A review of mathematical representations of biomolecular data

DD Nguyen, Z Cang, GW Wei - Physical Chemistry Chemical Physics, 2020‏ - pubs.rsc.org
Recently, machine learning (ML) has established itself in various worldwide benchmarking
competitions in computational biology, including Critical Assessment of Structure Prediction …

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

Z Cang, GW Wei - PLoS computational biology, 2017‏ - journals.plos.org
Although deep learning approaches have had tremendous success in image, video and
audio processing, computer vision, and speech recognition, their applications to three …

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

Z Cang, L Mu, GW Wei - PLoS computational biology, 2018‏ - journals.plos.org
This work introduces a number of algebraic topology approaches, including multi-
component persistent homology, multi-level persistent homology, and electrostatic …

Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges

DD Nguyen, Z Cang, K Wu, M Wang, Y Cao… - Journal of computer …, 2019‏ - Springer
Advanced mathematics, such as multiscale weighted colored subgraph and element specific
persistent homology, and machine learning including deep neural networks were integrated …

Quantitative toxicity prediction using topology based multitask deep neural networks

K Wu, GW Wei - Journal of chemical information and modeling, 2018‏ - ACS Publications
The understanding of toxicity is of paramount importance to human health and
environmental protection. Quantitative toxicity analysis has become a new standard in the …

MathDL: mathematical deep learning for D3R Grand Challenge 4

DD Nguyen, K Gao, M Wang, GW Wei - Journal of computer-aided …, 2020‏ - Springer
We present the performances of our mathematical deep learning (MathDL) models for D3R
Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free …

Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology

Z Cang, GW Wei - Bioinformatics, 2017‏ - academic.oup.com
Motivation Site directed mutagenesis is widely used to understand the structure and function
of biomolecules. Computational prediction of mutation impacts on protein stability offers a …

Persistent spectral based ensemble learning (PerSpect-EL) for protein–protein binding affinity prediction

JJ Wee, K **a - Briefings in Bioinformatics, 2022‏ - academic.oup.com
Protein–protein interactions (PPIs) play a significant role in nearly all cellular and biological
activities. Data-driven machine learning models have demonstrated great power in PPIs …

Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation

JJ Wee, J Chen, K **a, GW Wei - Computers in biology and medicine, 2024‏ - Elsevier
Protein mutations can significantly influence protein solubility, which results in altered
protein functions and leads to various diseases. Despite tremendous effort, machine …

A review of geometric, topological and graph theory apparatuses for the modeling and analysis of biomolecular data

K **a, GW Wei - arxiv preprint arxiv:1612.01735, 2016‏ - arxiv.org
Geometric, topological and graph theory modeling and analysis of biomolecules are of
essential importance in the conceptualization of molecular structure, function, dynamics, and …