AstraZeneca

chemicalx

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

rexmex

A general purpose recommender metrics library for fair evaluation.

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)

SubTab

The official implementation of the paper, "SubTab: Subsetting Features of Tabular Data for Self-Supervised Representation Learning"

awesome-shapley-value

Reading list for "The Shapley Value in Machine Learning" (JCAI 2022)

awesome-drug-pair-scoring

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

biology-for-ai

learning biology syllabus, geared for machine learning folks

skywalkR

code for Gogleva et al manuscript

StarGazer

StarGazer is a tool designed for rapidly assessing drug repositioning opportunities. It combines multi-source, multi-omics data with a novel target prioritization scoring system in an interactive Python-based Streamlit dashboard. StarGazer displays target prioritization scores for genes associated with 1844 phenotypic traits.

Omicsfold

Multi-omics data normalisation, model fitting and visualisation.

VecNER

A library of tools for dictionary-based Named Entity Recognition (NER), based on word vector representations to expand dictionary terms.

data-science-python-course

ibd-interpret

We trained high performing open source models on image scans of tissue biopsies to predict endoscopic categories in inflammatory bowel disease. These predictive models can help us better understand the disease pathology and represent a step towards automated clinical recruitment strategies.

NESS

Official implementation of "NESS: Node Embeddings from Static Subgraphs"

detectIS

A pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data

UnlockingHeart

This repository accompanies our paper Unlocking the Heart Using Adaptive Locked Agnostic Networks and enables replication of the key results.

hsqc_structure_elucidation

Implementation of the SGNN graph neural network for 1H and 13C NMR prediction and a tool for distinguishing different molecules based on HSQC simulations

Multimodal_NSCLC

multi-omics data integration helps improving patient survival prediction. We provide a pipeline allowing for early integration of multiple omics plus clinical modalities in order to predict patient survival for NSCLC. The pipeline utilizes autoencoders, and helps identify main driving factor in survival prediction

Siamese-Regression-Pairing

Siamese Neural Networks for Regression: Similarity-Based Pairing and Uncertainty Quantification

fragler

magnus-extensions

Extensions packages for magnus

PatientSafetyKG

molecular-complexity

Python implementation of the molecular complexity metric described by Proudfoot 2017 (http://dx.doi.org/10.1016/j.bmcl.2017.03.008).

multitask_impute

Supplementary code for 'Deep Learning Imputation for Multi Task Learning'

OCT_publication

This repository contains the source code for the image analysis of optical coherence tomography images, as stated in the publication of Volumetric wound healing by machine learning and optical coherence tomography in type 2 diabetes.

survextrap-excesshazards

Demonstration of excess hazard and excess hazard cure models for survival extrapolation

GIM

gene interaction matrices, a novel approach to using ConvNets on gene expression data

AdaptedGraphDTA

gonogo

Implement Go/No-Go policies using multiple endpoints, and simulate the outcome under different scenarios.

INSPECTumours

This is a shiny tool to classify and analyse pre-clinical tumour data automatically.