Repository Index

Official repository for the Boltz biomolecular interaction models

• binding-prediction
• drug-discovery
• protein-structure

Message Passing Neural Networks for Molecule Property Prediction

• machine-learning
• chemistry
• neural-networks
• drug-discovery

Chai-1, SOTA model for biomolecular structure prediction

The Control Toolbox - An Open-Source C++ Library for Robotics, Optimal and Model Predictive Control

• optimal-control
• model-predictive-control
• ilqr
• ilqg

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

• drug-repurposing
• deep-learning
• drug-target-interactions
• toolkit

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

• computational-chemistry
• computational-biology
• deep-learning
• deep-neural-networks

Nonconvex embedded optimization: code generation for fast real-time optimization + ROS support

• embedded-optimization
• nonconvex
• model-predictive-control
• rust-library

ACADO Toolkit is a software environment and algorithm collection for automatic control and dynamic optimization. It provides a general framework for using a great variety of algorithms for direct optimal control, including model predictive control, state and parameter estimation and robust optimization.

Sequential regulatory activity predictions with deep convolutional neural networks.

Iterative Linear Quadratic Regulator with auto-differentiatiable dynamics models

• trajectory-optimization
• differential-dynamic-programming
• theano
• dynamics-models

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

• dna
• language-model
• variant-effect-prediction
• genomics

The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)

• ai-for-science
• diffusion-models
• drug-design
• equivariant-networks

GraphDTA: Predicting drug-target binding affinity with graph neural networks

Source code for "DeepDTA: deep drug-target binding affinity prediction"

• protein-ligand-interactions
• convolutional-neural-networks

RNA-seq prediction with deep convolutional neural networks.

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

• cancer-imaging-research
• radiomics
• radiomics-features
• machine-learning

A Network Integration Approach for Drug-Target Interaction Prediction

AI-based pathology predicts origins for cancers of unknown primary - Nature

• histology
• pathology
• wsi-images
• histopathology

An automatic code generator for nonlinear model predictive control (NMPC) and the continuation/GMRES method (C/GMRES) based numerical solvers for NMPC

• model-predictive-control
• nonlinear-model-predictive-control
• mpc
• nmpc

OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

• disentanglement
• drug-discovery
• genomics
• perturbation

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening