Ecosyste.ms: Issues

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GitHub / agemagician/ProtTrans issues and pull requests

#164 - ProtT5 model training loss function

Issue - State: open - Opened by Alex2975 2 months ago - 6 comments

#163 - fix syntax error

Pull Request - State: closed - Opened by kamurani 2 months ago - 1 comment

#162 - Generate embedding for unnatural amino acid

Issue - State: open - Opened by Frank-LIU-520 3 months ago - 1 comment

#160 - Fine-tuning for antibody dataset

Issue - State: open - Opened by Frank-LIU-520 3 months ago - 2 comments

#159 - link for downloading ProtElektra does not work

Issue - State: open - Opened by aryankeluskar 3 months ago - 1 comment

#158 - T5 fine-tuning special tokens

Issue - State: open - Opened by tombosc 4 months ago - 3 comments

#157 - Missing `example_seqs.fasta` file in the Colab example

Issue - State: open - Opened by zt20001126 5 months ago - 3 comments

#156 - Prediction meanings

Issue - State: open - Opened by lhkhiem28 5 months ago - 1 comment

#155 - Error while saving the fine-tuned model

Issue - State: closed - Opened by Chinjuj2017 6 months ago - 2 comments

#154 - About prot_t5

Issue - State: closed - Opened by yelou2022 6 months ago - 2 comments

#152 - IndexError in generate protein notebook

Issue - State: open - Opened by ekiefl 8 months ago - 3 comments

#151 - What was the pretraining split for the ProtT5-UniRef50 model?

Issue - State: open - Opened by speydril 8 months ago - 1 comment

#150 - What is the `./protT5` directory in the Colab example?

Issue - State: closed - Opened by ekiefl 10 months ago - 4 comments

#149 - Feature order

Issue - State: closed - Opened by abelavit 11 months ago - 2 comments

#148 - How was ProtT5 trained?

Issue - State: closed - Opened by Sspandau 11 months ago - 1 comment

#147 - ProtT5 model generate

Issue - State: open - Opened by BSharmi 11 months ago - 2 comments

#146 - Generating embedding from finetuned model

Issue - State: open - Opened by abelavit 11 months ago - 3 comments

#145 - Issue running PT5_LoRA_Finetuning_per_residue_reg.ipynb

Issue - State: closed - Opened by abelavit 11 months ago - 3 comments

#144 - (Question) Can I use this for protein homology to UniRef50?

Issue - State: open - Opened by jolespin 12 months ago - 2 comments

#143 - Error while running Finetuning script

Issue - State: closed - Opened by suresh-pokharel 12 months ago - 2 comments

#142 - per_residue and per_protein embedding comparison

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

#141 - Link to finetune colab and license info

Pull Request - State: closed - Opened by RSchmirler about 1 year ago

#140 - Added link to Colab version

Pull Request - State: closed - Opened by RSchmirler about 1 year ago

#139 - Fix full precision casting on cpu

Pull Request - State: closed - Opened by li-yq about 1 year ago - 1 comment

#138 - Mixed-precision and Preprint link

Pull Request - State: closed - Opened by RSchmirler about 1 year ago

#137 - Formatting for ProtT5 labels

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

#136 - Fine tuning with Lora on multi GPU

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

#135 - Fine-tuning smaller models in half-precision

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

#134 - Error in Generation of Embeddings from list of sequences via ProtT5

Issue - State: open - Opened by amalislam675 over 1 year ago - 5 comments

#132 - Added LoRA per residue regression

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

#131 - Tokenising multi-chain proteins

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

#130 - RuntimeError: "addmm_impl_cpu_" not implemented for 'Half'

Issue - State: closed - Opened by Mjvolk3 over 1 year ago - 2 comments

#129 - Sequence extraction from embedding representation

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

#128 - Fix quick start

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

#127 - Improvements on Quick Start in README

Issue - State: closed - Opened by delta2323 over 1 year ago - 1 comment

#126 - Gene Ontology (GO) prediction

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

#125 - New364 dataset

Issue - State: closed - Opened by SamarthGarg09 over 1 year ago - 1 comment

#124 - Adding LoRA Finetuning Notebooks

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

#123 - Sequence processing

Issue - State: closed - Opened by BSharmi over 1 year ago - 6 comments

#122 - Availability of Seq2Seq Autoencoder Models for Protein Sequences

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

#121 - OSError: Can't load tokenizer for 'Rostlab/prot_t5_xl_uniref50'

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

#120 - Speed up via xformers

Issue - State: open - Opened by mortonjt over 1 year ago - 6 comments

#119 - Training a T5 tokenizer

Issue - State: closed - Opened by ideasbyjin over 1 year ago - 5 comments

#118 - I want the prottrans training code.

