Daily Papers

Teamwork in workspace for complex tasks requires diverse communication strategies, but current multi-agent LLM systems lack systematic frameworks for task oriented communication. We introduce Communication to Completion (C2C), a scalable framework that addresses this gap through two key innovations: (1) the Alignment Factor (AF), a novel metric quantifying agent task alignment that directly impacts work efficiency, and (2) a Sequential Action Framework that integrates stepwise execution with intelligent communication decisions. C2C enables agents to make cost aware communication choices, dynamically improving task understanding through targeted interactions. We evaluated C2C on realistic coding workflows across three complexity tiers and team sizes from 5 to 17 agents, comparing against no communication and fixed steps baselines. The results show that C2C reduces the task completion time by about 40% with acceptable communication costs. The framework completes all tasks successfully in standard configurations and maintains effectiveness at scale. C2C establishes both a theoretical foundation for measuring communication effectiveness in multi-agent systems and a practical framework for complex collaborative tasks.

Forced alignment (FA) plays a key role in speech research through the automatic time alignment of speech signals with corresponding text transcriptions. Despite the move towards end-to-end architectures for speech technology, FA is still dominantly achieved through a classic GMM-HMM acoustic model. This work directly compares alignment performance from leading automatic speech recognition (ASR) methods, WhisperX and Massively Multilingual Speech Recognition (MMS), against a Kaldi-based GMM-HMM system, the Montreal Forced Aligner (MFA). Performance was assessed on the manually aligned TIMIT and Buckeye datasets, with comparisons conducted only on words correctly recognized by WhisperX and MMS. The MFA outperformed both WhisperX and MMS, revealing a shortcoming of modern ASR systems. These findings highlight the need for advancements in forced alignment and emphasize the importance of integrating traditional expertise with modern innovation to foster progress. Index Terms: forced alignment, phoneme alignment, word alignment

Aligning foundation models is essential for their safe and trustworthy deployment. However, traditional fine-tuning methods are computationally intensive and require updating billions of model parameters. A promising alternative, alignment via decoding, adjusts the response distribution directly without model updates to maximize a target reward r, thus providing a lightweight and adaptable framework for alignment. However, principled decoding methods rely on oracle access to an optimal Q-function (Q^*), which is often unavailable in practice. Hence, prior SoTA methods either approximate this Q^* using Q^{pi_{sft}} (derived from the reference SFT model) or rely on short-term rewards, resulting in sub-optimal decoding performance. In this work, we propose Transfer Q^*, which implicitly estimates the optimal value function for a target reward r through a baseline model rho_{BL} aligned with a baseline reward rho_{BL} (which can be different from the target reward r). Theoretical analyses of Transfer Q^* provide a rigorous characterization of its optimality, deriving an upper bound on the sub-optimality gap and identifying a hyperparameter to control the deviation from the pre-trained reference SFT model based on user needs. Our approach significantly reduces the sub-optimality gap observed in prior SoTA methods and demonstrates superior empirical performance across key metrics such as coherence, diversity, and quality in extensive tests on several synthetic and real datasets.

AI alignment aims to make AI systems behave in line with human intentions and values. As AI systems grow more capable, so do risks from misalignment. To provide a comprehensive and up-to-date overview of the alignment field, in this survey, we delve into the core concepts, methodology, and practice of alignment. First, we identify four principles as the key objectives of AI alignment: Robustness, Interpretability, Controllability, and Ethicality (RICE). Guided by these four principles, we outline the landscape of current alignment research and decompose them into two key components: forward alignment and backward alignment. The former aims to make AI systems aligned via alignment training, while the latter aims to gain evidence about the systems' alignment and govern them appropriately to avoid exacerbating misalignment risks. On forward alignment, we discuss techniques for learning from feedback and learning under distribution shift. On backward alignment, we discuss assurance techniques and governance practices. We also release and continually update the website (www.alignmentsurvey.com) which features tutorials, collections of papers, blog posts, and other resources.

Recent vision-language foundation models still frequently produce outputs misaligned with their inputs, evidenced by object hallucination in captioning and prompt misalignment in the text-to-image generation model. Recent studies have explored methods for identifying misaligned elements, aiming not only to enhance interpretability but also to improve model performance. However, current approaches primarily rely on large foundation models in a zero-shot manner or fine-tuned models with human annotations, which limits scalability due to significant computational costs. This work proposes a novel approach, dubbed CLIP4DM, for detecting dense misalignments from pre-trained CLIP, specifically focusing on pinpointing misaligned words between image and text. We carefully revamp the gradient-based attribution computation method, enabling negative gradient of individual text tokens to indicate misalignment. We also propose F-CLIPScore, which aggregates misaligned attributions with a global alignment score. We evaluate our method on various dense misalignment detection benchmarks, covering various image and text domains and misalignment types. Our method demonstrates state-of-the-art performance among zero-shot models and competitive performance with fine-tuned models while maintaining superior efficiency. Our qualitative examples show that our method has a unique strength to detect entity-level objects, intangible objects, and attributes that can not be easily detected for existing works. We conduct ablation studies and analyses to highlight the strengths and limitations of our approach. Our code is publicly available at https://github.com/naver-ai/CLIP4DM.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein structure prediction, AF2's accuracy is significantly influenced by the depth of multiple sequence alignment (MSA), which requires extensive exploration of a large protein database for similar sequences. However, not all protein sequences possess abundant homologous families, and consequently, AF2's performance can degrade on such queries, at times failing to produce meaningful results. To address this, we introduce a novel generative language model, MSA-Augmenter, which leverages protein-specific attention mechanisms and large-scale MSAs to generate useful, novel protein sequences not currently found in databases. These sequences supplement shallow MSAs, enhancing the accuracy of structural property predictions. Our experiments on CASP14 demonstrate that MSA-Augmenter can generate de novo sequences that retain co-evolutionary information from inferior MSAs, thereby improving protein structure prediction quality on top of strong AF2.

As Large Language Models (LLMs) become increasingly integrated into real-world applications, ensuring their outputs align with human values and safety standards has become critical. The field has developed diverse alignment approaches including traditional fine-tuning methods (RLHF, instruction tuning), post-hoc correction systems, and inference-time interventions, each with distinct advantages and limitations. However, the lack of unified evaluation frameworks makes it difficult to systematically compare these paradigms and guide deployment decisions. This paper introduces a multi-dimensional evaluation of alignment techniques for LLMs, a comprehensive evaluation framework that provides a systematic comparison across all major alignment paradigms. Our framework assesses methods along four key dimensions: alignment detection, alignment quality, computational efficiency, and robustness. Through experiments across diverse base models and alignment strategies, we demonstrate the utility of our framework in identifying strengths and limitations of current state-of-the-art models, providing valuable insights for future research directions.

We introduce Baichuan Alignment, a detailed analysis of the alignment techniques employed in the Baichuan series of models. This represents the industry's first comprehensive account of alignment methodologies, offering valuable insights for advancing AI research. We investigate the critical components that enhance model performance during the alignment process, including optimization methods, data strategies, capability enhancements, and evaluation processes. The process spans three key stages: Prompt Augmentation System (PAS), Supervised Fine-Tuning (SFT), and Preference Alignment. The problems encountered, the solutions applied, and the improvements made are thoroughly recorded. Through comparisons across well-established benchmarks, we highlight the technological advancements enabled by Baichuan Alignment. Baichuan-Instruct is an internal model, while Qwen2-Nova-72B and Llama3-PBM-Nova-70B are instruct versions of the Qwen2-72B and Llama-3-70B base models, optimized through Baichuan Alignment. Baichuan-Instruct demonstrates significant improvements in core capabilities, with user experience gains ranging from 17% to 28%, and performs exceptionally well on specialized benchmarks. In open-source benchmark evaluations, both Qwen2-Nova-72B and Llama3-PBM-Nova-70B consistently outperform their respective official instruct versions across nearly all datasets. This report aims to clarify the key technologies behind the alignment process, fostering a deeper understanding within the community. Llama3-PBM-Nova-70B model is available at https://huggingface.co/PKU-Baichuan-MLSystemLab/Llama3-PBM-Nova-70B.

Although deep learning and end-to-end models have been widely used and shown superiority in automatic speech recognition (ASR) and text-to-speech (TTS) synthesis, state-of-the-art forced alignment (FA) models are still based on hidden Markov model (HMM). HMM has limited view of contextual information and is developed with long pipelines, leading to error accumulation and unsatisfactory performance. Inspired by the capability of attention mechanism in capturing long term contextual information and learning alignments in ASR and TTS, we propose a neural network based end-to-end forced aligner called NeuFA, in which a novel bidirectional attention mechanism plays an essential role. NeuFA integrates the alignment learning of both ASR and TTS tasks in a unified framework by learning bidirectional alignment information from a shared attention matrix in the proposed bidirectional attention mechanism. Alignments are extracted from the learnt attention weights and optimized by the ASR, TTS and FA tasks in a multi-task learning manner. Experimental results demonstrate the effectiveness of our proposed model, with mean absolute error on test set drops from 25.8 ms to 23.7 ms at word level, and from 17.0 ms to 15.7 ms at phoneme level compared with state-of-the-art HMM based model.

This work presents the first quantitative study of alignment errors between small uncrewed aerial systems (sUAS) geospatial imagery and a priori building polygons and finds that alignment errors are non-uniform and irregular. The work also introduces a publicly available dataset of imagery, building polygons, and human-generated and curated adjustments that can be used to evaluate existing strategies for aligning building polygons with sUAS imagery. There are no efforts that have aligned pre-existing spatial data with sUAS imagery, and thus, there is no clear state of practice. However, this effort and analysis show that the translational alignment errors present in this type of data, averaging 82px and an intersection over the union of 0.65, which would induce further errors and biases in downstream machine learning systems unless addressed. This study identifies and analyzes the translational alignment errors of 21,619 building polygons in fifty-one orthomosaic images, covering 16787.2 Acres (26.23 square miles), constructed from sUAS raw imagery from nine wide-area disasters (Hurricane Ian, Hurricane Harvey, Hurricane Michael, Hurricane Ida, Hurricane Idalia, Hurricane Laura, the Mayfield Tornado, the Musset Bayou Fire, and the Kilauea Eruption). The analysis finds no uniformity among the angle and distance metrics of the building polygon alignments as they present an average degree variance of 0.4 and an average pixel distance variance of 0.45. This work alerts the sUAS community to the problem of spatial alignment and that a simple linear transform, often used to align satellite imagery, will not be sufficient to align spatial data in sUAS orthomosaic imagery.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

Efforts to align Large Language Models (LLMs) are mainly conducted via Reinforcement Learning from Human Feedback (RLHF) methods. However, RLHF encounters major challenges including training reward models, actor-critic engineering, and importantly, it requires access to LLM parameters. Here we introduce Aligner, a new efficient alignment paradigm that bypasses the whole RLHF process by learning the correctional residuals between the aligned and the unaligned answers. Our Aligner offers several key advantages. Firstly, it is an autoregressive seq2seq model that is trained on the query-answer-correction dataset via supervised learning; this offers a parameter-efficient alignment solution with minimal resources. Secondly, the Aligner facilitates weak-to-strong generalization; finetuning large pretrained models by Aligner's supervisory signals demonstrates strong performance boost. Thirdly, Aligner functions as a model-agnostic plug-and-play module, allowing for its direct application on different open-source and API-based models. Remarkably, Aligner-7B improves 11 different LLMs by 21.9% in helpfulness and 23.8% in harmlessness on average (GPT-4 by 17.5% and 26.9%). When finetuning (strong) Llama2-70B with (weak) Aligner-13B's supervision, we can improve Llama2 by 8.2% in helpfulness and 61.6% in harmlessness. See our dataset and code at https://aligner2024.github.io

Language promptable X-ray image segmentation would enable greater flexibility for human-in-the-loop workflows in diagnostic and interventional precision medicine. Prior efforts have contributed task-specific models capable of solving problems within a narrow scope, but expanding to broader use requires additional data, annotations, and training time. Recently, language-aligned foundation models (LFMs) -- machine learning models trained on large amounts of highly variable image and text data thus enabling broad applicability -- have emerged as promising tools for automated image analysis. Existing foundation models for medical image analysis focus on scenarios and modalities where large, richly annotated datasets are available. However, the X-ray imaging modality features highly variable image appearance and applications, from diagnostic chest X-rays to interventional fluoroscopy, with varying availability of data. To pave the way toward an LFM for comprehensive and language-aligned analysis of arbitrary medical X-ray images, we introduce FluoroSAM, a language-promptable variant of the Segment Anything Model, trained from scratch on 3M synthetic X-ray images from a wide variety of human anatomies, imaging geometries, and viewing angles. These include pseudo-ground truth masks for 128 organ types and 464 tools with associated text descriptions. FluoroSAM is capable of segmenting myriad anatomical structures and tools based on natural language prompts, thanks to the novel incorporation of vector quantization (VQ) of text embeddings in the training process. We demonstrate FluoroSAM's performance quantitatively on real X-ray images and showcase on several applications how FluoroSAM is a key enabler for rich human-machine interaction in the X-ray image acquisition and analysis context. Code is available at https://github.com/arcadelab/fluorosam.

Despite advancements in Large Language Model (LLM) alignment, understanding the reasons behind LLM preferences remains crucial for bridging the gap between desired and actual behavior. LLMs often exhibit biases or tendencies that diverge from human preferences, such as favoring certain writing styles or producing overly verbose outputs. However, current methods for evaluating preference alignment often lack explainability, relying on coarse-grained comparisons. To address this, we introduce PROFILE (PRObing Factors of InfLuence for Explainability), a novel framework that uncovers and quantifies the influence of specific factors driving preferences. PROFILE's factor level analysis explains the 'why' behind human-model alignment and misalignment, offering insights into the direction of model improvement. We apply PROFILE to analyze human and LLM preferences across three tasks: summarization, helpful response generation, and document-based question-answering. Our factor level analysis reveals a substantial discrepancy between human and LLM preferences in generation tasks, whereas LLMs show strong alignment with human preferences in evaluation tasks. We demonstrate how leveraging factor level insights, including addressing misaligned factors or exploiting the generation-evaluation gap, can improve alignment with human preferences. This work underscores the importance of explainable preference analysis and highlights PROFILE's potential to provide valuable training signals, driving further improvements in human-model alignment.

