ppi-networks

There are 3 repositories under ppi-networks topic.

graphein
a-r-j / graphein
Protein Graph Library
protein protein-structure deep-learning pytorch graph-neural-networks dgl computational-biology bioinformatics structural-biology protein-data-bank protein-design geometric-deep-learning pytorch-geometric python interactomics interactome rna ppi-networks gene-regulatory-networks drug-discovery
Language:Jupyter Notebook 989
LirongWu / MAPE-PPI
Code for ICLR 2024 (Spotlight) paper "MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding"
codebook masked-modeling microenvironment ppi-networks protein-embedding protein-protein-interaction protein-representation-learning vocabulary
Language:Python 163
pulimeng / CancerOmicsNet
A Graph Neural Network Model for prediction of the effectiveness of a drug on a given cancer cell lines
graph-neural-network drug-discovery cancer-genomics ppi-networks systems-biology
Language:Python 14
chao1224 / SGNN-EBM
Structured Multi-task Learning for Molecular Property Prediction, AISTATS'22 (https://proceedings.mlr.press/v151/liu22e.html)
knowledge-graph molecule multitask-learning energy-based-model ppi-networks string chembl chembl-string
Language:Python 13
paulmorio / protclus
Python 3 library implementing a number of topological clustering techniques used on protein-protein interaction networks.
ppi-networks clustering
Language:Python 9
pievos101 / Ensemble-GNN
Ensemble learning with graph neural networks for disease module discovery and classification
ensemble-learning graph-neural-networks ppi-networks
Language:Python 9
THinnerichs / DTI-VOODOO
A PPI network driven approach to drug-target-interaction prediction using deep graph learning methods.
dti-prediction graph-neural-networks ontologies ppi-networks
Language:TeX 9
ylaboratory / ETNA
Embeddings to Network Alignment - align biological networks between two species
bioinformatics-tool computational-biology network-alignment ppi-networks protein-protein-interaction-network
Language:Python 8
Barabasi-Lab / NonCoding
Codes for the paper entitled: Non-Coding RNAs Improve the Predictive Power of Network Medicine
disease-modules ncrna ncrna-protein-interactions netsci network network-medicine ppi-networks
Language:HTML 2
aGalhoz / wppi
Gene prioritisation tool using a weighted network methodology based on Gene Ontology and Human Phenotype Ontology annotations to infer closely related genes to given genes of interest.
ppi-networks gene-ontology human-phenotype-ontology random-walk-with-restart gene-prioritization omnipath
Language:R 1
pulimeng / Biology-Network-Reduction
Graph representation for system biology networks and the reduction of them for machine learning purposes
ppi-networks systemsbiology
Language:Python 1
sevmardi / Protein-Protein-Networks
Evaluate a strategy for predicting cancer-related proteins in PPI networks.
python-3 ppi ppi-networks prediction
Language:Python 1
giuliapalmaa / PPI-Networks-Clustering
New implementation of the Girvan-Newman edge-betweenness' algorithm and study of the clustering structure through modularity. Based on "A MapReduce-Based Parallel Clustering Algorithm for Large Protein-Protein Interaction Networks", by Liu and others
clustering edge-betweenness modularity ppi-networks
Language:Java 0
MateJozsaPhys / CNDinvestigation
Opportunities and challenges in partitioning the graph measure space of real-world networks
networks complex-networks network-analysis network-measures networkx igraph brain-networks social-networks affiliation-networks web-networks metabolic-networks transportation-networks ppi-networks network-classification machine-learning feature-selection relevant-feature-analysis feature-extraction skewed-data unbalanced-datasets
Language:Jupyter Notebook 0
ylaboratory / splitpea
A tool for calculating PPI network rewiring due to alternative splicing
bioinformatics cancer ppi-networks protein-protein-interaction splicing
Language:Jupyter Notebook 0
sysbiolux / MD_network_map
paper ppi-networks
Language:Python

ppi-networks

a-r-j / graphein

LirongWu / MAPE-PPI

pulimeng / CancerOmicsNet

chao1224 / SGNN-EBM

paulmorio / protclus

pievos101 / Ensemble-GNN

THinnerichs / DTI-VOODOO

ylaboratory / ETNA

Barabasi-Lab / NonCoding

aGalhoz / wppi

pulimeng / Biology-Network-Reduction

sevmardi / Protein-Protein-Networks

giuliapalmaa / PPI-Networks-Clustering

MateJozsaPhys / CNDinvestigation

ylaboratory / splitpea

sysbiolux / MD_network_map