34 citations · 49 across the 14 of their papers we have counts for
7 papers · 1 filter
A review of topological data analysis and topological deep learning in molecular sciences
JunJie Wee, Jian Jiang
Topological Data Analysis (TDA) has emerged as a powerful framework for extracting robust, multiscale, and interpretable features from complex molecular data for artificial intelli…
CAML: Commutative algebra machine learning -- a case study on protein-ligand binding affinity prediction
Hongsong Feng, Faisal Suwayyid, Mushal Zia +4
Recently, Suwayyid and Wei have introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we integrate commutative algebra machine…
Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning
JunJie Wee, Guo-Wei Wei
The fast evolution of SARS-CoV-2 and other infectious viruses poses a grand challenge to the rapid response in terms of viral tracking, diagnostics, and design and manufacture of m…
Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation
JunJie Wee, Guo-Wei Wei
AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug di…
Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation
JunJie Wee, Jiahui Chen, Kelin Xia +1
Protein mutations can significantly influence protein solubility, which results in altered protein functions and leads to various diseases. Despite of tremendous effort, machine le…
Persistent Dirac for molecular representation
JunJie Wee, Ginestra Bianconi, Kelin Xia
Molecular representations are of fundamental importance for the modeling and analysis of molecular systems. Representation models and in general approaches based on topological dat…
Ollivier persistent Ricci curvature (OPRC) based molecular representation for drug design
JunJie Wee, Kelin Xia
Efficient molecular featurization is one of the major issues for machine learning models in drug design. Here we propose persistent Ricci curvature (PRC), in particular Ollivier pe…