jerryji1993 DNABERT issues

jerryji1993 / DNABERT

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

https://doi.org/10.1093/bioinformatics/btab083

Apache License 2.0

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Using DNABert to predict expression

#125 saninta0212 opened 2 weeks ago
0
Understand the attention design

#124 HelloWorldLTY opened 2 weeks ago
0
The highest possible pytorch which can run DNABERT?

#123 HelloWorldLTY closed 3 weeks ago
1
Which model to use for genomic variants analysis?

#122 nc1m opened 2 months ago
1
Creating a dataset needs very long time

#121 HelloWorldLTY closed 2 months ago
1
Installation Issues.

#120 CodelyUnicorn opened 4 months ago
0
what is the masking ratio

#119 abhidipbhattacharyya opened 5 months ago
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Release pretraining data?

#118 leannmlindsey opened 5 months ago
0
Request for Detailed Information on Training the Tokenizer

#117 a-green-hand-jack opened 6 months ago
1
Add Plotting tool section to README

#116 terryluan12 opened 7 months ago
0
Unable to get motif image

#115 wangyb97 opened 7 months ago
3
Create LICENSE

#114 Zhihan1996 closed 11 months ago
0
the seq longer than 512

#113 SSHH007 opened 12 months ago
0
install packages using pip

#112 lingfengxu opened 1 year ago
2
Shape of atten.npy

#111 salehsereshkiucr opened 1 year ago
0
benchmark for the time and computation cost during the fine-tuning

#110 Shicheng-Guo closed 1 year ago
0
Pretraining error

#109 liu3zhenlab opened 1 year ago
0
attention maps generated in pre-training stage or fine-turning stage

#108 Shicheng-Guo opened 1 year ago
0
Update README.md

#107 Zhihan1996 closed 1 year ago
0
Update README.md

#106 Zhihan1996 closed 1 year ago
0
AssertionError in kmer2seq for motif search

#105 Vejni opened 1 year ago
0
How to get the high attention regions of a given sequence.

#104 ytye2010 opened 1 year ago
0
Importing error of Transformers

#103 Rofidagamal opened 1 year ago
4
There is a bug about attention mask in source code

#102 Jason941 opened 1 year ago
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How can I create my own processor?

#101 dominiclopez391 opened 1 year ago
1
Fix typo in modeling_utils.py

#100 xxchenxx opened 1 year ago
1
How Can I track model loss and accuracy of each epoch during fine-tuning, to make sure model is stable?

#99 XuanrZhang opened 1 year ago
0
early_stop not being triggered?

#98 jackievaleri opened 1 year ago
0
Changing max_seq_length does not update max_length in config.json

#97 jackievaleri opened 1 year ago
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How to divide our own dataset into test, dev and train data and assign them labels for fine tuning process

#96 smruti241 opened 1 year ago
2
provided example does not use GPU

#95 ekg opened 1 year ago
1
Can you use the pre-trained BERT models, but add novel tokens to the vocabulary?

#94 mepster opened 1 year ago
0
comparing DNABERT to where it was forked from transformers

#93 mepster opened 1 year ago
0
Transformers not recognized in test run

#92 leannmlindsey opened 1 year ago
0
Reverse complement of a sequence

#91 ariannap88 opened 1 year ago
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How to use `--task_name dnasplice`?

#90 ajoudaki opened 1 year ago
0
Readme section 5.2

#89 mepster opened 1 year ago
4
Is there an implementation in huggingface?

#88 yyou1996 opened 1 year ago
1
Feature/mayo

#87 rohandavidg opened 1 year ago
0
Your masking of 6 consecutive tokens lets MLM pre-training trivially learn from the adjacent tokens

#86 rcasero closed 1 year ago
0
Steps required for pre-training completion

#85 smruti241 opened 1 year ago
0
cannot import name 'BertForLongSequenceClassification'

#84 vedashreebhandare opened 1 year ago
4
Pre-train

#83 morningsun77 opened 2 years ago
1
Trained on mouse?

#82 gdolsten opened 2 years ago
1
training with different k-mer

#81 berkuva opened 2 years ago
3
Intermdiate layers output

#80 FAhtisham opened 2 years ago
0
Add custom tokens to DNATokenizer

#79 WENHUAN22 opened 2 years ago
0
Finetuning Issue with Example Data

#78 mosala777 opened 2 years ago
4
DNATokenizer

#77 ChengkuiZhao opened 2 years ago
3
Adding a license?

#76 ksarmentrout opened 2 years ago
1