songlab-cal/tape issues and pull requests

#138 - Datasets are invalid and cannot be downloaded

Issue - State: open - Opened by KQDtianxiaK 3 months ago

#137 - BUG

Issue - State: open - Opened by dezhi0730 5 months ago

#136 - support OMP_NUM_THREADS for CPU limit

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

#135 - Usability questions

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

#134 - Data splits for stability task

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

#133 - How to use embedding of BERT pretrain model for my classification task?

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

#132 - quick-fix of typo in README.md (Issue #97)

Pull Request - State: open - Opened by keith-flynn almost 2 years ago

#131 - wild type sequence for stability dataset

Issue - State: open - Opened by lzhangUT over 2 years ago - 1 comment

#130 - Use TRRosetta to predict protein structure for a sequence

Issue - State: open - Opened by heavenAsk over 2 years ago

#129 - Distributed training does not exit properly after completion

Issue - State: open - Opened by Licko0909 over 2 years ago

#128 - How to fine-tune a new task？

Issue - State: closed - Opened by Binyun-Z over 2 years ago - 1 comment

#127 - the size of pre-train model 's input data

Issue - State: open - Opened by willow-yll over 2 years ago - 1 comment

#126 - attention masks tokenizer

Issue - State: open - Opened by Ch-rode over 2 years ago - 2 comments

#125 - Adding other metrics for validation steps

Issue - State: closed - Opened by marcmk6 over 2 years ago - 2 comments

#124 - cannot import tape

Issue - State: closed - Opened by willow-yll over 2 years ago - 2 comments

#123 - babbler-1900 model doesnt work!

Issue - State: open - Opened by hkoohy almost 3 years ago - 1 comment

#122 - results of contact prediction, medium&long range or short&medium&long range

Issue - State: open - Opened by apeterswu almost 3 years ago

#121 - EOFError: Ran out of input

Issue - State: open - Opened by ZhengYang-00 about 3 years ago

#120 - about proteins emb

Issue - State: closed - Opened by viko-3 about 3 years ago

#119 - About different length proteins

Issue - State: closed - Opened by viko-3 about 3 years ago

#118 - Filtered Remote Homology Pretraining Dataset

Issue - State: closed - Opened by cutecows about 3 years ago

#117 - Issue downloading weights

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

#116 - Runtime error when trying to train on contact prediction task with FP16

Issue - State: open - Opened by pocuca about 3 years ago

#115 - about ProteinBertModel

Issue - State: closed - Opened by viko-3 over 3 years ago - 11 comments

#114 - How to run with file in Gitlab

Issue - State: closed - Opened by willow-yll over 3 years ago - 9 comments

#113 - Update version and pip package

Issue - State: closed - Opened by rmrao over 3 years ago

#112 - some wrong with url of config.json

Issue - State: closed - Opened by willow-yll over 3 years ago - 9 comments

#111 - feat: S3 buckets update with relaxed requirements.

Pull Request - State: closed - Opened by drugilsberg over 3 years ago

#110 - Update data and model paths to new s3 bucket

Pull Request - State: closed - Opened by thomas-a-neil over 3 years ago

#109 - One-hot vocab

Issue - State: open - Opened by erika-alden over 3 years ago - 1 comment

#108 - Remove invalid UniRep token

Pull Request - State: open - Opened by joshim5 over 3 years ago

#107 - Fix spelling (wiht -> with).