The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

The transcriptional response to genetic perturbation reveals fundamental insights into complex cellular systems. While current approaches have made progress in predicting genetic perturbation responses, they provide limited biological understanding and cannot systematically refine existing knowledge. Overcoming these limitations requires an end-to-end integration of data-driven learning and existing knowledge. However, this integration is challenging due to inconsistencies between data and knowledge bases, such as noise, misannotation, and incompleteness. To address this challenge, we propose ALIGNED (Adaptive aLignment for Inconsistent Genetic kNowledgE and Data), a neuro-symbolic framework based on the Abductive Learning (ABL) paradigm. This end-to-end framework aligns neural and symbolic components and performs systematic knowledge refinement. We introduce a balanced consistency metric to evaluate the predictions' consistency against both data and knowledge. Our results show that ALIGNED outperforms state-of-the-art methods by achieving the highest balanced consistency, while also re-discovering biologically meaningful knowledge. Our work advances beyond existing methods to enable both the transparency and the evolution of mechanistic biological understanding.

AI alignment research is the field of study dedicated to ensuring that artificial intelligence (AI) benefits humans. As machine intelligence gets more advanced, this research is becoming increasingly important. Researchers in the field share ideas across different media to speed up the exchange of information. However, this focus on speed means that the research landscape is opaque, making it difficult for young researchers to enter the field. In this project, we collected and analyzed existing AI alignment research. We found that the field is growing quickly, with several subfields emerging in parallel. We looked at the subfields and identified the prominent researchers, recurring topics, and different modes of communication in each. Furthermore, we found that a classifier trained on AI alignment research articles can detect relevant articles that we did not originally include in the dataset. We are sharing the dataset with the research community and hope to develop tools in the future that will help both established researchers and young researchers get more involved in the field.

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

Text-to-image generation has advanced rapidly, yet aligning complex textual prompts with generated visuals remains challenging, especially with intricate object relationships and fine-grained details. This paper introduces Fast Prompt Alignment (FPA), a prompt optimization framework that leverages a one-pass approach, enhancing text-to-image alignment efficiency without the iterative overhead typical of current methods like OPT2I. FPA uses large language models (LLMs) for single-iteration prompt paraphrasing, followed by fine-tuning or in-context learning with optimized prompts to enable real-time inference, reducing computational demands while preserving alignment fidelity. Extensive evaluations on the COCO Captions and PartiPrompts datasets demonstrate that FPA achieves competitive text-image alignment scores at a fraction of the processing time, as validated through both automated metrics (TIFA, VQA) and human evaluation. A human study with expert annotators further reveals a strong correlation between human alignment judgments and automated scores, underscoring the robustness of FPA's improvements. The proposed method showcases a scalable, efficient alternative to iterative prompt optimization, enabling broader applicability in real-time, high-demand settings. The codebase is provided to facilitate further research: https://github.com/tiktok/fast_prompt_alignment

Large Language Models (LLMs) have achieved significant advancements, however, the common learning paradigm treats LLMs as passive information repositories, neglecting their potential for active learning and alignment. Some approaches train LLMs using their own generated synthetic data, exploring the possibility of active alignment. However, there is still a huge gap between these one-time alignment methods and the continuous automatic alignment of humans. In this paper, we introduce I-SHEEP, an Iterative Self-EnHancEmEnt Paradigm.This human-like paradigm enables LLMs to continuously self-align from scratch with nothing. Compared to the one-time alignment method Dromedary sun2023principledriven, which refers to the first iteration in this paper, I-SHEEP can significantly enhance capacities on both Qwen and Llama models. I-SHEEP achieves a maximum relative improvement of 78.2\% in the Alpaca Eval, 24.0\% in the MT Bench, and an absolute increase of 8.88\% in the IFEval accuracy over subsequent iterations in Qwen-1.5 72B model. Additionally, I-SHEEP surpasses the base model in various standard benchmark generation tasks, achieving an average improvement of 24.77\% in code generation tasks, 12.04\% in TrivialQA, and 20.29\% in SQuAD. We also provide new insights based on the experiment results. Our codes, datasets, and models are available at https://anonymous.4open.science/r/I-SHEEP.

In AI alignment, extensive latitude must be granted to annotators, either human or algorithmic, to judge which model outputs are `better' or `safer.' We refer to this latitude as alignment discretion. Such discretion remains largely unexamined, posing two risks: (i) annotators may use their power of discretion arbitrarily, and (ii) models may fail to mimic this discretion. To study this phenomenon, we draw on legal concepts of discretion that structure how decision-making authority is conferred and exercised, particularly in cases where principles conflict or their application is unclear or irrelevant. Extended to AI alignment, discretion is required when alignment principles and rules are (inevitably) conflicting or indecisive. We present a set of metrics to systematically analyze when and how discretion in AI alignment is exercised, such that both risks (i) and (ii) can be observed. Moreover, we distinguish between human and algorithmic discretion and analyze the discrepancy between them. By measuring both human and algorithmic discretion over safety alignment datasets, we reveal layers of discretion in the alignment process that were previously unaccounted for. Furthermore, we demonstrate how algorithms trained on these datasets develop their own forms of discretion in interpreting and applying these principles, which challenges the purpose of having any principles at all. Our paper presents the first step towards formalizing this core gap in current alignment processes, and we call on the community to further scrutinize and control alignment discretion.

We introduce Aligner, a novel Parameter-Efficient Fine-Tuning (PEFT) method for aligning multi-billion-parameter-sized Large Language Models (LLMs). Aligner employs a unique design that constructs a globally shared set of tunable tokens that modify the attention of every layer. Remarkably with this method, even when using one token accounting for a mere 5,000 parameters, Aligner can still perform comparably well to state-of-the-art LLM adaptation methods like LoRA that require millions of parameters. This capacity is substantiated in both instruction following and value alignment tasks. Besides the multiple order-of-magnitude improvement in parameter efficiency, the insight Aligner provides into the internal mechanisms of LLMs is also valuable. The architectural features and efficacy of our method, in addition to our experiments demonstrate that an LLM separates its internal handling of "form" and "knowledge" in a somewhat orthogonal manner. This finding promises to motivate new research into LLM mechanism understanding and value alignment.

Low-rank adaptation (LoRA) has become a standard tool for efficiently fine-tuning large language models (LLMs). Yet, even minor LoRA updates can induce alignment drift, weakening safety and behavioral constraints through entangled parameter changes. To address this, we propose AlignGuard-LoRA (AGL), a principled framework for preserving alignment during finetuning. AGL introduces several key components: a primary task loss for supervision, Fisher Information Matrix-based regularization to restrict updates in alignment-sensitive subspaces, and task-specific regularization to stabilize the integration of new knowledge. We further introduce collision-aware regularization, blending Riemannian overlap -- which penalizes coordinate-wise interference -- and geodesic separation -- which encourages disjoint update geometry. We curate DriftCaps, a targeted diagnostic benchmark of safe and unsafe prompts designed to quantify alignment drift and safety degradation. Empirical evaluations show that AGL mitigates alignment drift by up to 50% on safety-critical benchmarks without degrading downstream task performance. Comprehensive ablation confirms that each component contributes distinctly to preserving latent safety behaviors. Finally, we derive and validate a scaling law for catastrophic forgetting, revealing that AGL flattens post-finetuning loss escalation while preserving adaptation dynamics. AGL is a structurally grounded refinement of LoRA, ensuring alignment preservation with minimal trade-offs. To encourage further exploration and development, we open-source our implementation.

Radiologists play a crucial role by translating medical images into medical reports. However, the field faces staffing shortages and increasing workloads. While automated approaches using vision-language models (VLMs) show promise as assistants, they require exceptionally high accuracy. Most current VLMs in radiology rely solely on supervised fine-tuning (SFT). Meanwhile, in the general domain, additional preference fine-tuning has become standard practice. The challenge in radiology lies in the prohibitive cost of obtaining radiologist feedback. We propose a scalable automated preference alignment technique for VLMs in radiology, focusing on chest X-ray (CXR) report generation. Our method leverages publicly available datasets with an LLM-as-a-Judge mechanism, eliminating the need for additional expert radiologist feedback. We evaluate and benchmark five direct alignment algorithms (DAAs). Our results show up to a 57.4% improvement in average GREEN scores, a LLM-based metric for evaluating CXR reports, and a 9.2% increase in an average across six metrics (domain specific and general), compared to the SFT baseline. We study reward overoptimization via length exploitation, with reports lengthening by up to 3.2x. To assess a potential alignment tax, we benchmark on six additional diverse tasks, finding no significant degradations. A reader study involving four board-certified radiologists indicates win rates of up to 0.62 over the SFT baseline, while significantly penalizing verbosity. Our analysis provides actionable insights for the development of VLMs in high-stakes fields like radiology.

Big models, exemplified by Large Language Models (LLMs), are models typically pre-trained on massive data and comprised of enormous parameters, which not only obtain significantly improved performance across diverse tasks but also present emergent capabilities absent in smaller models. However, the growing intertwining of big models with everyday human lives poses potential risks and might cause serious social harm. Therefore, many efforts have been made to align LLMs with humans to make them better follow user instructions and satisfy human preferences. Nevertheless, `what to align with' has not been fully discussed, and inappropriate alignment goals might even backfire. In this paper, we conduct a comprehensive survey of different alignment goals in existing work and trace their evolution paths to help identify the most essential goal. Particularly, we investigate related works from two perspectives: the definition of alignment goals and alignment evaluation. Our analysis encompasses three distinct levels of alignment goals and reveals a goal transformation from fundamental abilities to value orientation, indicating the potential of intrinsic human values as the alignment goal for enhanced LLMs. Based on such results, we further discuss the challenges of achieving such intrinsic value alignment and provide a collection of available resources for future research on the alignment of big models.

Large Language Models (LLMs) fine-tuned to align with human values often exhibit alignment drift, producing unsafe or policy-violating completions when exposed to adversarial prompts, decoding perturbations, or paraphrased jailbreaks. While prior work has behaviorally characterized alignment failure, little is known about the training-time belief sources underlying these failures. We introduce TraceAlign, a unified framework for tracing unsafe completions back to their root causes in the model's training corpus. Central to our approach is the Belief Conflict Index (BCI), which quantifies semantic inconsistency between generated spans and aligned policies, based on retrieved training documents using suffix-array matching. We propose three complementary interventions: (i) TraceShield, an inference-time safety filter that refuses completions with high-BCI spans, (ii) Contrastive Belief Deconfliction Loss, a contrastive fine-tuning objective penalizing high-BCI continuations during DPO, and (iii) Prov-Decode, a provenance-aware decoding strategy that vetoes beam expansions predicted to yield high-BCI spans. Together, these defenses reduce alignment drift by up to 85% on our curated Alignment Drift Benchmark (ADB) while preserving utility on standard tasks, with delta less than 0.2 and improved refusal quality. We further derive a theoretical upper bound on drift likelihood via suffix-array span statistics, linking memorization frequency and length to adversarial reactivation risk. TraceAlign thus provides the first scalable, traceable, and grounded toolkit for understanding and mitigating alignment failures at source. To encourage further exploration and development, we open-source our implementation at: https://anonymous.4open.science/r/tracealign-2DA7

Alignment is no longer a luxury, it is a necessity. As large language models (LLMs) enter high-stakes domains like education, healthcare, governance, and law, their behavior must reliably reflect human-aligned values and safety constraints. Yet current evaluations rely heavily on behavioral proxies such as refusal rates, G-Eval scores, and toxicity classifiers, all of which have critical blind spots. Aligned models are often vulnerable to jailbreaking, stochasticity of generation, and alignment faking. To address this issue, we introduce the Alignment Quality Index (AQI). This novel geometric and prompt-invariant metric empirically assesses LLM alignment by analyzing the separation of safe and unsafe activations in latent space. By combining measures such as the Davies-Bouldin Score (DBS), Dunn Index (DI), Xie-Beni Index (XBI), and Calinski-Harabasz Index (CHI) across various formulations, AQI captures clustering quality to detect hidden misalignments and jailbreak risks, even when outputs appear compliant. AQI also serves as an early warning signal for alignment faking, offering a robust, decoding invariant tool for behavior agnostic safety auditing. Additionally, we propose the LITMUS dataset to facilitate robust evaluation under these challenging conditions. Empirical tests on LITMUS across different models trained under DPO, GRPO, and RLHF conditions demonstrate AQI's correlation with external judges and ability to reveal vulnerabilities missed by refusal metrics. We make our implementation publicly available to foster future research in this area.

Recent advancements in general-purpose AI have highlighted the importance of guiding AI systems towards the intended goals, ethical principles, and values of individuals and groups, a concept broadly recognized as alignment. However, the lack of clarified definitions and scopes of human-AI alignment poses a significant obstacle, hampering collaborative efforts across research domains to achieve this alignment. In particular, ML- and philosophy-oriented alignment research often views AI alignment as a static, unidirectional process (i.e., aiming to ensure that AI systems' objectives match humans) rather than an ongoing, mutual alignment problem [429]. This perspective largely neglects the long-term interaction and dynamic changes of alignment. To understand these gaps, we introduce a systematic review of over 400 papers published between 2019 and January 2024, spanning multiple domains such as Human-Computer Interaction (HCI), Natural Language Processing (NLP), Machine Learning (ML), and others. We characterize, define and scope human-AI alignment. From this, we present a conceptual framework of "Bidirectional Human-AI Alignment" to organize the literature from a human-centered perspective. This framework encompasses both 1) conventional studies of aligning AI to humans that ensures AI produces the intended outcomes determined by humans, and 2) a proposed concept of aligning humans to AI, which aims to help individuals and society adjust to AI advancements both cognitively and behaviorally. Additionally, we articulate the key findings derived from literature analysis, including discussions about human values, interaction techniques, and evaluations. To pave the way for future studies, we envision three key challenges for future directions and propose examples of potential future solutions.

The rapid advancement of Large Language Models (LLMs) necessitates robust evaluation methodologies. Current benchmarking approaches often rely on comparing model outputs against predefined prompts and reference outputs. Relying on predefined reference outputs hinders flexible adaptation of benchmarks to the rapidly evolving capabilities of LLMs. This limitation necessitates periodic efforts to prepare new benchmarks. To keep pace with rapidly evolving LLM capabilities, we propose a more flexible benchmarking approach. Our method, \textbf{Varco Arena}, provides reference-free benchmarking of LLMs in tournament style. \textbf{Varco Arena} directly compares LLM outputs across a diverse set of prompts, determining model rankings through a single-elimination tournament structure. This direct pairwise comparison offers two key advantages: (1) Direct comparison, unmediated by reference text, more effectively orders competing LLMs, resulting in more reliable rankings, and (2) reference-free approach to benchmarking adds flexibility in updating benchmark prompts by eliminating the need for quality references. Our empirical results, supported by simulation experiments, demonstrate that the \textbf{Varco Arena} tournament approach aligns better with the current Elo model for benchmarking LLMs. The alignment is measured in terms of Spearman correlation, showing improvement over current practice of benchmarking that use reference outputs as comparison anchors.

Human-object interactions (HOI) detection aims at capturing human-object pairs in images and corresponding actions. It is an important step toward high-level visual reasoning and scene understanding. However, due to the natural bias from the real world, existing methods mostly struggle with rare human-object pairs and lead to sub-optimal results. Recently, with the development of the generative model, a straightforward approach is to construct a more balanced dataset based on a group of supplementary samples. Unfortunately, there is a significant domain gap between the generated data and the original data, and simply merging the generated images into the original dataset cannot significantly boost the performance. To alleviate the above problem, we present a novel model-agnostic framework called Context-Enhanced Feature Alignment (CEFA) module, which can effectively align the generated data with the original data at the feature level and bridge the domain gap. Specifically, CEFA consists of a feature alignment module and a context enhancement module. On one hand, considering the crucial role of human-object pairs information in HOI tasks, the feature alignment module aligns the human-object pairs by aggregating instance information. On the other hand, to mitigate the issue of losing important context information caused by the traditional discriminator-style alignment method, we employ a context-enhanced image reconstruction module to improve the model's learning ability of contextual cues. Extensive experiments have shown that our method can serve as a plug-and-play module to improve the detection performance of HOI models on rare categorieshttps://github.com/LijunZhang01/CEFA.

Connectionist temporal classification (CTC) models are known to have peaky output distributions. Such behavior is not a problem for automatic speech recognition (ASR), but it can cause inaccurate forced alignments (FA), especially at finer granularity, e.g., phoneme level. This paper aims at alleviating the peaky behavior for CTC and improve its suitability for forced alignment generation, by leveraging label priors, so that the scores of alignment paths containing fewer blanks are boosted and maximized during training. As a result, our CTC model produces less peaky posteriors and is able to more accurately predict the offset of the tokens besides their onset. It outperforms the standard CTC model and a heuristics-based approach for obtaining CTC's token offset timestamps by 12-40% in phoneme and word boundary errors (PBE and WBE) measured on the Buckeye and TIMIT data. Compared with the most widely used FA toolkit Montreal Forced Aligner (MFA), our method performs similarly on PBE/WBE on Buckeye, yet falls behind MFA on TIMIT. Nevertheless, our method has a much simpler training pipeline and better runtime efficiency. Our training recipe and pretrained model are released in TorchAudio.

Recent work discovered Emergent Misalignment (EM): fine-tuning large language models on narrowly harmful datasets can lead them to become broadly misaligned. A survey of experts prior to publication revealed this was highly unexpected, demonstrating critical gaps in our understanding of model alignment. In this work, we both advance understanding and provide tools for future research. Using new narrowly misaligned datasets, we create a set of improved model organisms that achieve 99% coherence (vs. 67% prior), work with smaller 0.5B parameter models (vs. 32B), and that induce misalignment using a single rank-1 LoRA adapter. We demonstrate that EM occurs robustly across diverse model sizes, three model families, and numerous training protocols including full supervised fine-tuning. Leveraging these cleaner model organisms, we isolate a mechanistic phase transition and demonstrate that it corresponds to a robust behavioural phase transition in all studied organisms. Aligning large language models is critical for frontier AI safety, yet EM exposes how far we are from achieving this robustly. By distilling clean model organisms that isolate a minimal alignment-compromising change, and where this is learnt, we establish a foundation for future research into understanding and mitigating alignment risks in LLMs.

Large Language Models (LLMs) are expected to produce safe, helpful, and honest content during interaction with human users, but they frequently fail to align with such values when given flawed instructions, e.g., missing context, ambiguous directives, or inappropriate tone, leaving substantial room for improvement along multiple dimensions. A cost-effective yet high-impact way is to pre-align instructions before the model begins decoding. Existing approaches either rely on prohibitive test-time search costs or end-to-end model rewrite, which is powered by a customized training corpus with unclear objectives. In this work, we demonstrate that the goal of efficient and effective preference alignment can be achieved by P-Aligner, a lightweight module generating instructions that preserve the original intents while being expressed in a more human-preferred form. P-Aligner is trained on UltraPrompt, a new dataset synthesized via a proposed principle-guided pipeline using Monte-Carlo Tree Search, which systematically explores the space of candidate instructions that are closely tied to human preference. Experiments across different methods show that P-Aligner generally outperforms strong baselines across various models and benchmarks, including average win-rate gains of 28.35% and 8.69% on GPT-4-turbo and Gemma-2-SimPO, respectively. Further analyses validate its effectiveness and efficiency through multiple perspectives, including data quality, search strategies, iterative deployment, and time overhead.

The most common tools for word-alignment rely on a large amount of parallel sentences, which are then usually processed according to one of the IBM model algorithms. The training data is, however, the same as for machine translation (MT) systems, especially for neural MT (NMT), which itself is able to produce word-alignments using the trained attention heads. This is convenient because word-alignment is theoretically a viable byproduct of any attention-based NMT, which is also able to provide decoder scores for a translated sentence pair. We summarize different approaches on how word-alignment can be extracted from alignment scores and then explore ways in which scores can be extracted from NMT, focusing on inferring the word-alignment scores based on output sentence and token probabilities. We compare this to the extraction of alignment scores from attention. We conclude with aggregating all of the sources of alignment scores into a simple feed-forward network which achieves the best results when combined alignment extractors are used.

The reward model has become increasingly important in alignment, assessment, and data construction for large language models (LLMs). Most existing researchers focus on enhancing reward models through data improvements, following the conventional training framework for reward models that directly optimizes the predicted rewards. In this paper, we propose a hybrid alignment framework HaF-RM for reward model training by introducing an additional constraint on token-level policy probabilities in addition to the reward score. It can simultaneously supervise the internal preference model at the token level and optimize the mapping layer of the reward model at the sequence level. Theoretical justifications and experiment results on five datasets show the validity and effectiveness of our proposed hybrid framework for training a high-quality reward model. By decoupling the reward modeling procedure and incorporating hybrid supervision, our HaF-RM framework offers a principled and effective approach to enhancing the performance and alignment of reward models, a critical component in the responsible development of powerful language models. We release our code at https://haf-rm.github.io.

The importance of qualitative parallel data in machine translation has long been determined but it has always been very difficult to obtain such in sufficient quantity for the majority of world languages, mainly because of the associated cost and also the lack of accessibility to these languages. Despite the potential for obtaining parallel datasets from online articles using automatic approaches, forensic investigations have found a lot of quality-related issues such as misalignment, and wrong language codes. In this work, we present a simple but qualitative parallel sentence aligner that carefully leveraged the closed-access Cohere multilingual embedding, a solution that ranked second in the just concluded #CoHereAIHack 2023 Challenge (see https://ai6lagos.devpost.com). The proposed approach achieved 94.96 and 54.83 f1 scores on FLORES and MAFAND-MT, compared to 3.64 and 0.64 of LASER respectively. Our method also achieved an improvement of more than 5 BLEU scores over LASER, when the resulting datasets were used with MAFAND-MT dataset to train translation models. Our code and data are available for research purposes here (https://github.com/abumafrim/Cohere-Align).

Assessing image-text alignment models such as CLIP is crucial for bridging visual and linguistic representations. Yet existing benchmarks rely on rule-based perturbations or short captions, limiting their ability to measure fine-grained alignment. We introduce AlignBench, a benchmark that provides a new indicator of image-text alignment by evaluating detailed image-caption pairs generated by diverse image-to-text and text-to-image models. Each sentence is annotated for correctness, enabling direct assessment of VLMs as alignment evaluators. Benchmarking a wide range of decoder-based VLMs reveals three key findings: (i) CLIP-based models, even those tailored for compositional reasoning, remain nearly blind; (ii) detectors systematically over-score early sentences; and (iii) they show strong self-preference, favoring their own outputs and harming detection performance. Our project page will be available at https://dahlian00.github.io/AlignBench/.

Joint Alignment (JA) of images aims to align a collection of images into a unified coordinate frame, such that semantically-similar features appear at corresponding spatial locations. Most existing approaches often require long training times, large-capacity models, and extensive hyperparameter tuning. We introduce FastJAM, a rapid, graph-based method that drastically reduces the computational complexity of joint alignment tasks. FastJAM leverages pairwise matches computed by an off-the-shelf image matcher, together with a rapid nonparametric clustering, to construct a graph representing intra- and inter-image keypoint relations. A graph neural network propagates and aggregates these correspondences, efficiently predicting per-image homography parameters via image-level pooling. Utilizing an inverse-compositional loss, that eliminates the need for a regularization term over the predicted transformations (and thus also obviates the hyperparameter tuning associated with such terms), FastJAM performs image JA quickly and effectively. Experimental results on several benchmarks demonstrate that FastJAM achieves results better than existing modern JA methods in terms of alignment quality, while reducing computation time from hours or minutes to mere seconds. Our code is available at our project webpage, https://bgu-cs-vil.github.io/FastJAM/

The rapid advancement of text-to-image (T2I) diffusion models has enabled them to generate unprecedented results from given texts. However, as text inputs become longer, existing encoding methods like CLIP face limitations, and aligning the generated images with long texts becomes challenging. To tackle these issues, we propose LongAlign, which includes a segment-level encoding method for processing long texts and a decomposed preference optimization method for effective alignment training. For segment-level encoding, long texts are divided into multiple segments and processed separately. This method overcomes the maximum input length limits of pretrained encoding models. For preference optimization, we provide decomposed CLIP-based preference models to fine-tune diffusion models. Specifically, to utilize CLIP-based preference models for T2I alignment, we delve into their scoring mechanisms and find that the preference scores can be decomposed into two components: a text-relevant part that measures T2I alignment and a text-irrelevant part that assesses other visual aspects of human preference. Additionally, we find that the text-irrelevant part contributes to a common overfitting problem during fine-tuning. To address this, we propose a reweighting strategy that assigns different weights to these two components, thereby reducing overfitting and enhancing alignment. After fine-tuning 512 times 512 Stable Diffusion (SD) v1.5 for about 20 hours using our method, the fine-tuned SD outperforms stronger foundation models in T2I alignment, such as PixArt-alpha and Kandinsky v2.2. The code is available at https://github.com/luping-liu/LongAlign.

Connectionist Temporal Classification (CTC) is a widely used criterion for training supervised sequence-to-sequence (seq2seq) models. It enables learning the relations between input and output sequences, termed alignments, by marginalizing over perfect alignments (that yield the ground truth), at the expense of imperfect alignments. This binary differentiation of perfect and imperfect alignments falls short of capturing other essential alignment properties that hold significance in other real-world applications. Here we propose Align With Purpose, a general Plug-and-Play framework for enhancing a desired property in models trained with the CTC criterion. We do that by complementing the CTC with an additional loss term that prioritizes alignments according to a desired property. Our method does not require any intervention in the CTC loss function, enables easy optimization of a variety of properties, and allows differentiation between both perfect and imperfect alignments. We apply our framework in the domain of Automatic Speech Recognition (ASR) and show its generality in terms of property selection, architectural choice, and scale of training dataset (up to 280,000 hours). To demonstrate the effectiveness of our framework, we apply it to two unrelated properties: emission time and word error rate (WER). For the former, we report an improvement of up to 570ms in latency optimization with a minor reduction in WER, and for the latter, we report a relative improvement of 4.5% WER over the baseline models. To the best of our knowledge, these applications have never been demonstrated to work on a scale of data as large as ours. Notably, our method can be implemented using only a few lines of code, and can be extended to other alignment-free loss functions and to domains other than ASR.

The alignment tuning process of large language models (LLMs) typically involves instruction learning through supervised fine-tuning (SFT) and preference tuning via reinforcement learning from human feedback (RLHF). A recent study, LIMA (Zhou et al. 2023), shows that using merely 1K examples for SFT can achieve significant alignment performance as well, suggesting that the effect of alignment tuning might be "superficial." This raises questions about how exactly the alignment tuning transforms a base LLM. We analyze the effect of alignment tuning by examining the token distribution shift between base LLMs and their aligned counterpart. Our findings reveal that base LLMs and their alignment-tuned versions perform nearly identically in decoding on the majority of token positions. Most distribution shifts occur with stylistic tokens. These direct evidence strongly supports the Superficial Alignment Hypothesis suggested by LIMA. Based on these findings, we rethink the alignment of LLMs by posing the research question: how effectively can we align base LLMs without SFT or RLHF? To address this, we introduce a simple, tuning-free alignment method, URIAL. URIAL achieves effective alignment purely through in-context learning (ICL) with base LLMs, requiring as few as three constant stylistic examples and a system prompt. We conduct a fine-grained and interpretable evaluation on a diverse set of examples, named JUST-EVAL-INSTRUCT. Results demonstrate that base LLMs with URIAL can match or even surpass the performance of LLMs aligned with SFT or SFT+RLHF. We show that the gap between tuning-free and tuning-based alignment methods can be significantly reduced through strategic prompting and ICL. Our findings on the superficial nature of alignment tuning and results with URIAL suggest that deeper analysis and theoretical understanding of alignment is crucial to future LLM research.

Preference learning is critical for aligning large language models (LLMs) with human values, yet its success hinges on high-quality datasets comprising three core components: Preference Annotations, Instructions, and Response Pairs. Current approaches conflate these components, obscuring their individual impacts and hindering systematic optimization. In this work, we propose AIR, a component-wise analysis framework that systematically isolates and optimizes each component while evaluating their synergistic effects. Through rigorous experimentation, AIR reveals actionable principles: annotation simplicity (point-wise generative scoring), instruction inference stability (variance-based filtering across LLMs), and response pair quality (moderate margins + high absolute scores). When combined, these principles yield +5.3 average gains over baseline method, even with only 14k high-quality pairs. Our work shifts preference dataset design from ad hoc scaling to component-aware optimization, offering a blueprint for efficient, reproducible alignment.

Aligning language models with human preferences is crucial for reducing errors and biases in these models. Alignment techniques, such as reinforcement learning from human feedback (RLHF), are typically cast as optimizing a tradeoff between human preference rewards and a proximity regularization term that encourages staying close to the unaligned model. Selecting an appropriate level of regularization is critical: insufficient regularization can lead to reduced model capabilities due to reward hacking, whereas excessive regularization hinders alignment. Traditional methods for finding the optimal regularization level require retraining multiple models with varying regularization strengths. This process, however, is resource-intensive, especially for large models. To address this challenge, we propose decoding-time realignment (DeRa), a simple method to explore and evaluate different regularization strengths in aligned models without retraining. DeRa enables control over the degree of alignment, allowing users to smoothly transition between unaligned and aligned models. It also enhances the efficiency of hyperparameter tuning by enabling the identification of effective regularization strengths using a validation dataset.

Mining parallel document pairs poses a significant challenge because existing sentence embedding models often have limited context windows, preventing them from effectively capturing document-level information. Another overlooked issue is the lack of concrete evaluation benchmarks comprising high-quality parallel document pairs for assessing document-level mining approaches, particularly for Indic languages. In this study, we introduce Pralekha, a large-scale benchmark for document-level alignment evaluation. Pralekha includes over 2 million documents, with a 1:2 ratio of unaligned to aligned pairs, covering 11 Indic languages and English. Using Pralekha, we evaluate various document-level mining approaches across three dimensions: the embedding models, the granularity levels, and the alignment algorithm. To address the challenge of aligning documents using sentence and chunk-level alignments, we propose a novel scoring method, Document Alignment Coefficient (DAC). DAC demonstrates substantial improvements over baseline pooling approaches, particularly in noisy scenarios, achieving average gains of 20-30% in precision and 15-20% in F1 score. These results highlight DAC's effectiveness in parallel document mining for Indic languages.

Precise alignment in Text-to-Image (T2I) systems is crucial to ensure that generated visuals not only accurately encapsulate user intents but also conform to stringent ethical and aesthetic benchmarks. Incidents like the Google Gemini fiasco, where misaligned outputs triggered significant public backlash, underscore the critical need for robust alignment mechanisms. In contrast, Large Language Models (LLMs) have achieved notable success in alignment. Building on these advancements, researchers are eager to apply similar alignment techniques, such as Direct Preference Optimization (DPO), to T2I systems to enhance image generation fidelity and reliability. We present YinYangAlign, an advanced benchmarking framework that systematically quantifies the alignment fidelity of T2I systems, addressing six fundamental and inherently contradictory design objectives. Each pair represents fundamental tensions in image generation, such as balancing adherence to user prompts with creative modifications or maintaining diversity alongside visual coherence. YinYangAlign includes detailed axiom datasets featuring human prompts, aligned (chosen) responses, misaligned (rejected) AI-generated outputs, and explanations of the underlying contradictions.

Direct Alignment Algorithms (DAAs) simplify language model alignment by replacing reinforcement learning (RL) and reward modeling (RM) in Reinforcement Learning from Human Feedback (RLHF) with direct policy optimization. DAAs can be classified by their ranking losses (pairwise vs. pointwise), by the rewards used in those losses (e.g., likelihood ratios of policy and reference policy, or odds ratios), or by whether a Supervised Fine-Tuning (SFT) phase is required (two-stage vs. one-stage). We first show that one-stage methods underperform two-stage methods. To address this, we incorporate an explicit SFT phase and introduce the beta parameter, controlling the strength of preference optimization, into single-stage ORPO and ASFT. These modifications improve their performance in Alpaca Eval 2 by +3.46 (ORPO) and +8.27 (ASFT), matching two-stage methods like DPO. Further analysis reveals that the key factor is whether the approach uses pairwise or pointwise objectives, rather than the specific implicit reward or loss function. These results highlight the importance of careful evaluation to avoid premature claims of performance gains or overall superiority in alignment algorithms.

Alignment with human preference is a desired property of large language models (LLMs). Currently, the main alignment approach is based on reinforcement learning from human feedback (RLHF). Despite the effectiveness of RLHF, it is intricate to implement and train, thus recent studies explore how to develop alternative alignment approaches based on supervised fine-tuning (SFT). A major limitation of SFT is that it essentially does imitation learning, which cannot fully understand what are the expected behaviors. To address this issue, we propose an improved alignment approach named FIGA. Different from prior methods, we incorporate fine-grained (i.e., token or phrase level) quality signals that are derived by contrasting good and bad responses. Our approach has made two major contributions. Firstly, we curate a refined alignment dataset that pairs initial responses and the corresponding revised ones. Secondly, we devise a new loss function can leverage fine-grained quality signals to instruct the learning of LLMs for alignment. Extensive experiments have demonstrated the effectiveness of our approaches by comparing a number of competitive baselines.

We present PyMAF-X, a regression-based approach to recovering parametric full-body models from monocular images. This task is very challenging since minor parametric deviation may lead to noticeable misalignment between the estimated mesh and the input image. Moreover, when integrating part-specific estimations into the full-body model, existing solutions tend to either degrade the alignment or produce unnatural wrist poses. To address these issues, we propose a Pyramidal Mesh Alignment Feedback (PyMAF) loop in our regression network for well-aligned human mesh recovery and extend it as PyMAF-X for the recovery of expressive full-body models. The core idea of PyMAF is to leverage a feature pyramid and rectify the predicted parameters explicitly based on the mesh-image alignment status. Specifically, given the currently predicted parameters, mesh-aligned evidence will be extracted from finer-resolution features accordingly and fed back for parameter rectification. To enhance the alignment perception, an auxiliary dense supervision is employed to provide mesh-image correspondence guidance while spatial alignment attention is introduced to enable the awareness of the global contexts for our network. When extending PyMAF for full-body mesh recovery, an adaptive integration strategy is proposed in PyMAF-X to produce natural wrist poses while maintaining the well-aligned performance of the part-specific estimations. The efficacy of our approach is validated on several benchmark datasets for body, hand, face, and full-body mesh recovery, where PyMAF and PyMAF-X effectively improve the mesh-image alignment and achieve new state-of-the-art results. The project page with code and video results can be found at https://www.liuyebin.com/pymaf-x.

We consider the task of generating diverse and realistic videos guided by natural audio samples from a wide variety of semantic classes. For this task, the videos are required to be aligned both globally and temporally with the input audio: globally, the input audio is semantically associated with the entire output video, and temporally, each segment of the input audio is associated with a corresponding segment of that video. We utilize an existing text-conditioned video generation model and a pre-trained audio encoder model. The proposed method is based on a lightweight adaptor network, which learns to map the audio-based representation to the input representation expected by the text-to-video generation model. As such, it also enables video generation conditioned on text, audio, and, for the first time as far as we can ascertain, on both text and audio. We validate our method extensively on three datasets demonstrating significant semantic diversity of audio-video samples and further propose a novel evaluation metric (AV-Align) to assess the alignment of generated videos with input audio samples. AV-Align is based on the detection and comparison of energy peaks in both modalities. In comparison to recent state-of-the-art approaches, our method generates videos that are better aligned with the input sound, both with respect to content and temporal axis. We also show that videos produced by our method present higher visual quality and are more diverse.

It has recently been discovered that using a pre-trained vision-language model (VLM), e.g., CLIP, to align a whole query image with several finer text descriptions generated by a large language model can significantly enhance zero-shot performance. However, in this paper, we empirically find that the finer descriptions tend to align more effectively with local areas of the query image rather than the whole image, and then we theoretically validate this finding. Thus, we present a method called weighted visual-text cross alignment (WCA). This method begins with a localized visual prompting technique, designed to identify local visual areas within the query image. The local visual areas are then cross-aligned with the finer descriptions by creating a similarity matrix using the pre-trained VLM. To determine how well a query image aligns with each category, we develop a score function based on the weighted similarities in this matrix. Extensive experiments demonstrate that our method significantly improves zero-shot performance across various datasets, achieving results that are even comparable to few-shot learning methods.

Despite their impressive capabilities, aligned large language models (LLMs) often generate outputs that lack diversity. What drives this stability in the generation? We investigate this phenomenon through the lens of probability concentration in the model's output distribution. To quantify this concentration, we introduce the Branching Factor (BF) -- a token-invariant measure of the effective number of plausible next steps during generation. Our empirical analysis reveals two key findings: (1) BF often decreases as generation progresses, suggesting that LLMs become more predictable as they generate. (2) alignment tuning substantially sharpens the model's output distribution from the outset, reducing BF by nearly an order of magnitude (e.g., from 12 to 1.2) relative to base models. This stark reduction helps explain why aligned models often appear less sensitive to decoding strategies. Building on this insight, we find this stability has surprising implications for complex reasoning. Aligned Chain-of-Thought (CoT) models (e.g., DeepSeek-distilled models), for instance, leverage this effect; by generating longer reasoning chains, they push generation into later, more deterministic (lower BF) stages, resulting in more stable outputs. We hypothesize that alignment tuning does not fundamentally change a model's behavior, but instead steers it toward stylistic tokens (e.g., "Sure") that unlock low-entropy trajectories already present in the base model. This view is supported by nudging experiments, which show that prompting base models with such tokens can similarly reduce BF. Together, our findings establish BF as a powerful diagnostic for understanding and controlling LLM outputs - clarifying how alignment reduces variability, how CoT promotes stable generations, and how base models can be steered away from diversity.

Multi-modal foundation models combining vision and language models such as Flamingo or GPT-4 have recently gained enormous interest. Alignment of foundation models is used to prevent models from providing toxic or harmful output. While malicious users have successfully tried to jailbreak foundation models, an equally important question is if honest users could be harmed by malicious third-party content. In this paper we show that imperceivable attacks on images in order to change the caption output of a multi-modal foundation model can be used by malicious content providers to harm honest users e.g. by guiding them to malicious websites or broadcast fake information. This indicates that countermeasures to adversarial attacks should be used by any deployed multi-modal foundation model.

Layout-guided text-to-image models offer greater control over the generation process by explicitly conditioning image synthesis on the spatial arrangement of elements. As a result, their adoption has increased in many computer vision applications, ranging from content creation to synthetic data generation. A critical challenge is achieving precise alignment between the image, textual prompt, and layout, ensuring semantic fidelity and spatial accuracy. Although recent benchmarks assess text alignment, layout alignment remains overlooked, and no existing benchmark jointly evaluates both. This gap limits the ability to evaluate a model's spatial fidelity, which is crucial when using layout-guided generation for synthetic data, as errors can introduce noise and degrade data quality. In this work, we introduce 7Bench, the first benchmark to assess both semantic and spatial alignment in layout-guided text-to-image generation. It features text-and-layout pairs spanning seven challenging scenarios, investigating object generation, color fidelity, attribute recognition, inter-object relationships, and spatial control. We propose an evaluation protocol that builds on existing frameworks by incorporating the layout alignment score to assess spatial accuracy. Using 7Bench, we evaluate several state-of-the-art diffusion models, uncovering their respective strengths and limitations across diverse alignment tasks. The benchmark is available at https://github.com/Elizzo/7Bench.

Image-text matching plays a critical role in bridging the vision and language, and great progress has been made by exploiting the global alignment between image and sentence, or local alignments between regions and words. However, how to make the most of these alignments to infer more accurate matching scores is still underexplored. In this paper, we propose a novel Similarity Graph Reasoning and Attention Filtration (SGRAF) network for image-text matching. Specifically, the vector-based similarity representations are firstly learned to characterize the local and global alignments in a more comprehensive manner, and then the Similarity Graph Reasoning (SGR) module relying on one graph convolutional neural network is introduced to infer relation-aware similarities with both the local and global alignments. The Similarity Attention Filtration (SAF) module is further developed to integrate these alignments effectively by selectively attending on the significant and representative alignments and meanwhile casting aside the interferences of non-meaningful alignments. We demonstrate the superiority of the proposed method with achieving state-of-the-art performances on the Flickr30K and MSCOCO datasets, and the good interpretability of SGR and SAF modules with extensive qualitative experiments and analyses.

Large Language Models (LLMs) require alignment with human preferences to avoid generating offensive, false, or meaningless content. Recently, low-resource methods for LLM alignment have been popular, while still facing challenges in obtaining both high-quality and aligned content. Motivated by the observation that the difficulty of generating aligned responses is concentrated at the beginning of decoding, we propose a novel framework, Weak-to-Strong Decoding (WSD), to enhance the alignment ability of base models by the guidance of a small aligned model. The small model first drafts well-aligned beginnings, followed by the large base model to continue the rest, controlled by a well-designed auto-switch mechanism. We also collect a new dataset, GenerAlign, to fine-tune a small-sized Pilot-3B as the draft model, which effectively enhances different base models under the WSD framework to outperform all baseline methods, while avoiding degradation on downstream tasks, termed as the alignment tax. Extensive experiments are further conducted to examine the impact of different settings and time efficiency, as well as analyses on the intrinsic mechanisms of WSD in depth.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

Recent advances in learning aligned multimodal representations have been primarily driven by training large neural networks on massive, noisy paired-modality datasets. In this work, we ask whether it is possible to achieve similar results with substantially less training time and data. We achieve this by taking advantage of existing pretrained unimodal encoders and careful curation of alignment data relevant to the downstream task of interest. We study a natural approach to aligning existing encoders via small auxiliary functions, and we find that this method is competitive with (or outperforms) state of the art in many settings while being less prone to overfitting, less costly to train, and more robust to distribution shift. With a properly chosen alignment distribution, our method surpasses prior state of the art for ImageNet zero-shot classification on public data while using two orders of magnitude less time and data and training 77% fewer parameters.

