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

#698 - ESMFold crashing with specific FASTA files

Issue - State: open - Opened by npcooley 6 months ago

#696 - esmfold_v1() error in pl_upgrades branch for pytorch v2 and cuda v12

Issue - State: open - Opened by MaxChu719 7 months ago - 1 comment

#694 - Codes to fine-tune ESM-IF1

Issue - State: open - Opened by tuln128 7 months ago

#692 - Runtime in half precision

Issue - State: open - Opened by Hrovatin 8 months ago

#688 - Missing CUDA availability check in ESM-1v example

Issue - State: open - Opened by ebeurer 8 months ago

#686 - Fine tuning on sequencing classification data

Issue - State: open - Opened by BIOBRICK 8 months ago

#683 - Different result with esmfold server

Issue - State: open - Opened by lzygitk7 9 months ago - 1 comment

#679 - Why the inpu size of embedding is 33?

Issue - State: open - Opened by fulacse 10 months ago - 1 comment

#678 - Contact prediction for multimeric proteins

Issue - State: open - Opened by AnjaliSetiya 10 months ago - 1 comment

#677 - Failed to build openfold

Issue - State: open - Opened by AlejandroSanchezCano 10 months ago - 3 comments

#674 - Error when predicting contacts for heterodimer

Issue - State: open - Opened by AnjaliSetiya 10 months ago

#670 - RuntimeError

Issue - State: open - Opened by tonyageall 11 months ago - 5 comments

#669 - the specific code of the ESM2 model

Issue - State: open - Opened by GriffithLin 11 months ago

#661 - Embedding

Issue - State: closed - Opened by anonimoustt 12 months ago

#660 - fold.py in naming pdb file

Issue - State: open - Opened by yzhang-github-pub 12 months ago

#658 - add max len option to BatchConverter

Pull Request - State: closed - Opened by timydaley 12 months ago - 1 comment

#656 - ESMFold for multimer fails when using HuggingFace installation

Issue - State: open - Opened by eliottpark 12 months ago - 1 comment

#654 - requests.exceptions.SSLError :: Streamlit

Issue - State: open - Opened by tcchola about 1 year ago

#653 - Expecting multiple model of single sequence input

Issue - State: closed - Opened by Hossen-sahadot97 about 1 year ago

#652 - AttributeError: module 'deepspeed' has no attribute 'comm'

Issue - State: open - Opened by YvetteJxy about 1 year ago - 3 comments

#651 - how to input cropped protein for ESM-2 ?

Issue - State: open - Opened by GriffithLin about 1 year ago - 1 comment

#650 - [Variant effect prediction] Fix CPU inference

Pull Request - State: open - Opened by anton-bushuiev about 1 year ago - 1 comment
Labels: CLA Signed

#649 - index out of bounds during zero-shot with msa1b

Issue - State: open - Opened by Maxwell-downtown about 1 year ago

#648 - ESM2 pretrain

Issue - State: open - Opened by ZJL0111 about 1 year ago

#647 - HuggingFace EsmForProteinFolding inference raises exception on Windows

Issue - State: open - Opened by shimooper about 1 year ago - 1 comment

#645 - Move the scripts folder into esm package and revise on einops version

Pull Request - State: open - Opened by gefei-qian-nih about 1 year ago - 1 comment
Labels: CLA Signed

#643 - esm2_t6_8M_UR50D model results in an empty representation

Issue - State: open - Opened by Amels404 about 1 year ago - 1 comment

#641 - ESMFold fails for some long sequence?

Issue - State: open - Opened by yuanqm55 about 1 year ago

#640 - Can you share a dataset of ESM2 coding for UniRef90?

Issue - State: open - Opened by JiangLab2020 about 1 year ago - 1 comment

#638 - "model_name" is not defined - ESM-2

Issue - State: closed - Opened by bdabykov about 1 year ago - 1 comment

#637 - esm-fold interface: SyntaxError: invalid syntax

Issue - State: open - Opened by johnnytam100 about 1 year ago - 1 comment

#636 - How to convert folded_positions -> PDB file format?

