lucidrains/enformer-pytorch

Issues

• OOM after consecutive forward passes

  #47 opened a month ago by Andrei-Aksionov
  1

• Training process

  #28 opened a year ago by maksimallist
  23

• The pytorch-enformer has much lower performance than the tensorflow-enformer

  #44 opened 2 months ago by biginfor
  0

• AssertionError: if using tf gamma, only sequence length of 1536 allowed for now

  #40 opened 9 months ago by jerome-f
  2

• metric for enformer

  #9 opened 2 years ago by Rachel66666
  6

• Correlation Coefficient Calculation

  #36 opened a year ago by adamcatto
  4

• example data files

  #7 opened 2 years ago by yingyuan830
  3

• minor question on extract sequence embeddings

  #39 opened 9 months ago by Azai-yx
  1

• Is there a recommended approach to extract embeddings for the starting and ending regions?

  #43 opened 7 months ago by santule
  0

• Computing Contribution Scores

  #13 opened 2 years ago by Prakash2403
  5

• How to retrieve neular with ACTG information from the dataset

  #42 opened 9 months ago by HelloWorldLTY
  0

• How to retreive the sequence of genes?

  #38 opened 10 months ago by HelloWorldLTY
  0

• Problems during fine-tuing on my own ATAC-seq data

  #37 opened 10 months ago by Aut-eve
  0

• Using transformers[torch] to limit dependencies

  #27 opened a year ago by gokceneraslan
  1

• Hard coded input sequence length to the transformer blocks with using use_tf_gamma = True

  #32 opened a year ago by zhhhhahahaha
  14

• Gradient checkpoint

  #33 opened a year ago by fransilvionGenomica
  2

• Rounding errors in the positional encodings

  #31 opened a year ago by johahi
  6

• Would using FlashAttention(2) help?

  #30 opened a year ago by jmschrei
  4

• Fail to read .bed file

  #29 opened a year ago by kchl5
  0

• GenomeIntervalDataset problems

  #26 opened 2 years ago by tcztzy
  1

• Reverse Complement Fails when return_seq_indices=True

  #25 opened 2 years ago by Vejni
  3

• CUDA out of memory in unexpected cases

  #24 opened 2 years ago by havu73
  2

• rounding errors fixed?

  #17 opened 2 years ago by mepster
  3

• Fine-tuning without freezing transformer parameter leads to poor performance

  #16 opened 2 years ago by Zehui127
  27

• Distribution of embedding values

  #18 opened 2 years ago by sofroniewn
  5

• Initializing AttentionPool weights with 2 * Identity matrix, again!

  #22 opened 2 years ago by dohlee
  3

• Initializing AttentionPool weights with 2 * Identity matrix.

  #21 opened 2 years ago by dohlee
  1

• Error in fine-tuning

  #20 opened 2 years ago by joonan30
  3

• Minor typo in data.py

  #19 opened 2 years ago by icdh99
  2

• Using EleutherAI/enformer-official-rough PyTorch implementation to just get human output head

  #15 opened 2 years ago by aaronwtr
  4

• Minor potential typo in `FastaInterval` class

  #14 opened 2 years ago by sofroniewn
  2

• Models in training splits

  #12 opened 2 years ago by luciabarb
  0

• enformer TF pretrained weights

  #11 opened 2 years ago by naumanjaved
  1

• AttentionPool bug?

  #10 opened 2 years ago by cmlakhan
  1

• error loading enformer package

  #8 opened 2 years ago by cmlakhan
  1

• Why do we need Residual here while we have residual connection inside conv block

  #6 opened 3 years ago by inspirit
  2

• How to load the pre-trained Enfromer model?

  #3 opened 3 years ago by yzJiang9
  2