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github deepgraphlearning torchdrug a powerful and flexible machine learning platform for drug discovery github skip to content navigation menu toggle navigation sign in appearance settings platform ai code creation github copilot write better code with ai github copilot app direct agents from issue to merge mcp registry new integrate external tools developer workflows actions automate any workflow codespaces instant dev environments issues plan and track work code review manage code changes code quality enforce quality at merge application security github advanced security find and fix vulnerabilities code security secure your code as you build secret protection stop leaks before they start explore why github documentation blog changelog marketplace view all features solutions by company size enterprises small and medium teams startups nonprofits by use case app modernization devsecops devops ci cd view all use cases by industry healthcare financial services manufacturing government 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contacted cancel submit feedback saved searches use saved searches to filter your results more quickly name query to see all available qualifiers see our documentation cancel create saved search sign in sign up appearance settings resetting focus you signed in with another tab or window reload to refresh your session you signed out in another tab or window reload to refresh your session you switched accounts on another tab or window reload to refresh your session dismiss alert message uh oh there was an error while loading please reload this page deepgraphlearning torchdrug public notifications you must be signed in to change notification settings fork 220 star 1 6k code issues 113 pull requests 11 actions projects security and quality 0 insights additional navigation options code issues pull requests actions projects security and quality insights deepgraphlearning torchdrug master branches tags go to file code open more actions menu folders and files name name last commit message last commit date latest commit history 115 commits 115 commits asset asset conda torchdrug conda torchdrug doc source doc source docker docker test test torchdrug torchdrug gitignore gitignore citation citation code_of_conduct md code_of_conduct md contributing md contributing md license license readme md readme md requirements txt requirements txt setup py setup py view all files repository files navigation readme code of conduct contributing apache 2 0 license more items with docs tutorials benchmarks papers implemented torchdrug is a pytorch based machine learning toolbox designed for several purposes easy implementation of graph operations in a pytorchic style with gpu support being friendly to practitioners with minimal knowledge about drug discovery rapid prototyping of machine learning research installation torchdrug can be installed on either linux windows or macos it is compatible with 3 7 python 3 10 and pytorch 1 8 0 from conda conda install torchdrug c milagraph c conda forge c pytorch c pyg from pip pip install torch 1 9 0 pip install torch scatter torch cluster f https pytorch geometric com whl torch 1 9 0 cu102 html pip install torchdrug to install torch scatter for other pytorch or cuda versions please see the instructions in https github com rusty1s pytorch_scatter from source git clone https github com deepgraphlearning torchdrug cd torchdrug pip install r requirements txt python setup py install windows powershell we need to first install the build tools for visual studio we then install the following modules in powershell install module pscx allowclobber install module vssetup initialize visual studio in powershell with the following commands we may setup this for all powershell sessions by writing it to the powershell profile change the library path according to your own case import visualstudiovars architecture x64 env lib c program files python37 libs apple silicon m1 m2 chips we need pytorch 1 13 to run torchdrug on apple silicon for torch scatter and torch cluster they can be compiled from their sources note torchdrug doesn t support mps devices pip install torch 1 13 0 pip install git https github com rusty1s pytorch_scatter git pip install git https github com rusty1s pytorch_cluster git pip install torchdrug quick start torchdrug is designed for humans and focused on graph structured data it enables easy implementation of graph operations in machine learning models all the operations in torchdrug are backed by pytorch framework and support gpu acceleration and auto differentiation from torchdrug import data edge_list 0 1 1 2 2 3 3 4 4 5 5 0 graph data graph edge_list num_node 6 graph graph cuda the subgraph induced by nodes 2 3 4 subgraph graph subgraph 2 3 4 molecules are also supported in torchdrug you can get the desired molecule properties without any domain knowledge mol data molecule from_smiles ccoc o n atom_feature default bond_feature default print mol node_feature print mol atom_type print mol to_scaffold you may also register custom node edge or graph attributes they will be automatically processed during indexing operations with mol edge mol is_cc_bond mol edge_list 2 td carbon all dim 1 sub_mol mol subgraph mol atom_type td nitrogen print sub_mol is_cc_bond torchdrug provides a wide range of common datasets and building blocks for drug discovery with minimal code you can apply standard models to solve your own problem import torch from torchdrug import datasets dataset datasets tox21 dataset 0 visualize lengths int 0 8 len dataset int 0 1 len dataset lengths len dataset sum lengths train_set valid_set test_set torch utils data random_split dataset lengths from torchdrug import models tasks model models gin dataset node_feature_dim hidden_dims 256 256 256 256 task tasks propertyprediction model task dataset tasks training and inference are accelerated by multiple cpus or gpus this can be seamlessly switched in torchdrug by just a line of code from torchdrug import core single cpu multiple cpus distributed cpus solver core engine task train_set valid_set test_set optimizer single gpu solver core engine task train_set valid_set test_set optimizer gpus 0 multiple gpus solver core engine task train_set valid_set test_set optimizer gpus 0 1 2 3 distributed gpus solver core engine task train_set valid_set test_set optimizer gpus 0 1 2 3 0 1 2 3 experiments can be easily tracked and managed through weights biases platform solver core engine task train_set valid_set test_set optimizer logger wandb contributing everyone is welcome to contribute to the development of torchdrug please refer to contributing guidelines for more details license torchdrug is released under apache 2 0 license about a powerful and flexible machine learning platform for drug discovery torchdrug ai topics deep learning pytorch drug discovery graph neural networks resources readme license apache 2 0 license code of conduct code of conduct contributing contributing uh oh there was an error while loading 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