer-based seq2seq GEC system. The code and trained models are publicly available.

Vision transformer (ViT) recently has drawn great attention in computer vision due to its remarkable model capability. However, most prevailing ViT models suffer from huge number of parameters, restricting their applicability on devices with limited resources. To alleviate this issue, we propose TinyViT, a new family of tiny and efficient small vision transformers pretrained on large-scale datasets with our proposed fast distillation framework. The central idea is to transfer knowledge from large pretrained models to small ones, while enabling small models to get the dividends of massive pretraining data. More specifically, we apply distillation during pretraining for knowledge transfer. The logits of large teacher models are sparsified and stored in disk in advance to save the memory cost and computation overheads. The tiny student transformers are automatically scaled down from a large pretrained model with computation and parameter constraints. Comprehensive experiments demonstrate the efficacy of TinyViT. It achieves a top-1 accuracy of 84.8% on ImageNet-1k with only 21M parameters, being comparable to Swin-B pretrained on ImageNet-21k while using 4.2 times fewer parameters. Moreover, increasing image resolutions, TinyViT can reach 86.5% accuracy, being slightly better than Swin-L while using only 11% parameters. Last but not the least, we demonstrate a good transfer ability of TinyViT on various downstream tasks. Code and models are available at https://github.com/microsoft/Cream/tree/main/TinyViT.

Autoregressive next-token prediction is a standard pretraining method for large-scale language models, but its application to vision tasks is hindered by the non-sequential nature of image data, leading to cumulative errors. Most vision models employ masked autoencoder (MAE) based pretraining, which faces scalability issues. To address these challenges, we introduce TokenUnify, a novel pretraining method that integrates random token prediction, next-token prediction, and next-all token prediction. We provide theoretical evidence demonstrating that TokenUnify mitigates cumulative errors in visual autoregression. Cooperated with TokenUnify, we have assembled a large-scale electron microscopy (EM) image dataset with ultra-high resolution, ideal for creating spatially correlated long sequences. This dataset includes over 120 million annotated voxels, making it the largest neuron segmentation dataset to date and providing a unified benchmark for experimental validation. Leveraging the Mamba network inherently suited for long-sequence modeling on this dataset, TokenUnify not only reduces the computational complexity but also leads to a significant 45\% improvement in segmentation performance on downstream EM neuron segmentation tasks compared to existing methods. Furthermore, TokenUnify demonstrates superior scalability over MAE and traditional autoregressive methods, effectively bridging the gap between pretraining strategies for language and vision models. Code is available at https://github.com/ydchen0806/TokenUnify.

Spotting facial micro-expression from videos finds various potential applications in fields including clinical diagnosis and interrogation, meanwhile this task is still difficult due to the limited scale of training data. To solve this problem, this paper tries to formulate a new task called micro-expression generation and then presents a strong baseline which combines the first order motion model with facial prior knowledge. Given a target face, we intend to drive the face to generate micro-expression videos according to the motion patterns of source videos. Specifically, our new model involves three modules. First, we extract facial prior features from a region focusing module. Second, we estimate facial motion using key points and local affine transformations with a motion prediction module. Third, expression generation module is used to drive the target face to generate videos. We train our model on public CASME II, SAMM and SMIC datasets and then use the model to generate new micro-expression videos for evaluation. Our model achieves the first place in the Facial Micro-Expression Challenge 2021 (MEGC2021), where our superior performance is verified by three experts with Facial Action Coding System certification. Source code is provided in https://github.com/Necolizer/Facial-Prior-Based-FOMM.

Training native 3D texture generative models remains a fundamental yet challenging problem, largely due to the limited availability of large-scale, high-quality 3D texture datasets. This scarcity hinders generalization to real-world scenarios. To address this, most existing methods finetune foundation image generative models to exploit their learned visual priors. However, these approaches typically generate only multi-view images and rely on post-processing to produce UV texture maps -- an essential representation in modern graphics pipelines. Such two-stage pipelines often suffer from error accumulation and spatial inconsistencies across the 3D surface. In this paper, we introduce SeqTex, a novel end-to-end framework that leverages the visual knowledge encoded in pretrained video foundation models to directly generate complete UV texture maps. Unlike previous methods that model the distribution of UV textures in isolation, SeqTex reformulates the task as a sequence generation problem, enabling the model to learn the joint distribution of multi-view renderings and UV textures. This design effectively transfers the consistent image-space priors from video foundation models into the UV domain. To further enhance performance, we propose several architectural innovations: a decoupled multi-view and UV branch design, geometry-informed attention to guide cross-domain feature alignment, and adaptive token resolution to preserve fine texture details while maintaining computational efficiency. Together, these components allow SeqTex to fully utilize pretrained video priors and synthesize high-fidelity UV texture maps without the need for post-processing. Extensive experiments show that SeqTex achieves state-of-the-art performance on both image-conditioned and text-conditioned 3D texture generation tasks, with superior 3D consistency, texture-geometry alignment, and real-world generalization.

Multimodal pathology-genomic analysis is critical for cancer survival prediction. However, existing approaches predominantly integrate formalin-fixed paraffin-embedded (FFPE) slides with genomic data, while neglecting the availability of other preservation slides, such as Fresh Froze (FF) slides. Moreover, as the high-resolution spatial nature of pathology data tends to dominate the cross-modality fusion process, it hinders effective multimodal fusion and leads to modality imbalance challenges between pathology and genomics. These methods also typically require complete data modalities, limiting their clinical applicability with incomplete modalities, such as missing either pathology or genomic data. In this paper, we propose a multimodal survival prediction framework that leverages hypergraph learning to effectively integrate multi-WSI information and cross-modality interactions between pathology slides and genomics data while addressing modality imbalance. In addition, we introduce a memory mechanism that stores previously learned paired pathology-genomic features and dynamically compensates for incomplete modalities. Experiments on five TCGA datasets demonstrate that our model outperforms advanced methods by over 2.3% in C-Index. Under incomplete modality scenarios, our approach surpasses pathology-only (3.3%) and gene-only models (7.9%). Code: https://github.com/MCPathology/M2Surv

Computational pathology (CPath) digitizes pathology slides into whole slide images (WSIs), enabling analysis for critical healthcare tasks such as cancer diagnosis and prognosis. However, WSIs possess extremely long sequence lengths (up to 200K), significant length variations (from 200 to 200K), and limited supervision. These extreme variations in sequence length lead to high data heterogeneity and redundancy. Conventional methods often compromise on training efficiency and optimization to preserve such heterogeneity under limited supervision. To comprehensively address these challenges, we propose a pack-based MIL framework. It packs multiple sampled, variable-length feature sequences into fixed-length ones, enabling batched training while preserving data heterogeneity. Moreover, we introduce a residual branch that composes discarded features from multiple slides into a hyperslide which is trained with tailored labels. It offers multi-slide supervision while mitigating feature loss from sampling. Meanwhile, an attention-driven downsampler is introduced to compress features in both branches to reduce redundancy. By alleviating these challenges, our approach achieves an accuracy improvement of up to 8% while using only 12% of the training time in the PANDA(UNI). Extensive experiments demonstrate that focusing data challenges in CPath holds significant potential in the era of foundation models. The code is https://github.com/FangHeng/PackMIL

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

We present the Pathways Autoregressive Text-to-Image (Parti) model, which generates high-fidelity photorealistic images and supports content-rich synthesis involving complex compositions and world knowledge. Parti treats text-to-image generation as a sequence-to-sequence modeling problem, akin to machine translation, with sequences of image tokens as the target outputs rather than text tokens in another language. This strategy can naturally tap into the rich body of prior work on large language models, which have seen continued advances in capabilities and performance through scaling data and model sizes. Our approach is simple: First, Parti uses a Transformer-based image tokenizer, ViT-VQGAN, to encode images as sequences of discrete tokens. Second, we achieve consistent quality improvements by scaling the encoder-decoder Transformer model up to 20B parameters, with a new state-of-the-art zero-shot FID score of 7.23 and finetuned FID score of 3.22 on MS-COCO. Our detailed analysis on Localized Narratives as well as PartiPrompts (P2), a new holistic benchmark of over 1600 English prompts, demonstrate the effectiveness of Parti across a wide variety of categories and difficulty aspects. We also explore and highlight limitations of our models in order to define and exemplify key areas of focus for further improvements. See https://parti.research.google/ for high-resolution images.

We study lossless acceleration for seq2seq generation with a novel decoding algorithm -- Aggressive Decoding. Unlike the previous efforts (e.g., non-autoregressive decoding) speeding up seq2seq generation at the cost of quality loss, our approach aims to yield the identical (or better) generation compared with autoregressive decoding but in a significant speedup, achieved by innovative cooperation of aggressive decoding and verification that are both efficient due to parallel computing. We propose two Aggressive Decoding paradigms for 2 kinds of seq2seq tasks: 1) For the seq2seq tasks whose inputs and outputs are highly similar (e.g., Grammatical Error Correction), we propose Input-guided Aggressive Decoding (IAD) that aggressively copies from the input sentence as drafted decoded tokens to verify in parallel; 2) For other general seq2seq tasks (e.g., Machine Translation), we propose Generalized Aggressive Decoding (GAD) that first employs an additional non-autoregressive decoding model for aggressive decoding and then verifies in parallel in the autoregressive manner. We test Aggressive Decoding on the most popular 6-layer Transformer model on GPU in multiple seq2seq tasks: 1) For IAD, we show that it can introduce a 7x-9x speedup for the Transformer in Grammatical Error Correction and Text Simplification tasks with the identical results as greedy decoding; 2) For GAD, we observe a 3x-5x speedup with the identical or even better quality in two important seq2seq tasks: Machine Translation and Abstractive Summarization. Moreover, Aggressive Decoding can benefit even more from stronger computing devices that are better at parallel computing. Given the lossless quality as well as significant and promising speedup, we believe Aggressive Decoding may potentially evolve into a de facto standard for efficient and lossless seq2seq generation in the near future.

As a powerful tool for characterizing cellular subpopulations and cellular heterogeneity, single cell RNA sequencing (scRNA-seq) technology offers advantages of high throughput and multidimensional analysis. However, the process of data acquisition is often constrained by high cost and limited sample availability. To overcome these limitations, we propose a hybrid model based on Diffusion model and White-Box transformer that aims to generate synthetic and biologically plausible scRNA-seq data. Diffusion model progressively introduce noise into the data and then recover the original data through a denoising process, a forward and reverse process that is particularly suitable for generating complex data distributions. White-Box transformer is a deep learning architecture that emphasizes mathematical interpretability. By minimizing the encoding rate of the data and maximizing the sparsity of the representation, it not only reduces the computational burden, but also provides clear insight into underlying structure. Our White-Box Diffusion Transformer combines the generative capabilities of Diffusion model with the mathematical interpretability of White-Box transformer. Through experiments using six different single-cell RNA-Seq datasets, we visualize both generated and real data using t-SNE dimensionality reduction technique, as well as quantify similarity between generated and real data using various metrics to demonstrate comparable performance of White-Box Diffusion Transformer and Diffusion Transformer in generating scRNA-seq data alongside significant improvements in training efficiency and resource utilization. Our code is available at https://github.com/lingximamo/White-Box-Diffusion-Transformer

In this work, we study the problem of Text-to-Image In-Context Learning (T2I-ICL). While Unified Multimodal LLMs (MLLMs) have advanced rapidly in recent years, they struggle with contextual reasoning in T2I-ICL scenarios. To address this limitation, we propose a novel framework that incorporates a thought process called ImageGen-CoT prior to image generation. To avoid generating unstructured ineffective reasoning steps, we develop an automatic pipeline to curate a high-quality ImageGen-CoT dataset. We then fine-tune MLLMs using this dataset to enhance their contextual reasoning capabilities. To further enhance performance, we explore test-time scale-up strategies and propose a novel hybrid scaling approach. This approach first generates multiple ImageGen-CoT chains and then produces multiple images for each chain via sampling. Extensive experiments demonstrate the effectiveness of our proposed method. Notably, fine-tuning with the ImageGen-CoT dataset leads to a substantial 80\% performance gain for SEED-X on T2I-ICL tasks. See our project page at https://ImageGen-CoT.github.io/. Code and model weights will be open-sourced.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

Various Seq2Seq learning models designed for machine translation were applied for abstractive summarization task recently. Despite these models provide high ROUGE scores, they are limited to generate comprehensive summaries with a high level of abstraction due to its degenerated attention distribution. We introduce Diverse Convolutional Seq2Seq Model(DivCNN Seq2Seq) using Determinantal Point Processes methods(Micro DPPs and Macro DPPs) to produce attention distribution considering both quality and diversity. Without breaking the end to end architecture, DivCNN Seq2Seq achieves a higher level of comprehensiveness compared to vanilla models and strong baselines. All the reproducible codes and datasets are available online.

Multiple Instance Learning (MIL) has emerged as a dominant paradigm to extract discriminative feature representations within Whole Slide Images (WSIs) in computational pathology. Despite driving notable progress, existing MIL approaches suffer from limitations in facilitating comprehensive and efficient interactions among instances, as well as challenges related to time-consuming computations and overfitting. In this paper, we incorporate the Selective Scan Space State Sequential Model (Mamba) in Multiple Instance Learning (MIL) for long sequence modeling with linear complexity, termed as MambaMIL. By inheriting the capability of vanilla Mamba, MambaMIL demonstrates the ability to comprehensively understand and perceive long sequences of instances. Furthermore, we propose the Sequence Reordering Mamba (SR-Mamba) aware of the order and distribution of instances, which exploits the inherent valuable information embedded within the long sequences. With the SR-Mamba as the core component, MambaMIL can effectively capture more discriminative features and mitigate the challenges associated with overfitting and high computational overhead. Extensive experiments on two public challenging tasks across nine diverse datasets demonstrate that our proposed framework performs favorably against state-of-the-art MIL methods. The code is released at https://github.com/isyangshu/MambaMIL.

Diffusion model, a new generative modelling paradigm, has achieved great success in image, audio, and video generation. However, considering the discrete categorical nature of text, it is not trivial to extend continuous diffusion models to natural language, and text diffusion models are less studied. Sequence-to-sequence text generation is one of the essential natural language processing topics. In this work, we apply diffusion models to approach sequence-to-sequence text generation, and explore whether the superiority generation performance of diffusion model can transfer to natural language domain. We propose SeqDiffuSeq, a text diffusion model for sequence-to-sequence generation. SeqDiffuSeq uses an encoder-decoder Transformers architecture to model denoising function. In order to improve generation quality, SeqDiffuSeq combines the self-conditioning technique and a newly proposed adaptive noise schedule technique. The adaptive noise schedule has the difficulty of denoising evenly distributed across time steps, and considers exclusive noise schedules for tokens at different positional order. Experiment results illustrate the good performance on sequence-to-sequence generation in terms of text quality and inference time.

Recently, diffusion models have emerged as a new paradigm for generative models. Despite the success in domains using continuous signals such as vision and audio, adapting diffusion models to natural language is under-explored due to the discrete nature of texts, especially for conditional generation. We tackle this challenge by proposing DiffuSeq: a diffusion model designed for sequence-to-sequence (Seq2Seq) text generation tasks. Upon extensive evaluation over a wide range of Seq2Seq tasks, we find DiffuSeq achieving comparable or even better performance than six established baselines, including a state-of-the-art model that is based on pre-trained language models. Apart from quality, an intriguing property of DiffuSeq is its high diversity during generation, which is desired in many Seq2Seq tasks. We further include a theoretical analysis revealing the connection between DiffuSeq and autoregressive/non-autoregressive models. Bringing together theoretical analysis and empirical evidence, we demonstrate the great potential of diffusion models in complex conditional language generation tasks. Code is available at https://github.com/Shark-NLP/DiffuSeq

Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and diversity of chromosomal abnormalities, requiring extensive annotation efforts, while automated methods remain task-specific and lack generalizability due to the scarcity of comprehensive datasets spanning diverse resource conditions. Here, we introduce CHROMA, a foundation model for cytogenomics, designed to overcome these challenges by learning generalizable representations of chromosomal abnormalities. Pre-trained on over 84,000 specimens (~4 million chromosomal images) via self-supervised learning, CHROMA outperforms other methods across all types of abnormalities, even when trained on fewer labelled data and more imbalanced datasets. By facilitating comprehensive mapping of instability and clonal leisons across various aberration types, CHROMA offers a scalable and generalizable solution for reliable and automated clinical analysis, reducing the annotation workload for experts and advancing precision oncology through the early detection of rare genomic abnormalities, enabling broad clinical AI applications and making advanced genomic analysis more accessible.

We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have achieved remarkable success in natural language generation, their application to DNA sequence generation remains largely underexplored. In this work, we introduce ATGC-Gen, an Automated Transformer Generator for Controllable Generation, which leverages cross-modal encoding to integrate diverse biological signals. ATGC-Gen is instantiated with both decoder-only and encoder-only transformer architectures, allowing flexible training and generation under either autoregressive or masked recovery objectives. We evaluate ATGC-Gen on representative tasks including promoter and enhancer sequence design, and further introduce a new dataset based on ChIP-Seq experiments for modeling protein binding specificity. Our experiments demonstrate that ATGC-Gen can generate fluent, diverse, and biologically relevant sequences aligned with the desired properties. Compared to prior methods, our model achieves notable improvements in controllability and functional relevance, highlighting the potential of language models in advancing programmable genomic design. The source code is released at (https://github.com/divelab/AIRS/blob/main/OpenBio/ATGC_Gen).

We propose Speculative Decoding (SpecDec), for the first time ever, to formally study exploiting the idea of speculative execution to accelerate autoregressive (AR) decoding. Speculative Decoding has two innovations: Spec-Drafter -- an independent model specially optimized for efficient and accurate drafting -- and Spec-Verification -- a reliable method for verifying the drafted tokens efficiently in the decoding paradigm. Experimental results on various seq2seq tasks including machine translation and abstractive summarization show our approach can achieve around 5times speedup for the popular Transformer architectures with comparable generation quality to beam search decoding, refreshing the impression that the draft-then-verify paradigm introduces only 1.4timessim2times speedup. In addition to the remarkable speedup, we also demonstrate 3 additional advantages of SpecDec, revealing its practical value for accelerating generative models in real-world applications. Our models and codes are available at https://github.com/hemingkx/SpecDec.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

While generative modeling has become prevalent across numerous research fields, its integration into the realm of image retrieval remains largely unexplored and underjustified. In this paper, we present a novel methodology, reframing image retrieval as a variant of generative modeling and employing a sequence-to-sequence model. This approach is harmoniously aligned with the current trend towards unification in research, presenting a cohesive framework that allows for end-to-end differentiable searching. This, in turn, facilitates superior performance via direct optimization techniques. The development of our model, dubbed IRGen, addresses the critical technical challenge of converting an image into a concise sequence of semantic units, which is pivotal for enabling efficient and effective search. Extensive experiments demonstrate that our model achieves state-of-the-art performance on three widely-used image retrieval benchmarks as well as two million-scale datasets, yielding significant improvement compared to prior competitive retrieval methods. In addition, the notable surge in precision scores facilitated by generative modeling presents the potential to bypass the reranking phase, which is traditionally indispensable in practical retrieval workflows.

As large language models (LLMs) become more prevalent, there is a growing need for new and improved quantization methods that can meet the computationalast layer demands of these modern architectures while maintaining the accuracy. In this paper, we present TEQ, a trainable equivalent transformation that preserves the FP32 precision of the model output while taking advantage of low-precision quantization, especially 3 and 4 bits weight-only quantization. The training process is lightweight, requiring only 1K steps and fewer than 0.1 percent of the original model's trainable parameters. Furthermore, the transformation does not add any computational overhead during inference. Our results are on-par with the state-of-the-art (SOTA) methods on typical LLMs. Our approach can be combined with other methods to achieve even better performance. The code is available at https://github.com/intel/neural-compressor.

Zero-shot and prompt-based technologies capitalized on using frequently occurring images to transform visual reasoning tasks, which explains why such technologies struggle with valuable yet scarce scientific image sets. In this work, we propose Zenesis, a comprehensive no-code interactive platform designed to minimize barriers posed by data readiness for scientific images. We develop lightweight multi-modal adaptation techniques that enable zero-shot operation on raw scientific data, along with human-in-the-loop refinement and heuristic-based temporal enhancement options. We demonstrate the performance of our approach through comprehensive comparison and validation on challenging Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) data of catalyst-loaded membranes. Zenesis significantly outperforms baseline methods, achieving an average accuracy of 0.947, an Intersection over Union (IOU) of 0.858, and a Dice score of 0.923 for amorphous catalyst samples and accuracy of 0.987, an IOU of 0.857, and a Dice score of 0.923 for crystalline samples. These results mark a substantial improvement over traditional methods like Otsu thresholding and even advanced models like Segment Anything Model (SAM) when used in isolation. Our results demonstrate that Zenesis is a powerful tool for scientific applications, particularly in fields where high-quality annotated datasets are unavailable, accelerating accurate analysis of experimental imaging.

Few-shot class-incremental learning (FSCIL) confronts the challenge of integrating new classes into a model with minimal training samples while preserving the knowledge of previously learned classes. Traditional methods widely adopt static adaptation relying on a fixed parameter space to learn from data that arrive sequentially, prone to overfitting to the current session. Existing dynamic strategies require the expansion of the parameter space continually, leading to increased complexity. To address these challenges, we integrate the recently proposed selective state space model (SSM) into FSCIL. Concretely, we propose a dual selective SSM projector that dynamically adjusts the projection parameters based on the intermediate features for dynamic adaptation. The dual design enables the model to maintain the robust features of base classes, while adaptively learning distinctive feature shifts for novel classes. Additionally, we develop a class-sensitive selective scan mechanism to guide dynamic adaptation. It minimizes the disruption to base-class representations caused by training on novel data, and meanwhile, forces the selective scan to perform in distinct patterns between base and novel classes. Experiments on miniImageNet, CUB-200, and CIFAR-100 demonstrate that our framework outperforms the existing state-of-the-art methods. The code is available at https://github.com/xiaojieli0903/Mamba-FSCIL.

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

Single-cell RNA sequencing (scRNA-seq) data are often confounded by technical or biological batch effects. Existing deep learning models mitigate these effects but often discard batch-specific information, potentially losing valuable biological insights. We propose a Mixed Effects Deep Learning (MEDL) autoencoder framework that separately models batch-invariant (fixed effects) and batch-specific (random effects) components. By decoupling batch-invariant biological states from batch variations, our framework integrates both into predictive models. Our approach also generates 2D visualizations of how the same cell appears across batches, enhancing interpretability. Retaining both fixed and random effect latent spaces improves classification accuracy. We applied our framework to three datasets spanning the cardiovascular system (Healthy Heart), Autism Spectrum Disorder (ASD), and Acute Myeloid Leukemia (AML). With 147 batches in the Healthy Heart dataset, far exceeding typical numbers, we tested our framework's ability to handle many batches. In the ASD dataset, our approach captured donor heterogeneity between autistic and healthy individuals. In the AML dataset, it distinguished donor heterogeneity despite missing cell types and diseased donors exhibiting both healthy and malignant cells. These results highlight our framework's ability to characterize fixed and random effects, enhance batch effect visualization, and improve prediction accuracy across diverse datasets.

This paper presents MedSegFactory, a versatile medical synthesis framework that generates high-quality paired medical images and segmentation masks across modalities and tasks. It aims to serve as an unlimited data repository, supplying image-mask pairs to enhance existing segmentation tools. The core of MedSegFactory is a dual-stream diffusion model, where one stream synthesizes medical images and the other generates corresponding segmentation masks. To ensure precise alignment between image-mask pairs, we introduce Joint Cross-Attention (JCA), enabling a collaborative denoising paradigm by dynamic cross-conditioning between streams. This bidirectional interaction allows both representations to guide each other's generation, enhancing consistency between generated pairs. MedSegFactory unlocks on-demand generation of paired medical images and segmentation masks through user-defined prompts that specify the target labels, imaging modalities, anatomical regions, and pathological conditions, facilitating scalable and high-quality data generation. This new paradigm of medical image synthesis enables seamless integration into diverse medical imaging workflows, enhancing both efficiency and accuracy. Extensive experiments show that MedSegFactory generates data of superior quality and usability, achieving competitive or state-of-the-art performance in 2D and 3D segmentation tasks while addressing data scarcity and regulatory constraints.

We introduce LlamaGen, a new family of image generation models that apply original ``next-token prediction'' paradigm of large language models to visual generation domain. It is an affirmative answer to whether vanilla autoregressive models, e.g., Llama, without inductive biases on visual signals can achieve state-of-the-art image generation performance if scaling properly. We reexamine design spaces of image tokenizers, scalability properties of image generation models, and their training data quality. The outcome of this exploration consists of: (1) An image tokenizer with downsample ratio of 16, reconstruction quality of 0.94 rFID and codebook usage of 97% on ImageNet benchmark. (2) A series of class-conditional image generation models ranging from 111M to 3.1B parameters, achieving 2.18 FID on ImageNet 256x256 benchmarks, outperforming the popular diffusion models such as LDM, DiT. (3) A text-conditional image generation model with 775M parameters, from two-stage training on LAION-COCO and high aesthetics quality images, demonstrating competitive performance of visual quality and text alignment. (4) We verify the effectiveness of LLM serving frameworks in optimizing the inference speed of image generation models and achieve 326% - 414% speedup. We release all models and codes to facilitate open-source community of visual generation and multimodal foundation models.

Despite excellent average-case performance of many image classifiers, their performance can substantially deteriorate on semantically coherent subgroups of the data that were under-represented in the training data. These systematic errors can impact both fairness for demographic minority groups as well as robustness and safety under domain shift. A major challenge is to identify such subgroups with subpar performance when the subgroups are not annotated and their occurrence is very rare. We leverage recent advances in text-to-image models and search in the space of textual descriptions of subgroups ("prompts") for subgroups where the target model has low performance on the prompt-conditioned synthesized data. To tackle the exponentially growing number of subgroups, we employ combinatorial testing. We denote this procedure as PromptAttack as it can be interpreted as an adversarial attack in a prompt space. We study subgroup coverage and identifiability with PromptAttack in a controlled setting and find that it identifies systematic errors with high accuracy. Thereupon, we apply PromptAttack to ImageNet classifiers and identify novel systematic errors on rare subgroups.

Spatial Transcriptomics (ST) technologies provide biologists with rich insights into single-cell biology by preserving spatial context of cells. Building foundational models for ST can significantly enhance the analysis of vast and complex data sources, unlocking new perspectives on the intricacies of biological tissues. However, modeling ST data is inherently challenging due to the need to extract multi-scale information from tissue slices containing vast numbers of cells. This process requires integrating macro-scale tissue morphology, micro-scale cellular microenvironment, and gene-scale gene expression profile. To address this challenge, we propose SToFM, a multi-scale Spatial Transcriptomics Foundation Model. SToFM first performs multi-scale information extraction on each ST slice, to construct a set of ST sub-slices that aggregate macro-, micro- and gene-scale information. Then an SE(2) Transformer is used to obtain high-quality cell representations from the sub-slices. Additionally, we construct SToCorpus-88M, the largest high-resolution spatial transcriptomics corpus for pretraining. SToFM achieves outstanding performance on a variety of downstream tasks, such as tissue region semantic segmentation and cell type annotation, demonstrating its comprehensive understanding of ST data through capturing and integrating multi-scale information.

Transformer-based vision models typically tokenize images into fixed-size square patches as input units, which lacks the adaptability to image content and overlooks the inherent pixel grouping structure. Inspired by the subword tokenization widely adopted in language models, we propose an image tokenizer at a subobject level, where the subobjects are represented by semantically meaningful image segments obtained by segmentation models (e.g., segment anything models). To implement a learning system based on subobject tokenization, we first introduced a Sequence-to-sequence AutoEncoder (SeqAE) to compress subobject segments of varying sizes and shapes into compact embedding vectors, then fed the subobject embeddings into a large language model for vision language learning. Empirical results demonstrated that our subobject-level tokenization significantly facilitates efficient learning of translating images into object and attribute descriptions compared to the traditional patch-level tokenization. Codes and models will be open-sourced at https://github.com/ChenDelong1999/subobjects.

We introduce BiGR, a novel conditional image generation model using compact binary latent codes for generative training, focusing on enhancing both generation and representation capabilities. BiGR is the first conditional generative model that unifies generation and discrimination within the same framework. BiGR features a binary tokenizer, a masked modeling mechanism, and a binary transcoder for binary code prediction. Additionally, we introduce a novel entropy-ordered sampling method to enable efficient image generation. Extensive experiments validate BiGR's superior performance in generation quality, as measured by FID-50k, and representation capabilities, as evidenced by linear-probe accuracy. Moreover, BiGR showcases zero-shot generalization across various vision tasks, enabling applications such as image inpainting, outpainting, editing, interpolation, and enrichment, without the need for structural modifications. Our findings suggest that BiGR unifies generative and discriminative tasks effectively, paving the way for further advancements in the field.

The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. Almost all research on large-scale biosequence transformers has focused on one domain at a time (single-omic), usually nucleotides or peptides. These models have seen incredible success in downstream tasks in each domain and have achieved particularly noteworthy breakthroughs in sequences of peptides and structural modeling. However, these single-omic models are naturally incapable of modeling multi-omic tasks, one of the most biologically critical being nucleotide-peptide interactions. We present our work training the first multi-omic nucleotide-peptide foundation models. We show that these multi-omic models (MOMs) can learn joint representations between various single-omic distributions that are emergently consistent with the Central Dogma of molecular biology, despite only being trained on unlabeled biosequences. We further demonstrate that MOMs can be fine-tuned to achieve state-of-the-art results on peptide-nucleotide interaction tasks, namely predicting the change in Gibbs free energy ({\Delta}G) of the binding interaction between a given oligonucleotide and peptide, as well as the effect on this binding interaction due to mutations in the oligonucleotide sequence ({\Delta}{\Delta}G). Remarkably, we show that multi-omic biosequence transformers emergently learn useful structural information without any prior structural training, allowing us to predict which peptide residues are most involved in the peptide-nucleotide binding interaction. Lastly, we provide evidence that multi-omic biosequence models are non-inferior to foundation models trained on single-omics distributions, suggesting a more generalized or foundational approach to building these models.

Spatial transcriptomics enables simultaneous measurement of gene expression and tissue morphology, offering unprecedented insights into cellular organization and disease mechanisms. However, the field lacks comprehensive benchmarks for evaluating multimodal learning methods that leverage both histology images and gene expression data. Here, we present HESCAPE, a large-scale benchmark for cross-modal contrastive pretraining in spatial transcriptomics, built on a curated pan-organ dataset spanning 6 different gene panels and 54 donors. We systematically evaluated state-of-the-art image and gene expression encoders across multiple pretraining strategies and assessed their effectiveness on two downstream tasks: gene mutation classification and gene expression prediction. Our benchmark demonstrates that gene expression encoders are the primary determinant of strong representational alignment, and that gene models pretrained on spatial transcriptomics data outperform both those trained without spatial data and simple baseline approaches. However, downstream task evaluation reveals a striking contradiction: while contrastive pretraining consistently improves gene mutation classification performance, it degrades direct gene expression prediction compared to baseline encoders trained without cross-modal objectives. We identify batch effects as a key factor that interferes with effective cross-modal alignment. Our findings highlight the critical need for batch-robust multimodal learning approaches in spatial transcriptomics. To accelerate progress in this direction, we release HESCAPE, providing standardized datasets, evaluation protocols, and benchmarking tools for the community

Lightweight inference is critical for biomolecular structure prediction and other downstream tasks, enabling efficient real-world deployment and inference-time scaling for large-scale applications. In this work, we address the challenge of balancing model efficiency and prediction accuracy by making several key modifications, 1) Multi-step AF3 sampler is replaced by a few-step ODE sampler, significantly reducing computational overhead for the diffusion module part during inference; 2) In the open-source Protenix framework, a subset of pairformer or diffusion transformer blocks doesn't make contributions to the final structure prediction, presenting opportunities for architectural pruning and lightweight redesign; 3) A model incorporating an ESM module is trained to substitute the conventional MSA module, reducing MSA preprocessing time. Building on these key insights, we present Protenix-Mini, a compact and optimized model designed for efficient protein structure prediction. This streamlined version incorporates a more efficient architectural design with a two-step Ordinary Differential Equation (ODE) sampling strategy. By eliminating redundant Transformer components and refining the sampling process, Protenix-Mini significantly reduces model complexity with slight accuracy drop. Evaluations on benchmark datasets demonstrate that it achieves high-fidelity predictions, with only a negligible 1 to 5 percent decrease in performance on benchmark datasets compared to its full-scale counterpart. This makes Protenix-Mini an ideal choice for applications where computational resources are limited but accurate structure prediction remains crucial.

Machine learning applications on extremely low-power devices, commonly referred to as tiny machine learning (TinyML), promises a smarter and more connected world. However, the advancement of current TinyML research is hindered by the limited size and quality of pertinent datasets. To address this challenge, we introduce Wake Vision, a large-scale, diverse dataset tailored for person detection -- the canonical task for TinyML visual sensing. Wake Vision comprises over 6 million images, which is a hundredfold increase compared to the previous standard, and has undergone thorough quality filtering. Using Wake Vision for training results in a 2.41\% increase in accuracy compared to the established benchmark. Alongside the dataset, we provide a collection of five detailed benchmark sets that assess model performance on specific segments of the test data, such as varying lighting conditions, distances from the camera, and demographic characteristics of subjects. These novel fine-grained benchmarks facilitate the evaluation of model quality in challenging real-world scenarios that are often ignored when focusing solely on overall accuracy. Through an evaluation of a MobileNetV2 TinyML model on the benchmarks, we show that the input resolution plays a more crucial role than the model width in detecting distant subjects and that the impact of quantization on model robustness is minimal, thanks to the dataset quality. These findings underscore the importance of a detailed evaluation to identify essential factors for model development. The dataset, benchmark suite, code, and models are publicly available under the CC-BY 4.0 license, enabling their use for commercial use cases.

Whole Slide Image (WSI) classification with multiple instance learning (MIL) in digital pathology faces significant computational challenges. Current methods mostly rely on extensive self-supervised learning (SSL) for satisfactory performance, requiring long training periods and considerable computational resources. At the same time, no pre-training affects performance due to domain shifts from natural images to WSIs. We introduce Snuffy architecture, a novel MIL-pooling method based on sparse transformers that mitigates performance loss with limited pre-training and enables continual few-shot pre-training as a competitive option. Our sparsity pattern is tailored for pathology and is theoretically proven to be a universal approximator with the tightest probabilistic sharp bound on the number of layers for sparse transformers, to date. We demonstrate Snuffy's effectiveness on CAMELYON16 and TCGA Lung cancer datasets, achieving superior WSI and patch-level accuracies. The code is available on https://github.com/jafarinia/snuffy.

Mitotic figure (MF) detection in histopathology images is challenging due to large variations in slide scanners, staining protocols, tissue types, and the presence of artifacts. This paper presents a collection of training techniques - a bag of tricks - that enable robust, real-time MF detection across diverse domains. We build on the efficient RTMDet single stage object detector to achieve high inference speed suitable for clinical deployment. Our method addresses scanner variability and tumor heterogeneity via extensive multi-domain training data, balanced sampling, and careful augmentation. Additionally, we employ targeted, hard negative mining on necrotic and debris tissue to reduce false positives. In a grouped 5-fold cross-validation across multiple MF datasets, our model achieves an F1 score between 0.78 and 0.84. On the preliminary test set of the MItosis DOmain Generalization (MIDOG) 2025 challenge, our single-stage RTMDet-S based approach reaches an F1 of 0.81, outperforming larger models and demonstrating adaptability to new, unfamiliar domains. The proposed solution offers a practical trade-off between accuracy and speed, making it attractive for real-world clinical adoption.

This report introduces PixelBytes Embedding, a novel approach for unified multimodal representation learning. Our method captures diverse inputs in a single, cohesive representation, enabling emergent properties for multimodal sequence generation, particularly for text and pixelated images. Inspired by state-of-the-art sequence models such as Image Transformers, PixelCNN, and Mamba-Bytes, PixelBytes aims to address the challenges of integrating different data types. We explore various model architectures, including Recurrent Neural Networks (RNNs), State Space Models (SSMs), and Attention-based models, focusing on bidirectional processing and our innovative PxBy embedding technique. Our experiments, conducted on a specialized PixelBytes Pok{\'e}mon dataset, demonstrate that bidirectional sequence models with PxBy embedding and convolutional layers can generate coherent multimodal sequences. This work contributes to the advancement of integrated AI models capable of understanding and generating multimodal data in a unified manner.

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include > 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Masked Generative Image Transformers (MaskGIT) have emerged as a scalable and efficient image generation framework, able to deliver high-quality visuals with low inference costs. However, MaskGIT's token unmasking scheduler, an essential component of the framework, has not received the attention it deserves. We analyze the sampling objective in MaskGIT, based on the mutual information between tokens, and elucidate its shortcomings. We then propose a new sampling strategy based on our Halton scheduler instead of the original Confidence scheduler. More precisely, our method selects the token's position according to a quasi-random, low-discrepancy Halton sequence. Intuitively, that method spreads the tokens spatially, progressively covering the image uniformly at each step. Our analysis shows that it allows reducing non-recoverable sampling errors, leading to simpler hyper-parameters tuning and better quality images. Our scheduler does not require retraining or noise injection and may serve as a simple drop-in replacement for the original sampling strategy. Evaluation of both class-to-image synthesis on ImageNet and text-to-image generation on the COCO dataset demonstrates that the Halton scheduler outperforms the Confidence scheduler quantitatively by reducing the FID and qualitatively by generating more diverse and more detailed images. Our code is at https://github.com/valeoai/Halton-MaskGIT.

Long-range dependencies are critical for understanding genomic structure and function, yet most conventional methods struggle with them. Widely adopted transformer-based models, while excelling at short-context tasks, are limited by the attention module's quadratic computational complexity and inability to extrapolate to sequences longer than those seen in training. In this work, we explore State Space Models (SSMs) as a promising alternative by benchmarking two SSM-inspired architectures, Caduceus and Hawk, on long-range genomics modeling tasks under conditions parallel to a 50M parameter transformer baseline. We discover that SSMs match transformer performance and exhibit impressive zero-shot extrapolation across multiple tasks, handling contexts 10 to 100 times longer than those seen during training, indicating more generalizable representations better suited for modeling the long and complex human genome. Moreover, we demonstrate that these models can efficiently process sequences of 1M tokens on a single GPU, allowing for modeling entire genomic regions at once, even in labs with limited compute. Our findings establish SSMs as efficient and scalable for long-context genomic analysis.

