8 papers
ToxReason: A Benchmark for Mechanistic Chemical Toxicity Reasoning via Adverse Outcome Pathway
Jueon Park, Wonjune Jang, Chanhwi Kim +2
Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemica…
ATTNSOM: Learning Cross-Isoform Attention for Cytochrome P450 Site-of-Metabolism
Hajung Kim, Eunha Lee, Sohyun Chung +3
Identifying metabolic sites where cytochrome P450 enzymes metabolize small-molecule drugs is essential for drug discovery. Although existing computational approaches have been prop…
GraphCliff: Short-Long Range Gating for Modeling Critical Activity Changes Caused by Subtle Molecular Differences
Hajung Kim, Jueon Park, Junseok Choe +4
The quantitative structure-activity relationship assumes a smooth mapping between molecular structure and biological activity. However, activity cliffs, defined as pairs of structu…
CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction
Jueon Park, Yein Park, Minju Song +4
Drug toxicity remains a major challenge in pharmaceutical development. Recent machine learning models have improved in silico toxicity prediction, but their reliance on annotated d…
Understanding and Tackling Over-Dilution in Graph Neural Networks
Junhyun Lee, Veronika Thost, Bumsoo Kim +2
Message Passing Neural Networks (MPNNs) hold a key position in machine learning on graphs, but they struggle with unintended behaviors, such as over-smoothing and over-squashing, d…
HiRef: Leveraging Hierarchical Ontology and Network Refinement for Robust Medication Recommendation
Yan Ting Chok, Soyon Park, Seungheun Baek +3
Medication recommendation is a crucial task for assisting physicians in making timely decisions from longitudinal patient medical records. However, real-world EHR data present sign…