Issue - State: closed - Opened by miderxi over 1 year ago - 15 comments

#117 - Fine-Tune T5 for Residue Classification

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

#116 - Multi-Mask Inference in ProtBert via HF Pipeline Function

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

#115 - Sanity check of inputs

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

#114 - Sanity check of data processing

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

#113 - Finetuning ProtT5

Issue - State: closed - Opened by BSharmi almost 2 years ago - 7 comments

#111 - How to Fine-tune Rostlab/prot_t5_xl_uniref50 Model for Sequence Generation

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

#110 - ZeroDivisionError when running prott5_embedder.py

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

#109 - How to prevent the residue X to be generated

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

#108 - Questions for generating sequence using ProtXLNet pertained-model

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

#107 - can i using pretraining for some regression problems?

Issue - State: closed - Opened by morestart almost 2 years ago - 16 comments

#106 - FineTuning of Model for Allosteric Site Prediction

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

#105 - 1D amino acid sequence generation from encoder output

Issue - State: closed - Opened by bg-uni about 2 years ago - 1 comment

#104 - ProtT5 Fine-Tuning

Issue - State: closed - Opened by TheBil99 about 2 years ago - 3 comments

#103 - Exception: Label encoder found an unknown label.

Issue - State: closed - Opened by skr3178 about 2 years ago - 2 comments

#102 - can't set attribute

Issue - State: closed - Opened by skr3178 about 2 years ago - 2 comments

#100 - Bert pretraining approach

Issue - State: closed - Opened by shu1273 about 2 years ago - 1 comment

#99 - Sequence-level embeddings using ProtTrans models

Issue - State: closed - Opened by josephyu12 about 2 years ago - 3 comments

#98 - Generating protein sequences

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

#97 - Protein-protein interaction

Issue - State: closed - Opened by Moeinh77 about 2 years ago - 3 comments

#96 - Generating embeddings in T5

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

#95 - Cross Attention Query

Issue - State: closed - Opened by lhallee over 2 years ago - 9 comments

#93 - question about prot T5 denoising objective

Issue - State: closed - Opened by zzk1st over 2 years ago - 3 comments

#92 - about the decoder of prott5 model

Issue - State: closed - Opened by xiebaoshu058 over 2 years ago - 4 comments

#91 - Precomputed embedding for all huuman proteins

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

#90 - ProtT5 vs fine-tuned ProtBERT for classification

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

#89 - Using subnets of ProtTrans for protein understanding/classification tasks

Issue - State: closed - Opened by xinshao-wang over 2 years ago - 1 comment

#88 - Using [CLS] token for classification task?

Issue - State: closed - Opened by gitwangxf over 2 years ago - 9 comments

#87 - CNN classifier for supervised learning

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

#86 - Fine tuning ProtBert model for language modelling task

Issue - State: closed - Opened by shu1273 over 2 years ago - 7 comments

#85 - Error downloading pre-trained model (prot_t5_xl_uniref50)

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

#84 - Positional Encoding in ProtBERT

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

#83 - Model names in "Models Availability" and "Original downstream Predictions" Tables

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

#82 - Dealing with PDB files

Issue - State: closed - Opened by sky-2002 over 2 years ago - 1 comment

#81 - About prot_t5_xl_half_uniref50-enc on HuggingFace

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

#79 - RuntimeError: CUDA out of memory.

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

#78 - Error running fine tune notebooks

Issue - State: closed - Opened by BSharmi almost 3 years ago - 1 comment

#77 - Cuda out of memory

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

#75 - BFD_FineTune_Loc attributeError

Issue - State: closed - Opened by wvdon almost 3 years ago - 1 comment

#74 - About 2-chars characters in DeepLoc's protein strings

Issue - State: closed - Opened by ratthachat almost 3 years ago - 17 comments

#73 - U class in "membrane" vs. "water soluble" dataset

Issue - State: closed - Opened by ratthachat almost 3 years ago - 1 comment

#72 - Embedding to sequence?

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

#71 - About predictprotein.org

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

#70 - Long Protein sequences embeddings

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

#69 - 2D t-SNE projections of single amino acids in figure 3A

Issue - State: closed - Opened by wuwo007 almost 3 years ago - 1 comment

#68 - ProtElectra Tokenizer

Issue - State: closed - Opened by CeciLyu about 3 years ago - 1 comment

#67 - Details on Rostlab/prot_t5_base_mt_uniref50

Issue - State: closed - Opened by ArcaneEmergence about 3 years ago - 1 comment

#66 - How to train a new model using my own sequence data? train.py missing?

Issue - State: closed - Opened by usccolumbia about 3 years ago - 1 comment

#65 - protein sequence embedding for t-sne

Issue - State: closed - Opened by ddongminstar about 3 years ago - 1 comment

#64 - Checkpoints of pre-trained models

Issue - State: closed - Opened by pzhang84 about 3 years ago - 2 comments