Large Multimodal Models (LMMs) demonstrate impressive capabilities. However, current benchmarks predominantly focus on image comprehension in specific domains, and these benchmarks are labor-intensive to construct. Moreover, their answers tend to be brief, making it difficult to assess the ability of LMMs to generate detailed descriptions of images. To address these limitations, we propose the MMGenBench-Pipeline, a straightforward and fully automated evaluation pipeline. This involves generating textual descriptions from input images, using these descriptions to create auxiliary images via text-to-image generative models, and then comparing the original and generated images. Furthermore, to ensure the effectiveness of MMGenBench-Pipeline, we design MMGenBench-Test, evaluating LMMs across 13 distinct image patterns, and MMGenBench-Domain, focusing on generative image performance. A thorough evaluation involving over 50 popular LMMs demonstrates the effectiveness and reliability of both the pipeline and benchmark. Our observations indicate that numerous LMMs excelling in existing benchmarks fail to adequately complete the basic tasks related to image understanding and description. This finding highlights the substantial potential for performance improvement in current LMMs and suggests avenues for future model optimization. Concurrently, MMGenBench-Pipeline can efficiently assess the performance of LMMs across diverse domains using only image inputs.

We introduce a novel meme generation system, which given any image can produce a humorous and relevant caption. Furthermore, the system can be conditioned on not only an image but also a user-defined label relating to the meme template, giving a handle to the user on meme content. The system uses a pretrained Inception-v3 network to return an image embedding which is passed to an attention-based deep-layer LSTM model producing the caption - inspired by the widely recognised Show and Tell Model. We implement a modified beam search to encourage diversity in the captions. We evaluate the quality of our model using perplexity and human assessment on both the quality of memes generated and whether they can be differentiated from real ones. Our model produces original memes that cannot on the whole be differentiated from real ones.

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

Instruction tuning, a new learning paradigm that fine-tunes pre-trained language models on tasks specified through instructions, has shown promising zero-shot performance on various natural language processing tasks. However, it has yet to be explored for vision and multimodal tasks. In this work, we introduce MUL-TIINSTRUCT, the first multimodal instruction tuning benchmark dataset that consists of 62 diverse multimodal tasks in a unified seq-to-seq format covering 10 broad categories. The tasks are derived from 21 existing open-source datasets and each task is equipped with 5 expert-written instructions. We take OFA as the base pre-trained model for multimodal instruction tuning, and to further improve its zero-shot performance, we explore multiple transfer learning strategies to leverage the large-scale NATURAL INSTRUCTIONS dataset. Experimental results demonstrate strong zero-shot performance on various unseen multimodal tasks and the benefit of transfer learning from a text-only instruction dataset. We also design a new evaluation metric - Sensitivity, to evaluate how sensitive the model is to the variety of instructions. Our results indicate that fine-tuning the model on a diverse set of tasks and instructions leads to a reduced sensitivity to variations in instructions for each task.

Although deep generative models have gained a lot of attention, most of the existing works are designed for unimodal generation. In this paper, we explore a new method for unconditional image-text pair generation. We design Multimodal Cross-Quantization VAE (MXQ-VAE), a novel vector quantizer for joint image-text representations, with which we discover that a joint image-text representation space is effective for semantically consistent image-text pair generation. To learn a multimodal semantic correlation in a quantized space, we combine VQ-VAE with a Transformer encoder and apply an input masking strategy. Specifically, MXQ-VAE accepts a masked image-text pair as input and learns a quantized joint representation space, so that the input can be converted to a unified code sequence, then we perform unconditional image-text pair generation with the code sequence. Extensive experiments show the correlation between the quantized joint space and the multimodal generation capability on synthetic and real-world datasets. In addition, we demonstrate the superiority of our approach in these two aspects over several baselines. The source code is publicly available at: https://github.com/ttumyche/MXQ-VAE.

For autoregressive (AR) modeling of high-resolution images, vector quantization (VQ) represents an image as a sequence of discrete codes. A short sequence length is important for an AR model to reduce its computational costs to consider long-range interactions of codes. However, we postulate that previous VQ cannot shorten the code sequence and generate high-fidelity images together in terms of the rate-distortion trade-off. In this study, we propose the two-stage framework, which consists of Residual-Quantized VAE (RQ-VAE) and RQ-Transformer, to effectively generate high-resolution images. Given a fixed codebook size, RQ-VAE can precisely approximate a feature map of an image and represent the image as a stacked map of discrete codes. Then, RQ-Transformer learns to predict the quantized feature vector at the next position by predicting the next stack of codes. Thanks to the precise approximation of RQ-VAE, we can represent a 256times256 image as 8times8 resolution of the feature map, and RQ-Transformer can efficiently reduce the computational costs. Consequently, our framework outperforms the existing AR models on various benchmarks of unconditional and conditional image generation. Our approach also has a significantly faster sampling speed than previous AR models to generate high-quality images.

The sequence-to-sequence (seq2seq) task aims at generating the target sequence based on the given input source sequence. Traditionally, most of the seq2seq task is resolved by the Encoder-Decoder framework which requires an encoder to encode the source sequence and a decoder to generate the target text. Recently, a bunch of new approaches have emerged that apply decoder-only language models directly to the seq2seq task. Despite the significant advancements in applying language models to the seq2seq task, there is still a lack of thorough analysis on the effectiveness of the decoder-only language model architecture. This paper aims to address this gap by conducting a detailed comparison between the encoder-decoder architecture and the decoder-only language model framework through the analysis of a regularized encoder-decoder structure. This structure is designed to replicate all behaviors in the classical decoder-only language model but has an encoder and a decoder making it easier to be compared with the classical encoder-decoder structure. Based on the analysis, we unveil the attention degeneration problem in the language model, namely, as the generation step number grows, less and less attention is focused on the source sequence. To give a quantitative understanding of this problem, we conduct a theoretical sensitivity analysis of the attention output with respect to the source input. Grounded on our analysis, we propose a novel partial attention language model to solve the attention degeneration problem. Experimental results on machine translation, summarization, and data-to-text generation tasks support our analysis and demonstrate the effectiveness of our proposed model.

Multi-omics research has enhanced our understanding of cancer heterogeneity and progression. Investigating molecular data through multi-omics approaches is crucial for unraveling the complex biological mechanisms underlying cancer, thereby enabling effective diagnosis, treatment, and prevention strategies. However, predicting patient outcomes through integration of all available multi-omics data is an under-study research direction. Here, we present SeNMo (Self-normalizing Network for Multi-omics), a deep neural network trained on multi-omics data across 33 cancer types. SeNMo is efficient in handling multi-omics data characterized by high-width (many features) and low-length (fewer samples) attributes. We trained SeNMo for the task of overall survival using pan-cancer data involving 33 cancer sites from Genomics Data Commons (GDC). The training data includes gene expression, DNA methylation, miRNA expression, DNA mutations, protein expression modalities, and clinical data. We evaluated the model's performance in predicting overall survival using concordance index (C-Index). SeNMo performed consistently well in training regime, with the validation C-Index of 0.76 on GDC's public data. In the testing regime, SeNMo performed with a C-Index of 0.758 on a held-out test set. The model showed an average accuracy of 99.8% on the task of classifying the primary cancer type on the pan-cancer test cohort. SeNMo proved to be a mini-foundation model for multi-omics oncology data because it demonstrated robust performance, and adaptability not only across molecular data types but also on the classification task of predicting the primary cancer type of patients. SeNMo can be further scaled to any cancer site and molecular data type. We believe SeNMo and similar models are poised to transform the oncology landscape, offering hope for more effective, efficient, and patient-centric cancer care.

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Contrastive self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address unique problems in pathology that involve synthesizing images; overcoming annotated data scarcity, enabling privacy-preserving data sharing, and performing inherently generative tasks, such as virtual staining. We introduce PixCell, the first diffusion-based generative foundation model for histopathology. We train PixCell on PanCan-30M, a vast, diverse dataset derived from 69,184 H\&E-stained whole slide images covering various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any annotated data. PixCell generates diverse and high-quality images across multiple cancer types, which we find can be used in place of real data to train a self-supervised discriminative model. Synthetic images shared between institutions are subject to fewer regulatory barriers than would be the case with real clinical images. Furthermore, we showcase the ability to precisely control image generation using a small set of annotated images, which can be used for both data augmentation and educational purposes. Testing on a cell segmentation task, a mask-guided PixCell enables targeted data augmentation, improving downstream performance. Finally, we demonstrate PixCell's ability to use H\&E structural staining to infer results from molecular marker studies; we use this capability to infer IHC staining from H\&E images. Our trained models are publicly released to accelerate research in computational pathology.

We introduce Seedream 4.0, an efficient and high-performance multimodal image generation system that unifies text-to-image (T2I) synthesis, image editing, and multi-image composition within a single framework. We develop a highly efficient diffusion transformer with a powerful VAE which also can reduce the number of image tokens considerably. This allows for efficient training of our model, and enables it to fast generate native high-resolution images (e.g., 1K-4K). Seedream 4.0 is pretrained on billions of text-image pairs spanning diverse taxonomies and knowledge-centric concepts. Comprehensive data collection across hundreds of vertical scenarios, coupled with optimized strategies, ensures stable and large-scale training, with strong generalization. By incorporating a carefully fine-tuned VLM model, we perform multi-modal post-training for training both T2I and image editing tasks jointly. For inference acceleration, we integrate adversarial distillation, distribution matching, and quantization, as well as speculative decoding. It achieves an inference time of up to 1.8 seconds for generating a 2K image (without a LLM/VLM as PE model). Comprehensive evaluations reveal that Seedream 4.0 can achieve state-of-the-art results on both T2I and multimodal image editing. In particular, it demonstrates exceptional multimodal capabilities in complex tasks, including precise image editing and in-context reasoning, and also allows for multi-image reference, and can generate multiple output images. This extends traditional T2I systems into an more interactive and multidimensional creative tool, pushing the boundary of generative AI for both creativity and professional applications. Seedream 4.0 is now accessible on https://www.volcengine.com/experience/ark?launch=seedream.

Unlike color photography images, which are consistently encoded into RGB channels, biological images encompass various modalities, where the type of microscopy and the meaning of each channel varies with each experiment. Importantly, the number of channels can range from one to a dozen and their correlation is often comparatively much lower than RGB, as each of them brings specific information content. This aspect is largely overlooked by methods designed out of the bioimage field, and current solutions mostly focus on intra-channel spatial attention, often ignoring the relationship between channels, yet crucial in most biological applications. Importantly, the variable channel type and count prevent the projection of several experiments to a unified representation for large scale pre-training. In this study, we propose ChAda-ViT, a novel Channel Adaptive Vision Transformer architecture employing an Inter-Channel Attention mechanism on images with an arbitrary number, order and type of channels. We also introduce IDRCell100k, a bioimage dataset with a rich set of 79 experiments covering 7 microscope modalities, with a multitude of channel types, and channel counts varying from 1 to 10 per experiment. Our proposed architecture, trained in a self-supervised manner, outperforms existing approaches in several biologically relevant downstream tasks. Additionally, it can be used to bridge the gap for the first time between assays with different microscopes, channel numbers or types by embedding various image and experimental modalities into a unified biological image representation. The latter should facilitate interdisciplinary studies and pave the way for better adoption of deep learning in biological image-based analyses. Code and Data to be released soon.

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

Sparse autoencoders (SAEs) emerged as a promising tool for mechanistic interpretability of transformer-based foundation models. Very recently, SAEs were also adopted for the visual domain, enabling the discovery of visual concepts and their patch-wise attribution to tokens in the transformer model. While a growing number of foundation models emerged for medical imaging, tools for explaining their inferences are still lacking. In this work, we show the applicability of SAEs for hematology. We propose CytoSAE, a sparse autoencoder which is trained on over 40,000 peripheral blood single-cell images. CytoSAE generalizes to diverse and out-of-domain datasets, including bone marrow cytology, where it identifies morphologically relevant concepts which we validated with medical experts. Furthermore, we demonstrate scenarios in which CytoSAE can generate patient-specific and disease-specific concepts, enabling the detection of pathognomonic cells and localized cellular abnormalities at the patch level. We quantified the effect of concepts on a patient-level AML subtype classification task and show that CytoSAE concepts reach performance comparable to the state-of-the-art, while offering explainability on the sub-cellular level. Source code and model weights are available at https://github.com/dynamical-inference/cytosae.

Generative modeling of single-cell RNA-seq data has shown invaluable potential in community-driven tasks such as trajectory inference, batch effect removal and gene expression generation. However, most recent deep models generating synthetic single cells from noise operate on pre-processed continuous gene expression approximations, ignoring the inherently discrete and over-dispersed nature of single-cell data, which limits downstream applications and hinders the incorporation of robust noise models. Moreover, crucial aspects of deep-learning-based synthetic single-cell generation remain underexplored, such as controllable multi-modal and multi-label generation and its role in the performance enhancement of downstream tasks. This work presents Cell Flow for Generation (CFGen), a flow-based conditional generative model for multi-modal single-cell counts, which explicitly accounts for the discrete nature of the data. Our results suggest improved recovery of crucial biological data characteristics while accounting for novel generative tasks such as conditioning on multiple attributes and boosting rare cell type classification via data augmentation. By showcasing CFGen on a diverse set of biological datasets and settings, we provide evidence of its value to the fields of computational biology and deep generative models.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

Remarkable strides in computational pathology have been made in the task-agnostic foundation model that advances the performance of a wide array of downstream clinical tasks. Despite the promising performance, there are still several challenges. First, prior works have resorted to either vision-only or image-caption data, disregarding pathology reports with more clinically authentic information from pathologists and gene expression profiles which respectively offer distinct knowledge for versatile clinical applications. Second, the current progress in pathology FMs predominantly concentrates on the patch level, where the restricted context of patch-level pretraining fails to capture whole-slide patterns. Even recent slide-level FMs still struggle to provide whole-slide context for patch representation. In this study, for the first time, we develop a pathology foundation model incorporating three levels of modalities: pathology slides, pathology reports, and gene expression data, which resulted in 26,169 slide-level modality pairs from 10,275 patients across 32 cancer types, amounting to over 116 million pathological patch images. To leverage these data for CPath, we propose a novel whole-slide pretraining paradigm that injects the multimodal whole-slide context into the patch representation, called Multimodal Self-TAught PRetraining (mSTAR). The proposed paradigm revolutionizes the pretraining workflow for CPath, enabling the pathology FM to acquire the whole-slide context. To the best of our knowledge, this is the first attempt to incorporate three modalities at the whole-slide context for enhancing pathology FMs. To systematically evaluate the capabilities of mSTAR, we built the largest spectrum of oncological benchmark, spanning 7 categories of oncological applications in 15 types of 97 practical oncological tasks.

Personalized image generation aims to integrate user-provided concepts into text-to-image models, enabling the generation of customized content based on a given prompt. Recent zero-shot approaches, particularly those leveraging diffusion transformers, incorporate reference image information through multi-modal attention mechanism. This integration allows the generated output to be influenced by both the textual prior from the prompt and the visual prior from the reference image. However, we observe that when the prompt and reference image are misaligned, the generated results exhibit a stronger bias toward the textual prior, leading to a significant loss of reference content. To address this issue, we propose AlignGen, a Cross-Modality Prior Alignment mechanism that enhances personalized image generation by: 1) introducing a learnable token to bridge the gap between the textual and visual priors, 2) incorporating a robust training strategy to ensure proper prior alignment, and 3) employing a selective cross-modal attention mask within the multi-modal attention mechanism to further align the priors. Experimental results demonstrate that AlignGen outperforms existing zero-shot methods and even surpasses popular test-time optimization approaches.

Diffusion models, such as Stable Diffusion, have made significant strides in visual generation, yet their paradigm remains fundamentally different from autoregressive language models, complicating the development of unified language-vision models. Recent efforts like LlamaGen have attempted autoregressive image generation using discrete VQVAE tokens, but the large number of tokens involved renders this approach inefficient and slow. In this work, we present Meissonic, which elevates non-autoregressive masked image modeling (MIM) text-to-image to a level comparable with state-of-the-art diffusion models like SDXL. By incorporating a comprehensive suite of architectural innovations, advanced positional encoding strategies, and optimized sampling conditions, Meissonic substantially improves MIM's performance and efficiency. Additionally, we leverage high-quality training data, integrate micro-conditions informed by human preference scores, and employ feature compression layers to further enhance image fidelity and resolution. Our model not only matches but often exceeds the performance of existing models like SDXL in generating high-quality, high-resolution images. Extensive experiments validate Meissonic's capabilities, demonstrating its potential as a new standard in text-to-image synthesis. We release a model checkpoint capable of producing 1024 times 1024 resolution images.

The rapid advancement of single-cell ATAC sequencing (scATAC-seq) technologies holds great promise for investigating the heterogeneity of epigenetic landscapes at the cellular level. The amplification process in scATAC-seq experiments often introduces noise due to dropout events, which results in extreme sparsity that hinders accurate analysis. Consequently, there is a significant demand for the generation of high-quality scATAC-seq data in silico. Furthermore, current methodologies are typically task-specific, lacking a versatile framework capable of handling multiple tasks within a single model. In this work, we propose ATAC-Diff, a versatile framework, which is based on a latent diffusion model conditioned on the latent auxiliary variables to adapt for various tasks. ATAC-Diff is the first diffusion model for the scATAC-seq data generation and analysis, composed of auxiliary modules encoding the latent high-level variables to enable the model to learn the semantic information to sample high-quality data. Gaussian Mixture Model (GMM) as the latent prior and auxiliary decoder, the yield variables reserve the refined genomic information beneficial for downstream analyses. Another innovation is the incorporation of mutual information between observed and hidden variables as a regularization term to prevent the model from decoupling from latent variables. Through extensive experiments, we demonstrate that ATAC-Diff achieves high performance in both generation and analysis tasks, outperforming state-of-the-art models.

Existing methods for uncertainty quantification incur massive memory and compute overhead, often requiring multiple models/inferences. Hence they are impractical on ultra-low-power KB-sized TinyML devices. To reduce overhead, prior works have proposed the use of early-exit networks as ensembles to quantify uncertainty in a single forward-pass. However, they still have a prohibitive cost for tinyML. To address these challenges, we propose QUTE, a novel resource-efficient early-exit-assisted ensemble architecture optimized for tinyML models. QUTE adds additional output blocks at the final exit of the base network and distills the knowledge of early-exits into these blocks to create a diverse and lightweight ensemble architecture. Our results show that QUTE outperforms popular prior works, and improves the quality of uncertainty estimates by 6% with 3.1x lower model size on average compared to the most relevant prior work. Furthermore, we demonstrate that QUTE is also effective in detecting co-variate shifted and out-of-distribution inputs, and shows competitive performance relative to G-ODIN, a state-of-the-art generalized OOD detector.

Image tokenization plays a critical role in reducing the computational demands of modeling high-resolution images, significantly improving the efficiency of image and multimodal understanding and generation. Recent advances in 1D latent spaces have reduced the number of tokens required by eliminating the need for a 2D grid structure. In this paper, we further advance compact discrete image representation by introducing 1D binary image latents. By representing each image as a sequence of binary vectors, rather than using traditional one-hot codebook tokens, our approach preserves high-resolution details while maintaining the compactness of 1D latents. To the best of our knowledge, our text-to-image models are the first to achieve competitive performance in both diffusion and auto-regressive generation using just 128 discrete tokens for images up to 1024x1024, demonstrating up to a 32-fold reduction in token numbers compared to standard VQ-VAEs. The proposed 1D binary latent space, coupled with simple model architectures, achieves marked improvements in speed training and inference speed. Our text-to-image models allow for a global batch size of 4096 on a single GPU node with 8 AMD MI300X GPUs, and the training can be completed within 200 GPU days. Our models achieve competitive performance compared to modern image generation models without any in-house private training data or post-training refinements, offering a scalable and efficient alternative to conventional tokenization methods.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

Efficient image tokenization with high compression ratios remains a critical challenge for training generative models. We present SoftVQ-VAE, a continuous image tokenizer that leverages soft categorical posteriors to aggregate multiple codewords into each latent token, substantially increasing the representation capacity of the latent space. When applied to Transformer-based architectures, our approach compresses 256x256 and 512x512 images using as few as 32 or 64 1-dimensional tokens. Not only does SoftVQ-VAE show consistent and high-quality reconstruction, more importantly, it also achieves state-of-the-art and significantly faster image generation results across different denoising-based generative models. Remarkably, SoftVQ-VAE improves inference throughput by up to 18x for generating 256x256 images and 55x for 512x512 images while achieving competitive FID scores of 1.78 and 2.21 for SiT-XL. It also improves the training efficiency of the generative models by reducing the number of training iterations by 2.3x while maintaining comparable performance. With its fully-differentiable design and semantic-rich latent space, our experiment demonstrates that SoftVQ-VAE achieves efficient tokenization without compromising generation quality, paving the way for more efficient generative models. Code and model are released.

