--- 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*. --- ## 📂 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 | --- ## 📑 Data Format | Task Type | Fields | Description | |-----------|--------|-------------| | **Classification** | `sequence` | DNA sequence (string) | | | `label` | Binary label: `0 = negative`, `1 = positive` | | **Recovery** | `sequence` | DNA sequence (string) | --- ## 📊 Data Splits | Split | Description | |-------|-------------| | `test` | General test data | | `test_maize` | Zea mays (corn)-specific test data | | `test_tomato` | Solanum lycopersicum (tomato)-specific test data | --- ## 🚀 Usage Example ```python 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)}") ```