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
#692 - Runtime in half precision
Issue -
State: open - Opened by Hrovatin 19 days ago
#691 - [BUG] Fasta header with special characters alter output path
Issue -
State: open - Opened by jspaezp 22 days ago
#688 - Missing CUDA availability check in ESM-1v example
Issue -
State: open - Opened by ebeurer about 1 month ago
#686 - Fine tuning on sequencing classification data
Issue -
State: open - Opened by BIOBRICK about 1 month ago
#683 - Different result with esmfold server
Issue -
State: open - Opened by lzygitk7 about 1 month ago
- 1 comment
#680 - offset=24 in [Zero-shot variant prediction with protein language models]
Issue -
State: open - Opened by yinshiyi 2 months ago
#679 - Why the inpu size of embedding is 33?
Issue -
State: open - Opened by fulacse 2 months ago
- 1 comment
#678 - Contact prediction for multimeric proteins
Issue -
State: open - Opened by AnjaliSetiya 2 months ago
- 1 comment
#677 - Failed to build openfold
Issue -
State: open - Opened by AlejandroSanchezCano 3 months ago
- 2 comments
#674 - Error when predicting contacts for heterodimer
Issue -
State: open - Opened by AnjaliSetiya 3 months ago
#670 - RuntimeError
Issue -
State: open - Opened by tonyageall 4 months ago
- 5 comments
#669 - the specific code of the ESM2 model
Issue -
State: open - Opened by GriffithLin 4 months ago
#668 - Query on Alphabet Consistency Across Different Scales of ESM2 Models [8M, 35M, 150M, 650M, 3B, 150B]
Issue -
State: open - Opened by CNwangbin 4 months ago
#661 - Embedding
Issue -
State: closed - Opened by anonimoustt 4 months ago
#660 - fold.py in naming pdb file
Issue -
State: open - Opened by yzhang-github-pub 5 months ago
#658 - add max len option to BatchConverter
Pull Request -
State: closed - Opened by timydaley 5 months ago
- 1 comment
#656 - ESMFold for multimer fails when using HuggingFace installation
Issue -
State: open - Opened by eliottpark 5 months ago
- 1 comment
#655 - How to train LinearProjectionDistogramModel for my dataοΌ
Issue -
State: open - Opened by hasaiki136 5 months ago
#654 - requests.exceptions.SSLError :: Streamlit
Issue -
State: open - Opened by tcchola 5 months ago
#653 - Expecting multiple model of single sequence input
Issue -
State: closed - Opened by Hossen-sahadot97 5 months ago
#652 - AttributeError: module 'deepspeed' has no attribute 'comm'
Issue -
State: open - Opened by YvetteJxy 5 months ago
- 3 comments
#651 - how to input cropped protein for ESM-2 ?
Issue -
State: open - Opened by GriffithLin 6 months ago
- 1 comment
#650 - [Variant effect prediction] Fix CPU inference
Pull Request -
State: open - Opened by anton-bushuiev 6 months ago
- 1 comment
Labels: CLA Signed
#649 - index out of bounds during zero-shot with msa1b
Issue -
State: open - Opened by Maxwell-downtown 6 months ago
#648 - ESM2 pretrain
Issue -
State: open - Opened by ZJL0111 6 months ago
#647 - HuggingFace EsmForProteinFolding inference raises exception on Windows
Issue -
State: open - Opened by shimooper 6 months 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 6 months ago
- 1 comment
Labels: CLA Signed
#643 - esm2_t6_8M_UR50D model results in an empty representation
Issue -
State: open - Opened by Amels404 7 months ago
- 1 comment
#641 - ESMFold fails for some long sequence?
Issue -
State: open - Opened by yuanqm55 7 months ago
#640 - Can you share a dataset of ESM2 coding for UniRef90?
Issue -
State: open - Opened by JiangLab2020 7 months ago
#638 - "model_name" is not defined - ESM-2
Issue -
State: closed - Opened by bdabykov 7 months ago
- 1 comment
#637 - esm-fold interface: SyntaxError: invalid syntax
Issue -
State: open - Opened by johnnytam100 8 months ago
- 1 comment
#636 - How to convert folded_positions -> PDB file format?
Issue -
State: open - Opened by johnnytam100 8 months ago
- 1 comment
#635 - Discrepancy between ESMFold predicted `distogram_logits` and final output atomic coordinates
Issue -
State: open - Opened by Hejl19 8 months ago
#634 - ESMFold API SSL Ceritifcate Error
Issue -
State: closed - Opened by falatfernando 8 months ago
- 2 comments
#633 - Inverse folding samples from all tokens instead of just amino acids
Issue -
State: open - Opened by smitchell556 8 months ago
#632 - Getting multiple structures from one esmfold prediction?