In this paper, we introduce PixArt-\Sigma, a Diffusion Transformer model~(DiT) capable of directly generating images at 4K resolution. PixArt-\Sigma represents a significant advancement over its predecessor, PixArt-\alpha, offering images of markedly higher fidelity and improved alignment with text prompts. A key feature of PixArt-\Sigma is its training efficiency. Leveraging the foundational pre-training of PixArt-\alpha, it evolves from the `weaker' baseline to a `stronger' model via incorporating higher quality data, a process we term "weak-to-strong training". The advancements in PixArt-\Sigma are twofold: (1) High-Quality Training Data: PixArt-\Sigma incorporates superior-quality image data, paired with more precise and detailed image captions. (2) Efficient Token Compression: we propose a novel attention module within the DiT framework that compresses both keys and values, significantly improving efficiency and facilitating ultra-high-resolution image generation. Thanks to these improvements, PixArt-\Sigma achieves superior image quality and user prompt adherence capabilities with significantly smaller model size (0.6B parameters) than existing text-to-image diffusion models, such as SDXL (2.6B parameters) and SD Cascade (5.1B parameters). Moreover, PixArt-\Sigma's capability to generate 4K images supports the creation of high-resolution posters and wallpapers, efficiently bolstering the production of high-quality visual content in industries such as film and gaming.

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making them unable to benefit from transfer learning across families. To address this, we propose Protein Evolutionary Transformer (PoET), an autoregressive generative model of whole protein families that learns to generate sets of related proteins as sequences-of-sequences across tens of millions of natural protein sequence clusters. PoET can be used as a retrieval-augmented language model to generate and score arbitrary modifications conditioned on any protein family of interest, and can extrapolate from short context lengths to generalize well even for small families. This is enabled by a unique Transformer layer; we model tokens sequentially within sequences while attending between sequences order invariantly, allowing PoET to scale to context lengths beyond those used during training. In extensive experiments on deep mutational scanning datasets, we show that PoET outperforms existing protein language models and evolutionary sequence models for variant function prediction across proteins of all MSA depths. We also demonstrate PoET's ability to controllably generate new protein sequences.

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

Vision Language Models (VLMs) like CLIP have attracted substantial attention in pathology, serving as backbones for applications such as zero-shot image classification and Whole Slide Image (WSI) analysis. Additionally, they can function as vision encoders when combined with large language models (LLMs) to support broader capabilities. Current efforts to train pathology VLMs rely on pathology image-text pairs from platforms like PubMed, YouTube, and Twitter, which provide limited, unscalable data with generally suboptimal image quality. In this work, we leverage large-scale WSI datasets like TCGA to extract numerous high-quality image patches. We then train a large multimodal model to generate captions for these images, creating PathGen-1.6M, a dataset containing 1.6 million high-quality image-caption pairs. Our approach involves multiple agent models collaborating to extract representative WSI patches, generating and refining captions to obtain high-quality image-text pairs. Extensive experiments show that integrating these generated pairs with existing datasets to train a pathology-specific CLIP model, PathGen-CLIP, significantly enhances its ability to analyze pathological images, with substantial improvements across nine pathology-related zero-shot image classification tasks and three whole-slide image tasks. Furthermore, we construct 200K instruction-tuning data based on PathGen-1.6M and integrate PathGen-CLIP with the Vicuna LLM to create more powerful multimodal models through instruction tuning. Overall, we provide a scalable pathway for high-quality data generation in pathology, paving the way for next-generation general pathology models.

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our Species-Profile Adaptive Collaborative Experts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

This paper proposes a fundamentally new paradigm for image generation through set-based tokenization and distribution modeling. Unlike conventional methods that serialize images into fixed-position latent codes with a uniform compression ratio, we introduce an unordered token set representation to dynamically allocate coding capacity based on regional semantic complexity. This TokenSet enhances global context aggregation and improves robustness against local perturbations. To address the critical challenge of modeling discrete sets, we devise a dual transformation mechanism that bijectively converts sets into fixed-length integer sequences with summation constraints. Further, we propose Fixed-Sum Discrete Diffusion--the first framework to simultaneously handle discrete values, fixed sequence length, and summation invariance--enabling effective set distribution modeling. Experiments demonstrate our method's superiority in semantic-aware representation and generation quality. Our innovations, spanning novel representation and modeling strategies, advance visual generation beyond traditional sequential token paradigms. Our code and models are publicly available at https://github.com/Gengzigang/TokenSet.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Domain generalization is critical for real-world applications of machine learning to microscopy images, including histopathology and fluorescence imaging. Artifacts in these modalities arise through a complex combination of factors relating to tissue collection and laboratory processing, as well as factors intrinsic to patient samples. In fluorescence imaging, these artifacts stem from variations across experimental batches. The complexity and subtlety of these artifacts make the enumeration of data domains intractable. Therefore, augmentation-based methods of domain generalization that require domain identifiers and manual fine-tuning are inadequate in this setting. To overcome this challenge, we introduce ContriMix, a domain generalization technique that learns to generate synthetic images by disentangling and permuting the biological content ("content") and technical variations ("attributes") in microscopy images. ContriMix does not rely on domain identifiers or handcrafted augmentations and makes no assumptions about the input characteristics of images. We assess the performance of ContriMix on two pathology datasets dealing with patch classification and Whole Slide Image label prediction tasks respectively (Camelyon17-WILDS and RCC subtyping), and one fluorescence microscopy dataset (RxRx1-WILDS). Without any access to domain identifiers at train or test time, ContriMix performs similar or better than current state-of-the-art methods in all these datasets, motivating its usage for microscopy image analysis in real-world settings where domain information is hard to come by. The code for ContriMix can be found at https://gitlab.com/huutan86/contrimix

We study the problem of optimizing biological sequences, e.g., proteins, DNA, and RNA, to maximize a black-box score function that is only evaluated in an offline dataset. We propose a novel solution, bootstrapped training of score-conditioned generator (BootGen) algorithm. Our algorithm repeats a two-stage process. In the first stage, our algorithm trains the biological sequence generator with rank-based weights to enhance the accuracy of sequence generation based on high scores. The subsequent stage involves bootstrapping, which augments the training dataset with self-generated data labeled by a proxy score function. Our key idea is to align the score-based generation with a proxy score function, which distills the knowledge of the proxy score function to the generator. After training, we aggregate samples from multiple bootstrapped generators and proxies to produce a diverse design. Extensive experiments show that our method outperforms competitive baselines on biological sequential design tasks. We provide reproducible source code: https://github.com/kaist-silab/bootgen{https://github.com/kaist-silab/bootgen}.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

Efficient computation or approximation of Levenshtein distance, a widely-used metric for evaluating sequence similarity, has attracted significant attention with the emergence of DNA storage and other biological applications. Sequence embedding, which maps Levenshtein distance to a conventional distance between embedding vectors, has emerged as a promising solution. In this paper, a novel neural network-based sequence embedding technique using Poisson regression is proposed. We first provide a theoretical analysis of the impact of embedding dimension on model performance and present a criterion for selecting an appropriate embedding dimension. Under this embedding dimension, the Poisson regression is introduced by assuming the Levenshtein distance between sequences of fixed length following a Poisson distribution, which naturally aligns with the definition of Levenshtein distance. Moreover, from the perspective of the distribution of embedding distances, Poisson regression approximates the negative log likelihood of the chi-squared distribution and offers advancements in removing the skewness. Through comprehensive experiments on real DNA storage data, we demonstrate the superior performance of the proposed method compared to state-of-the-art approaches.

This paper presents the challenge report for the 2021 Kidney and Kidney Tumor Segmentation Challenge (KiTS21) held in conjunction with the 2021 international conference on Medical Image Computing and Computer Assisted Interventions (MICCAI). KiTS21 is a sequel to its first edition in 2019, and it features a variety of innovations in how the challenge was designed, in addition to a larger dataset. A novel annotation method was used to collect three separate annotations for each region of interest, and these annotations were performed in a fully transparent setting using a web-based annotation tool. Further, the KiTS21 test set was collected from an outside institution, challenging participants to develop methods that generalize well to new populations. Nonetheless, the top-performing teams achieved a significant improvement over the state of the art set in 2019, and this performance is shown to inch ever closer to human-level performance. An in-depth meta-analysis is presented describing which methods were used and how they faired on the leaderboard, as well as the characteristics of which cases generally saw good performance, and which did not. Overall KiTS21 facilitated a significant advancement in the state of the art in kidney tumor segmentation, and provides useful insights that are applicable to the field of semantic segmentation as a whole.

Personalized text-to-image generation has emerged as a powerful and sought-after tool, empowering users to create customized images based on their specific concepts and prompts. However, existing approaches to personalization encounter multiple challenges, including long tuning times, large storage requirements, the necessity for multiple input images per identity, and limitations in preserving identity and editability. To address these obstacles, we present PhotoVerse, an innovative methodology that incorporates a dual-branch conditioning mechanism in both text and image domains, providing effective control over the image generation process. Furthermore, we introduce facial identity loss as a novel component to enhance the preservation of identity during training. Remarkably, our proposed PhotoVerse eliminates the need for test time tuning and relies solely on a single facial photo of the target identity, significantly reducing the resource cost associated with image generation. After a single training phase, our approach enables generating high-quality images within only a few seconds. Moreover, our method can produce diverse images that encompass various scenes and styles. The extensive evaluation demonstrates the superior performance of our approach, which achieves the dual objectives of preserving identity and facilitating editability. Project page: https://photoverse2d.github.io/

Speculative decoding has emerged as a powerful method to improve latency and throughput in hosting large language models. However, most existing implementations focus on generating a single sequence. Real-world generative AI applications often require multiple responses and how to perform speculative decoding in a batched setting while preserving its latency benefits poses non-trivial challenges. This paper describes a system of batched speculative decoding that sets a new state of the art in multi-sequence generation latency and that demonstrates superior GPU utilization as well as quality of generations within a time budget. For example, for a 7.8B-size model on a single A100 GPU and with a batch size of 8, each sequence is generated at an average speed of 5.8ms per token, the overall throughput being 1.1K tokens per second. These results represent state-of-the-art latency and a 2.15X speed-up over optimized regular decoding. Within a time budget that regular decoding does not finish, our system is able to generate sequences with HumanEval Pass@First of 43% and Pass@All of 61%, far exceeding what's feasible with single-sequence speculative decoding. Our peak GPU utilization during decoding reaches as high as 15.8%, more than 3X the highest of that of regular decoding and around 10X of single-sequence speculative decoding.

Since the introduction of Vision Transformer (ViT), patchification has long been regarded as a de facto image tokenization approach for plain visual architectures. By compressing the spatial size of images, this approach can effectively shorten the token sequence and reduce the computational cost of ViT-like plain architectures. In this work, we aim to thoroughly examine the information loss caused by this patchification-based compressive encoding paradigm and how it affects visual understanding. We conduct extensive patch size scaling experiments and excitedly observe an intriguing scaling law in patchification: the models can consistently benefit from decreased patch sizes and attain improved predictive performance, until it reaches the minimum patch size of 1x1, i.e., pixel tokenization. This conclusion is broadly applicable across different vision tasks, various input scales, and diverse architectures such as ViT and the recent Mamba models. Moreover, as a by-product, we discover that with smaller patches, task-specific decoder heads become less critical for dense prediction. In the experiments, we successfully scale up the visual sequence to an exceptional length of 50,176 tokens, achieving a competitive test accuracy of 84.6% with a base-sized model on the ImageNet-1k benchmark. We hope this study can provide insights and theoretical foundations for future works of building non-compressive vision models. Code is available at https://github.com/wangf3014/Patch_Scaling.

Recent advancements in generative models have highlighted the crucial role of image tokenization in the efficient synthesis of high-resolution images. Tokenization, which transforms images into latent representations, reduces computational demands compared to directly processing pixels and enhances the effectiveness and efficiency of the generation process. Prior methods, such as VQGAN, typically utilize 2D latent grids with fixed downsampling factors. However, these 2D tokenizations face challenges in managing the inherent redundancies present in images, where adjacent regions frequently display similarities. To overcome this issue, we introduce Transformer-based 1-Dimensional Tokenizer (TiTok), an innovative approach that tokenizes images into 1D latent sequences. TiTok provides a more compact latent representation, yielding substantially more efficient and effective representations than conventional techniques. For example, a 256 x 256 x 3 image can be reduced to just 32 discrete tokens, a significant reduction from the 256 or 1024 tokens obtained by prior methods. Despite its compact nature, TiTok achieves competitive performance to state-of-the-art approaches. Specifically, using the same generator framework, TiTok attains 1.97 gFID, outperforming MaskGIT baseline significantly by 4.21 at ImageNet 256 x 256 benchmark. The advantages of TiTok become even more significant when it comes to higher resolution. At ImageNet 512 x 512 benchmark, TiTok not only outperforms state-of-the-art diffusion model DiT-XL/2 (gFID 2.74 vs. 3.04), but also reduces the image tokens by 64x, leading to 410x faster generation process. Our best-performing variant can significantly surpasses DiT-XL/2 (gFID 2.13 vs. 3.04) while still generating high-quality samples 74x faster.

Online continual learning aims to get closer to a live learning experience by learning directly on a stream of data with temporally shifting distribution and by storing a minimum amount of data from that stream. In this empirical evaluation, we evaluate various methods from the literature that tackle online continual learning. More specifically, we focus on the class-incremental setting in the context of image classification, where the learner must learn new classes incrementally from a stream of data. We compare these methods on the Split-CIFAR100 and Split-TinyImagenet benchmarks, and measure their average accuracy, forgetting, stability, and quality of the representations, to evaluate various aspects of the algorithm at the end but also during the whole training period. We find that most methods suffer from stability and underfitting issues. However, the learned representations are comparable to i.i.d. training under the same computational budget. No clear winner emerges from the results and basic experience replay, when properly tuned and implemented, is a very strong baseline. We release our modular and extensible codebase at https://github.com/AlbinSou/ocl_survey based on the avalanche framework to reproduce our results and encourage future research.

Understanding the performance of machine learning models across diverse data distributions is critically important for reliable applications. Motivated by this, there is a growing focus on curating benchmark datasets that capture distribution shifts. While valuable, the existing benchmarks are limited in that many of them only contain a small number of shifts and they lack systematic annotation about what is different across different shifts. We present MetaShift--a collection of 12,868 sets of natural images across 410 classes--to address this challenge. We leverage the natural heterogeneity of Visual Genome and its annotations to construct MetaShift. The key construction idea is to cluster images using its metadata, which provides context for each image (e.g. "cats with cars" or "cats in bathroom") that represent distinct data distributions. MetaShift has two important benefits: first, it contains orders of magnitude more natural data shifts than previously available. Second, it provides explicit explanations of what is unique about each of its data sets and a distance score that measures the amount of distribution shift between any two of its data sets. We demonstrate the utility of MetaShift in benchmarking several recent proposals for training models to be robust to data shifts. We find that the simple empirical risk minimization performs the best when shifts are moderate and no method had a systematic advantage for large shifts. We also show how MetaShift can help to visualize conflicts between data subsets during model training.

Self-supervised deep learning has accelerated 2D natural image analysis but remains difficult to translate into 3D MRI, where data are scarce and pre-trained 2D backbones cannot capture volumetric context. We present a sequence-invariant self-supervised framework leveraging quantitative MRI (qMRI). By simulating multiple MRI contrasts from a single 3D qMRI scan and enforcing consistent representations across these contrasts, we learn anatomy-centric rather than sequence-specific features. The result is a single 3D encoder that excels across tasks and protocols. Experiments on healthy brain segmentation (IXI), stroke lesion segmentation (ARC), and MRI denoising show significant gains over baseline SSL approaches, especially in low-data settings (up to +8.3\% Dice, +4.2 dB PSNR). It also generalises to unseen sites, supporting scalable clinical use. Code and trained models are publicly available at https://github.com/liamchalcroft/contrast-squared

Recently, Stitchable Neural Networks (SN-Net) is proposed to stitch some pre-trained networks for quickly building numerous networks with different complexity and performance trade-offs. In this way, the burdens of designing or training the variable-sized networks, which can be used in application scenarios with diverse resource constraints, are alleviated. However, SN-Net still faces a few challenges. 1) Stitching from multiple independently pre-trained anchors introduces high storage resource consumption. 2) SN-Net faces challenges to build smaller models for low resource constraints. 3). SN-Net uses an unlearned initialization method for stitch layers, limiting the final performance. To overcome these challenges, motivated by the recently proposed Learngene framework, we propose a novel method called Learngene Pool. Briefly, Learngene distills the critical knowledge from a large pre-trained model into a small part (termed as learngene) and then expands this small part into a few variable-sized models. In our proposed method, we distill one pretrained large model into multiple small models whose network blocks are used as learngene instances to construct the learngene pool. Since only one large model is used, we do not need to store more large models as SN-Net and after distilling, smaller learngene instances can be created to build small models to satisfy low resource constraints. We also insert learnable transformation matrices between the instances to stitch them into variable-sized models to improve the performance of these models. Exhaustive experiments have been implemented and the results validate the effectiveness of the proposed Learngene Pool compared with SN-Net.

Generative Adversarial Networks (GAN) boast impressive capacity to generate realistic images. However, like much of the field of deep learning, they require an inordinate amount of data to produce results, thereby limiting their usefulness in generating novelty. In the same vein, recent advances in meta-learning have opened the door to many few-shot learning applications. In the present work, we propose Few-shot Image Generation using Reptile (FIGR), a GAN meta-trained with Reptile. Our model successfully generates novel images on both MNIST and Omniglot with as little as 4 images from an unseen class. We further contribute FIGR-8, a new dataset for few-shot image generation, which contains 1,548,944 icons categorized in over 18,409 classes. Trained on FIGR-8, initial results show that our model can generalize to more advanced concepts (such as "bird" and "knife") from as few as 8 samples from a previously unseen class of images and as little as 10 training steps through those 8 images. This work demonstrates the potential of training a GAN for few-shot image generation and aims to set a new benchmark for future work in the domain.

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

Extracting single-cell information from microscopy data requires accurate instance-wise segmentations. Obtaining pixel-wise segmentations from microscopy imagery remains a challenging task, especially with the added complexity of microstructured environments. This paper presents a novel dataset for segmenting yeast cells in microstructures. We offer pixel-wise instance segmentation labels for both cells and trap microstructures. In total, we release 493 densely annotated microscopy images. To facilitate a unified comparison between novel segmentation algorithms, we propose a standardized evaluation strategy for our dataset. The aim of the dataset and evaluation strategy is to facilitate the development of new cell segmentation approaches. The dataset is publicly available at https://christophreich1996.github.io/yeast_in_microstructures_dataset/ .

