arXiv subjects

Zhaohan Meng

Publications and source records attributed to Zhaohan Meng.

4 recordsLinked to original sources

arXiv2026

SSE-Bio: A Structured Self-Evolving Agent with Agentic Retrieval Policy for Multi-Hop Biomedical Reasoning

Biomedical multi-hop question answering (QA) requires models to connect evidence across intermediate entities such as diseases, drugs, proteins, and phenotypes. Existing agents typically rely on static retrieval workflows or coarse-grained prompt rewriting, which can lead to instruction drift when reasoning procedures need to be updated. We propose SSE-Bio, a structured self-evolving agent with an agentic retrieval policy for multi-hop biomedical reasoning. Instead of globally rewriting agent instructions, SSE-Bio maintains a structured state, selectively retrieves knowledge triplets and prior templates through a trainable proxy policy, and improves its reasoning memory through fine-grained template editing. To optimise retrieval decisions, we introduce a proxy-training strategy based on group relative policy optimization, where the proxy is improved through decision-contrastive groups over alternative retrieval choices. Experiments on three biomedical multi-hop QA benchmarks show that SSE-Bio consistently outperforms existing baselines, achieving an improvement of 6.56 absolute points over the strongest self-evolving baseline on BioHopR.

cs.CL↗

arXiv2026

A Large-Scale Dataset and Benchmark: Do Protein-Ligand Models Learn Binding Sites or Just Binding Likelihood?

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary binding prediction and affinity regression. However, these evaluations provide limited evidence of whether models can localize binding sites or identify the non-covalent interactions underlying molecular recognition. To address this gap, we introduce InteractBind, a large-scale protein-ligand dataset comprising approximately 100k protein-ligand pairs, together with a benchmark for fine-grained evaluation. The core fine-grained task is that of binding-site localization, which uses protein-residue and ligand-atom interaction maps spanning six major types of non-covalent interactions to assess whether model-derived interaction maps localize binding sites. InteractBind further includes binding affinity and protein similarity-controlled splits to support realistic generalization assessment. Using InteractBind, we evaluate eight existing sequence-based and interaction-aware models, assessing binary binding prediction and binding-site localization. Results reveal limited binding-site localization despite strong binary binding prediction, with marked variation across non-covalent interaction types. Overall, InteractBind establishes a benchmark paradigm that encourages the development of more interpretable and physically grounded protein-ligand models.

cs.LG↗

arXiv2025

GraphMed-LT: Patient-Specific Graph Memory with Latent Clinical Thought Refinement for Multi-Turn Medical Conversations

Multi-turn medical question answering (QA) aims to model realistic clinical diagnosis, where a doctor gathers patient information across multiple turns of conversation. Existing multi-turn medical conversation systems have shown promising progress, but they often rely on accumulated conversation histories as memory, leaving clinical evidence fragmented across turns. We propose GraphMed-LT, a patient-specific graph memory approach with latent clinical thought refinement for multi-turn medical conversations. GraphMed-LT extracts patient-specific clinical triplets from patient responses, retrieves relevant knowledge triplets, and organises them into an incrementally updated graph memory. The graph memory is projected into graph-conditioned evidence tokens and refined inside a trainable doctor agent through hidden-state feedback, enabling the agent to update its internal clinical context before asking follow-up questions or producing the final answer. Experiments on three multi-turn medical QA benchmarks show that GraphMed-LT consistently outperforms existing multi-turn medical conversation baselines across multiple LLM backbones, achieving up to a 6.3 percentage-point absolute improvement over the strongest baseline. Further analyses show that GraphMed-LT asks more answerable follow-up questions and provides consistent gains across medical specialties.

cs.CL↗

arXiv2024

FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction

Predicting drug-target interaction (DTI) is critical in the drug discovery process. Despite remarkable advances in recent DTI models through the integration of representations from diverse drug and target encoders, such models often struggle to capture the fine-grained interactions between drugs and protein, i.e. the binding of specific drug atoms (or substructures) and key amino acids of proteins, which is crucial for understanding the binding mechanisms and optimising drug design. To address this issue, this paper introduces a novel model, called FusionDTI, which uses a token-level Fusion module to effectively learn fine-grained information for Drug-Target Interaction. In particular, our FusionDTI model uses the SELFIES representation of drugs to mitigate sequence fragment invalidation and incorporates the structure-aware (SA) vocabulary of target proteins to address the limitation of amino acid sequences in structural information, additionally leveraging pre-trained language models extensively trained on large-scale biomedical datasets as encoders to capture the complex information of drugs and targets. Experiments on three well-known benchmark datasets show that our proposed FusionDTI model achieves the best performance in DTI prediction compared with seven existing state-of-the-art baselines. Furthermore, our case study indicates that FusionDTI could highlight the potential binding sites, enhancing the explainability of the DTI prediction.

q-bio.QM↗