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Hello! I was wondering if you would release your pretraining code for DNABERT-2 and NT? The DNABERT-2 website does not release the actual code that they used to pre-train, just a suggestion of two sim…
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Hi, I found that there exist several errors in the pre-training code (the file run.sh) and corresponding code. I have mentioned one in the pull request.Furthermore, it seems that we should use $PATH_T…
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Trying to get predictions using the ReadME tutorial and getting the below error during run_prediction.py
```
09/23/2024 21:12:42 - INFO - __main__ - ***** Running prediction *****
09/23/2024 2…
nal10 updated
1 month ago
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Dear authors,
first thank you for your work!
I'm trying to recreate the results from section "3.5 Identifying functional genetic variants with DNABERT".
Which model should be used to compute the …
nc1m updated
2 months ago
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**Part 1: Tokenization and Dataset Preparation**
```python
from transformers import AutoTokenizer, BertForSequenceClassification
from torch.utils.data import Dataset
tokenizer = AutoTokenizer.…
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Hi,
I use deep learning model which is written using specifically triton version 2.0.0.dev20221202. Now, I tried to set up environment into new location, but the version 2.0.0.dev20221202 binaries …
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Hi Ziqi,
Thank you and your team for providing this valuable evaluation framework. However, I encountered some issues while trying to build the environment.
Here is one example, the GPN enviro…
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I am trying to train the model on my own data, which consists of 10-mers. Running part 2.2 with the following command:
> cd examples
>
> export KMER=10
> export TRAIN_FILE=PATH_TO_MY_10MER_FILE…
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Hi,
I'm trying to finetune this for a regression problem with continuous labels. For that, I changed the 'num_labels' to 1 in the model as follows.
```
model = transformers.AutoModelForSequenceC…
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Hi there,
I am running the DNABERT pretrain.py as instructed by the readme file, once it worked well and started the model training, while when I re-build the environment after a week, the system o…