downstream task
nucleotide_transformer_downstream_tasks
Dataset Card for Dataset Name
The nucleotide_transformer_downstream_tasks dataset features the 18 downstream tasks presented in the Nucleotide Transformer paper. They consist of both binary and multi-class classification tasks that aim at providing a consistent genomics benchmark.
⚠️We note that we have revised and improved our benchmark during the peer-review process. The datasets featured in this repository are used up to this release. We highly encourage to move to the new… See the full description on the dataset page: https://huggingface.co/datasets/InstaDeepAI/nucleotide_transformer_downstream_tasks.nucleotide_transformer_downstream_tasks_revised
Dataset Card for Dataset Name
The nucleotide_transformer_downstream_tasks dataset features the 18 downstream tasks presented in the Nucleotide Transformer paper. They consist of both binary and multi-class classification tasks that aim at providing a consistent genomics benchmark.
We note that this is an updated version of this benchmark after the paper has been through peer-review. We highly encourage to move to this version in detriment of the older version.Keypoints about the… See the full description on the dataset page: https://huggingface.co/datasets/InstaDeepAI/nucleotide_transformer_downstream_tasks_revised.cell-downstream-tasksversion https://git-lfs.github.com/spec/v1
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rna-downstream-tasks
GB.RNA Benchmark Datasets
mRNA related tasks
Translation efficiency prediction from Chu et al.(2024) [1]
3 cell lines: Muscle, pc3, HEK
input sequence: 5'UTR
10-fold cross-validation split
mRNA expression level prediction from Chu et al.(2024) [1]
3 cell lines: Muscle, pc3, HEK
input sequence: 5'UTR
10-fold cross-validation split
Mean ribosome load prediction from Sample et al. (2019) [2]
input sequence: 5'UTR
ouput: mean ribosome load
the original data… See the full description on the dataset page: https://huggingface.co/datasets/genbio-ai/rna-downstream-tasks.LucaOne-Downstream-Task-Datasets
split: devpath: dataset/ncRNAFam/gene/multi_class/dev/dev.csv
split: testpath: dataset/ncRNAFam/gene/multi_class/test/test.csv
split: labelpath: dataset/ncRNAFam/gene/multi_class/label.txt
config_name: ncRPIdata_files:
split: trainpath: dataset/ncRPI/gene_protein/binary_class/train/train.csv
split: devpath: dataset/ncRPI/gene_protein/binary_class/dev/dev.csv
split: testpath:… See the full description on the dataset page: https://huggingface.co/datasets/LucaGroup/LucaOne-Downstream-Task-Datasets.tissue-downstream-tasks
GB.Tissue Dataset Collection
niche type classification
Niche is the microenvironment in which each cell exists and is able to keep its own peculiar characteristics (Giacomo Donati, 2015). Based on spatial transcriptomic data, one can annotate niche label with established tools, which integrates similarity in gene expression profiles, spatial neighborhood structures and histological information in the tissue.
The task is to predict niche type of each cell given… See the full description on the dataset page: https://huggingface.co/datasets/genbio-ai/tissue-downstream-tasks.