The performance of Latent Diffusion Models (LDMs) is critically dependent on the quality of their visual tokenizer. While recent works have explored incorporating Vision Foundation Models (VFMs) via distillation, we identify a fundamental flaw in this approach: it inevitably weakens the robustness of alignment with the original VFM, causing the aligned latents to deviate semantically under distribution shifts. In this paper, we bypass distillation by proposing a more direct approach: Vision Foundation Model Variational Autoencoder (VFM-VAE). To resolve the inherent tension between the VFM's semantic focus and the need for pixel-level fidelity, we redesign the VFM-VAE decoder with Multi-Scale Latent Fusion and Progressive Resolution Reconstruction blocks, enabling high-quality reconstruction from spatially coarse VFM features. Furthermore, we provide a comprehensive analysis of representation dynamics during diffusion training, introducing the proposed SE-CKNNA metric as a more precise tool for this diagnosis. This analysis allows us to develop a joint tokenizer-diffusion alignment strategy that dramatically accelerates convergence. Our innovations in tokenizer design and training strategy lead to superior performance and efficiency: our system reaches a gFID (w/o CFG) of 2.20 in merely 80 epochs (a 10x speedup over prior tokenizers). With continued training to 640 epochs, it further attains a gFID (w/o CFG) of 1.62, establishing direct VFM integration as a superior paradigm for LDMs.

Alignment, endowing a pre-trained Large language model (LLM) with the ability to follow instructions, is crucial for its real-world applications. Conventional supervised fine-tuning (SFT) methods formalize it as causal language modeling typically with a cross-entropy objective, requiring a large amount of high-quality instruction-response pairs. However, the quality of widely used SFT datasets can not be guaranteed due to the high cost and intensive labor for the creation and maintenance in practice. To overcome the limitations associated with the quality of SFT datasets, we introduce a novel preference-oriented supervised fine-tuning approach, namely PoFT. The intuition is to boost SFT by imposing a particular preference: favoring the target model over aligned LLMs on the same SFT data. This preference encourages the target model to predict a higher likelihood than that predicted by the aligned LLMs, incorporating assessment information on data quality (i.e., predicted likelihood by the aligned LLMs) into the training process. Extensive experiments are conducted, and the results validate the effectiveness of the proposed method. PoFT achieves stable and consistent improvements over the SFT baselines across different training datasets and base models. Moreover, we prove that PoFT can be integrated with existing SFT data filtering methods to achieve better performance, and further improved by following preference optimization procedures, such as DPO.

Ensuring precise multimodal alignment between diffusion-generated images and input prompts has been a long-standing challenge. Earlier works finetune diffusion weight using high-quality preference data, which tends to be limited and difficult to scale up. Recent editing-based methods further refine local regions of generated images but may compromise overall image quality. In this work, we propose Implicit Multimodal Guidance (IMG), a novel re-generation-based multimodal alignment framework that requires no extra data or editing operations. Specifically, given a generated image and its prompt, IMG a) utilizes a multimodal large language model (MLLM) to identify misalignments; b) introduces an Implicit Aligner that manipulates diffusion conditioning features to reduce misalignments and enable re-generation; and c) formulates the re-alignment goal into a trainable objective, namely Iteratively Updated Preference Objective. Extensive qualitative and quantitative evaluations on SDXL, SDXL-DPO, and FLUX show that IMG outperforms existing alignment methods. Furthermore, IMG acts as a flexible plug-and-play adapter, seamlessly enhancing prior finetuning-based alignment methods. Our code will be available at https://github.com/SHI-Labs/IMG-Multimodal-Diffusion-Alignment.

Existing perceptual similarity metrics assume an image and its reference are well aligned. As a result, these metrics are often sensitive to a small alignment error that is imperceptible to the human eyes. This paper studies the effect of small misalignment, specifically a small shift between the input and reference image, on existing metrics, and accordingly develops a shift-tolerant similarity metric. This paper builds upon LPIPS, a widely used learned perceptual similarity metric, and explores architectural design considerations to make it robust against imperceptible misalignment. Specifically, we study a wide spectrum of neural network elements, such as anti-aliasing filtering, pooling, striding, padding, and skip connection, and discuss their roles in making a robust metric. Based on our studies, we develop a new deep neural network-based perceptual similarity metric. Our experiments show that our metric is tolerant to imperceptible shifts while being consistent with the human similarity judgment.

Regression-based methods have recently shown promising results in reconstructing human meshes from monocular images. By directly mapping raw pixels to model parameters, these methods can produce parametric models in a feed-forward manner via neural networks. However, minor deviation in parameters may lead to noticeable misalignment between the estimated meshes and image evidences. To address this issue, we propose a Pyramidal Mesh Alignment Feedback (PyMAF) loop to leverage a feature pyramid and rectify the predicted parameters explicitly based on the mesh-image alignment status in our deep regressor. In PyMAF, given the currently predicted parameters, mesh-aligned evidences will be extracted from finer-resolution features accordingly and fed back for parameter rectification. To reduce noise and enhance the reliability of these evidences, an auxiliary pixel-wise supervision is imposed on the feature encoder, which provides mesh-image correspondence guidance for our network to preserve the most related information in spatial features. The efficacy of our approach is validated on several benchmarks, including Human3.6M, 3DPW, LSP, and COCO, where experimental results show that our approach consistently improves the mesh-image alignment of the reconstruction. The project page with code and video results can be found at https://hongwenzhang.github.io/pymaf.

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

Aligning large language models with human objectives is paramount, yet common approaches including RLHF suffer from unstable and resource-intensive training. In response to this challenge, we introduce ARGS, Alignment as Reward-Guided Search, a novel framework that integrates alignment into the decoding process, eliminating the need for expensive RL training. By adjusting the model's probabilistic predictions using a reward signal, ARGS generates texts with semantic diversity while being aligned with human preferences, offering a promising and flexible solution for aligning language models. Notably, ARGS demonstrates consistent enhancements in average reward compared to baselines across diverse alignment tasks and various model dimensions. For example, under the same greedy-based decoding strategy, our method improves the average reward by 19.56% relative to the baseline and secures a preference or tie score of 64.33% in GPT-4 evaluation. We believe that our framework, emphasizing decoding-time alignment, paves the way for more responsive language models in the future. Code is publicly available at: https://github.com/deeplearning-wisc/args.

Foundation Vision Encoders have become essential for a wide range of dense vision tasks. However, their low-resolution spatial feature outputs necessitate feature upsampling to produce the high-resolution modalities required for downstream tasks. In this work, we introduce JAFAR, a lightweight and flexible feature upsampler that enhances the spatial resolution of visual features from any Foundation Vision Encoder to an arbitrary target resolution. JAFAR employs an attention-based module designed to promote semantic alignment between high-resolution queries, derived from low-level image features, and semantically enriched low-resolution keys, using Spatial Feature Transform (SFT) modulation. Notably, despite the absence of high-resolution supervision, we demonstrate that learning at low upsampling ratios and resolutions generalizes remarkably well to significantly higher output scales. Extensive experiments show that JAFAR effectively recovers fine-grained spatial details and consistently outperforms existing feature upsampling methods across a diverse set of downstream tasks. Project page at https://jafar-upsampler.github.io

Aiming to enhance Face Recognition (FR) on Low-Quality (LQ) inputs, recent studies suggest incorporating synthetic LQ samples into training. Although promising, the quality factors that are considered in these works are general rather than FR-specific, \eg, atmospheric turbulence, resolution, \etc. Motivated by the observation of the vulnerability of current FR models to even small Face Alignment Errors (FAE) in LQ images, we present a simple yet effective method that considers FAE as another quality factor that is tailored to FR. We seek to improve LQ FR by enhancing FR models' robustness to FAE. To this aim, we formalize the problem as a combination of differentiable spatial transformations and adversarial data augmentation in FR. We perturb the alignment of the training samples using a controllable spatial transformation and enrich the training with samples expressing FAE. We demonstrate the benefits of the proposed method by conducting evaluations on IJB-B, IJB-C, IJB-S (+4.3\% Rank1), and TinyFace (+2.63\%). https://github.com/msed-Ebrahimi/ARoFace{https://github.com/msed-Ebrahimi/ARoFace}

A key concern with the concept of "alignment" is the implicit question of "alignment to what?". AI systems are increasingly used across the world, yet safety alignment is often focused on homogeneous monolingual settings. Additionally, preference training and safety measures often overfit to harms common in Western-centric datasets. Here, we explore the viability of different alignment approaches when balancing dual objectives: addressing and optimizing for a non-homogeneous set of languages and cultural preferences while minimizing both global and local harms. We collect the first set of human annotated red-teaming prompts in different languages distinguishing between global and local harm, which serve as a laboratory for understanding the reliability of alignment techniques when faced with preference distributions that are non-stationary across geographies and languages. While this setting is seldom covered by the literature to date, which primarily centers on English harm mitigation, it captures real-world interactions with AI systems around the world. We establish a new precedent for state-of-the-art alignment techniques across 6 languages with minimal degradation in general performance. Our work provides important insights into cross-lingual transfer and novel optimization approaches to safeguard AI systems designed to serve global populations.

The success of AI assistants based on Language Models (LLMs) hinges on Reinforcement Learning from Human Feedback (RLHF) to comprehend and align with user intentions. However, traditional alignment algorithms, such as PPO, are hampered by complex annotation and training requirements. This reliance limits the applicability of RLHF and hinders the development of professional assistants tailored to diverse human preferences. In this work, we introduce Linear Alignment, a novel algorithm that aligns language models with human preferences in one single inference step, eliminating the reliance on data annotation and model training. Linear alignment incorporates a new parameterization for policy optimization under divergence constraints, which enables the extraction of optimal policy in a closed-form manner and facilitates the direct estimation of the aligned response. Extensive experiments on both general and personalized preference datasets demonstrate that linear alignment significantly enhances the performance and efficiency of LLM alignment across diverse scenarios. Our code and dataset will be published on https://github.com/Wizardcoast/Linear_Alignment.git.

Full-reference image quality assessment (FR-IQA) generally assumes that reference images are of perfect quality. However, this assumption is flawed due to the sensor and optical limitations of modern imaging systems. Moreover, recent generative enhancement methods are capable of producing images of higher quality than their original. All of these challenge the effectiveness and applicability of current FR-IQA models. To relax the assumption of perfect reference image quality, we build a large-scale IQA database, namely DiffIQA, containing approximately 180,000 images generated by a diffusion-based image enhancer with adjustable hyper-parameters. Each image is annotated by human subjects as either worse, similar, or better quality compared to its reference. Building on this, we present a generalized FR-IQA model, namely Adaptive Fidelity-Naturalness Evaluator (A-FINE), to accurately assess and adaptively combine the fidelity and naturalness of a test image. A-FINE aligns well with standard FR-IQA when the reference image is much more natural than the test image. We demonstrate by extensive experiments that A-FINE surpasses standard FR-IQA models on well-established IQA datasets and our newly created DiffIQA. To further validate A-FINE, we additionally construct a super-resolution IQA benchmark (SRIQA-Bench), encompassing test images derived from ten state-of-the-art SR methods with reliable human quality annotations. Tests on SRIQA-Bench re-affirm the advantages of A-FINE. The code and dataset are available at https://tianhewu.github.io/A-FINE-page.github.io/.

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

We investigate whether Alfv\'enic fluctuations (AFs) can affect the structure of magnetic ejecta (MEs) within interplanetary coronal mass ejections (ICMEs). We study an ICME observed on 2001 December 29 at 1 au by ACE and Wind, at a total angular separation of sim0.8^circ (sim0.014~au). We focus on the correlation and complexity of its magnetic structure measured between two spacecraft in association with large-amplitude AFs. The Alfv\'enicity of the ME is investigated in terms of the residual energy and cross helicity of fluctuations. We find that as for the event of interest, large-amplitude AFs occur in the rear region of the ME at both Wind and ACE with a duration of about six hours. We compare the correlation of the magnetic field strength and vector components measured between Wind and ACE, and investigate complexity in terms of the magnetic hodograms. The region showing AFs is found to be associated with a decreased correlation of the magnetic field components and an increased complexity of the ME magnetic configuration detected at ACE and Wind, which may be due to the fact that the two spacecraft crossing the same ME along different trajectories likely sampled AFs in different oscillation phases. Combining multi-point in-situ measurements and remote-sensing observations of the ICME source region, we further discuss different potential sources of the AFs.

Large language models (LLMs) can handle a wide variety of general tasks with simple prompts, without the need for task-specific training. Multimodal Large Language Models (MLLMs), built upon LLMs, have demonstrated impressive potential in tackling complex tasks involving visual, auditory, and textual data. However, critical issues related to truthfulness, safety, o1-like reasoning, and alignment with human preference remain insufficiently addressed. This gap has spurred the emergence of various alignment algorithms, each targeting different application scenarios and optimization goals. Recent studies have shown that alignment algorithms are a powerful approach to resolving the aforementioned challenges. In this paper, we aim to provide a comprehensive and systematic review of alignment algorithms for MLLMs. Specifically, we explore four key aspects: (1) the application scenarios covered by alignment algorithms, including general image understanding, multi-image, video, and audio, and extended multimodal applications; (2) the core factors in constructing alignment datasets, including data sources, model responses, and preference annotations; (3) the benchmarks used to evaluate alignment algorithms; and (4) a discussion of potential future directions for the development of alignment algorithms. This work seeks to help researchers organize current advancements in the field and inspire better alignment methods. The project page of this paper is available at https://github.com/BradyFU/Awesome-Multimodal-Large-Language-Models/tree/Alignment.

Due to the remarkable capabilities and growing impact of large language models (LLMs), they have been deeply integrated into many aspects of society. Thus, ensuring their alignment with human values and intentions has emerged as a critical challenge. This survey provides a comprehensive overview of practical alignment techniques, training protocols, and empirical findings in LLM alignment. We analyze the development of alignment methods across diverse paradigms, characterizing the fundamental trade-offs between core alignment objectives. Our analysis shows that while supervised fine-tuning enables basic instruction-following, preference-based methods offer more flexibility for aligning with nuanced human intent. We discuss state-of-the-art techniques, including Direct Preference Optimization (DPO), Constitutional AI, brain-inspired methods, and alignment uncertainty quantification (AUQ), highlighting their approaches to balancing quality and efficiency. We review existing evaluation frameworks and benchmarking datasets, emphasizing limitations such as reward misspecification, distributional robustness, and scalable oversight. We summarize strategies adopted by leading AI labs to illustrate the current state of practice. We conclude by outlining open problems in oversight, value pluralism, robustness, and continuous alignment. This survey aims to inform both researchers and practitioners navigating the evolving landscape of LLM alignment.

