Genomic Benchmarks Dataset

by ComputingNotes
Large Language Models
  • Benchmarks for classification of genomic sequences

https://github.com/ML-Bioinfo-CEITEC/genomic_benchmarks

Accessing:

1.list_datasets 
from genomic_benchmarks.data_check import list_datasets
list_datasets()

2. Pytorch
from genomic_benchmarks.dataset_getters.pytorch_datasets import HumanNontataPromoters
dset = HumanNontataPromoters(split='train', version=0)
dset[0]

output:
('CAATCTCACAGGCTCCTGGTTGTCTACCCATGGACCCAGAGGTTCTTTGACAGCTTTGGCAACCTGTCCTCTGCCTCTGCCATCATGGGCAACCCCAAAGTCAAGGCACATGGCAAGAAGGTGCTGACTTCCTTGGGAGATGCCATAAAGCACCTGGATGATCTCAAGGGCACCTTTGCCCAGCTGAGTGAACTGCACTGTGACAAGCTGCATGTGGATCCTGAGAACTTCAAGGTGAGTCCAGGAGATGT', 0)

3. HuggingFace Hub
https://github.com/ML-Bioinfo-CEITEC/genomic_benchmarks/blob/main/notebooks/How_To_Use_Datasets_From_HF.ipynb

Training Benchmark genomic datasets resources:

  1. https://github.com/ML-Bioinfo-CEITEC/genomic_benchmarks/blob/main/notebooks/How_To_Train_CNN_Classifier_With_Pytorch.ipynb
  2. https://github.com/ML-Bioinfo-CEITEC/genomic_benchmarks/tree/main/notebooks
error: