README.md

metadata

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
  - 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
  - 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
  - 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
  - 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
  - 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
  - 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
  - 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
        path: 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
  - 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
  - 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
  - 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
  - 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
        path: 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
  - 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
  - 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

LucaOne-Downstream-Task-Datasets

This directory includes all the downstream task datasets of the LucaOne paper (https://www.nature.com/articles/s42256-025-01044-4).

Dataset Structure

This dataset includes three splits and a label info file:

• train(training dataset)
• dev (validation dataset)
• test (testing dataset)
• label.txt (label name to label index in *.csv, label_idx=${the line number of label_name - 1})

Usage:

from datasets import load_dataset

# load ncRPI dataset
ds = load_dataset("LucaGroup/LucaOne-Downstream-Task-Datasets", name="ncRPI")