Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / facebookresearch/esm issues and pull requests

#538 - Fix MSA reading in predict.py

Pull Request - State: open - Opened by alex-hh over 1 year ago - 2 comments
Labels: CLA Signed

#537 - AttributeError: 'NoneType' object has no attribute 'arch'

Issue - State: open - Opened by linyuheng594 over 1 year ago - 1 comment

#536 - Fix small typo

Pull Request - State: closed - Opened by amorehead over 1 year ago - 2 comments
Labels: CLA Signed

#535 - Torch module no longer supported

Issue - State: open - Opened by thype2000 over 1 year ago - 5 comments

#532 - Question about ESM-1v results.

Issue - State: closed - Opened by elttaes over 1 year ago - 1 comment

#531 - 'esm.pretrained' has no attribute 'esm2_t6_8M_UR50D'

Issue - State: open - Opened by LZhang98 over 1 year ago - 2 comments

#529 - Canonicalize all license headers, small README fixes

Pull Request - State: closed - Opened by tomsercu over 1 year ago - 1 comment
Labels: CLA Signed

#528 - Code release for protein programming language paper

Pull Request - State: closed - Opened by brianhie over 1 year ago
Labels: CLA Signed

#527 - Code release for "Language Models Generalize Beyond Natural Proteins".

Pull Request - State: closed - Opened by robert-verkuil over 1 year ago
Labels: CLA Signed

#526 - Fix link and repeat Atlas license

Pull Request - State: closed - Opened by tomsercu over 1 year ago
Labels: CLA Signed

#525 - ESM2 pretrained model in torch hub not accessible

Issue - State: closed - Opened by lordim over 1 year ago

#521 - 'esm-fold' error from command line execution

Issue - State: open - Opened by amoroso2 over 1 year ago - 1 comment

#520 - ESM is failed for the protein Ccnd1 (Q790L7)

Issue - State: closed - Opened by hust220 over 1 year ago - 1 comment

#519 - esm_contact_prediction.ipynb -FileNotFoundError

Issue - State: closed - Opened by 313king over 1 year ago - 2 comments

#518 - 400 Bad Request for foldseekdb

Issue - State: open - Opened by mjoh223 over 1 year ago - 3 comments

#517 - when i use esm_contact_prediction.ipynb ,it has a ' ModuleNotFoundError '

Issue - State: closed - Opened by 313king over 1 year ago - 3 comments

#516 - Add atlas bulk embeddings and v2023_02 backfills

Pull Request - State: closed - Opened by w3ntinglu over 1 year ago
Labels: CLA Signed

#515 - Code "Language models generalize beyond natural proteins"

Issue - State: closed - Opened by zas97 over 1 year ago - 2 comments

#512 - Update atlas science citation

Pull Request - State: closed - Opened by tomsercu over 1 year ago
Labels: CLA Signed

#508 - HTTP Error 403 when downloading some Atlas tarballs via aria2c

Issue - State: closed - Opened by naailkhan28 over 1 year ago - 2 comments

#505 - Atlas update v2023_02

Pull Request - State: closed - Opened by tomsercu over 1 year ago
Labels: CLA Signed

#502 - methods to plot UMAP for ~200,000 protein structures

Issue - State: open - Opened by avilella over 1 year ago - 2 comments

#501 - 'GVPTransformerModel' object has no attribute 'num_layers'

Issue - State: open - Opened by bg-uni over 1 year ago - 1 comment

#500 - Broken/outdated URIs in contact_prediction.ipynb

Issue - State: closed - Opened by DanBuchan over 1 year ago - 1 comment

#499 - ESM-IF sampling for dimer

Issue - State: open - Opened by adrienchaton over 1 year ago

#498 - Create missing __init__.py file in model module

Pull Request - State: closed - Opened by moritzschaefer over 1 year ago - 3 comments
Labels: CLA Signed

#497 - allow the user to select a CUDA device when running esmfold_inference.py

Pull Request - State: closed - Opened by decarboxy over 1 year ago - 2 comments

#496 - Release ESMFold IPA only models

Pull Request - State: closed - Opened by ebetica over 1 year ago
Labels: CLA Signed

#488 - Fix sampling and scoring device bugs

Pull Request - State: closed - Opened by naailkhan28 over 1 year ago
Labels: CLA Signed

#487 - The device problem when running the ESM-IF

Issue - State: open - Opened by a96123155 over 1 year ago - 1 comment

#484 - How to evaluate the confidence of a multimer ？

Issue - State: open - Opened by genomicsgroup over 1 year ago - 3 comments

#483 - ESMFold - Masking specific residues in input FASTA?

