Daily Papers

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

This paper proposes a novel approach to few-shot semantic segmentation for machinery with multiple parts that exhibit spatial and hierarchical relationships. Our method integrates the foundation models CLIPSeg and Segment Anything Model (SAM) with the interest point detector SuperPoint and a graph convolutional network (GCN) to accurately segment machinery parts. By providing 1 to 25 annotated samples, our model, evaluated on a purely synthetic dataset depicting a truck-mounted loading crane, achieves effective segmentation across various levels of detail. Training times are kept under five minutes on consumer GPUs. The model demonstrates robust generalization to real data, achieving a qualitative synthetic-to-real generalization with a J&F score of 92.2 on real data using 10 synthetic support samples. When benchmarked on the DAVIS 2017 dataset, it achieves a J&F score of 71.5 in semi-supervised video segmentation with three support samples. This method's fast training times and effective generalization to real data make it a valuable tool for autonomous systems interacting with machinery and infrastructure, and illustrate the potential of combined and orchestrated foundation models for few-shot segmentation tasks.

While the popularity of physics-informed neural networks (PINNs) is steadily rising, to this date PINNs have not been successful in simulating dynamical systems whose solution exhibits multi-scale, chaotic or turbulent behavior. In this work we attribute this shortcoming to the inability of existing PINNs formulations to respect the spatio-temporal causal structure that is inherent to the evolution of physical systems. We argue that this is a fundamental limitation and a key source of error that can ultimately steer PINN models to converge towards erroneous solutions. We address this pathology by proposing a simple re-formulation of PINNs loss functions that can explicitly account for physical causality during model training. We demonstrate that this simple modification alone is enough to introduce significant accuracy improvements, as well as a practical quantitative mechanism for assessing the convergence of a PINNs model. We provide state-of-the-art numerical results across a series of benchmarks for which existing PINNs formulations fail, including the chaotic Lorenz system, the Kuramoto-Sivashinsky equation in the chaotic regime, and the Navier-Stokes equations in the turbulent regime. To the best of our knowledge, this is the first time that PINNs have been successful in simulating such systems, introducing new opportunities for their applicability to problems of industrial complexity.

We present HILGEN, a Hierarchically-Informed Data Generation approach that combines domain knowledge from the Unified Medical Language System (UMLS) with synthetic data generated by large language models (LLMs), specifically GPT-3.5. Our approach leverages UMLS's hierarchical structure to expand training data with related concepts, while incorporating contextual information from LLMs through targeted prompts aimed at automatically generating synthetic examples for sparsely occurring named entities. The performance of the HILGEN approach was evaluated across four biomedical NER datasets (MIMIC III, BC5CDR, NCBI-Disease, and Med-Mentions) using BERT-Large and DANN (Data Augmentation with Nearest Neighbor Classifier) models, applying various data generation strategies, including UMLS, GPT-3.5, and their best ensemble. For the BERT-Large model, incorporating UMLS led to an average F1 score improvement of 40.36%, while using GPT-3.5 resulted in a comparable average increase of 40.52%. The Best-Ensemble approach using BERT-Large achieved the highest improvement, with an average increase of 42.29%. DANN model's F1 score improved by 22.74% on average using the UMLS-only approach. The GPT-3.5-based method resulted in a 21.53% increase, and the Best-Ensemble DANN model showed a more notable improvement, with an average increase of 25.03%. Our proposed HILGEN approach improves NER performance in few-shot settings without requiring additional manually annotated data. Our experiments demonstrate that an effective strategy for optimizing biomedical NER is to combine biomedical knowledge curated in the past, such as the UMLS, and generative LLMs to create synthetic training instances. Our future research will focus on exploring additional innovative synthetic data generation strategies for further improving NER performance.

Traditionally, training neural networks to perform semantic segmentation required expensive human-made annotations. But more recently, advances in the field of unsupervised learning have made significant progress on this issue and towards closing the gap to supervised algorithms. To achieve this, semantic knowledge is distilled by learning to correlate randomly sampled features from images across an entire dataset. In this work, we build upon these advances by incorporating information about the structure of the scene into the training process through the use of depth information. We achieve this by (1) learning depth-feature correlation by spatially correlate the feature maps with the depth maps to induce knowledge about the structure of the scene and (2) implementing farthest-point sampling to more effectively select relevant features by utilizing 3D sampling techniques on depth information of the scene. Finally, we demonstrate the effectiveness of our technical contributions through extensive experimentation and present significant improvements in performance across multiple benchmark datasets.

We introduce neural lithography to address the 'design-to-manufacturing' gap in computational optics. Computational optics with large design degrees of freedom enable advanced functionalities and performance beyond traditional optics. However, the existing design approaches often overlook the numerical modeling of the manufacturing process, which can result in significant performance deviation between the design and the fabricated optics. To bridge this gap, we, for the first time, propose a fully differentiable design framework that integrates a pre-trained photolithography simulator into the model-based optical design loop. Leveraging a blend of physics-informed modeling and data-driven training using experimentally collected datasets, our photolithography simulator serves as a regularizer on fabrication feasibility during design, compensating for structure discrepancies introduced in the lithography process. We demonstrate the effectiveness of our approach through two typical tasks in computational optics, where we design and fabricate a holographic optical element (HOE) and a multi-level diffractive lens (MDL) using a two-photon lithography system, showcasing improved optical performance on the task-specific metrics.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6% increase in drug response prediction correlation, 9.6% improvement in single-cell drug classification AUC, and 1.1% average gain in gene perturbation prediction accuracy.

This paper presents a pioneering methodology, termed StructTuning, to efficiently transform foundation Large Language Models (LLMs) into domain specialists. It significantly minimizes the training corpus requirement to a mere 0.3% while achieving an impressive 50% of traditional knowledge injection performance. Our method is inspired by the educational processes for human students, particularly how structured domain knowledge from textbooks is absorbed and then applied to tackle real-world challenges through specific exercises. Based on this, we propose a novel two-stage knowledge injection strategy: Structure-aware Continual Pre-Training (SCPT) and Structure-aware Supervised Fine-Tuning (SSFT). In the SCPT phase, we organize the training data into an auto-generated taxonomy of domain knowledge, enabling LLMs to effectively memorize textual segments linked to specific expertise within the taxonomy's architecture. Subsequently, in the SSFT phase, we explicitly prompt models to reveal the underlying knowledge structure in their outputs, leveraging this structured domain insight to address practical problems adeptly. Our ultimate method has undergone extensive evaluations across model architectures and scales, using closed-book question-answering tasks on LongBench and MMedBench datasets. Remarkably, our method matches 50% of the improvement displayed by the state-of-the-art MMedLM2 on MMedBench, but with only 0.3% quantity of the training corpus. This breakthrough showcases the potential to scale up our StructTuning for stronger domain-specific LLMs. Code will be made public soon.

Structure information is critical for understanding the semantics of text-rich images, such as documents, tables, and charts. Existing Multimodal Large Language Models (MLLMs) for Visual Document Understanding are equipped with text recognition ability but lack general structure understanding abilities for text-rich document images. In this work, we emphasize the importance of structure information in Visual Document Understanding and propose the Unified Structure Learning to boost the performance of MLLMs. Our Unified Structure Learning comprises structure-aware parsing tasks and multi-grained text localization tasks across 5 domains: document, webpage, table, chart, and natural image. To better encode structure information, we design a simple and effective vision-to-text module H-Reducer, which can not only maintain the layout information but also reduce the length of visual features by merging horizontal adjacent patches through convolution, enabling the LLM to understand high-resolution images more efficiently. Furthermore, by constructing structure-aware text sequences and multi-grained pairs of texts and bounding boxes for publicly available text-rich images, we build a comprehensive training set DocStruct4M to support structure learning. Finally, we construct a small but high-quality reasoning tuning dataset DocReason25K to trigger the detailed explanation ability in the document domain. Our model DocOwl 1.5 achieves state-of-the-art performance on 10 visual document understanding benchmarks, improving the SOTA performance of MLLMs with a 7B LLM by more than 10 points in 5/10 benchmarks. Our codes, models, and datasets are publicly available at https://github.com/X-PLUG/mPLUG-DocOwl/tree/main/DocOwl1.5.

We propose a novel interpretation technique to explain the behavior of structured output models, which learn mappings between an input vector to a set of output variables simultaneously. Because of the complex relationship between the computational path of output variables in structured models, a feature can affect the value of output through other ones. We focus on one of the outputs as the target and try to find the most important features utilized by the structured model to decide on the target in each locality of the input space. In this paper, we assume an arbitrary structured output model is available as a black box and argue how considering the correlations between output variables can improve the explanation performance. The goal is to train a function as an interpreter for the target output variable over the input space. We introduce an energy-based training process for the interpreter function, which effectively considers the structural information incorporated into the model to be explained. The effectiveness of the proposed method is confirmed using a variety of simulated and real data sets.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

A growing body of research has demonstrated the inability of NLP models to generalize compositionally and has tried to alleviate it through specialized architectures, training schemes, and data augmentation, among other approaches. In this work, we study a different approach: training on instances with diverse structures. We propose a model-agnostic algorithm for subsampling such sets of instances from a labeled instance pool with structured outputs. Evaluating on both compositional template splits and traditional IID splits of 5 semantic parsing datasets of varying complexity, we show that structurally diverse training using our algorithm leads to comparable or better generalization than prior algorithms in 9 out of 10 dataset-split type pairs. In general, we find structural diversity to consistently improve sample efficiency compared to random train sets. Moreover, we show that structurally diverse sampling yields comprehensive test sets that are a lot more challenging than IID test sets. Finally, we provide two explanations for improved generalization from diverse train sets: 1) improved coverage of output substructures, and 2) a reduction in spurious correlations between these substructures.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in a way such that they can be captured by PLMs. Prior work on structured prediction with PLMs typically flattens the structured output into a sequence, which limits the quality of structural information being learned and leads to inferior performance compared to classic discriminative models. In this work, we describe an approach to model structures as sequences of actions in an autoregressive manner with PLMs, allowing in-structure dependencies to be learned without any loss. Our approach achieves the new state-of-the-art on all the structured prediction tasks we looked at, namely, named entity recognition, end-to-end relation extraction, and coreference resolution.

Although many pretrained models exist for text or images, there have been relatively fewer attempts to train representations specifically for dialog understanding. Prior works usually relied on finetuned representations based on generic text representation models like BERT or GPT-2. But such language modeling pretraining objectives do not take the structural information of conversational text into consideration. Although generative dialog models can learn structural features too, we argue that the structure-unaware word-by-word generation is not suitable for effective conversation modeling. We empirically demonstrate that such representations do not perform consistently across various dialog understanding tasks. Hence, we propose a structure-aware Mutual Information based loss-function DMI (Discourse Mutual Information) for training dialog-representation models, that additionally captures the inherent uncertainty in response prediction. Extensive evaluation on nine diverse dialog modeling tasks shows that our proposed DMI-based models outperform strong baselines by significant margins.

Despite rapid advancements in the capabilities of generative models, pretrained text-to-image models still struggle in capturing the semantics conveyed by complex prompts that compound multiple objects and instance-level attributes. Consequently, we are witnessing growing interests in integrating additional structural constraints, typically in the form of coarse bounding boxes, to better guide the generation process in such challenging cases. In this work, we take the idea of structural guidance a step further by making the observation that contemporary image generation models can directly provide a plausible fine-grained structural initialization. We propose a technique that couples this image-based structural guidance with LLM-based instance-level instructions, yielding output images that adhere to all parts of the text prompt, including object counts, instance-level attributes, and spatial relations between instances.

We present Probabilistic Structure Integration (PSI), a system for learning richly controllable and flexibly promptable world models from data. PSI consists of a three-step cycle. The first step, Probabilistic prediction, involves building a probabilistic graphical model Psi of the data, in the form of a random-access autoregressive sequence model. Psi supports a complete set of learned conditional distributions describing the dependence of any variables in the data on any other set of variables. In step 2, Structure extraction, we show how to extract underlying low-dimensional properties in the data, corresponding to a diverse set of meaningful "intermediate structures", in a zero-shot fashion via causal inference on Psi. Step 3, Integration, completes the cycle by converting these structures into new token types that are then continually mixed back into the training diet as conditioning signals and prediction targets. Each such cycle augments the capabilities of Psi, both allowing it to model the underlying data better, and creating new control handles -- akin to an LLM-like universal prompting language. We train an instance of Psi on 1.4 trillion tokens of internet video data; we use it to perform a variety of useful video prediction and understanding inferences; we extract state-of-the-art optical flow, self-supervised depth and object segmentation; and we use these structures to support a full cycle of predictive improvements.

