Noelia Ferruz

#47 opened 4 months ago by

jashton1315

How to finetune models on GPU?

#46 opened 5 months ago by

Jonathanlin

Introducing protgpt2-distilled-tiny: A Leaner, Faster Approach to Protein Sequence Generation

#45 opened 5 months ago by

New activity in nferruz/UR50_2021_04 5 months ago

Guidance Needed for Training with nferruz/UR50_2021_04

#4 opened 5 months ago by

New activity in nferruz/ProtGPT2 6 months ago

how can i fine tune the model on the colab?

#43 opened 6 months ago by

TomLong

New activity in nferruz/ProtGPT2 7 months ago

How can I generate a new sequence by fixing some of the residues ?

#42 opened 8 months ago by

polytide

New activity in nferruz/ProtGPT2 8 months ago

Problems encountered when fine-tuning model validation

#41 opened 8 months ago by

ysy2002

Inquiry on ProtGPT2 Model Performance and Fine-Tuning Evaluation

#38 opened 9 months ago by

How to change the first generate amino acid?

#40 opened 8 months ago by

Jonathanlin

How to create embeddings using ProtGPT2

#39 opened 8 months ago by

PurvaTijare

New activity in nferruz/ProtGPT2 10 months ago

how to define the compute_metrics function in fine-tuning

#37 opened 10 months ago by

Biohebb

New activity in AI4PD/ZymCTRL 10 months ago

Many generated sequences are highly similar to WT sequences

#10 opened 10 months ago by

ShanGao

New activity in nferruz/ProtGPT2 10 months ago

Questions regarding fine tuning protgpt2

#35 opened 10 months ago by

xenidisv

New activity in nferruz/1.24.3.1 10 months ago

How to provide the prompt

#1 opened 10 months ago by

ShanGao

New activity in nferruz/ProtGPT2 10 months ago

How to fine-tune with dataset of multiple .csv.gz files and had some features or labels? Exemple with OAS database (antibody db)

5

#34 opened 11 months ago by

BioinfoProteo

New activity in nferruz/ProtGPT2 about 1 year ago

Example of `training.txt` and `validation.txt` for fine tuning ProtGPT2

4

#24 opened over 1 year ago by

pre-training code sharing

#32 opened about 1 year ago by

Eric2333

Predicting end of sequence

#31 opened about 1 year ago by

pipparichter

Generate mutation by define specific stations

#15 opened over 1 year ago by

Aviv

How to work training and generating on GPU environment

#29 opened over 1 year ago by

Jonathanlin

New activity in AI4PD/ZymCTRL over 1 year ago

fine-tuning the model with orphan sequences

#6 opened over 1 year ago by

rqh

New activity in nferruz/ProtGPT2 over 1 year ago

Model fine-tuning does not work well

#28 opened over 1 year ago by

rqh

Discrepancy between num_samples when fine tuning and the number of samples in my training file

#27 opened over 1 year ago by

codev

New activity in AI4PD/ZymCTRL over 1 year ago

Example 2: Fine-tuning on a set of user-defined sequences

#5 opened over 1 year ago by

ipark

Can we do the inferences on ZymCTRL with multi GPUs?

#4 opened over 1 year ago by

guruace

New activity in nferruz/ProtGPT2 over 1 year ago

Inquiry Regarding ProtGPT2 Prompt and Output Length

#26 opened over 1 year ago by

Making ProtGPT2-medium and ProtGPT2-small available?

#25 opened over 1 year ago by

New activity in nferruz/UR50_2021_04 over 1 year ago

🚩 Report

#3 opened over 1 year ago by

shellx

New activity in nferruz/ProtGPT2 over 1 year ago

There is an 'X' in generated sequences.

#23 opened over 1 year ago by

SweetGAN

Conserving the end of a protein sequence

#21 opened over 1 year ago by

codev

New line characters in generated sequences

#20 opened over 1 year ago by

emrecicekyurt

Recommended GPU architecture for fine tuning

7

#19 opened over 1 year ago by

codev

New activity in AI4PD/ZymCTRL over 1 year ago

Fine-tuning memory and custom tokenizer

#2 opened over 1 year ago by

ipark

New activity in nferruz/ProtGPT2 over 1 year ago

Finetune without using run_clm.py

#16 opened over 1 year ago by

TianlaiChen

New activity in nferruz/UR50_2021_04 over 1 year ago

nferruz/UR50_2021_04_Text

#2 opened over 1 year ago by

alex6095

New activity in nferruz/ProtGPT2 over 1 year ago

Basic sequence generation usage

#13 opened over 1 year ago by

kevinky

clarification question- sequence with invalid proteins

#14 opened over 1 year ago by

skr3178

Embedding sequences

4

#12 opened over 1 year ago by

flpgrz

Unable to finetune ProtGPT2 model

#11 opened over 1 year ago by

Sirisha

New activity in nferruz/ProtGPT2 almost 2 years ago

Finetuning ProtGPT2 on a set of user-defined sequences

4

#9 opened almost 2 years ago by

SweetGAN

can protgpt2 be used in "Fill-Mask" tasks?

#10 opened almost 2 years ago by

likun

New activity in AI4PD/ZymCTRL almost 2 years ago

Output of ZymCTRL

#1 opened almost 2 years ago by

0jj0

New activity in nferruz/ProtGPT2 almost 2 years ago

Generation of sequences based on one input sequence

#8 opened almost 2 years ago by

0jj0

New activity in evaluate-metric/perplexity almost 2 years ago

Different values observed wrt HF PPL documentation

#3 opened almost 2 years ago by

nferruz

New activity in nferruz/ProtGPT2 about 2 years ago

Lengths of designed proteins

#6 opened about 2 years ago by

SenyorDrew

Minimal number of sequences for fine tuning

#2 opened about 2 years ago by

ShanGao

Generating Sequences Pre-conditioned on Embeddings from MSA Transformer

6

#5 opened about 2 years ago by

hunarbatra

Use model for calculating sequence perplexity

#4 opened about 2 years ago by

avuhong

ProtGPT2 QA Task for Mutation Generation

#3 opened about 2 years ago by

hunarbatra

New activity in nferruz/UR50_2021_04 about 2 years ago

Fix `license` metadata

#1 opened about 2 years ago by

julien-c

New activity in nferruz/ProtGPT2 about 2 years ago

End-to-end example for AA sequence vectorization