Daily Papers

Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries, and 2) the confusion of mimics and debris as nuclei. In this work, we proposed a De-overlapping Network (DoNet) in a decompose-and-recombined strategy. A Dual-path Region Segmentation Module (DRM) explicitly decomposes the cell clusters into intersection and complement regions, followed by a Semantic Consistency-guided Recombination Module (CRM) for integration. To further introduce the containment relationship of the nucleus in the cytoplasm, we design a Mask-guided Region Proposal Strategy (MRP) that integrates the cell attention maps for inner-cell instance prediction. We validate the proposed approach on ISBI2014 and CPS datasets. Experiments show that our proposed DoNet significantly outperforms other state-of-the-art (SOTA) cell instance segmentation methods. The code is available at https://github.com/DeepDoNet/DoNet.

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

A hallmark of human innovation is the process of recombination -- creating original ideas by integrating elements of existing mechanisms and concepts. In this work, we automatically mine the scientific literature and build CHIMERA: a large-scale knowledge base (KB) of recombination examples. CHIMERA can be used to empirically explore at scale how scientists recombine concepts and take inspiration from different areas, or to train supervised machine learning models that learn to predict new creative cross-domain directions. To build this KB, we present a novel information extraction task of extracting recombination from scientific paper abstracts, collect a high-quality corpus of hundreds of manually annotated abstracts, and use it to train an LLM-based extraction model. The model is applied to a large corpus of papers in the AI domain, yielding a KB of over 28K recombination examples. We analyze CHIMERA to explore the properties of recombination in different subareas of AI. Finally, we train a scientific hypothesis generation model using the KB, which predicts new recombination directions that real-world researchers find inspiring. Our data and code are available at https://github.cs.huji.ac.il/tomhope-lab/CHIMERA

RAG systems are increasingly deployed in high-stakes domains where users expect outputs to be consistent across semantically equivalent queries. However, existing systems often exhibit significant inconsistencies due to variability in both the retriever and generator (LLM), undermining trust and reliability. In this work, we focus on information consistency, i.e., the requirement that outputs convey the same core content across semantically equivalent inputs. We introduce a principled evaluation framework that decomposes RAG consistency into retriever-level, generator-level, and end-to-end components, helping identify inconsistency sources. To improve consistency, we propose Paraphrased Set Group Relative Policy Optimization (PS-GRPO), an RL approach that leverages multiple rollouts across paraphrased set to assign group similarity rewards. We leverage PS-GRPO to achieve Information Consistent RAG (Con-RAG), training the generator to produce consistent outputs across paraphrased queries and remain robust to retrieval-induced variability. Because exact reward computation over paraphrase sets is computationally expensive, we also introduce a scalable approximation method that retains effectiveness while enabling efficient, large-scale training. Empirical evaluations across short-form, multi-hop, and long-form QA benchmarks demonstrate that Con-RAG significantly improves both consistency and accuracy over strong baselines, even in the absence of explicit ground-truth supervision. Our work provides practical solutions for evaluating and building reliable RAG systems for safety-critical deployments.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

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.

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.

Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language foundation models, which thrive on substantially larger scales. Furthermore, genome understanding involves numerous downstream genome annotation tasks with inherent data heterogeneity, thereby necessitating more efficient and robust fine-tuning methods tailored for genomics. Here, we present Lingo: Language prefix fIne-tuning for GenOmes. Unlike DNA foundation models, Lingo strategically leverages natural language foundation models' contextual cues, recalibrating their linguistic knowledge to genomic sequences. Lingo further accommodates numerous, heterogeneous downstream fine-tune tasks by an adaptive rank sampling method that prunes and stochastically reintroduces pruned singular vectors within small computational budgets. Adaptive rank sampling outperformed existing fine-tuning methods on all benchmarked 14 genome understanding tasks, while requiring fewer than 2\% of trainable parameters as genomic-specific adapters. Impressively, applying these adapters on natural language foundation models matched or even exceeded the performance of DNA foundation models. Lingo presents a new paradigm of efficient and scalable genome understanding via genomic-specific adapters on language models.

Large Transformer models are capable of implementing a plethora of so-called in-context learning algorithms. These include gradient descent, classification, sequence completion, transformation, and improvement. In this work, we investigate whether large language models (LLMs), which never explicitly encountered the task of black-box optimization, are in principle capable of implementing evolutionary optimization algorithms. While previous works have solely focused on language-based task specification, we move forward and focus on the zero-shot application of LLMs to black-box optimization. We introduce a novel prompting strategy, consisting of least-to-most sorting of discretized population members and querying the LLM to propose an improvement to the mean statistic, i.e. perform a type of black-box recombination operation. Empirically, we find that our setup allows the user to obtain an LLM-based evolution strategy, which we call `EvoLLM', that robustly outperforms baseline algorithms such as random search and Gaussian Hill Climbing on synthetic BBOB functions as well as small neuroevolution tasks. Hence, LLMs can act as `plug-in' in-context recombination operators. We provide several comparative studies of the LLM's model size, prompt strategy, and context construction. Finally, we show that one can flexibly improve EvoLLM's performance by providing teacher algorithm information via instruction fine-tuning on previously collected teacher optimization trajectories.

Previous works have explored various customized generation tasks given a reference image, but they still face limitations in generating consistent fine-grained details. In this paper, our aim is to solve the inconsistency problem of generated images by applying a reference-guided post-editing approach and present our ImageCritic. We first construct a dataset of reference-degraded-target triplets obtained via VLM-based selection and explicit degradation, which effectively simulates the common inaccuracies or inconsistencies observed in existing generation models. Furthermore, building on a thorough examination of the model's attention mechanisms and intrinsic representations, we accordingly devise an attention alignment loss and a detail encoder to precisely rectify inconsistencies. ImageCritic can be integrated into an agent framework to automatically detect inconsistencies and correct them with multi-round and local editing in complex scenarios. Extensive experiments demonstrate that ImageCritic can effectively resolve detail-related issues in various customized generation scenarios, providing significant improvements over existing methods.

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.

Large Language Models (LLMs) excel at generating synthetic data, but ensuring its quality and diversity remains challenging. We propose Genetic Prompt, a novel framework that combines genetic algorithms with LLMs to augment synthetic data generation. Our approach treats semantic text attributes as gene sequences and leverages the LLM to simulate crossover and mutation operations. This genetic process enhances data quality and diversity by creating novel attribute combinations, yielding synthetic distributions closer to real-world data. To optimize parent selection, we also integrate an active learning scheme that expands the offspring search space. Our experiments on multiple NLP tasks reveal several key findings: Genetic Prompt not only significantly outperforms state-of-the-art baselines but also shows robust performance across various generator model sizes and scales. Moreover, we demonstrate that fusing our synthetic data with the original training set significantly boosts downstream model performance, particularly for class-imbalanced scenarios. Our findings validate that Genetic Prompt is an effective method for producing high-quality synthetic data for a wide range of NLP applications.

As large language models (LLMs) continue to advance, ensuring their alignment with human values becomes increasingly critical. Traditional alignment methods heavily rely on human feedback to fine-tune models. With the emergence of superhuman models whose outputs may surpass human understanding, evaluating and aligning these models using human judgments poses significant challenges. To address the challenges, recent works use weak supervisors to elicit knowledge from much stronger models. However, there are important disanalogies between the empirical setup in the existing works and the genuine goal of alignment. We remark that existing works investigate the phenomenon of weak-to-strong generation in analogous setup (i.e., binary classification), rather than practical alignment-relevant tasks (e.g., safety). In this paper, we bridge this gap by extending weak-to-strong generation to the context of practical alignment. We empirically demonstrate the widespread phenomenon of weak-to-strong generation in three complicated alignment tasks: safety, toxicity, and legal reasoning}. Furthermore, we explore efficient strategies for improving alignment performance to enhance the quality of model outcomes. Lastly, we summarize and analyze the challenges and potential solutions in regard to specific alignment tasks, which we hope to catalyze the research progress on the topic of weak-to-strong generalization. Our code is released at https://github.com/yeruimeng/WTS.git.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

Despite remarkable progress in Text-to-Image models, many real-world applications require generating coherent image sets with diverse consistency requirements. Existing consistent methods often focus on a specific domain with specific aspects of consistency, which significantly constrains their generalizability to broader applications. In this paper, we propose a more challenging problem, Text-to-ImageSet (T2IS) generation, which aims to generate sets of images that meet various consistency requirements based on user instructions. To systematically study this problem, we first introduce T2IS-Bench with 596 diverse instructions across 26 subcategories, providing comprehensive coverage for T2IS generation. Building on this, we propose T2IS-Eval, an evaluation framework that transforms user instructions into multifaceted assessment criteria and employs effective evaluators to adaptively assess consistency fulfillment between criteria and generated sets. Subsequently, we propose AutoT2IS, a training-free framework that maximally leverages pretrained Diffusion Transformers' in-context capabilities to harmonize visual elements to satisfy both image-level prompt alignment and set-level visual consistency. Extensive experiments on T2IS-Bench reveal that diverse consistency challenges all existing methods, while our AutoT2IS significantly outperforms current generalized and even specialized approaches. Our method also demonstrates the ability to enable numerous underexplored real-world applications, confirming its substantial practical value. Visit our project in https://chengyou-jia.github.io/T2IS-Home.

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.

Semantic control entails steering LM generations towards satisfying subtle non-lexical constraints, e.g., toxicity, sentiment, or politeness, attributes that can be captured by a sequence-level verifier. It can thus be viewed as sampling from the LM distribution conditioned on the target attribute, a computationally intractable problem due to the non-decomposable nature of the verifier. Existing approaches to LM control either only deal with syntactic constraints which cannot capture the aforementioned attributes, or rely on sampling to explore the conditional LM distribution, an ineffective estimator for low-probability events. In this work, we leverage a verifier's gradient information to efficiently reason over all generations that satisfy the target attribute, enabling precise steering of LM generations by reweighing the next-token distribution. Starting from an initial sample, we create a local LM distribution favoring semantically similar sentences. This approximation enables the tractable computation of an expected sentence embedding. We use this expected embedding, informed by the verifier's evaluation at the initial sample, to estimate the probability of satisfying the constraint, which directly informs the update to the next-token distribution. We evaluated the effectiveness of our approach in controlling the toxicity, sentiment, and topic-adherence of LMs yielding generations satisfying the constraint with high probability (>95%) without degrading their quality.

