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lucidrains
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enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
MIT License
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OOM after consecutive forward passes
#47
Andrei-Aksionov
closed
1 week ago
1
small fix to disable future warning with torch.load
#46
johahi
closed
1 month ago
1
Fixed edge case in shift augmentation
#45
johahi
closed
1 month ago
0
The pytorch-enformer has much lower performance than the tensorflow-enformer
#44
biginfor
closed
1 month ago
0
Is there a recommended approach to extract embeddings for the starting and ending regions?
#43
santule
opened
6 months ago
0
How to retrieve neular with ACTG information from the dataset
#42
HelloWorldLTY
opened
8 months ago
0
updated the assert to check if the seq_length == 196_608 when use_tf_…
#41
jerome-f
closed
8 months ago
0
AssertionError: if using tf gamma, only sequence length of 1536 allowed for now
#40
jerome-f
closed
8 months ago
2
minor question on extract sequence embeddings
#39
Azai-yx
opened
8 months ago
1
How to retreive the sequence of genes?
#38
HelloWorldLTY
opened
9 months ago
0
Problems during fine-tuing on my own ATAC-seq data
#37
Aut-eve
opened
9 months ago
0
Correlation Coefficient Calculation
#36
adamcatto
opened
10 months ago
4
support for bfloat16
#35
yang-dongxu
closed
11 months ago
1
Remove depreciated torchmetrics __init__ argument and fix str_to_one_hot for CUDA devices
#34
Vance-Raiti
closed
1 year ago
0
Gradient checkpoint
#33
fransilvionGenomica
closed
1 year ago
2
Hard coded input sequence length to the transformer blocks with using use_tf_gamma = True
#32
zhhhhahahaha
closed
11 months ago
14
Rounding errors in the positional encodings
#31
johahi
closed
1 year ago
6
Would using FlashAttention(2) help?
#30
jmschrei
closed
1 year ago
4
Fail to read .bed file
#29
kchl5
closed
1 year ago
0
Training process
#28
maksimallist
opened
1 year ago
23
Using transformers[torch] to limit dependencies
#27
gokceneraslan
closed
11 months ago
1
GenomeIntervalDataset problems
#26
tcztzy
closed
1 year ago
1
Reverse Complement Fails when return_seq_indices=True
#25
Vejni
closed
1 year ago
3
CUDA out of memory in unexpected cases
#24
havu73
opened
1 year ago
2
Make the output activation in HeadAdapterWrapper adjustable
#23
gokceneraslan
closed
1 year ago
4
Initializing AttentionPool weights with 2 * Identity matrix, again!
#22
dohlee
closed
1 year ago
3
Initializing AttentionPool weights with 2 * Identity matrix.
#21
dohlee
closed
1 year ago
1
Error in fine-tuning
#20
joonan30
closed
1 year ago
3
Minor typo in data.py
#19
icdh99
closed
1 year ago
2
Distribution of embedding values
#18
sofroniewn
closed
1 year ago
5
rounding errors fixed?
#17
mepster
closed
1 year ago
3
Fine-tuning without freezing transformer parameter leads to poor performance
#16
Zehui127
closed
1 year ago
27
Using EleutherAI/enformer-official-rough PyTorch implementation to just get human output head
#15
aaronwtr
closed
1 year ago
4
Minor potential typo in `FastaInterval` class
#14
sofroniewn
closed
1 year ago
2
Computing Contribution Scores
#13
Prakash2403
opened
1 year ago
5
Models in training splits
#12
luciabarb
opened
2 years ago
0
enformer TF pretrained weights
#11
naumanjaved
closed
2 years ago
1
AttentionPool bug?
#10
cmlakhan
closed
2 years ago
1
metric for enformer
#9
Rachel66666
opened
2 years ago
6
error loading enformer package
#8
cmlakhan
opened
2 years ago
1
example data files
#7
yingyuan830
closed
2 years ago
3
Why do we need Residual here while we have residual connection inside conv block
#6
inspirit
closed
2 years ago
2
Colab notebook for computing the correlation across different basenji2 dataset splits.
#5
jstjohn
closed
2 years ago
0
Add base_model_prefix
#4
NielsRogge
closed
2 years ago
2
How to load the pre-trained Enfromer model?
#3
yzJiang9
closed
2 years ago
2
tiny tiny nit
#2
julien-c
closed
2 years ago
1
Host weights on HuggingFace hub
#1
NielsRogge
closed
2 years ago
4