Spatial transcriptomics (ST) enables interrogating the molecular composition of tissue with ever-increasing resolution, depth, and sensitivity. However, costs, rapidly evolving technology, and lack of standards have constrained computational methods in ST to narrow tasks and small cohorts. In addition, the underlying tissue morphology as reflected by H&E-stained whole slide images (WSIs) encodes rich information often overlooked in ST studies. Here, we introduce HEST-1k, a collection of 1,108 spatial transcriptomic profiles, each linked to a WSI and metadata. HEST-1k was assembled using HEST-Library from 131 public and internal cohorts encompassing 25 organs, two species (Homo Sapiens and Mus Musculus), and 320 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 1.5 million expression--morphology pairs and 60 million nuclei. HEST-1k is tested on three use cases: (1) benchmarking foundation models for histopathology (HEST-Benchmark), (2) biomarker identification, and (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed via https://github.com/mahmoodlab/hest.

Flow matching and diffusion models have shown impressive results in text-to-image generation, producing photorealistic images through an iterative denoising process. A common strategy to speed up synthesis is to perform early denoising at lower resolutions. However, traditional methods that downscale and upscale in pixel space often introduce artifacts and distortions. These issues arise when the upscaled images are re-encoded into the latent space, leading to degraded final image quality. To address this, we propose {\bf Latent Space Scaling Generation (LSSGen)}, a framework that performs resolution scaling directly in the latent space using a lightweight latent upsampler. Without altering the Transformer or U-Net architecture, LSSGen improves both efficiency and visual quality while supporting flexible multi-resolution generation. Our comprehensive evaluation covering text-image alignment and perceptual quality shows that LSSGen significantly outperforms conventional scaling approaches. When generating 1024^2 images at similar speeds, it achieves up to 246\% TOPIQ score improvement.

Cancer is a genetic disorder whose clonal evolution can be monitored by tracking noisy genome-wide copy number variants. We introduce the Copy Number Stochastic Block Model (CN-SBM), a probabilistic framework that jointly clusters samples and genomic regions based on discrete copy number states using a bipartite categorical block model. Unlike models relying on Gaussian or Poisson assumptions, CN-SBM respects the discrete nature of CNV calls and captures subpopulation-specific patterns through block-wise structure. Using a two-stage approach, CN-SBM decomposes CNV data into primary and residual components, enabling detection of both large-scale chromosomal alterations and finer aberrations. We derive a scalable variational inference algorithm for application to large cohorts and high-resolution data. Benchmarks on simulated and real datasets show improved model fit over existing methods. Applied to TCGA low-grade glioma data, CN-SBM reveals clinically relevant subtypes and structured residual variation, aiding patient stratification in survival analysis. These results establish CN-SBM as an interpretable, scalable framework for CNV analysis with direct relevance for tumor heterogeneity and prognosis.

Recent text-to-image diffusion models are able to learn and synthesize images containing novel, personalized concepts (e.g., their own pets or specific items) with just a few examples for training. This paper tackles two interconnected issues within this realm of personalizing text-to-image diffusion models. First, current personalization techniques fail to reliably extend to multiple concepts -- we hypothesize this to be due to the mismatch between complex scenes and simple text descriptions in the pre-training dataset (e.g., LAION). Second, given an image containing multiple personalized concepts, there lacks a holistic metric that evaluates performance on not just the degree of resemblance of personalized concepts, but also whether all concepts are present in the image and whether the image accurately reflects the overall text description. To address these issues, we introduce Gen4Gen, a semi-automated dataset creation pipeline utilizing generative models to combine personalized concepts into complex compositions along with text-descriptions. Using this, we create a dataset called MyCanvas, that can be used to benchmark the task of multi-concept personalization. In addition, we design a comprehensive metric comprising two scores (CP-CLIP and TI-CLIP) for better quantifying the performance of multi-concept, personalized text-to-image diffusion methods. We provide a simple baseline built on top of Custom Diffusion with empirical prompting strategies for future researchers to evaluate on MyCanvas. We show that by improving data quality and prompting strategies, we can significantly increase multi-concept personalized image generation quality, without requiring any modifications to model architecture or training algorithms.

Instance segmentation is critical in biomedical imaging to accurately distinguish individual objects like cells, which often overlap and vary in size. Recent query-based methods, where object queries guide segmentation, have shown strong performance. While U-Net has been a go-to architecture in medical image segmentation, its potential in query-based approaches remains largely unexplored. In this work, we present IAUNet, a novel query-based U-Net architecture. The core design features a full U-Net architecture, enhanced by a novel lightweight convolutional Pixel decoder, making the model more efficient and reducing the number of parameters. Additionally, we propose a Transformer decoder that refines object-specific features across multiple scales. Finally, we introduce the 2025 Revvity Full Cell Segmentation Dataset, a unique resource with detailed annotations of overlapping cell cytoplasm in brightfield images, setting a new benchmark for biomedical instance segmentation. Experiments on multiple public datasets and our own show that IAUNet outperforms most state-of-the-art fully convolutional, transformer-based, and query-based models and cell segmentation-specific models, setting a strong baseline for cell instance segmentation tasks. Code is available at https://github.com/SlavkoPrytula/IAUNet

We propose expanding the shared Transformer module to produce and initialize Transformers of varying depths, enabling adaptation to diverse resource constraints. Drawing an analogy to genetic expansibility, we term such module as learngene. To identify the expansion mechanism, we delve into the relationship between the layer's position and its corresponding weight value, and find that linear function appropriately approximates this relationship. Building on this insight, we present Transformer as Linear Expansion of learnGene (TLEG), a novel approach for flexibly producing and initializing Transformers of diverse depths. Specifically, to learn learngene, we firstly construct an auxiliary Transformer linearly expanded from learngene, after which we train it through employing soft distillation. Subsequently, we can produce and initialize Transformers of varying depths via linearly expanding the well-trained learngene, thereby supporting diverse downstream scenarios. Extensive experiments on ImageNet-1K demonstrate that TLEG achieves comparable or better performance in contrast to many individual models trained from scratch, while reducing around 2x training cost. When transferring to several downstream classification datasets, TLEG surpasses existing initialization methods by a large margin (e.g., +6.87% on iNat 2019 and +7.66% on CIFAR-100). Under the situation where we need to produce models of varying depths adapting for different resource constraints, TLEG achieves comparable results while reducing around 19x parameters stored to initialize these models and around 5x pre-training costs, in contrast to the pre-training and fine-tuning approach. When transferring a fixed set of parameters to initialize different models, TLEG presents better flexibility and competitive performance while reducing around 2.9x parameters stored to initialize, compared to the pre-training approach.

We present ILLUME+ that leverages dual visual tokenization and a diffusion decoder to improve both deep semantic understanding and high-fidelity image generation. Existing unified models have struggled to simultaneously handle the three fundamental capabilities in a unified model: understanding, generation, and editing. Models like Chameleon and EMU3 utilize VQGAN for image discretization, due to the lack of deep semantic interaction, they lag behind specialist models like LLaVA in visual understanding tasks. To mitigate this, LaViT and ILLUME employ semantic encoders for tokenization, but they struggle with image editing due to poor texture preservation. Meanwhile, Janus series decouples the input and output image representation, limiting their abilities to seamlessly handle interleaved image-text understanding and generation. In contrast, ILLUME+ introduces a unified dual visual tokenizer, DualViTok, which preserves both fine-grained textures and text-aligned semantics while enabling a coarse-to-fine image representation strategy for multimodal understanding and generation. Additionally, we employ a diffusion model as the image detokenizer for enhanced generation quality and efficient super-resolution. ILLUME+ follows a continuous-input, discrete-output scheme within the unified MLLM and adopts a progressive training procedure that supports dynamic resolution across the vision tokenizer, MLLM, and diffusion decoder. This design allows for flexible and efficient context-aware image editing and generation across diverse tasks. ILLUME+ (3B) exhibits competitive performance against existing unified MLLMs and specialized models across multimodal understanding, generation, and editing benchmarks. With its strong performance, ILLUME+ provides a scalable and versatile foundation for future multimodal applications. Project Page: https://illume-unified-mllm.github.io/.

Developing self-supervised learning (SSL) models that can learn universal and transferable representations of H&E gigapixel whole-slide images (WSIs) is becoming increasingly valuable in computational pathology. These models hold the potential to advance critical tasks such as few-shot classification, slide retrieval, and patient stratification. Existing approaches for slide representation learning extend the principles of SSL from small images (e.g., 224 x 224 patches) to entire slides, usually by aligning two different augmentations (or views) of the slide. Yet the resulting representation remains constrained by the limited clinical and biological diversity of the views. Instead, we postulate that slides stained with multiple markers, such as immunohistochemistry, can be used as different views to form a rich task-agnostic training signal. To this end, we introduce Madeleine, a multimodal pretraining strategy for slide representation learning. Madeleine is trained with a dual global-local cross-stain alignment objective on large cohorts of breast cancer samples (N=4,211 WSIs across five stains) and kidney transplant samples (N=12,070 WSIs across four stains). We demonstrate the quality of slide representations learned by Madeleine on various downstream evaluations, ranging from morphological and molecular classification to prognostic prediction, comprising 21 tasks using 7,299 WSIs from multiple medical centers. Code is available at https://github.com/mahmoodlab/MADELEINE.

This paper addresses complex challenges in histopathological image analysis through three key contributions. Firstly, it introduces a fast patch selection method, FPS, for whole-slide image (WSI) analysis, significantly reducing computational cost while maintaining accuracy. Secondly, it presents PathDino, a lightweight histopathology feature extractor with a minimal configuration of five Transformer blocks and only 9 million parameters, markedly fewer than alternatives. Thirdly, it introduces a rotation-agnostic representation learning paradigm using self-supervised learning, effectively mitigating overfitting. We also show that our compact model outperforms existing state-of-the-art histopathology-specific vision transformers on 12 diverse datasets, including both internal datasets spanning four sites (breast, liver, skin, and colorectal) and seven public datasets (PANDA, CAMELYON16, BRACS, DigestPath, Kather, PanNuke, and WSSS4LUAD). Notably, even with a training dataset of 6 million histopathology patches from The Cancer Genome Atlas (TCGA), our approach demonstrates an average 8.5% improvement in patch-level majority vote performance. These contributions provide a robust framework for enhancing image analysis in digital pathology, rigorously validated through extensive evaluation. Project Page: https://rhazeslab.github.io/PathDino-Page/

Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming manual curation. As deep-learning methods outperformed classical state-of-the-art algorithms in various domains and have also been successfully applied to life science problems including medicine and biology, we here propose Deep SNP, a novel Deep Neural Network to learn from genomic data. Specifically, we used a manually curated dataset from 12 genomic single nucleotide polymorphism array (SNPa) profiles as truth-set and aimed at predicting the presence or absence of genomic breakpoints, an indicator of structural chromosomal variations, in windows of 40,000 probes. We compare our results with well-known neural network models as well as Rawcopy though this tool is designed to predict breakpoints and in addition genomic segments with high sensitivity. We show, that Deep SNP is capable of successfully predicting the presence or absence of a breakpoint in large genomic windows and outperforms state-of-the-art neural network models. Qualitative examples suggest that integration of a localization unit may enable breakpoint detection and prediction of genomic segments, even if the breakpoint coordinates were not provided for network training. These results warrant further evaluation of DeepSNP for breakpoint localization and subsequent calling of genomic segments.

Despite a big leap forward in capability, multimodal large language models (MLLMs) tend to behave like a sloth in practical use, i.e., slow response and large latency. Recent efforts are devoted to building tiny MLLMs for better efficiency, but the plethora of visual tokens still used limit their actual speedup. In this paper, we propose a powerful and fast tiny MLLM called FlashSloth. Different from previous efforts, FlashSloth focuses on improving the descriptive power of visual tokens in the process of compressing their redundant semantics. In particular, FlashSloth introduces embedded visual compression designs to capture both visually salient and instruction-related image information, so as to achieving superior multimodal performance with fewer visual tokens. Extensive experiments are conducted to validate the proposed FlashSloth, and a bunch of tiny but strong MLLMs are also comprehensively compared, e.g., InternVL2, MiniCPM-V2 and Qwen2-VL. The experimental results show that compared with these advanced tiny MLLMs, our FlashSloth can greatly reduce the number of visual tokens, training memory and computation complexity while retaining high performance on various VL tasks.

Recently, there has been significant interest in enhancing the capability of multimodal large language models (MLLMs) to process high-resolution images. Most existing methods focus on adopting a cropping strategy to improve the ability of multimodal large language models to understand image details. However, this cropping operation inevitably causes the segmentation of objects and connected areas, which impairs the MLLM's ability to recognize small or irregularly shaped objects or text. This issue is particularly evident in lightweight MLLMs. Addressing this issue, we propose Mini-Monkey, a lightweight MLLM that incorporates a plug-and-play method called multi-scale adaptive crop strategy (MSAC). Mini-Monkey adaptively generates multi-scale representations, allowing it to select non-segmented objects from various scales. To mitigate the computational overhead introduced by MSAC, we propose a Scale Compression Mechanism (SCM), which effectively compresses image tokens. Mini-Monkey achieves state-of-the-art performance among 2B-parameter MLLMs. It not only demonstrates leading performance on a variety of general multimodal understanding tasks but also shows consistent improvements in document understanding capabilities. On the OCRBench, Mini-Monkey achieves a score of 802, outperforming 8B-parameter state-of-the-art model InternVL2-8B. Besides, our model and training strategy are very efficient, which can be trained with only eight RTX 3090. The code is available at https://github.com/Yuliang-Liu/Monkey.

Brain tumors, particularly gliomas, pose significant chall-enges due to their complex growth patterns, infiltrative nature, and the variability in brain structure across individuals, which makes accurate diagnosis and monitoring difficult. Deep learning models have been developed to accurately delineate these tumors. However, most of these models were trained on relatively homogenous high-resource datasets, limiting their robustness when deployed in underserved regions. In this study, we performed segmentation-aware offline data augmentation on the BraTS-Africa dataset to increase the data sample size and diversity to enhance generalization. We further constructed an ensemble of three distinct architectures, MedNeXt, SegMamba, and Residual-Encoder U-Net, to leverage their complementary strengths. Our best-performing model, MedNeXt, was trained on 1000 epochs and achieved the highest average lesion-wise dice and normalized surface distance scores of 0.86 and 0.81 respectively. However, the ensemble model trained for 500 epochs produced the most balanced segmentation performance across the tumour subregions. This work demonstrates that a combination of advanced augmentation and model ensembling can improve segmentation accuracy and robustness on diverse and underrepresented datasets. Code available at: https://github.com/SPARK-Academy-2025/SPARK-2025/tree/main/SPARK2025_BraTs_MODELS/SPARK_NeuroAshanti

Micro-expression recognition (MER), a critical subfield of affective computing, presents greater challenges than macro-expression recognition due to its brief duration and low intensity. While incorporating prior knowledge has been shown to enhance MER performance, existing methods predominantly rely on simplistic, singular sources of prior knowledge, failing to fully exploit multi-source information. This paper introduces the Multi-Prior Fusion Network (MPFNet), leveraging a progressive training strategy to optimize MER tasks. We propose two complementary encoders: the Generic Feature Encoder (GFE) and the Advanced Feature Encoder (AFE), both based on Inflated 3D ConvNets (I3D) with Coordinate Attention (CA) mechanisms, to improve the model's ability to capture spatiotemporal and channel-specific features. Inspired by developmental psychology, we present two variants of MPFNet--MPFNet-P and MPFNet-C--corresponding to two fundamental modes of infant cognitive development: parallel and hierarchical processing. These variants enable the evaluation of different strategies for integrating prior knowledge. Extensive experiments demonstrate that MPFNet significantly improves MER accuracy while maintaining balanced performance across categories, achieving accuracies of 0.811, 0.924, and 0.857 on the SMIC, CASME II, and SAMM datasets, respectively. To the best of our knowledge, our approach achieves state-of-the-art performance on the SMIC and SAMM datasets.

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Digital pathology enables automatic analysis of histopathological sections using artificial intelligence (AI). Automatic evaluation could improve diagnostic efficiency and help find associations between morphological features and clinical outcome. For development of such prediction models, identifying invasive epithelial cells, and separating these from benign epithelial cells and in situ lesions would be the first step. In this study, we aimed to develop an AI model for segmentation of epithelial cells in sections from breast cancer. We generated epithelial ground truth masks by restaining hematoxylin and eosin (HE) sections with cytokeratin (CK) AE1/AE3, and by pathologists' annotations. HE/CK image pairs were used to train a convolutional neural network, and data augmentation was used to make the model more robust. Tissue microarrays (TMAs) from 839 patients, and whole slide images from two patients were used for training and evaluation of the models. The sections were derived from four cohorts of breast cancer patients. TMAs from 21 patients from a fifth cohort was used as a second test set. In quantitative evaluation, a mean Dice score of 0.70, 0.79, and 0.75 for invasive epithelial cells, benign epithelial cells, and in situ lesions, respectively, were achieved. In qualitative scoring (0-5) by pathologists, results were best for all epithelium and invasive epithelium, with scores of 4.7 and 4.4. Scores for benign epithelium and in situ lesions were 3.7 and 2.0. The proposed model segmented epithelial cells in HE stained breast cancer slides well, but further work is needed for accurate division between the classes. Immunohistochemistry, together with pathologists' annotations, enabled the creation of accurate ground truths. The model is made freely available in FastPathology and the code is available at https://github.com/AICAN-Research/breast-epithelium-segmentation

Breast cancer survival prediction in computational pathology presents a remarkable challenge due to tumor heterogeneity. For instance, different regions of the same tumor in the pathology image can show distinct morphological and molecular characteristics. This makes it difficult to extract representative features from whole slide images (WSIs) that truly reflect the tumor's aggressive potential and likely survival outcomes. In this paper, we present PathoHR, a novel pipeline for accurate breast cancer survival prediction that enhances any size of pathological images to enable more effective feature learning. Our approach entails (1) the incorporation of a plug-and-play high-resolution Vision Transformer (ViT) to enhance patch-wise WSI representation, enabling more detailed and comprehensive feature extraction, (2) the systematic evaluation of multiple advanced similarity metrics for comparing WSI-extracted features, optimizing the representation learning process to better capture tumor characteristics, (3) the demonstration that smaller image patches enhanced follow the proposed pipeline can achieve equivalent or superior prediction accuracy compared to raw larger patches, while significantly reducing computational overhead. Experimental findings valid that PathoHR provides the potential way of integrating enhanced image resolution with optimized feature learning to advance computational pathology, offering a promising direction for more accurate and efficient breast cancer survival prediction. Code will be available at https://github.com/AIGeeksGroup/PathoHR.

