Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models
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 …
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
Despite tremendous efforts in the past two years, our understanding of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune …
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
Although deep learning approaches have had tremendous success in image, video and
audio processing, computer vision, and speech recognition, their applications to three …
audio processing, computer vision, and speech recognition, their applications to three …
Persistent-homology-based machine learning: a survey and a comparative study
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 …
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
This work introduces a number of algebraic topology approaches, including multi-
component persistent homology, multi-level persistent homology, and electrostatic …
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
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 …
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 …
symmetric applications among the most significant sources of new data in the future. In this …
Persistence weighted Gaussian kernel for topological data analysis
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 …
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
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 …
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
Protein‐ligand binding is a fundamental biological process that is paramount to many other
biological processes, such as signal transduction, metabolic pathways, enzyme …
biological processes, such as signal transduction, metabolic pathways, enzyme …