Image registration is important for medical imaging, the estimation of the spatial transformation between different images. Many previous studies have used learning-based methods for coarse-to-fine registration to efficiently perform 3D image registration. The coarse-to-fine approach, however, is limited when dealing with the different motions of nearby objects. Here we propose a novel Motion-Aware (MA) structure that captures the different motions in a region. The MA structure incorporates a novel Residual Aligner (RA) module which predicts the multi-head displacement field used to disentangle the different motions of multiple neighbouring objects. Compared with other deep learning methods, the network based on the MA structure and RA module achieve one of the most accurate unsupervised inter-subject registration on the 9 organs of assorted sizes in abdominal CT scans, with the highest-ranked registration of the veins (Dice Similarity Coefficient / Average surface distance: 62\%/4.9mm for the vena cava and 34\%/7.9mm for the portal and splenic vein), with a half-sized structure and more efficient computation. Applied to the segmentation of lungs in chest CT scans, the new network achieves results which were indistinguishable from the best-ranked networks (94\%/3.0mm). Additionally, the theorem on predicted motion pattern and the design of MA structure are validated by further analysis.

Diffusion models have demonstrated great success in the field of text-to-image generation. However, alleviating the misalignment between the text prompts and images is still challenging. The root reason behind the misalignment has not been extensively investigated. We observe that the misalignment is caused by inadequate token attention activation. We further attribute this phenomenon to the diffusion model's insufficient condition utilization, which is caused by its training paradigm. To address the issue, we propose CoMat, an end-to-end diffusion model fine-tuning strategy with an image-to-text concept matching mechanism. We leverage an image captioning model to measure image-to-text alignment and guide the diffusion model to revisit ignored tokens. A novel attribute concentration module is also proposed to address the attribute binding problem. Without any image or human preference data, we use only 20K text prompts to fine-tune SDXL to obtain CoMat-SDXL. Extensive experiments show that CoMat-SDXL significantly outperforms the baseline model SDXL in two text-to-image alignment benchmarks and achieves start-of-the-art performance.

Despite their generative power, diffusion models struggle to maintain style consistency across images conditioned on the same style prompt, hindering their practical deployment in creative workflows. While several training-free methods attempt to solve this, they are constrained to the U-Net architecture, which not only leads to low-quality results and artifacts like object repetition but also renders them incompatible with superior Diffusion Transformer (DiT). To address these issues, we introduce AlignedGen, a novel training-free framework that enhances style consistency across images generated by DiT models. Our work first reveals a critical insight: naive attention sharing fails in DiT due to conflicting positional signals from improper position embeddings. We introduce Shifted Position Embedding (ShiftPE), an effective solution that resolves this conflict by allocating a non-overlapping set of positional indices to each image. Building on this foundation, we develop Advanced Attention Sharing (AAS), a suite of three techniques meticulously designed to fully unleash the potential of attention sharing within the DiT. Furthermore, to broaden the applicability of our method, we present an efficient query, key, and value feature extraction algorithm, enabling our method to seamlessly incorporate external images as style references. Extensive experimental results validate that our method effectively enhances style consistency across generated images while maintaining precise text-to-image alignment.

Vision-language models (VLMs) often produce chain-of-thought (CoT) explanations that sound plausible yet fail to reflect the underlying decision process, undermining trust in high-stakes clinical use. Existing evaluations rarely catch this misalignment, prioritizing answer accuracy or adherence to formats. We present a clinically grounded framework for chest X-ray visual question answering (VQA) that probes CoT faithfulness via controlled text and image modifications across three axes: clinical fidelity, causal attribution, and confidence calibration. In a reader study (n=4), evaluator-radiologist correlations fall within the observed inter-radiologist range for all axes, with strong alignment for attribution (Kendall's tau_b=0.670), moderate alignment for fidelity (tau_b=0.387), and weak alignment for confidence tone (tau_b=0.091), which we report with caution. Benchmarking six VLMs shows that answer accuracy and explanation quality are decoupled, acknowledging injected cues does not ensure grounding, and text cues shift explanations more than visual cues. While some open-source models match final answer accuracy, proprietary models score higher on attribution (25.0% vs. 1.4%) and often on fidelity (36.1% vs. 31.7%), highlighting deployment risks and the need to evaluate beyond final answer accuracy.

With the rapid development of large language models (LLMs), they are not only used as general-purpose AI assistants but are also customized through further fine-tuning to meet the requirements of different applications. A pivotal factor in the success of current LLMs is the alignment process. Current alignment methods, such as supervised fine-tuning (SFT) and reinforcement learning from human feedback (RLHF), focus on training-time alignment and are often complex and cumbersome to implement. Therefore, we develop InferAligner, a novel inference-time alignment method that utilizes cross-model guidance for harmlessness alignment. InferAligner utilizes safety steering vectors extracted from safety-aligned model to modify the activations of the target model when responding to harmful inputs, thereby guiding the target model to provide harmless responses. Experimental results show that our method can be very effectively applied to domain-specific models in finance, medicine, and mathematics, as well as to multimodal large language models (MLLMs) such as LLaVA. It significantly diminishes the Attack Success Rate (ASR) of both harmful instructions and jailbreak attacks, while maintaining almost unchanged performance in downstream tasks.

Foundation models rely on large-scale web-crawled datasets, which frequently contain noisy data, biases, and irrelevant content. Existing data selection techniques typically use human heuristics, downstream evaluation datasets, or specialized scoring models, and can overlook samples' utility in the training process. Instead, we propose a new approach, Mimic Score, a data quality metric that uses a pretrained reference model as a guide to assess the usefulness of data samples for training a new model. It relies on the alignment between the gradient of the new model parameters and the vector pointing toward the reference model in weight space. Samples that misalign with this direction are considered low-value and can be filtered out. Motivated by the Mimic score, we develop Grad-Mimic, a data selection framework that identifies and prioritizes useful samples, automating the selection process to create effective filters. Empirically, using Mimic scores to guide model training results in consistent performance gains across six image datasets and enhances the performance of CLIP models. Moreover, Mimic scores and their associated filters improve upon existing filtering methods and offer accurate estimation of dataset quality.

Despite notable advancements in Multimodal Large Language Models (MLLMs), most state-of-the-art models have not undergone thorough alignment with human preferences. This gap exists because current alignment research has primarily achieved progress in specific areas (e.g., hallucination reduction), while the broader question of whether aligning models with human preferences can systematically enhance MLLM capability remains largely unexplored. To this end, we introduce MM-RLHF, a dataset containing 120k fine-grained, human-annotated preference comparison pairs. This dataset represents a substantial advancement over existing resources, offering superior size, diversity, annotation granularity, and quality. Leveraging this dataset, we propose several key innovations to improve both the quality of reward models and the efficiency of alignment algorithms. Notably, we introduce a Critique-Based Reward Model, which generates critiques of model outputs before assigning scores, offering enhanced interpretability and more informative feedback compared to traditional scalar reward mechanisms. Additionally, we propose Dynamic Reward Scaling, a method that adjusts the loss weight of each sample according to the reward signal, thereby optimizing the use of high-quality comparison pairs. Our approach is rigorously evaluated across 10 distinct dimensions and 27 benchmarks, with results demonstrating significant and consistent improvements in model performance. Specifically, fine-tuning LLaVA-ov-7B with MM-RLHF and our alignment algorithm leads to a 19.5% increase in conversational abilities and a 60% improvement in safety. We have open-sourced the preference dataset, reward model, training and evaluation code, as well as reward modeling and safety benchmarks. For more details, please visit our project page: https://mm-rlhf.github.io.

Monolingual word alignment is crucial to model semantic interactions between sentences. In particular, null alignment, a phenomenon in which words have no corresponding counterparts, is pervasive and critical in handling semantically divergent sentences. Identification of null alignment is useful on its own to reason about the semantic similarity of sentences by indicating there exists information inequality. To achieve unbalanced word alignment that values both alignment and null alignment, this study shows that the family of optimal transport (OT), i.e., balanced, partial, and unbalanced OT, are natural and powerful approaches even without tailor-made techniques. Our extensive experiments covering unsupervised and supervised settings indicate that our generic OT-based alignment methods are competitive against the state-of-the-arts specially designed for word alignment, remarkably on challenging datasets with high null alignment frequencies.

Alignment of the language model with human preferences is a common approach to making a language model useful to end users. However, most alignment work is done in English, and human preference datasets are dominated by English, reflecting only the preferences of English-speaking annotators. Nevertheless, it is common practice to use the English preference data, either directly or by translating it into the target language, when aligning a multilingual language model. The question is whether such an alignment strategy marginalizes the preference of non-English speaking users. To this end, we investigate the effect of aligning Japanese language models with (mostly) English resources. In particular, we focus on evaluating whether the commonsense morality of the resulting fine-tuned models is aligned with Japanese culture using the JCommonsenseMorality (JCM) and ETHICS datasets. The experimental results show that the fine-tuned model outperforms the SFT model. However, it does not demonstrate the same level of improvement as a model fine-tuned using the JCM, suggesting that while some aspects of commonsense morality are transferable, others may not be.

Fine-tuning a pre-trained Text-to-Image (T2I) model on a tailored portrait dataset is the mainstream method for text-driven customization of portrait attributes. Due to Semantic Pollution during fine-tuning, existing methods struggle to maintain the original model's behavior and achieve incremental learning while customizing target attributes. To address this issue, we propose SPF-Portrait, a pioneering work to purely understand customized semantics while eliminating semantic pollution in text-driven portrait customization. In our SPF-Portrait, we propose a dual-path pipeline that introduces the original model as a reference for the conventional fine-tuning path. Through contrastive learning, we ensure adaptation to target attributes and purposefully align other unrelated attributes with the original portrait. We introduce a novel Semantic-Aware Fine Control Map, which represents the precise response regions of the target semantics, to spatially guide the alignment process between the contrastive paths. This alignment process not only effectively preserves the performance of the original model but also avoids over-alignment. Furthermore, we propose a novel response enhancement mechanism to reinforce the performance of target attributes, while mitigating representation discrepancy inherent in direct cross-modal supervision. Extensive experiments demonstrate that SPF-Portrait achieves state-of-the-art performance. Project webpage: https://spf-portrait.github.io/SPF-Portrait/

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Word alignments are useful for tasks like statistical and neural machine translation (NMT) and cross-lingual annotation projection. Statistical word aligners perform well, as do methods that extract alignments jointly with translations in NMT. However, most approaches require parallel training data, and quality decreases as less training data is available. We propose word alignment methods that require no parallel data. The key idea is to leverage multilingual word embeddings, both static and contextualized, for word alignment. Our multilingual embeddings are created from monolingual data only without relying on any parallel data or dictionaries. We find that alignments created from embeddings are superior for four and comparable for two language pairs compared to those produced by traditional statistical aligners, even with abundant parallel data; e.g., contextualized embeddings achieve a word alignment F1 for English-German that is 5 percentage points higher than eflomal, a high-quality statistical aligner, trained on 100k parallel sentences.

The crux of learning vision-language models is to extract semantically aligned information from visual and linguistic data. Existing attempts usually face the problem of coarse alignment, e.g., the vision encoder struggles in localizing an attribute-specified object. In this work, we propose an embarrassingly simple approach to better align image and text features with no need of additional data formats other than image-text pairs. Concretely, given an image and its paired text, we manage to parse objects (e.g., cat) and attributes (e.g., black) from the description, which are highly likely to exist in the image. It is noteworthy that the parsing pipeline is fully automatic and thus enjoys good scalability. With these parsed semantics as supervision signals, we can complement the commonly used image-text contrastive loss with the multi-tag classification loss. Extensive experimental results on a broad suite of semantic segmentation datasets substantiate the average 3.65\% improvement of our framework over existing alternatives. Furthermore, the visualization results indicate that attribute supervision makes vision-language models accurately localize attribute-specified objects. Project page and code can be found at https://qinying-liu.github.io/Tag-Align.

Foundation Models (FMs) have demonstrated unprecedented capabilities including zero-shot learning, high fidelity data synthesis, and out of domain generalization. However, as we show in this paper, FMs still have poor out-of-the-box performance on expert tasks (e.g. retrieval of car manuals technical illustrations from language queries), data for which is either unseen or belonging to a long-tail part of the data distribution of the huge datasets used for FM pre-training. This underlines the necessity to explicitly evaluate and finetune FMs on such expert tasks, arguably ones that appear the most in practical real-world applications. In this paper, we propose a first of its kind FETA benchmark built around the task of teaching FMs to understand technical documentation, via learning to match their graphical illustrations to corresponding language descriptions. Our FETA benchmark focuses on text-to-image and image-to-text retrieval in public car manuals and sales catalogue brochures. FETA is equipped with a procedure for completely automatic annotation extraction (code would be released upon acceptance), allowing easy extension of FETA to more documentation types and application domains in the future. Our automatic annotation leads to an automated performance metric shown to be consistent with metrics computed on human-curated annotations (also released). We provide multiple baselines and analysis of popular FMs on FETA leading to several interesting findings that we believe would be very valuable to the FM community, paving the way towards real-world application of FMs for practical expert tasks currently 'overlooked' by standard benchmarks focusing on common objects.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

Recent advancements in text-to-image models, particularly diffusion models, have shown significant promise. However, compositional text-to-image models frequently encounter difficulties in generating high-quality images that accurately align with input texts describing multiple objects, variable attributes, and intricate spatial relationships. To address this limitation, we employ large vision-language models (LVLMs) for multi-dimensional assessment of the alignment between generated images and their corresponding input texts. Utilizing this assessment, we fine-tune the diffusion model to enhance its alignment capabilities. During the inference phase, an initial image is produced using the fine-tuned diffusion model. The LVLM is then employed to pinpoint areas of misalignment in the initial image, which are subsequently corrected using the image editing algorithm until no further misalignments are detected by the LVLM. The resultant image is consequently more closely aligned with the input text. Our experimental results validate that the proposed methodology significantly improves text-image alignment in compositional image generation, particularly with respect to object number, attribute binding, spatial relationships, and aesthetic quality.

High-quality instruction data is critical for aligning large language models (LLMs). Although some models, such as Llama-3-Instruct, have open weights, their alignment data remain private, which hinders the democratization of AI. High human labor costs and a limited, predefined scope for prompting prevent existing open-source data creation methods from scaling effectively, potentially limiting the diversity and quality of public alignment datasets. Is it possible to synthesize high-quality instruction data at scale by extracting it directly from an aligned LLM? We present a self-synthesis method for generating large-scale alignment data named Magpie. Our key observation is that aligned LLMs like Llama-3-Instruct can generate a user query when we input only the left-side templates up to the position reserved for user messages, thanks to their auto-regressive nature. We use this method to prompt Llama-3-Instruct and generate 4 million instructions along with their corresponding responses. We perform a comprehensive analysis of the extracted data and select 300K high-quality instances. To compare Magpie data with other public instruction datasets, we fine-tune Llama-3-8B-Base with each dataset and evaluate the performance of the fine-tuned models. Our results indicate that in some tasks, models fine-tuned with Magpie perform comparably to the official Llama-3-8B-Instruct, despite the latter being enhanced with 10 million data points through supervised fine-tuning (SFT) and subsequent feedback learning. We also show that using Magpie solely for SFT can surpass the performance of previous public datasets utilized for both SFT and preference optimization, such as direct preference optimization with UltraFeedback. This advantage is evident on alignment benchmarks such as AlpacaEval, ArenaHard, and WildBench.

Targeting at both high efficiency and performance, we propose AlignTTS to predict the mel-spectrum in parallel. AlignTTS is based on a Feed-Forward Transformer which generates mel-spectrum from a sequence of characters, and the duration of each character is determined by a duration predictor.Instead of adopting the attention mechanism in Transformer TTS to align text to mel-spectrum, the alignment loss is presented to consider all possible alignments in training by use of dynamic programming. Experiments on the LJSpeech dataset show that our model achieves not only state-of-the-art performance which outperforms Transformer TTS by 0.03 in mean option score (MOS), but also a high efficiency which is more than 50 times faster than real-time.

Recently, Text-to-Image (T2I) generation models have achieved significant advancements. Correspondingly, many automated metrics have emerged to evaluate the image-text alignment capabilities of generative models. However, the performance comparison among these automated metrics is limited by existing small datasets. Additionally, these datasets lack the capacity to assess the performance of automated metrics at a fine-grained level. In this study, we contribute an EvalMuse-40K benchmark, gathering 40K image-text pairs with fine-grained human annotations for image-text alignment-related tasks. In the construction process, we employ various strategies such as balanced prompt sampling and data re-annotation to ensure the diversity and reliability of our benchmark. This allows us to comprehensively evaluate the effectiveness of image-text alignment metrics for T2I models. Meanwhile, we introduce two new methods to evaluate the image-text alignment capabilities of T2I models: FGA-BLIP2 which involves end-to-end fine-tuning of a vision-language model to produce fine-grained image-text alignment scores and PN-VQA which adopts a novel positive-negative VQA manner in VQA models for zero-shot fine-grained evaluation. Both methods achieve impressive performance in image-text alignment evaluations. We also use our methods to rank current AIGC models, in which the results can serve as a reference source for future study and promote the development of T2I generation. The data and code will be made publicly available.

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language models can efficiently process sequential data, offering an alternative approach to molecular representation. In the current study, we introduce BAPULM, an innovative sequence-based framework that leverages the chemical latent representations of proteins via ProtT5-XL-U50 and ligands through MolFormer, eliminating reliance on complex 3D configurations. Our approach was validated extensively on benchmark datasets, achieving scoring power (R) values of 0.925 pm 0.043, 0.914 pm 0.004, and 0.8132 pm 0.001 on benchmark1k2101, Test2016_290, and CSAR-HiQ_36, respectively. These findings indicate the robustness and accuracy of BAPULM across diverse datasets and underscore the potential of sequence-based models in-silico drug discovery, offering a scalable alternative to 3D-centric methods for screening potential ligands.

Inference-time alignment provides an efficient alternative for aligning LLMs with humans. However, these approaches still face challenges, such as limited scalability due to policy-specific value functions and latency during the inference phase. In this paper, we propose a novel approach, Diffusion-styled Preference Optimization (\model), which provides an efficient and policy-agnostic solution for aligning LLMs with humans. By directly performing alignment at sentence level, \model~avoids the time latency associated with token-level generation. Designed as a plug-and-play module, \model~can be seamlessly integrated with various base models to enhance their alignment. Extensive experiments on AlpacaEval 2, MT-bench, and HH-RLHF demonstrate that \model~achieves superior alignment performance across various settings, achieving a favorable trade-off between alignment quality and inference-time latency. Furthermore, \model~demonstrates model-agnostic scalability, significantly improving the performance of large models such as Llama-3-70B.

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

Existing video recognition algorithms always conduct different training pipelines for inputs with different frame numbers, which requires repetitive training operations and multiplying storage costs. If we evaluate the model using other frames which are not used in training, we observe the performance will drop significantly (see Fig.1), which is summarized as Temporal Frequency Deviation phenomenon. To fix this issue, we propose a general framework, named Frame Flexible Network (FFN), which not only enables the model to be evaluated at different frames to adjust its computation, but also reduces the memory costs of storing multiple models significantly. Concretely, FFN integrates several sets of training sequences, involves Multi-Frequency Alignment (MFAL) to learn temporal frequency invariant representations, and leverages Multi-Frequency Adaptation (MFAD) to further strengthen the representation abilities. Comprehensive empirical validations using various architectures and popular benchmarks solidly demonstrate the effectiveness and generalization of FFN (e.g., 7.08/5.15/2.17% performance gain at Frame 4/8/16 on Something-Something V1 dataset over Uniformer). Code is available at https://github.com/BeSpontaneous/FFN.

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

Recent work by Baratin et al. (2021) sheds light on an intriguing pattern that occurs during the training of deep neural networks: some layers align much more with data compared to other layers (where the alignment is defined as the euclidean product of the tangent features matrix and the data labels matrix). The curve of the alignment as a function of layer index (generally) exhibits an ascent-descent pattern where the maximum is reached for some hidden layer. In this work, we provide the first explanation for this phenomenon. We introduce the Equilibrium Hypothesis which connects this alignment pattern to signal propagation in deep neural networks. Our experiments demonstrate an excellent match with the theoretical predictions.

Vision Foundation Models (VFMs) and Vision-Language Models (VLMs) have gained traction in Domain Generalized Semantic Segmentation (DGSS) due to their strong generalization capabilities. However, existing DGSS methods often rely exclusively on either VFMs or VLMs, overlooking their complementary strengths. VFMs (e.g., DINOv2) excel at capturing fine-grained features, while VLMs (e.g., CLIP) provide robust text alignment but struggle with coarse granularity. Despite their complementary strengths, effectively integrating VFMs and VLMs with attention mechanisms is challenging, as the increased patch tokens complicate long-sequence modeling. To address this, we propose MFuser, a novel Mamba-based fusion framework that efficiently combines the strengths of VFMs and VLMs while maintaining linear scalability in sequence length. MFuser consists of two key components: MVFuser, which acts as a co-adapter to jointly fine-tune the two models by capturing both sequential and spatial dynamics; and MTEnhancer, a hybrid attention-Mamba module that refines text embeddings by incorporating image priors. Our approach achieves precise feature locality and strong text alignment without incurring significant computational overhead. Extensive experiments demonstrate that MFuser significantly outperforms state-of-the-art DGSS methods, achieving 68.20 mIoU on synthetic-to-real and 71.87 mIoU on real-to-real benchmarks. The code is available at https://github.com/devinxzhang/MFuser.

As large language models rapidly evolve to support longer context, there is a notable disparity in their capability to generate output at greater lengths. Recent study suggests that the primary cause for this imbalance may arise from the lack of data with long-output during alignment training. In light of this observation, attempts are made to re-align foundation models with data that fills the gap, which result in models capable of generating lengthy output when instructed. In this paper, we explore the impact of data-quality in tuning a model for long output, and the possibility of doing so from the starting points of human-aligned (instruct or chat) models. With careful data curation, we show that it possible to achieve similar performance improvement in our tuned models, with only a small fraction of training data instances and compute. In addition, we assess the generalizability of such approaches by applying our tuning-recipes to several models. our findings suggest that, while capacities for generating long output vary across different models out-of-the-box, our approach to tune them with high-quality data using lite compute, consistently yields notable improvement across all models we experimented on. We have made public our curated dataset for tuning long-writing capability, the implementations of model tuning and evaluation, as well as the fine-tuned models, all of which can be openly-accessed.

Prior work has shown that fine-tuning models on a narrow domain with misaligned data can lead to broad misalignment - a phenomenon termed "emergent misalignment" (Betley et al. 2025). While all tested models were susceptible to emergent misalignment, some models showed more resistance than others. Specifically the Qwen-2.5 family proved to be relatively resistant, while GPT-4o exhibited the strongest misalignment. In this paper we evaluate if current-generation open-weights models exhibit similar resistance to the Qwen-2.5 family and measure misalignment robustness over a range of model architectures and scales. We replicate the effect across nine modern open-weights models (Gemma 3 and Qwen 3 families, 1B-32B parameters). Models fine-tuned on insecure code generation show a 0.68% misalignment rate (compared to 0.07% for base models), matching the lower end of prior open-model results but dramatically lower than GPT-4o's 20%. We identify a critical format-dependent vulnerability: requiring JSON output doubles misalignment rates compared to natural language prompts (0.96% vs 0.42%). This suggests that structural constraints may bypass safety training by reducing the model's 'degrees of freedom' to refuse. These findings confirm emergent misalignment as a reproducible phenomenon in modern open-weights models, with rates substantially lower than observed in proprietary systems.

Instruction tuning is a standard technique employed to align large language models to end tasks and user preferences after the initial pretraining phase. Recent research indicates the critical role of data engineering in instruction tuning -- when appropriately selected, only limited data is necessary to achieve superior performance. However, we still lack a principled understanding of what makes good instruction tuning data for alignment, and how we should select data automatically and effectively. In this work, we delve deeply into automatic data selection strategies for alignment. We start with controlled studies to measure data across three dimensions: complexity, quality, and diversity, along which we examine existing methods and introduce novel techniques for enhanced data measurement. Subsequently, we propose a simple strategy to select data samples based on the measurement. We present deita (short for Data-Efficient Instruction Tuning for Alignment), a series of models fine-tuned from LLaMA and Mistral models using data samples automatically selected with our proposed approach. Empirically, deita performs better or on par with the state-of-the-art open-source alignment models with only 6K SFT training data samples -- over 10x less than the data used in the baselines. When further trained with direct preference optimization (DPO), deita-Mistral-7B + DPO trained with 6K SFT and 10K DPO samples achieve 7.55 MT-Bench and 90.06% AlpacaEval scores. We anticipate this work to provide tools on automatic data selection, facilitating data-efficient alignment. We release our models as well as the selected datasets for future researches to effectively align models more efficiently.

We present 850 {\mu}m thermal dust polarization observations with a resolution of 14.4"(~ 0.13 pc) towards an infrared dark cloud G16.96+0.27 using JCMT/POL-2. The average magnetic field orientation, which roughly agrees with the larger-scale magnetic field orientation traced by the Planck 353 GHz data, is approximately perpendicular to the filament structure. The estimated plane-of-sky magnetic field strength is ~ 96 {\mu}G and ~ 60 {\mu}G using two variants of the Davis-Chandrasekhar-Fermi methods. We calculate the virial and magnetic critical parameters to evaluate the relative importance of gravity, the magnetic field, and turbulence. The magnetic field and turbulence are both weaker than gravity, but magnetic fields and turbulence together are equal to gravity, suggesting that G16.96+0.27 is in a quasi-equilibrium state. The cloud-magnetic-field alignment is found to have a trend moving away from perpendicularity in the dense regions, which may serve as a tracer of potential fragmentation in such quiescent filaments.

Decompilation transforms compiled code back into a high-level programming language for analysis when source code is unavailable. Previous work has primarily focused on enhancing decompilation performance by increasing the scale of model parameters or training data for pre-training. Based on the characteristics of the decompilation task, we propose two methods: (1) Without fine-tuning, the Self-Constructed Context Decompilation (sc^2dec) method recompiles the LLM's decompilation results to construct pairs for in-context learning, helping the model improve decompilation performance. (2) Fine-grained Alignment Enhancement (FAE), which meticulously aligns assembly code with source code at the statement level by leveraging debugging information, is employed during the fine-tuning phase to achieve further improvements in decompilation. By integrating these two methods, we achieved a Re-Executability performance improvement of approximately 7.35\% on the Decompile-Eval benchmark, establishing a new state-of-the-art performance of 55.03\%.

In this work, we explore a multimodal semi-supervised learning approach for punctuation prediction by learning representations from large amounts of unlabelled audio and text data. Conventional approaches in speech processing typically use forced alignment to encoder per frame acoustic features to word level features and perform multimodal fusion of the resulting acoustic and lexical representations. As an alternative, we explore attention based multimodal fusion and compare its performance with forced alignment based fusion. Experiments conducted on the Fisher corpus show that our proposed approach achieves ~6-9% and ~3-4% absolute improvement (F1 score) over the baseline BLSTM model on reference transcripts and ASR outputs respectively. We further improve the model robustness to ASR errors by performing data augmentation with N-best lists which achieves up to an additional ~2-6% improvement on ASR outputs. We also demonstrate the effectiveness of semi-supervised learning approach by performing ablation study on various sizes of the corpus. When trained on 1 hour of speech and text data, the proposed model achieved ~9-18% absolute improvement over baseline model.