We need billion-scale images to achieve more generalizable and ground-breaking vision models, as well as massive dataset storage to ship the images (e.g., the LAION-4B dataset needs 240TB storage space). However, it has become challenging to deal with unlimited dataset storage with limited storage infrastructure. A number of storage-efficient training methods have been proposed to tackle the problem, but they are rarely scalable or suffer from severe damage to performance. In this paper, we propose a storage-efficient training strategy for vision classifiers for large-scale datasets (e.g., ImageNet) that only uses 1024 tokens per instance without using the raw level pixels; our token storage only needs <1% of the original JPEG-compressed raw pixels. We also propose token augmentations and a Stem-adaptor module to make our approach able to use the same architecture as pixel-based approaches with only minimal modifications on the stem layer and the carefully tuned optimization settings. Our experimental results on ImageNet-1k show that our method significantly outperforms other storage-efficient training methods with a large gap. We further show the effectiveness of our method in other practical scenarios, storage-efficient pre-training, and continual learning. Code is available at https://github.com/naver-ai/seit

This report introduces xGen-MM (also known as BLIP-3), a framework for developing Large Multimodal Models (LMMs). The framework comprises meticulously curated datasets, a training recipe, model architectures, and a resulting suite of LMMs. xGen-MM, short for xGen-MultiModal, expands the Salesforce xGen initiative on foundation AI models. Our models undergo rigorous evaluation across a range of tasks, including both single and multi-image benchmarks. Our pre-trained base model exhibits strong in-context learning capabilities and the instruction-tuned model demonstrates competitive performance among open-source LMMs with similar model sizes. In addition, we introduce a safety-tuned model with DPO, aiming to mitigate harmful behaviors such as hallucinations and improve safety. We open-source our models, curated large-scale datasets, and our fine-tuning codebase to facilitate further advancements in LMM research. Associated resources will be available on our project page above.

Generating ultra-long sequences with large language models (LLMs) has become increasingly crucial but remains a highly time-intensive task, particularly for sequences up to 100K tokens. While traditional speculative decoding methods exist, simply extending their generation limits fails to accelerate the process and can be detrimental. Through an in-depth analysis, we identify three major challenges hindering efficient generation: frequent model reloading, dynamic key-value (KV) management and repetitive generation. To address these issues, we introduce TOKENSWIFT, a novel framework designed to substantially accelerate the generation process of ultra-long sequences while maintaining the target model's inherent quality. Experimental results demonstrate that TOKENSWIFT achieves over 3 times speedup across models of varying scales (1.5B, 7B, 8B, 14B) and architectures (MHA, GQA). This acceleration translates to hours of time savings for ultra-long sequence generation, establishing TOKENSWIFT as a scalable and effective solution at unprecedented lengths. Code can be found at https://github.com/bigai-nlco/TokenSwift.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

We present SEED, an elaborate image tokenizer that empowers Large Language Models (LLMs) with the emergent ability to SEE and Draw at the same time. Research on image tokenizers has previously reached an impasse, as frameworks employing quantized visual tokens have lost prominence due to subpar performance and convergence in multimodal comprehension (compared to BLIP-2, etc.) or generation (compared to Stable Diffusion, etc.). Despite the limitations, we remain confident in its natural capacity to unify visual and textual representations, facilitating scalable multimodal training with LLM's original recipe. In this study, we identify two crucial principles for the architecture and training of SEED that effectively ease subsequent alignment with LLMs. (1) Image tokens should be independent of 2D physical patch positions and instead be produced with a 1D causal dependency, exhibiting intrinsic interdependence that aligns with the left-to-right autoregressive prediction mechanism in LLMs. (2) Image tokens should capture high-level semantics consistent with the degree of semantic abstraction in words, and be optimized for both discriminativeness and reconstruction during the tokenizer training phase. As a result, the off-the-shelf LLM is able to perform both image-to-text and text-to-image generation by incorporating our SEED through efficient LoRA tuning. Comprehensive multimodal pretraining and instruction tuning, which may yield improved results, are reserved for future investigation. This version of SEED was trained in 5.7 days using only 64 V100 GPUs and 5M publicly available image-text pairs. Our preliminary study emphasizes the great potential of discrete visual tokens in versatile multimodal LLMs and the importance of proper image tokenizers in broader research.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

To help address the growing demand for ever-longer sequence lengths in transformer models, Liu et al. recently proposed Ring Attention, an exact attention algorithm capable of overcoming per-device memory bottle- necks by distributing self-attention across multiple devices. In this paper, we study the performance characteristics of Ring Attention in the important special case of causal transformer models, and identify a key workload imbal- ance due to triangular structure of causal attention computations. We propose a simple extension to Ring Attention, which we call Striped Attention to fix this imbalance. Instead of devices having contiguous subsequences, each device has a subset of tokens distributed uniformly throughout the sequence, which we demonstrate leads to more even workloads. In experiments running Striped Attention on A100 GPUs and TPUv4s, we are able to achieve up to 1.45x end-to-end throughput improvements over the original Ring Attention algorithm on causal transformer training at a sequence length of 256k. Furthermore, on 16 TPUv4 chips, we were able to achieve 1.65x speedups at sequence lengths of 786k. We release the code for our experiments as open source

Deploying NMT models on mobile devices is essential for privacy, low latency, and offline scenarios. For high model capacity, NMT models are rather large. Running these models on devices is challenging with limited storage, memory, computation, and power consumption. Existing work either only focuses on a single metric such as FLOPs or general engine which is not good at auto-regressive decoding. In this paper, we present MobileNMT, a system that can translate in 15MB and 30ms on devices. We propose a series of principles for model compression when combined with quantization. Further, we implement an engine that is friendly to INT8 and decoding. With the co-design of model and engine, compared with the existing system, we speed up 47.0x and save 99.5% of memory with only 11.6% loss of BLEU. The code is publicly available at https://github.com/zjersey/Lightseq-ARM.

Recent advances in video generation have shown remarkable progress in open-domain settings, yet medical video generation remains largely underexplored. Medical videos are critical for applications such as clinical training, education, and simulation, requiring not only high visual fidelity but also strict medical accuracy. However, current models often produce unrealistic or erroneous content when applied to medical prompts, largely due to the lack of large-scale, high-quality datasets tailored to the medical domain. To address this gap, we introduce MedVideoCap-55K, the first large-scale, diverse, and caption-rich dataset for medical video generation. It comprises over 55,000 curated clips spanning real-world medical scenarios, providing a strong foundation for training generalist medical video generation models. Built upon this dataset, we develop MedGen, which achieves leading performance among open-source models and rivals commercial systems across multiple benchmarks in both visual quality and medical accuracy. We hope our dataset and model can serve as a valuable resource and help catalyze further research in medical video generation. Our code and data is available at https://github.com/FreedomIntelligence/MedGen

Nucleus instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current dominant algorithms rely on regression of nuclear proxy maps. Distinguishing nucleus instances from the estimated maps requires carefully curated post-processing, which is error-prone and parameter-sensitive. Recently, the Segment Anything Model (SAM) has earned huge attention in medical image segmentation, owing to its impressive generalization ability and promptable property. Nevertheless, its potential on nucleus instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a nucleus prompter and SAM for automatic nucleus instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine-tuned to output the corresponding mask for the prompted nucleus. Furthermore, we propose the inclusion of adjacent nuclei as negative prompts to enhance the model's capability to identify overlapping nuclei. Without complicated post-processing, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Code is available at github.com/windygoo/PromptNucSeg

We present a simple, highly modularized network architecture for image classification. Our network is constructed by repeating a building block that aggregates a set of transformations with the same topology. Our simple design results in a homogeneous, multi-branch architecture that has only a few hyper-parameters to set. This strategy exposes a new dimension, which we call "cardinality" (the size of the set of transformations), as an essential factor in addition to the dimensions of depth and width. On the ImageNet-1K dataset, we empirically show that even under the restricted condition of maintaining complexity, increasing cardinality is able to improve classification accuracy. Moreover, increasing cardinality is more effective than going deeper or wider when we increase the capacity. Our models, named ResNeXt, are the foundations of our entry to the ILSVRC 2016 classification task in which we secured 2nd place. We further investigate ResNeXt on an ImageNet-5K set and the COCO detection set, also showing better results than its ResNet counterpart. The code and models are publicly available online.

In this work, we are interested in achieving both high text controllability and overall appearance consistency in the generation of personalized human characters. We propose a novel framework, named SerialGen, which is a serial generation method consisting of two stages: first, a standardization stage that standardizes reference images, and then a personalized generation stage based on the standardized reference. Furthermore, we introduce two modules aimed at enhancing the standardization process. Our experimental results validate the proposed framework's ability to produce personalized images that faithfully recover the reference image's overall appearance while accurately responding to a wide range of text prompts. Through thorough analysis, we highlight the critical contribution of the proposed serial generation method and standardization model, evidencing enhancements in appearance consistency between reference and output images and across serial outputs generated from diverse text prompts. The term "Serial" in this work carries a double meaning: it refers to the two-stage method and also underlines our ability to generate serial images with consistent appearance throughout.

There is a constant need for high-performing and computationally efficient neural network models for image super-resolution: computationally efficient models can be used via low-capacity devices and reduce carbon footprints. One way to obtain such models is to compress models, e.g. quantization. Another way is a neural architecture search that automatically discovers new, more efficient solutions. We propose a novel quantization-aware procedure, the QuantNAS that combines pros of these two approaches. To make QuantNAS work, the procedure looks for quantization-friendly super-resolution models. The approach utilizes entropy regularization, quantization noise, and Adaptive Deviation for Quantization (ADQ) module to enhance the search procedure. The entropy regularization technique prioritizes a single operation within each block of the search space. Adding quantization noise to parameters and activations approximates model degradation after quantization, resulting in a more quantization-friendly architectures. ADQ helps to alleviate problems caused by Batch Norm blocks in super-resolution models. Our experimental results show that the proposed approximations are better for search procedure than direct model quantization. QuantNAS discovers architectures with better PSNR/BitOps trade-off than uniform or mixed precision quantization of fixed architectures. We showcase the effectiveness of our method through its application to two search spaces inspired by the state-of-the-art SR models and RFDN. Thus, anyone can design a proper search space based on an existing architecture and apply our method to obtain better quality and efficiency. The proposed procedure is 30\% faster than direct weight quantization and is more stable.

Alzheimer's disease (AD) is a chronic neurodegenerative disorder and the leading cause of dementia, significantly impacting cost, mortality, and burden worldwide. The advent of high-throughput omics technologies, such as genomics, transcriptomics, proteomics, and epigenomics, has revolutionized the molecular understanding of AD. Conventional AI approaches typically require the completion of all omics data at the outset to achieve optimal AD diagnosis, which are inefficient and may be unnecessary. To reduce the clinical cost and improve the accuracy of AD diagnosis using multi-omics data, we propose a novel staged graph convolutional network with uncertainty quantification (SGUQ). SGUQ begins with mRNA and progressively incorporates DNA methylation and miRNA data only when necessary, reducing overall costs and exposure to harmful tests. Experimental results indicate that 46.23% of the samples can be reliably predicted using only single-modal omics data (mRNA), while an additional 16.04% of the samples can achieve reliable predictions when combining two omics data types (mRNA + DNA methylation). In addition, the proposed staged SGUQ achieved an accuracy of 0.858 on ROSMAP dataset, which outperformed existing methods significantly. The proposed SGUQ can not only be applied to AD diagnosis using multi-omics data but also has the potential for clinical decision-making using multi-viewed data. Our implementation is publicly available at https://github.com/chenzhao2023/multiomicsuncertainty.

Histopathological analysis is a cornerstone of cancer diagnosis, with Hematoxylin and Eosin (H&E) staining routinely acquired for every patient to visualize cell morphology and tissue architecture. On the other hand, multiplex immunofluorescence (mIF) enables more precise cell type identification via proteomic markers, but has yet to achieve widespread clinical adoption due to cost and logistical constraints. To bridge this gap, we introduce MIPHEI (Multiplex Immunofluorescence Prediction from H&E), a U-Net-inspired architecture that integrates state-of-the-art ViT foundation models as encoders to predict mIF signals from H&E images. MIPHEI targets a comprehensive panel of markers spanning nuclear content, immune lineages (T cells, B cells, myeloid), epithelium, stroma, vasculature, and proliferation. We train our model using the publicly available ORION dataset of restained H&E and mIF images from colorectal cancer tissue, and validate it on two independent datasets. MIPHEI achieves accurate cell-type classification from H&E alone, with F1 scores of 0.88 for Pan-CK, 0.57 for CD3e, 0.56 for SMA, 0.36 for CD68, and 0.30 for CD20, substantially outperforming both a state-of-the-art baseline and a random classifier for most markers. Our results indicate that our model effectively captures the complex relationships between nuclear morphologies in their tissue context, as visible in H&E images and molecular markers defining specific cell types. MIPHEI offers a promising step toward enabling cell-type-aware analysis of large-scale H&E datasets, in view of uncovering relationships between spatial cellular organization and patient outcomes.

Segmenting biomarkers in medical images is crucial for various biotech applications. Despite advances, Transformer and CNN based methods often struggle with variations in staining and morphology, limiting feature extraction. In medical image segmentation, where datasets often have limited sample availability, recent state-of-the-art (SOTA) methods achieve higher accuracy by leveraging pre-trained encoders, whereas end-to-end methods tend to underperform. This is due to challenges in effectively transferring rich multiscale features from encoders to decoders, as well as limitations in decoder efficiency. To address these issues, we propose an architecture that captures multi-scale local and global contextual information and a novel decoder design, which effectively integrates features from the encoder, emphasizes important channels and regions, and reconstructs spatial dimensions to enhance segmentation accuracy. Our method, compatible with various encoders, outperforms SOTA methods, as demonstrated by experiments on four datasets and ablation studies. Specifically, our method achieves absolute performance gains of 2.76% on MoNuSeg, 3.12% on DSB, 2.87% on Electron Microscopy, and 4.03% on TNBC datasets compared to existing SOTA methods. Code: https://github.com/saadwazir/MCADS-Decoder

The remarkable success of Large Language Models (LLMs) has extended to the multimodal domain, achieving outstanding performance in image understanding and generation. Recent efforts to develop unified Multimodal Large Language Models (MLLMs) that integrate these capabilities have shown promising results. However, existing approaches often involve complex designs in model architecture or training pipeline, increasing the difficulty of model training and scaling. In this paper, we propose SynerGen-VL, a simple yet powerful encoder-free MLLM capable of both image understanding and generation. To address challenges identified in existing encoder-free unified MLLMs, we introduce the token folding mechanism and the vision-expert-based progressive alignment pretraining strategy, which effectively support high-resolution image understanding while reducing training complexity. After being trained on large-scale mixed image-text data with a unified next-token prediction objective, SynerGen-VL achieves or surpasses the performance of existing encoder-free unified MLLMs with comparable or smaller parameter sizes, and narrows the gap with task-specific state-of-the-art models, highlighting a promising path toward future unified MLLMs. Our code and models shall be released.

Large Language Models (LLMs) have become ubiquitous across various domains, transforming the way we interact with information and conduct research. However, most high-performing LLMs remain confined behind proprietary walls, hindering scientific progress. Most open-source LLMs, on the other hand, are limited in their ability to support longer sequence lengths, which is a key requirement for many tasks that require inference over an input context. To address this, we have trained XGen, a series of 7B parameter models on up to 8K sequence length for up to 1.5T tokens. We have also finetuned the XGen models on public-domain instructional data, creating their instruction-tuned counterparts (XGen-Inst). We open-source our models for both research advancements and commercial applications. Our evaluation on standard benchmarks shows that XGen models achieve comparable or better results when compared with state-of-the-art open-source LLMs. Our targeted evaluation on long sequence modeling tasks shows the benefits of our 8K-sequence models over 2K-sequence open-source LLMs.

Generative modeling of discrete variables is challenging yet crucial for applications in natural language processing and biological sequence design. We introduce the Shortlisting Model (SLM), a novel simplex-based diffusion model inspired by progressive candidate pruning. SLM operates on simplex centroids, reducing generation complexity and enhancing scalability. Additionally, SLM incorporates a flexible implementation of classifier-free guidance, enhancing unconditional generation performance. Extensive experiments on DNA promoter and enhancer design, protein design, character-level and large-vocabulary language modeling demonstrate the competitive performance and strong potential of SLM. Our code can be found at https://github.com/GenSI-THUAIR/SLM

Keyphrase Generation (KPG) is a longstanding task in NLP with widespread applications. The advent of sequence-to-sequence (seq2seq) pre-trained language models (PLMs) has ushered in a transformative era for KPG, yielding promising performance improvements. However, many design decisions remain unexplored and are often made arbitrarily. This paper undertakes a systematic analysis of the influence of model selection and decoding strategies on PLM-based KPG. We begin by elucidating why seq2seq PLMs are apt for KPG, anchored by an attention-driven hypothesis. We then establish that conventional wisdom for selecting seq2seq PLMs lacks depth: (1) merely increasing model size or performing task-specific adaptation is not parameter-efficient; (2) although combining in-domain pre-training with task adaptation benefits KPG, it does partially hinder generalization. Regarding decoding, we demonstrate that while greedy search achieves strong F1 scores, it lags in recall compared with sampling-based methods. Based on these insights, we propose DeSel, a likelihood-based decode-select algorithm for seq2seq PLMs. DeSel improves greedy search by an average of 4.7% semantic F1 across five datasets. Our collective findings pave the way for deeper future investigations into PLM-based KPG.

We present any4, a learned 4-bit weight quantization solution for large language models (LLMs) providing arbitrary numeric representations without requiring pre-processing of weights or activations. any4 yields higher accuracy compared to other related 4-bit numeric representation types: int4, fp4 and nf4, as evaluated on a range of model sizes, generations and families (Llama 2, Llama 3, Mistral and Mixtral). While any4 does not require preprocessing of weights or activations, it is also competitive with orthogonal techniques that require such preprocessing (e.g., AWQ and GPTQ). We also experiment with any3 and any2 and show competitiveness at lower bits. Additionally, we show that we can calibrate using a single curated diverse sample rather than hundreds of samples from a dataset as done in most quantization approaches. We also open source tinygemm, a latency optimized GPU matrix multiplication library for LLMs, that implements any4 using a GPU-efficient lookup table strategy along with other common quantization methods. We open source our code at https://github.com/facebookresearch/any4 .

Precision medicine, such as patient-adaptive treatments assisted by medical image analysis, poses new challenges for segmentation algorithms in adapting to new patients, due to the large variability across different patients and the limited availability of annotated data for each patient. In this work, we propose a data-efficient segmentation algorithm, namely Part-aware Prompted Segment Anything Model (P^2SAM). Without any model fine-tuning, P^2SAM enables seamless adaptation to any new patients relying only on one-shot patient-specific data. We introduce a novel part-aware prompt mechanism to select multiple-point prompts based on the part-level features of the one-shot data, which can be extensively integrated into different promptable segmentation models, such as SAM and SAM 2. Moreover, to determine the optimal number of parts for each specific case, we propose a distribution-guided retrieval approach that further enhances the robustness of the part-aware prompt mechanism. P^2SAM improves the performance by +8.0% and +2.0% mean Dice score for two different patient-adaptive segmentation applications, respectively. In addition, P^2SAM also exhibits impressive generalizability in other adaptive segmentation tasks in the natural image domain, e.g., +6.4% mIoU within personalized object segmentation task. The code is available at: https://github.com/Zch0414/p2sam

Recent image generation schemes typically capture image distribution in a pre-constructed latent space relying on a frozen image tokenizer. Though the performance of tokenizer plays an essential role to the successful generation, its current evaluation metrics (e.g. rFID) fail to precisely assess the tokenizer and correlate its performance to the generation quality (e.g. gFID). In this paper, we comprehensively analyze the reason for the discrepancy of reconstruction and generation qualities in a discrete latent space, and, from which, we propose a novel plug-and-play tokenizer training scheme to facilitate latent space construction. Specifically, a latent perturbation approach is proposed to simulate sampling noises, i.e., the unexpected tokens sampled, from the generative process. With the latent perturbation, we further propose (1) a novel tokenizer evaluation metric, i.e., pFID, which successfully correlates the tokenizer performance to generation quality and (2) a plug-and-play tokenizer training scheme, which significantly enhances the robustness of tokenizer thus boosting the generation quality and convergence speed. Extensive benchmarking are conducted with 11 advanced discrete image tokenizers with 2 autoregressive generation models to validate our approach. The tokenizer trained with our proposed latent perturbation achieve a notable 1.60 gFID with classifier-free guidance (CFG) and 3.45 gFID without CFG with a sim400M generator. Code: https://github.com/lxa9867/ImageFolder.

Vision Transformer (ViT) models have recently drawn much attention in computer vision due to their high model capability. However, ViT models suffer from huge number of parameters, restricting their applicability on devices with limited memory. To alleviate this problem, we propose MiniViT, a new compression framework, which achieves parameter reduction in vision transformers while retaining the same performance. The central idea of MiniViT is to multiplex the weights of consecutive transformer blocks. More specifically, we make the weights shared across layers, while imposing a transformation on the weights to increase diversity. Weight distillation over self-attention is also applied to transfer knowledge from large-scale ViT models to weight-multiplexed compact models. Comprehensive experiments demonstrate the efficacy of MiniViT, showing that it can reduce the size of the pre-trained Swin-B transformer by 48\%, while achieving an increase of 1.0\% in Top-1 accuracy on ImageNet. Moreover, using a single-layer of parameters, MiniViT is able to compress DeiT-B by 9.7 times from 86M to 9M parameters, without seriously compromising the performance. Finally, we verify the transferability of MiniViT by reporting its performance on downstream benchmarks. Code and models are available at here.

Text-guided image editing involves modifying a source image based on a language instruction and, typically, requires changes to only small local regions. However, existing approaches generate the entire target image rather than selectively regenerate only the intended editing areas. This results in (1) unnecessary computational costs and (2) a bias toward reconstructing non-editing regions, which compromises the quality of the intended edits. To resolve these limitations, we propose to formulate image editing as Next Editing-token Prediction (NEP) based on autoregressive image generation, where only regions that need to be edited are regenerated, thus avoiding unintended modification to the non-editing areas. To enable any-region editing, we propose to pre-train an any-order autoregressive text-to-image (T2I) model. Once trained, it is capable of zero-shot image editing and can be easily adapted to NEP for image editing, which achieves a new state-of-the-art on widely used image editing benchmarks. Moreover, our model naturally supports test-time scaling (TTS) through iteratively refining its generation in a zero-shot manner. The project page is: https://nep-bigai.github.io/

In this work, we share the insights for achieving state-of-the-art quality in our text-to-image anime image generative model, called Illustrious. To achieve high resolution, dynamic color range images, and high restoration ability, we focus on three critical approaches for model improvement. First, we delve into the significance of the batch size and dropout control, which enables faster learning of controllable token based concept activations. Second, we increase the training resolution of images, affecting the accurate depiction of character anatomy in much higher resolution, extending its generation capability over 20MP with proper methods. Finally, we propose the refined multi-level captions, covering all tags and various natural language captions as a critical factor for model development. Through extensive analysis and experiments, Illustrious demonstrates state-of-the-art performance in terms of animation style, outperforming widely-used models in illustration domains, propelling easier customization and personalization with nature of open source. We plan to publicly release updated Illustrious model series sequentially as well as sustainable plans for improvements.

Multimodal large language models (MLLMs) extend the success of language models to visual understanding, and recent efforts have sought to build unified MLLMs that support both understanding and generation. However, constructing such models remains challenging: hybrid approaches combine continuous embeddings with diffusion or flow-based objectives, producing high-quality images but breaking the autoregressive paradigm, while pure autoregressive approaches unify text and image prediction over discrete visual tokens but often face trade-offs between semantic alignment and pixel-level fidelity. In this work, we present Bridge, a pure autoregressive unified MLLM that augments pre-trained visual understanding models with generative ability through a Mixture-of-Transformers architecture, enabling both image understanding and generation within a single next-token prediction framework. To further improve visual generation fidelity, we propose a semantic-to-pixel discrete representation that integrates compact semantic tokens with fine-grained pixel tokens, achieving strong language alignment and precise description of visual details with only a 7.9% increase in sequence length. Extensive experiments across diverse multimodal benchmarks demonstrate that Bridge achieves competitive or superior results in both understanding and generation benchmarks, while requiring less training data and reduced training time compared to prior unified MLLMs.

Autoregressive (AR) models, long dominant in language generation, are increasingly applied to image synthesis but are often considered less competitive than Diffusion-based models. A primary limitation is the substantial number of image tokens required for AR models, which constrains both training and inference efficiency, as well as image resolution. To address this, we present Token-Shuffle, a novel yet simple method that reduces the number of image tokens in Transformer. Our key insight is the dimensional redundancy of visual vocabularies in Multimodal Large Language Models (MLLMs), where low-dimensional visual codes from visual encoder are directly mapped to high-dimensional language vocabularies. Leveraging this, we consider two key operations: token-shuffle, which merges spatially local tokens along channel dimension to decrease the input token number, and token-unshuffle, which untangles the inferred tokens after Transformer blocks to restore the spatial arrangement for output. Jointly training with textual prompts, our strategy requires no additional pretrained text-encoder and enables MLLMs to support extremely high-resolution image synthesis in a unified next-token prediction way while maintaining efficient training and inference. For the first time, we push the boundary of AR text-to-image generation to a resolution of 2048x2048 with gratifying generation performance. In GenAI-benchmark, our 2.7B model achieves 0.77 overall score on hard prompts, outperforming AR models LlamaGen by 0.18 and diffusion models LDM by 0.15. Exhaustive large-scale human evaluations also demonstrate our prominent image generation ability in terms of text-alignment, visual flaw, and visual appearance. We hope that Token-Shuffle can serve as a foundational design for efficient high-resolution image generation within MLLMs.

Image tokenization has enabled major advances in autoregressive image generation by providing compressed, discrete representations that are more efficient to process than raw pixels. While traditional approaches use 2D grid tokenization, recent methods like TiTok have shown that 1D tokenization can achieve high generation quality by eliminating grid redundancies. However, these methods typically use a fixed number of tokens and thus cannot adapt to an image's inherent complexity. We introduce FlexTok, a tokenizer that projects 2D images into variable-length, ordered 1D token sequences. For example, a 256x256 image can be resampled into anywhere from 1 to 256 discrete tokens, hierarchically and semantically compressing its information. By training a rectified flow model as the decoder and using nested dropout, FlexTok produces plausible reconstructions regardless of the chosen token sequence length. We evaluate our approach in an autoregressive generation setting using a simple GPT-style Transformer. On ImageNet, this approach achieves an FID<2 across 8 to 128 tokens, outperforming TiTok and matching state-of-the-art methods with far fewer tokens. We further extend the model to support to text-conditioned image generation and examine how FlexTok relates to traditional 2D tokenization. A key finding is that FlexTok enables next-token prediction to describe images in a coarse-to-fine "visual vocabulary", and that the number of tokens to generate depends on the complexity of the generation task.

Identifying key pathological features in brain MRIs is crucial for the long-term survival of glioma patients. However, manual segmentation is time-consuming, requiring expert intervention and is susceptible to human error. Therefore, significant research has been devoted to developing machine learning methods that can accurately segment tumors in 3D multimodal brain MRI scans. Despite their progress, state-of-the-art models are often limited by the data they are trained on, raising concerns about their reliability when applied to diverse populations that may introduce distribution shifts. Such shifts can stem from lower quality MRI technology (e.g., in sub-Saharan Africa) or variations in patient demographics (e.g., children). The BraTS-2024 challenge provides a platform to address these issues. This study presents our methodology for segmenting tumors in the BraTS-2024 SSA and Pediatric Tumors tasks using MedNeXt, comprehensive model ensembling, and thorough postprocessing. Our approach demonstrated strong performance on the unseen validation set, achieving an average Dice Similarity Coefficient (DSC) of 0.896 on the BraTS-2024 SSA dataset and an average DSC of 0.830 on the BraTS Pediatric Tumor dataset. Additionally, our method achieved an average Hausdorff Distance (HD95) of 14.682 on the BraTS-2024 SSA dataset and an average HD95 of 37.508 on the BraTS Pediatric dataset. Our GitHub repository can be accessed here: Project Repository : https://github.com/python-arch/BioMbz-Optimizing-Brain-Tumor-Segmentation-with-MedNeXt-BraTS-2024-SSA-and-Pediatrics

We propose a novel approach to image generation by decomposing an image into a structured sequence, where each element in the sequence shares the same spatial resolution but differs in the number of unique tokens used, capturing different level of visual granularity. Image generation is carried out through our newly introduced Next Visual Granularity (NVG) generation framework, which generates a visual granularity sequence beginning from an empty image and progressively refines it, from global layout to fine details, in a structured manner. This iterative process encodes a hierarchical, layered representation that offers fine-grained control over the generation process across multiple granularity levels. We train a series of NVG models for class-conditional image generation on the ImageNet dataset and observe clear scaling behavior. Compared to the VAR series, NVG consistently outperforms it in terms of FID scores (3.30 -> 3.03, 2.57 ->2.44, 2.09 -> 2.06). We also conduct extensive analysis to showcase the capability and potential of the NVG framework. Our code and models will be released.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

Recent advancements in artificial intelligence (AI) have precipitated significant breakthroughs in healthcare, particularly in refining diagnostic procedures. However, previous studies have often been constrained to limited functionalities. This study introduces MiniGPT-Med, a vision-language model derived from large-scale language models and tailored for medical applications. MiniGPT-Med demonstrates remarkable versatility across various imaging modalities, including X-rays, CT scans, and MRIs, enhancing its utility. The model is capable of performing tasks such as medical report generation, visual question answering (VQA), and disease identification within medical imagery. Its integrated processing of both image and textual clinical data markedly improves diagnostic accuracy. Our empirical assessments confirm MiniGPT-Med's superior performance in disease grounding, medical report generation, and VQA benchmarks, representing a significant step towards reducing the gap in assisting radiology practice. Furthermore, it achieves state-of-the-art performance on medical report generation, higher than the previous best model by 19\% accuracy. MiniGPT-Med promises to become a general interface for radiology diagnoses, enhancing diagnostic efficiency across a wide range of medical imaging applications.

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

Image tokenizers are crucial for visual generative models, e.g., diffusion models (DMs) and autoregressive (AR) models, as they construct the latent representation for modeling. Increasing token length is a common approach to improve the image reconstruction quality. However, tokenizers with longer token lengths are not guaranteed to achieve better generation quality. There exists a trade-off between reconstruction and generation quality regarding token length. In this paper, we investigate the impact of token length on both image reconstruction and generation and provide a flexible solution to the tradeoff. We propose ImageFolder, a semantic tokenizer that provides spatially aligned image tokens that can be folded during autoregressive modeling to improve both generation efficiency and quality. To enhance the representative capability without increasing token length, we leverage dual-branch product quantization to capture different contexts of images. Specifically, semantic regularization is introduced in one branch to encourage compacted semantic information while another branch is designed to capture the remaining pixel-level details. Extensive experiments demonstrate the superior quality of image generation and shorter token length with ImageFolder tokenizer.

We present Infinity, a Bitwise Visual AutoRegressive Modeling capable of generating high-resolution, photorealistic images following language instruction. Infinity redefines visual autoregressive model under a bitwise token prediction framework with an infinite-vocabulary tokenizer & classifier and bitwise self-correction mechanism, remarkably improving the generation capacity and details. By theoretically scaling the tokenizer vocabulary size to infinity and concurrently scaling the transformer size, our method significantly unleashes powerful scaling capabilities compared to vanilla VAR. Infinity sets a new record for autoregressive text-to-image models, outperforming top-tier diffusion models like SD3-Medium and SDXL. Notably, Infinity surpasses SD3-Medium by improving the GenEval benchmark score from 0.62 to 0.73 and the ImageReward benchmark score from 0.87 to 0.96, achieving a win rate of 66%. Without extra optimization, Infinity generates a high-quality 1024x1024 image in 0.8 seconds, making it 2.6x faster than SD3-Medium and establishing it as the fastest text-to-image model. Models and codes will be released to promote further exploration of Infinity for visual generation and unified tokenizer modeling.

Digitizing pathological images into gigapixel Whole Slide Images (WSIs) has opened new avenues for Computational Pathology (CPath). As positive tissue comprises only a small fraction of gigapixel WSIs, existing Multiple Instance Learning (MIL) methods typically focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting challenging ones. Recent studies have shown that hard examples are crucial for accurately modeling discriminative boundaries. Applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which utilizes a Siamese structure with a consistency constraint to explore the hard instances. Using a class-aware instance probability, MHIM-MIL employs a momentum teacher to mask salient instances and implicitly mine hard instances for training the student model. To obtain diverse, non-redundant hard instances, we adopt large-scale random masking while utilizing a global recycle network to mitigate the risk of losing key features. Furthermore, the student updates the teacher using an exponential moving average, which identifies new hard instances for subsequent training iterations and stabilizes optimization. Experimental results on cancer diagnosis, subtyping, survival analysis tasks, and 12 benchmarks demonstrate that MHIM-MIL outperforms the latest methods in both performance and efficiency. The code is available at: https://github.com/DearCaat/MHIM-MIL.

Selecting appropriate datasets is critical in modern computer vision. However, no general-purpose tools exist to evaluate the extent to which two datasets differ. For this, we propose representing images - and by extension datasets - using Distributions of Neuron Activations (DNAs). DNAs fit distributions, such as histograms or Gaussians, to activations of neurons in a pre-trained feature extractor through which we pass the image(s) to represent. This extractor is frozen for all datasets, and we rely on its generally expressive power in feature space. By comparing two DNAs, we can evaluate the extent to which two datasets differ with granular control over the comparison attributes of interest, providing the ability to customise the way distances are measured to suit the requirements of the task at hand. Furthermore, DNAs are compact, representing datasets of any size with less than 15 megabytes. We demonstrate the value of DNAs by evaluating their applicability on several tasks, including conditional dataset comparison, synthetic image evaluation, and transfer learning, and across diverse datasets, ranging from synthetic cat images to celebrity faces and urban driving scenes.

Advanced autoregressive models have reshaped multimodal AI. However, their transformative potential in medical imaging remains largely untapped due to the absence of a unified visual tokenizer -- one capable of capturing fine-grained visual structures for faithful image reconstruction and realistic image synthesis, as well as rich semantics for accurate diagnosis and image interpretation. To this end, we present MedITok, the first unified tokenizer tailored for medical images, encoding both low-level structural details and high-level clinical semantics within a unified latent space. To balance these competing objectives, we introduce a novel two-stage training framework: a visual representation alignment stage that cold-starts the tokenizer reconstruction learning with a visual semantic constraint, followed by a textual semantic representation alignment stage that infuses detailed clinical semantics into the latent space. Trained on the meticulously collected large-scale dataset with over 30 million medical images and 2 million image-caption pairs, MedITok achieves state-of-the-art performance on more than 30 datasets across 9 imaging modalities and 4 different tasks. By providing a unified token space for autoregressive modeling, MedITok supports a wide range of tasks in clinical diagnostics and generative healthcare applications. Model and code will be made publicly available at: https://github.com/Masaaki-75/meditok.

Image recognition and generation have long been developed independently of each other. With the recent trend towards general-purpose representation learning, the development of general representations for both recognition and generation tasks is also promoted. However, preliminary attempts mainly focus on generation performance, but are still inferior on recognition tasks. These methods are modeled in the vector-quantized (VQ) space, whereas leading recognition methods use pixels as inputs. Our key insights are twofold: (1) pixels as inputs are crucial for recognition tasks; (2) VQ tokens as reconstruction targets are beneficial for generation tasks. These observations motivate us to propose an Alternating Denoising Diffusion Process (ADDP) that integrates these two spaces within a single representation learning framework. In each denoising step, our method first decodes pixels from previous VQ tokens, then generates new VQ tokens from the decoded pixels. The diffusion process gradually masks out a portion of VQ tokens to construct the training samples. The learned representations can be used to generate diverse high-fidelity images and also demonstrate excellent transfer performance on recognition tasks. Extensive experiments show that our method achieves competitive performance on unconditional generation, ImageNet classification, COCO detection, and ADE20k segmentation. Importantly, our method represents the first successful development of general representations applicable to both generation and dense recognition tasks. Code shall be released.

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological research. Prior results have shown that deep vision models can capture biological signal better than hand-crafted features. This work explores how self-supervised deep learning approaches scale when training larger models on larger microscopy datasets. Our results show that both CNN- and ViT-based masked autoencoders significantly outperform weakly supervised baselines. At the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops sampled from 93-million microscopy images achieves relative improvements as high as 28% over our best weakly supervised baseline at inferring known biological relationships curated from public databases. Relevant code and select models released with this work can be found at: https://github.com/recursionpharma/maes_microscopy.

Although two-stage Vector Quantized (VQ) generative models allow for synthesizing high-fidelity and high-resolution images, their quantization operator encodes similar patches within an image into the same index, resulting in a repeated artifact for similar adjacent regions using existing decoder architectures. To address this issue, we propose to incorporate the spatially conditional normalization to modulate the quantized vectors so as to insert spatially variant information to the embedded index maps, encouraging the decoder to generate more photorealistic images. Moreover, we use multichannel quantization to increase the recombination capability of the discrete codes without increasing the cost of model and codebook. Additionally, to generate discrete tokens at the second stage, we adopt a Masked Generative Image Transformer (MaskGIT) to learn an underlying prior distribution in the compressed latent space, which is much faster than the conventional autoregressive model. Experiments on two benchmark datasets demonstrate that our proposed modulated VQGAN is able to greatly improve the reconstructed image quality as well as provide high-fidelity image generation.

Cell instance segmentation (CIS) is crucial for identifying individual cell morphologies in histopathological images, providing valuable insights for biological and medical research. While unsupervised CIS (UCIS) models aim to reduce the heavy reliance on labor-intensive image annotations, they fail to accurately capture cell boundaries, causing missed detections and poor performance. Recognizing the absence of error-free instances as a key limitation, we present COIN (COnfidence score-guided INstance distillation), a novel annotation-free framework with three key steps: (1) Increasing the sensitivity for the presence of error-free instances via unsupervised semantic segmentation with optimal transport, leveraging its ability to discriminate spatially minor instances, (2) Instance-level confidence scoring to measure the consistency between model prediction and refined mask and identify highly confident instances, offering an alternative to ground truth annotations, and (3) Progressive expansion of confidence with recursive self-distillation. Extensive experiments across six datasets show COIN outperforming existing UCIS methods, even surpassing semi- and weakly-supervised approaches across all metrics on the MoNuSeg and TNBC datasets. The code is available at https://github.com/shjo-april/COIN.

Large vision-language models (VLMs) such as GPT-4 have achieved exceptional performance across various multi-modal tasks. However, the deployment of VLMs necessitates substantial energy consumption and computational resources. Once attackers maliciously induce high energy consumption and latency time (energy-latency cost) during inference of VLMs, it will exhaust computational resources. In this paper, we explore this attack surface about availability of VLMs and aim to induce high energy-latency cost during inference of VLMs. We find that high energy-latency cost during inference of VLMs can be manipulated by maximizing the length of generated sequences. To this end, we propose verbose images, with the goal of crafting an imperceptible perturbation to induce VLMs to generate long sentences during inference. Concretely, we design three loss objectives. First, a loss is proposed to delay the occurrence of end-of-sequence (EOS) token, where EOS token is a signal for VLMs to stop generating further tokens. Moreover, an uncertainty loss and a token diversity loss are proposed to increase the uncertainty over each generated token and the diversity among all tokens of the whole generated sequence, respectively, which can break output dependency at token-level and sequence-level. Furthermore, a temporal weight adjustment algorithm is proposed, which can effectively balance these losses. Extensive experiments demonstrate that our verbose images can increase the length of generated sequences by 7.87 times and 8.56 times compared to original images on MS-COCO and ImageNet datasets, which presents potential challenges for various applications. Our code is available at https://github.com/KuofengGao/Verbose_Images.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C^2LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.

