Sharmi Banerjee

Hi, Is there an example on running `prediction.py` with the model under output/models? I tried running it via the command `python prediction.py --input_sequence='MKNLISFGVKPWWAARWETVEPEPEEPVYT' --model_path="/home/openprotein/output/models/2019-01-30_00_38_46-TRAIN-LR0_01-MB1.model"` but get error that `ModuleNotFoundError: No...

confidence interval on train data

2

Hello, I am trying to compare the RF error on train and test data for a regression problem. After fitting the model (rf_model), I estimate the error as follows (np...

error in node2vec fit

14

Hello, I ran the commands using the default data in the package and get the following error in the embed node step in the `node2vec.fit` step `import networkx as nx`...

Data processing script is not working

4

Hi there! I am getting the following error in MaSIF data processing. I followed the demo example ``` root@dc2aa58b2fb5:/masif/data/masif_site# ./data_prepare_one.sh 4ZQK_A Downloading PDB structure '4ZQK'... Desired structure doesn't exists Empty...

Hi there! I followed training a T5 model with FSDP on Sagemaker from the example `https://github.com/huggingface/notebooks/blob/main/sagemaker/25_pytorch_fsdp_model_parallelism/scripts/run_clm.py` I noticed that checkpointing is not done with `save_strategy="no"`. Is it intentional(line `https://github.com/huggingface/notebooks/blob/main/sagemaker/25_pytorch_fsdp_model_parallelism/scripts/run_clm.py#L93`)? In...

Cannot open louvain.csv.gz

2

Hi, I have downloaded the louvain.csv.gz file. But I cannot extract it. Tried gunzip, reading it through python and R but getting the error that it is Not a gzipped...

Hi there! Awesome work! Quick question, in the paper you mention > performed a full demasking/reconstruction of the sequence (i.e., all tokens are reconstructed as individual tokens). Isn't it different...

ProtT5 model generate

2

Hi there! Was ProtT5 trained to predict just the masked position or the full sequence? When I use the `generate` function with masked sequences I noticed the model returns full...

Training SaProt with a smaller ESM model

3

Hi there! Awesome work! Do you have a script that I can use to train SaProt with a smaller ESM model? I think I can use the config https://github.com/westlake-repl/SaProt/blob/main/config/pretrain/saprot.yaml but...