Logic-Regularized Verifier Elicits Reasoning from LLMs

Verifiers are crucial components for enhancing modern LLMs' reasoning capability. Typicalverifiers require resource-intensive superviseddataset construction, which is costly and faceslimitations in data diversity. In this paper, wepropose LOVER, an unsupervised verifier regularized by logical rules. LOVER treats theverifier as a binary latent variable, utilizinginternal activations and enforcing three logical constraints on multiple reasoning paths:negation consistency, intra-group consistency,and inter-group consistency (grouped by thefinal answer). By incorporating logical rulesas priors, LOVER can leverage unlabeled examples and is directly compatible with any offthe-shelf LLMs. Experiments on 10 datasetsdemonstrate that LOVER significantly outperforms unsupervised baselines, achieving performance comparable to the supervised verifier(reaching its 95% level on average). The sourcecode is publicly available at https://github.com/wangxinyufighting/llm-lover.

Stabilizing LLM Supervised Fine-Tuning via Explicit Distributional Control

Post-training large language models (LLMs) often suffers from catastrophic forgetting, where improvements on a target objective degrade previously acquired capabilities. Recent evidence suggests that this phenomenon is primarily driven by excessive distributional drift during optimization. Motivated by this perspective, we propose Anchored Learning, a simple framework that explicitly controls distributional updates during offline fine-tuning via a dynamically evolving moving anchor. Instead of matching a fixed reference distribution, the anchor interpolates between the current model and a frozen reference to construct an intermediate target that the model distills toward, transforming global fine-tuning into a sequence of local trust-region updates in distribution space. Theoretically, we prove this anchor-based update admits a linear KL-divergence upper bound per iteration, ensuring a stable transition between model distributions. Extensive experiments on iGSM, MedCalc, and IFEval show that Anchored Learning consistently lies on the Pareto frontier of gain-stability trade-offs, achieving near-optimal performance improvements while substantially reducing degradation compared to strong baselines. For example, while standard SFT suffers from over 53% performance degradation on iGSM and MedCalc, Anchored Learning slashes this drop to under 5% while maintaining near-optimal gains (e.g., 75.2% on iGSM).

On Support Samples of Next Word Prediction

Language models excel in various tasks by making complex decisions, yet understanding the rationale behind these decisions remains a challenge. This paper investigates \emph{data-centric interpretability} in language models, focusing on the next-word prediction task. Using representer theorem, we identify two types of \emph{support samples}-those that either promote or deter specific predictions. Our findings reveal that being a support sample is an intrinsic property, predictable even before training begins. Additionally, while non-support samples are less influential in direct predictions, they play a critical role in preventing overfitting and shaping generalization and representation learning. Notably, the importance of non-support samples increases in deeper layers, suggesting their significant role in intermediate representation formation. These insights shed light on the interplay between data and model decisions, offering a new dimension to understanding language model behavior and interpretability.

PDFBench: A Benchmark for De novo Protein Design from Function

In recent years, while natural language processing and multimodal learning have seen rapid advancements, the field of de novo protein design has also experienced significant growth. However, most current methods rely on proprietary datasets and evaluation rubrics, making fair comparisons between different approaches challenging. Moreover, these methods often employ evaluation metrics that capture only a subset of the desired properties of designed proteins, lacking a comprehensive assessment framework. To address these, we introduce PDFBench, the first comprehensive benchmark for evaluating de novo protein design from function. PDFBench supports two tasks: description-guided design and keyword-guided design. To ensure fair and multifaceted evaluation, we compile 22 metrics covering sequence plausibility, structural fidelity, and language-protein alignment, along with measures of novelty and diversity. We evaluate five state-of-the-art baselines, revealing their respective strengths and weaknesses across tasks. Finally, we analyze inter-metric correlations, exploring the relationships between four categories of metrics, and offering guidelines for metric selection. PDFBench establishes a unified framework to drive future advances in function-driven de novo protein design.

Protein Design with Dynamic Protein Vocabulary

Protein design is a fundamental challenge in biotechnology, aiming to design novel sequences with specific functions within the vast space of possible proteins. Recent advances in deep generative models have enabled function-based protein design from textual descriptions, yet struggle with structural plausibility. Inspired by classical protein design methods that leverage natural protein structures, we explore whether incorporating fragments from natural proteins can enhance foldability in generative models. Our empirical results show that even random incorporation of fragments improves foldability. Building on this insight, we introduce ProDVa, a novel protein design approach that integrates a text encoder for functional descriptions, a protein language model for designing proteins, and a fragment encoder to dynamically retrieve protein fragments based on textual functional descriptions. Experimental results demonstrate that our approach effectively designs protein sequences that are both functionally aligned and structurally plausible. Compared to state-of-the-art models, ProDVa achieves comparable function alignment using less than 0.04% of the training data, while designing significantly more well-folded proteins, with the proportion of proteins having pLDDT above 70 increasing by 7.38% and those with PAE below 10 increasing by 9.6%.

