This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention
☆59Sep 30, 2022Updated 3 years ago
Alternatives and similar repositories for factored-attention
Users that are interested in factored-attention are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆26May 9, 2022Updated 3 years ago
- ☆10Sep 13, 2021Updated 4 years ago
- GREMLIN - learn MRF/potts model from input multiple sequence alignment! Implementation now available in C++ and Tensorflow/Python!☆59Oct 17, 2022Updated 3 years ago
- a pytorch version for GREMLIN, used to predict the protein contacts by coevolution method.☆17May 30, 2021Updated 4 years ago
- ☆20Jun 10, 2024Updated last year
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- ☆14Feb 13, 2023Updated 3 years ago
- Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different dom…☆736Dec 11, 2022Updated 3 years ago
- Code for Fold2Seq paper from ICML 2021☆50May 25, 2022Updated 3 years ago
- ☆34Oct 5, 2020Updated 5 years ago
- Training multi resolution GAN using MsCeleb datasets.☆12May 2, 2018Updated 7 years ago
- code repo for Set2Gaussian☆17Jun 19, 2020Updated 5 years ago
- To be a next-generation DL-based phenotype prediction from genome mutations.☆19May 17, 2021Updated 4 years ago
- PaccMann models for protein language modeling☆43Nov 10, 2021Updated 4 years ago
- Code of our JC paper: "Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted cont…☆76Mar 1, 2022Updated 4 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- ☆10Nov 10, 2023Updated 2 years ago
- ☆10Jun 29, 2021Updated 4 years ago
- functional genomic data integration☆10Sep 22, 2019Updated 6 years ago
- Code for the paper "DLAB - Deep learning methods for structure-basedvirtual screening of antibodies"☆30Oct 28, 2022Updated 3 years ago
- ☆35Nov 4, 2021Updated 4 years ago
- SWift and Optimized Recognition of protein Domains☆30Mar 24, 2026Updated 2 weeks ago
- Extract ligand binding sites from PDB. Match the binding sites to de novo scaffolds.☆12Dec 29, 2020Updated 5 years ago
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆11Oct 2, 2025Updated 6 months ago
- ☆34Jul 3, 2024Updated last year
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- PARCE version 1.0☆12Feb 1, 2021Updated 5 years ago
- A benchmark for comprehensive evaluation on protein structure tokenization methods☆53Aug 2, 2025Updated 8 months ago
- The standalone version / cli-tool of SPOT-Contact-Single available for public use for research purposes.☆16Feb 1, 2024Updated 2 years ago
- Note that current version does not include search of very large metagenome data. For some proteins, metagenome data is important. We will…☆99Jan 26, 2022Updated 4 years ago
- Codebase for our preprint using trRosetta to design proteins with discontinuous functional sites, found here: https://www.biorxiv.org/con…☆16Oct 27, 2021Updated 4 years ago
- some tools for working with protein (PDB) files in tensorflow☆11Jul 9, 2019Updated 6 years ago
- Make interactive LocusZoom plots from a local GWAS file☆10May 9, 2025Updated 11 months ago
- xxhash wrapper for Nim☆19Mar 20, 2025Updated last year
- ☆137Jun 3, 2025Updated 10 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- using graph convolutional neural network and spaital transcriptomics data to infer cell-cell interactions☆55Jun 15, 2021Updated 4 years ago
- ☆13Aug 13, 2020Updated 5 years ago
- Graph neural network for predicting energy of known and hypothetical crystal structures☆10Jan 26, 2022Updated 4 years ago
- An official implementation of Protein Representation Learning via Knowledge Enhanced Primary Structure Reasoning☆28Jul 14, 2023Updated 2 years ago
- Local Attention - Flax module for Jax☆22May 26, 2021Updated 4 years ago
- Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019☆262Jun 16, 2021Updated 4 years ago
- Ultra-fast in-silico structure mutation☆36Apr 9, 2025Updated last year