plantcad/PlantCAD2_zero_shot_tasks

🌱 PlantCAD2 Zero-Shot Tasks

Zero-shot evaluation tasks for plant genomics using PlantCAD2.
This dataset contains tasks designed to evaluate model performance without task-specific training.

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📂 Available Tasks

🔬 Cross-species Evolutionary Conservation

Task Name	Description	Samples	Metric
conservation_within_andropogoneae	Predict conserved vs non-conserved sites using alignments within 35 Andropogoneae genomes	19,030 vs 19,030	AUROC
conservation_within_poaceae_non_tis	Predict conserved vs non-conserved coding sites (excluding TIS) within Poaceae	103,368 vs 80,317	AUROC
conservation_within_poaceae_tis	Predict conserved vs non-conserved TIS sites	26,650 vs 10,012	AUROC

🧬 Key Junction Recovery

Task Name	Description	Samples	Metric
tis_recovery	Recover masked ATG start codon (maize)	39,035	Accuracy
tts_recovery	Recover masked TAG/TAA/TGA stop codon (maize)	39,035	Accuracy
donor_recovery	Recover masked GT splice donor motif (maize)	153,869	Accuracy
acceptor_recovery	Recover masked AG splice acceptor motif (maize)	153,869	Accuracy

🌽 Within-species Conservation (Maize)

Task Name	Description	Samples	Metric
tis_core_noncore_classification	Predict core TIS vs non-core TIS	28,291 vs 8,118	AUROC
tts_core_noncore_classification	Predict core TTS vs non-core TTS	28,291 vs 8,118	AUROC
donor_core_noncore_classification	Predict core splice donor vs non-core splice donor	123,183 vs 21,367	AUROC
acceptor_core_noncore_classification	Predict core splice acceptor vs non-core splice acceptor	123,183 vs 21,367	AUROC

🧩 Structural Variant Effect

Task Name	Description	Samples	Metric
structural_variant_effect_prediction	Predict conserved deletions vs non-conserved deletions	7,662 vs 10,413	AUPRC

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📑 Data Format

Task Type	Fields	Description
Classification	sequence	DNA sequence (string)
	label	Binary label: 0 = negative, 1 = positive
Recovery	sequence	DNA sequence (string)

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📊 Data Splits

Split	Description
test	General test data
test_maize	Zea mays (corn)-specific test data
test_tomato	Solanum lycopersicum (tomato)-specific test data

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🚀 Usage Example

from datasets import load_dataset, get_dataset_config_names

# List all available tasks
tasks = get_dataset_config_names("plantcad/PlantCAD2_zero_shot_tasks")
print("Available tasks:", tasks)

# Example: Classification task
classification_data = load_dataset("plantcad/PlantCAD2_zero_shot_tasks", "conservation_within_poaceae_tis")
test_split = classification_data['test']
print(f"Test samples: {len(test_split)}")
print(f"Sample: {test_split[0]}")

# Example: TIS recovery task
recovery_data = load_dataset("plantcad/PlantCAD2_zero_shot_tasks", "tis_recovery")
if 'test_maize' in recovery_data:
    maize_data = recovery_data['test_maize']
    print(f"Maize recovery samples: {len(maize_data)}")