Xingyuan Wei

Congying Liu, Xingyuan Wei, Peipei Liu et al.

Biomedical queries often rely on a deep understanding of specialized knowledge such as gene regulatory mechanisms and pathological processes of diseases. They require detailed analysis of complex physiological processes and effective integration of information from multiple data sources to support accurate retrieval and reasoning. Although large language models (LLMs) perform well in general reasoning tasks, their generated biomedical content often lacks scientific rigor due to the inability to access authoritative biomedical databases and frequently fabricates protein functions, interactions, and structural details that deviate from authentic information. Therefore, we present BioMedSearch, a multi-source biomedical information retrieval framework based on LLMs. The method integrates literature retrieval, protein database and web search access to support accurate and efficient handling of complex biomedical queries. Through sub-queries decomposition, keywords extraction, task graph construction, and multi-source information filtering, BioMedSearch generates high-quality question-answering results. To evaluate the accuracy of question answering, we constructed a multi-level dataset, BioMedMCQs, consisting of 3,000 questions. The dataset covers three levels of reasoning: mechanistic identification, non-adjacent semantic integration, and temporal causal reasoning, and is used to assess the performance of BioMedSearch and other methods on complex QA tasks. Experimental results demonstrate that BioMedSearch consistently improves accuracy over all baseline models across all levels. Specifically, at Level 1, the average accuracy increases from 59.1% to 91.9%; at Level 2, it rises from 47.0% to 81.0%; and at the most challenging Level 3, the average accuracy improves from 36.3% to 73.4%. The code and BioMedMCQs are available at: https://github.com/CyL-ucas/BioMed_Search

Congying Liu, Taihao Li, Ming Huang et al.

Protein analysis tasks arising in healthcare settings often require accurate reasoning under protein sequence constraints, involving tasks such as functional interpretation of disease-related variants, protein-level analysis for clinical research, and similar scenarios. To address such tasks, search agents are introduced to search protein-related information, providing support for disease-related variant analysis and protein function reasoning in protein-centric inference. However, such search agents are mostly limited to single-round, text-only modality search, which prevents the protein sequence modality from being incorporated as a multimodal input into the search decision-making process. Meanwhile, their reliance on reinforcement learning (RL) supervision that focuses solely on the final answer results in a lack of search process constraints, making deviations in keyword selection and reasoning directions difficult to identify and correct in a timely manner. To address these limitations, we propose ProtRLSearch, a multi-round protein search agent trained with multi-dimensional reward based RL, which jointly leverages protein sequence and text as multimodal inputs during real-time search to produce high quality reports. To evaluate the ability of models to integrate protein sequence information and text-based multimodal inputs in realistic protein query settings, we construct ProtMCQs, a benchmark of 3,000 multiple choice questions (MCQs) organized into three difficulty levels. The benchmark evaluates protein query tasks that range from sequence constrained reasoning about protein function and phenotype changes to comprehensive protein reasoning that integrates multi-dimensional sequence features with signal pathways and regulatory networks.

Congying Liu, Gaosheng Wang, Peipei Liu et al.

Few-shot named entity recognition can identify new types of named entities based on a few labeled examples. Previous methods employing token-level or span-level metric learning suffer from the computational burden and a large number of negative sample spans. In this paper, we propose the Hybrid Multi-stage Decoding for Few-shot NER with Entity-aware Contrastive Learning (MsFNER), which splits the general NER into two stages: entity-span detection and entity classification. There are 3 processes for introducing MsFNER: training, finetuning, and inference. In the training process, we train and get the best entity-span detection model and the entity classification model separately on the source domain using meta-learning, where we create a contrastive learning module to enhance entity representations for entity classification. During finetuning, we finetune the both models on the support dataset of target domain. In the inference process, for the unlabeled data, we first detect the entity-spans, then the entity-spans are jointly determined by the entity classification model and the KNN. We conduct experiments on the open FewNERD dataset and the results demonstrate the advance of MsFNER.