Structured data sources, such as tables, graphs, and databases, are ubiquitous knowledge sources. Despite the demonstrated capabilities of large language models (LLMs) on plain text, their proficiency in interpreting and utilizing structured data remains limited. Our investigation reveals a notable deficiency in LLMs' ability to process structured data, e.g., ChatGPT lags behind state-of-the-art (SoTA) model by an average of 35%. To augment the Structured Knowledge Grounding (SKG) capabilities in LLMs, we have developed a comprehensive instruction tuning dataset comprising 1.1 million examples. Utilizing this dataset, we train a series of models, referred to as StructLM, based on the Code-LLaMA architecture, ranging from 7B to 34B parameters. Our StructLM series surpasses task-specific models on 14 out of 18 evaluated datasets and establishes new SoTA achievements on 7 SKG tasks. Furthermore, StructLM demonstrates exceptional generalization across 6 novel SKG tasks. Contrary to expectations, we observe that scaling model size offers marginal benefits, with StructLM-34B showing only slight improvements over StructLM-7B. This suggests that structured knowledge grounding is still a challenging task and requires more innovative design to push to a new level.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

Strong inductive biases enable learning from little data and help generalization outside of the training distribution. Popular neural architectures such as Transformers lack strong structural inductive biases for seq2seq NLP tasks on their own. Consequently, they struggle with systematic generalization beyond the training distribution, e.g. with extrapolating to longer inputs, even when pre-trained on large amounts of text. We show how a structural inductive bias can be efficiently injected into a seq2seq model by pre-training it to simulate structural transformations on synthetic data. Specifically, we inject an inductive bias towards Finite State Transducers (FSTs) into a Transformer by pre-training it to simulate FSTs given their descriptions. Our experiments show that our method imparts the desired inductive bias, resulting in improved systematic generalization and better few-shot learning for FST-like tasks. Our analysis shows that fine-tuned models accurately capture the state dynamics of the unseen underlying FSTs, suggesting that the simulation process is internalized by the fine-tuned model.

Large Language Models (LLMs) have demonstrated remarkable capabilities in natural language generation and reasoning. However, their integration into automated software ecosystems is often hindered by the "Structure Gap" - the inherent tension between the probabilistic nature of token generation and the deterministic requirements of structured data formats (e.g., JSON, XML). Traditional Supervised Fine-Tuning (SFT) often fails to enforce strict syntactic constraints, leading to "hallucinated" keys or malformed structures, while constrained decoding methods impose significant inference latency. In this paper, we propose a lightweight, efficient Reinforcement Learning (RL) framework to bridge this gap. We introduce a novel Multi-dimensional Reward Function that decomposes the structured output task into a hierarchy of constraints: structural integrity, format correctness, content accuracy, and validity. Leveraging Gradient Regularized Policy Optimization (GRPO), we enable the model to internalize these constraints without the need for a separate critic network, reducing peak VRAM usage by 40% compared to PPO. We validate our approach on multiple tasks, including complex recipe generation and structured math reasoning (GSM8K-JSON). Experimental results demonstrate that our method achieves 89.7% structural accuracy and 92.1% JSON validity, significantly outperforming both zero-shot baselines (e.g., GPT-3.5) and SFT on larger models like LLaMA-3-8B. Furthermore, we provide a detailed analysis of training dynamics, revealing a distinct self-paced curriculum where the model sequentially acquires syntactic proficiency before semantic accuracy. Our model is publicly available at https://huggingface.co/Freakz3z/Qwen-JSON.

Large-scale vision-language pre-training has achieved significant performance in multi-modal understanding and generation tasks. However, existing methods often perform poorly on image-text matching tasks that require structured representations, i.e., representations of objects, attributes, and relations. As illustrated in Fig.~reffig:case (a), the models cannot make a distinction between ``An astronaut rides a horse" and ``A horse rides an astronaut". This is because they fail to fully leverage structured knowledge when learning representations in multi-modal scenarios. In this paper, we present an end-to-end framework Structure-CLIP, which integrates Scene Graph Knowledge (SGK) to enhance multi-modal structured representations. Firstly, we use scene graphs to guide the construction of semantic negative examples, which results in an increased emphasis on learning structured representations. Moreover, a Knowledge-Enhance Encoder (KEE) is proposed to leverage SGK as input to further enhance structured representations. To verify the effectiveness of the proposed framework, we pre-train our model with the aforementioned approaches and conduct experiments on downstream tasks. Experimental results demonstrate that Structure-CLIP achieves state-of-the-art (SOTA) performance on VG-Attribution and VG-Relation datasets, with 12.5% and 4.1% ahead of the multi-modal SOTA model respectively. Meanwhile, the results on MSCOCO indicate that Structure-CLIP significantly enhances the structured representations while maintaining the ability of general representations. Our code is available at https://github.com/zjukg/Structure-CLIP.

Document layout understanding remains data-intensive despite advances in semi-supervised learning. We present a framework that enhances semi-supervised detection by fusing visual predictions with structural priors from text-pretrained LLMs via principled probabilistic weighting. Given unlabeled documents, an OCR-LLM pipeline infers hierarchical regions which are combined with teacher detector outputs through inverse-variance fusion to generate refined pseudo-labels.Our method demonstrates consistent gains across model scales. With a lightweight SwiftFormer backbone (26M params), we achieve 88.2pm0.3 AP using only 5\% labels on PubLayNet. When applied to document-pretrained LayoutLMv3 (133M params), our fusion framework reaches 89.7pm0.4 AP, surpassing both LayoutLMv3 with standard semi-supervised learning (89.1pm0.4 AP, p=0.02) and matching UDOP~udop (89.8 AP) which requires 100M+ pages of multimodal pretraining. This demonstrates that LLM structural priors are complementary to both lightweight and pretrained architectures. Key findings include: (1) learned instance-adaptive gating improves over fixed weights by +0.9 AP with data-dependent PAC bounds correctly predicting convergence; (2) open-source LLMs enable privacy-preserving deployment with minimal loss (Llama-3-70B: 87.1 AP lightweight, 89.4 AP with LayoutLMv3); (3) LLMs provide targeted semantic disambiguation (18.7\% of cases, +3.8 AP gain) beyond simple text heuristics.Total system cost includes \$12 for GPT-4o-mini API or 17 GPU-hours for local Llama-3-70B per 50K pages, amortized across training runs.

Large language models record impressive performance on many natural language processing tasks. However, their knowledge capacity is limited to the pretraining corpus. Retrieval augmentation offers an effective solution by retrieving context from external knowledge sources to complement the language model. However, existing retrieval augmentation techniques ignore the structural relationships between these documents. Furthermore, retrieval models are not explored much in scientific tasks, especially in regard to the faithfulness of retrieved documents. In this paper, we propose a novel structure-aware retrieval augmented language model that accommodates document structure during retrieval augmentation. We create a heterogeneous document graph capturing multiple types of relationships (e.g., citation, co-authorship, etc.) that connect documents from more than 15 scientific disciplines (e.g., Physics, Medicine, Chemistry, etc.). We train a graph neural network on the curated document graph to act as a structural encoder for the corresponding passages retrieved during the model pretraining. Particularly, along with text embeddings of the retrieved passages, we obtain structural embeddings of the documents (passages) and fuse them together before feeding them to the language model. We evaluate our model extensively on various scientific benchmarks that include science question-answering and scientific document classification tasks. Experimental results demonstrate that structure-aware retrieval improves retrieving more coherent, faithful and contextually relevant passages, while showing a comparable performance in the overall accuracy.

Language models have the ability to perform in-context learning (ICL), allowing them to flexibly adapt their behavior based on context. This contrasts with in-weights learning, where information is statically encoded in model parameters from iterated observations of the data. Despite this apparent ability to learn in-context, language models are known to struggle when faced with unseen or rarely seen tokens. Hence, we study structural in-context learning, which we define as the ability of a model to execute in-context learning on arbitrary tokens -- so called because the model must generalize on the basis of e.g. sentence structure or task structure, rather than semantic content encoded in token embeddings. An ideal model would be able to do both: flexibly deploy in-weights operations (in order to robustly accommodate ambiguous or unknown contexts using encoded semantic information) and structural in-context operations (in order to accommodate novel tokens). We study structural in-context algorithms in a simple part-of-speech setting using both practical and toy models. We find that active forgetting, a technique that was recently introduced to help models generalize to new languages, forces models to adopt structural in-context learning solutions. Finally, we introduce temporary forgetting, a straightforward extension of active forgetting that enables one to control how much a model relies on in-weights vs. in-context solutions. Importantly, temporary forgetting allows us to induce a dual process strategy where in-context and in-weights solutions coexist within a single model.

Multimodal models have demonstrated powerful capabilities in complex tasks requiring multimodal alignment including zero-shot classification and cross-modal retrieval. However, existing models typically rely on millions of paired multimodal samples, which are prohibitively expensive or infeasible to obtain in many domains. In this work, we explore the feasibility of building multimodal models with limited amount of paired data by aligning pretrained unimodal foundation models. We show that high-quality alignment is possible with as few as tens of thousands of paired samplesx2013less than 1% of the data typically used in the field. To achieve this, we introduce STRUCTURE, an effective regularization technique that preserves the neighborhood geometry of the latent space of unimodal encoders. Additionally, we show that aligning last layers is often suboptimal and demonstrate the benefits of aligning the layers with the highest representational similarity across modalities. These two components can be readily incorporated into existing alignment methods, yielding substantial gains across 24 zero-shot image classification and retrieval benchmarks, with average relative improvement of 51.6% in classification and 91.8% in retrieval tasks. Our results highlight the effectiveness and broad applicability of our framework for limited-sample multimodal learning and offer a promising path forward for resource-constrained domains.

Recently, the pre-trained language model, BERT (and its robustly optimized version RoBERTa), has attracted a lot of attention in natural language understanding (NLU), and achieved state-of-the-art accuracy in various NLU tasks, such as sentiment classification, natural language inference, semantic textual similarity and question answering. Inspired by the linearization exploration work of Elman [8], we extend BERT to a new model, StructBERT, by incorporating language structures into pre-training. Specifically, we pre-train StructBERT with two auxiliary tasks to make the most of the sequential order of words and sentences, which leverage language structures at the word and sentence levels, respectively. As a result, the new model is adapted to different levels of language understanding required by downstream tasks. The StructBERT with structural pre-training gives surprisingly good empirical results on a variety of downstream tasks, including pushing the state-of-the-art on the GLUE benchmark to 89.0 (outperforming all published models), the F1 score on SQuAD v1.1 question answering to 93.0, the accuracy on SNLI to 91.7.

The chain-structured long short-term memory (LSTM) has showed to be effective in a wide range of problems such as speech recognition and machine translation. In this paper, we propose to extend it to tree structures, in which a memory cell can reflect the history memories of multiple child cells or multiple descendant cells in a recursive process. We call the model S-LSTM, which provides a principled way of considering long-distance interaction over hierarchies, e.g., language or image parse structures. We leverage the models for semantic composition to understand the meaning of text, a fundamental problem in natural language understanding, and show that it outperforms a state-of-the-art recursive model by replacing its composition layers with the S-LSTM memory blocks. We also show that utilizing the given structures is helpful in achieving a performance better than that without considering the structures.

Vision-Language Pretraining (VLP) has achieved remarkable success across various downstream tasks, but such gains are largely driven by scaling up on training data. Yet, literature methods treat image-text pairs as isolated training examples; this neglects the rich relational structure naturally present in many domains, such as e-commerce product co-purchase graphs and social recommendation networks. Inspired by neuroscientific evidence that human encodes knowledge as relationship cognitive maps, we introduce Structure-aware Language-Image Pretraining (SLIP). SLIP integrates a structural contrastive loss to align modalities while also modeling relationships between neighboring entities in a structured graph. To support this paradigm, we construct a large-scale Amazon Product Co-purchase Multimodal Graph Dataset, enabling structured cross-modality supervision at scale. Experiment results show that SLIP consistently outperforms CLIP on cross-modal retrieval and classification tasks in both zero-shot and few-shot settings, showing the value of relational supervision for cross-modal alignment.

