Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models

Y Qiu, GW Wei - Briefings in bioinformatics, 2023 - academic.oup.com
Protein engineering is an emerging field in biotechnology that has the potential to
revolutionize various areas, such as antibody design, drug discovery, food security, ecology …

Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2

K Gao, R Wang, J Chen, L Cheng, J Frishcosy… - Chemical …, 2022 - ACS Publications
Despite tremendous efforts in the past two years, our understanding of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune …

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 …

Persistent-homology-based machine learning: a survey and a comparative study

CS Pun, SX Lee, K Xia - Artificial Intelligence Review, 2022 - Springer
A suitable feature representation that can both preserve the data intrinsic information and
reduce data complexity and dimensionality is key to the performance of machine learning …

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 …

A topology-based network tree for the prediction of protein–protein binding affinity changes following mutation

M Wang, Z Cang, GW Wei - Nature Machine Intelligence, 2020 - nature.com
The ability to predict protein–protein interactions is crucial to our understanding of a wide
range of biological activities and functions in the human body, and for guiding drug …

Machine learning algorithms for smart data analysis in internet of things environment: taxonomies and research trends

MH Alsharif, AH Kelechi, K Yahya, SA Chaudhry - Symmetry, 2020 - mdpi.com
Machine learning techniques will contribution towards making Internet of Things (IoT)
symmetric applications among the most significant sources of new data in the future. In this …

Persistence weighted Gaussian kernel for topological data analysis

G Kusano, Y Hiraoka… - … conference on machine …, 2016 - proceedings.mlr.press
Topological data analysis (TDA) is an emerging mathematical concept for characterizing
shapes in complex data. In TDA, persistence diagrams are widely recognized as a useful …

Coupled dynamics on hypergraphs: Master stability of steady states and synchronization

R Mulas, C Kuehn, J Jost - Physical Review E, 2020 - APS
In the study of dynamical systems on networks or graphs, a key theme is how the network
topology influences stability for steady states or synchronized states. Ideally, one would like …

Integration of element specific persistent homology and machine learning for protein‐ligand binding affinity prediction

Z Cang, GW Wei - … journal for numerical methods in biomedical …, 2018 - Wiley Online Library
Protein‐ligand binding is a fundamental biological process that is paramount to many other
biological processes, such as signal transduction, metabolic pathways, enzyme …