Issue - State: open - Opened by johnnytam100 about 1 year ago - 1 comment

#634 - ESMFold API SSL Ceritifcate Error

Issue - State: closed - Opened by falatfernando about 1 year ago - 2 comments

#629 - SSL certificate problem: unable to get local issuer certificate

Issue - State: open - Opened by coliva92 over 1 year ago - 1 comment

#626 - Einops 0.7.0 syntax error

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

#623 - Erroneous characters generated by ESM-IF1

Issue - State: open - Opened by JonathanLV123 over 1 year ago

#622 - FlashAttention support

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

#621 - No module named 'torch._six'

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

#620 - Dataset for Remote Homology Evaluation

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

#619 - Questions about the precomputed embeddings

Issue - State: open - Opened by Lisa314159 over 1 year ago

#618 - docs: fixing citation rendering

Pull Request - State: open - Opened by drugilsberg over 1 year ago - 1 comment

#617 - Fst

Pull Request - State: closed - Opened by LeonHermann322 over 1 year ago - 1 comment

#615 - Error while compute embeddings in bulk from FASTA

Issue - State: closed - Opened by smruti241 over 1 year ago - 2 comments

#614 - Loading Embeddings error Supervised variant prediction with ESM

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

#611 - Is facebook going to discontinue the esm development?

Issue - State: open - Opened by johnnytam100 over 1 year ago - 2 comments

#610 - Added a basic Dockerfile to improve dev experience

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

#605 - Inverse Folding Training Dataset

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

#596 - add flag for torch device

Pull Request - State: open - Opened by misko-diffuse over 1 year ago - 1 comment

#595 - How do we represent a deletion event in ESM-1v?

Issue - State: open - Opened by Chonghao98 over 1 year ago - 1 comment

#594 - How to install esmfold for A100 on cuda 10.1

Issue - State: closed - Opened by linda5mith over 1 year ago - 3 comments

#593 - Sample source for ESM metagenomic atlas records

Issue - State: closed - Opened by ntnn19 over 1 year ago - 1 comment

#590 - Local installation help?

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

#588 - How to use Zero-shot variant prediction for other protein sequences

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

#586 - ESM-IF and ESMFold in the same conda environnment

Issue - State: open - Opened by Baldwin-disso over 1 year ago

#584 - Google Colab "TypeError: 'str' object is not callable"

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

#582 - Provide predicted aligned error (PAE) for locally folded proteins

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

#578 - Make programming language reporting less confusing. πŸ˜΅β€πŸ’«

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

#577 - How to install the esm-fold interface?

Issue - State: open - Opened by johnnytam100 over 1 year ago - 3 comments

#576 - guard torch_scatter dependency

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

#575 - ValueError: too many values to unpack (expected 2)

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

#573 - Error installing OpenFold

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

#572 - Fst

Pull Request - State: closed - Opened by LeonHermann322 over 1 year ago - 1 comment

#570 - confused about the model used

Issue - State: open - Opened by daisykuma22 over 1 year ago - 1 comment

#569 - Update util.py

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

#567 - Methods to plot/visualize structure for generated protein

Issue - State: open - Opened by adaga06 over 1 year ago

#564 - Installation Error - OpenFold

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

#562 - RuntimeError: "LayerNormKernelImpl" not implemented for 'Half'

Issue - State: open - Opened by ziyujiang818 over 1 year ago - 2 comments

#561 - Can't run ESMFold

Issue - State: open - Opened by melody666666 over 1 year ago

#560 - Folded structure from `esm-fold` has overlapping atoms

Issue - State: open - Opened by em255 over 1 year ago - 1 comment

#557 - details about finetuning

Issue - State: open - Opened by xtzhang0216 over 1 year ago

#554 - Weird error when computing embedding for sequences

Issue - State: closed - Opened by Joey-Xue over 1 year ago

#553 - NameError: name 'PartialState' is not defined

Issue - State: closed - Opened by francescopatane96 over 1 year ago - 1 comment

#552 - v2023_02 tarballs have less structures than listed in metadata-rc2.parquet

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

#551 - Linux process status is D

Issue - State: open - Opened by bj600800 over 1 year ago - 1 comment

#548 - RAM crashes by fine tuning with pretrain ESM model on large dataset.

Issue - State: open - Opened by amalislam675 over 1 year ago - 3 comments

#547 - Issue when building wheel? Not sure if on my end

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

#546 - KeyErroer: 'States'

Issue - State: open - Opened by liaojing1111 over 1 year ago

#545 - Check if partial embeddings file exist before recomputing

Pull Request - State: closed - Opened by JuLieAlgebra over 1 year ago - 1 comment

#544 - esm2 with .csv files

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

#543 - Potential source of GPU memory leak in `ESMFold`

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

#541 - Training codes for ESM inverse folding

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

#539 - Error when importing batch_encode_sequences

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