Emily Nguyen
Publications
Trustworthy Protein-Ligand Binding Affinity Prediction via Reliability-Aware Multi-Engine Fusion
Accurate protein-ligand binding affinity prediction is central to computational drug discovery, yet modern docking engines frequently disagree without indicating which prediction to trust. Consensus scoring and ensemble methods improve mean accuracy but treat all predictions identically without interpretable confidence measures or uncertainty decomposition, ignoring the chemical context of each protein-ligand pair. To address this limitation, we introduce RELIABLE-BA (RELIABiLity-aware Evidential fusion for Binding Affinity), an evidential framework for multi-engine binding affinity prediction. Our model comprises three steps: (1) modeling each engine as an evidential expert via Normal-Inverse-Gamma distributions, (2) scaling epistemic uncertainty through learned reliability from molecular context while preserving each expert's predictive mean, and (3) fusing experts through closed-form aggregation that captures both individual uncertainty and inter-engine disagreement. Experiments on the PDBBind and BDB2020+ benchmarks demonstrate competitive point prediction with substantially improved uncertainty calibration, and additional validation on the SARS-CoV-2 Mpro dataset and 5HT2A receptor demonstrates applicability to clinically relevant drug targets. Crucially, these uncertainty estimates enable reliable filtering of protein-ligand pairs, reducing prediction error by up to 25% when retaining only high-confidence pairs. To our knowledge, RELIABLE-BA is the first multi-engine binding affinity prediction framework to combine evidential fusion with context-dependent reliability, offering a principled path toward trustworthy AI-guided drug discovery. Our code is publicly available at https://github.com/yongchand/RELIABLE-BA.
De-conflating Preference and Qualification: Constrained Dual-Perspective Reasoning for Job Recommendation with Large Language Models
Professional job recommendation involves a complex bipartite matching process that must reconcile a candidate's subjective preference with an employer's objective qualification. While Large Language Models (LLMs) are well-suited for modeling the rich semantics of resumes and job descriptions, existing paradigms often collapse these two decision dimensions into a single interaction signal, yielding confounded supervision under recruitment-funnel censoring and limiting policy controllability. To address these challenges, We propose JobRec, a generative job recommendation framework for de-conflating preference and qualification via constrained dual-perspective reasoning. JobRec introduces a Unified Semantic Alignment Schema that aligns candidate and job attributes into structured semantic layers, and a Two-Stage Cooperative Training Strategy that learns decoupled experts to separately infer preference and qualification. Building on these experts, a Lagrangian-based Policy Alignment module optimizes recommendations under explicit eligibility requirements, enabling controllable trade-offs. To mitigate data scarcity, we construct a synthetic dataset refined by experts. Experiments show that JobRec consistently outperforms strong baselines and provides improved controllability for strategy-aware professional matching.