Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step reasoning and lack transparent, biologically meaningful explanations. BioReason addresses this by tightly integrating a DNA foundation model with a large language model (LLM), enabling the LLM to directly interpret and reason over genomic information. Through supervised fine-tuning and reinforcement learning, BioReason learns to produce logical, biologically coherent deductions. It achieves major performance gains, boosting KEGG-based disease pathway prediction accuracy from 86% to 98% and improving variant effect prediction by an average of 15% over strong baselines. BioReason can reason over unseen biological entities and explain its decisions step by step, offering a transformative framework for interpretable, mechanistic AI in biology.

Inductive reasoning infers general rules from observed evidence, which is one of the most critical intelligence abilities. Previous works have succeeded in formal languages but suffer from onerous and error-prone conversions between a particular formal language and the working language. As large language models (LLMs) have emerged, direct reasoning with various kinds of languages, especially natural languages, without formal language involvement has become feasible. However, existing LLM-based inductive reasoning usually relies on LLM's intrinsic generation ability, which is prone to LLM's hallucination and lacks systematic guidance according to the nature of inductive reasoning. To this end, we propose HypoBootstrap, an integrated framework for inductive reasoning that generates and confirms hypotheses both in a bootstrapping manner. Regarding hypothesis generation, we propose a novel bootstrapping generation strategy, bootstrapping object hypotheses, relational hypotheses, and functional hypotheses successively, which assists LLM in observing the evidence from trivial patterns to non-trivial patterns. Regarding hypothesis confirmation, we utilize Glymour's theory of bootstrap confirmation, a hypothesis confirmation theory from the philosophy of science that can confirm a set of hypotheses. We use its principles to confirm the object hypotheses, relational hypotheses, and functional hypotheses. Empirical studies on four inductive reasoning scenarios of different natures, involving causal induction, concept learning, grammar learning, and abstract reasoning, demonstrate that HypoBootstrap significantly outperforms existing methods.

Large language models (LLMs) have enabled agents to perform complex reasoning and decision-making through free-form language interactions. However, in open-ended language action environments (e.g., negotiation or question-asking games), the action space can be formulated as a joint distribution over tokens, resulting in an extremely large and combinatorial action space. Sampling actions in such a space can lead to extreme reward sparsity, which brings large reward variance, hindering effective reinforcement learning (RL).

Probabilistic reasoning is a key aspect of both human and artificial intelligence that allows for handling uncertainty and ambiguity in decision-making. In this paper, we introduce a new numerical reasoning task under uncertainty for large language models, focusing on estimating the privacy risk of user-generated documents containing privacy-sensitive information. We propose BRANCH, a new LLM methodology that estimates the $k$-privacy value of a text--the size of the population matching the given information.

Despite recent advances in machine learning, many scientific discoveries in chemistry still rely on manually curated datasets extracted from the scientific literature. Automation of information extraction in specialized chemistry domains has the potential to scale up machine learning applications and improve the quality of predictions, enabling data-driven scientific discoveries at a faster pace. In this paper, we present ChemX, a collection of 10 benchmarking datasets across several domains of chemistry providing a reliable basis for evaluating and fine-tuning automated information extraction methods. The datasets encompassing various properties of small molecules and nanomaterials have been manually extracted from peer-reviewed publications and systematically validated by domain experts through a cross-verification procedure allowing for identification and correction of errors at sources. In order to demonstrate the utility of the resulting datasets, we evaluate the extraction performance of the state-of-the-art large language models (LLMs). Moreover, we design our own agentic approach to take full control of the document preprocessing before LLM-based information extraction.

Vision-based intrusion detection has multiple applications in practical scenarios, e.g., autonomous driving, intelligent monitoring, and security. Previous works mainly focus on improving the intrusion detection performance, without a comprehensive and in-depth understanding of the intrusion scene. To fill this gap, we explore a novel task called Multimodal Large Language Models based Intrusion Scene Understanding (MLLM-ISU) and report a comprehensive benchmark for the task.

