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David McDonald's Projects

off-target-p-ml icon off-target-p-ml

This repository contains the necessary scripts to derive off-target models through (1) A neural network framework based on Keras and Tensorflow (2)An autmomated machine learning framework based on AutoGluon

openane icon openane

OpenANE: the first Open source framework specialized in Attributed Network Embedding (ANE)

pharml icon pharml

PharML is a framework for predicting compound affinity for protein structures. It utilizes a novel Molecular-Highway Graph Neural Network (MH-GNN) architecture based on state-of-the-art techniques in deep learning. This repository contains the visualization, preprocessing, training, and inference code written in Python and C. In addition, we provide an ensemble of pre-trained models which can readily be used for quickly generating rank-ordered predictions of compound affinity relative to a given target. DISCLAIMER: Compounds predicted by PharML.Bind should not be used without consulting a doctor or pharmacist - all results should be considered unverified and used only as a starting point for further investigation. Use at your own risk!

poincare-embeddings icon poincare-embeddings

PyTorch implementation of the NIPS-17 paper "Poincaré Embeddings for Learning Hierarchical Representations"

pyrmd icon pyrmd

AI-powered Virtual Screening

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