Vision and Language (VL) models have demonstrated remarkable zero-shot performance in a variety of tasks. However, some aspects of complex language understanding still remain a challenge. We introduce the collective notion of Structured Vision&Language Concepts (SVLC) which includes object attributes, relations, and states which are present in the text and visible in the image. Recent studies have shown that even the best VL models struggle with SVLC. A possible way of fixing this issue is by collecting dedicated datasets for teaching each SVLC type, yet this might be expensive and time-consuming. Instead, we propose a more elegant data-driven approach for enhancing VL models' understanding of SVLCs that makes more effective use of existing VL pre-training datasets and does not require any additional data. While automatic understanding of image structure still remains largely unsolved, language structure is much better modeled and understood, allowing for its effective utilization in teaching VL models. In this paper, we propose various techniques based on language structure understanding that can be used to manipulate the textual part of off-the-shelf paired VL datasets. VL models trained with the updated data exhibit a significant improvement of up to 15% in their SVLC understanding with only a mild degradation in their zero-shot capabilities both when training from scratch or fine-tuning a pre-trained model.

Graphs are able to model interconnected entities in many online services, supporting a wide range of applications on the Web. This raises an important question: How can we train a graph foundational model on multiple source domains and adapt to an unseen target domain? A major obstacle is that graphs from different domains often exhibit divergent characteristics. Some studies leverage large language models to align multiple domains based on textual descriptions associated with the graphs, limiting their applicability to text-attributed graphs. For text-free graphs, a few recent works attempt to align different feature distributions across domains, while generally neglecting structural differences. In this work, we propose a novel Structure Alignment framework for text-free Multi-domain Graph Pre-Training and cross-domain adaptation (SAMGPT). It is designed to learn multi-domain knowledge from graphs originating in multiple source domains, which can then be adapted to address applications in an unseen target domain. Specifically, we introduce a set of structure tokens to harmonize structure-based aggregation across source domains during the pre-training phase. Next, for cross-domain adaptation, we design dual prompts, namely, holistic prompts and specific prompts, which adapt unified multi-domain structural knowledge and fine-grained, domain-specific information, respectively, to a target domain. Finally, we conduct comprehensive experiments on seven public datasets to evaluate and analyze the effectiveness of SAMGPT.

Current language models tailored for code tasks often adopt the pre-training-then-fine-tuning paradigm from natural language processing, modeling source code as plain text. This approach, however, overlooks the unambiguous structures inherent in programming languages. In this work, we explore data-efficient adaptation of pre-trained code models by further pre-training and fine-tuning them with program structures. Specifically, we represent programs as parse trees -- also known as concrete syntax trees (CSTs) -- and adapt pre-trained models on serialized CSTs. Although the models that we adapt have been pre-trained only on the surface form of programs, we find that a small amount of continual pre-training and fine-tuning on CSTs without changing the model architecture yields improvements over the baseline approach across various code tasks. The improvements are found to be particularly significant when there are limited training examples, demonstrating the effectiveness of integrating program structures with plain-text representation even when working with backbone models that have not been pre-trained with structures.

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

In recent times, Vision-Language Models (VLMs) have been trained under two predominant paradigms. Generative training has enabled Multimodal Large Language Models (MLLMs) to tackle various complex tasks, yet issues such as hallucinations and weak object discrimination persist. Discriminative training, exemplified by models like CLIP, excels in zero-shot image-text classification and retrieval, yet struggles with complex scenarios requiring fine-grained semantic differentiation. This paper addresses these challenges by proposing a unified approach that integrates the strengths of both paradigms. Considering interleaved image-text sequences as the general format of input samples, we introduce a structure-induced training strategy that imposes semantic relationships between input samples and the MLLM's hidden state. This approach enhances the MLLM's ability to capture global semantics and distinguish fine-grained semantics. By leveraging dynamic sequence alignment within the Dynamic Time Warping framework and integrating a novel kernel for fine-grained semantic differentiation, our method effectively balances generative and discriminative tasks. Extensive experiments demonstrate the effectiveness of our approach, achieving state-of-the-art results in multiple generative tasks, especially those requiring cognitive and discrimination abilities. Additionally, our method surpasses discriminative benchmarks in interleaved and fine-grained retrieval tasks. By employing a retrieval-augmented generation strategy, our approach further enhances performance in some generative tasks within one model, offering a promising direction for future research in vision-language modeling.

Post-training, which elicits a pretrained Base model into the corresponding Instruct model, is widely considered to be superficial. In this work, we first reinforce this hypothesis by providing novel quantitative evidence from the weight level that the effective rank (eRank) remains negligibly changed. However, this superficiality also suffers a critical trade-off, improving the exploitation capabilities at the cost of limiting its exploration. To tackle this issue, we propose Timber, a simple yet effective training-free method that enhances the exploration capability of the Instruct model while preserving its exploitation. The key insight is to partially revert Instruct towards the paired Base model by subtle yet targeted refinement of the weight deltas. Extensive experiments on Llama and Qwen series demonstrate that Timber consistently improves vanilla Instruct models, particularly on Pass@k performance. Our findings offer new insights into the post-training stage at the weight level and practical strategies to refine the Instruct model without training.

Motion trajectories offer reliable references for physics-based motion learning but suffer from sparsity, particularly in regions that lack sufficient data coverage. To address this challenge, we introduce a self-supervised, structured representation and generation method that extracts spatial-temporal relationships in periodic or quasi-periodic motions. The motion dynamics in a continuously parameterized latent space enable our method to enhance the interpolation and generalization capabilities of motion learning algorithms. The motion learning controller, informed by the motion parameterization, operates online tracking of a wide range of motions, including targets unseen during training. With a fallback mechanism, the controller dynamically adapts its tracking strategy and automatically resorts to safe action execution when a potentially risky target is proposed. By leveraging the identified spatial-temporal structure, our work opens new possibilities for future advancements in general motion representation and learning algorithms.

Learning spatial-temporal correspondences in cardiac motion from images is important for understanding the underlying dynamics of cardiac anatomical structures. Many methods explicitly impose smoothness constraints such as the L_2 norm on the displacement vector field (DVF), while usually ignoring biomechanical feasibility in the transformation. Other geometric constraints either regularize specific regions of interest such as imposing incompressibility on the myocardium or introduce additional steps such as training a separate network-based regularizer on physically simulated datasets. In this work, we propose an explicit biomechanics-informed prior as regularization on the predicted DVF in modeling a more generic biomechanically plausible transformation within all cardiac structures without introducing additional training complexity. We validate our methods on two publicly available datasets in the context of 2D MRI data and perform extensive experiments to illustrate the effectiveness and robustness of our proposed methods compared to other competing regularization schemes. Our proposed methods better preserve biomechanical properties by visual assessment and show advantages in segmentation performance using quantitative evaluation metrics. The code is publicly available at https://github.com/Voldemort108X/bioinformed_reg.

Recent developments in long-context large language models have attracted considerable attention. Yet, their real-world applications are often hindered by ineffective context information use. This work shows that structuring training data to increase semantic interdependence is an effective strategy for optimizing context utilization. To this end, we introduce Structured Packing for Long Context (SPLiCe), a method for creating training examples by using information retrieval methods to collate mutually relevant documents into a single training context. We empirically validate SPLiCe on large 3B and 7B models, showing perplexity improvements and better long-context utilization on downstream tasks. Remarkably, already relatively short fine-tuning with SPLiCe is enough to attain these benefits. Additionally, the comprehensive study of SPLiCe reveals intriguing transfer effects such as training on code data leading to perplexity improvements on text data.

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

State-of-the-art results in large language models (LLMs) often rely on scale, which becomes computationally expensive. This has sparked a research agenda to reduce these models' parameter counts and computational costs without significantly impacting their performance. Our study focuses on transformer-based LLMs, specifically targeting the computationally intensive feedforward networks (FFNs), which are less studied than attention blocks. We consider three structured linear parameterizations of the FFN using efficient low-rank and block-diagonal matrices. In contrast to many previous works that examined these approximations, our study i) explores these structures from a training-from-scratch perspective, ii) scales up to 1.3B parameters, and iii) is conducted within recent Transformer-based LLMs rather than convolutional architectures. We demonstrate that these structures can lead to actual computational gains in various scenarios, including online decoding when using a pre-merge technique. Additionally, we propose a novel training regime, called self-guided training, aimed at improving the poor training dynamics that these approximations exhibit when used from initialization. Interestingly, the scaling performance of structured matrices is explored, revealing steeper curves in scaling training FLOPs, along with a favorable scaling trend in the overtraining regime. Specifically, we show that wide and structured networks can utilize training FLOPs more efficiently, with fewer parameters and lower loss than dense models at their optimal trade-off. Our code is available at https://github.com/CLAIRE-Labo/StructuredFFN/tree/main.

We propose STRuCT-LLM, a unified framework for training large language models (LLMs) to perform structured reasoning over both relational and graph-structured data. Our approach jointly optimizes Text-to-SQL and Text-to-Cypher tasks using reinforcement learning (RL) combined with Chain-of-Thought (CoT) supervision. To support fine-grained optimization in graph-based parsing, we introduce a topology-aware reward function based on graph edit distance. Unlike prior work that treats relational and graph formalisms in isolation, STRuCT-LLM leverages shared abstractions between SQL and Cypher to induce cross-formalism transfer, enabling SQL training to improve Cypher performance and vice versa - even without shared schemas. Our largest model (QwQ-32B) achieves substantial relative improvements across tasks: on semantic parsing, Spider improves by 13.5\% and Text2Cypher by 73.1\%. The model also demonstrates strong zero-shot generalization, improving performance on downstream tabular QA (TableBench: 8.5\%) and knowledge graph QA (CR-LT-KGQA: 1.7\%) without any QA-specific supervision. These results demonstrate both the effectiveness of executable queries as scaffolds for structured reasoning and the synergistic benefits of jointly training on SQL and Cypher (code available at https://github.com/bouv/STRuCT-LLM).

When reading long-form text, human cognition is complex and structurized. While large language models (LLMs) process input contexts through a causal and sequential perspective, this approach can potentially limit their ability to handle intricate and complex inputs effectively. To enhance LLM's cognition capability, this paper presents a novel concept of context structurization. Specifically, we transform the plain, unordered contextual sentences into well-ordered and hierarchically structurized elements. By doing so, LLMs can better grasp intricate and extended contexts through precise attention and information-seeking along the organized structures. Extensive evaluations are conducted across various model architectures and sizes (including a series of auto-regressive LLMs as well as BERT-like masking models) on a diverse set of NLP tasks (e.g., context-based question-answering, exhaustive hallucination evaluation, and passage-level dense retrieval). Empirical results show consistent and significant performance gains afforded by a single-round structurization. In particular, we boost the open-sourced LLaMA2-70B model to achieve comparable performance against GPT-3.5-Turbo as the hallucination evaluator. Besides, we show the feasibility of distilling advanced LLMs' language processing abilities to a smaller yet effective StruXGPT-7B to execute structurization, addressing the practicality of our approach. Code is available at https://github.com/alibaba/struxgpt.

Visually-situated language is ubiquitous -- sources range from textbooks with diagrams to web pages with images and tables, to mobile apps with buttons and forms. Perhaps due to this diversity, previous work has typically relied on domain-specific recipes with limited sharing of the underlying data, model architectures, and objectives. We present Pix2Struct, a pretrained image-to-text model for purely visual language understanding, which can be finetuned on tasks containing visually-situated language. Pix2Struct is pretrained by learning to parse masked screenshots of web pages into simplified HTML. The web, with its richness of visual elements cleanly reflected in the HTML structure, provides a large source of pretraining data well suited to the diversity of downstream tasks. Intuitively, this objective subsumes common pretraining signals such as OCR, language modeling, image captioning. In addition to the novel pretraining strategy, we introduce a variable-resolution input representation and a more flexible integration of language and vision inputs, where language prompts such as questions are rendered directly on top of the input image. For the first time, we show that a single pretrained model can achieve state-of-the-art results in six out of nine tasks across four domains: documents, illustrations, user interfaces, and natural images.

