Hugging Face's logo
Noelia Ferruz's picture
58 14

Noelia Ferruz

nferruz
skr3178's profile picture saptawtf's profile picture 21world's profile picture
·
ferruz_noelia
noeliaferruz

AI & ML interests

artificial intelligence, protein design, structural biology.

Organizations

sdnf's profile picture AI for protein design's profile picture

nferruz's activity

New activity in nferruz/ProtGPT2 1 day ago

Error during Finetuning

8
#48 opened 27 days ago by pawanpc
New activity in nferruz/ProtGPT2 29 days ago

OOM During Finetuning on A100 GPU

2
#47 opened about 1 month ago by jashton1315
New activity in nferruz/ProtGPT2 about 2 months ago

How to finetune models on GPU?

1
#46 opened about 2 months ago by Jonathanlin

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

1
#45 opened about 2 months ago by littleworth
New activity in nferruz/UR50_2021_04 2 months ago

Guidance Needed for Training with nferruz/UR50_2021_04

1
#4 opened 2 months ago by littleworth
New activity in nferruz/ProtGPT2 3 months ago

how can i fine tune the model on the colab?

1
#43 opened 3 months ago by TomLong
New activity in nferruz/ProtGPT2 4 months ago

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

1
#42 opened 5 months ago by polytide
New activity in nferruz/ProtGPT2 5 months ago

Problems encountered when fine-tuning model validation

1
#41 opened 5 months ago by ysy2002

Inquiry on ProtGPT2 Model Performance and Fine-Tuning Evaluation

1
#38 opened 6 months ago by littleworth

How to change the first generate amino acid?

1
#40 opened 5 months ago by Jonathanlin
New activity in nferruz/ProtGPT2 6 months ago

How to create embeddings using ProtGPT2

1
#39 opened 6 months ago by PurvaTijare
New activity in nferruz/ProtGPT2 7 months ago

how to define the compute_metrics function in fine-tuning

1
#37 opened 7 months ago by Biohebb

Resources required for fine tuning Protgpt2

4
#36 opened 7 months ago by ChetnaA
New activity in AI4PD/ZymCTRL 7 months ago

Many generated sequences are highly similar to WT sequences

1
#10 opened 7 months ago by ShanGao
New activity in nferruz/ProtGPT2 7 months ago

Questions regarding fine tuning protgpt2

2
#35 opened 8 months ago by xenidisv
New activity in nferruz/1.24.3.1 8 months ago

How to provide the prompt

1
#1 opened 8 months ago by ShanGao
New activity in nferruz/ProtGPT2 8 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 8 months ago by BioinfoProteo
New activity in nferruz/ProtGPT2 10 months ago

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

4
#24 opened about 1 year ago by littleworth

pre-training code sharing

2
#32 opened 10 months ago by Eric2333
New activity in nferruz/ProtGPT2 11 months ago

Predicting end of sequence

1
#31 opened 11 months ago by pipparichter
New activity in nferruz/ProtGPT2 12 months ago

Generate mutation by define specific stations

3
#15 opened over 1 year ago by Aviv
New activity in nferruz/ProtGPT2 about 1 year ago

How to work training and generating on GPU environment

2
#29 opened about 1 year ago by Jonathanlin
New activity in AI4PD/ZymCTRL about 1 year ago

fine-tuning the model with orphan sequences

1
#6 opened about 1 year ago by rqh
New activity in AI4PD/REXzyme about 1 year ago

changed small thing in code snippet for reaction smile conversion
#5 opened about 1 year ago by Bienenwolf655

Update README.md
#4 opened about 1 year ago by Bienenwolf655
New activity in nferruz/ProtGPT2 about 1 year ago

Model fine-tuning does not work well

1
#28 opened about 1 year ago by rqh
New activity in AI4PD/REXzyme about 1 year ago

Upload figures__.004.jpeg
#3 opened about 1 year ago by Bienenwolf655

Update README.md
#2 opened about 1 year ago by Bienenwolf655
New activity in nferruz/ProtGPT2 about 1 year ago

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

2
#27 opened about 1 year ago by codev
New activity in AI4PD/ZymCTRL about 1 year ago

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

2
#5 opened about 1 year ago by ipark

Can we do the inferences on ZymCTRL with multi GPUs?

2
#4 opened about 1 year ago by guruace
New activity in nferruz/ProtGPT2 about 1 year ago

Inquiry Regarding ProtGPT2 Prompt and Output Length

2
#26 opened about 1 year ago by littleworth

Making ProtGPT2-medium and ProtGPT2-small available?

3
#25 opened about 1 year ago by littleworth
New activity in nferruz/UR50_2021_04 about 1 year ago

🚩 Report

1
#3 opened about 1 year ago by shellx
New activity in nferruz/ProtGPT2 about 1 year ago

There is an 'X' in generated sequences.

1
#23 opened about 1 year ago by SweetGAN

Conserving the end of a protein sequence

2
#21 opened about 1 year ago by codev

New line characters in generated sequences

1
#20 opened about 1 year ago by emrecicekyurt

Recommended GPU architecture for fine tuning

7
#19 opened about 1 year ago by codev
New activity in AI4PD/ZymCTRL over 1 year ago

Fine-tuning memory and custom tokenizer

2
#2 opened over 1 year ago by ipark
New activity in nferruz/ProtGPT2 over 1 year ago

Finetune without using run_clm.py

1
#16 opened over 1 year ago by TianlaiChen
New activity in nferruz/UR50_2021_04 over 1 year ago

nferruz/UR50_2021_04_Text

3
#2 opened over 1 year ago by alex6095
New activity in nferruz/ProtGPT2 over 1 year ago

Basic sequence generation usage

1
#13 opened over 1 year ago by kevinky

clarification question- sequence with invalid proteins

2
#14 opened over 1 year ago by skr3178

Embedding sequences

4
#12 opened over 1 year ago by flpgrz

Unable to finetune ProtGPT2 model

3
#11 opened over 1 year ago by Sirisha

Finetuning ProtGPT2 on a set of user-defined sequences

4
#9 opened over 1 year ago by SweetGAN

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

2
#10 opened over 1 year ago by likun
New activity in AI4PD/ZymCTRL over 1 year ago

Output of ZymCTRL

3
#1 opened over 1 year ago by 0jj0
New activity in nferruz/ProtGPT2 over 1 year ago

Generation of sequences based on one input sequence

3
#8 opened over 1 year ago by 0jj0
New activity in evaluate-metric/perplexity over 1 year ago

Different values observed wrt HF PPL documentation

2
#3 opened over 1 year ago by nferruz
New activity in nferruz/ProtGPT2 almost 2 years ago

Lengths of designed proteins

1
#6 opened almost 2 years ago by SenyorDrew

Minimal number of sequences for fine tuning

3
#2 opened almost 2 years ago by ShanGao

Generating Sequences Pre-conditioned on Embeddings from MSA Transformer

6
#5 opened almost 2 years ago by hunarbatra

Use model for calculating sequence perplexity

3
#4 opened almost 2 years ago by avuhong

ProtGPT2 QA Task for Mutation Generation

3
#3 opened almost 2 years ago by hunarbatra
New activity in nferruz/UR50_2021_04 almost 2 years ago

Fix `license` metadata

1
#1 opened almost 2 years ago by julien-c
New activity in nferruz/ProtGPT2 almost 2 years ago

End-to-end example for AA sequence vectorization

1
#1 opened almost 2 years ago by ptynecki
New activity in Gradio-Blocks/protGPT2_gradioFold about 2 years ago

Update app.py
#2 opened about 2 years ago by nferruz