Alignment has greatly improved large language models (LLMs)' output quality at the cost of diversity, yielding highly similar outputs across generations. We propose Base-Aligned Model Collaboration (BACo), an inference-time token-level model collaboration framework that dynamically combines a base LLM with its aligned counterpart to optimize diversity and quality. Inspired by prior work (Fei et al., 2025), BACo employs routing strategies that determine, at each token, from which model to decode based on next-token prediction uncertainty and predicted contents' semantic role. Prior diversity-promoting methods, such as retraining, prompt engineering, and multi-sampling methods, improve diversity but often degrade quality or require costly decoding or post-training. In contrast, BACo achieves both high diversity and quality post hoc within a single pass, while offering strong controllability. We explore a family of routing strategies, across three open-ended generation tasks and 13 metrics covering diversity and quality, BACo consistently surpasses state-of-the-art inference-time baselines. With our best router, BACo achieves a 21.3% joint improvement in diversity and quality. Human evaluations also mirror these improvements. The results suggest that collaboration between base and aligned models can optimize and control diversity and quality.

Recent advances in generative modeling enable image editing assistants that follow natural language instructions without additional user input. Their supervised training requires millions of triplets: original image, instruction, edited image. Yet mining pixel-accurate examples is hard. Each edit must affect only prompt-specified regions, preserve stylistic coherence, respect physical plausibility, and retain visual appeal. The lack of robust automated edit-quality metrics hinders reliable automation at scale. We present an automated, modular pipeline that mines high-fidelity triplets across domains, resolutions, instruction complexities, and styles. Built on public generative models and running without human intervention, our system uses a task-tuned Gemini validator to score instruction adherence and aesthetics directly, removing any need for segmentation or grounding models. Inversion and compositional bootstrapping enlarge the mined set by approximately 2.2x, enabling large-scale high-fidelity training data. By automating the most repetitive annotation steps, the approach allows a new scale of training without human labeling effort. To democratize research in this resource-intensive area, we release NHR-Edit: an open dataset of 358k high-quality triplets. In the largest cross-dataset evaluation, it surpasses all public alternatives. We also release Bagel-NHR-Edit, an open-source fine-tuned Bagel model, which achieves state-of-the-art metrics in our experiments.

Data quality and diversity are key to the construction of effective instruction-tuning datasets. % With the increasing availability of open-source instruction-tuning datasets, it is advantageous to automatically select high-quality and diverse subsets from a vast amount of data. % Existing methods typically prioritize instance quality and use heuristic rules to maintain diversity. % However, this absence of a comprehensive view of the entire collection often leads to suboptimal results. % Moreover, heuristic rules generally focus on distance or clustering within the embedding space, which fails to accurately capture the intent of complex instructions in the semantic space. % To bridge this gap, we propose a unified method for quantifying the information content of datasets. This method models the semantic space by constructing a label graph and quantifies diversity based on the distribution of information within the graph. % Based on such a measurement, we further introduce an efficient sampling method that selects data samples iteratively to Maximize the Information Gain (MIG) in semantic space. % Experiments on various datasets and base models demonstrate that MIG consistently outperforms state-of-the-art methods. % Notably, the model fine-tuned with 5\% Tulu3 data sampled by MIG achieves comparable performance to the official SFT model trained on the full dataset, with improvements of +5.73\% on AlpacaEval and +6.89\% on Wildbench.

We present LINGUIST, a method for generating annotated data for Intent Classification and Slot Tagging (IC+ST), via fine-tuning AlexaTM 5B, a 5-billion-parameter multilingual sequence-to-sequence (seq2seq) model, on a flexible instruction prompt. In a 10-shot novel intent setting for the SNIPS dataset, LINGUIST surpasses state-of-the-art approaches (Back-Translation and Example Extrapolation) by a wide margin, showing absolute improvement for the target intents of +1.9 points on IC Recall and +2.5 points on ST F1 Score. In the zero-shot cross-lingual setting of the mATIS++ dataset, LINGUIST out-performs a strong baseline of Machine Translation with Slot Alignment by +4.14 points absolute on ST F1 Score across 6 languages, while matching performance on IC. Finally, we verify our results on an internal large-scale multilingual dataset for conversational agent IC+ST and show significant improvements over a baseline which uses Back-Translation, Paraphrasing and Slot Catalog Resampling. To our knowledge, we are the first to demonstrate instruction fine-tuning of a large-scale seq2seq model to control the outputs of multilingual intent- and slot-labeled data generation.

Zero-shot learning strives to classify unseen categories for which no data is available during training. In the generalized variant, the test samples can further belong to seen or unseen categories. The state-of-the-art relies on Generative Adversarial Networks that synthesize unseen class features by leveraging class-specific semantic embeddings. During training, they generate semantically consistent features, but discard this constraint during feature synthesis and classification. We propose to enforce semantic consistency at all stages of (generalized) zero-shot learning: training, feature synthesis and classification. We first introduce a feedback loop, from a semantic embedding decoder, that iteratively refines the generated features during both the training and feature synthesis stages. The synthesized features together with their corresponding latent embeddings from the decoder are then transformed into discriminative features and utilized during classification to reduce ambiguities among categories. Experiments on (generalized) zero-shot object and action classification reveal the benefit of semantic consistency and iterative feedback, outperforming existing methods on six zero-shot learning benchmarks. Source code at https://github.com/akshitac8/tfvaegan.

The remarkable success of the autoregressive paradigm has made significant advancement in Multimodal Large Language Models (MLLMs), with powerful models like Show-o, Transfusion and Emu3 achieving notable progress in unified image understanding and generation. For the first time, we uncover a common phenomenon: the understanding capabilities of MLLMs are typically stronger than their generative capabilities, with a significant gap between the two. Building on this insight, we propose HermesFlow, a simple yet general framework designed to seamlessly bridge the gap between understanding and generation in MLLMs. Specifically, we take the homologous data as input to curate homologous preference data of both understanding and generation. Through Pair-DPO and self-play iterative optimization, HermesFlow effectively aligns multimodal understanding and generation using homologous preference data. Extensive experiments demonstrate the significant superiority of our approach over prior methods, particularly in narrowing the gap between multimodal understanding and generation. These findings highlight the potential of HermesFlow as a general alignment framework for next-generation multimodal foundation models. Code: https://github.com/Gen-Verse/HermesFlow

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.

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.

Diffusion large language models (dLLMs) generate text through iterative denoising, yet current decoding strategies discard rich intermediate predictions in favor of the final output. Our work here reveals a critical phenomenon, temporal oscillation, where correct answers often emerge in the middle process, but are overwritten in later denoising steps. To address this issue, we introduce two complementary methods that exploit temporal consistency: 1) Temporal Self-Consistency Voting, a training-free, test-time decoding strategy that aggregates predictions across denoising steps to select the most consistent output; and 2) a post-training method termed Temporal Consistency Reinforcement, which uses Temporal Semantic Entropy (TSE), a measure of semantic stability across intermediate predictions, as a reward signal to encourage stable generations. Empirical results across multiple benchmarks demonstrate the effectiveness of our approach. Using the negative TSE reward alone, we observe a remarkable average improvement of 24.7% on the Countdown dataset over an existing dLLM. Combined with the accuracy reward, we achieve absolute gains of 2.0% on GSM8K, 4.3% on MATH500, 6.6% on SVAMP, and 25.3% on Countdown, respectively. Our findings underscore the untapped potential of temporal dynamics in dLLMs and offer two simple yet effective tools to harness them.

Flow matching (FM) is a general framework for defining probability paths via Ordinary Differential Equations (ODEs) to transform between noise and data samples. Recent approaches attempt to straighten these flow trajectories to generate high-quality samples with fewer function evaluations, typically through iterative rectification methods or optimal transport solutions. In this paper, we introduce Consistency Flow Matching (Consistency-FM), a novel FM method that explicitly enforces self-consistency in the velocity field. Consistency-FM directly defines straight flows starting from different times to the same endpoint, imposing constraints on their velocity values. Additionally, we propose a multi-segment training approach for Consistency-FM to enhance expressiveness, achieving a better trade-off between sampling quality and speed. Preliminary experiments demonstrate that our Consistency-FM significantly improves training efficiency by converging 4.4x faster than consistency models and 1.7x faster than rectified flow models while achieving better generation quality. Our code is available at: https://github.com/YangLing0818/consistency_flow_matching

Pretrained visual-language models have demonstrated impressive zero-shot abilities in image captioning, when accompanied by hand-crafted prompts. Meanwhile, hand-crafted prompts utilize human prior knowledge to guide the model. However, due to the diversity between different domains, such hand-crafted prompt that provide invariant prior knowledge may result in mode collapse for some domains. Some researches attempted to incorporate expert knowledge and instruction datasets, but the results were costly and led to hallucinations. In this paper, we propose an unsupervised prompt learning method to improve Generalization of Image Captioning (GeneIC), which learns a domain-specific prompt vector for the target domain without requiring annotated data. GeneIC aligns visual and language modalities with a pre-trained Contrastive Language-Image Pre-Training (CLIP) model, thus optimizing the domain-specific prompt vector from two aspects: attribute and semantic consistency. Specifically, GeneIC first generates attribute-transferred images with differing attributes, while retaining semantic similarity with original images. Then, GeneIC uses CLIP to measure the similarity between the images and the generated sentences. By exploring the variable and invariant features in the original images and attribute-transferred images, attribute consistency constrains the attribute change direction of both images and sentences to learn domain-specific knowledge. The semantic consistency directly measures the similarity between the generated sentences and images to ensure the accuracy and comprehensiveness of the generated sentences. Consequently, GeneIC only optimizes the prompt vectors, which effectively retains the knowledge in the large model and introduces domain-specific knowledge.

Reward models (RMs) guide the alignment of large language models (LLMs), steering them toward behaviors preferred by humans. Evaluating RMs is the key to better aligning LLMs. However, the current evaluation of RMs may not directly correspond to their alignment performance due to the limited distribution of evaluation data and evaluation methods that are not closely related to alignment objectives. To address these limitations, we propose RMB, a comprehensive RM benchmark that covers over 49 real-world scenarios and includes both pairwise and Best-of-N (BoN) evaluations to better reflect the effectiveness of RMs in guiding alignment optimization. We demonstrate a positive correlation between our benchmark and the downstream alignment task performance. Based on our benchmark, we conduct extensive analysis on the state-of-the-art RMs, revealing their generalization defects that were not discovered by previous benchmarks, and highlighting the potential of generative RMs. Furthermore, we delve into open questions in reward models, specifically examining the effectiveness of majority voting for the evaluation of reward models and analyzing the impact factors of generative RMs, including the influence of evaluation criteria and instructing methods. Our evaluation code and datasets are available at https://github.com/Zhou-Zoey/RMB-Reward-Model-Benchmark.

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

Continuous-time Consistency Models (CMs) promise efficient few-step generation but face significant challenges with training instability. We argue this instability stems from a fundamental conflict: by training a network to learn only a shortcut across a probability flow, the model loses its grasp on the instantaneous velocity field that defines the flow. Our solution is to explicitly anchor the model in the underlying flow during training. We introduce the Flow-Anchored Consistency Model (FACM), a simple but effective training strategy that uses a Flow Matching (FM) task as an anchor for the primary CM shortcut objective. This Flow-Anchoring approach requires no architectural modifications and is broadly compatible with standard model architectures. By distilling a pre-trained LightningDiT model, our method achieves a state-of-the-art FID of 1.32 with two steps (NFE=2) and 1.76 with just one step (NFE=1) on ImageNet 256x256, significantly outperforming previous methods. This provides a general and effective recipe for building high-performance, few-step generative models. Our code and pretrained models: https://github.com/ali-vilab/FACM.