Issue - State: closed - Opened by amorehead over 1 year ago - 2 comments

#481 - Issue with Typing-extensions during run of batch submission.

Issue - State: closed - Opened by coopersvajda over 1 year ago - 4 comments

#480 - Hey There,

Issue - State: closed - Opened by coopersvajda over 1 year ago

#479 - CUDA error

Issue - State: closed - Opened by sbassi over 1 year ago - 4 comments

#477 - ESM atlas length limit

Issue - State: open - Opened by y-hwang over 1 year ago - 4 comments

#476 - pre-train with ELECTRA rather than BERT

Issue - State: closed - Opened by Joseph-Vineland over 1 year ago - 3 comments

#475 - touching up the readmes a bit regarding Atlas and blogpost

Pull Request - State: closed - Opened by tomsercu over 1 year ago
Labels: CLA Signed

#474 - RuntimeError: File cannot be opened

Issue - State: closed - Opened by HyprValent over 1 year ago - 1 comment

#473 - ESM-IF1 installation

Issue - State: closed - Opened by sahakyanhk over 1 year ago - 1 comment

#472 - Questions about row self-attention implementation

Issue - State: open - Opened by gdolsten over 1 year ago

#471 - Initialization of paired representation inputs to the ESMFold folding block

Issue - State: closed - Opened by amyxlu over 1 year ago - 3 comments

#461 - Error while installing ESM-2

Issue - State: closed - Opened by anpanche over 1 year ago - 2 comments

#460 - fair-esm 1.0.3 does not provide the extra 'esmfold'

Issue - State: open - Opened by thyol over 1 year ago - 12 comments

#457 - Out of memory - upper limit on sequence length?

Issue - State: open - Opened by jennastanislaw over 1 year ago - 4 comments

#456 - openfold installation

Issue - State: open - Opened by saeid976 over 1 year ago - 11 comments

#455 - Update data.py

Pull Request - State: closed - Opened by Chenjw99 over 1 year ago - 2 comments

#453 - ESM-2 Model checkpoints during training run

Issue - State: closed - Opened by tomsercu over 1 year ago

#451 - Only CPU Malfunction -- HF Colab Notebook

Issue - State: open - Opened by coopersvajda over 1 year ago - 1 comment

#448 - Protein design papers added

Pull Request - State: closed - Opened by tomsercu over 1 year ago
Labels: CLA Signed

#447 - download model from huggingface

Issue - State: closed - Opened by saeid976 over 1 year ago - 3 comments

#445 - Adjust header in output file

Pull Request - State: closed - Opened by dawsonhunt almost 2 years ago - 6 comments
Labels: CLA Signed

#443 - EMSIF1-Encoder output as structure representation

Issue - State: open - Opened by LDAIprotein almost 2 years ago

#442 - can't download the contact-regression.pt for those ESM models

Issue - State: open - Opened by imSeaton almost 2 years ago - 1 comment

#438 - Fix sampling error with partial_seq

Pull Request - State: closed - Opened by chloechsu almost 2 years ago
Labels: CLA Signed

#431 - atom name all left justified

Issue - State: open - Opened by kad-ecoli almost 2 years ago - 2 comments

#426 - Question about confidence determination

Issue - State: closed - Opened by alpha-omega-labs almost 2 years ago - 3 comments

#423 - Question about mean-pooled protein embeddings

Issue - State: closed - Opened by y-hwang almost 2 years ago

#421 - RuntimeError: view size is not compatible with input tensor's on MPS backend

Issue - State: closed - Opened by shaharec almost 2 years ago - 1 comment

#418 - Why is `lm_head` in ESM-2 (35M) (480, 480)?

