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Phuc Pham

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Review Jul 2026

Evaluating Agentic Bioinformatics through Function, Evidence, and Validation

It is argued that agentic bioinformatics should be assessed through workflow correctness rather than final-answer correctness alone, and the Function--Evidence--Validation (FEV) framework is introduced, which separates demonstrated workflow operations, traceable support for actions and claims, and use-case-specific validation.

Phuc Pham, Truong-Son Hy · 0 citations
Open access Sep 2025

LINKER: Learning Interactions between Functional Groups and Residues with Chemical Knowledge‑Enhanced Reasoning and Explainability

LINKER is the first sequence-based model to predict residue-functional group interactions according to biologically defined interaction types, using only a protein sequence and the SMILES representation of the ligand, and requires only sequence-level input at inference.

Phuc Pham, Viet Thanh Duy Nguyen, Truong-Son Hy · 1 citation