README.md

metadata

license: apache-2.0
task_categories:
  - text-classification
  - sequence-modeling
language:
  - en
tags:
  - biology
  - genomics
  - dna
  - plants
  - zero-shot
  - conservation
configs:
  - config_name: acceptor_core_noncore_classification
    data_files:
      - split: test_maize
        path: acceptor_core_noncore_classification/test_maize-*
      - split: test_tomato
        path: acceptor_core_noncore_classification/test_tomato-*
  - config_name: acceptor_recovery
    data_files:
      - split: test_maize
        path: acceptor_recovery/test_maize-*
      - split: test_tomato
        path: acceptor_recovery/test_tomato-*
  - config_name: conservation_within_poaceae_non_tis
    data_files:
      - split: test
        path: conservation_within_poaceae_non_tis/test-*
  - config_name: conservation_within_andropogoneae
    data_files:
      - split: test
        path: conservation_within_andropogoneae/test-*
  - config_name: conservation_within_poaceae_tis
    data_files:
      - split: test
        path: conservation_within_poaceae_tis/test-*
  - config_name: structural_variant_effect_prediction
    data_files:
      - split: test
        path: structural_variant_effect_prediction/test-*
  - config_name: donor_core_noncore_classification
    data_files:
      - split: test_maize
        path: donor_core_noncore_classification/test_maize-*
      - split: test_tomato
        path: donor_core_noncore_classification/test_tomato-*
  - config_name: donor_recovery
    data_files:
      - split: test_maize
        path: donor_recovery/test_maize-*
      - split: test_tomato
        path: donor_recovery/test_tomato-*
  - config_name: tis_core_noncore_classification
    data_files:
      - split: test_maize
        path: tis_core_noncore_classification/test_maize-*
      - split: test_tomato
        path: tis_core_noncore_classification/test_tomato-*
  - config_name: tis_recovery
    data_files:
      - split: test_maize
        path: tis_recovery/test_maize-*
      - split: test_tomato
        path: tis_recovery/test_tomato-*
  - config_name: tts_core_noncore_classification
    data_files:
      - split: test_maize
        path: tts_core_noncore_classification/test_maize-*
      - split: test_tomato
        path: tts_core_noncore_classification/test_tomato-*
  - config_name: tts_recovery
    data_files:
      - split: test_maize
        path: tts_recovery/test_maize-*
      - split: test_tomato
        path: tts_recovery/test_tomato-*
dataset_info:
  - config_name: acceptor_core_noncore_classification
    features:
      - name: sequence
        dtype: string
      - name: label
        dtype: int64
    splits:
      - name: test_maize
        num_bytes: 1185888200
        num_examples: 144550
      - name: test_tomato
        num_bytes: 1152260004
        num_examples: 140451
    download_size: 778025325
    dataset_size: 2338148204
  - config_name: acceptor_recovery
    features:
      - name: sequence
        dtype: string
    splits:
      - name: test_maize
        num_bytes: 1261110324
        num_examples: 153869
      - name: test_tomato
        num_bytes: 1151169180
        num_examples: 140455
    download_size: 810355602
    dataset_size: 2412279504
  - config_name: conservation_within_poaceae_non_tis
    features:
      - name: sequence
        dtype: string
      - name: label
        dtype: int64
    splits:
      - name: test
        num_bytes: 1506951740
        num_examples: 183685
    download_size: 575528297
    dataset_size: 1506951740
  - config_name: conservation_within_poaceae_tis
    features:
      - name: sequence
        dtype: string
      - name: label
        dtype: int64
    splits:
      - name: test
        num_bytes: 300775048
        num_examples: 36662
    download_size: 139559957
    dataset_size: 300775048
  - config_name: donor_core_noncore_classification
    features:
      - name: sequence
        dtype: string
      - name: label
        dtype: int64
    splits:
      - name: test_maize
        num_bytes: 1185888200
        num_examples: 144550
      - name: test_tomato
        num_bytes: 1152260004
        num_examples: 140451
    download_size: 780485274
    dataset_size: 2338148204
  - config_name: donor_recovery
    features:
      - name: sequence
        dtype: string
    splits:
      - name: test_maize
        num_bytes: 1261110324
        num_examples: 153869
      - name: test_tomato
        num_bytes: 1151177376
        num_examples: 140456
    download_size: 812414184
    dataset_size: 2412287700
  - config_name: tis_core_noncore_classification
    features:
      - name: sequence
        dtype: string
      - name: label
        dtype: int64
    splits:
      - name: test_maize
        num_bytes: 298699436
        num_examples: 36409
      - name: test_tomato
        num_bytes: 291061512
        num_examples: 35478
    download_size: 259785500
    dataset_size: 589760948
  - config_name: tis_recovery
    features:
      - name: sequence
        dtype: string
    splits:
      - name: test_maize
        num_bytes: 319930860
        num_examples: 39035
      - name: test_tomato
        num_bytes: 290826864
        num_examples: 35484
    download_size: 269457351
    dataset_size: 610757724
  - config_name: tts_core_noncore_classification
    features:
      - name: sequence
        dtype: string
      - name: label
        dtype: int64
    splits:
      - name: test_maize
        num_bytes: 298699436
        num_examples: 36409
      - name: test_tomato
        num_bytes: 291053308
        num_examples: 35477
    download_size: 260010533
    dataset_size: 589752744
  - config_name: tts_recovery
    features:
      - name: sequence
        dtype: string
    splits:
      - name: test_maize
        num_bytes: 319930860
        num_examples: 39035
      - name: test_tomato
        num_bytes: 290818668
        num_examples: 35483
    download_size: 269872033
    dataset_size: 610749528

🌱 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)}")