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Datasets:
LucaGroup
/
LucaOne-Downstream-Task-Datasets

Tasks:
Text Classification
Modalities:
Text
Languages:
English
Tags:
LucaOne
Bioinformatics
Protein
Gene
RNA
DNA
License:
Dataset card Data Studio Files
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+
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+ # Datasets
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+ This directory includes all the downstream task datasets of the LucaOne paper (https://www.nature.com/articles/s42256-025-01044-4).
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+
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+ ---
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+ configs:
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+
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+ - config_name: CentralDogma
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+ data_files:
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+ - split: train
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+ path: dataset/CentralDogma/gene_protein/binary_class/train/train.csv
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+ - split: dev
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+ path: dataset/CentralDogma/gene_protein/binary_class/dev/dev.csv
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+ - split: test
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+ path: dataset/CentralDogma/gene_protein/binary_class/test/test.csv
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+ - split: label_info
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+ dataset/CentralDogma/gene_protein/binary_class/label.txt
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+
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+ - config_name: CentralDogmaCDSProtein
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+ data_files:
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+ - split: train
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+ path: dataset/CentralDogmaCDSProtein/gene_protein/binary_class/train/train.csv
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+ - split: dev
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+ path: dataset/CentralDogmaCDSProtein/gene_protein/binary_class/dev/dev.csv
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+ - split: test
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+ path: dataset/CentralDogmaCDSProtein/gene_protein/binary_class/test/test.csv
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+ - split: label_info
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+ dataset/CentralDogmaCDSProtein/gene_protein/binary_class/label.txt
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+
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+ - config_name: CentralDogmaV2
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+ data_files:
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+ - split: train
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+ path: dataset/CentralDogmaV2/gene_protein/binary_class/train/train.csv
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+ - split: dev
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+ path: dataset/CentralDogmaV2/gene_protein/binary_class/dev/dev.csv
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+ - split: test
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+ path: dataset/CentralDogmaV2/gene_protein/binary_class/test/test.csv
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+ - split: label_info
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+ dataset/CentralDogmaV2/gene_protein/binary_class/label.txt
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+
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+ - config_name: CrossSpeciesHomologousGenePairsV1
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+ data_files:
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+ - split: train
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+ path: dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/train/train.csv
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+ - split: dev
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+ path: dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/dev/dev.csv
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+ - split: test
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+ path: dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/test/test.csv
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+ - split: label_info
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+ dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/label.txt
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+
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+ - config_name: CrossSpeciesHomologousGenePairsV2
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+ data_files:
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+ - split: train
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+ path: dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/train/train.csv
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+ - split: dev
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+ path: dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/dev/dev.csv
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+ - split: test
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+ path: dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/test/test.csv
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+ - split: label_info
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+ dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/label.txt
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+
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+ - config_name: GenusTax
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+ data_files:
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+ - split: train
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+ path: dataset/GenusTax/gene/multi_class/train/train.csv
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+ - split: dev
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+ path: dataset/GenusTax/gene/multi_class/dev/dev.csv
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+ - split: test
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+ path: dataset/GenusTax/gene/multi_class/test/test.csv
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+ - split: label_info
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+ dataset/GenusTax/gene/multi_class/label.txt
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+
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+ - config_name: InfA
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+ data_files:
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+ - split: train
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+ path: dataset/InfA/gene_gene/binary_class/train/train.csv
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+ - split: dev
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+ path: dataset/InfA/gene_gene/binary_class/dev/dev.csv
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+ - split: test
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+ path: dataset/InfA/gene_gene/binary_class/test/test.csv
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+ - split: label_info
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+ dataset/InfA/gene_gene/binary_class/label.txt
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+
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+ - config_name: ncRNAFam
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+ data_files:
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+ - split: train
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+ path: dataset/ncRNAFam/gene/multi_class/train/train.csv
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+ - split: dev
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+ path: dataset/ncRNAFam/gene/multi_class/dev/dev.csv
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+ - split: test
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+ path: dataset/ncRNAFam/gene/multi_class/test/test.csv
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+ - split: label_info