Issue -
State: open - Opened by johnnytam100 8 months ago
#629 - SSL certificate problem: unable to get local issuer certificate
Issue -
State: open - Opened by coliva92 8 months ago
- 1 comment
#628 - The length limitation of protein sequences for different size of ESM2 (8M, 35M, 150M,,,,,,,,)?
Issue -
State: open - Opened by liudan111 8 months ago
- 1 comment
#626 - Einops 0.7.0 syntax error
Issue -
State: open - Opened by ivanpmartell 9 months ago
#625 - Locally Installed v1 Pretrained Model for Structure Prediction
Issue -
State: open - Opened by SkwisgaarSkwigelf 9 months ago
#623 - Erroneous characters generated by ESM-IF1
Issue -
State: open - Opened by JonathanLV123 9 months ago
#622 - FlashAttention support
Issue -
State: open - Opened by kklemon 9 months ago
#621 - No module named 'torch._six'
Issue -
State: open - Opened by DipBobDar 9 months ago
- 2 comments
#620 - Dataset for Remote Homology Evaluation
Issue -
State: open - Opened by amoldwin 9 months ago
#619 - Questions about the precomputed embeddings
Issue -
State: open - Opened by Lisa314159 9 months ago
#618 - docs: fixing citation rendering
Pull Request -
State: open - Opened by drugilsberg 9 months ago
- 1 comment
#617 - Fst
Pull Request -
State: closed - Opened by LeonHermann322 9 months ago
- 1 comment
#616 - PDB files not readable because chemical element symbol in columns 77-78 is incorrectly left-justified
Issue -
State: open - Opened by elmar-k 10 months ago
#615 - Error while compute embeddings in bulk from FASTA
Issue -
State: closed - Opened by smruti241 10 months ago
- 2 comments
#614 - Loading Embeddings error Supervised variant prediction with ESM
Issue -
State: open - Opened by CwilsonBroad 10 months ago
- 2 comments
#611 - Is facebook going to discontinue the esm development?
Issue -
State: open - Opened by johnnytam100 10 months ago
- 2 comments
#610 - Added a basic Dockerfile to improve dev experience
Pull Request -
State: open - Opened by ankitvgupta 10 months ago
- 3 comments
Labels: CLA Signed
#606 - EsmForSequenceClassification does not support gradient checkpointing
Issue -
State: open - Opened by Amelie-Schreiber 10 months ago
- 1 comment
#605 - Inverse Folding Training Dataset
Issue -
State: open - Opened by realfenston 10 months ago
#599 - There is abnormal hot line in the embedding along the sequence length dimension?
Issue -
State: open - Opened by chemgeeklian 11 months ago
#596 - add flag for torch device
Pull Request -
State: open - Opened by misko-diffuse 11 months ago
- 1 comment
#595 - How do we represent a deletion event in ESM-1v?
Issue -
State: open - Opened by Chonghao98 11 months ago
- 1 comment
#594 - How to install esmfold for A100 on cuda 10.1
Issue -
State: closed - Opened by linda5mith 11 months ago
- 3 comments
#593 - Sample source for ESM metagenomic atlas records
Issue -
State: closed - Opened by ntnn19 11 months ago
- 1 comment
#592 - ERROR: Could not find a version that satisfies the requirement openfold (unavailable) (from versions: 0.0.1)
Issue -
State: open - Opened by xiha-haxi 11 months ago
- 1 comment
#590 - Local installation help?
Issue -
State: closed - Opened by immunoliver 12 months ago
- 4 comments
#588 - How to use Zero-shot variant prediction for other protein sequences
Issue -
State: open - Opened by geng-lee 12 months ago
- 2 comments
#586 - ESM-IF and ESMFold in the same conda environnment
Issue -
State: open - Opened by Baldwin-disso 12 months ago
#584 - Google Colab "TypeError: 'str' object is not callable"
Issue -
State: closed - Opened by DaRinker 12 months ago
#583 - Difference between embeddings fetched from api vs embeddings calculated locally
Issue -
State: open - Opened by zas97 12 months ago
#582 - Provide predicted aligned error (PAE) for locally folded proteins
Issue -
State: open - Opened by jolakopec 12 months ago
- 1 comment
#579 - [Feature] MSA Transformer implementation of self_attn_mask
Issue -
State: open - Opened by rmaguire31 about 1 year ago
#578 - Make programming language reporting less confusing. π΅βπ«
Pull Request -
State: closed - Opened by scandido about 1 year ago
Labels: CLA Signed
#577 - How to install the esm-fold interface?
Issue -
State: open - Opened by johnnytam100 about 1 year ago
- 3 comments
#576 - guard torch_scatter dependency
Pull Request -
State: closed - Opened by rmrao about 1 year ago
Labels: CLA Signed
#575 - ValueError: too many values to unpack (expected 2)
Issue -
State: open - Opened by limpidzhao about 1 year ago
- 1 comment
#574 - How to use ESM models to generate new protein sequences similar to the training set
Issue -
State: closed - Opened by francescopatane96 about 1 year ago
- 6 comments
#573 - Error installing OpenFold
Issue -
State: closed - Opened by DaRinker about 1 year ago
- 2 comments
#572 - Fst
Pull Request -
State: closed - Opened by LeonHermann322 about 1 year ago
- 1 comment
#570 - confused about the model used
Issue -
State: open - Opened by daisykuma22 about 1 year ago
- 1 comment
#569 - Update util.py
Pull Request -
State: closed - Opened by latticetower about 1 year ago
- 2 comments
Labels: CLA Signed
#567 - Methods to plot/visualize structure for generated protein
Issue -
State: open - Opened by adaga06 about 1 year ago
#564 - Installation Error - OpenFold
Issue -
State: open - Opened by tamimmurad about 1 year ago
- 4 comments
#562 - RuntimeError: "LayerNormKernelImpl" not implemented for 'Half'
Issue -
State: open - Opened by ziyujiang818 about 1 year ago
- 2 comments
#561 - Can't run ESMFold
Issue -
State: open - Opened by melody666666 about 1 year ago
#560 - Folded structure from `esm-fold` has overlapping atoms
Issue -
State: open - Opened by em255 about 1 year ago
- 1 comment
#557 - details about finetuning
Issue -
State: open - Opened by xtzhang0216 about 1 year ago
#554 - Weird error when computing embedding for sequences
Issue -
State: closed - Opened by Joey-Xue about 1 year ago
#553 - NameError: name 'PartialState' is not defined
Issue -
State: closed - Opened by francescopatane96 about 1 year ago
- 1 comment
#552 - v2023_02 tarballs have less structures than listed in metadata-rc2.parquet
Issue -
State: open - Opened by Khalimat about 1 year ago
- 1 comment
#551 - Linux process status is D
Issue -
State: open - Opened by bj600800 about 1 year ago
- 1 comment
#548 - RAM crashes by fine tuning with pretrain ESM model on large dataset.
Issue -
State: open - Opened by amalislam675 about 1 year ago
- 3 comments
#547 - Issue when building wheel? Not sure if on my end
Issue -
State: open - Opened by bpizzano about 1 year ago
- 2 comments
#546 - KeyErroer: 'States'
Issue -
State: open - Opened by liaojing1111 about 1 year ago
#545 - Check if partial embeddings file exist before recomputing
Pull Request -
State: closed - Opened by JuLieAlgebra about 1 year ago
- 1 comment
#544 - esm2 with .csv files
Issue -
State: closed - Opened by nayeemmz about 1 year ago
- 3 comments
#543 - Potential source of GPU memory leak in `ESMFold`
Issue -
State: closed - Opened by amorehead about 1 year ago
- 1 comment
#541 - Training codes for ESM inverse folding
Issue -
State: open - Opened by adrienchaton about 1 year ago
- 3 comments
#539 - Error when importing batch_encode_sequences
Issue -
State: open - Opened by yangkky about 1 year ago
#538 - Fix MSA reading in predict.py
Pull Request -
State: open - Opened by alex-hh about 1 year ago
- 2 comments
Labels: CLA Signed
#537 - AttributeError: 'NoneType' object has no attribute 'arch'
Issue -
State: open - Opened by linyuheng594 about 1 year ago
- 1 comment
#536 - Fix small typo
Pull Request -
State: closed - Opened by amorehead about 1 year ago
- 2 comments
Labels: CLA Signed
#535 - Torch module no longer supported
Issue -
State: open - Opened by thype2000 about 1 year ago
- 5 comments
#532 - Question about ESM-1v results.
Issue -
State: open - Opened by elttaes about 1 year ago