MAGICS-LAB DNABERT_2 issues

MAGICS-LAB / DNABERT_2

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

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Got negative train loss when do pretrain process

#97 Jingyao711 opened 1 week ago
0
Attention error

#96 HelloWorldLTY opened 2 weeks ago
0
Random issues still come up in use

#95 josecar24 closed 2 weeks ago
1
About the motif prediction function

#94 josecar24 opened 3 weeks ago
0
GUE labels

#93 nehmea opened 3 weeks ago
0
TypeError: __init__() got an unexpected keyword argument 'token'

#92 Jingyao711 closed 3 weeks ago
1
About random factor in the embedding/tokenization process

#91 josecar24 closed 3 weeks ago
7
CUDA out of memory

#90 chenruipu closed 2 weeks ago
8
Getting embedding of a sequence

#89 CorvusVaine closed 1 month ago
2
Is it neccessary to train a specific BPE tokenizer on own datasets?

#88 amssljc closed 1 month ago
1
GUE+ datasets?

#87 leannmlindsey closed 1 month ago
2
Cannot Reproduce DNA-BERT2‘s Result

#86 KatarinaYuan closed 1 month ago
1
Unable to Retrieve ' hidden_states ' Despite ' Setting return_dict=True ' and ' output_hidden_states=True '

#85 biglittleme opened 1 month ago
3
Added package versions to requirements.txt

#84 TommasoTarchi opened 2 months ago
0
splice site predictions

#83 amitpande74 opened 2 months ago
0
Special token treatment.

#81 prwoolley closed 1 month ago
1
How do I output the attention from the model?

#80 jkb-ag opened 2 months ago
1
Fine-tune for continuous labels

#79 buwanim opened 2 months ago
3
I always encounter this error during the fine-tuning evaluation phase

#78 zlw1747832053 opened 3 months ago
1
Abnormal memory increase in eval step

#77 aaron1aaron2 opened 3 months ago
0
Pretraining, Pretraining, Pretraining!!!

#76 multydoffer closed 1 month ago
2
Quickstart Does not work and Embedding Dim is not 768

#75 Leo-T-Zang closed 1 month ago
1
When will the code for pre-training model and training BPE tokenizer be available?

#74 a-green-hand-jack closed 1 month ago
1
Discuss a question about k-mer

#73 xueleecs closed 1 month ago
1
hidden_states = model(inputs)[0] # [1, sequence_length, 768]-- Is the second dimension really the sequence length?

#72 xueleecs opened 3 months ago
1
problem stll in environment

#71 xueleecs closed 3 months ago
6
environment about torch version

#70 xueleecs closed 3 months ago
1
nproc_per_node typo

#69 tnmygrwl opened 4 months ago
0
.

#68 Buntzen-uni closed 4 months ago
0
When will the pretraining code be available?

#67 chenwydj opened 5 months ago
0
While Doing Quick Start, I Encountered an AssertionError:

#66 Jingyao711 closed 3 weeks ago
2
Debug issue

#65 jimmylihui opened 5 months ago
1
Flash Attention 2

#64 jacobfulano closed 5 months ago
0
Wrong tokens at the end of the sequence

#63 pabloacera opened 5 months ago
0
token split issue

#62 HITzhongyu opened 6 months ago
0
"indexSelectLargeIndex: block: [313,0,0], thread: [32,0,0] Assertion `srcIndex < srcSelectDimSize` failed." after evaluation.

#61 Time-Rune opened 6 months ago
0
Triton version issue

#60 yuddecho closed 6 months ago
1
Fine tuning for plants

#59 lucaskbobadilla closed 6 months ago
0
dtype=next(self.parameters()).dtype) # fp16 compatibility StopIteration

#58 csm276 closed 7 months ago
1
Triton flash attention error

#57 Atrix21 opened 7 months ago
13
AssertionError: libcuda.so cannot found!

#56 aaronmaiww opened 7 months ago
1
ValueError: The model class you are passing has a `config_class` attribute that is not consistent with the config class you passed

#55 rohan-sonthalia closed 8 months ago
2
AssertionError in model(inputs)

#54 ZhaoyueZhang closed 7 months ago
6
Get logits and LM loss from the DNABert

#53 JinyuanSun closed 8 months ago
1
Train Dev Test Splits for GUE Benchmark Differ from Reported Paper Splits

#52 o-turbitt-mdc closed 7 months ago
2
Pre-training Data

#51 leannmlindsey closed 6 months ago
2
Pre-training code

#50 alexpancheva closed 1 month ago
1
config_class error

#49 yudizhangzyd closed 8 months ago
3
Inference fails with output_all_encoded_layers=True

#48 princethewinner opened 9 months ago
0
install triton

#47 lingfengxu opened 9 months ago
2