medical informatics engineers

Abstract: High-dimensional bioinformatics data, characterized by a large number of features relative to the number of samples, pose major challenges such as the ``curse of dimensionality,'' leading to overfitting, high computational cost, and poor generalization. Traditional feature selection methods often suffer from limited scalability and adaptability in such domains. We propose an LLM-in-the-loop reinforcement learning (RL) framework for bioinformatics feature selection, where the RL agent formulates feature selection as a sequential decision-making task, while the large language model (LLM) enhances the process in two ways: (1) guiding exploration through domain-informed advice, and (2) providing hybrid rewards that integrate data-driven performance with knowledge-driven evaluation. The LLM also produces explanations to improve interpretability for human experts without altering the RL policy update. Experiments on diverse bioinformatics datasets show that the LLM-in-the-loop framework outperforms baselines, achieves stable performance across downstream models, and converges faster than pure RL.

Abstract: Multi-source knowledge graphs (KGs) need query mechanisms that expose reliability and exploit domain structure. This paper presents TCMaster, a property-graph query substrate for confidence-aware traversal and workload-guided physical design over Traditional Chinese Medicine KGs. TCMaster integrates pharmacopoeias, prescriptions, molecular databases, and LLM-extracted micro-semantics into a KG with approximately 221K entities and 723K base edges. It annotates edges with provenance-level confidence, rewrites Cypher queries with confidence predicates, ranks multi-hop paths under PRODUCT, MIN, or weighted-average policies, and uses ontology skew through direction selection, herb-attribute bitmaps, and materialized shortcut edges. On Neo4j, direction selection improves attribute lookup by a factor of 1.47, shortcuts accelerate high-fanout target counting by a factor of 4.42, confidence filtering removes 39.3 percent of low-quality heterogeneous paths, and KG retrieval improves TCMbench QA accuracy by 20.0 percentage points.