Alexander Goncearenco's repositories
graph2vec
A parallel implementation of "graph2vec: Learning Distributed Representations of Graphs" (MLGWorkshop 2017).
bio_embeddings
Get protein embeddings from protein sequences
opentargets-py
Python client for the Open Targets REST API at targetvalidation.org
biovec
A new approach for representing biological sequences
poetry
Python dependency management and packaging made easy.
SPServer
Assessment of the quality of protein folds and protein-protein interaction interfaces using statistical potentials
protein-sequence-motifs
Tools to derive prototypical sequence motifs of functional and structural protein units of sub-domain size
int3dInterfaces
Pipeline to extract protein interfaces from Interactome3d structures
reproducible-research-guidelines
Guidelines for accountable and reproducible computational research
molmimic
Predict Host Pathogen Protein Protein Interactions using 3D Fully Convolutional Neural Networks
openfda-faers
FAERS Adverse Reaction Events database and OpenFDA API
twobitreader
A fast python class for reading 2-bit files (used by UCSC genome browser)
freesasa
C-library for calculating Solvent Accessible Surface Areas
interactome
Structural Interactome pipeline
DeepExplain
A unified framework of perturbation and gradient-based attribution methods for Deep Neural Networks interpretability. DeepExplain also includes support for Shapley Values sampling. (ICLR 2018)
KAN
An implementation of Knowledge-aware attention networks (KAN) for protein-protein extraction task
MutaBindv2.0
dataset for MutaBindv2.0
elementary-functions
Online Supplementary Materials and scripts for the Physical Biology paper on proteins and their elementary functions
molecule_discovery
matter.farm, 7x7 beijing project w/ Sean Raspet
ml101
intro to machine learning - reverse engineering phenomena
Enolase
Elementary functions in Enolase enzyme superfamily