The Role of Visual Modality in Multimodal Mathematical Reasoning: Challenges and Insights

Recent research has increasingly focused on multimodal mathematical reasoning, particularly emphasizing the creation of relevant datasets and benchmarks. Despite this, the role of visual information in reasoning has been underexplored. Our findings show that existing multimodal mathematical models minimally leverage visual information, and model performance remains largely unaffected by changes to or removal of images in the dataset. We attribute this to the dominance of textual information and answer options that inadvertently guide the model to correct answers. To improve evaluation methods, we introduce the HC-M3D dataset, specifically designed to require image reliance for problem-solving and to challenge models with similar, yet distinct, images that change the correct answer. In testing leading models, their failure to detect these subtle visual differences suggests limitations in current visual perception capabilities. Additionally, we observe that the common approach of improving general VQA capabilities by combining various types of image encoders does not contribute to math reasoning performance. This finding also presents a challenge to enhancing visual reliance during math reasoning. Our benchmark and code would be available at \href{https://github.com/Yufang-Liu/visual_modality_role}{https://github.com/Yufang-Liu/visual\_modality\_role}.

Towards Economical Inference: Enabling DeepSeek's Multi-Head Latent Attention in Any Transformer-based LLMs

Multi-head Latent Attention (MLA) is an innovative architecture proposed by DeepSeek, designed to ensure efficient and economical inference by significantly compressing the Key-Value (KV) cache into a latent vector. Compared to MLA, standard LLMs employing Multi-Head Attention (MHA) and its variants such as Grouped-Query Attention (GQA) exhibit significant cost disadvantages. Enabling well-trained LLMs (e.g., Llama) to rapidly adapt to MLA without pre-training from scratch is both meaningful and challenging. This paper proposes the first data-efficient fine-tuning method for transitioning from MHA to MLA (MHA2MLA), which includes two key components: for partial-RoPE, we remove RoPE from dimensions of queries and keys that contribute less to the attention scores, for low-rank approximation, we introduce joint SVD approximations based on the pre-trained parameters of keys and values. These carefully designed strategies enable MHA2MLA to recover performance using only a small fraction (0.3% to 0.6%) of the data, significantly reducing inference costs while seamlessly integrating with compression techniques such as KV cache quantization. For example, the KV cache size of Llama2-7B is reduced by 92.19%, with only a 0.5% drop in LongBench performance.

EvoLlama: Enhancing LLMs' Understanding of Proteins via Multimodal Structure and Sequence Representations

Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from the universe of natural protein sequences. Furthermore, structure-based encoders like ProteinMPNN learn the structural information of proteins through Graph Neural Networks. However, whether the incorporation of protein encoders can enhance the protein understanding of LLMs has not been explored. To bridge this gap, we propose EvoLlama, a multimodal framework that connects a structure-based encoder, a sequence-based protein encoder and an LLM for protein understanding. EvoLlama consists of a ProteinMPNN structure encoder, an ESM-2 protein sequence encoder, a multimodal projector to align protein and text representations and a Llama-3 text decoder. To train EvoLlama, we fine-tune it on protein-oriented instructions and protein property prediction datasets verbalized via natural language instruction templates. Our experiments show that EvoLlama's protein understanding capabilities have been significantly enhanced, outperforming other fine-tuned protein-oriented LLMs in zero-shot settings by an average of 1%-8% and surpassing the state-of-the-art baseline with supervised fine-tuning by an average of 6%. On protein property prediction datasets, our approach achieves promising results that are competitive with state-of-the-art task-specific baselines. We will release our code in a future version.

AntLM: Bridging Causal and Masked Language Models

Causal Language Modeling (CLM) and Masked Language Modeling (MLM) are two mainstream learning paradigms based on Transformer networks, specifically the Decoder-only and Encoder-only architectures. The strengths of each paradigm in downstream tasks have shown a mix of advantages and disadvantages. In the past BabyLM Challenge 2023, although the MLM paradigm achieved the best average performance, the CLM paradigm demonstrated significantly faster convergence rates. For the BabyLM Challenge 2024, we propose a novel language modeling paradigm named $\textbf{AntLM}$, which integrates both CLM and MLM to leverage the advantages of these two classic paradigms. We chose the strict-small track and conducted experiments on two foundation models: BabyLlama, representing CLM, and LTG-BERT, representing MLM. During the training process for specific foundation models, we alternate between applying CLM or MLM training objectives and causal or bidirectional attention masks. Experimental results show that combining the two pretraining objectives leverages their strengths, enhancing overall training performance. Under the same epochs, $AntLM_{BabyLlama}$ improves Macro-average by 1%, and $AntLM_{LTG-BERT}$ achieves a 2.2% increase over the baselines.

Generation with Dynamic Vocabulary

We introduce a new dynamic vocabulary for language models. It can involve arbitrary text spans during generation. These text spans act as basic generation bricks, akin to tokens in the traditional static vocabularies. We show that, the ability to generate multi-tokens atomically improve both generation quality and efficiency (compared to the standard language model, the MAUVE metric is increased by 25%, the latency is decreased by 20%). The dynamic vocabulary can be deployed in a plug-and-play way, thus is attractive for various downstream applications. For example, we demonstrate that dynamic vocabulary can be applied to different domains in a training-free manner. It also helps to generate reliable citations in question answering tasks (substantially enhancing citation results without compromising answer accuracy).