jerryji1993/DNABERT
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
PythonApache-2.0
Issues
- 0
Using DNABert to predict expression
#125 opened by saninta0212 - 0
Understand the attention design
#124 opened by HelloWorldLTY - 1
- 1
Which model to use for genomic variants analysis?
#122 opened by nc1m - 3
training with different k-mer
#81 opened by berkuva - 1
Creating a dataset needs very long time
#121 opened by HelloWorldLTY - 1
- 0
Installation Issues.
#120 opened by CodelyUnicorn - 0
what is the masking ratio
#119 opened by abhidipbhattacharyya - 0
Release pretraining data?
#118 opened by leannmlindsey - 4
Importing error of Transformers
#103 opened by Rofidagamal - 3
Unable to get motif image
#115 opened by wangyb97 - 1
pre-training perplexity
#74 opened by gianfilippo - 1
Pre-train
#83 opened by morningsun77 - 3
DNATokenizer
#77 opened by ChengkuiZhao - 0
the seq longer than 512
#113 opened by SSHH007 - 2
install packages using pip
#112 opened by lingfengxu - 0
Shape of atten.npy
#111 opened by salehsereshkiucr - 0
- 0
Pretraining error
#109 opened by liu3zhenlab - 0
- 4
Finetuning Issue with Example Data
#78 opened by mosala777 - 1
Trained on mouse?
#82 opened by gdolsten - 1
How can I create my own processor?
#101 opened by dominiclopez391 - 0
AssertionError in kmer2seq for motif search
#105 opened by Vejni - 0
- 0
There is a bug about attention mask in source code
#102 opened by Jason941 - 0
How Can I track model loss and accuracy of each epoch during fine-tuning, to make sure model is stable?
#99 opened by XuanrZhang - 0
early_stop not being triggered?
#98 opened by jackievaleri - 0
- 2
How to divide our own dataset into test, dev and train data and assign them labels for fine tuning process
#96 opened by smruti241 - 1
Is there an implementation in huggingface?
#88 opened by yyou1996 - 1
provided example does not use GPU
#95 opened by ekg - 1
- 4
Readme section 5.2
#89 opened by mepster - 0
Can you use the pre-trained BERT models, but add novel tokens to the vocabulary?
#94 opened by mepster - 0
- 0
Transformers not recognized in test run
#92 opened by leannmlindsey - 4
- 0
Reverse complement of a sequence
#91 opened by ariannap88 - 0
How to use `--task_name dnasplice`?
#90 opened by ajoudaki - 0
Your masking of 6 consecutive tokens lets MLM pre-training trivially learn from the adjacent tokens
#86 opened by rcasero - 0
Steps required for pre-training completion
#85 opened by smruti241 - 0
Intermdiate layers output
#80 opened by FAhtisham - 0
Add custom tokens to DNATokenizer
#79 opened by WENHUAN22 - 1
Adding a license?
#76 opened by ksarmentrout - 0
Long DNA seqs embeddings
#72 opened by rominaappierdo - 1
Getting the last hidden state of the encoder
#71 opened by bill-95 - 0
DNA BERT : MISMATCH in the saved fine_tuned model and the model loaded after fine tuning
#70 opened by FAhtisham - 0