Discovering the underlying relationships among variables from temporal observations has been a longstanding challenge in numerous scientific disciplines, including biology, finance, and climate science. The dynamics of such systems are often best described using continuous-time stochastic processes. Unfortunately, most existing structure learning approaches assume that the underlying process evolves in discrete-time and/or observations occur at regular time intervals. These mismatched assumptions can often lead to incorrect learned structures and models. In this work, we introduce a novel structure learning method, SCOTCH, which combines neural stochastic differential equations (SDE) with variational inference to infer a posterior distribution over possible structures. This continuous-time approach can naturally handle both learning from and predicting observations at arbitrary time points. Theoretically, we establish sufficient conditions for an SDE and SCOTCH to be structurally identifiable, and prove its consistency under infinite data limits. Empirically, we demonstrate that our approach leads to improved structure learning performance on both synthetic and real-world datasets compared to relevant baselines under regular and irregular sampling intervals.

Graph contrastive learning (GCL) has become a powerful tool for learning graph data, but its scalability remains a significant challenge. In this work, we propose a simple yet effective training framework called Structural Compression (StructComp) to address this issue. Inspired by a sparse low-rank approximation on the diffusion matrix, StructComp trains the encoder with the compressed nodes. This allows the encoder not to perform any message passing during the training stage, and significantly reduces the number of sample pairs in the contrastive loss. We theoretically prove that the original GCL loss can be approximated with the contrastive loss computed by StructComp. Moreover, StructComp can be regarded as an additional regularization term for GCL models, resulting in a more robust encoder. Empirical studies on seven benchmark datasets show that StructComp greatly reduces the time and memory consumption while improving model performance compared to the vanilla GCL models and scalable training methods.

We introduce "pointer-guided segment ordering" (SO), a novel pre-training technique aimed at enhancing the contextual understanding of paragraph-level text representations in large language models. Our methodology leverages a self-attention-driven pointer network to restore the original sequence of shuffled text segments, addressing the challenge of capturing the structural coherence and contextual dependencies within documents. This pre-training approach is complemented by a fine-tuning methodology that incorporates dynamic sampling, augmenting the diversity of training instances and improving sample efficiency for various downstream applications. We evaluate our method on a diverse set of datasets, demonstrating its efficacy in tasks requiring sequential text classification across scientific literature and financial reporting domains. Our experiments show that pointer-guided pre-training significantly enhances the model's ability to understand complex document structures, leading to state-of-the-art performance in downstream classification tasks.

In this paper we present APEX-Embedding-7B (Advanced Processing for Epistemic eXtraction), a 7-billion parameter decoder-only text Feature Extraction Model, specifically designed for Document Retrieval-Augmented Generation (RAG) tasks. Our approach employs two training techniques that yield an emergent improvement in factual focus: (1) Pre-convergence interrupted fine-tuning using Structured Entity Relationship Maps as training data input: designed to shift the model's attention and create a bias towards factual content rather than semantic style - this enhances plain text performance despite not being directly trained for it; and (2) Model-Aware Contrastive Sampling, creating a balanced and evenly distributed collation map of hard and soft negatives directly informed by the base model's competency. This combined methodology yields significant improvements, enhancing plain text query/document pair retrieval to achieve an absolute rank@1 accuracy of 90.86% (an increase of 6.26% compared to the next leading model) in our evaluation, and reducing training data input context size by an average of 37.71% compared to plain text for both queries and document texts. Based on our evaluations, our model establishes a new state-of-the-art standard in text feature extraction for longer context document retrieval tasks.

In this work, we present a naive initialization scheme for word vectors based on a dense, independent co-occurrence model and provide preliminary results that suggest it is competitive and warrants further investigation. Specifically, we demonstrate through information-theoretic minimum description length (MDL) probing that our model, EigenNoise, can approach the performance of empirically trained GloVe despite the lack of any pre-training data (in the case of EigenNoise). We present these preliminary results with interest to set the stage for further investigations into how this competitive initialization works without pre-training data, as well as to invite the exploration of more intelligent initialization schemes informed by the theory of harmonic linguistic structure. Our application of this theory likewise contributes a novel (and effective) interpretation of recent discoveries which have elucidated the underlying distributional information that linguistic representations capture from data and contrast distributions.

Recent advancements in Large Language Models (LLMs) such as GPT4 have displayed exceptional multi-modal capabilities in following open-ended instructions given images. However, the performance of these models heavily relies on design choices such as network structures, training data, and training strategies, and these choices have not been extensively discussed in the literature, making it difficult to quantify progress in this field. To address this issue, this paper presents a systematic and comprehensive study, quantitatively and qualitatively, on training such models. We implement over 20 variants with controlled settings. Concretely, for network structures, we compare different LLM backbones and model designs. For training data, we investigate the impact of data and sampling strategies. For instructions, we explore the influence of diversified prompts on the instruction-following ability of the trained models. For benchmarks, we contribute the first, to our best knowledge, comprehensive evaluation set including both image and video tasks through crowd-sourcing. Based on our findings, we present Lynx, which performs the most accurate multi-modal understanding while keeping the best multi-modal generation ability compared to existing open-sourced GPT4-style models.

Large language models (LLMs) excel in language tasks, especially with supervised fine-tuning after pre-training. However, their substantial memory and computational requirements hinder practical applications. Structural pruning, which reduces less significant weight dimensions, is one solution. Yet, traditional post-hoc pruning often leads to significant performance loss, with limited recovery from further fine-tuning due to reduced capacity. Since the model fine-tuning refines the general and chaotic knowledge in pre-trained models, we aim to incorporate structural pruning with the fine-tuning, and propose the Pruning-Aware Tuning (PAT) paradigm to eliminate model redundancy while preserving the model performance to the maximum extend. Specifically, we insert the innovative Hybrid Sparsification Modules (HSMs) between the Attention and FFN components to accordingly sparsify the upstream and downstream linear modules. The HSM comprises a lightweight operator and a globally shared trainable mask. The lightweight operator maintains a training overhead comparable to that of LoRA, while the trainable mask unifies the channels to be sparsified, ensuring structural pruning. Additionally, we propose the Identity Loss which decouples the transformation and scaling properties of the HSMs to enhance training robustness. Extensive experiments demonstrate that PAT excels in both performance and efficiency. For example, our Llama2-7b model with a 25\% pruning ratio achieves 1.33times speedup while outperforming the LoRA-finetuned model by up to 1.26\% in accuracy with a similar training cost. Code: https://github.com/kriskrisliu/PAT_Pruning-Aware-Tuning

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

We present an approach for assessing how multilingual large language models (LLMs) learn syntax in terms of multi-formalism syntactic structures. We aim to recover constituent and dependency structures by casting parsing as sequence labeling. To do so, we select a few LLMs and study them on 13 diverse UD treebanks for dependency parsing and 10 treebanks for constituent parsing. Our results show that: (i) the framework is consistent across encodings, (ii) pre-trained word vectors do not favor constituency representations of syntax over dependencies, (iii) sub-word tokenization is needed to represent syntax, in contrast to character-based models, and (iv) occurrence of a language in the pretraining data is more important than the amount of task data when recovering syntax from the word vectors.

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

This paper investigates efficient deep neural networks (DNNs) to replace dense unstructured weight matrices with structured ones that possess desired properties. The challenge arises because the optimal weight matrix structure in popular neural network models is obscure in most cases and may vary from layer to layer even in the same network. Prior structured matrices proposed for efficient DNNs were mostly hand-crafted without a generalized framework to systematically learn them. To address this issue, we propose a generalized and differentiable framework to learn efficient structures of weight matrices by gradient descent. We first define a new class of structured matrices that covers a wide range of structured matrices in the literature by adjusting the structural parameters. Then, the frequency-domain differentiable parameterization scheme based on the Gaussian-Dirichlet kernel is adopted to learn the structural parameters by proximal gradient descent. On the image and language tasks, our method learns efficient DNNs with structured matrices, achieving lower complexity and/or higher performance than prior approaches that employ low-rank, block-sparse, or block-low-rank matrices.

Large language models (LLMs) learn a vast amount of knowledge during pretraining, but they are often oblivious to the source(s) of such knowledge. We investigate the problem of intrinsic source citation, where LLMs are required to cite the pretraining source supporting a generated response. Intrinsic source citation can enhance LLM transparency, interpretability, and verifiability. To give LLMs such ability, we explore source-aware training -- a post pretraining recipe that involves (i) training the LLM to associate unique source document identifiers with the knowledge in each document, followed by (ii) an instruction-tuning to teach the LLM to cite a supporting pretraining source when prompted. Source-aware training can easily be applied to pretrained LLMs off the shelf, and diverges minimally from existing pretraining/fine-tuning frameworks. Through experiments on carefully curated data, we demonstrate that our training recipe can enable faithful attribution to the pretraining data without a substantial impact on the model's quality compared to standard pretraining. Our results also highlight the importance of data augmentation in achieving attribution.

Large language models (LLMs) have shown impressive capabilities across various tasks. However, training LLMs from scratch requires significant computational power and extensive memory capacity. Recent studies have explored low-rank structures on weights for efficient fine-tuning in terms of parameters and memory, either through low-rank adaptation or factorization. While effective for fine-tuning, low-rank structures are generally less suitable for pretraining because they restrict parameters to a low-dimensional subspace. In this work, we propose to parameterize the weights as a sum of low-rank and sparse matrices for pretraining, which we call SLTrain. The low-rank component is learned via matrix factorization, while for the sparse component, we employ a simple strategy of uniformly selecting the sparsity support at random and learning only the non-zero entries with the fixed support. While being simple, the random fixed-support sparse learning strategy significantly enhances pretraining when combined with low-rank learning. Our results show that SLTrain adds minimal extra parameters and memory costs compared to pretraining with low-rank parameterization, yet achieves substantially better performance, which is comparable to full-rank training. Remarkably, when combined with quantization and per-layer updates, SLTrain can reduce memory requirements by up to 73% when pretraining the LLaMA 7B model.

Models need appropriate inductive biases to effectively learn from small amounts of data and generalize systematically outside of the training distribution. While Transformers are highly versatile and powerful, they can still benefit from enhanced structural inductive biases for seq2seq tasks, especially those involving syntactic transformations, such as converting active to passive voice or semantic parsing. In this paper, we propose to strengthen the structural inductive bias of a Transformer by intermediate pre-training to perform synthetically generated syntactic transformations of dependency trees given a description of the transformation. Our experiments confirm that this helps with few-shot learning of syntactic tasks such as chunking, and also improves structural generalization for semantic parsing. Our analysis shows that the intermediate pre-training leads to attention heads that keep track of which syntactic transformation needs to be applied to which token, and that the model can leverage these attention heads on downstream tasks.

This article explores the adaptive relationship between Encoder Layers and Decoder Layers using the SOTA model Helsinki-NLP/opus-mt-de-en, which translates German to English. The specific method involves introducing a bias-free fully connected layer between the Encoder and Decoder, with different initializations of the layer's weights, and observing the outcomes of fine-tuning versus retraining. Four experiments were conducted in total. The results suggest that directly modifying the pre-trained model structure for fine-tuning yields suboptimal performance. However, upon observing the outcomes of the experiments with retraining, this structural adjustment shows significant potential.

A salient characteristic of pre-trained language models (PTLMs) is a remarkable improvement in their generalization capability and emergence of new capabilities with increasing model capacity and pre-training dataset size. Consequently, we are witnessing the development of enormous models pushing the state-of-the-art. It is, however, imperative to realize that this inevitably leads to prohibitively long training times, extortionate computing costs, and a detrimental environmental impact. Significant efforts are underway to make PTLM training more efficient through innovations in model architectures, training pipelines, and loss function design, with scant attention being paid to optimizing the utility of training data. The key question that we ask is whether it is possible to train PTLMs by employing only highly informative subsets of the training data while maintaining downstream performance? Building upon the recent progress in informative data subset selection, we show how we can employ submodular optimization to select highly representative subsets of the training corpora and demonstrate that the proposed framework can be applied to efficiently train multiple PTLMs (BERT, BioBERT, GPT-2) using only a fraction of data. Further, we perform a rigorous empirical evaluation to show that the resulting models achieve up to sim99% of the performance of the fully-trained models. We made our framework publicly available at https://github.com/Efficient-AI/ingenious.

The automated analysis of chemical literature holds promise to accelerate discovery in fields such as material science and drug development. In particular, search capabilities for chemical structures and Markush structures (chemical structure templates) within patent documents are valuable, e.g., for prior-art search. Advancements have been made in the automatic extraction of chemical structures from text and images, yet the Markush structures remain largely unexplored due to their complex multi-modal nature. In this work, we present MarkushGrapher, a multi-modal approach for recognizing Markush structures in documents. Our method jointly encodes text, image, and layout information through a Vision-Text-Layout encoder and an Optical Chemical Structure Recognition vision encoder. These representations are merged and used to auto-regressively generate a sequential graph representation of the Markush structure along with a table defining its variable groups. To overcome the lack of real-world training data, we propose a synthetic data generation pipeline that produces a wide range of realistic Markush structures. Additionally, we present M2S, the first annotated benchmark of real-world Markush structures, to advance research on this challenging task. Extensive experiments demonstrate that our approach outperforms state-of-the-art chemistry-specific and general-purpose vision-language models in most evaluation settings. Code, models, and datasets will be available.

The quality of training data impacts the performance of pre-trained large language models (LMs). Given a fixed budget of tokens, we study how to best select data that leads to good downstream model performance across tasks. We develop a new framework based on a simple hypothesis: just as humans acquire interdependent skills in a deliberate order, language models also follow a natural order when learning a set of skills from their training data. If such an order exists, it can be utilized for improved understanding of LMs and for data-efficient training. Using this intuition, our framework formalizes the notion of a skill and of an ordered set of skills in terms of the associated data. First, using both synthetic and real data, we demonstrate that these ordered skill sets exist, and that their existence enables more advanced skills to be learned with less data when we train on their prerequisite skills. Second, using our proposed framework, we introduce an online data sampling algorithm, Skill-It, over mixtures of skills for both continual pre-training and fine-tuning regimes, where the objective is to efficiently learn multiple skills in the former and an individual skill in the latter. On the LEGO synthetic in the continual pre-training setting, Skill-It obtains 36.5 points higher accuracy than random sampling. On the Natural Instructions dataset in the fine-tuning setting, Skill-It reduces the validation loss on the target skill by 13.6% versus training on data associated with the target skill itself. We apply our skills framework on the recent RedPajama dataset to continually pre-train a 3B-parameter LM, achieving higher accuracy on the LM Evaluation Harness with 1B tokens than the baseline approach of sampling uniformly over data sources with 3B tokens.

Pre-trained language models (LMs) are capable of in-context learning (ICL): they can adapt to a task with only a few examples given in the prompt without any parameter update. However, it is unclear where this capability comes from as there is a stark distribution shift between pre-training text and ICL prompts. In this work, we study what patterns of the pre-training data contribute to ICL. We find that LMs' ICL ability depends on parallel structures in the pre-training data -- pairs of phrases following similar templates in the same context window. Specifically, we detect parallel structures by checking whether training on one phrase improves prediction of the other, and conduct ablation experiments to study their effect on ICL. We show that removing parallel structures in the pre-training data reduces LMs' ICL accuracy by 51% (vs 2% from random ablation). This drop persists even when excluding common patterns such as n-gram repetitions and long-range dependency, showing the diversity and generality of parallel structures. A closer look at the detected parallel structures indicates that they cover diverse linguistic tasks and span long distances in the data.

Multi-task learning has the potential to improve generalization by maximizing positive transfer between tasks while reducing task interference. Fully achieving this potential is hindered by manually designed architectures that remain static throughout training. On the contrary, learning in the brain occurs through structural changes that are in tandem with changes in synaptic strength. Thus, we propose Multi-Task Structural Learning (MTSL) that simultaneously learns the multi-task architecture and its parameters. MTSL begins with an identical single-task network for each task and alternates between a task-learning phase and a structural-learning phase. In the task learning phase, each network specializes in the corresponding task. In each of the structural learning phases, starting from the earliest layer, locally similar task layers first transfer their knowledge to a newly created group layer before being removed. MTSL then uses the group layer in place of the corresponding removed task layers and moves on to the next layers. Our empirical results show that MTSL achieves competitive generalization with various baselines and improves robustness to out-of-distribution data.

Large language model (LLM) based knowledge graph completion (KGC) aims to predict the missing triples in the KGs with LLMs and enrich the KGs to become better web infrastructure, which can benefit a lot of web-based automatic services. However, research about LLM-based KGC is limited and lacks effective utilization of LLM's inference capabilities, which ignores the important structural information in KGs and prevents LLMs from acquiring accurate factual knowledge. In this paper, we discuss how to incorporate the helpful KG structural information into the LLMs, aiming to achieve structrual-aware reasoning in the LLMs. We first transfer the existing LLM paradigms to structural-aware settings and further propose a knowledge prefix adapter (KoPA) to fulfill this stated goal. KoPA employs structural embedding pre-training to capture the structural information of entities and relations in the KG. Then KoPA informs the LLMs of the knowledge prefix adapter which projects the structural embeddings into the textual space and obtains virtual knowledge tokens as a prefix of the input prompt. We conduct comprehensive experiments on these structural-aware LLM-based KGC methods and provide an in-depth analysis comparing how the introduction of structural information would be better for LLM's knowledge reasoning ability. Our code is released at https://github.com/zjukg/KoPA.

Current Multimodal Large Language Models (MLLMs) typically integrate a pre-trained LLM with another pre-trained vision transformer through a connector, such as an MLP, endowing the LLM with visual capabilities. However, the misalignment between two embedding strategies in MLLMs -- the structural textual embeddings based on an embedding look-up table and the continuous embeddings generated directly by the vision encoder -- makes challenges for a more seamless fusion of visual and textual information. We propose Ovis, a novel MLLM architecture designed to structurally align visual and textual embeddings. Ovis integrates an additional learnable visual embedding table into the visual encoder's process. To capture rich visual semantics, each image patch indexes the visual embedding table multiple times, resulting in a final visual embedding that is a probabilistic combination of the indexed embeddings. This structural approach mirrors the method used for generating textual embeddings. Empirical evaluations on various multimodal benchmarks demonstrate that Ovis outperforms open-source MLLMs of similar parameter scales and even surpasses the proprietary model Qwen-VL-Plus overall. These results highlight the potential of Ovis' structured visual representation for advancing MLLM architectural design and promoting more effective multimodal learning. Both the source code and the training dataset of Ovis will be made publicly available.

For an LLM to correctly respond to an instruction it must understand both the semantics and the domain (i.e., subject area) of a given task-instruction pair. However, syntax can also convey implicit information Recent work shows that syntactic templates -- frequent sequences of Part-of-Speech (PoS) tags -- are prevalent in training data and often appear in model outputs. In this work we characterize syntactic templates, domain, and semantics in task-instruction pairs. We identify cases of spurious correlations between syntax and domain, where models learn to associate a domain with syntax during training; this can sometimes override prompt semantics. Using a synthetic training dataset, we find that the syntactic-domain correlation can lower performance (mean 0.51 +/- 0.06) on entity knowledge tasks in OLMo-2 models (1B-13B). We introduce an evaluation framework to detect this phenomenon in trained models, and show that it occurs on a subset of the FlanV2 dataset in open (OLMo-2-7B; Llama-4-Maverick), and closed (GPT-4o) models. Finally, we present a case study on the implications for safety finetuning, showing that unintended syntactic-domain correlations can be used to bypass refusals in OLMo-2-7B Instruct and GPT-4o. Our findings highlight two needs: (1) to explicitly test for syntactic-domain correlations, and (2) to ensure syntactic diversity in training data, specifically within domains, to prevent such spurious correlations.

As the size of deep learning models continues to grow, finding optimal models under memory and computation constraints becomes increasingly more important. Although usually the architecture and constituent building blocks of neural networks allow them to be used in a modular way, their training process is not aware of this modularity. Consequently, conventional neural network training lacks the flexibility to adapt the computational load of the model during inference. This paper proposes SortedNet, a generalized and scalable solution to harness the inherent modularity of deep neural networks across various dimensions for efficient dynamic inference. Our training considers a nested architecture for the sub-models with shared parameters and trains them together with the main model in a sorted and probabilistic manner. This sorted training of sub-networks enables us to scale the number of sub-networks to hundreds using a single round of training. We utilize a novel updating scheme during training that combines random sampling of sub-networks with gradient accumulation to improve training efficiency. Furthermore, the sorted nature of our training leads to a search-free sub-network selection at inference time; and the nested architecture of the resulting sub-networks leads to minimal storage requirement and efficient switching between sub-networks at inference. Our general dynamic training approach is demonstrated across various architectures and tasks, including large language models and pre-trained vision models. Experimental results show the efficacy of the proposed approach in achieving efficient sub-networks while outperforming state-of-the-art dynamic training approaches. Our findings demonstrate the feasibility of training up to 160 different sub-models simultaneously, showcasing the extensive scalability of our proposed method while maintaining 96% of the model performance.

We argue that progress toward general intelligence requires complementary foundation models grounded in language, the physical world, and structured data. This report presents LimiX, the first installment of our large structured-data models (LDMs). LimiX treats structured data as a joint distribution over variables and missingness, thus capable of addressing a wide range of tabular tasks through query-based conditional prediction via a single model. LimiX is pretrained using masked joint-distribution modeling with an episodic, context-conditional objective, where the model predicts for query subsets conditioned on dataset-specific contexts, supporting rapid, training-free adaptation at inference. We evaluate LimiX across 10 large structured-data benchmarks with broad regimes of sample size, feature dimensionality, class number, categorical-to-numerical feature ratio, missingness, and sample-to-feature ratios. With a single model and a unified interface, LimiX consistently surpasses strong baselines including gradient-boosting trees, deep tabular networks, recent tabular foundation models, and automated ensembles, as shown in Figure 1 and Figure 2. The superiority holds across a wide range of tasks, such as classification, regression, missing value imputation, and data generation, often by substantial margins, while avoiding task-specific architectures or bespoke training per task. All LimiX models are publicly accessible under Apache 2.0.

Heterogeneous tabular data poses unique challenges in generative modelling due to its fundamentally different underlying data structure compared to homogeneous modalities, such as images and text. Although previous research has sought to adapt the successes of generative modelling in homogeneous modalities to the tabular domain, defining an effective generator for tabular data remains an open problem. One major reason is that the evaluation criteria inherited from other modalities often fail to adequately assess whether tabular generative models effectively capture or utilise the unique structural information encoded in tabular data. In this paper, we carefully examine the limitations of the prevailing evaluation framework and introduce TabStruct, a novel evaluation benchmark that positions structural fidelity as a core evaluation dimension. Specifically, TabStruct evaluates the alignment of causal structures in real and synthetic data, providing a direct measure of how effectively tabular generative models learn the structure of tabular data. Through extensive experiments using generators from eight categories on seven datasets with expert-validated causal graphical structures, we show that structural fidelity offers a task-independent, domain-agnostic evaluation dimension. Our findings highlight the importance of tabular data structure and offer practical guidance for developing more effective and robust tabular generative models. Code is available at https://github.com/SilenceX12138/TabStruct.

Dense linear layers are the dominant computational bottleneck in foundation models. Identifying more efficient alternatives to dense matrices has enormous potential for building more compute-efficient models, as exemplified by the success of convolutional networks in the image domain. In this work, we systematically explore structured matrices as replacements for dense matrices. We show that different structures often require drastically different initialization scales and learning rates, which are crucial to performance, especially as models scale. Using insights from the Maximal Update Parameterization, we determine the optimal scaling for initialization and learning rates of these unconventional layers. Finally, we measure the scaling laws of different structures to compare how quickly their performance improves with compute. We propose a novel matrix family containing Monarch matrices, the Block Tensor-Train (BTT), which we show performs better than dense matrices for the same compute on multiple tasks. On CIFAR-10/100 with augmentation, BTT achieves exponentially lower training loss than dense when training MLPs and ViTs. BTT matches dense ViT-S/32 performance on ImageNet-1k with 3.8 times less compute and is more efficient than dense for training small GPT-2 language models.

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and others parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

Large language models show impressive results on few-shot NLP tasks. However, these models are memory and computation-intensive. Meta-training allows one to leverage smaller models for few-shot generalization in a domain-general and task-agnostic manner; however, these methods alone results in models that may not have sufficient parameterization or knowledge to adapt quickly to a large variety of tasks. To overcome this issue, we propose meta-training with demonstration retrieval, where we use a dense passage retriever to retrieve semantically similar labeled demonstrations to each example for more varied supervision. By separating external knowledge from model parameters, we can use meta-training to train parameter-efficient models that generalize well on a larger variety of tasks. We construct a meta-training set from UnifiedQA and CrossFit, and propose a demonstration bank based on UnifiedQA tasks. To our knowledge, our work is the first to combine retrieval with meta-training, to use DPR models to retrieve demonstrations, and to leverage demonstrations from many tasks simultaneously, rather than randomly sampling demonstrations from the training set of the target task. Our approach outperforms a variety of targeted parameter-efficient and retrieval-augmented few-shot methods on QA, NLI, and text classification tasks (including SQuAD, QNLI, and TREC). Our approach can be meta-trained and fine-tuned quickly on a single GPU.

This paper investigates the ability of transformer-based models to learn structural recursion from examples. Recursion is a universal concept in both natural and formal languages. Structural recursion is central to the programming language and formal mathematics tasks where symbolic tools currently excel beyond neural models, such as inferring semantic relations between datatypes and emulating program behavior. We introduce a general framework that nicely connects the abstract concepts of structural recursion in the programming language domain to concrete sequence modeling problems and learned models' behavior. The framework includes a representation that captures the general syntax of structural recursion, coupled with two different frameworks for understanding their semantics -- one that is more natural from a programming languages perspective and one that helps bridge that perspective with a mechanistic understanding of the underlying transformer architecture. With our framework as a powerful conceptual tool, we identify different issues under various set-ups. The models trained to emulate recursive computations cannot fully capture the recursion yet instead fit short-cut algorithms and thus cannot solve certain edge cases that are under-represented in the training distribution. In addition, it is difficult for state-of-the-art large language models (LLMs) to mine recursive rules from in-context demonstrations. Meanwhile, these LLMs fail in interesting ways when emulating reduction (step-wise computation) of the recursive function.

Transformers generalize to novel compositions of structures and entities after being trained on a complex dataset, but easily overfit on datasets of insufficient complexity. We observe that when the training set is sufficiently complex, the model encodes sentences that have a common syntactic structure using a systematic attention pattern. Inspired by this observation, we propose SQ-Transformer (Structurally Quantized) that explicitly encourages systematicity in the embeddings and attention layers, even with a training set of low complexity. At the embedding level, we introduce Structure-oriented Vector Quantization (SoVQ) to cluster word embeddings into several classes of structurally equivalent entities. At the attention level, we devise the Systematic Attention Layer (SAL) and an alternative, Systematically Regularized Layer (SRL) that operate on the quantized word embeddings so that sentences of the same structure are encoded with invariant or similar attention patterns. Empirically, we show that SQ-Transformer achieves stronger compositional generalization than the vanilla Transformer on multiple low-complexity semantic parsing and machine translation datasets. In our analysis, we show that SoVQ indeed learns a syntactically clustered embedding space and SAL/SRL induces generalizable attention patterns, which lead to improved systematicity.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

Fine-tuning pre-trained language models (PLMs) has recently shown a potential to improve knowledge graph completion (KGC). However, most PLM-based methods focus solely on encoding textual information, neglecting the long-tailed nature of knowledge graphs and their various topological structures, e.g., subgraphs, shortest paths, and degrees. We claim that this is a major obstacle to achieving higher accuracy of PLMs for KGC. To this end, we propose a Subgraph-Aware Training framework for KGC (SATKGC) with two ideas: (i) subgraph-aware mini-batching to encourage hard negative sampling and to mitigate an imbalance in the frequency of entity occurrences during training, and (ii) new contrastive learning to focus more on harder in-batch negative triples and harder positive triples in terms of the structural properties of the knowledge graph. To the best of our knowledge, this is the first study to comprehensively incorporate the structural inductive bias of the knowledge graph into fine-tuning PLMs. Extensive experiments on three KGC benchmarks demonstrate the superiority of SATKGC. Our code is available.

Training models with varying capacities can be advantageous for deploying them in different scenarios. While high-capacity models offer better performance, low-capacity models require fewer computing resources for training and inference. In this work, we propose a novel one-stop training framework to jointly train high-capacity and low-capactiy models. This framework consists of two composite model architectures and a joint training algorithm called Two-Stage Joint-Training (TSJT). Unlike knowledge distillation, where multiple capacity models are trained from scratch separately, our approach integrates supervisions from different capacity models simultaneously, leading to faster and more efficient convergence. Extensive experiments on the multilingual machine translation benchmark WMT10 show that our method outperforms low-capacity baseline models and achieves comparable or better performance on high-capacity models. Notably, the analysis demonstrates that our method significantly influences the initial training process, leading to more efficient convergence and superior solutions.

Abstract meaning representation (AMR) highlights the core semantic information of text in a graph structure. Recently, pre-trained language models (PLMs) have advanced tasks of AMR parsing and AMR-to-text generation, respectively. However, PLMs are typically pre-trained on textual data, thus are sub-optimal for modeling structural knowledge. To this end, we investigate graph self-supervised training to improve the structure awareness of PLMs over AMR graphs. In particular, we introduce two graph auto-encoding strategies for graph-to-graph pre-training and four tasks to integrate text and graph information during pre-training. We further design a unified framework to bridge the gap between pre-training and fine-tuning tasks. Experiments on both AMR parsing and AMR-to-text generation show the superiority of our model. To our knowledge, we are the first to consider pre-training on semantic graphs.

Large Language Models (LLMs) have shown strong potential for tabular data generation by modeling textualized feature-value pairs. However, tabular data inherently exhibits sparse feature-level dependencies, where many feature interactions are structurally insignificant. This creates a fundamental mismatch as LLMs' self-attention mechanism inevitably distributes focus across all pairs, diluting attention on critical relationships, particularly in datasets with complex dependencies or semantically ambiguous features. To address this limitation, we propose GraDe (Graph-Guided Dependency Learning), a novel method that explicitly integrates sparse dependency graphs into LLMs' attention mechanism. GraDe employs a lightweight dynamic graph learning module guided by externally extracted functional dependencies, prioritizing key feature interactions while suppressing irrelevant ones. Our experiments across diverse real-world datasets demonstrate that GraDe outperforms existing LLM-based approaches by up to 12% on complex datasets while achieving competitive results with state-of-the-art approaches in synthetic data quality. Our method is minimally intrusive yet effective, offering a practical solution for structure-aware tabular data modeling with LLMs.

Large language models (LLMs) are typically developed through large-scale pre-training followed by task-specific fine-tuning. Recent advances highlight the importance of an intermediate mid-training stage, where models undergo multiple annealing-style phases that refine data quality, adapt optimization schedules, and extend context length. This stage mitigates diminishing returns from noisy tokens, stabilizes convergence, and expands model capability in late training. Its effectiveness can be explained through gradient noise scale, the information bottleneck, and curriculum learning, which together promote generalization and abstraction. Despite widespread use in state-of-the-art systems, there has been no prior survey of mid-training as a unified paradigm. We introduce the first taxonomy of LLM mid-training spanning data distribution, learning-rate scheduling, and long-context extension. We distill practical insights, compile evaluation benchmarks, and report gains to enable structured comparisons across models. We also identify open challenges and propose avenues for future research and practice.

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

Large Language Models (LLMs) have achieved significant success across various NLP tasks. However, their massive computational costs limit their widespread use, particularly in real-time applications. Structured pruning offers an effective solution by compressing models and directly providing end-to-end speed improvements, regardless of the hardware environment. Meanwhile, different components of the model exhibit varying sensitivities towards pruning, calling for non-uniform model compression. However, a pruning method should not only identify a capable substructure, but also account for post-compression training. To this end, we propose \sysname, a method for training-aware structured pruning. \sysname builds upon an evolutionary search process, generating multiple offspring models in each generation through mutation, and selecting the fittest for survival. To assess the effect of post-training, we incorporate a lightweight, multistep training process within the offspring population, progressively increasing the number of tokens and eliminating poorly performing models in each selection stage. We validate our method through extensive experiments on Llama-2-7B, Llama-3.1-8B and Qwen-2.5-14B-Instruct, achieving state-of-the-art performance for structured pruning. For instance, \sysname surpasses ShearedLlama while requiring 5times less training data during post-compression training.

Large vision-language models are generally applicable to many downstream tasks, but come at an exorbitant training cost that only large institutions can afford. This paper trades generality for efficiency and presents Curation in Training (CiT), a simple and efficient vision-text learning algorithm that couples a data objective into training. CiT automatically yields quality data to speed-up contrastive image-text training and alleviates the need for an offline data filtering pipeline, allowing broad data sources (including raw image-text pairs from the web). CiT contains two loops: an outer loop curating the training data and an inner loop consuming the curated training data. The text encoder connects the two loops. Given metadata for tasks of interest, e.g., class names, and a large pool of image-text pairs, CiT alternatively selects relevant training data from the pool by measuring the similarity of their text embeddings and embeddings of the metadata. In our experiments, we observe that CiT can speed up training by over an order of magnitude, especially if the raw data size is large.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.

We introduce Image2Struct, a benchmark to evaluate vision-language models (VLMs) on extracting structure from images. Our benchmark 1) captures real-world use cases, 2) is fully automatic and does not require human judgment, and 3) is based on a renewable stream of fresh data. In Image2Struct, VLMs are prompted to generate the underlying structure (e.g., LaTeX code or HTML) from an input image (e.g., webpage screenshot). The structure is then rendered to produce an output image (e.g., rendered webpage), which is compared against the input image to produce a similarity score. This round-trip evaluation allows us to quantitatively evaluate VLMs on tasks with multiple valid structures. We create a pipeline that downloads fresh data from active online communities upon execution and evaluates the VLMs without human intervention. We introduce three domains (Webpages, LaTeX, and Musical Scores) and use five image metrics (pixel similarity, cosine similarity between the Inception vectors, learned perceptual image patch similarity, structural similarity index measure, and earth mover similarity) that allow efficient and automatic comparison between pairs of images. We evaluate Image2Struct on 14 prominent VLMs and find that scores vary widely, indicating that Image2Struct can differentiate between the performances of different VLMs. Additionally, the best score varies considerably across domains (e.g., 0.402 on sheet music vs. 0.830 on LaTeX equations), indicating that Image2Struct contains tasks of varying difficulty. For transparency, we release the full results at https://crfm.stanford.edu/helm/image2struct/v1.0.1/.

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Pre-training techniques have been verified successfully in a variety of NLP tasks in recent years. Despite the widespread use of pre-training models for NLP applications, they almost exclusively focus on text-level manipulation, while neglecting layout and style information that is vital for document image understanding. In this paper, we propose the LayoutLM to jointly model interactions between text and layout information across scanned document images, which is beneficial for a great number of real-world document image understanding tasks such as information extraction from scanned documents. Furthermore, we also leverage image features to incorporate words' visual information into LayoutLM. To the best of our knowledge, this is the first time that text and layout are jointly learned in a single framework for document-level pre-training. It achieves new state-of-the-art results in several downstream tasks, including form understanding (from 70.72 to 79.27), receipt understanding (from 94.02 to 95.24) and document image classification (from 93.07 to 94.42). The code and pre-trained LayoutLM models are publicly available at https://aka.ms/layoutlm.

In large language model training, input documents are typically concatenated together and then split into sequences of equal length to avoid padding tokens. Despite its efficiency, the concatenation approach compromises data integrity -- it inevitably breaks many documents into incomplete pieces, leading to excessive truncations that hinder the model from learning to compose logically coherent and factually consistent content that is grounded on the complete context. To address the issue, we propose Best-fit Packing, a scalable and efficient method that packs documents into training sequences through length-aware combinatorial optimization. Our method completely eliminates unnecessary truncations while retaining the same training efficiency as concatenation. Empirical results from both text and code pre-training show that our method achieves superior performance (e.g., relatively +4.7% on reading comprehension; +16.8% in context following; and +9.2% on program synthesis), and reduces closed-domain hallucination effectively by up to 58.3%.

Recent advances in foundation models have highlighted the significant benefits of multi-stage training, with a particular emphasis on the emergence of mid-training as a vital stage that bridges pre-training and post-training. Mid-training is distinguished by its use of intermediate data and computational resources, systematically enhancing specified capabilities such as mathematics, coding, reasoning, and long-context extension, while maintaining foundational competencies. This survey provides a formal definition of mid-training for large language models (LLMs) and investigates optimization frameworks that encompass data curation, training strategies, and model architecture optimization. We analyze mainstream model implementations in the context of objective-driven interventions, illustrating how mid-training serves as a distinct and critical stage in the progressive development of LLM capabilities. By clarifying the unique contributions of mid-training, this survey offers a comprehensive taxonomy and actionable insights, supporting future research and innovation in the advancement of LLMs.

The dominant paradigm for instruction tuning is the random-shuffled training of maximally diverse instruction-response pairs. This paper explores the potential benefits of applying a structured cognitive learning approach to instruction tuning in contemporary large language models like ChatGPT and GPT-4. Unlike the previous conventional randomized instruction dataset, we propose a highly structured synthetic dataset that mimics the progressive and organized nature of human education. We curate our dataset by aligning it with educational frameworks, incorporating meta information including its topic and cognitive rigor level for each sample. Our dataset covers comprehensive fine-grained topics spanning diverse educational stages (from middle school to graduate school) with various questions for each topic to enhance conceptual depth using Bloom's taxonomy-a classification framework distinguishing various levels of human cognition for each concept. The results demonstrate that this cognitive rigorous training approach yields significant performance enhancements - +3.06 on the MMLU benchmark and an additional +1.28 on AI2 Reasoning Challenge (hard set) - compared to conventional randomized training, all while avoiding additional computational costs. This research highlights the potential of leveraging human learning principles to enhance the capabilities of language models in comprehending and responding to complex instructions and tasks.

LLMs have demonstrated commendable performance across diverse domains. Nevertheless, formulating high-quality prompts to assist them in their work poses a challenge for non-AI experts. Existing research in prompt engineering suggests somewhat scattered optimization principles and designs empirically dependent prompt optimizers. Unfortunately, these endeavors lack a structural design, incurring high learning costs and it is not conducive to the iterative updating of prompts, especially for non-AI experts. Inspired by structured reusable programming languages, we propose LangGPT, a structural prompt design framework. Furthermore, we introduce Minstrel, a multi-generative agent system with reflection to automate the generation of structural prompts. Experiments and the case study illustrate that structural prompts generated by Minstrel or written manually significantly enhance the performance of LLMs. Furthermore, we analyze the ease of use of structural prompts through a user survey in our online community.

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled sequence-only (e.g., SMILES or SELFIES) generalist molecular LLMs, and researchers are now exploring multimodal approaches that incorporate molecular structural information for further gains. However, a genuinely multimodal, generalist LLM that covers a broad spectrum of molecular tasks has yet to be fully investigated. We observe that naive next token prediction training ignores graph-structural information, limiting an LLM's ability to exploit molecular graphs. To address this, we propose (i) Molecular structure Preference Optimization (MolPO), which facilitates graph usage by optimizing preferences between pairs of correct and perturbed molecular structures, and (ii) an advanced graph encoder with a tailored pre-training strategy to improve the effect of graph utilization by MolPO. Building on these contributions, we introduce Mol-LLM, the first multimodal generalist model that (a) handles a broad spectrum of molecular tasks among molecular LLMs, (b) explicitly leverages molecular-structure information, and (c) takes advantage of extensive instruction tuning. Mol-LLM attains state-of-the-art or comparable results across the most comprehensive molecular-LLM benchmark-even on out-of-distribution datasets for reaction and property prediction, where it surpasses prior generalist molecular LLMs by a large margin.

Graphs are a fundamental data structure for representing relationships in real-world scenarios. With the success of Large Language Models (LLMs) across various natural language processing (NLP) tasks, there has been growing interest in integrating LLMs for graph learning. However, applying LLMs to graph-related tasks poses significant challenges, as these models are not inherently designed to capture the complex structural information present in graphs. Existing approaches address this challenge through two strategies: the chain of tasks approach, which uses Graph Neural Networks (GNNs) to encode the graph structure so that LLMs are relieved from understanding spatial positions; and Graph-to-Text Conversion, which translates graph structures into semantic text representations that LLMs can process. Despite their progress, these methods often struggle to fully preserve the topological information of graphs or require extensive computational resources, limiting their practical applicability. In this work, we introduce Node Tokenizer for Large Language Models (NT-LLM), a novel framework that efficiently encodes graph structures by selecting key nodes as anchors and representing each node based on its relative distance to these anchors. This position-anchored encoding effectively captures the graph topology, enabling enhanced reasoning capabilities in LLMs over graph data. Additionally, we implement a task-specific tuning procedure to further improve structural understanding within LLMs. Through extensive empirical evaluations, NT-LLM demonstrates significant performance improvements across a variety of graph-related tasks.

Tabular data underpins decisions across science, industry, and public services. Despite rapid progress, advances in deep learning have not fully carried over to the tabular domain, where gradient-boosted decision trees (GBDTs) remain a default choice in practice. We present iLTM, an integrated Large Tabular Model that unifies tree-derived embeddings, dimensionality-agnostic representations, a meta-trained hypernetwork, multilayer perceptrons (MLPs), and retrieval within a single architecture. Pretrained on more than 1,800 heterogeneous classification datasets, iLTM achieves consistently superior performance across tabular classification and regression tasks, from small datasets to large and high-dimensional tasks. After light fine-tuning, the meta-trained hypernetwork transfers to regression targets, matching or surpassing strong baselines. Extensive experiments show that iLTM outperforms well-tuned GBDTs and leading deep tabular models while requiring less task-specific tuning. By bridging the gap between tree-based and neural methods, iLTM offers a new framework for tabular foundation models for robust, adaptable, and scalable tabular learning.

We present LEAF ("Lightweight Embedding Alignment Framework"), a knowledge distillation framework for text embedding models. A key distinguishing feature is that our distilled leaf models are aligned to their teacher. In the context of information retrieval, this allows for flexible asymmetric architectures where documents are encoded with the larger teacher model, while queries can be served with the smaller leaf models. We also show that leaf models automatically inherit MRL and robustness to output quantization whenever these properties are present in the teacher model, without explicitly training for them. To demonstrate the capability of our framework we publish leaf-ir, a 23M parameters information retrieval oriented text embedding model trained using LEAF, which sets a new state-of-the-art (SOTA) on BEIR, ranking #1 on the public leaderboard for this benchmark and for models of its size. When run in asymmetric mode, its retrieval performance is further increased. Our scheme is however not restricted to the information retrieval setting, and we demonstrate its wider applicability by synthesizing the multi-task leaf-mt model. This also sets a new SOTA, ranking #1 on the public MTEB v2 (English) leaderboard for its size. LEAF is applicable to black-box models and in contrast to other embedding model training frameworks, it does not require judgments nor hard negatives, and training can be conducted using small batch sizes. Thus, dataset and training infrastructure requirements for our framework are modest. We make our models publicly available under a permissive Apache 2.0 license.

Non-exemplar class-incremental learning is to recognize both the old and new classes when old class samples cannot be saved. It is a challenging task since representation optimization and feature retention can only be achieved under supervision from new classes. To address this problem, we propose a novel self-sustaining representation expansion scheme. Our scheme consists of a structure reorganization strategy that fuses main-branch expansion and side-branch updating to maintain the old features, and a main-branch distillation scheme to transfer the invariant knowledge. Furthermore, a prototype selection mechanism is proposed to enhance the discrimination between the old and new classes by selectively incorporating new samples into the distillation process. Extensive experiments on three benchmarks demonstrate significant incremental performance, outperforming the state-of-the-art methods by a margin of 3%, 3% and 6%, respectively.

Recently, multi-modal content generation has attracted lots of attention from researchers by investigating the utilization of visual instruction tuning based on large language models (LLMs). To enhance the performance and generalization ability of such LLMs, the practice of distilling knowledge from pretrained multi-modal models (a.k.a. teachers) to more compact multi-modal LLMs (students) has gained considerable interest. However, the prevailing paradigm of instructiontuning in multi-modal LLMs knowledge distillation is resource-intensive and unidirectional, neglecting the potential for mutual feedback between the student and teacher models. Thus, we propose an innovative Competitive Multi-modal Distillation framework (CoMD), which captures bidirectional feedback between teacher and student models and continually updates the multi-modal capabilities that the student model has learned. It comprises two stages: multi-modal pre-training and multi-modal competitive distillation. The first stage pre-trains the student model on a large number of filtered multi-modal datasets. The second stage facilitates a bidirectional knowledge transfer between the student and teacher models. Our experimental analysis of diverse datasets shows that our knowledge transfer method consistently improves the capabilities of the student model. Finally, the 7B-sized student model after four distillations surpassed the current state-of-the-art model LLaVA-13B on the ScienceQA and LLaVA Test dataset, also outperforms other strong baselines in the zero-shot setting.

The rapid advancement of large language models (LLMs) demands robust, unbiased, and scalable evaluation methods. However, human annotations are costly to scale, model-based evaluations are susceptible to stylistic biases, and target-answer-based benchmarks are vulnerable to data contamination and cheating. To address these limitations, we propose StructTest, a novel benchmark that evaluates LLMs on their ability to follow compositional instructions and generate structured outputs, providing an unbiased, cost-effective, and difficult-to-cheat evaluation framework. Assessments are conducted deterministically using a rule-based evaluator, which can be easily extended to new tasks and datasets. By testing structured outputs across diverse domains including Summarization, Code, HTML, and Math, and evaluating 17 popular LLMs, we demonstrate that StructTest remains challenging even for top-performing models like Deepseek-V3/R1 and GPT-4o, establishing it as a robust proxy for measuring reasoning capabilities. We believe StructTest offers a critical and complementary approach to achieving objective and comprehensive model evaluation.

In this paper, we study how to improve the zero-shot reasoning ability of large language models~(LLMs) over structured data in a unified way. Inspired by the study on tool augmentation for LLMs, we develop an Iterative Reading-then-Reasoning~(IRR) approach for solving question answering tasks based on structured data, called StructGPT. In our approach, we construct the specialized function to collect relevant evidence from structured data (\ie reading), and let LLMs concentrate the reasoning task based on the collected information (\ie reasoning). Specially, we propose an invoking-linearization-generation procedure to support LLMs in reasoning on the structured data with the help of the external interfaces. By iterating this procedures with provided interfaces, our approach can gradually approach the target answer to a given query. Extensive experiments conducted on three types of structured data demonstrate the effectiveness of our approach, which can significantly boost the performance of ChatGPT and achieve comparable performance against the full-data supervised-tuning baselines. Our codes and data are publicly available at~https://github.com/RUCAIBox/StructGPT.

The growing prevalence of visually rich documents, such as webpages and scanned/digital-born documents (images, PDFs, etc.), has led to increased interest in automatic document understanding and information extraction across academia and industry. Although various document modalities, including image, text, layout, and structure, facilitate human information retrieval, the interconnected nature of these modalities presents challenges for neural networks. In this paper, we introduce WebLM, a multimodal pre-training network designed to address the limitations of solely modeling text and structure modalities of HTML in webpages. Instead of processing document images as unified natural images, WebLM integrates the hierarchical structure of document images to enhance the understanding of markup-language-based documents. Additionally, we propose several pre-training tasks to model the interaction among text, structure, and image modalities effectively. Empirical results demonstrate that the pre-trained WebLM significantly surpasses previous state-of-the-art pre-trained models across several webpage understanding tasks. The pre-trained models and code are available at https://github.com/X-LANCE/weblm.

Language models pretrained on large collections of tabular data have demonstrated their effectiveness in several downstream tasks. However, many of these models do not take into account the row/column permutation invariances, hierarchical structure, etc. that exist in tabular data. To alleviate these limitations, we propose HYTREL, a tabular language model, that captures the permutation invariances and three more structural properties of tabular data by using hypergraphs - where the table cells make up the nodes and the cells occurring jointly together in each row, column, and the entire table are used to form three different types of hyperedges. We show that HYTREL is maximally invariant under certain conditions for tabular data, i.e., two tables obtain the same representations via HYTREL iff the two tables are identical up to permutations. Our empirical results demonstrate that HYTREL consistently outperforms other competitive baselines on four downstream tasks with minimal pretraining, illustrating the advantages of incorporating the inductive biases associated with tabular data into the representations. Finally, our qualitative analyses showcase that HYTREL can assimilate the table structures to generate robust representations for the cells, rows, columns, and the entire table.