Recent work shows that Sparse Autoencoders (SAE) applied to large language model (LLM) layers have neurons corresponding to interpretable concepts. These SAE neurons can be modified to align generated outputs, but only towards pre-identified topics and with some parameter tuning. Our approach leverages the observational and modification properties of SAEs to enable alignment for any topic. This method 1) scores each SAE neuron by its semantic similarity to an alignment text and uses them to 2) modify SAE-layer-level outputs by emphasizing topic-aligned neurons. We assess the alignment capabilities of this approach on diverse public topic datasets including Amazon reviews, Medicine, and Sycophancy, across the currently available open-source LLMs and SAE pairs (GPT2 and Gemma) with multiple SAEs configurations. Experiments aligning to medical prompts reveal several benefits over fine-tuning, including increased average language acceptability (0.25 vs. 0.5), reduced training time across multiple alignment topics (333.6s vs. 62s), and acceptable inference time for many applications (+0.00092s/token). Our open-source code is available at github.com/IBM/sae-steering.

The ability to translate diverse patterns of inputs into structured patterns of behavior has been thought to rest on both humans' and machines' ability to learn robust representations of relevant concepts. The rapid advancement of transformer-based large language models (LLMs) has led to a diversity of computational ingredients -- architectures, fine tuning methods, and training datasets among others -- but it remains unclear which of these ingredients are most crucial for building models that develop human-like representations. Further, most current LLM benchmarks are not suited to measuring representational alignment between humans and models, making benchmark scores unreliable for assessing if current LLMs are making progress towards becoming useful cognitive models. We address these limitations by first evaluating a set of over 70 models that widely vary in their computational ingredients on a triplet similarity task, a method well established in the cognitive sciences for measuring human conceptual representations, using concepts from the THINGS database. Comparing human and model representations, we find that models that undergo instruction-finetuning and which have larger dimensionality of attention heads are among the most human aligned, while multimodal pretraining and parameter size have limited bearing on alignment. Correlations between alignment scores and scores on existing benchmarks reveal that while some benchmarks (e.g., MMLU) are better suited than others (e.g., MUSR) for capturing representational alignment, no existing benchmark is capable of fully accounting for the variance of alignment scores, demonstrating their insufficiency in capturing human-AI alignment. Taken together, our findings help highlight the computational ingredients most essential for advancing LLMs towards models of human conceptual representation and address a key benchmarking gap in LLM evaluation.

A network-based approach is presented to investigate the cerebrovascular flow patterns during atrial fibrillation (AF) with respect to normal sinus rhythm (NSR). AF, the most common cardiac arrhythmia with faster and irregular beating, has been recently and independently associated with the increased risk of dementia. However, the underlying hemodynamic mechanisms relating the two pathologies remain mainly undetermined so far; thus the contribution of modeling and refined statistical tools is valuable. Pressure and flow rate temporal series in NSR and AF are here evaluated along representative cerebral sites (from carotid arteries to capillary brain circulation), exploiting reliable artificially built signals recently obtained from an in silico approach. The complex network analysis evidences, in a synthetic and original way, a dramatic signal variation towards the distal/capillary cerebral regions during AF, which has no counterpart in NSR conditions. At the large artery level, networks obtained from both AF and NSR hemodynamic signals exhibit elongated and chained features, which are typical of pseudo-periodic series. These aspects are almost completely lost towards the microcirculation during AF, where the networks are topologically more circular and present random-like characteristics. As a consequence, all the physiological phenomena at microcerebral level ruled by periodicity - such as regular perfusion, mean pressure per beat, and average nutrient supply at cellular level - can be strongly compromised, since the AF hemodynamic signals assume irregular behaviour and random-like features. Through a powerful approach which is complementary to the classical statistical tools, the present findings further strengthen the potential link between AF hemodynamic and cognitive decline.

While recent advancements in generative modeling have significantly improved text-image alignment, some residual misalignment between text and image representations still remains. Although many approaches have attempted to address this issue by fine-tuning models using various reward models, etc., we revisit the challenge from the perspective of representation alignment-an approach that has gained popularity with the success of REPresentation Alignment (REPA). We first argue that conventional text-to-image (T2I) diffusion models, typically trained on paired image and text data (i.e., positive pairs) by minimizing score matching or flow matching losses, is suboptimal from the standpoint of representation alignment. Instead, a better alignment can be achieved through contrastive learning that leverages both positive and negative pairs. To achieve this efficiently even with pretrained models, we introduce a lightweight contrastive fine tuning strategy called SoftREPA that uses soft text tokens. This approach improves alignment with minimal computational overhead by adding fewer than 1M trainable parameters to the pretrained model. Our theoretical analysis demonstrates that our method explicitly increases the mutual information between text and image representations, leading to enhanced semantic consistency. Experimental results across text-to-image generation and text-guided image editing tasks validate the effectiveness of our approach in improving the semantic consistency of T2I generative models.

Alignment has become a critical step for instruction-tuned Large Language Models (LLMs) to become helpful assistants. However, effective evaluation of alignment for emerging Chinese LLMs is still significantly lacking, calling for real-scenario grounded, open-ended, challenging and automatic evaluations tailored for alignment. To fill in this gap, we introduce AlignBench, a comprehensive multi-dimensional benchmark for evaluating LLMs' alignment in Chinese. Equipped with a human-in-the-loop data curation pipeline, our benchmark employs a rule-calibrated multi-dimensional LLM-as-Judge with Chain-of-Thought to generate explanations and final ratings as evaluations, ensuring high reliability and interpretability. Furthermore, we report AlignBench evaluated by CritiqueLLM, a dedicated Chinese evaluator LLM that recovers 95% of GPT-4's evaluation ability. We will provide public APIs for evaluating AlignBench with CritiqueLLM to facilitate the evaluation of LLMs' Chinese alignment. All evaluation codes, data, and LLM generations are available at https://github.com/THUDM/AlignBench.

We present a corpus of sentence-aligned triples of German audio, German text, and English translation, based on German audiobooks. The speech translation data consist of 110 hours of audio material aligned to over 50k parallel sentences. An even larger dataset comprising 547 hours of German speech aligned to German text is available for speech recognition. The audio data is read speech and thus low in disfluencies. The quality of audio and sentence alignments has been checked by a manual evaluation, showing that speech alignment quality is in general very high. The sentence alignment quality is comparable to well-used parallel translation data and can be adjusted by cutoffs on the automatic alignment score. To our knowledge, this corpus is to date the largest resource for German speech recognition and for end-to-end German-to-English speech translation.

As humans, we consistently engage in interactions with our peers and receive feedback in the form of natural language. This language feedback allows us to reflect on our actions, maintain appropriate behavior, and rectify our errors. The question arises naturally: can we use language feedback to align large language models (LLMs)? In contrast to previous research that aligns LLMs with reward or preference data, we present the first systematic exploration of alignment through the lens of language feedback (i.e., judgment). We commence with an in-depth investigation of potential methods that can be adapted for aligning LLMs with judgments, revealing that these methods are unable to fully capitalize on the judgments. To facilitate more effective utilization of judgments, we propose a novel framework, Contrastive Unlikelihood Training (CUT), that allows for fine-grained inappropriate content detection and correction based on judgments. Our offline alignment results show that, with merely 1317 off-the-shelf judgment data, CUT (LLaMA2-13b) can beat the 175B DaVinci003 and surpass the best baseline by 52.34 points on AlpacaEval. The online alignment results demonstrate that CUT can align LLMs (LLaMA2-chat-13b) in an iterative fashion using model-specific judgment data, with a steady performance improvement from 81.09 to 91.36 points on AlpacaEval. Our analysis further suggests that judgments exhibit greater potential than rewards for LLM alignment and warrant future research.

While recent preference alignment algorithms for language models have demonstrated promising results, supervised fine-tuning (SFT) remains imperative for achieving successful convergence. In this paper, we study the crucial role of SFT within the context of preference alignment, emphasizing that a minor penalty for the disfavored generation style is sufficient for preference-aligned SFT. Building on this foundation, we introduce a straightforward and innovative reference model-free monolithic odds ratio preference optimization algorithm, ORPO, eliminating the necessity for an additional preference alignment phase. We demonstrate, both empirically and theoretically, that the odds ratio is a sensible choice for contrasting favored and disfavored styles during SFT across the diverse sizes from 125M to 7B. Specifically, fine-tuning Phi-2 (2.7B), Llama-2 (7B), and Mistral (7B) with ORPO on the UltraFeedback alone surpasses the performance of state-of-the-art language models with more than 7B and 13B parameters: achieving up to 12.20% on AlpacaEval_{2.0} (Figure 1), 66.19% on IFEval (instruction-level loose, Table 6), and 7.32 in MT-Bench (Figure 12). We release code and model checkpoints for Mistral-ORPO-alpha (7B) and Mistral-ORPO-beta (7B).

Pre-trained Vision Foundation Models (VFMs) provide strong visual representations for a wide range of applications. In this paper, we continually pre-train prevailing VFMs in a multimodal manner such that they can effortlessly process visual inputs of varying sizes and produce visual representations that are more aligned with language representations, regardless of their original pre-training process. To this end, we introduce CoMP, a carefully designed multimodal pre-training pipeline. CoMP uses a Continual Rotary Position Embedding to support native resolution continual pre-training, and an Alignment Loss between visual and textual features through language prototypes to align multimodal representations. By three-stage training, our VFMs achieve remarkable improvements not only in multimodal understanding but also in other downstream tasks such as classification and segmentation. Remarkably, CoMP-SigLIP achieves scores of 66.7 on ChartQA and 75.9 on DocVQA with a 0.5B LLM, while maintaining an 87.4% accuracy on ImageNet-1K and a 49.5 mIoU on ADE20K under frozen chunk evaluation.

Person retrieval has attracted rising attention. Existing methods are mainly divided into two retrieval modes, namely image-only and text-only. However, they are unable to make full use of the available information and are difficult to meet diverse application requirements. To address the above limitations, we propose a new Composed Person Retrieval (CPR) task, which combines visual and textual queries to identify individuals of interest from large-scale person image databases. Nevertheless, the foremost difficulty of the CPR task is the lack of available annotated datasets. Therefore, we first introduce a scalable automatic data synthesis pipeline, which decomposes complex multimodal data generation into the creation of textual quadruples followed by identity-consistent image synthesis using fine-tuned generative models. Meanwhile, a multimodal filtering method is designed to ensure the resulting SynCPR dataset retains 1.15 million high-quality and fully synthetic triplets. Additionally, to improve the representation of composed person queries, we propose a novel Fine-grained Adaptive Feature Alignment (FAFA) framework through fine-grained dynamic alignment and masked feature reasoning. Moreover, for objective evaluation, we manually annotate the Image-Text Composed Person Retrieval (ITCPR) test set. The extensive experiments demonstrate the effectiveness of the SynCPR dataset and the superiority of the proposed FAFA framework when compared with the state-of-the-art methods. All code and data will be provided at https://github.com/Delong-liu-bupt/Composed_Person_Retrieval.

In this paper, we propose a novel soft and monotonic alignment mechanism used for sequence transduction. It is inspired by the integrate-and-fire model in spiking neural networks and employed in the encoder-decoder framework consists of continuous functions, thus being named as: Continuous Integrate-and-Fire (CIF). Applied to the ASR task, CIF not only shows a concise calculation, but also supports online recognition and acoustic boundary positioning, thus suitable for various ASR scenarios. Several support strategies are also proposed to alleviate the unique problems of CIF-based model. With the joint action of these methods, the CIF-based model shows competitive performance. Notably, it achieves a word error rate (WER) of 2.86% on the test-clean of Librispeech and creates new state-of-the-art result on Mandarin telephone ASR benchmark.

We present the Swiss Parliaments Corpus (SPC), an automatically aligned Swiss German speech to Standard German text corpus. This first version of the corpus is based on publicly available data of the Bernese cantonal parliament and consists of 293 hours of data. It was created using a novel forced sentence alignment procedure and an alignment quality estimator, which can be used to trade off corpus size and quality. We trained Automatic Speech Recognition (ASR) models as baselines on different subsets of the data and achieved a Word Error Rate (WER) of 0.278 and a BLEU score of 0.586 on the SPC test set. The corpus is freely available for download.

Direct Preference Optimization (DPO) is a method for enhancing model performance by directly optimizing for the preferences or rankings of outcomes, instead of traditional loss functions. This approach has proven effective in aligning Large Language Models (LLMs) with human preferences. Despite its widespread use across various tasks, DPO has been criticized for its sensitivity to the effectiveness of Supervised Fine-Tuning (SFT) and its limitations in enabling models to learn human-preferred responses, leading to less satisfactory performance. To address these limitations, we propose Aligned Supervised Fine-Tuning (ASFT), an effective approach that better aligns LLMs with pair-wise datasets by optimizing absolute likelihood for each response, rather than using the Bradley-Terry model, and eliminates the need for a reference model. Through theoretical gradient analysis, we demonstrate that ASFT mitigates the issue where the DPO loss function decreases the probability of generating human-dispreferred data at a faster rate than it increases the probability of producing preferred data. Additionally, we compare ASFT to DPO and its latest variants, such as the single-step approach ORPO, using the latest instruction-tuned model Llama3, which has been fine-tuned on UltraFeedback and HH-RLHF. We evaluated performance on instruction-following benchmarks like MT-Bench and traditional text generation metrics such as BLEU-4 and ROUGE-L. Extensive experiments demonstrate that ASFT is an effective alignment approach, consistently outperforming existing methods.

In the latest advancements in multimodal learning, effectively addressing the spatial and semantic losses of visual data after encoding remains a critical challenge. This is because the performance of large multimodal models is positively correlated with the coupling between visual encoders and large language models. Existing approaches often face issues such as vector gaps or semantic disparities, resulting in information loss during the propagation process. To address these issues, we propose MAGE (Multimodal Alignment and Generation Enhancement), a novel framework that bridges the semantic spaces of vision and text through an innovative alignment mechanism. By introducing the Intelligent Alignment Network (IAN), MAGE achieves dimensional and semantic alignment. To reduce the gap between synonymous heterogeneous data, we employ a training strategy that combines cross-entropy and mean squared error, significantly enhancing the alignment effect. Moreover, to enhance MAGE's "Any-to-Any" capability, we developed a fine-tuning dataset for multimodal tool-calling instructions to expand the model's output capability boundaries. Finally, our proposed multimodal large model architecture, MAGE, achieved significantly better performance compared to similar works across various evaluation benchmarks, including MME, MMBench, and SEED. Complete code and appendix are available at: https://github.com/GTCOM-NLP/MAGE.