2025
Torsion Graph Neural Networks.
IEEE Trans. Pattern Anal. Mach. Intell., April, 2025
Commutative algebra-enhanced topological data analysis.
CoRR, April, 2025
Join Persistent Homology (JPH)-Based Machine Learning for Metalloprotein-Ligand Binding Affinity Prediction.
J. Chem. Inf. Model., 2025
Topology-Enhanced Machine Learning Model (Top-ML) for Anticancer Peptide Prediction.
J. Chem. Inf. Model., 2025
Quotient Complex (QC)-Based Machine Learning for 2D Hybrid Perovskite Design.
J. Chem. Inf. Model., 2025
TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment.
Briefings Bioinform., 2025
Path Complex Neural Networks for Sequential Process Activities Classification.
Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining, V.1, 2025
2024
Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation.
Comput. Biol. Medicine, February, 2024
A cohomology-based Gromov-Hausdorff metric approach for quantifying molecular similarity.
CoRR, 2024
KA-GNN: Kolmogorov-Arnold Graph Neural Networks for Molecular Property Prediction.
CoRR, 2024
Molecular topological deep learning for polymer property prediction.
CoRR, 2024
Quotient complex (QC)-based machine learning for 2D perovskite design.
CoRR, 2024
Multi-Cover Persistence (MCP)-based machine learning for polymer property prediction.
Briefings Bioinform., 2024
Graph Neural Networks with a Distribution of Parametrized Graphs.
Proceedings of the Forty-first International Conference on Machine Learning, 2024
2023
Multiscale Topological Indices for the Quantitative Prediction of SARS CoV-2 Binding Affinity Change upon Mutations.
J. Chem. Inf. Model., July, 2023
Laplacian Spectra of Persistent Structures in Taiwan, Singapore, and US Stock Markets.
Entropy, June, 2023
Fingerprint-Enhanced Graph Attention Network (FinGAT) Model for Antibiotic Discovery.
J. Chem. Inf. Model., May, 2023
Persistent Tor-algebra for protein-protein interaction analysis.
Briefings Bioinform., March, 2023
Molecular geometric deep learning.
CoRR, 2023
Curvature-enhanced Graph Convolutional Network for Biomolecular Interaction Prediction.
CoRR, 2023
2022
Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction.
PLoS Comput. Biol., 2022
<i>Hom</i>-Complex-Based Machine Learning (HCML) for the Prediction of Protein-Protein Binding Affinity Changes upon Mutation.
J. Chem. Inf. Model., 2022
Flexibility and rigidity index for chromosome packing, flexibility and dynamics analysis.
Frontiers Comput. Sci., 2022
Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction.
Briefings Bioinform., 2022
Multiphysical graph neural network (MP-GNN) for COVID-19 drug design.
Briefings Bioinform., 2022
Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design.
Briefings Bioinform., 2022
Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation.
Briefings Bioinform., 2022
Persistent-homology-based machine learning: a survey and a comparative study.
Artif. Intell. Rev., 2022
Persistent tor-algebra based stacking ensemble learning (PTA-SEL) for protein-protein binding affinity prediction.
Proceedings of the Topological, 2022
2021
Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein-Ligand Binding Affinity Prediction.
J. Chem. Inf. Model., 2021
Understanding Changes in the Topology and Geometry of Financial Market Correlations during a Market Crash.
Entropy, 2021
Fast random algorithms for manifold based optimization in reconstructing 3D chromosomal structures.
Commun. Inf. Syst., 2021
Forman persistent Ricci curvature (FPRC)-based machine learning models for protein-ligand binding affinity prediction.
Briefings Bioinform., 2021
Hypergraph-based persistent cohomology (HPC) for molecular representations in drug design.
Briefings Bioinform., 2021
Persistent spectral hypergraph based machine learning (PSH-ML) for protein-ligand binding affinity prediction.
Briefings Bioinform., 2021
Neighborhood Complex Based Machine Learning (NCML) Models for Drug Design.
Proceedings of the Interpretability of Machine Intelligence in Medical Image Computing, and Topological Data Analysis and Its Applications for Medical Data, 2021
2020
Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes.
J. Comput. Chem., 2020
Persistent spectral based machine learning (PerSpect ML) for drug design.
CoRR, 2020
2019
Understanding Attack Trends from Security Blog Posts Using Guided-topic Model.
J. Inf. Process., 2019
A Malicious Web Site Identification Technique Using Web Structure Clustering.
IEICE Trans. Inf. Syst., 2019
2018
Persistent similarity for biomolecular structure comparison.
Commun. Inf. Syst., 2018
2017
Geometric and electrostatic modeling using molecular rigidity functions.
J. Comput. Appl. Math., 2017
Finite volume formulation of the MIB method for elliptic interface problems.
J. Comput. Appl. Math., 2017
2016
Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.
J. Comput. Chem., 2016
2015
Second order method for solving 3D elasticity equations with complex interfaces.
J. Comput. Phys., 2015
Multidimensional persistence in biomolecular data.
J. Comput. Chem., 2015
Persistent homology for the quantitative prediction of fullerene stability.
J. Comput. Chem., 2015
Multiresolution Topological Simplification.
J. Comput. Biol., 2015
Matched interface and boundary method for elasticity interface problems.
J. Comput. Appl. Math., 2015
2014
Multiscale geometric modeling of macromolecules I: Cartesian representation.
J. Comput. Phys., 2014
MIB Galerkin method for elliptic interface problems.
J. Comput. Appl. Math., 2014
A Galerkin formulation of the MIB method for three dimensional elliptic interface problems.
Comput. Math. Appl., 2014
2013
Multiscale geometric modeling of macromolecules II: Lagrangian representation.
J. Comput. Chem., 2013
2012
Variational Multiscale Models for Charge Transport.
SIAM Rev., 2012
Adaptively deformed mesh based interface method for elliptic equations with discontinuous coefficients.
J. Comput. Phys., 2012
2011
MIB method for elliptic equations with multi-material interfaces.
J. Comput. Phys., 2011