Hanmeng Zhong

Hanmeng Zhong, Linqing Chen, Wentao Wu et al.

Recent development in Retrieval-Augmented Large Language Models (LLMs) have shown great promise in biomedical applications. How ever, a critical gap persists in reliably evaluating their curation ability the process by which models select and integrate relevant references while filtering out noise. To address this, we introduce the benchmark for Curation of Retrieval-Augmented LLMs in Biomedicine (CRAB), the first multilingual benchmark tailored for evaluating the biomedical curation of retrieval-augmented LLMs, available in English, French, German and Chinese. By incorporating a novel citation-based evaluation metric, CRAB quantifies the curation performance of retrieval-augmented LLMs in biomedicine. Experimental results reveal significant discrepancies in the curation performance of mainstream LLMs, underscoring the urgent need to improve it in the domain of biomedicine. Our dataset is available at https://huggingface.co/datasets/zhm0/CRAB.

Linqing Chen, Weilei Wang, Yubin Xia et al.

In this paper, we propose a novel system that integrates state-of-the-art, domain-specific large language models with advanced information retrieval techniques to deliver comprehensive and context-aware responses. Our approach facilitates seamless interaction among diverse components, enabling cross-validation of outputs to produce accurate, high-quality responses enriched with relevant data, images, tables, and other modalities. We demonstrate the system's capability to enhance response precision by leveraging a robust question-answering model, significantly improving the quality of dialogue generation. The system provides an accessible platform for real-time, high-fidelity interactions, allowing users to benefit from efficient human-computer interaction, precise retrieval, and simultaneous access to a wide range of literature and data. This dramatically improves the research efficiency of professionals in the biomedical and pharmaceutical domains and facilitates faster, more informed decision-making throughout the R\&D process. Furthermore, the system proposed in this paper is available at https://synapse-chat.patsnap.com.

Linqing Chen, Hanmeng Zhong, Wentao Wu et al.

Large language model (LLM) training faces a critical bottleneck: the scarcity of high-quality, reasoning-intensive question-answer pairs, especially from sparse, domain-specific sources like PubMed papers or legal documents. Existing methods rely on surface patterns, fundamentally failing to generate controllable, complex multi-hop reasoning questions that test genuine understanding-essential for advancing LLM training paradigms. We present \textbf{Semantic Bridge}, the first universal framework for controllably generating sophisticated multi-hop reasoning questions from arbitrary sources. Our breakthrough innovation is \textit{semantic graph weaving}-three complementary bridging mechanisms (entity bridging for role-varying shared entities, predicate chain bridging for temporal/causal/logical sequences, and causal bridging for explicit reasoning chains)-that systematically construct complex pathways across documents, with fine-grained control over complexity and types via AMR-driven analysis. Our multi-modal AMR pipeline achieves up to 9.5% better round-trip quality, enabling production-ready controllable QA generation. Extensive evaluation demonstrates performance across both general-purpose datasets (Wikipedia) and specialized domains (biomedicine) It yields consistent 18.3%-25.4% gains over baselines across four languages (English, Chinese, French, German). Question pairs generated from 200 sources outperform 600 native human annotation examples with 67% fewer materials. Human evaluation shows 23.4% higher complexity, 18.7% better answerability, and 31.2% improved pattern coverage. Semantic Bridge establishes a new paradigm for LLM training data synthesis, enabling controllable generation of targeted reasoning questions from sparse sources. We will release our core code and semantic bridge model.

Wentao Wu, Linqing Chen, Hanmeng Zhong et al.

BalancedBio is a theoretically grounded framework for parameter-efficient biomedical reasoning, addressing multi-capability integration in domain-specific AI alignment. It establishes the Biomedical Multi-Capability Convergence Theorem, proving orthogonal gradient spaces are essential to prevent capability interference for safe deployment. Key innovations include: (1) Medical Knowledge Grounded Synthetic Generation (MKGSG), extending Source2Synth with clinical workflow constraints and medical ontology validation for factual accuracy and safety; and (2) Capability Aware Group Relative Policy Optimization, deriving optimal hybrid reward weighting to maintain orthogonality in RL, using a reward model with rule-based and model-based scores adapted to biomedical tasks. Mathematical analysis proves Pareto-optimal convergence, preserving performance across capabilities. It achieves state-of-the-art results in its parameter class: domain expertise (80.95% BIOMED-MMLU, +15.32% over baseline), reasoning (61.94%, +7.75%), instruction following (67.95%, +6.44%), and integration (86.7%, +18.5%). Theoretical safety guarantees include bounds on capability preservation and clinical accuracy. Real-world deployment yields 78% cost reduction, 23% improved diagnostic accuracy, and 89% clinician acceptance. This work provides a principled methodology for biomedical AI alignment, enabling efficient reasoning with essential safety and reliability, with the 0.5B model version to be released.

Linqing Chen, Weilei Wang, Wentao Wu et al.

Hierarchical Extreme Multi-Label Classification poses greater difficulties compared to traditional multi-label classification because of the intricate hierarchical connections of labels within a domain-specific taxonomy and the substantial number of labels. Some of the prior research endeavors centered on classifying text through several ancillary stages such as the cluster algorithm and multiphase classification. Others made attempts to leverage the assistance of generative methods yet were unable to properly control the output of the generative model. We redefine the task from hierarchical multi-Label classification to Hierarchical Multi-Label Generation (HMG) and employ a generative framework with Probabilistic Level Constraints (PLC) to generate hierarchical labels within a specific taxonomy that have complex hierarchical relationships. The approach we proposed in this paper enables the framework to generate all relevant labels across levels for each document without relying on preliminary operations like clustering. Meanwhile, it can control the model output precisely in terms of count, length, and level aspects. Experiments demonstrate that our approach not only achieves a new SOTA performance in the HMG task, but also has a much better performance in constrained the output of model than previous research work.