BIOME-Bench: A Benchmark for Biomolecular Interaction Inference and Multi-Omics Pathway Mechanism Elucidation from Scientific Literature

Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional redundancy, and limited sensitivity to molecular states and interventions. Although recent work has explored using large language models (LLMs) to improve PE-based interpretation, the lack of a standardized benchmark for end-to-end multi-omics pathway mechanism elucidation has largely confined evaluation to small, manually curated datasets or ad hoc case studies, hindering reproducible progress. To address this issue, we introduce BIOME-Bench, constructed via a rigorous four-stage workflow, to evaluate two core capabilities of LLMs in multi-omics analysis: Biomolecular Interaction Inference and end-to-end Multi-Omics Pathway Mechanism Elucidation. We develop evaluation protocols for both tasks and conduct comprehensive experiments across multiple strong contemporary models. Experimental results demonstrate that existing models still exhibit substantial deficiencies in multi-omics analysis, struggling to reliably distinguish fine-grained biomolecular relation types and to generate faithful, robust pathway-level mechanistic explanations.

BianCang: A Traditional Chinese Medicine Large Language Model

The rise of large language models (LLMs) has driven significant progress in medical applications, including traditional Chinese medicine (TCM). However, current medical LLMs struggle with TCM diagnosis and syndrome differentiation due to substantial differences between TCM and modern medical theory, and the scarcity of specialized, high-quality corpora. This paper addresses these challenges by proposing BianCang, a TCM-specific LLM, using a two-stage training process that first injects domain-specific knowledge and then aligns it through targeted stimulation. To enhance diagnostic and differentiation capabilities, we constructed pre-training corpora, instruction-aligned datasets based on real hospital records, and the ChP-TCM dataset derived from the Pharmacopoeia of the People's Republic of China. We compiled extensive TCM and medical corpora for continuous pre-training and supervised fine-tuning, building a comprehensive dataset to refine the model's understanding of TCM. Evaluations across 11 test sets involving 29 models and 4 tasks demonstrate the effectiveness of BianCang, offering valuable insights for future research. Code, datasets, and models are available at https://github.com/QLU-NLP/BianCang.

Medical Question Summarization with Entity-driven Contrastive Learning

By summarizing longer consumer health questions into shorter and essential ones, medical question answering (MQA) systems can more accurately understand consumer intentions and retrieve suitable answers. However, medical question summarization is very challenging due to obvious distinctions in health trouble descriptions from patients and doctors. Although existing works have attempted to utilize Seq2Seq, reinforcement learning, or contrastive learning to solve the problem, two challenges remain: how to correctly capture question focus to model its semantic intention, and how to obtain reliable datasets to fairly evaluate performance. To address these challenges, this paper proposes a novel medical question summarization framework using entity-driven contrastive learning (ECL). ECL employs medical entities in frequently asked questions (FAQs) as focuses and devises an effective mechanism to generate hard negative samples. This approach forces models to pay attention to the crucial focus information and generate more ideal question summarization. Additionally, we find that some MQA datasets suffer from serious data leakage problems, such as the iCliniq dataset's 33% duplicate rate. To evaluate the related methods fairly, this paper carefully checks leaked samples to reorganize more reasonable datasets. Extensive experiments demonstrate that our ECL method outperforms state-of-the-art methods by accurately capturing question focus and generating medical question summaries. The code and datasets are available at https://github.com/yrbobo/MQS-ECL.