Betty Xiong
Publications
LLM-Guided Retrieval for Prediction of Molecular Perturbation Responses
Predicting transcriptomic responses to small-molecule perturbations across cell lines is central to drug discovery, but exhaustive profiling of drug-cell combinations is infeasible. We frame molecular perturbation prediction as retrieve-and-aggregate: approximate an unmeasured drug's response in a cell line by aggregating measured responses of a small set of biologically related compounds. We propose LLM-Guided Retrieval (LGR), where a large language model (LLM) ranks candidate neighbor drugs (restricted to those profiled in the target cell line); after which a fixed mean aggregator combines their observed expression deltas to form the prediction. We evaluate on the Tahoe-100M single-cell perturbation atlas under unseen-drug, unseen-cell-line, and open-world regimes. LGR consistently improves over drug mean, ChemCPA, and chemistry-based kNN baselines, with the strongest gains for unseen cell-line generalization, where it achieves higher correlation and lower error than mean baselines. Across settings, LGR improves directional (sign) accuracy of gene regulation, indicating better recovery of biologically meaningful perturbation effects even when magnitude-based metrics are similar. These results suggest that retrieval quality, rather than predictor complexity, is a key driver of zero-shot molecular perturbation prediction, and that LLMs can provide a useful biological prior when used as constrained retrieval modules.
FDARxBench: Benchmarking Regulatory and Clinical Reasoning on FDA Generic Drug Assessment
We introduce an expert curated, real-world benchmark for evaluating document-grounded question-answering (QA) motivated by generic drug assessment, using the U.S. Food and Drug Administration (FDA) drug label documents. Drug labels contain rich but heterogeneous clinical and regulatory information, making accurate question answering difficult for current language models. In collaboration with FDA regulatory assessors, we introduce FDARxBench, and construct a multi-stage pipeline for generating high-quality, expert curated, QA examples spanning factual, multi-hop, and refusal tasks, and design evaluation protocols to assess both open-book and closed-book reasoning. Experiments across proprietary and open-weight models reveal substantial gaps in factual grounding, long-context retrieval, and safe refusal behavior. While motivated by FDA generic drug assessment needs, this benchmark also provides a substantial foundation for challenging regulatory-grade evaluation of label comprehension. The benchmark is designed to support evaluation of LLM behavior on drug-label questions.