lucidrains / enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

lucidrains/enformer-pytorch Issues

Computing Contribution Scores
Updated a month ago5
How to retrieve neular with ACTG information from the dataset
Updated 2 months ago
AssertionError: if using tf gamma, only sequence length of 1536 allowed for now
Closed 2 months ago
minor question on extract sequence embeddings
Updated 3 months ago
How to retreive the sequence of genes?
Updated 3 months ago
Correlation Coefficient Calculation
Updated 3 months ago3
Problems during fine-tuing on my own ATAC-seq data
Updated 3 months ago
Using transformers[torch] to limit dependencies
Closed 6 months ago1
Hard coded input sequence length to the transformer blocks with using use_tf_gamma = True
Closed 6 months ago14
Training process
Updated 6 months ago22
Gradient checkpoint
Closed 7 months ago2
Rounding errors in the positional encodings
Closed 8 months ago6
Would using FlashAttention(2) help?
Closed 9 months ago4
Fail to read .bed file
Closed 10 months ago
GenomeIntervalDataset problems
Closed a year ago1
metric for enformer
Updated a year ago1
Reverse Complement Fails when return_seq_indices=True
Closed a year ago3
CUDA out of memory in unexpected cases
Updated a year ago2
rounding errors fixed?
Closed a year ago3
Fine-tuning without freezing transformer parameter leads to poor performance
Closed a year ago27
Distribution of embedding values
Closed a year ago5
Initializing AttentionPool weights with 2 * Identity matrix, again!
Closed a year ago3
Initializing AttentionPool weights with 2 * Identity matrix.
Closed a year ago1
Error in fine-tuning
Closed a year ago3
Minor typo in data.py
Closed a year ago2
Using EleutherAI/enformer-official-rough PyTorch implementation to just get human output head
Closed a year ago4
Minor potential typo in `FastaInterval` class
Closed a year ago2
Models in training splits
Updated 2 years ago
enformer TF pretrained weights
Closed 2 years ago1
AttentionPool bug?
Closed 2 years ago1
error loading enformer package
Updated 2 years ago1
example data files
Closed 2 years ago2
Why do we need Residual here while we have residual connection inside conv block
Closed 2 years ago2
How to load the pre-trained Enfromer model?
Closed 2 years ago2