enformer-pytorch

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metric for enformer

6

Hello, can I ask how you find of the human pearson R is 0.625 for validation, and 0.65 for test? Couldn't find any information in the paper. Is there any...

Rachel66666

error loading enformer package

1

I am trying to install the enformer package but seem to be getting the following error: ``` >>> import torch >>> from enformer_pytorch import Enformer Traceback (most recent call last):...

cmlakhan

Hey, Is there a way of getting the models trained in each training set, as mentioned in the "Model training and evaluation" paragraph of the Enformer paper? Thanks!

luciabarb

minor question on extract sequence embeddings

1

Thanks for adopting the Enformer model to PyTorch. Recently, I've needed to extract sequence embeddings from Enformer. Do I have to use one-hot encoding as input, or can I directly...

Azai-yx

Hi, since enformer can be used to predict gene expression values, I am looking for the index of model output to describe the relationship between genes and genome regions. Could...

HelloWorldLTY

Correlation Coefficient Calculation

4

I ran the `test_pretrained.py` script to calculate the correlation coefficient on a validation sample, and got `0.5963` as expected. However, when I inspected the target and predictions, the shapes were...

adamcatto

Hi, I'm now trying to fine-tune the pretrained model on my own ATAC-seq data using HeadAdapterWrapper. Due to device limitations and long training time, I set finetune_last_n_layers_only to 2, and...

Aut-eve

Training process

23

Hello. Can you share the details of neural model training? Did you train it yourself? Did you collect data for training from basenji dataset files? I am unable to reproduce...

maksimallist

Computing Contribution Scores

5

From the paper: > To better understand what sequence elements Enformer is utilizing when making predictions, we computed two different gene expression contribution scores — input gradients (gradient × input...

Prakash2403

CUDA out of memory in unexpected cases

2

Hi! Thank you so much for providing this implementation and documentations. I have been looking for the pytorch implementation of enformer for a while. When I run the provided code...

havu73