State-of-the-art medical multi-modal LLMs (med-MLLMs), such as LLaVA-Med and BioMedGPT, primarily depend on scaling model size and data volume, with training driven largely by autoregressive objectives. However, we reveal that this approach can lead to weak vision-language alignment, making these models overly dependent on costly instruction-following data. To address this, we introduce ExGra-Med, a novel multi-graph alignment framework that jointly aligns images, instruction responses, and extended captions in the latent space, advancing semantic grounding and cross-modal coherence. To scale to large LLMs (e.g., LLaMa-7B), we develop an efficient end-to-end training scheme using black-box gradient estimation, enabling fast and scalable optimization. Empirically, ExGra-Med matches LLaVA-Med's performance using just 10\% of pre-training data, achieving a 20.13\% gain on VQA-RAD and approaching full-data performance. It also outperforms strong baselines like BioMedGPT and RadFM on visual chatbot and zero-shot classification tasks, demonstrating its promise for efficient, high-quality vision-language integration in medical AI.

Addressing the critical need for robust safety in Large Language Models (LLMs), particularly against adversarial attacks and in-distribution errors, we introduce Reinforcement Learning with Backtracking Feedback (RLBF). This framework advances upon prior methods, such as BSAFE, by primarily leveraging a Reinforcement Learning (RL) stage where models learn to dynamically correct their own generation errors. Through RL with critic feedback on the model's live outputs, LLMs are trained to identify and recover from their actual, emergent safety violations by emitting an efficient backtrack by x tokens signal, then continuing generation autoregressively. This RL process is crucial for instilling resilience against sophisticated adversarial strategies, including middle filling, Greedy Coordinate Gradient (GCG) attacks, and decoding parameter manipulations. To further support the acquisition of this backtracking capability, we also propose an enhanced Supervised Fine-Tuning (SFT) data generation strategy (BSAFE+). This method improves upon previous data creation techniques by injecting violations into coherent, originally safe text, providing more effective initial training for the backtracking mechanism. Comprehensive empirical evaluations demonstrate that RLBF significantly reduces attack success rates across diverse benchmarks and model scales, achieving superior safety outcomes while critically preserving foundational model utility.

Fine-tuning large language models (LLMs) using diverse datasets is crucial for enhancing their overall performance across various domains. In practical scenarios, existing methods based on modeling the mixture proportions of data composition often struggle with data whose domain labels are missing, imprecise or non-normalized, while methods based on data selection usually encounter difficulties in balancing multi-domain performance. To address these challenges, in this work, we investigate the role of data diversity in enhancing the overall abilities of LLMs by empirically constructing contrastive data pools and theoretically deriving explanations. Building upon the insights gained, we propose a new method that gives the LLM a dual identity: an output model to cognitively probe and select data based on diversity reward, as well as an input model to be tuned with the selected data. Extensive experiments show that the proposed method notably boosts performance across domain-undetermined data and a series of foundational downstream tasks when applied to various advanced LLMs. We release our code and hope this study can shed light on the understanding of data diversity and advance feedback-driven data-model co-design for LLMs.

Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies have explored the integration of MRL with LLMs and achieved promising results. However, the increasing availability of diverse LLMs and molecular structure encoders has significantly expanded the model space, presenting major challenges for benchmarking. Currently, there is no LLM framework that supports both flexible molecular input formats and dynamic architectural switching. To address these challenges, reduce redundant coding, and ensure fair model comparison, we propose ModuLM, a framework designed to support flexible LLM-based model construction and diverse molecular representations. ModuLM provides a rich suite of modular components, including 8 types of 2D molecular graph encoders, 11 types of 3D molecular conformation encoders, 7 types of interaction layers, and 7 mainstream LLM backbones. Owing to its highly flexible model assembly mechanism, ModuLM enables the dynamic construction of over 50,000 distinct model configurations. In addition, we provide comprehensive benchmark results to demonstrate the effectiveness of ModuLM in supporting LLM-based MRL tasks.