Implementation of Graph Transformer in Pytorch, for potential use in replicating Alphafold2
☆239Jun 22, 2023Updated 3 years ago
Alternatives and similar repositories for graph-transformer-pytorch
Users that are interested in graph-transformer-pytorch are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- An unofficial implementation of Graph Transformer (Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classificat…☆36Apr 20, 2024Updated 2 years ago
- Implementation of E(n)-Transformer, which incorporates attention mechanisms into Welling's E(n)-Equivariant Graph Neural Network☆226Jun 2, 2024Updated 2 years ago
- Implementation of Invariant Point Attention, used for coordinate refinement in the structure module of Alphafold2, as a standalone Pytorc…☆171Nov 25, 2022Updated 3 years ago
- Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein…☆290Dec 17, 2024Updated last year
- Implementation of SE3-Transformers for Equivariant Self-Attention, in Pytorch. This specific repository is geared towards integration wit…☆331Aug 28, 2025Updated 11 months ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Graph neural network message passing reframed as a Transformer with local attention☆70Dec 24, 2022Updated 3 years ago
- Graph Transformer Architecture. Source code for "A Generalization of Transformer Networks to Graphs", DLG-AAAI'21.☆1,028Jul 27, 2021Updated 5 years ago
- Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pyt…☆76Jun 8, 2021Updated 5 years ago
- Implementation of Tranception, an attention network, paired with retrieval, that is SOTA for protein fitness prediction☆32Jun 19, 2022Updated 4 years ago
- Implementation of E(n)-Equivariant Graph Neural Networks, in Pytorch☆532Dec 6, 2024Updated last year
- Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure☆326Nov 15, 2025Updated 8 months ago
- Graphormer is a general-purpose deep learning backbone for molecular modeling.☆2,469Jun 12, 2026Updated last month
- code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503☆580Apr 3, 2026Updated 4 months ago
- Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion☆59May 6, 2024Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Pytorch reimplementation of Molecule Attention Transformer, which uses a transformer to tackle the graph-like structure of molecules☆58Dec 2, 2020Updated 5 years ago
- An all-atom protein structure dataset for machine learning.☆365Mar 16, 2024Updated 2 years ago
- Attempt at reproduction of AlphaFold2☆98Updated this week
- Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design☆83Aug 27, 2021Updated 4 years ago
- To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released☆1,632Oct 29, 2022Updated 3 years ago
- De novo protein structure prediction using iteratively predicted structural constraints☆60Jan 30, 2022Updated 4 years ago
- FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation☆297Dec 10, 2024Updated last year
- Graph Transformer Networks (Authors' PyTorch implementation for the NeurIPS 19 paper)☆1,083Feb 15, 2023Updated 3 years ago
- PLaTITO is an open-source model for generative molecular dynamics of proteins.☆25May 6, 2026Updated 2 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- A deep neural network with hybrid architecture (EGNN + Transformer) for molecular properties prediction.☆23Dec 9, 2023Updated 2 years ago
- Training neural network potentials☆480Jul 13, 2026Updated 3 weeks ago
- The official implementation of NeurIPS22 spotlight paper "NodeFormer: A Scalable Graph Structure Learning Transformer for Node Classifica…☆312Mar 4, 2024Updated 2 years ago
- A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms☆143Apr 20, 2022Updated 4 years ago
- [ICLR 2023 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs☆287Feb 11, 2025Updated last year
- Some personal experiments around routing tokens to different autoregressive attention, akin to mixture-of-experts☆122Oct 17, 2024Updated last year
- [NeurIPS 2025 spotlight] Efficient factorized variant of the IPA module.☆47Nov 14, 2025Updated 8 months ago
- An implementation of local windowed attention for language modeling☆503Jul 16, 2025Updated last year
- Generative Models for Graph-Based Protein Design☆291Dec 24, 2020Updated 5 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Energy-based models for atomic-resolution protein conformations☆105Mar 22, 2022Updated 4 years ago
- Implementation of Lie Transformer, Equivariant Self-Attention, in Pytorch☆98Feb 19, 2021Updated 5 years ago
- Official Pytorch Implementation of GraphiT☆111Jul 6, 2021Updated 5 years ago
- ☆34Sep 19, 2025Updated 10 months ago
- This repository contains a set of scripts for performing singular value decomposition on protein multiple sequence alignments, and analyz…☆11Aug 12, 2024Updated last year
- PyTorch library of layers acting on protein representations☆119Jun 30, 2024Updated 2 years ago
- Implementation of Cross Transformer for spatially-aware few-shot transfer, in Pytorch☆54Mar 30, 2021Updated 5 years ago