Following natural instructions is crucial for the effective application of Retrieval-Augmented Generation (RAG) systems. Despite recent advancements in Large Language Models (LLMs), research on assessing and improving instruction-following (IF) alignment within the RAG domain remains limited. To address this issue, we propose VIF-RAG, the first automated, scalable, and verifiable synthetic pipeline for instruction-following alignment in RAG systems. We start by manually crafting a minimal set of atomic instructions (<100) and developing combination rules to synthesize and verify complex instructions for a seed set. We then use supervised models for instruction rewriting while simultaneously generating code to automate the verification of instruction quality via a Python executor. Finally, we integrate these instructions with extensive RAG and general data samples, scaling up to a high-quality VIF-RAG-QA dataset (>100k) through automated processes. To further bridge the gap in instruction-following auto-evaluation for RAG systems, we introduce FollowRAG Benchmark, which includes approximately 3K test samples, covering 22 categories of general instruction constraints and four knowledge-intensive QA datasets. Due to its robust pipeline design, FollowRAG can seamlessly integrate with different RAG benchmarks. Using FollowRAG and eight widely-used IF and foundational abilities benchmarks for LLMs, we demonstrate that VIF-RAG markedly enhances LLM performance across a broad range of general instruction constraints while effectively leveraging its capabilities in RAG scenarios. Further analysis offers practical insights for achieving IF alignment in RAG systems. Our code and datasets are released at https://FollowRAG.github.io.

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.

Self-consistency-based approaches, which involve repeatedly sampling multiple outputs and selecting the most consistent one as the final response, prove to be remarkably effective in improving the factual accuracy of large language models. Nonetheless, existing methods usually have strict constraints on the task format, largely limiting their applicability. In this paper, we present Integrative Decoding (ID), to unlock the potential of self-consistency in open-ended generation tasks. ID operates by constructing a set of inputs, each prepended with a previously sampled response, and then processes them concurrently, with the next token being selected by aggregating of all their corresponding predictions at each decoding step. In essence, this simple approach implicitly incorporates self-consistency in the decoding objective. Extensive evaluation shows that ID consistently enhances factuality over a wide range of language models, with substantial improvements on the TruthfulQA (+11.2%), Biographies (+15.4%) and LongFact (+8.5%) benchmarks. The performance gains amplify progressively as the number of sampled responses increases, indicating the potential of ID to scale up with repeated sampling.

Employing a single, unified model (UM) for both visual understanding (image-to-text: I2T) and and visual generation (text-to-image: T2I) has opened a new direction in Visual Language Model (VLM) research. While UMs can also support broader unimodal tasks (e.g., text-to-text, image-to-image), we focus on the core cross-modal pair T2I and I2T, as consistency between understanding and generation is critical for downstream use. Existing evaluations consider these capabilities in isolation: FID and GenEval for T2I, and benchmarks such as MME, MMBench for I2T. These single-pass metrics do not reveal whether a model that understands a concept can also render it, nor whether meaning is preserved when cycling between image and text modalities. To address this, we introduce the Unified Consistency Framework for Unified Models (UCF-UM), a cyclic evaluation protocol that alternates I2T and T2I over multiple generations to quantify semantic drift. UCF formulates 3 metrics: (i) Mean Cumulative Drift (MCD), an embedding-based measure of overall semantic loss; (ii) Semantic Drift Rate (SDR), that summarizes semantic decay rate; and (iii) Multi-Generation GenEval (MGG), an object-level compliance score extending GenEval. To assess generalization beyond COCO, which is widely used in training; we create a new benchmark ND400, sampled from NoCaps and DOCCI and evaluate on seven recent models. UCF-UM reveals substantial variation in cross-modal stability: some models like BAGEL maintain semantics over many alternations, whereas others like Vila-u drift quickly despite strong single-pass scores. Our results highlight cyclic consistency as a necessary complement to standard I2T and T2I evaluations, and provide practical metrics to consistently assess unified model's cross-modal stability and strength of their shared representations. Code: https://github.com/mollahsabbir/Semantic-Drift-in-Unified-Models

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

Large Language Models (LLMs) exhibit remarkable fluency and competence across various natural language tasks. However, recent research has highlighted their sensitivity to variations in input prompts. To deploy LLMs in a safe and reliable manner, it is crucial for their outputs to be consistent when prompted with expressions that carry the same meaning or intent. While some existing work has explored how state-of-the-art LLMs address this issue, their evaluations have been confined to assessing lexical equality of single- or multi-word answers, overlooking the consistency of generative text sequences. For a more comprehensive understanding of the consistency of LLMs in open-ended text generation scenarios, we introduce a general measure of semantic consistency, and formulate multiple versions of this metric to evaluate the performance of various LLMs. Our proposal demonstrates significantly higher consistency and stronger correlation with human evaluations of output consistency than traditional metrics based on lexical consistency. Finally, we propose a novel prompting strategy, called Ask-to-Choose (A2C), to enhance semantic consistency. When evaluated for closed-book question answering based on answer variations from the TruthfulQA benchmark, A2C increases accuracy metrics for pretrained and finetuned LLMs by up to 47%, and semantic consistency metrics for instruction-tuned models by up to 7-fold.

Sequence generation applications require satisfying semantic constraints, such as ensuring that programs are correct, using certain keywords, or avoiding undesirable content. Language models, whether fine-tuned or prompted with few-shot demonstrations, frequently violate these constraints, and lack a mechanism to iteratively revise their outputs. Moreover, some powerful language models are of extreme scale or inaccessible, making it inefficient, if not infeasible, to update their parameters for task-specific adaptation. We present Self-Correction, an approach that decouples an imperfect base generator (an off-the-shelf language model or supervised sequence-to-sequence model) from a separate corrector that learns to iteratively correct imperfect generations. To train the corrector, we propose an online training procedure that can use either scalar or natural language feedback on intermediate imperfect generations. We show that Self-Correction improves upon the base generator in three diverse generation tasks - mathematical program synthesis, lexically-constrained generation, and toxicity control - even when the corrector is much smaller than the base generator.

Reward models are central to aligning LLMs with human preferences, but they are costly to train, requiring large-scale human-labeled preference data and powerful pretrained LLM backbones. Meanwhile, the increasing availability of high-quality synthetic instruction-following datasets raises the question: can simpler, reference-based metrics serve as viable alternatives to reward models during RL-based alignment? In this paper, we show first that BLEU, a basic string-matching metric, surprisingly matches strong reward models in agreement with human preferences on general instruction-following datasets. Based on this insight, we develop BLEUBERI, a method that first identifies challenging instructions and then applies Group Relative Policy Optimization (GRPO) using BLEU directly as the reward function. We demonstrate that BLEUBERI-trained models are competitive with models trained via reward model-guided RL across four challenging instruction-following benchmarks and three different base language models. A human evaluation further supports that the quality of BLEUBERI model outputs is on par with those from reward model-aligned models. Moreover, BLEUBERI models generate outputs that are more factually grounded than competing methods. Overall, we show that given access to high-quality reference outputs (easily obtained via existing instruction-following datasets or synthetic data generation), string matching-based metrics are cheap yet effective proxies for reward models during alignment. We release our code and data at https://github.com/lilakk/BLEUBERI.

The democratization of machine learning systems has made the process of fine-tuning accessible to practitioners, leading to a wide range of open-source models fine-tuned on specialized tasks and datasets. Recent work has proposed to merge such models to combine their functionalities. However, prior approaches are usually restricted to models that are fine-tuned from the same base model. Furthermore, the final merged model is typically required to be of the same size as the original models. In this work, we propose a new two-step algorithm to merge models -- termed PLeaS -- which relaxes these constraints. First, leveraging the Permutation symmetries inherent in the two models, PLeaS partially matches nodes in each layer by maximizing alignment. Next, PLeaS computes the weights of the merged model as a layer-wise Least Squares solution to minimize the approximation error between the features of the merged model and the permuted features of the original models. PLeaS allows a practitioner to merge two models sharing the same architecture into a single performant model of a desired size, even when the two original models are fine-tuned from different base models. We also demonstrate how our method can be extended to address a challenging scenario where no data is available from the fine-tuning domains. We demonstrate our method to merge ResNet and ViT models trained with shared and different label spaces, and show improvement over the state-of-the-art merging methods of up to 15 percentage points for the same target compute while merging models trained on DomainNet and fine-grained classification tasks. Our code is open-sourced at https://github.com/SewoongLab/PLeaS-Merging .

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

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

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

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

In this article, we introduce a new parameterized family of topological invariants, taking the form of candidate decompositions, for multi-parameter persistence modules. We prove that our candidate decompositions are controllable approximations: when restricting to modules that can be decomposed into interval summands, we establish theoretical results about the approximation error between our candidate decompositions and the true underlying module in terms of the standard interleaving and bottleneck distances. Moreover, even when the underlying module does not admit such a decomposition, our candidate decompositions are nonetheless stable invariants; small perturbations in the underlying module lead to small perturbations in the candidate decomposition. Then, we introduce MMA (Multipersistence Module Approximation): an algorithm for computing stable instances of such invariants, which is based on fibered barcodes and exact matchings, two constructions that stem from the theory of single-parameter persistence. By design, MMA can handle an arbitrary number of filtrations, and has bounded complexity and running time. Finally, we present empirical evidence validating the generalization capabilities and running time speed-ups of MMA on several data sets.

We present M^3-Bench, the first benchmark for evaluating multimodal tool use under the Model Context Protocol. The benchmark targets realistic, multi-hop and multi-threaded workflows that require visual grounding and textual reasoning, cross-tool dependencies, and persistence of intermediate resources across steps. We introduce a similarity-driven alignment that serializes each tool call, embeds signatures with a sentence encoder, and performs similarity-bucketed Hungarian matching to obtain auditable one-to-one correspondences. On top of this alignment, we report interpretable metrics that decouple semantic fidelity from workflow consistency. The benchmark spans 28 servers with 231 tools, and provides standardized trajectories curated through an Executor & Judge pipeline with human verification; an auxiliary four large language models (LLMs) judge ensemble reports end-task Task Completion and information grounding. Evaluations of representative state-of-the-art Multimodal LLMs (MLLMs) reveal persistent gaps in multimodal MCP tool use, particularly in argument fidelity and structure consistency, underscoring the need for methods that jointly reason over images, text, and tool graphs. Our Benchmark's anonymous repository is at https://github.com/EtaYang10th/Open-M3-Bench

Antibodies are proteins produced by the immune system that can identify and neutralise a wide variety of antigens with high specificity and affinity, and constitute the most successful class of biotherapeutics. With the advent of next-generation sequencing, billions of antibody sequences have been collected in recent years, though their application in the design of better therapeutics has been constrained by the sheer volume and complexity of the data. To address this challenge, we present IgBert and IgT5, the best performing antibody-specific language models developed to date which can consistently handle both paired and unpaired variable region sequences as input. These models are trained comprehensively using the more than two billion unpaired sequences and two million paired sequences of light and heavy chains present in the Observed Antibody Space dataset. We show that our models outperform existing antibody and protein language models on a diverse range of design and regression tasks relevant to antibody engineering. This advancement marks a significant leap forward in leveraging machine learning, large scale data sets and high-performance computing for enhancing antibody design for therapeutic development.

