sbonner0

awesome-drug-discovery-knowledge-graphs

A collection of research papers, datasets and software related to knowledge graphs for drug discovery. Accompanies the paper "A review of biomedical datasets relating to drug discovery: a knowledge graph perspective" (Briefings in Bioinformatics, 2022)

awesome-drug-pair-scoring

Readings for "A Unified View of Relational Deep Learning for Drug Pair Scoring." (IJCAI 2022)

biomedical-kg-topological-imbalance

Code to accompany the "Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphs" (Briefings in Bioinformatics, 2022)

kgem-in-drug-discovery

Code to accompany the "Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery" manuscript (Artificial Intelligence in the Life Sciences, 2022)

reco-gym

Code for reco-gym: A Reinforcement Learning Environment for the problem of Product Recommendation in Online Advertising

DeepTopologyClassification

The code and datasets for the IEEE Big Data 2016 paper entitled - " Deep Topology Classification: A New Approach for Massive Graph Classification"

gae_in_pytorch

Graph Auto-Encoder in PyTorch

GraphFingerprintComparison

A repository for the graph finger print comparison code, written in python and graph-tool.

temporal-neighbourhood-aggregation

Code for the Big Data 2019 Paper - Temporal Neighbourhood Aggregation: Predicting Future Links in Temporal Graphs via Recurrent Variational Graph Convolutions

unsupervised-graph-embedding

Code for both the IEEE Big Data 2017 Paper: Evaluating the quality of graph embeddings via topological feature reconstruction and the Springer Data Science and Engineering paper: Exploring the Semantic Content of Unsupervised Graph Embeddings: An Empirical Study

sbonner0/GraphFingerprintComparison

A repository for the graph finger print comparison code, written in python and graph-tool.

sbonner0/temporal-neighbourhood-aggregation

Code for the Big Data 2019 Paper - Temporal Neighbourhood Aggregation: Predicting Future Links in Temporal Graphs via Recurrent Variational Graph Convolutions

sbonner0/unsupervised-graph-embedding

Code for both the IEEE Big Data 2017 Paper: Evaluating the quality of graph embeddings via topological feature reconstruction and the Springer Data Science and Engineering paper: Exploring the Semantic Content of Unsupervised Graph Embeddings: An Empirical Study

sbonner0/DeepTopologyClassification

The code and datasets for the IEEE Big Data 2016 paper entitled - " Deep Topology Classification: A New Approach for Massive Graph Classification"

sbonner0/gae_in_pytorch

Graph Auto-Encoder in PyTorch

sbonner0/GFPX-GraphSimilarity

The code for measuring the similarity of graphs using Apache Spark and GraphX

sbonner0/temporal-offset-reconstruction

Code the Big Data 2018 Paper: Temporal Graph Offset Reconstruction: Towards Temporally Robust Graph Representation Learning

sbonner0/pytorch_geometric

Geometric Deep Learning Extension Library for PyTorch

sbonner0/SemNetCon

Semantic Enabled Python Tool For The Construction Of Complex Networks From Disperse Data Sources (SemNetCon)

sbonner0/awesome-explainable-graph-reasoning

A collection of research papers and software related to explainability in graph machine learning.

sbonner0/dotfiles

Config files for my Arch i3-gaps + Polybar setup

sbonner0/DynamicGEM

sbonner0/esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

sbonner0/NBFNet

Official implementation of Neural Bellman-Ford Networks (NeurIPS 2021)

sbonner0/NBFNet-PyG

PyG re-implementation of Neural Bellman-Ford Networks (NeurIPS 2021)

sbonner0/pykeen

🤖 A Python library for learning and evaluating knowledge graph embeddings

sbonner0/pytorch-apex-experiment

Simple experiment of Apex (A PyTorch Extension)

sbonner0/rexmex

A general purpose recommender metrics library for fair evaluation.

sbonner0/RNNLogic

sbonner0/sbonner0

sbonner0/skywalkR

code for Gogleva et al manuscript