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+ dataset/ncRNAFam/gene/multi_class/label.txt
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+
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+ - config_name: ncRPI
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+ data_files:
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+ - split: train
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+ path: dataset/ncRPI/gene_protein/binary_class/train/train.csv
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+ - split: dev
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+ path: dataset/ncRPI/gene_protein/binary_class/dev/dev.csv
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+ - split: test
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+ path: dataset/ncRPI/gene_protein/binary_class/test/test.csv
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+ - split: label_info
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+ dataset/ncRPI/gene_protein/binary_class/label.txt
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+
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+ - config_name: PPI
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+ data_files:
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+ - split: train
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+ path: dataset/PPI/protein/binary_class/train/train.csv
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+ - split: dev
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+ path: dataset/PPI/protein/binary_class/dev/dev.csv
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+ - split: test
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+ path: dataset/PPI/protein/binary_class/test/test.csv
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+ - split: label_info
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+ dataset/PPI/protein/binary_class/label.txt
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+
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+ - config_name: ProtLoc
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+ data_files:
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+ - split: train
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+ path: dataset/ProtLoc/protein/multi_class/train/train.csv
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+ - split: dev
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+ path: dataset/ProtLoc/protein/multi_class/dev/dev.csv
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+ - split: test
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+ path: dataset/ProtLoc/protein/multi_class/test/test.csv
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+ - split: label_info
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+ dataset/ProtLoc/protein/multi_class/label.txt
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+
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+ - config_name: ProtLocCDSGene
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+ data_files:
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+ - split: train
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+ path: dataset/ProtLocCDSGene/gene/multi_class/train/train.csv
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+ - split: dev
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+ path: dataset/ProtLocCDSGene/gene/multi_class/dev/dev.csv
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+ - split: test
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+ path: dataset/ProtLocCDSGene/gene/multi_class/test/test.csv
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+ - split: label_info
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+ dataset/ProtLocCDSGene/gene/multi_class/label.txt
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+
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+ - config_name: ProtLocCDSProt
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+ data_files:
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+ - split: train
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+ path: dataset/ProtLocCDSProt/protein/multi_class/train/train.csv
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+ - split: dev
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+ path: dataset/ProtLocCDSProt/protein/multi_class/dev/dev.csv
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+ - split: test
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+ path: dataset/ProtLocCDSProt/protein/multi_class/test/test.csv
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+ - split: label_info
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+ dataset/ProtLocCDSProt/protein/multi_class/label.txt
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+
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+ - config_name: ProtStab
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+ data_files:
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+ - split: train
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+ path: dataset/ProtStab/protein/regression/train/train.csv
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+ - split: dev
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+ path: dataset/ProtStab/protein/regression/dev/dev.csv
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+ - split: test
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+ path: dataset/ProtStab/protein/regression/test/test.csv
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+ - split: label_info
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+ dataset/ProtStab/protein/regression/label.txt
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+
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+ - config_name: SpeciesTax
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+ data_files:
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+ - split: train
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+ path: dataset/SpeciesTax/gene/multi_class/train/train.csv
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+ - split: dev
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+ path: dataset/SpeciesTax/gene/multi_class/dev/dev.csv
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+ - split: test
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+ path: dataset/SpeciesTax/gene/multi_class/test/test.csv
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+ - split: label_info
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+ dataset/SpeciesTax/gene/multi_class/label.txt
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+
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+ - config_name: SupKTax
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+ data_files:
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+ - split: train
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+ path: dataset/SupKTax/gene/multi_class/train/train.csv
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+ - split: dev
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+ path: dataset/SupKTax/gene/multi_class/dev/dev.csv
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+ - split: test
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+ path: dataset/SupKTax/gene/multi_class/test/test.csv
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+ - split: label_info
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+ dataset/SupKTax/gene/multi_class/label.txt
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+
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+ ---
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+
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+ # LucaOne-Downstream-Task-Datasets
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+ Usage:
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+
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+ ```python
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+ from datasets import load_dataset
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+
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+ # load PPI dataset
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+ ds = load_dataset("LucaGroup/LucaOne-Downstream-Task-Datasets", name="ncRPI")
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+ ```