Issue - State: closed - Opened by jasperhyp almost 2 years ago - 1 comment

#410 - name of protein != entirety of header

Issue - State: open - Opened by flowers9 almost 2 years ago - 1 comment
Labels: good first issue

#408 - fix typo in README.md

Pull Request - State: closed - Opened by eltociear almost 2 years ago - 1 comment
Labels: CLA Signed

#407 - CUDA out of memory error for long sequences

Issue - State: closed - Opened by gbrown40 almost 2 years ago - 5 comments

#405 - High quality ESM atlas contains some pdb files without ATOM records.

Issue - State: open - Opened by khb7840 almost 2 years ago - 1 comment

#404 - Some pdbfile ATOM sections are missing Spaces

Issue - State: open - Opened by bearmin almost 2 years ago - 1 comment

#402 - Some pdbfile ATOM sections are missing Spaces

Issue - State: closed - Opened by bearmin almost 2 years ago

#399 - Issue with ESM_advanced Colab

Issue - State: open - Opened by jfbazan almost 2 years ago

#398 - document esmfold version

Pull Request - State: closed - Opened by tomsercu almost 2 years ago
Labels: CLA Signed

#395 - Separation of model config and weights

Issue - State: closed - Opened by kklemon almost 2 years ago - 2 comments

#386 - Further CUDA support for IF-1

Pull Request - State: closed - Opened by naailkhan28 almost 2 years ago - 5 comments
Labels: CLA Signed

#379 - update IF1 readme colab link to multichain

Pull Request - State: closed - Opened by tomsercu almost 2 years ago - 1 comment
Labels: CLA Signed

#375 - ESMAtlas api access: Rate limit?

Issue - State: closed - Opened by fteufel almost 2 years ago - 11 comments

#374 - Configuring device in Inverse Folding model

Issue - State: closed - Opened by adrienchaton almost 2 years ago - 4 comments

#372 - download pretrained models in a local disk storage?

Issue - State: open - Opened by ryao-mdanderson almost 2 years ago - 11 comments

#364 - Error when setting chunk size for ESMFold

Issue - State: closed - Opened by martinez-zacharya almost 2 years ago - 5 comments

#362 - Fix typo in README.md

Pull Request - State: closed - Opened by amorehead almost 2 years ago

#350 - metadata dataframe content, add sequence crc64

Issue - State: open - Opened by tomsercu almost 2 years ago - 1 comment
Labels: enhancement

#348 - Obtaining a embedding for sequence

Issue - State: closed - Opened by SalvatoreRa almost 2 years ago - 2 comments

#336 - No module named 'openfold'

Issue - State: closed - Opened by yesols almost 2 years ago - 2 comments

#331 - Adding console scripts

Pull Request - State: closed - Opened by andersoncarlosfs almost 2 years ago - 7 comments
Labels: CLA Signed

#312 - Wrong colab link for inverse folding multichain notebook

Issue - State: closed - Opened by chloechsu almost 2 years ago - 1 comment

#299 - use of bos and eos token when training

Issue - State: closed - Opened by zhenyuhe00 about 2 years ago - 4 comments

#267 - Token dropout is set to Ture duing inference?

Issue - State: closed - Opened by zhenyuhe00 about 2 years ago - 5 comments

#262 - Layer weights for ESM-Fold

Issue - State: closed - Opened by zhenyuhe00 about 2 years ago - 6 comments

#255 - ESM2 embedding extraction error: 'NoneType' object has no attribute 'arch'

Issue - State: closed - Opened by HannesStark about 2 years ago - 3 comments

#244 - MSA dataset

Issue - State: closed - Opened by EBGU about 2 years ago - 2 comments

#236 - Inverse Folding Feature Request: Fixing parts of the protein sequence

Issue - State: closed - Opened by chanjed about 2 years ago - 5 comments
Labels: enhancement, good first issue

#234 - MSA batch converter does not accept pre-masked MSAs

Issue - State: open - Opened by seanrjohnson about 2 years ago - 5 comments
Labels: bug, good first issue

#228 - Inconsistent result between multi-MSAs and single-MSAs

Issue - State: open - Opened by huangtinglin about 2 years ago - 2 comments

#164 - KeyError: 'J'

Issue - State: closed - Opened by liudan111 over 2 years ago - 6 comments

#152 - Huggingface Transformers model compatibility?

Issue - State: closed - Opened by ddofer almost 3 years ago - 2 comments