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GitHub / agemagician/ProtTrans issues and pull requests

#55 - Loading model prot_t5_xxl_uniref50/Rostlab/prot_t5_xxl_bfd

Issue - State: closed - Opened by timfraseratg about 3 years ago - 1 comment
Labels: question

#54 - Generating embeddings in batches

Issue - State: closed - Opened by Xinxinatg about 3 years ago - 1 comment
Labels: question

#53 - XLNetTokenizer removes multiple 'X' character in a row.

Issue - State: closed - Opened by iwyoo about 3 years ago - 1 comment
Labels: bug

#52 - Using ProtTrans

Issue - State: closed - Opened by dukkakc about 3 years ago - 3 comments
Labels: question

#51 - Please help with fine tuning of T5 model

Issue - State: closed - Opened by yzhang-github-pub about 3 years ago - 1 comment
Labels: question

#50 - Running the ProtAlbert-TF.ipynb and getting NoneType Object error

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

#49 - Details on T5

Issue - State: closed - Opened by Turakar about 3 years ago - 2 comments
Labels: question

#48 - Using ProtXLNet for Protein Variant Generation

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

#47 - Question about using ProtXLNet

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

#46 - The problem of T5 when Fine-Tuning

Issue - State: closed - Opened by houzl3416 about 3 years ago

#45 - T5 fine tune memory error

Issue - State: closed - Opened by sacombs about 3 years ago - 1 comment
Labels: question

#44 - Strange indexing for ProtT5 embeddings?

Issue - State: closed - Opened by Turakar over 3 years ago - 2 comments
Labels: question

#43 - Why not use the Hugginface Hub ELECTRA?

Issue - State: closed - Opened by Turakar over 3 years ago - 1 comment
Labels: question

#42 - Which mask token is used in T5 training?

Issue - State: closed - Opened by StephanHeijl over 3 years ago - 1 comment

#41 - Should I always convert the rarely occured amino acid token (B O U Z)?

Issue - State: closed - Opened by wangwwno1 over 3 years ago - 1 comment

#40 - How to ignore the warning

Issue - State: closed - Opened by SamieeS over 3 years ago - 3 comments
Labels: question

#39 - Mask tokens for T5 models

Issue - State: closed - Opened by joshim5 over 3 years ago - 1 comment
Labels: question

#37 - A suggestion for Fine-Tuning code

Issue - State: closed - Opened by hailong23-jin over 3 years ago - 1 comment
Labels: bug

#36 - Question about run ProtTrans in multiproces mode

Issue - State: closed - Opened by ZeroDesigner over 3 years ago - 2 comments
Labels: question

#35 - Add performer and reformer model

Issue - State: closed - Opened by behroozazarkhalili over 3 years ago - 2 comments
Labels: enhancement

#34 - Fine tuning code might have a small bug (just printing)

Issue - State: closed - Opened by danpf over 3 years ago - 1 comment
Labels: bug

#33 - Truncation

Issue - State: closed - Opened by udibgui over 3 years ago - 1 comment
Labels: question

#32 - Is batch inference helpful for performance?

Issue - State: closed - Opened by yzhang-github-pub over 3 years ago - 2 comments
Labels: question

#31 - masking prediction help

Issue - State: closed - Opened by danpf over 3 years ago - 1 comment
Labels: question

#29 - Where to find code for training prot_bert_bfd?

Issue - State: closed - Opened by MJimitater over 3 years ago - 1 comment
Labels: duplicate

#28 - Distilled version?

Issue - State: closed - Opened by anindabitm over 3 years ago - 1 comment
Labels: enhancement

#27 - paper figure6A

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

#26 - ValueError: The first argument to `Layer.call` must always be passed.

Issue - State: closed - Opened by Trishna-Chakraborty over 3 years ago - 1 comment
Labels: bug

#25 - ResourceExhaustedError : OOM when allocating tensor

Issue - State: closed - Opened by Trishna-Chakraborty over 3 years ago - 4 comments
Labels: question

#24 - Pooler output - Question

Issue - State: closed - Opened by anindabitm almost 4 years ago - 1 comment
Labels: question

#23 - Will the prot_bert or prot_bert_BFD model provide classification support or any other API in the future?

Issue - State: closed - Opened by shysuen almost 4 years ago - 1 comment
Labels: question

#22 - Maximum number of sequences_Example

Issue - State: closed - Opened by sailfish009 almost 4 years ago - 2 comments
Labels: question

#21 - Default feature length 1024?

Issue - State: closed - Opened by sailfish009 almost 4 years ago - 4 comments
Labels: question

#20 - Usage Questions

Issue - State: closed - Opened by bhavaygg almost 4 years ago - 1 comment
Labels: question

#19 - Model Freezing

Issue - State: closed - Opened by wjs20 almost 4 years ago - 1 comment
Labels: question

#18 - Does prot_bert have Classifier output layer?

Issue - State: closed - Opened by yzhang-github-pub almost 4 years ago - 1 comment
Labels: question

#17 - Predicting the properties of bacteria

Issue - State: closed - Opened by slgero almost 4 years ago - 4 comments
Labels: question

#16 - Question about input data for ProtBert-FineTuning-Localization.ipynb

Issue - State: closed - Opened by yzhang-github-pub almost 4 years ago - 2 comments
Labels: bug

#15 - DefaultCPUAllocator: not enough memory

Issue - State: closed - Opened by bhavaygg almost 4 years ago - 1 comment
Labels: question

#14 - Error loading 'pytorch_lightning.metrics.sklearns'

Issue - State: closed - Opened by yzhang-github-pub almost 4 years ago - 3 comments
Labels: question

#13 - Replicating a basic Protrans model

Issue - State: closed - Opened by donal1 almost 4 years ago - 4 comments
Labels: question

#12 - Predicting protein distance map

Issue - State: closed - Opened by akirasosa almost 4 years ago - 2 comments
Labels: community use-case

#11 - Source code of the models

Issue - State: closed - Opened by hadim almost 4 years ago - 6 comments
Labels: question

#10 - XLNet produces incorrect output dimensions when there are consecutive X tokens

Issue - State: closed - Opened by konstin almost 4 years ago - 2 comments
Labels: bug

#9 - Add more pre-trained models for tensorflow 2

Issue - State: closed - Opened by deepgradient almost 4 years ago - 1 comment
Labels: question

#8 - Unsupervised LM fine-tuning

Issue - State: closed - Opened by fteufel almost 4 years ago - 3 comments
Labels: question

#7 - Language modeling heads

Issue - State: closed - Opened by jaekor91 almost 4 years ago - 4 comments
Labels: question

#6 - Pretrained Model

Issue - State: closed - Opened by cztay about 4 years ago - 1 comment
Labels: question

#5 - Is there a correct way to use ProtBert with FillMaskPipeline

Issue - State: closed - Opened by adsodemelk about 4 years ago - 2 comments
Labels: question

#4 - Do you have a plan to release the trained models for secondary structure prediction etc.?

Issue - State: closed - Opened by zzhongzz about 4 years ago - 4 comments
Labels: question

#3 - Load ProtBert or ProtBert-BFD in TensorFlow

Issue - State: closed - Opened by JoeRRPhillips about 4 years ago - 4 comments
Labels: question

#2 - Do you have plan to include reformer in ProtTrans?

Issue - State: closed - Opened by qwu01 about 4 years ago - 1 comment
Labels: question

#1 - Dropbox links to model weights and Embeddings not working

Issue - State: closed - Opened by Gurpreethgnis about 4 years ago - 1 comment
Labels: bug