Datasets:
Datasets
This directory includes all the downstream task datasets of the LucaOne paper (https://www.nature.com/articles/s42256-025-01044-4).
configs:
config_name: CentralDogma
data_files:- split: train path: dataset/CentralDogma/gene_protein/binary_class/train/train.csv
- split: dev path: dataset/CentralDogma/gene_protein/binary_class/dev/dev.csv
- split: test path: dataset/CentralDogma/gene_protein/binary_class/test/test.csv
- split: label_info dataset/CentralDogma/gene_protein/binary_class/label.txt
config_name: CentralDogmaCDSProtein
data_files:- split: train path: dataset/CentralDogmaCDSProtein/gene_protein/binary_class/train/train.csv
- split: dev path: dataset/CentralDogmaCDSProtein/gene_protein/binary_class/dev/dev.csv
- split: test path: dataset/CentralDogmaCDSProtein/gene_protein/binary_class/test/test.csv
- split: label_info dataset/CentralDogmaCDSProtein/gene_protein/binary_class/label.txt
config_name: CentralDogmaV2
data_files:- split: train path: dataset/CentralDogmaV2/gene_protein/binary_class/train/train.csv
- split: dev path: dataset/CentralDogmaV2/gene_protein/binary_class/dev/dev.csv
- split: test path: dataset/CentralDogmaV2/gene_protein/binary_class/test/test.csv
- split: label_info dataset/CentralDogmaV2/gene_protein/binary_class/label.txt
config_name: CrossSpeciesHomologousGenePairsV1
data_files:- split: train path: dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/train/train.csv
- split: dev path: dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/dev/dev.csv
- split: test path: dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/test/test.csv
- split: label_info dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/label.txt
config_name: CrossSpeciesHomologousGenePairsV2
data_files:- split: train path: dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/train/train.csv
- split: dev path: dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/dev/dev.csv
- split: test path: dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/test/test.csv
- split: label_info dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/label.txt
config_name: GenusTax
data_files:- split: train path: dataset/GenusTax/gene/multi_class/train/train.csv
- split: dev path: dataset/GenusTax/gene/multi_class/dev/dev.csv
- split: test path: dataset/GenusTax/gene/multi_class/test/test.csv
- split: label_info dataset/GenusTax/gene/multi_class/label.txt
config_name: InfA
data_files:- split: train path: dataset/InfA/gene_gene/binary_class/train/train.csv
- split: dev path: dataset/InfA/gene_gene/binary_class/dev/dev.csv
- split: test path: dataset/InfA/gene_gene/binary_class/test/test.csv
- split: label_info dataset/InfA/gene_gene/binary_class/label.txt
config_name: ncRNAFam
data_files:- split: train path: dataset/ncRNAFam/gene/multi_class/train/train.csv
- split: dev path: dataset/ncRNAFam/gene/multi_class/dev/dev.csv
- split: test path: dataset/ncRNAFam/gene/multi_class/test/test.csv
- split: label_info dataset/ncRNAFam/gene/multi_class/label.txt
config_name: ncRPI
data_files:- split: train path: dataset/ncRPI/gene_protein/binary_class/train/train.csv
- split: dev path: dataset/ncRPI/gene_protein/binary_class/dev/dev.csv
- split: test path: dataset/ncRPI/gene_protein/binary_class/test/test.csv
- split: label_info dataset/ncRPI/gene_protein/binary_class/label.txt
config_name: PPI
data_files:- split: train path: dataset/PPI/protein/binary_class/train/train.csv
- split: dev path: dataset/PPI/protein/binary_class/dev/dev.csv
- split: test path: dataset/PPI/protein/binary_class/test/test.csv
- split: label_info dataset/PPI/protein/binary_class/label.txt
config_name: ProtLoc data_files:
- split: train path: dataset/ProtLoc/protein/multi_class/train/train.csv
- split: dev path: dataset/ProtLoc/protein/multi_class/dev/dev.csv
- split: test path: dataset/ProtLoc/protein/multi_class/test/test.csv
- split: label_info dataset/ProtLoc/protein/multi_class/label.txt
config_name: ProtLocCDSGene
data_files:- split: train path: dataset/ProtLocCDSGene/gene/multi_class/train/train.csv
- split: dev path: dataset/ProtLocCDSGene/gene/multi_class/dev/dev.csv
- split: test path: dataset/ProtLocCDSGene/gene/multi_class/test/test.csv
- split: label_info dataset/ProtLocCDSGene/gene/multi_class/label.txt
config_name: ProtLocCDSProt
data_files:- split: train path: dataset/ProtLocCDSProt/protein/multi_class/train/train.csv
- split: dev path: dataset/ProtLocCDSProt/protein/multi_class/dev/dev.csv
- split: test path: dataset/ProtLocCDSProt/protein/multi_class/test/test.csv
- split: label_info dataset/ProtLocCDSProt/protein/multi_class/label.txt
config_name: ProtStab
data_files:- split: train path: dataset/ProtStab/protein/regression/train/train.csv
- split: dev path: dataset/ProtStab/protein/regression/dev/dev.csv
- split: test path: dataset/ProtStab/protein/regression/test/test.csv
- split: label_info dataset/ProtStab/protein/regression/label.txt
config_name: SpeciesTax
data_files:- split: train path: dataset/SpeciesTax/gene/multi_class/train/train.csv
- split: dev path: dataset/SpeciesTax/gene/multi_class/dev/dev.csv
- split: test path: dataset/SpeciesTax/gene/multi_class/test/test.csv
- split: label_info dataset/SpeciesTax/gene/multi_class/label.txt
config_name: SupKTax
data_files:- split: train path: dataset/SupKTax/gene/multi_class/train/train.csv
- split: dev path: dataset/SupKTax/gene/multi_class/dev/dev.csv
- split: test path: dataset/SupKTax/gene/multi_class/test/test.csv
- split: label_info dataset/SupKTax/gene/multi_class/label.txt
LucaOne-Downstream-Task-Datasets
Usage:
from datasets import load_dataset
# load PPI dataset
ds = load_dataset("LucaGroup/LucaOne-Downstream-Task-Datasets", name="ncRPI")