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PlantCAD2_zero_shot_tasks

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Languages:
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Tags:
biology
genomics
dna
plants
zero-shot
conservation
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Yangximiao JingjingZhai commited on
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Duplicate from plantcad/PlantCAD2_zero_shot_tasks

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Co-authored-by: Jingjing Zhai <JingjingZhai@users.noreply.huggingface.co>

Files changed (41) hide show
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  2. README.md +298 -0
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  14. acceptor_recovery/test_tomato-00002-of-00003.parquet +3 -0
  15. conservation_within_andropogoneae/test-00000-of-00001.parquet +3 -0
  16. conservation_within_poaceae_non_tis/test-00000-of-00004.parquet +3 -0
  17. conservation_within_poaceae_non_tis/test-00001-of-00004.parquet +3 -0
  18. conservation_within_poaceae_non_tis/test-00002-of-00004.parquet +3 -0
  19. conservation_within_poaceae_non_tis/test-00003-of-00004.parquet +3 -0
  20. conservation_within_poaceae_tis/test-00000-of-00001.parquet +3 -0
  21. donor_core_noncore_classification/test_maize-00000-of-00003.parquet +3 -0
  22. donor_core_noncore_classification/test_maize-00001-of-00003.parquet +3 -0
  23. donor_core_noncore_classification/test_maize-00002-of-00003.parquet +3 -0
  24. donor_core_noncore_classification/test_tomato-00000-of-00003.parquet +3 -0
  25. donor_core_noncore_classification/test_tomato-00001-of-00003.parquet +3 -0
  26. donor_core_noncore_classification/test_tomato-00002-of-00003.parquet +3 -0
  27. donor_recovery/test_maize-00000-of-00003.parquet +3 -0
  28. donor_recovery/test_maize-00001-of-00003.parquet +3 -0
  29. donor_recovery/test_maize-00002-of-00003.parquet +3 -0
  30. donor_recovery/test_tomato-00000-of-00003.parquet +3 -0
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  33. structural_variant_effect_prediction/test-00000-of-00001.parquet +3 -0
  34. tis_core_noncore_classification/test_maize-00000-of-00001.parquet +3 -0
  35. tis_core_noncore_classification/test_tomato-00000-of-00001.parquet +3 -0
  36. tis_recovery/test_maize-00000-of-00001.parquet +3 -0
  37. tis_recovery/test_tomato-00000-of-00001.parquet +3 -0
  38. tts_core_noncore_classification/test_maize-00000-of-00001.parquet +3 -0
  39. tts_core_noncore_classification/test_tomato-00000-of-00001.parquet +3 -0
  40. tts_recovery/test_maize-00000-of-00001.parquet +3 -0
  41. tts_recovery/test_tomato-00000-of-00001.parquet +3 -0
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1
+ ---
2
+ license: apache-2.0
3
+ task_categories:
4
+ - text-classification
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+ - sequence-modeling
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+ language:
7
+ - en
8
+ tags:
9
+ - biology
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+ - genomics
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+ - dna
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+ - plants
13
+ - zero-shot
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+ - conservation
15
+ configs:
16
+ - config_name: acceptor_core_noncore_classification
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+ data_files:
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+ - split: test_maize
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+ path: acceptor_core_noncore_classification/test_maize-*
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+ - split: test_tomato
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+ path: acceptor_core_noncore_classification/test_tomato-*
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+ - config_name: acceptor_recovery
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+ data_files:
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+ - split: test_maize
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+ path: acceptor_recovery/test_maize-*
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+ - split: test_tomato
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+ path: acceptor_recovery/test_tomato-*
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+ - config_name: conservation_within_poaceae_non_tis
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+ data_files:
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+ - split: test
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+ path: conservation_within_poaceae_non_tis/test-*
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+ - config_name: conservation_within_andropogoneae
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+ data_files:
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+ - split: test
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+ path: conservation_within_andropogoneae/test-*
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+ - config_name: conservation_within_poaceae_tis
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+ data_files:
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+ - split: test
39
+ path: conservation_within_poaceae_tis/test-*
40
+ - config_name: structural_variant_effect_prediction
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+ data_files:
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+ - split: test
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+ path: structural_variant_effect_prediction/test-*
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+ - config_name: donor_core_noncore_classification
45
+ data_files:
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+ - split: test_maize
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+ path: donor_core_noncore_classification/test_maize-*
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+ - split: test_tomato
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+ path: donor_core_noncore_classification/test_tomato-*
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+ - config_name: donor_recovery
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+ data_files:
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+ - split: test_maize
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+ path: donor_recovery/test_maize-*
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+ - split: test_tomato
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+ path: donor_recovery/test_tomato-*
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+ - config_name: tis_core_noncore_classification
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+ data_files:
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+ - split: test_maize
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+ path: tis_core_noncore_classification/test_maize-*
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+ - split: test_tomato
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+ path: tis_core_noncore_classification/test_tomato-*
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+ - config_name: tis_recovery
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+ data_files:
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+ - split: test_maize
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+ path: tis_recovery/test_maize-*
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+ - split: test_tomato
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+ path: tis_recovery/test_tomato-*
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+ - config_name: tts_core_noncore_classification
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+ data_files:
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+ - split: test_maize
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+ path: tts_core_noncore_classification/test_maize-*
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+ - split: test_tomato
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+ path: tts_core_noncore_classification/test_tomato-*
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+ - config_name: tts_recovery
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+ data_files:
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+ - split: test_maize
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+ path: tts_recovery/test_maize-*
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+ - split: test_tomato
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+ path: tts_recovery/test_tomato-*
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+ dataset_info:
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+ - config_name: acceptor_core_noncore_classification
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+ features:
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+ - name: sequence
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+ dtype: string
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+ - name: label
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+ dtype: int64
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+ - name: test_tomato
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+ num_examples: 140451
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+ download_size: 778025325
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+ dataset_size: 2338148204
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+ - config_name: acceptor_recovery
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+ features:
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+ - name: sequence
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+ dtype: string
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+ splits:
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+ - name: test_maize
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+ num_bytes: 1261110324
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+ num_examples: 153869
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+ - name: test_tomato
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+ num_bytes: 1151169180
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+ num_examples: 140455
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+ download_size: 810355602
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+ dataset_size: 2412279504
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+ - config_name: conservation_within_poaceae_non_tis
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+ features:
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+ - name: sequence
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+ dtype: string
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+ - name: label
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+ dtype: int64
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+ splits:
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+ - name: test
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+ num_bytes: 1506951740
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+ num_examples: 183685
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+ download_size: 575528297
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+ dataset_size: 1506951740
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+ - config_name: conservation_within_poaceae_tis
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+ features:
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+ dtype: string
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+ - name: label
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+ dtype: int64
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+ - name: test
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+ num_bytes: 300775048
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+ num_examples: 36662
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+ download_size: 139559957
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+ dataset_size: 300775048
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+ - config_name: donor_core_noncore_classification
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+ features:
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+ - name: sequence
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+ dtype: string
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+ - name: label
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+ dtype: int64
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+ num_bytes: 1185888200
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+ num_examples: 144550
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+ - name: test_tomato
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+ num_examples: 140451
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+ download_size: 780485274
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+ dataset_size: 2338148204
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+ - config_name: donor_recovery
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+ num_examples: 140456
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+ download_size: 812414184
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+ dataset_size: 2412287700
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+ - config_name: tis_core_noncore_classification
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+ features:
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+ - name: sequence
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+ dtype: string
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+ - name: label
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+ dtype: int64
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+ splits:
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+ - name: test_tomato
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+ num_examples: 35478
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+ download_size: 259785500
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+ dataset_size: 589760948
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+ - config_name: tis_recovery
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+ features:
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+ dtype: string
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+ - name: test_tomato
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+ num_examples: 35484
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+ download_size: 269457351
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+ dataset_size: 610757724
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+ - config_name: tts_core_noncore_classification
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+ features:
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+ - name: sequence
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+ dtype: string
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+ - name: label
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+ dtype: int64
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+ - name: test_tomato
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+ num_examples: 35477
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+ download_size: 260010533
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+ dataset_size: 589752744
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+ - config_name: tts_recovery
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+ features:
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+ - name: sequence
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+ dtype: string
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+ splits:
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+ - name: test_maize
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+ num_bytes: 319930860
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+ - name: test_tomato
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+ num_examples: 35483
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+ download_size: 269872033
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+ dataset_size: 610749528
217
+ ---
218
+
219
+ # 🌱 PlantCAD2 Zero-Shot Tasks
220
+
221
+ Zero-shot evaluation tasks for **plant genomics** using **PlantCAD2**.
222
+ This dataset contains tasks designed to evaluate model performance *without task-specific training*.
223
+
224
+ ---
225
+
226
+ ## 📂 Available Tasks
227
+
228
+ ### 🔬 Cross-species Evolutionary Conservation
229
+ | Task Name | Description | Samples | Metric |
230
+ |-----------|-------------|---------|--------|
231
+ | `conservation_within_andropogoneae` | Predict conserved vs non-conserved sites using alignments within 35 Andropogoneae genomes | 19,030 vs 19,030 | AUROC |
232
+ | `conservation_within_poaceae_non_tis` | Predict conserved vs non-conserved coding sites (excluding TIS) within Poaceae | 103,368 vs 80,317 | AUROC |
233
+ | `conservation_within_poaceae_tis` | Predict conserved vs non-conserved TIS sites | 26,650 vs 10,012 | AUROC |
234
+
235
+ ### 🧬 Key Junction Recovery
236
+ | Task Name | Description | Samples | Metric |
237
+ |-----------|-------------|---------|--------|
238
+ | `tis_recovery` | Recover masked **ATG start codon** (maize) | 39,035 | Accuracy |
239
+ | `tts_recovery` | Recover masked **TAG/TAA/TGA stop codon** (maize) | 39,035 | Accuracy |
240
+ | `donor_recovery` | Recover masked **GT splice donor motif** (maize) | 153,869 | Accuracy |
241
+ | `acceptor_recovery` | Recover masked **AG splice acceptor motif** (maize) | 153,869 | Accuracy |
242
+
243
+ ### 🌽 Within-species Conservation (Maize)
244
+ | Task Name | Description | Samples | Metric |
245
+ |-----------|-------------|---------|--------|
246
+ | `tis_core_noncore_classification` | Predict **core TIS vs non-core TIS** | 28,291 vs 8,118 | AUROC |
247
+ | `tts_core_noncore_classification` | Predict **core TTS vs non-core TTS** | 28,291 vs 8,118 | AUROC |
248
+ | `donor_core_noncore_classification` | Predict **core splice donor vs non-core splice donor** | 123,183 vs 21,367 | AUROC |
249
+ | `acceptor_core_noncore_classification` | Predict **core splice acceptor vs non-core splice acceptor** | 123,183 vs 21,367 | AUROC |
250
+
251
+ ### 🧩 Structural Variant Effect
252
+ | Task Name | Description | Samples | Metric |
253
+ |-----------|-------------|---------|--------|
254
+ | `structural_variant_effect_prediction` | Predict **conserved deletions vs non-conserved deletions** | 7,662 vs 10,413 | AUPRC |
255
+
256
+ ---
257
+
258
+ ## 📑 Data Format
259
+
260
+ | Task Type | Fields | Description |
261
+ |-----------|--------|-------------|
262
+ | **Classification** | `sequence` | DNA sequence (string) |
263
+ | | `label` | Binary label: `0 = negative`, `1 = positive` |
264
+ | **Recovery** | `sequence` | DNA sequence (string) |
265
+
266
+ ---
267
+
268
+ ## 📊 Data Splits
269
+
270
+ | Split | Description |
271
+ |-------|-------------|
272
+ | `test` | General test data |
273
+ | `test_maize` | Zea mays (corn)-specific test data |
274
+ | `test_tomato` | Solanum lycopersicum (tomato)-specific test data |
275
+
276
+ ---
277
+
278
+ ## 🚀 Usage Example
279
+
280
+ ```python
281
+ from datasets import load_dataset, get_dataset_config_names
282
+
283
+ # List all available tasks
284
+ tasks = get_dataset_config_names("plantcad/PlantCAD2_zero_shot_tasks")
285
+ print("Available tasks:", tasks)
286
+
287
+ # Example: Classification task
288
+ classification_data = load_dataset("plantcad/PlantCAD2_zero_shot_tasks", "conservation_within_poaceae_tis")
289
+ test_split = classification_data['test']
290
+ print(f"Test samples: {len(test_split)}")
291
+ print(f"Sample: {test_split[0]}")
292
+
293
+ # Example: TIS recovery task
294
+ recovery_data = load_dataset("plantcad/PlantCAD2_zero_shot_tasks", "tis_recovery")
295
+ if 'test_maize' in recovery_data:
296
+ maize_data = recovery_data['test_maize']
297
+ print(f"Maize recovery samples: {len(maize_data)}")
298
+ ```
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