Pull Request - State: closed - Opened by chrislengerich over 3 years ago - 1 comment

#106 - update setup.py

Pull Request - State: closed - Opened by hmkim over 3 years ago

#105 - Fine-Tune Downstream Tasks

Issue - State: closed - Opened by yuanenming over 3 years ago - 2 comments

#104 - Pfam dataset version and preprocess

Issue - State: closed - Opened by apeterswu over 3 years ago - 4 comments

#103 - tape training on fluorescence-dataset seemingly yield bad predictions

Issue - State: closed - Opened by ekvall93 over 3 years ago - 5 comments

#102 - Positional embedding

Issue - State: closed - Opened by linnlii almost 4 years ago - 1 comment

#101 - protein embedding is odd

Issue - State: closed - Opened by jxzly almost 4 years ago - 3 comments

#100 - Sequence to Sequence Bert Classification Model

Issue - State: closed - Opened by markpb2-ai almost 4 years ago - 1 comment

#99 - Where can I download the training and testing for the GFP fluorescence task?

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

#98 - Hyper-parameter setting for fine-tuning on contact prediction task

Issue - State: closed - Opened by wuzhen247 almost 4 years ago - 2 comments

#97 - Typo in README file

Issue - State: open - Opened by simoncorrea almost 4 years ago - 1 comment
Labels: documentation, quick-fix

#96 - Cannot run the provided examples for creating new models

Issue - State: open - Opened by rocketsfallonrocketfalls about 4 years ago - 1 comment
Labels: bug

#95 - Make Bert Large available as pretrained models

Issue - State: closed - Opened by changecreator about 4 years ago - 1 comment

#94 - Creating new embedding with a portion of data

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

#93 - A potential bug that may mask the start and stop tokens

Issue - State: open - Opened by lishen about 4 years ago - 1 comment
Labels: bug, quick-fix

#92 - length of transformer's output cannot match input's

Issue - State: closed - Opened by quailwwk about 4 years ago - 1 comment

#91 - Allow torch 1.5 and 1.6

Pull Request - State: open - Opened by konstin about 4 years ago

#90 - Vocabulary used for Pre-Trained BERT Model

Issue - State: closed - Opened by simolanzi about 4 years ago - 1 comment

#89 - How to declare "ProteinBertModel" model without pretrained ?

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

#88 - OOM when calling pretrained models on sequences

Issue - State: closed - Opened by wward97 about 4 years ago - 4 comments

#87 - Update README.md

Pull Request - State: closed - Opened by rmrao about 4 years ago

#86 - Mutli GPU takes 10 times longer than single GPU

Issue - State: closed - Opened by donal1 about 4 years ago - 2 comments

#85 - can't start pretrain with --nproc_per_node > 1

Issue - State: closed - Opened by FTD007 about 4 years ago - 2 comments

#84 - Question about ProteinNet dataset

Issue - State: closed - Opened by akirasosa over 4 years ago

#83 - Training LSTM language model on own data

Issue - State: closed - Opened by kodrzywolek over 4 years ago - 1 comment

#82 - tape-eval vs. huggingface api?

Issue - State: closed - Opened by hyeh20 over 4 years ago - 7 comments

#81 - Is It Possible to Use TAPE for Sequence Generation?

Issue - State: closed - Opened by brucejwittmann over 4 years ago - 1 comment

#80 - cuda out of memory when increasing samplesize

Issue - State: closed - Opened by kkpsiren over 4 years ago - 5 comments

#79 - Generate Secondary Structure prediction from fasta file directly.

Issue - State: closed - Opened by jas-preet over 4 years ago - 1 comment

#78 - Sequence length varies when generating an embeding.

Issue - State: closed - Opened by jas-preet over 4 years ago - 1 comment

#77 - Difficulties replicating pre-trained results from scratch

Issue - State: closed - Opened by psturmfels over 4 years ago - 3 comments

#76 - How use Huggingface API for Loading Pretrained Models?

Issue - State: closed - Opened by binarywz over 4 years ago - 1 comment

#75 - Mapping to Pfam IDs

Issue - State: open - Opened by christophfeinauer over 4 years ago - 7 comments
Labels: documentation, quick-fix

#74 - Loss and Perplexity

Issue - State: closed - Opened by AmeenAli over 4 years ago - 3 comments

#73 - UniRep pretrained weights

Issue - State: closed - Opened by fteufel over 4 years ago - 1 comment

#72 - Loss and perplexity

Issue - State: closed - Opened by AmeenAli over 4 years ago - 1 comment

#71 - UniRep or BERT fine tuning examples?