The structure of causal language model training assumes that each token can be accurately predicted from the previous context. This contrasts with humans' natural writing and reasoning process, where goals are typically known before the exact argument or phrasings. While this mismatch has been well studied in the literature, the working assumption has been that architectural changes are needed to address this mismatch. We argue that rearranging and processing the training data sequences can allow models to more accurately imitate the true data-generating process, and does not require any other changes to the architecture or training infrastructure. We demonstrate that this technique, Trelawney, and the inference algorithms derived from it allow us to improve performance on several key benchmarks that span planning, algorithmic reasoning, and story generation tasks. Finally, our method naturally enables the generation of long-term goals at no additional cost. We investigate how using the model's goal-generation capability can further improve planning and reasoning. Additionally, we believe Trelawney could potentially open doors to new capabilities beyond the current language modeling paradigm.

Structural priming is a cognitive phenomenon where exposure to a particular syntactic structure increases the likelihood of producing the same structure in subsequent utterances. While humans consistently demonstrate structural priming effects across various linguistic contexts, it remains unclear whether multimodal large language models (MLLMs) exhibit similar syntactic preservation behaviors. We introduce PRISMATIC, the first multimodal structural priming dataset, which advances computational linguistics by providing a standardized benchmark for investigating syntax-vision interactions. We propose the Syntactic Preservation Index (SPI), a novel reference-free evaluation metric designed specifically to assess structural priming effects in sentence level. Using this metric, we constructed and tested models with two different multimodal encoding architectures to investigate their structural preservation capabilities. Our experimental results demonstrate that models with both encoding methods show comparable syntactic priming effects. However, only fusion-encoded models exhibit robust positive correlations between priming effects and visual similarity, suggesting a cognitive process more aligned with human psycholinguistic patterns. This work provides new insights into evaluating and understanding how syntactic information is processed in multimodal language models.

Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and nonidentifiability of the parameters due to rotation invariance properties of the likelihood. We address these concerns by proposing a fast correlation thresholding (CT) algorithm that simultaneously learns the number of latent factors and a rotationally identifiable model structure. Our novel approach translates this structure learning problem into the search for so-called independent maximal cliques in a thresholded correlation graph that can be easily constructed from the observed data. Our clique analysis technique scales well up to thousands of variables, while competing methods are not applicable in a reasonable amount of running time. We establish a finite-sample error bound and high-dimensional consistency for the structure learning of our method. Through a series of simulation studies and a real data example, we show that the CT algorithm is an accurate method for learning the structure of factor analysis models and is robust to violations of its assumptions.

Large language models (LLMs) have demonstrated exceptional performance in text generation within current NLP research. However, the lack of factual accuracy is still a dark cloud hanging over the LLM skyscraper. Structural knowledge prompting (SKP) is a prominent paradigm to integrate external knowledge into LLMs by incorporating structural representations, achieving state-of-the-art results in many knowledge-intensive tasks. However, existing methods often focus on specific problems, lacking a comprehensive exploration of the generalization and capability boundaries of SKP. This paper aims to evaluate and rethink the generalization capability of the SKP paradigm from four perspectives including Granularity, Transferability, Scalability, and Universality. To provide a thorough evaluation, we introduce a novel multi-granular, multi-level benchmark called SUBARU, consisting of 9 different tasks with varying levels of granularity and difficulty.

Web search is an essential way for humans to obtain information, but it's still a great challenge for machines to understand the contents of web pages. In this paper, we introduce the task of structural reading comprehension (SRC) on web. Given a web page and a question about it, the task is to find the answer from the web page. This task requires a system not only to understand the semantics of texts but also the structure of the web page. Moreover, we proposed WebSRC, a novel Web-based Structural Reading Comprehension dataset. WebSRC consists of 400K question-answer pairs, which are collected from 6.4K web pages. Along with the QA pairs, corresponding HTML source code, screenshots, and metadata are also provided in our dataset. Each question in WebSRC requires a certain structural understanding of a web page to answer, and the answer is either a text span on the web page or yes/no. We evaluate various baselines on our dataset to show the difficulty of our task. We also investigate the usefulness of structural information and visual features. Our dataset and baselines have been publicly available at https://x-lance.github.io/WebSRC/.

Vision-Language Models have made significant progress on many perception-focused tasks, however, their progress on reasoning-focused tasks seem to be limited due to the lack of high-quality and diverse training data. In this work, we aim to address the scarcity issue of reasoning-focused multimodal datasets. We propose VisualWebInstruct - a novel approach that leverages search engine to create a diverse, and high-quality dataset spanning multiple disciplines like math, physics, finance, chemistry, etc. Starting with meticulously selected 30,000 seed images, we employ Google Image search to identify websites containing similar images. We collect and process the HTMLs from over 700K unique URL sources. Through a pipeline of content extraction, filtering and synthesis, we build a dataset of approximately 900K question-answer pairs, with 40% being visual QA pairs and the rest as text QA pairs. Models fine-tuned on VisualWebInstruct demonstrate significant performance gains: (1) training from Llava-OV-mid shows 10-20% absolute point gains across benchmarks, (2) training from MAmmoTH-VL shows 5% absoluate gain. Our best model MAmmoTH-VL2 shows state-of-the-art performance within the 10B parameter class on MMMU-Pro-std (40.7%), MathVerse (42.6%), and DynaMath (55.7%). These remarkable results highlight the effectiveness of our dataset in enhancing VLMs' reasoning capabilities for complex multimodal tasks.

Recently, it was shown that small, looped architectures, such as Tiny Recursive Models (TRMs), can outperform Large Language Models (LLMs) on complex reasoning tasks, including the Abstraction and Reasoning Corpus (ARC). In this work, we investigate a core question: how can we further improve the efficiency of these methods with minimal changes? To address this, we frame the latent reasoning of TRMs as a form of classifier-free guidance and implicit policy improvement algorithm. Building on these insights, we propose a novel training scheme that provides a target for each loop during training. We demonstrate that our approach significantly enhances training efficiency. Our method reduces the total number of forward passes by 18x and eliminates halting mechanisms, while maintaining quality comparable to standard TRMs. Notably, we achieve 24% accuracy on ARC-1 with only 0.8M parameters, outperforming most LLMs.

The goal of knowledge graph completion (KGC) is to predict missing links in a KG using trained facts that are already known. In recent, pre-trained language model (PLM) based methods that utilize both textual and structural information are emerging, but their performances lag behind state-of-the-art (SOTA) structure-based methods or some methods lose their inductive inference capabilities in the process of fusing structure embedding to text encoder. In this paper, we propose a novel method to effectively unify structure information and language semantics without losing the power of inductive reasoning. We adopt entity anchors and these anchors and textual description of KG elements are fed together into the PLM-based encoder to learn unified representations. In addition, the proposed method utilizes additional random negative samples which can be reused in the each mini-batch during contrastive learning to learn a generalized entity representations. We verify the effectiveness of the our proposed method through various experiments and analysis. The experimental results on standard benchmark widely used in link prediction task show that the proposed model outperforms existing the SOTA KGC models. Especially, our method show the largest performance improvement on FB15K-237, which is competitive to the SOTA of structure-based KGC methods.

Large language models (LLMs) have achieved remarkable success across various domains, driving significant technological advancements and innovations. Despite the rapid growth in model scale and capability, systematic, data-driven research on how structural configurations affect performance remains scarce. To address this gap, we present a large-scale dataset encompassing diverse open-source LLM structures and their performance across multiple benchmarks. Leveraging this dataset, we conduct a systematic, data mining-driven analysis to validate and quantify the relationship between structural configurations and performance. Our study begins with a review of the historical development of LLMs and an exploration of potential future trends. We then analyze how various structural choices impact performance across benchmarks and further corroborate our findings using mechanistic interpretability techniques. By providing data-driven insights into LLM optimization, our work aims to guide the targeted development and application of future models. We will release our dataset at https://huggingface.co/datasets/DX0369/LLM-Structure-Performance-Dataset

Curriculum learning has shown promise in improving training efficiency and generalization in various machine learning domains, yet its potential in pretraining language models remains underexplored, prompting our work as the first systematic investigation in this area. We experimented with different settings, including vanilla curriculum learning, pacing-based sampling, and interleaved curricula-guided by six difficulty metrics spanning linguistic and information-theoretic perspectives. We train models under these settings and evaluate their performance on eight diverse benchmarks. Our experiments reveal that curriculum learning consistently improves convergence in early and mid-training phases, and can yield lasting gains when used as a warmup strategy with up to 3.5% improvement. Notably, we identify compression ratio, lexical diversity, and readability as effective difficulty signals across settings. Our findings highlight the importance of data ordering in large-scale pretraining and provide actionable insights for scalable, data-efficient model development under realistic training scenarios.

Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but lack the structural knowledge essential for many biological applications. To address this, we integrate structural insights from pre-trained protein graph neural networks (pGNNs) into pLMs through a latent-level contrastive learning task. This task aligns residue representations from pLMs with those from pGNNs across multiple proteins, enriching pLMs with inter-protein structural knowledge. Additionally, we incorporate a physical-level task that infuses intra-protein structural knowledge by optimizing pLMs to predict structural tokens. The proposed dual-task framework effectively incorporates both inter-protein and intra-protein structural knowledge into pLMs. Given the variability in the quality of protein structures in PDB, we further introduce a residue loss selection module, which uses a small model trained on high-quality structures to select reliable yet challenging residue losses for the pLM to learn. Applying our structure alignment method to the state-of-the-art ESM2 and AMPLIFY results in notable performance gains across a wide range of tasks, including a 12.7% increase in ESM2 contact prediction. The data, code, and resulting SaESM2 and SaAMPLIFY models will be released on Hugging Face.

Recent advancements in NLP have witnessed the groundbreaking impact of pretrained models, yielding impressive outcomes across various tasks. This study seeks to extend the power of pretraining methodologies to facilitating the prediction over tables in data science, a domain traditionally overlooked, yet inherently challenging due to the plethora of table schemas intrinsic to different tasks. The primary research questions underpinning this work revolve around the establishment of a universal pretraining protocol for tables with varied structures, the generalizability and transferability of learned knowledge across tasks, the adaptation to diverse downstream applications, and the incorporation of incremental columns over time. In response to these challenges, we introduce UniTabE, a straightforward yet effective method designed to process tables in a uniform manner, devoid of constraints imposed by specific table structures. UniTabE's core concept relies on representing each basic table element with a module, termed TabUnit. This is subsequently followed by a Transformer encoder to refine the representation. Moreover, our model is designed to facilitate pretraining and finetuning through the utilization of free-form prompts. In order to implement the pretraining phase, we curated an expansive tabular dataset comprising approximately 13B samples, meticulously gathered from the Kaggle platform. This research primarily centers on classification and regression tasks involving tabular data, and conducts rigorous experimental testing and analyses to validate the effectiveness of our methodology. The experimental results demonstrate UniTabE's superior performance against several baselines across massive benchmarks. This, therefore, underscores UniTabE's potential to significantly enhance the semantic representation of tabular data, thereby marking a significant stride for tabular data analysis.

Large language models (LLMs) have demonstrated remarkable abilities in representation learning for program synthesis and understanding tasks. The quality of the learned representations appears to be dictated by the neural scaling laws as a function of the number of model parameters and observations, while imposing upper bounds on the model performance by the amount of available data and compute, which is costly. In this study, we attempt to render the training of LLMs for program synthesis more efficient by unifying four key components: (1) model architectures, (2) learning methods, (3) infill sampling, and, (4) data distributions. Specifically, for the model architecture, we attempt to unify encoder and decoder-based models into a single prefix-LM. For learning methods, (i) causal language modeling, (ii) span corruption, (iii) infilling are unified into a simple learning algorithm. For infill sampling, we explore the claim of a "free lunch" hypothesis. For data distributions, the effect of a mixture distribution of programming and natural languages on model performance is explored. We conduct a comprehensive series of empirical experiments on 1B LLMs, for which failures and successes of this exploration are distilled into four lessons. We will provide a final recipe for training and release CodeGen2 models in size 1B, 3.7B, 7B, and, 16B parameters, along with the training framework as open-source: https://github.com/salesforce/CodeGen2.