Protein function prediction using a variational autoencoder

A nextflow pipeline to cluster sets of proteins.

Protein function prediction based on protein-protein interaction network topology and deep maxout neural networks

Graph Embedding Evaluation / Code and Datasets for "Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations"

A nextflow pipeline to cluster sets of proteins.

Classification of protein function based on their sequences with Artificial Neural Networks

Improving protein function prediction with synthetic feature samples created by generative adversarial networks

Epistatic Net is an algorithm which allows for spectral regularization of deep neural networks to predict biological fitness functions (e.g., protein functions).

DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction

python package to encode protein using different methods for machine learning

python package to train CNN and DenseNet for protein function prediction

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN. This repository is for portfolio purposes only. For currently maintained version go to Małopolskie Centrum Biotechnologii repository - https://github.com/bioinf-mcb/Metagenomic-DeepFRI

A platfrom supplies various machine learning algorithms and datasets and evaluation metrics for Protein Function Prediction

Deep Critical Learning. Implementation of ProSelfLC, IMAE, DM, etc.

Automated protein function prediction is critical for the annotation of uncharacterized protein sequences, where accurate prediction methods are still required.we expect to create an accurate prediction model that assigns the best sub-graph of the gene ontology to each new protein and output a prediction score for this sub-graph and/or each pred…

[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding

This repository contains the FPredX models for the prediction of excitation maximum, emission maximum, brightness and oligomeric state of fluorescent proteins.

Multi-label protein function annotation

Benchmarking uncertainty quantification methods on proteins.

An efficient attention-based approach for Protein Function Prediction using skip-gram features. Proposing two novel approaches, namely, OntoPred and OntoPredPlus capable to annotate protein sequences accurately.