While Retrieval-Augmented Generation (RAG) has become a standard paradigm for mitigating hallucinations in Large Language Models (LLMs), its effectiveness in complex medical reasoning remains limited. Existing RAG methods suffer from two main challenges: First, **Semantic Drift**: without explicit domain constraints, LLM-driven query decomposition often deviates from the original clinical intent, introducing substantial noise that degrades retrieval relevance. Second, **Concatenation Fallacy**: retrieved evidence from different semantic aspects is aggregated in a naive, unstructured manner, without modeling their inter-dependencies and potential conflicts, which ultimately undermines downstream reasoning. To address these challenges, we propose **Med-SRAF**, a multi-agent retrieval augmentation framework guided by medical domain knowledge. This framework reconstructs the traditional RAG process through two core mechanisms: (1) Intent-driven Semantic Routing, where a UMLS-based NavigationAgent dynamically maps queries to medical dimensions for strategic search space pruning; and (2) Evidence-based Agentic Fusion, where a FusionAgent resolves conflicts among dimension-specific evidence to build logically consistent reasoning chains. Extensive experiments on five widely used medical benchmarks show that Med-SRAF consistently outperforms existing general RAG baselines, achieving an average accuracy improvement of over **4.9%**, highlighting its effectiveness in robust and interpretable medical reasoning. Our code is at https://anonymous.4open.science/r/MultiAgent_RAG-F6DC.

Recent advances in large language models (LLMs) have highlighted the effectiveness of chain-of-thought reasoning in symbolic domains such as mathematics and programming. However, our study shows that directly transferring such text-based reasoning paradigms to protein function understanding is ineffective: reinforcement learning mainly amplifies superficial keyword patterns while failing to introduce new biological knowledge, resulting in limited generalization. We argue that protein function prediction is a knowledge-intensive scientific task that fundamentally relies on external biological priors and computational tools rather than purely internal reasoning. To address this gap, we propose Protein Function Understanding Agent (PFUA), a tool-augmented protein reasoning agent that unifies problem decomposition, tool invocation, and grounded answer generation. Instead of relying on long unconstrained reasoning traces, PFUA integrates domain-specific tools to produce verifiable intermediate evidence. Experiments on four benchmarks demonstrate that PFUA consistently outperforms text-only reasoning models with an average performance improvement of 103%. We believe PFUA has the potential to become a standard paradigm for agentic reasoning in knowledge-intensive life science domains.

Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge repositories and advanced logical inference capabilities, has emerged as a promising way for efficient and effective MRL. Despite their potential, these methods predominantly rely on textual data, thus not fully harnessing the wealth of structural information inherent in molecular graphs. Moreover, the absence of a unified framework exacerbates the issue of insufficient data exploitation, as it hinders the sharing of interaction mechanism learned across various datasets. To address these challenges, this work proposes a novel LLM-based multi-modal framework for molecular interaction modeling following Chain-of-Thought (CoT) theory, termed MolTC, which effectively integrate graphical information of two molecules in pair. To train this integrated framework efficiently, we introduce a *multi-hierarchical CoT theory* to refine its training paradigm, and conduct a comprehensive *Molecular Interactive Instructions* dataset for the development of biochemical LLMs involving MRL.Our experiments,conducted across various datasets involving over 4,000,000 molecular pairs, exhibit the superiority of our method over current GNN and LLM-based baselines. Code is available at https://github.com/MangoKiller/MolTC.