Yuanzhi Lu

Fujian Jia, Xin Liu, Lixi Deng et al.

In the past year, there has been a growing trend in applying Large Language Models (LLMs) to the field of medicine, particularly with the advent of advanced language models such as ChatGPT developed by OpenAI. However, there is limited research on LLMs specifically addressing oncology-related queries. The primary aim of this research was to develop a specialized language model that demonstrates improved accuracy in providing advice related to oncology. We performed an extensive data collection of online question-answer interactions centered around oncology, sourced from reputable doctor-patient platforms. Following data cleaning and anonymization, a dataset comprising over 180K+ oncology-related conversations was established. The conversations were categorized and meticulously reviewed by field specialists and clinicians to ensure precision. Employing the LLaMA model and other selected open-source datasets, we conducted iterative fine-tuning to enhance the model's proficiency in basic medical conversation and specialized oncology knowledge. We observed a substantial enhancement in the model's understanding of genuine patient inquiries and its reliability in offering oncology-related advice through the utilization of real online question-answer interactions in the fine-tuning process. We release database and models to the research community (https://github.com/OncoGPT1).

Junwen Mo, Yuanzhi Lu, Yifang Xue et al.

Linguistic ambiguity is critical to the robustness of Large Language Models (LLMs), yet existing research focuses mostly on English, with limited attention devoted to Chinese. Existing Chinese ambiguity datasets (e.g., CHAmbi) suffer from poor scalability. Guided by Potential Ambiguity (PA) Theory, we design a semi-automatic pipeline to construct CHA-Gen. It is the first PA Theory-grounded Chinese ambiguity dataset, which comprises 5,712 sentences (2,414 ambiguous, 3,298 unambiguous) across 18 potential ambiguous structures. Evaluating LLMs (e.g. Gemma 3, Qwen 2.5/3 series) via direct querying and machine translation, we find that LLMs struggle with ambiguity detection (improved by CoT prompting). Analysis of Qwen3-32B's CoT rationales reveals three common failure modes: ambiguity blindness, misattribution, and premature resolution. Uncertainty quantification with semantic entropy metric shows higher uncertainty for ambiguous sentences. Moreover, instruction tuning induces overconfidence, whereas Base models better capture semantic diversity. We further observe that models exhibit a bias toward dominant interpretations. Our work provides a scalable approach for Chinese ambiguity corpus and insights into LLMs' ambiguity handling, laying a foundation for enhancing Chinese ambiguity research in LLMs.

Fujian Jia, Jiwen Gu, Cheng Lu et al.

Understanding mechanistic relationships among genes and their impacts on biological pathways is essential for elucidating disease mechanisms and advancing precision medicine. Despite the availability of extensive molecular interaction and pathway data in public databases, integrating heterogeneous knowledge sources and enabling interpretable multi-step reasoning across biological networks remain challenging. We present GIP-RAG (Gene Interaction Prediction through Retrieval-Augmented Generation), a computational framework that combines biomedical knowledge graphs with large language models (LLMs) to infer and interpret gene interactions. The framework constructs a unified gene interaction knowledge graph by integrating curated data from KEGG, WikiPathways, SIGNOR, Pathway Commons, and PubChem. Given user-specified genes, a query-driven module retrieves relevant subgraphs, which are incorporated into structured prompts to guide LLM-based stepwise reasoning. This enables identification of direct and indirect regulatory relationships and generation of mechanistic explanations supported by biological evidence. Beyond pairwise interactions, GIP-RAG includes a pathway-level functional impact module that simulates propagation of gene perturbations through signaling networks and evaluates potential pathway state changes. Evaluation across diverse biological scenarios demonstrates that the framework generates consistent, interpretable, and evidence-supported insights into gene regulatory mechanisms. Overall, GIP-RAG provides a general and interpretable approach for integrating knowledge graphs with retrieval-augmented LLMs to support mechanistic reasoning in complex molecular systems.