The emergence of Large Language Models (LLMs) has fundamentally transformed natural language processing, making them indispensable across domains ranging from conversational systems to scientific exploration. However, their pre-trained architectures often reveal limitations in specialized contexts, including restricted reasoning capacities, ethical uncertainties, and suboptimal domain-specific performance. These challenges necessitate advanced post-training language models (PoLMs) to address these shortcomings, such as OpenAI-o1/o3 and DeepSeek-R1 (collectively known as Large Reasoning Models, or LRMs). This paper presents the first comprehensive survey of PoLMs, systematically tracing their evolution across five core paradigms: Fine-tuning, which enhances task-specific accuracy; Alignment, which ensures alignment with human preferences; Reasoning, which advances multi-step inference despite challenges in reward design; Efficiency, which optimizes resource utilization amidst increasing complexity; and Integration and Adaptation, which extend capabilities across diverse modalities while addressing coherence issues. Charting progress from ChatGPT's foundational alignment strategies to DeepSeek-R1's innovative reasoning advancements, we illustrate how PoLMs leverage datasets to mitigate biases, deepen reasoning capabilities, and enhance domain adaptability. Our contributions include a pioneering synthesis of PoLM evolution, a structured taxonomy categorizing techniques and datasets, and a strategic agenda emphasizing the role of LRMs in improving reasoning proficiency and domain flexibility. As the first survey of its scope, this work consolidates recent PoLM advancements and establishes a rigorous intellectual framework for future research, fostering the development of LLMs that excel in precision, ethical robustness, and versatility across scientific and societal applications.

Large language models (LLMs) show the promise in supporting scientific research implementation, yet their ability to generate correct and executable code remains limited. Existing works largely adopt one-shot settings, ignoring the iterative and feedback-driven nature of realistic workflows of scientific research development. To address this gap, we present RECODE-H, a benchmark of 102 tasks from research papers and repositories that evaluates LLM agents through multi-turn interactions with LLM-simulated human feedback. It includes structured instructions,unit tests, and a five-level feedback hierarchy to reflect realistic researcher-agent collaboration. We further present ReCodeAgent, a framework that integrates feedback into iterative code generation. Experiments with leading LLMs, including GPT-5, Claude-Sonnet-4, DeepSeek-V3.1, and Gemini 2.5, show substantial performance gains with richer feedback, while also highlighting ongoing challenges in the generation of complex research code. RECODE-H establishes a foundation for developing adaptive, feedback-driven LLM agents in scientific research implementation

Large language models (LLMs) have had a transformative impact on a variety of scientific tasks across disciplines such as biology, chemistry, medicine, and physics. However, ensuring the safety alignment of these models in scientific research remains an underexplored area, with existing benchmarks primarily focus on textual content and overlooking key scientific representations such as molecular, protein, and genomic languages. Moreover, the safety mechanisms of LLMs in scientific tasks are insufficiently studied. To address these limitations, we introduce SciSafeEval, a comprehensive benchmark designed to evaluate the safety alignment of LLMs across a range of scientific tasks. SciSafeEval spans multiple scientific languages - including textual, molecular, protein, and genomic - and covers a wide range of scientific domains. We evaluate LLMs in zero-shot, few-shot and chain-of-thought settings, and introduce a 'jailbreak' enhancement feature that challenges LLMs equipped with safety guardrails, rigorously testing their defenses against malicious intention. Our benchmark surpasses existing safety datasets in both scale and scope, providing a robust platform for assessing the safety and performance of LLMs in scientific contexts. This work aims to facilitate the responsible development and deployment of LLMs, promoting alignment with safety and ethical standards in scientific research.

Large language models (LLMs) frequently refuse to respond to pseudo-malicious instructions: semantically harmless input queries triggering unnecessary LLM refusals due to conservative safety alignment, significantly impairing user experience. Collecting such instructions is crucial for evaluating and mitigating over-refusals, but existing instruction curation methods, like manual creation or instruction rewriting, either lack scalability or fail to produce sufficiently diverse and effective refusal-inducing prompts. To address these limitations, we introduce EVOREFUSE, a prompt optimization approach that generates diverse pseudo-malicious instructions consistently eliciting confident refusals across LLMs. EVOREFUSE employs an evolutionary algorithm exploring the instruction space in more diverse directions than existing methods via mutation strategies and recombination, and iteratively evolves seed instructions to maximize evidence lower bound on LLM refusal probability. Using EVOREFUSE, we create two novel datasets: EVOREFUSE-TEST, a benchmark of 582 pseudo-malicious instructions that outperforms the next-best benchmark with 140.41% higher average refusal triggering rate across 9 LLMs, 34.86% greater lexical diversity, and 40.03% improved LLM response confidence scores; and EVOREFUSE-ALIGN, which provides 3,000 pseudo-malicious instructions with responses for supervised and preference-based alignment training. LLAMA3.1-8B-INSTRUCT supervisedly fine-tuned on EVOREFUSE-ALIGN achieves up to 14.31% fewer over-refusals than models trained on the second-best alignment dataset, without compromising safety. Our analysis with EVOREFUSE-TEST reveals models trigger over-refusals by overly focusing on sensitive keywords while ignoring broader context.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

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 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.

Large Language Models (LLMs) have demonstrated remarkable capabilities, yet their transition to real-world applications reveals a critical limitation: the inability to adapt to individual preferences while maintaining alignment with universal human values. Current alignment techniques adopt a one-size-fits-all approach that fails to accommodate users' diverse backgrounds and needs. This paper presents the first comprehensive survey of personalized alignment-a paradigm that enables LLMs to adapt their behavior within ethical boundaries based on individual preferences. We propose a unified framework comprising preference memory management, personalized generation, and feedback-based alignment, systematically analyzing implementation approaches and evaluating their effectiveness across various scenarios. By examining current techniques, potential risks, and future challenges, this survey provides a structured foundation for developing more adaptable and ethically-aligned LLMs.

Large Language Models (LLMs) exhibit remarkably powerful capabilities. One of the crucial factors to achieve success is aligning the LLM's output with human preferences. This alignment process often requires only a small amount of data to efficiently enhance the LLM's performance. While effective, research in this area spans multiple domains, and the methods involved are relatively complex to understand. The relationships between different methods have been under-explored, limiting the development of the preference alignment. In light of this, we break down the existing popular alignment strategies into different components and provide a unified framework to study the current alignment strategies, thereby establishing connections among them. In this survey, we decompose all the strategies in preference learning into four components: model, data, feedback, and algorithm. This unified view offers an in-depth understanding of existing alignment algorithms and also opens up possibilities to synergize the strengths of different strategies. Furthermore, we present detailed working examples of prevalent existing algorithms to facilitate a comprehensive understanding for the readers. Finally, based on our unified perspective, we explore the challenges and future research directions for aligning large language models with human preferences.

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.

Advances in unsupervised probes such as Contrast-Consistent Search (CCS), which reveal latent beliefs without relying on token outputs, raise the question of whether these methods can reliably assess model alignment. We investigate this by examining the sensitivity of CCS to harmful vs. safe statements and by introducing Polarity-Aware CCS (PA-CCS), a method for evaluating whether a model's internal representations remain consistent under polarity inversion. We propose two alignment-oriented metrics, Polar-Consistency and the Contradiction Index, to quantify the semantic robustness of a model's latent knowledge. To validate PA-CCS, we curate two main datasets and one control dataset containing matched harmful-safe sentence pairs constructed using different methodologies (concurrent and antagonistic statements). We apply PA-CCS to 16 language models. Our results show that PA-CCS identifies both architectural and layer-specific differences in the encoding of latent harmful knowledge. Notably, replacing the negation token with a meaningless marker degrades PA-CCS scores for models with well-aligned internal representations, while models lacking robust internal calibration do not exhibit this degradation. Our findings highlight the potential of unsupervised probing for alignment evaluation and emphasize the need to incorporate structural robustness checks into interpretability benchmarks. Code and datasets are available at: https://github.com/SadSabrina/polarity-probing. WARNING: This paper contains potentially sensitive, harmful, and offensive content.

This paper presents a simple, effective, and cost-efficient strategy to improve LLM performance by scaling test-time compute. Our strategy builds upon the repeated-sampling-then-voting framework, with a novel twist: incorporating multiple models, even weaker ones, to leverage their complementary strengths that potentially arise from diverse training data and paradigms. By using consistency as a signal, our strategy dynamically switches between models. Theoretical analysis highlights the efficiency and performance advantages of our strategy. Extensive experiments on six datasets demonstrate that our strategy not only outperforms self-consistency and state-of-the-art multi-agent debate approaches, but also significantly reduces inference costs. Additionally, ModelSwitch requires only a few comparable LLMs to achieve optimal performance and can be extended with verification methods, demonstrating the potential of leveraging multiple LLMs in the generation-verification paradigm.

As development of large language models (LLM) progresses, aligning them with human preferences has become increasingly important. We propose stepwise DPO (sDPO), an extension of the recently popularized direct preference optimization (DPO) for alignment tuning. This approach involves dividing the available preference datasets and utilizing them in a stepwise manner, rather than employing it all at once. We demonstrate that this method facilitates the use of more precisely aligned reference models within the DPO training framework. Furthermore, sDPO trains the final model to be more performant, even outperforming other popular LLMs with more parameters.

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

Code generation techniques generate code snippets automatically based on the problem requirements in natural language. Recently, large language models (LLMs) achieve the SOTA performance on code generation. However, LLMs still struggle at times to generate accurate code, which diminishes their promised efficiency as developers must spend significant effort evaluating and debugging the generated code. To improve the reliability and quality of the generated codes, researchers propose to leverage Consistency to obtain a better code based on generating and ranking multiple candidates. The existing approach is problematic as Consistency thinks a code is better when (1) the code pass more tests (inter-consistency) (2) more codes share the same behavior (intra-consistency). However, because the tests are also generated by LLMs, they could be wrong as well. As a result, majority voting based on testing results is unreliable. Relying solely on consistency is insufficient to address this issue; integrating user feedback is essential for effectively guiding consistency. We show that with minimal human effort, performance can be significantly enhanced. We propose Consistency-Augmented Iterative Interaction Framework to Enhance the Reliability of Code Generation, ConAIR, which is an approach that aims to improve the performance of a code generator through two distinctive ingredients, i.e., (1) lightweight user effort for validating the correctness of selected tests; and (2) a dynamic strategy for ranking, localizing and correcting multiple tests and codes. Overall, we propose a lightweight interaction framework that incorporates user feedback to correct identified tests and guide the iterative process. The iteration rounds are only 4 in average with the help of consistency. With only lightweight human efforts, we can achieve an improvement of 33% towards the base model.

Multimodal protein language models deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In this paper, we propose a fine-tuning framework called InstructPLM-mu and try to answer a question: Can multimodal fine-tuning of a pretrained, sequence-only protein language model match the performance of models trained end-to-end? Surprisingly, our experiments show that fine-tuning ESM2 with structural inputs can reach performance comparable to ESM3. To understand how this is achieved, we systematically compare three different feature-fusion designs and fine-tuning recipes. Our results reveal that both the fusion method and the tuning strategy strongly affect final accuracy, indicating that the fine-tuning process is not trivial. We hope this work offers practical guidance for injecting structure into pretrained protein language models and motivates further research on better fusion mechanisms and fine-tuning protocols.

Existing large language models have to run K times to generate a sequence of K tokens. In this paper, we present RecycleGPT, a generative language model with fast decoding speed by recycling pre-generated model states without running the whole model in multiple steps. Our approach relies on the observation that adjacent tokens in a sequence usually have strong correlations and the next token in a sequence can be reasonably guessed or inferred based on the preceding ones. Through theoretical evaluations and practical tests on downstream text generation tasks, we demonstrate the effectiveness of our approach in lowering inference latency, achieving up to 1.4x speedup while preserving high performance.

Just like the previous generation of task-tuned models, large language models (LLMs) that are adapted to tasks via prompt-based methods like in-context-learning (ICL) perform well in some setups but not in others. This lack of consistency in prompt-based learning hints at a lack of robust generalisation. We here introduce the ICL consistency test -- a contribution to the GenBench collaborative benchmark task (CBT) -- which evaluates how consistent a model makes predictions across many different setups while using the same data. The test is based on different established natural language inference tasks. We provide preprocessed data constituting 96 different 'setups' and a metric that estimates model consistency across these setups. The metric is provided on a fine-grained level to understand what properties of a setup render predictions unstable and on an aggregated level to compare overall model consistency. We conduct an empirical analysis of eight state-of-the-art models, and our consistency metric reveals how all tested LLMs lack robust generalisation.

Model merging allows combining the capabilities of existing models into a new one - post hoc, without additional training. This has made it increasingly popular thanks to its low cost and the availability of libraries that support merging on consumer GPUs. Recent work shows that pairing merging with evolutionary algorithms can boost performance, but no framework currently supports flexible experimentation with such strategies in language models. We introduce Mergenetic, an open-source library for evolutionary model merging. Mergenetic enables easy composition of merging methods and evolutionary algorithms while incorporating lightweight fitness estimators to reduce evaluation costs. We describe its design and demonstrate that Mergenetic produces competitive results across tasks and languages using modest hardware.

Recent alignment algorithms such as direct preference optimization (DPO) have been developed to improve the safety of large language models (LLMs) by training these models to match human behaviors exemplified by preference data. However, these methods are both computationally intensive and lacking in controllability and transparency, making them prone to jailbreaking and inhibiting their widespread use. Furthermore, these tuning-based methods require large-scale preference data for training and are susceptible to noisy preference data. In this paper, we introduce a tuning-free alignment alternative (DeTox) and demonstrate its effectiveness under the use case of toxicity reduction. Grounded on theory from factor analysis, DeTox is a sample-efficient model editing approach that identifies a toxic subspace in the model parameter space and reduces model toxicity by projecting away the detected subspace. The toxic sub-space is identified by extracting preference data embeddings from the language model, and removing non-toxic information from these embeddings. We show that DeTox is more sample-efficient than DPO, further showcasing greater robustness to noisy data. Finally, we establish both theoretical and empirical connections between DeTox and DPO, showing that DeTox can be interpreted as a denoised version of a single DPO step.

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models nucleotide evolution on phylogenetic trees using multispecies whole-genome alignments. Our approach integrates an alignment into the loss function during training but does not require it for making predictions, thereby enhancing the model's applicability. We applied this framework to train PhyloGPN, a model that excels at predicting functionally disruptive variants from a single sequence alone and demonstrates strong transfer learning capabilities.

By compressing diverse narratives, LLMs go beyond memorization, achieving intelligence by capturing generalizable causal relationships. However, they suffer from local 'representation gaps' due to insufficient training data diversity, limiting their real-world utility, especially in tasks requiring strict alignment to rules. Traditional alignment methods relying on heavy human annotations are inefficient and unscalable. Recent self-alignment techniques also fall short, as they often depend on self-selection based prompting and memorization-based learning. To address these issues, we introduce Iterative Graph Alignment (IGA), an annotation-free rule-based alignment algorithm. A teacher model (VLM) employs Iterative Graph Prompting (IGP) to create logical graphs and reference answers. The student model (LLM) identifies local knowledge gaps by attempting to align its responses with these references, collaborating with helper models to generate diverse answers. These aligned responses are then used for iterative supervised fine-tuning (SFT). Our evaluations across five rule-based scenarios demonstrate IGP's effectiveness, with a 73.12\% alignment improvement in Claude Sonnet 3.5, and Llama3-8B-Instruct achieving an 86.20\% improvement, outperforming Claude Sonnet 3.5 in rule-based alignment.

Code Large Language Models (Code LLMs) are being increasingly employed in real-life applications, so evaluating them is critical. While the conventional accuracy evaluates the performance of Code LLMs on a set of individual tasks, their self-consistency across different tasks is overlooked. Intuitively, a trustworthy model should be self-consistent when generating natural language specifications for its own code and generating code for its own specifications. Failure to preserve self-consistency reveals a lack of understanding of the shared semantics underlying natural language and programming language, and therefore undermines the trustworthiness of a model. In this paper, we first formally define the self-consistency of Code LLMs and then design a framework, IdentityChain, which effectively and efficiently evaluates the self-consistency and conventional accuracy of a model at the same time. We study eleven Code LLMs and show that they fail to preserve self-consistency, which is indeed a distinct aspect from conventional accuracy. Furthermore, we show that IdentityChain can be used as a model debugging tool to expose weaknesses of Code LLMs by demonstrating three major weaknesses that we identify in current models using IdentityChain. Our code is available at https://github.com/marcusm117/IdentityChain.

Constraints are critical in text generation as LLM outputs are often unreliable when it comes to ensuring generated outputs adhere to user defined instruction or general safety guidelines. To address this gap, we present Constrained Discrete Diffusion (CDD), a novel method for enforcing constraints on natural language by integrating discrete diffusion models with differentiable optimization. Unlike conventional text generators, which often rely on post-hoc filtering or model retraining for controllable generation, we propose imposing constraints directly into the discrete diffusion sampling process. We illustrate how this technique can be applied to satisfy a variety of natural language constraints, including (i) toxicity mitigation by preventing harmful content from emerging, (ii) character and sequence level lexical constraints, and (iii) novel molecule sequence generation with specific property adherence. Experimental results show that our constraint-aware procedure achieves high fidelity in meeting these requirements while preserving fluency and semantic coherence, outperforming auto-regressive and existing discrete diffusion approaches.

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

We investigate how to teach large language models (LLMs) to perform scientific reasoning by leveraging expert discussions as a learning signal. Focusing on the genomics domain, we develop an automated pipeline to extract trainable data and introduce Genome-Bench, a new benchmark constructed from over a decade of scientific forum discussions on genome engineering. Our pipeline transforms raw interactions into a reinforcement learning-friendly multiple-choice questions format, supported by 3000+ high-quality question-answer pairs spanning foundational biology, experimental troubleshooting, tool usage, and beyond. We fine-tune an LLM using RL with a rule-based reward signal derived from the synthetic MCQ dataset to enhance domain-specific reasoning. Our results show that reinforcement learning from scientific discussions improves model performance by over 15% compared to the base model on Genome-Bench, narrowing the gap between open-source LLMs and expert-level reasoning. To our knowledge, this is the first end-to-end pipeline for teaching LLMs to reason from scientific discussions, with promising potential for generalization across scientific domains beyond biology.

Aligning large language models (LLMs) with human preferences is essential for their applications. Recently, decoding-time alignment has emerged as an effective plug-and-play technique that avoids fine-tuning model parameters. This approach retains the general utility of pretrained LLMs but often suffers from significant inefficiencies during decoding, primarily due to wasted token generation and excessive reward evaluations. To address these challenges, we introduce Cascade Reward Sampling (CARDS) to resolve both efficiency bottlenecks in decoding-time alignment. Specifically, we develop a segment-level rejection sampling algorithm that minimizes redundant computations of both LLMs and reward models (RMs). Central to CARDS is an uncertainty-based segmentation mechanism, which ensures the accuracy of RMs evaluations on incomplete segments. Furthermore, we provide a detailed analysis of reward scores on segments to elucidate the improved alignment performance. Experimental results demonstrate that CARDS significantly improves decoding efficiency, alignment quality, and general utility compared to existing decoding-time alignment methods, achieving approximately a 70% reduction in decoding time and over 90% win-ties in utility and safety benchmarks.

Large Language Models (LLMs) for formal theorem proving have shown significant promise, yet they often lack generalizability and are fragile to even minor transformations of problem statements. To address this limitation, we introduce a novel data augmentation pipeline designed to enhance model robustness from two perspectives: symmetry and difficulty. From the symmetry perspective, we propose two complementary methods: EvolAST, an Abstract Syntax Tree (AST) based approach that targets syntactic symmetry to generate semantically equivalent problem variants, and EvolDomain, which leverages LLMs to address semantic symmetry by translating theorems across mathematical domains. From the difficulty perspective, we propose EvolDifficulty, which uses carefully designed evolutionary instructions to guide LLMs in generating new theorems with a wider range of difficulty. We then use the evolved data to train EvolProver, a 7B-parameter non-reasoning theorem prover. EvolProver establishes a new state-of-the-art (SOTA) on FormalMATH-Lite with a 53.8% pass@32 rate, surpassing all models of comparable size, including reasoning-based models. It also sets new SOTA records for non-reasoning models on MiniF2F-Test (69.8% pass@32), Ineq-Comp-Seed (52.2% pass@32), and Ineq-Comp-Transformed (34.0% pass@32). Ablation studies further confirm our data augmentation pipeline's effectiveness across multiple benchmarks.

