| --- |
| license: apache-2.0 |
| task_categories: |
| - text-classification |
| language: |
| - en |
| tags: |
| - LucaOne |
| - Bioinformatics |
| - Protein |
| - Gene |
| - RNA |
| - DNA |
| - Nucleic Acid |
| - Interaction |
| - AI4Biology |
| - Bio |
| - Biology |
| - AI4Science |
| pretty_name: LucaGroup/LucaOne-Downstream-Task-Datasets |
| --- |
| - 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: |
|
|
|
|
| ```python |
| from datasets import load_dataset |
| |
| |
| # load ncRPI dataset |
| ds = load_dataset("LucaGroup/LucaOne-Downstream-Task-Datasets", name="ncRPI") |
| ``` |
|
|
|
|
| ## Github |
| https://github.com/LucaOne/ - 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: |
|
|
|
|
| ```python |
| from datasets import load_dataset |
| |
| |
| # load ncRPI dataset |
| ds = load_dataset("LucaGroup/LucaOne-Downstream-Task-Datasets", name="ncRPI") |
| ``` |
|
|
|
|
| ## Github |
| https://github.com/LucaOne/ |
