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I have used the code for computing embeddings. But it is showing the error.
dna = "ACGTAGCATCGGATCTATCTATCGACACTTGGTTATCGATCTACGAGCATCTCGTTAGC"
inputs = tokenizer(dna, return_tensors = 'pt')["input_…
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I am trying to run the finetuning example that you have on the github and I keep getting this error. I am able to successfully run the quickstart section of your github.
```Error:
The provided da…
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Hello, I was testing the finetune code but I got this error:
> Traceback (most recent call last):██████████████████████████████████████████████████████████████████████| 30/30 [00:00
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Dear Zhihan,
Thank you so much for the great contribution to the filed to develop this awesome pretraining model. The manuscript doesn't explicitly mention whether the attention maps (DNABERT-viz) …
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Hello! Congratulations on your work. I was so happy to see this come out!
I have a question about running the GUE tests according to your instructions. In DNABERT1 you had to physically download …
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Hi, do you have any examples of how to extract sequence embeddings using this model?
I tried the following code but get an error:
```python
import torch
from transformers import AutoTokenizer,…
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I recently came across your paper titled "Identification of Bacteriophage Genome Sequences with Representation Learning" and was fascinated by your work in utilizing representation learning for phage…
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Dear Zhihan,
I am curious is there any evaluation to identify the best ratio for human vs non-human data? GENA-LM model included human T2T and 1000 Genome project to make human vs non-human equal t…
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Hey,
Congrats on your contribution but the code isn't properly written. It might be that at the time of training for you, it must've worked but now, there are some severe issues. Please don't get …
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Hi,
I'm trying to use this model for microbiome data.
As a practice, I trained a model using a small dataset (10K sequences extracted from viruses genomes).
Unfortunately, fine-tuned model using …