With the rapid development of Large Language Models (LLMs), aligning these models with human preferences and values is critical to ensuring ethical and safe applications. However, existing alignment techniques such as RLHF or DPO often require direct fine-tuning on LLMs with billions of parameters, resulting in substantial computational costs and inefficiencies. To address this, we propose Micro token-level Accept-Reject Aligning (MARA) approach designed to operate independently of the language models. MARA simplifies the alignment process by decomposing sentence-level preference learning into token-level binary classification, where a compact three-layer fully-connected network determines whether candidate tokens are "Accepted" or "Rejected" as part of the response. Extensive experiments across seven different LLMs and three open-source datasets show that MARA achieves significant improvements in alignment performance while reducing computational costs.

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.

Controlled text perturbation is useful for evaluating and improving model generalizability. However, current techniques rely on training a model for every target perturbation, which is expensive and hard to generalize. We present Tailor, a semantically-controlled text generation system. Tailor builds on a pretrained seq2seq model and produces textual outputs conditioned on control codes derived from semantic representations. We craft a set of operations to modify the control codes, which in turn steer generation towards targeted attributes. These operations can be further composed into higher-level ones, allowing for flexible perturbation strategies. We demonstrate the effectiveness of these perturbations in multiple applications. First, we use Tailor to automatically create high-quality contrast sets for four distinct natural language processing (NLP) tasks. These contrast sets contain fewer spurious artifacts and are complementary to manually annotated ones in their lexical diversity. Second, we show that Tailor perturbations can improve model generalization through data augmentation. Perturbing just 2% of training data leads to a 5.8-point gain on an NLI challenge set measuring reliance on syntactic heuristics.

The widespread applicability and increasing omnipresence of LLMs have instigated a need to align LLM responses to user and stakeholder preferences. Many preference optimization approaches have been proposed that fine-tune LLM parameters to achieve good alignment. However, such parameter tuning is known to interfere with model performance on many tasks. Moreover, keeping up with shifting user preferences is tricky in such a situation. Decoding-time alignment with reward model guidance solves these issues at the cost of increased inference time. However, most of such methods fail to strike the right balance between exploration and exploitation of reward -- often due to the conflated formulation of these two aspects - to give well-aligned responses. To remedy this we decouple these two aspects and implement them in an evolutionary fashion: exploration is enforced by decoding from mutated instructions and exploitation is represented as the periodic replacement of poorly-rewarded generations with well-rewarded ones. Empirical evidences indicate that this strategy outperforms many preference optimization and decode-time alignment approaches on two widely accepted alignment benchmarks AlpacaEval 2 and MT-Bench. Our implementation will be available at: https://darwin-alignment.github.io.

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

Reinforcement Learning from Human Feedback (RLHF) has become a cornerstone for aligning large language models (LLMs). However, its effectiveness depends on high-quality instruction data. Most existing alignment datasets are either private or require costly human annotation, which limits reproducibility and scalability. Even with Reinforcement Learning from AI Feedback (RLAIF), concerns about data quality remain. Moreover, it is unclear how much data is actually required to fine-tune a base model into a strong instruction-following model. Current approaches often rely on over 300k examples even at the supervised fine-tuning (SFT) stage, yet they still underperform compared to proprietary models, creating barriers for academic and resource-limited communities. To address this gap, we introduce PiKa, a data-efficient family of expert-level alignment datasets. In particular, the PiKa-SFT dataset uses only 30k SFT examples, far fewer than state-of-the-art datasets like Magpie. Through evaluations by fine-tuning Llama-3-8B-Base on PiKa and other public datasets, we show that PiKa-SFT outperforms models trained on much larger data. On AlpacaEval 2.0 and Arena-Hard benchmarks, PiKa-SFT fine-tuning even surpasses the official Llama-3-8B-Instruct model trained on over 10 million proprietary examples. We further extend our study by training the Qwen2.5 series (0.5B to 7B) on PiKa-SFT, achieving consistent gains. These findings demonstrate that high-quality alignment can be achieved with significantly less data, offering a scalable path for open-source LLM alignment. Code and data: https://github.com/SJY8460/PiKa.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

Recent advances in multimodal models have demonstrated remarkable text-guided image editing capabilities, with systems like GPT-4o and Nano-Banana setting new benchmarks. However, the research community's progress remains constrained by the absence of large-scale, high-quality, and openly accessible datasets built from real images. We introduce Pico-Banana-400K, a comprehensive 400K-image dataset for instruction-based image editing. Our dataset is constructed by leveraging Nano-Banana to generate diverse edit pairs from real photographs in the OpenImages collection. What distinguishes Pico-Banana-400K from previous synthetic datasets is our systematic approach to quality and diversity. We employ a fine-grained image editing taxonomy to ensure comprehensive coverage of edit types while maintaining precise content preservation and instruction faithfulness through MLLM-based quality scoring and careful curation. Beyond single turn editing, Pico-Banana-400K enables research into complex editing scenarios. The dataset includes three specialized subsets: (1) a 72K-example multi-turn collection for studying sequential editing, reasoning, and planning across consecutive modifications; (2) a 56K-example preference subset for alignment research and reward model training; and (3) paired long-short editing instructions for developing instruction rewriting and summarization capabilities. By providing this large-scale, high-quality, and task-rich resource, Pico-Banana-400K establishes a robust foundation for training and benchmarking the next generation of text-guided image editing models.

Recent advancements in large language models (LLMs) have demonstrated remarkable reasoning capabilities. However, single-shot inference often yields unreliable results for complex reasoning tasks, leading researchers to explore multiple reasoning paths through methods such as perplexity and self-consistency. In this paper, we present the first theoretical error decomposition analysis of these techniques, breaking down their error into estimation error and model error. Our analysis reveals a fundamental trade-off: perplexity methods suffer from substantial model error due to the absence of a proper consistency function, while self-consistency exhibits high estimation error due to a slow error convergence rate. To overcome these limitations, we propose Reasoning-Pruning Perplexity Consistency (RPC). This approach combines Perplexity Consistency, which seamlessly integrates LLM perplexity with self-consistency, and Reasoning Pruning, which eliminates low-probability reasoning paths to effectively prevent the degeneration of estimation error reduction. Theoretical analysis demonstrates that RPC not only accelerates the convergence rate of estimation error to an exponential level but also holds strong potential for further reducing model error. Extensive empirical evaluations on seven benchmark datasets confirm that RPC can significantly improve reasoning performance, sample efficiency, and confidence reliability.

Recent advances in LLM-guided evolutionary computation, particularly AlphaEvolve (Novikov et al., 2025; Georgiev et al., 2025), have demonstrated remarkable success in discovering novel mathematical constructions and solving challenging optimization problems. However, the high-level descriptions in published work leave many implementation details unspecified, hindering reproducibility and further research. In this report we present GigaEvo, an extensible open-source framework that enables researchers to study and experiment with hybrid LLM-evolution approaches inspired by AlphaEvolve. Our system provides modular implementations of key components: MAP-Elites quality-diversity algorithms, asynchronous DAG-based evaluation pipelines, LLM-driven mutation operators with insight generation and bidirectional lineage tracking, and flexible multi-island evolutionary strategies. In order to assess reproducibility and validate our implementation we evaluate GigaEvo on challenging problems from the AlphaEvolve paper: Heilbronn triangle placement, circle packing in squares, and high-dimensional kissing numbers. The framework emphasizes modularity, concurrency, and ease of experimentation, enabling rapid prototyping through declarative configuration. We provide detailed descriptions of system architecture, implementation decisions, and experimental methodology to support further research in LLM driven evolutionary methods. The GigaEvo framework and all experimental code are available at https://github.com/AIRI-Institute/gigaevo-core.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

Aligning with personalized preferences, which vary significantly across cultural, educational, and political differences, poses a significant challenge due to the computational costs and data demands of traditional alignment methods. In response, this paper presents Personalized Alignment at Decoding-time (PAD), a novel framework designed to align LLM outputs with diverse personalized preferences during the inference phase, eliminating the need for additional training. By introducing a unique personalized reward modeling strategy, this framework decouples the text generation process from personalized preferences, facilitating the generation of generalizable token-level personalized rewards. The PAD algorithm leverages these rewards to guide the decoding process, dynamically tailoring the base model's predictions to personalized preferences. Extensive experimental results demonstrate that PAD not only outperforms existing training-based alignment methods in terms of aligning with diverse preferences but also shows significant generalizability to preferences unseen during training and scalability across different base models. This work advances the capability of LLMs to meet user needs in real-time applications, presenting a substantial step forward in personalized LLM alignment.

Recent years have witnessed remarkable progress made in large language models (LLMs). Such advancements, while garnering significant attention, have concurrently elicited various concerns. The potential of these models is undeniably vast; however, they may yield texts that are imprecise, misleading, or even detrimental. Consequently, it becomes paramount to employ alignment techniques to ensure these models to exhibit behaviors consistent with human values. This survey endeavors to furnish an extensive exploration of alignment methodologies designed for LLMs, in conjunction with the extant capability research in this domain. Adopting the lens of AI alignment, we categorize the prevailing methods and emergent proposals for the alignment of LLMs into outer and inner alignment. We also probe into salient issues including the models' interpretability, and potential vulnerabilities to adversarial attacks. To assess LLM alignment, we present a wide variety of benchmarks and evaluation methodologies. After discussing the state of alignment research for LLMs, we finally cast a vision toward the future, contemplating the promising avenues of research that lie ahead. Our aspiration for this survey extends beyond merely spurring research interests in this realm. We also envision bridging the gap between the AI alignment research community and the researchers engrossed in the capability exploration of LLMs for both capable and safe LLMs.

Large language models (LLMs) require continual knowledge updates to stay abreast of the ever-changing world facts, prompting the formulation of lifelong model editing task. While recent years have witnessed the development of various techniques for single and batch editing, these methods either fail to apply or perform sub-optimally when faced with lifelong editing. In this paper, we introduce LEMoE, an advanced Mixture of Experts (MoE) adaptor for lifelong model editing. We first analyze the factors influencing the effectiveness of conventional MoE adaptor in lifelong editing, including catastrophic forgetting, inconsistent routing and order sensitivity. Based on these insights, we propose a tailored module insertion method to achieve lifelong editing, incorporating a novel KV anchor routing to enhance routing consistency between training and inference stage, along with a concise yet effective clustering-based editing order planning. Experimental results demonstrate the effectiveness of our method in lifelong editing, surpassing previous model editing techniques while maintaining outstanding performance in batch editing task. Our code will be available.