Issue - State: closed - Opened by KirkDCO over 4 years ago - 4 comments

#70 - CUDA out of memory issue with contact map and masked_language_model training

Issue - State: closed - Opened by skyve2012 over 4 years ago - 2 comments

#69 - Force download install

Pull Request - State: closed - Opened by pravinrav over 4 years ago - 1 comment

#68 - Force Download Bug Fixed

Pull Request - State: closed - Opened by pravinrav over 4 years ago - 1 comment

#67 - Contact Prediction (ProteinNet) raw data download link not working

Issue - State: closed - Opened by nibtehaz over 4 years ago - 2 comments

#66 - Visualization

Issue - State: closed - Opened by simolanzi over 4 years ago - 1 comment

#65 - Examples for using code (not from command line?)

Issue - State: closed - Opened by ddofer over 4 years ago - 2 comments

#64 - Removed dependency on CUDA in training.

Pull Request - State: open - Opened by alexanderwhatley over 4 years ago

#63 - Added force re-download

Pull Request - State: closed - Opened by pravinrav over 4 years ago

#62 - Reading output_filename.npz

Issue - State: closed - Opened by simolanzi over 4 years ago - 2 comments

#61 - secondary structure dictionary

Issue - State: open - Opened by jcdelpiano over 4 years ago - 3 comments
Labels: documentation, quick-fix

#60 - UniRep model pooled output returns 3800 vector values

Issue - State: closed - Opened by ptynecki over 4 years ago - 1 comment

#59 - Extend list of models by SeqVec

Issue - State: open - Opened by ptynecki over 4 years ago - 1 comment
Labels: enhancement, good first issue, help wanted, wontfix

#58 - Corrupted raw remote homology dataset

Issue - State: closed - Opened by wbogud over 4 years ago - 1 comment

#57 - Fine-Tuning of Bert model

Issue - State: closed - Opened by simolanzi over 4 years ago - 3 comments

#56 - Data licenses

Issue - State: open - Opened by tdiethe over 4 years ago - 1 comment
Labels: enhancement, help wanted

#55 - CUDA oom with batch size 1

Issue - State: closed - Opened by jxmorris12 over 4 years ago - 5 comments

#54 - what does the from tape import data_utils refer?

Issue - State: closed - Opened by HadXu over 4 years ago - 1 comment

#53 - UniRep's representation

Issue - State: closed - Opened by SorteKanin over 4 years ago - 1 comment

#52 - Question about onehot contact prediction model

Issue - State: closed - Opened by jessevig over 4 years ago - 1 comment

#51 - v0.4

Pull Request - State: closed - Opened by rmrao over 4 years ago

#50 - Added .fna, .ffn, .faa, .frn as alternative fasta suffixes

Pull Request - State: closed - Opened by tdiethe over 4 years ago - 1 comment

#49 - Corrupted stability dataset (raw format)

Issue - State: closed - Opened by ikedim01 over 4 years ago - 6 comments

#48 - tape-embed fails under PyTorch 1.5.0

Issue - State: open - Opened by wbogud over 4 years ago - 2 comments
Labels: bug, wontfix

#47 - Unable to locate data_utils module

Issue - State: closed - Opened by jessevig over 4 years ago - 3 comments

#46 - Questions: About train BERT from scratch parameter?

Issue - State: closed - Opened by HadXu over 4 years ago - 1 comment

#45 - trRosetta problem with tape_embed

Issue - State: closed - Opened by serbulent over 4 years ago - 2 comments

#44 - Can I make some simple predictions directly (just like stability on my own datasets) using the sequence embedding results?

Issue - State: closed - Opened by goes0n over 4 years ago - 2 comments

GitHub / songlab-cal/tape issues and pull requests