We present HunyuanImage 3.0, a native multimodal model that unifies multimodal understanding and generation within an autoregressive framework, with its image generation module publicly available. The achievement of HunyuanImage 3.0 relies on several key components, including meticulous data curation, advanced architecture design, a native Chain-of-Thoughts schema, progressive model pre-training, aggressive model post-training, and an efficient infrastructure that enables large-scale training and inference. With these advancements, we successfully trained a Mixture-of-Experts (MoE) model comprising over 80 billion parameters in total, with 13 billion parameters activated per token during inference, making it the largest and most powerful open-source image generative model to date. We conducted extensive experiments and the results of automatic and human evaluation of text-image alignment and visual quality demonstrate that HunyuanImage 3.0 rivals previous state-of-the-art models. By releasing the code and weights of HunyuanImage 3.0, we aim to enable the community to explore new ideas with a state-of-the-art foundation model, fostering a dynamic and vibrant multimodal ecosystem. All open source assets are publicly available at https://github.com/Tencent-Hunyuan/HunyuanImage-3.0

With the rise of Transformers as the standard for language processing, and their advancements in computer vision, there has been a corresponding growth in parameter size and amounts of training data. Many have come to believe that because of this, transformers are not suitable for small sets of data. This trend leads to concerns such as: limited availability of data in certain scientific domains and the exclusion of those with limited resource from research in the field. In this paper, we aim to present an approach for small-scale learning by introducing Compact Transformers. We show for the first time that with the right size, convolutional tokenization, transformers can avoid overfitting and outperform state-of-the-art CNNs on small datasets. Our models are flexible in terms of model size, and can have as little as 0.28M parameters while achieving competitive results. Our best model can reach 98% accuracy when training from scratch on CIFAR-10 with only 3.7M parameters, which is a significant improvement in data-efficiency over previous Transformer based models being over 10x smaller than other transformers and is 15% the size of ResNet50 while achieving similar performance. CCT also outperforms many modern CNN based approaches, and even some recent NAS-based approaches. Additionally, we obtain a new SOTA result on Flowers-102 with 99.76% top-1 accuracy, and improve upon the existing baseline on ImageNet (82.71% accuracy with 29% as many parameters as ViT), as well as NLP tasks. Our simple and compact design for transformers makes them more feasible to study for those with limited computing resources and/or dealing with small datasets, while extending existing research efforts in data efficient transformers. Our code and pre-trained models are publicly available at https://github.com/SHI-Labs/Compact-Transformers.

In practice, we usually need to build variable-sized models adapting for diverse resource constraints in different application scenarios, where weight initialization is an important step prior to training. The Learngene framework, introduced recently, firstly learns one compact part termed as learngene from a large well-trained model, after which learngene is expanded to initialize variable-sized models. In this paper, we start from analysing the importance of guidance for the expansion of well-trained learngene layers, inspiring the design of a simple but highly effective Learngene approach termed SWS (Stage-wise Weight Sharing), where both learngene layers and their learning process critically contribute to providing knowledge and guidance for initializing models at varying scales. Specifically, to learn learngene layers, we build an auxiliary model comprising multiple stages where the layer weights in each stage are shared, after which we train it through distillation. Subsequently, we expand these learngene layers containing stage information at their corresponding stage to initialize models of variable depths. Extensive experiments on ImageNet-1K demonstrate that SWS achieves consistent better performance compared to many models trained from scratch, while reducing around 6.6x total training costs. In some cases, SWS performs better only after 1 epoch tuning. When initializing variable-sized models adapting for different resource constraints, SWS achieves better results while reducing around 20x parameters stored to initialize these models and around 10x pre-training costs, in contrast to the pre-training and fine-tuning approach.

Quantization is a promising approach for reducing the inference time and memory footprint of neural networks. However, most existing quantization methods require access to the original training dataset for retraining during quantization. This is often not possible for applications with sensitive or proprietary data, e.g., due to privacy and security concerns. Existing zero-shot quantization methods use different heuristics to address this, but they result in poor performance, especially when quantizing to ultra-low precision. Here, we propose ZeroQ , a novel zero-shot quantization framework to address this. ZeroQ enables mixed-precision quantization without any access to the training or validation data. This is achieved by optimizing for a Distilled Dataset, which is engineered to match the statistics of batch normalization across different layers of the network. ZeroQ supports both uniform and mixed-precision quantization. For the latter, we introduce a novel Pareto frontier based method to automatically determine the mixed-precision bit setting for all layers, with no manual search involved. We extensively test our proposed method on a diverse set of models, including ResNet18/50/152, MobileNetV2, ShuffleNet, SqueezeNext, and InceptionV3 on ImageNet, as well as RetinaNet-ResNet50 on the Microsoft COCO dataset. In particular, we show that ZeroQ can achieve 1.71\% higher accuracy on MobileNetV2, as compared to the recently proposed DFQ method. Importantly, ZeroQ has a very low computational overhead, and it can finish the entire quantization process in less than 30s (0.5\% of one epoch training time of ResNet50 on ImageNet). We have open-sourced the ZeroQ frameworkhttps://github.com/amirgholami/ZeroQ.

The transformer model is known to be computationally demanding, and prohibitively costly for long sequences, as the self-attention module uses a quadratic time and space complexity with respect to sequence length. Many researchers have focused on designing new forms of self-attention or introducing new parameters to overcome this limitation, however a large portion of them prohibits the model to inherit weights from large pretrained models. In this work, the transformer's inefficiency has been taken care of from another perspective. We propose Fourier Transformer, a simple yet effective approach by progressively removing redundancies in hidden sequence using the ready-made Fast Fourier Transform (FFT) operator to perform Discrete Cosine Transformation (DCT). Fourier Transformer is able to significantly reduce computational costs while retain the ability to inherit from various large pretrained models. Experiments show that our model achieves state-of-the-art performances among all transformer-based models on the long-range modeling benchmark LRA with significant improvement in both speed and space. For generative seq-to-seq tasks including CNN/DailyMail and ELI5, by inheriting the BART weights our model outperforms the standard BART and other efficient models. Our code is publicly available at \url{https://github.com/LUMIA-Group/FourierTransformer}

This work introduces a new framework, ProtoSAM, for one-shot medical image segmentation. It combines the use of prototypical networks, known for few-shot segmentation, with SAM - a natural image foundation model. The method proposed creates an initial coarse segmentation mask using the ALPnet prototypical network, augmented with a DINOv2 encoder. Following the extraction of an initial mask, prompts are extracted, such as points and bounding boxes, which are then input into the Segment Anything Model (SAM). State-of-the-art results are shown on several medical image datasets and demonstrate automated segmentation capabilities using a single image example (one shot) with no need for fine-tuning of the foundation model. Our code is available at: https://github.com/levayz/ProtoSAM

We present SegFormer, a simple, efficient yet powerful semantic segmentation framework which unifies Transformers with lightweight multilayer perception (MLP) decoders. SegFormer has two appealing features: 1) SegFormer comprises a novel hierarchically structured Transformer encoder which outputs multiscale features. It does not need positional encoding, thereby avoiding the interpolation of positional codes which leads to decreased performance when the testing resolution differs from training. 2) SegFormer avoids complex decoders. The proposed MLP decoder aggregates information from different layers, and thus combining both local attention and global attention to render powerful representations. We show that this simple and lightweight design is the key to efficient segmentation on Transformers. We scale our approach up to obtain a series of models from SegFormer-B0 to SegFormer-B5, reaching significantly better performance and efficiency than previous counterparts. For example, SegFormer-B4 achieves 50.3% mIoU on ADE20K with 64M parameters, being 5x smaller and 2.2% better than the previous best method. Our best model, SegFormer-B5, achieves 84.0% mIoU on Cityscapes validation set and shows excellent zero-shot robustness on Cityscapes-C. Code will be released at: github.com/NVlabs/SegFormer.

In this paper, we propose ProCreate, a simple and easy-to-implement method to improve sample diversity and creativity of diffusion-based image generative models and to prevent training data reproduction. ProCreate operates on a set of reference images and actively propels the generated image embedding away from the reference embeddings during the generation process. We propose FSCG-8 (Few-Shot Creative Generation 8), a few-shot creative generation dataset on eight different categories -- encompassing different concepts, styles, and settings -- in which ProCreate achieves the highest sample diversity and fidelity. Furthermore, we show that ProCreate is effective at preventing replicating training data in a large-scale evaluation using training text prompts. Code and FSCG-8 are available at https://github.com/Agentic-Learning-AI-Lab/procreate-diffusion-public. The project page is available at https://procreate-diffusion.github.io.

Recent advances in text-to-image generation have made remarkable progress in synthesizing realistic human photos conditioned on given text prompts. However, existing personalized generation methods cannot simultaneously satisfy the requirements of high efficiency, promising identity (ID) fidelity, and flexible text controllability. In this work, we introduce PhotoMaker, an efficient personalized text-to-image generation method, which mainly encodes an arbitrary number of input ID images into a stack ID embedding for preserving ID information. Such an embedding, serving as a unified ID representation, can not only encapsulate the characteristics of the same input ID comprehensively, but also accommodate the characteristics of different IDs for subsequent integration. This paves the way for more intriguing and practically valuable applications. Besides, to drive the training of our PhotoMaker, we propose an ID-oriented data construction pipeline to assemble the training data. Under the nourishment of the dataset constructed through the proposed pipeline, our PhotoMaker demonstrates better ID preservation ability than test-time fine-tuning based methods, yet provides significant speed improvements, high-quality generation results, strong generalization capabilities, and a wide range of applications. Our project page is available at https://photo-maker.github.io/

Transcriptomic foundation models (TFMs) have recently emerged as powerful tools for analyzing gene expression in cells and tissues, supporting key tasks such as cell-type annotation, batch correction, and perturbation prediction. However, the diversity of model implementations and training strategies across recent TFMs, though promising, makes it challenging to isolate the contribution of individual design choices or evaluate their potential synergies. This hinders the field's ability to converge on best practices and limits the reproducibility of insights across studies. We present BMFM-RNA, an open-source, modular software package that unifies diverse TFM pretraining and fine-tuning objectives within a single framework. Leveraging this capability, we introduce a novel training objective, whole cell expression decoder (WCED), which captures global expression patterns using an autoencoder-like CLS bottleneck representation. In this paper, we describe the framework, supported input representations, and training objectives. We evaluated four model checkpoints pretrained on CELLxGENE using combinations of masked language modeling (MLM), WCED and multitask learning. Using the benchmarking capabilities of BMFM-RNA, we show that WCED-based models achieve performance that matches or exceeds state-of-the-art approaches like scGPT across more than a dozen datasets in both zero-shot and fine-tuning tasks. BMFM-RNA, available as part of the biomed-multi-omics project ( https://github.com/BiomedSciAI/biomed-multi-omic ), offers a reproducible foundation for systematic benchmarking and community-driven exploration of optimal TFM training strategies, enabling the development of more effective tools to leverage the latest advances in AI for understanding cell biology.

We present the TinyLLaVA framework that provides a unified perspective in designing and analyzing the small-scale Large Multimodal Models (LMMs). We empirically study the effects of different vision encoders, connection modules, language models, training data and training recipes. Our extensive experiments showed that better quality of data combined with better training recipes, smaller LMMs can consistently achieve on-par performances compared to bigger LMMs. Under our framework, we train a family of small-scale LMMs. Our best model, TinyLLaVA-3.1B, achieves better overall performance against existing 7B models such as LLaVA-1.5 and Qwen-VL. We hope our findings can serve as baselines for future research in terms of data scaling, training setups and model selections. Our model weights and codes will be made public.

Medical image segmentation has recently demonstrated impressive progress with deep neural networks, yet the heterogeneous modalities and scarcity of mask annotations limit the development of segmentation models on unannotated modalities. This paper investigates a new paradigm for leveraging generative models in medical applications: controllably synthesizing data for unannotated modalities, without requiring registered data pairs. Specifically, we make the following contributions in this paper: (i) we collect and curate a large-scale radiology image-text dataset, MedGen-1M, comprising modality labels, attributes, region, and organ information, along with a subset of organ mask annotations, to support research in controllable medical image generation; (ii) we propose a diffusion-based data engine, termed MRGen, which enables generation conditioned on text prompts and masks, synthesizing MR images for diverse modalities lacking mask annotations, to train segmentation models on unannotated modalities; (iii) we conduct extensive experiments across various modalities, illustrating that our data engine can effectively synthesize training samples and extend MRI segmentation towards unannotated modalities.

It is natural to represent objects in terms of their parts. This has the potential to improve the performance of algorithms for object recognition and segmentation but can also help for downstream tasks like activity recognition. Research on part-based models, however, is hindered by the lack of datasets with per-pixel part annotations. This is partly due to the difficulty and high cost of annotating object parts so it has rarely been done except for humans (where there exists a big literature on part-based models). To help address this problem, we propose PartImageNet, a large, high-quality dataset with part segmentation annotations. It consists of 158 classes from ImageNet with approximately 24,000 images. PartImageNet is unique because it offers part-level annotations on a general set of classes including non-rigid, articulated objects, while having an order of magnitude larger size compared to existing part datasets (excluding datasets of humans). It can be utilized for many vision tasks including Object Segmentation, Semantic Part Segmentation, Few-shot Learning and Part Discovery. We conduct comprehensive experiments which study these tasks and set up a set of baselines. The dataset and scripts are released at https://github.com/TACJu/PartImageNet.

Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is primarily used for ER+ breast cancer, which is costly, tissue destructive, requires specialized platforms and takes several weeks to obtain a result. Deep learning algorithms can effectively extract morphological patterns in digital histopathology images to predict molecular phenotypes quickly and cost-effectively. We propose a new, computationally efficient approach called hist2RNA inspired by bulk RNA-sequencing techniques to predict the expression of 138 genes (incorporated from six commercially available molecular profiling tests), including luminal PAM50 subtype, from hematoxylin and eosin (H&E) stained whole slide images (WSIs). The training phase involves the aggregation of extracted features for each patient from a pretrained model to predict gene expression at the patient level using annotated H&E images from The Cancer Genome Atlas (TCGA, n=335). We demonstrate successful gene prediction on a held-out test set (n = 160, corr = 0.82 across patients, corr = 0.29 across genes) and perform exploratory analysis on an external tissue microarray (TMA) dataset (n = 498) with known IHC and survival information. Our model is able to predict gene expression and luminal PAM50 subtype (Luminal A versus Luminal B) on the TMA dataset with prognostic significance for overall survival in univariate analysis (c-index = 0.56, hazard ratio = 2.16 (95% CI 1.12-3.06), p < 5 x 10-3), and independent significance in multivariate analysis incorporating standard clinicopathological variables (c-index = 0.65, hazard ratio = 1.85 (95% CI 1.30-2.68), p < 5 x 10-3).

Recent advances in sequencing technologies have enabled researchers to explore cellular heterogeneity at single-cell resolution. Meanwhile, interpretability has gained prominence parallel to the rapid increase in the complexity and performance of deep learning models. In recent years, topic models have been widely used for interpretable single-cell embedding learning and clustering analysis, which we refer to as single-cell embedded topic models. However, previous studies evaluated the interpretability of the models mainly through qualitative analysis, and these single-cell embedded topic models suffer from the potential problem of interpretation collapse. Furthermore, their neglect of external biological knowledge constrains analytical performance. Here, we present scE2TM, an external knowledge-guided single-cell embedded topic model that provides a high-quality cell embedding and strong interpretation, contributing to comprehensive scRNA-seq data analysis. Our comprehensive evaluation across 20 scRNA-seq datasets demonstrates that scE2TM achieves significant clustering performance gains compared to 7 state-of-the-art methods. In addition, we propose a new interpretability evaluation benchmark that introduces 10 metrics to quantitatively assess the interpretability of single-cell embedded topic models. The results show that the interpretation provided by scE2TM performs encouragingly in terms of diversity and consistency with the underlying biological signals, contributing to a better revealing of the underlying biological mechanisms.

Recently, autoregressive (AR) image models have demonstrated remarkable generative capabilities, positioning themselves as a compelling alternative to diffusion models. However, their sequential nature leads to long inference times, limiting their practical scalability. In this work, we introduce Grouped Speculative Decoding (GSD), a novel, training-free acceleration method for AR image models. While recent studies have explored Speculative Decoding (SD) as a means to speed up AR image generation, existing approaches either provide only modest acceleration or require additional training. Our in-depth analysis reveals a fundamental difference between language and image tokens: image tokens exhibit inherent redundancy and diversity, meaning multiple tokens can convey valid semantics. However, traditional SD methods are designed to accept only a single most-likely token, which fails to leverage this difference, leading to excessive false-negative rejections. To address this, we propose a new SD strategy that evaluates clusters of visually valid tokens rather than relying on a single target token. Additionally, we observe that static clustering based on embedding distance is ineffective, which motivates our dynamic GSD approach. Extensive experiments show that GSD accelerates AR image models by an average of 3.7x while preserving image quality-all without requiring any additional training. The source code is available at https://github.com/junhyukso/GSD

This paper presents Tiny-toxic-detector, a compact transformer-based model designed for toxic content detection. Despite having only 2.1 million parameters, Tiny-toxic-detector achieves competitive performance on benchmark datasets, with 90.97% accuracy on ToxiGen and 86.98% accuracy on the Jigsaw dataset, rivaling models over 50 times its size. This efficiency enables deployment in resource-constrained environments, addressing the need for effective content moderation tools that balance performance with computational efficiency. The model architecture features 4 transformer encoder layers, each with 2 attention heads, an embedding dimension of 64, and a feedforward dimension of 128. Trained on both public and private datasets, Tiny-toxic-detector demonstrates the potential of efficient, task-specific models for addressing online toxicity. The paper covers the model architecture, training process, performance benchmarks, and limitations, underscoring its suitability for applications such as social media monitoring and content moderation. By achieving results comparable to much larger models while significantly reducing computational demands, Tiny-toxic-detector represents progress toward more sustainable and scalable AI-driven content moderation solutions.

Model size and inference speed/power have become a major challenge in the deployment of Neural Networks for many applications. A promising approach to address these problems is quantization. However, uniformly quantizing a model to ultra low precision leads to significant accuracy degradation. A novel solution for this is to use mixed-precision quantization, as some parts of the network may allow lower precision as compared to other layers. However, there is no systematic way to determine the precision of different layers. A brute force approach is not feasible for deep networks, as the search space for mixed-precision is exponential in the number of layers. Another challenge is a similar factorial complexity for determining block-wise fine-tuning order when quantizing the model to a target precision. Here, we introduce Hessian AWare Quantization (HAWQ), a novel second-order quantization method to address these problems. HAWQ allows for the automatic selection of the relative quantization precision of each layer, based on the layer's Hessian spectrum. Moreover, HAWQ provides a deterministic fine-tuning order for quantizing layers, based on second-order information. We show the results of our method on Cifar-10 using ResNet20, and on ImageNet using Inception-V3, ResNet50 and SqueezeNext models. Comparing HAWQ with state-of-the-art shows that we can achieve similar/better accuracy with 8times activation compression ratio on ResNet20, as compared to DNAS~wu2018mixed, and up to 1% higher accuracy with up to 14% smaller models on ResNet50 and Inception-V3, compared to recently proposed methods of RVQuant~park2018value and HAQ~wang2018haq. Furthermore, we show that we can quantize SqueezeNext to just 1MB model size while achieving above 68% top1 accuracy on ImageNet.