The widespread adoption of large language models (LLMs) across various regions underscores the urgent need to evaluate their alignment with human values. Current benchmarks, however, fall short of effectively uncovering safety vulnerabilities in LLMs. Despite numerous models achieving high scores and 'topping the chart' in these evaluations, there is still a significant gap in LLMs' deeper alignment with human values and achieving genuine harmlessness. To this end, this paper proposes a value alignment benchmark named Flames, which encompasses both common harmlessness principles and a unique morality dimension that integrates specific Chinese values such as harmony. Accordingly, we carefully design adversarial prompts that incorporate complex scenarios and jailbreaking methods, mostly with implicit malice. By prompting 17 mainstream LLMs, we obtain model responses and rigorously annotate them for detailed evaluation. Our findings indicate that all the evaluated LLMs demonstrate relatively poor performance on Flames, particularly in the safety and fairness dimensions. We also develop a lightweight specified scorer capable of scoring LLMs across multiple dimensions to efficiently evaluate new models on the benchmark. The complexity of Flames has far exceeded existing benchmarks, setting a new challenge for contemporary LLMs and highlighting the need for further alignment of LLMs. Our benchmark is publicly available at https://github.com/AIFlames/Flames.

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

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

The dominant approach to generating from language models subject to some constraint is locally constrained decoding (LCD), incrementally sampling tokens at each time step such that the constraint is never violated. Typically, this is achieved through token masking: looping over the vocabulary and excluding non-conforming tokens. There are two important problems with this approach. (i) Evaluating the constraint on every token can be prohibitively expensive -- LM vocabularies often exceed 100,000 tokens. (ii) LCD can distort the global distribution over strings, sampling tokens based only on local information, even if they lead down dead-end paths. This work introduces a new algorithm that addresses both these problems. First, to avoid evaluating a constraint on the full vocabulary at each step of generation, we propose an adaptive rejection sampling algorithm that typically requires orders of magnitude fewer constraint evaluations. Second, we show how this algorithm can be extended to produce low-variance, unbiased estimates of importance weights at a very small additional cost -- estimates that can be soundly used within previously proposed sequential Monte Carlo algorithms to correct for the myopic behavior of local constraint enforcement. Through extensive empirical evaluation in text-to-SQL, molecular synthesis, goal inference, pattern matching, and JSON domains, we show that our approach is superior to state-of-the-art baselines, supporting a broader class of constraints and improving both runtime and performance. Additional theoretical and empirical analyses show that our method's runtime efficiency is driven by its dynamic use of computation, scaling with the divergence between the unconstrained and constrained LM, and as a consequence, runtime improvements are greater for better models.

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

Large language models (LLMs) are increasingly deployed as agents, expected to decompose goals, invoke tools, and verify results in dynamic environments. Realizing these capabilities requires access to agentic data-structured interaction records that couple user intents with tool specifications, argument-grounded calls, and verifiable execution traces. However, collecting such data from human annotators is costly, time-consuming, and difficult to scale. We present a unified framework for synthesizing agentic data using only LLMs, without any human-in-the-loop supervision. This framework decomposes generation into modular pipelines that produce complete interaction records spanning task specifications, tool definitions, policy pseudocode, natural language exchanges, and execution traces. Records conform to strict syntactic and semantic constraints, ensuring machine-parseability and faithful alignment across inputs, outputs, and tool calls. Beyond single tasks, there is support for both multi-task and multi-turn agent interactions, enabling the construction of datasets that reflect the full spectrum of tool-use competencies. To ensure quality and consistency, the framework integrates constrained generation formats, JSON-schema validation, and judge-based filtering. This paper formalizes the schema for agentic records, details the prompt design principles that guide generation, and introduces scalable pipelines for high-quality synthetic data. By providing a reproducible, LLM-only alternative to manual collection, hence advancing the development of agentic LLMs capable of robust tool use.

Large Language Models (LLMs) excel in various natural language processing tasks but remain vulnerable to generating harmful content or being exploited for malicious purposes. Although safety alignment datasets have been introduced to mitigate such risks through supervised fine-tuning (SFT), these datasets often lack comprehensive risk coverage. Most existing datasets focus primarily on lexical diversity while neglecting other critical dimensions. To address this limitation, we propose a novel analysis framework to systematically measure the risk coverage of alignment datasets across three essential dimensions: Lexical Diversity, Malicious Intent, and Jailbreak Tactics. We further introduce TRIDENT, an automated pipeline that leverages persona-based, zero-shot LLM generation to produce diverse and comprehensive instructions spanning these dimensions. Each harmful instruction is paired with an ethically aligned response, resulting in two datasets: TRIDENT-Core, comprising 26,311 examples, and TRIDENT-Edge, with 18,773 examples. Fine-tuning Llama 3.1-8B on TRIDENT-Edge demonstrates substantial improvements, achieving an average 14.29% reduction in Harm Score, and a 20% decrease in Attack Success Rate compared to the best-performing baseline model fine-tuned on the WildBreak dataset.

Due to the scarcity of high-quality data, large language models (LLMs) are often trained on mixtures of data with varying quality levels, even after sophisticated data curation. A natural approach to better leverage high-quality data is curriculum-based pretraining, where the model is trained on data sorted in ascending order of quality as determined by a quality metric. However, prior studies have reported limited improvements from such curriculum-based pretraining strategies. This work identifies a critical factor constraining these methods: the incompatibility between the ascending data quality order and the decaying learning rate (LR) schedule. We find that while curriculum-based training substantially outperforms random shuffling when using a constant LR, its advantage diminishes under standard LR decay schedules. Our experiments show this incompatibility can be mitigated by two simple strategies: (1) employing a more moderate LR decay schedule, where the final LR is only moderately smaller than the peak LR, and (2) replacing LR decay with model averaging, i.e., computing a weighted average of the final few checkpoints. By combining these strategies, we improve the average score on a suite of standard benchmarks by 1.64% over random shuffling, without additional data refinement. Validated on 1.5B-parameter models trained over 30B tokens with various data-quality metrics, our findings call for a re-evaluation of curriculum-based LLM pretraining and underscore the potential of co-designing data curricula with optimization methods.

Using a nearly-frozen pretrained model, the continual representation learning paradigm reframes parameter updates as a similarity-matching problem to mitigate catastrophic forgetting. However, directly leveraging pretrained features for downstream tasks often suffers from multicollinearity in the similarity-matching stage, and more advanced methods can be computationally prohibitive for real-time, low-latency applications. Inspired by the fly olfactory circuit, we propose Fly-CL, a bio-inspired framework compatible with a wide range of pretrained backbones. Fly-CL substantially reduces training time while achieving performance comparable to or exceeding that of current state-of-the-art methods. We theoretically show how Fly-CL progressively resolves multicollinearity, enabling more effective similarity matching with low time complexity. Extensive simulation experiments across diverse network architectures and data regimes validate Fly-CL's effectiveness in addressing this challenge through a biologically inspired design. Code is available at https://github.com/gfyddha/Fly-CL.

Code generation models have achieved impressive performance. However, they tend to be brittle as slight edits to a prompt could lead to very different generations; these robustness properties, critical for user experience when deployed in real-life applications, are not well understood. Most existing works on robustness in text or code tasks have focused on classification, while robustness in generation tasks is an uncharted area and to date there is no comprehensive benchmark for robustness in code generation. In this paper, we propose ReCode, a comprehensive robustness evaluation benchmark for code generation models. We customize over 30 transformations specifically for code on docstrings, function and variable names, code syntax, and code format. They are carefully designed to be natural in real-life coding practice, preserve the original semantic meaning, and thus provide multifaceted assessments of a model's robustness performance. With human annotators, we verified that over 90% of the perturbed prompts do not alter the semantic meaning of the original prompt. In addition, we define robustness metrics for code generation models considering the worst-case behavior under each type of perturbation, taking advantage of the fact that executing the generated code can serve as objective evaluation. We demonstrate ReCode on SOTA models using HumanEval, MBPP, as well as function completion tasks derived from them. Interesting observations include: better robustness for CodeGen over InCoder and GPT-J; models are most sensitive to syntax perturbations; more challenging robustness evaluation on MBPP over HumanEval.

Recent advancements in diffusion models (DMs) have been propelled by alignment methods that post-train models to better conform to human preferences. However, these approaches typically require computation-intensive training of a base model and a reward model, which not only incurs substantial computational overhead but may also compromise model accuracy and training efficiency. To address these limitations, we propose Inversion-DPO, a novel alignment framework that circumvents reward modeling by reformulating Direct Preference Optimization (DPO) with DDIM inversion for DMs. Our method conducts intractable posterior sampling in Diffusion-DPO with the deterministic inversion from winning and losing samples to noise and thus derive a new post-training paradigm. This paradigm eliminates the need for auxiliary reward models or inaccurate appromixation, significantly enhancing both precision and efficiency of training. We apply Inversion-DPO to a basic task of text-to-image generation and a challenging task of compositional image generation. Extensive experiments show substantial performance improvements achieved by Inversion-DPO compared to existing post-training methods and highlight the ability of the trained generative models to generate high-fidelity compositionally coherent images. For the post-training of compostitional image geneation, we curate a paired dataset consisting of 11,140 images with complex structural annotations and comprehensive scores, designed to enhance the compositional capabilities of generative models. Inversion-DPO explores a new avenue for efficient, high-precision alignment in diffusion models, advancing their applicability to complex realistic generation tasks. Our code is available at https://github.com/MIGHTYEZ/Inversion-DPO

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

Enhancing the instruction-following ability of Large Language Models (LLMs) primarily demands substantial instruction-tuning datasets. However, the sheer volume of these imposes a considerable computational burden and annotation cost. To investigate a label-efficient instruction tuning method that allows the model itself to actively sample subsets that are equally or even more effective, we introduce a self-evolving mechanism DiverseEvol. In this process, a model iteratively augments its training subset to refine its own performance, without requiring any intervention from humans or more advanced LLMs. The key to our data sampling technique lies in the enhancement of diversity in the chosen subsets, as the model selects new data points most distinct from any existing ones according to its current embedding space. Extensive experiments across three datasets and benchmarks demonstrate the effectiveness of DiverseEvol. Our models, trained on less than 8% of the original dataset, maintain or improve performance compared with finetuning on full data. We also provide empirical evidence to analyze the importance of diversity in instruction data and the iterative scheme as opposed to one-time sampling. Our code is publicly available at https://github.com/OFA-Sys/DiverseEvol.git.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

In this paper, we present a novel approach for improving the quality and consistency of generated outputs from large-scale pre-trained language models (LLMs). Self-consistency has emerged as an effective approach for prompts with fixed answers, selecting the answer with the highest number of votes. In this paper, we introduce a generalized framework for self-consistency that extends its applicability beyond problems that have fixed-answer answers. Through extensive simulations, we demonstrate that our approach consistently recovers the optimal or near-optimal generation from a set of candidates. We also propose lightweight parameter-free similarity functions that show significant and consistent improvements across code generation, autoformalization, and summarization tasks, even without access to token log probabilities. Our method incurs minimal computational overhead, requiring no auxiliary reranker models or modifications to the existing model.

Aligning large language models (LLMs) with human intent is critical for enhancing their performance across a variety of tasks. Standard alignment techniques, such as Direct Preference Optimization (DPO), often rely on the binary Bradley-Terry (BT) model, which can struggle to capture the complexities of human preferences -- particularly in the presence of noisy or inconsistent labels and frequent ties. To address these limitations, we introduce the Tie-rank Oriented Bradley-Terry model (TOBT), an extension of the BT model that explicitly incorporates ties, enabling more nuanced preference representation. Building on this, we propose Tie-rank Oriented Direct Preference Optimization (TODO), a novel alignment algorithm that leverages TOBT's ternary ranking system to improve preference alignment. In evaluations on Mistral-7B and Llama 3-8B models, TODO consistently outperforms DPO in modeling preferences across both in-distribution and out-of-distribution datasets. Additional assessments using MT Bench and benchmarks such as Piqa, ARC-c, and MMLU further demonstrate TODO's superior alignment performance. Notably, TODO also shows strong results in binary preference alignment, highlighting its versatility and potential for broader integration into LLM alignment. The implementation details can be found in https://github.com/XXares/TODO.

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

Self-consistency (SC), leveraging multiple samples from LLMs, shows significant gains on various reasoning tasks but struggles with free-form generation due to the difficulty of aggregating answers. Its variants, UCS and USC, rely on sample selection or voting mechanisms to improve output quality. These methods, however, face limitations due to their inability to fully utilize the nuanced consensus knowledge present within multiple candidate samples, often resulting in suboptimal outputs. We propose Fine-Grained Self-Consistency (FSC) to addresses these limitations by extracting and integrating segment-level commonalities from candidate samples, enhancing the performance of LLMs both in open-ended and reasoning tasks. Based on this, we present two additional strategies: candidate filtering, which enhances overall quality by identifying highly similar candidate sets, and merging, which reduces input token requirements by combining similar samples. The effectiveness of FSC is demonstrated through extensive experiments on various tasks, including summarization, code generation, and mathematical reasoning, using GPT-3.5-turbo and GPT-4. The results indicate significant improvements over baseline methods, showcasing the potential of FSC to optimize output quality by effectively synthesizing fine-grained consensus knowledge from multiple samples.

In-context learning (ICL) -- the capacity of a model to infer and apply abstract patterns from examples provided within its input -- has been extensively studied in large language models trained for next-token prediction on human text. In fact, prior work often attributes this emergent behavior to distinctive statistical properties in human language. This raises a fundamental question: can ICL arise organically in other sequence domains purely through large-scale predictive training? To explore this, we turn to genomic sequences, an alternative symbolic domain rich in statistical structure. Specifically, we study the Evo2 genomic model, trained predominantly on next-nucleotide (A/T/C/G) prediction, at a scale comparable to mid-sized LLMs. We develop a controlled experimental framework comprising symbolic reasoning tasks instantiated in both linguistic and genomic forms, enabling direct comparison of ICL across genomic and linguistic models. Our results show that genomic models, like their linguistic counterparts, exhibit log-linear gains in pattern induction as the number of in-context demonstrations increases. To the best of our knowledge, this is the first evidence of organically emergent ICL in genomic sequences, supporting the hypothesis that ICL arises as a consequence of large-scale predictive modeling over rich data. These findings extend emergent meta-learning beyond language, pointing toward a unified, modality-agnostic view of in-context learning.

Direct alignment methods are increasingly used for aligning large language models (LLMs) with human preferences. However, these methods suffer from the issues of verbosity and likelihood displacement, which can be driven by the noisy preference pairs that induce similar likelihood for preferred and dispreferred responses. The contributions of this paper are two-fold. First, we propose a new preference alignment method based on comparison oracles and provide the convergence guarantee for its basic scheme. Second, we improve our method using some heuristics and conduct the experiments to demonstrate the flexibility and compatibility of practical scheme in improving the performance of LLMs using noisy preference pairs. Evaluations are conducted across multiple base and instruction-tuned models (Mistral-7B, Llama-3-8B and Gemma-2-9B) with benchmarks (AlpacaEval 2, MT-Bench and Arena-Hard). Experimental results show the effectiveness of our method as an alternative to addressing the limitations of existing direct alignment methods. A highlight of our work is that we evidence the importance of designing specialized methods for preference pairs with distinct likelihood margin, which complements the recent findings in Razin-2025-Unintentional.

Not a day goes by without hearing about the impressive feats of large language models (LLMs), and equally, not a day passes without hearing about their challenges. LLMs are notoriously vulnerable to biases in their dataset, leading to issues such as toxicity. While domain-adaptive training has been employed to mitigate these issues, these techniques often address all model parameters indiscriminately during the repair process, resulting in poor repair quality and reduced model versatility. In this paper, we introduce a novel dynamic slicing-based intent-aware LLM repair strategy, IRepair. This approach selectively targets the most error-prone sections of the model for repair. Specifically, we propose dynamically slicing the model's most sensitive layers that require immediate attention, concentrating repair efforts on those areas. This method enables more effective repairs with potentially less impact on the model's overall performance by altering a smaller portion of the model. We evaluated our technique on three models from the GPT2 and GPT-Neo families, with parameters ranging from 800M to 1.6B, in a toxicity mitigation setup. Our results show that IRepair repairs errors 43.6% more effectively while causing 46% less disruption to general performance compared to the closest baseline, direct preference optimization. Our empirical analysis also reveals that errors are more concentrated in a smaller section of the model, with the top 20% of layers exhibiting 773% more error density than the remaining 80\%. This highlights the need for selective repair. Additionally, we demonstrate that a dynamic selection approach is essential for addressing errors dispersed throughout the model, ensuring a robust and efficient repair.

This paper presents Okapi, a new dataset for Natural Language to executable web Application Programming Interfaces (NL2API). This dataset is in English and contains 22,508 questions and 9,019 unique API calls, covering three domains. We define new compositional generalization tasks for NL2API which explore the models' ability to extrapolate from simple API calls in the training set to new and more complex API calls in the inference phase. Also, the models are required to generate API calls that execute correctly as opposed to the existing approaches which evaluate queries with placeholder values. Our dataset is different than most of the existing compositional semantic parsing datasets because it is a non-synthetic dataset studying the compositional generalization in a low-resource setting. Okapi is a step towards creating realistic datasets and benchmarks for studying compositional generalization alongside the existing datasets and tasks. We report the generalization capabilities of sequence-to-sequence baseline models trained on a variety of the SCAN and Okapi datasets tasks. The best model achieves 15\% exact match accuracy when generalizing from simple API calls to more complex API calls. This highlights some challenges for future research. Okapi dataset and tasks are publicly available at https://aka.ms/nl2api/data.

Learning alignment between language and vision is a fundamental challenge, especially as multimodal data becomes increasingly detailed and complex. Existing methods often rely on collecting human or AI preferences, which can be costly and time-intensive. We propose an alternative approach that leverages cycle consistency as a supervisory signal. Given an image and generated text, we map the text back to image space using a text-to-image model and compute the similarity between the original image and its reconstruction. Analogously, for text-to-image generation, we measure the textual similarity between an input caption and its reconstruction through the cycle. We use the cycle consistency score to rank candidates and construct a preference dataset of 866K comparison pairs. The reward model trained on our dataset outperforms state-of-the-art alignment metrics on detailed captioning, with superior inference-time scalability when used as a verifier for Best-of-N sampling. Furthermore, performing DPO and Diffusion DPO using our dataset enhances performance across a wide range of vision-language tasks and text-to-image generation. Our dataset, model, and code are at https://cyclereward.github.io

Despite recent advances in diffusion models, achieving reliable image generation and editing remains challenging due to the inherent diversity induced by stochastic noise in the sampling process. Instruction-guided image editing with diffusion models offers user-friendly capabilities, yet editing failures, such as background distortion, frequently occur. Users often resort to trial and error, adjusting seeds or prompts to achieve satisfactory results, which is inefficient. While seed selection methods exist for Text-to-Image (T2I) generation, they depend on external verifiers, limiting applicability, and evaluating multiple seeds increases computational complexity. To address this, we first establish a multiple-seed-based image editing baseline using background consistency scores, achieving Best-of-N performance without supervision. Building on this, we introduce ELECT (Early-timestep Latent Evaluation for Candidate Selection), a zero-shot framework that selects reliable seeds by estimating background mismatches at early diffusion timesteps, identifying the seed that retains the background while modifying only the foreground. ELECT ranks seed candidates by a background inconsistency score, filtering unsuitable samples early based on background consistency while preserving editability. Beyond standalone seed selection, ELECT integrates into instruction-guided editing pipelines and extends to Multimodal Large-Language Models (MLLMs) for joint seed and prompt selection, further improving results when seed selection alone is insufficient. Experiments show that ELECT reduces computational costs (by 41 percent on average and up to 61 percent) while improving background consistency and instruction adherence, achieving around 40 percent success rates in previously failed cases - without any external supervision or training.

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.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Self-supervised learning on large-scale multi-modal datasets allows learning semantically meaningful embeddings in a joint multi-modal representation space without relying on human annotations. These joint embeddings enable zero-shot cross-modal tasks like retrieval and classification. However, these methods often struggle to generalize well on out-of-domain data as they ignore the semantic structure present in modality-specific embeddings. In this context, we propose a novel Semantic-Structure-Preserving Consistency approach to improve generalizability by preserving the modality-specific relationships in the joint embedding space. To capture modality-specific semantic relationships between samples, we propose to learn multiple anchors and represent the multifaceted relationship between samples with respect to their relationship with these anchors. To assign multiple anchors to each sample, we propose a novel Multi-Assignment Sinkhorn-Knopp algorithm. Our experimentation demonstrates that our proposed approach learns semantically meaningful anchors in a self-supervised manner. Furthermore, our evaluation on MSR-VTT and YouCook2 datasets demonstrates that our proposed multi-anchor assignment based solution achieves state-of-the-art performance and generalizes to both inand out-of-domain datasets. Code: https://github.com/Swetha5/Multi_Sinkhorn_Knopp

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Most research about natural language generation (NLG) relies on evaluation benchmarks with limited references for a sample, which may result in poor correlations with human judgements. The underlying reason is that one semantic meaning can actually be expressed in different forms, and the evaluation with a single or few references may not accurately reflect the quality of the model's hypotheses. To address this issue, this paper presents a simple and effective method, named Div-Ref, to enhance existing evaluation benchmarks by enriching the number of references. We leverage large language models (LLMs) to diversify the expression of a single reference into multiple high-quality ones to cover the semantic space of the reference sentence as much as possible. We conduct comprehensive experiments to empirically demonstrate that diversifying the expression of reference can significantly enhance the correlation between automatic evaluation and human evaluation. This idea is compatible with recent LLM-based evaluation which can similarly derive advantages from incorporating multiple references. We strongly encourage future generation benchmarks to include more references, even if they are generated by LLMs, which is once for all. We release all the code and data at https://github.com/RUCAIBox/Div-Ref to facilitate research.