nucleotide-transformer
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instadeepai
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Dear Team, I express my gratitude for your excellent work. Presently, I'm attempting to reproduce segmentNT (InstaDeepAI/segment_nt) on testing data (chr20 and chr21) to segment 5utr. I utilized the 5utr...
hi,thanks to your work! I read the paper SegmentNT and found this great idea of using unet to reach single-nucleotide resoltion. I notice to train SegmentNT you curated a dataset...
I am trying to tailor the script for the Gene of my interest. Repeatedly, I am getting this error: ValueError: Input length must be divisible by the 2 to the...
## Context Using the example Colab, running on a TPU instance, user get the following error running the second code chunk:  ## Attempted Fixes ### Updating the jax version...
Great work, and love that everything is easily runnable in Colab. However, I am not clear on what are the most direct real world applications of this for bioinformatics or...
Hi, When I looked at some examples of getting the pretrained models, I saw: ```python parameters, forward_fn, tokenizer, config = get_pretrained_model( model_name="500M_human_ref", embeddings_layers_to_save=(20,), max_positions=32, ) ``` ```python parameters, forward_fn, tokenizer,...
How do embeddings layers saved from inference notebook in the github and hidden states from the Hugging face inference notebook differ from each other? When I compare the these two...
Hi, Recently, I tried to implement a couple of downstream tasks where the data might not be sufficient to fine-tune the Nucleotide Transformer. However, with the release of SegmentNT, I...
Thank you for releasing this impressive work and providing pretrained models and code. I have a question regarding inference on short DNA sequences. Based on the documentation, SegmentNT was trained...
First of all, thank you for sharing this excellent paper. I have a question because I didn’t fully understand one part of the study. Regarding the section where the model...
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🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics