Add assay-specific seeded dataset splits

README.md

@@ -21,7 +21,7 @@ configs:
           - data/spr.jsonl
           - data/fpa.jsonl
           - data/rba.jsonl
-    features:
+    features: &bindingdb_features
       - name: reactant_set_id
         dtype: int64
       - name: pmid
@@ -60,6 +60,146 @@ configs:
         dtype: string
       - name: source_record_key
         dtype: string
+  - config_name: itc
+    data_files:
+      - split: full
+        path: data/itc.jsonl
+    features: *bindingdb_features
+  - config_name: spr
+    data_files:
+      - split: full
+        path: data/spr.jsonl
+    features: *bindingdb_features
+  - config_name: rba
+    data_files:
+      - split: full
+        path: data/rba.jsonl
+    features: *bindingdb_features
+  - config_name: fpa
+    data_files:
+      - split: full
+        path: data/fpa.jsonl
+    features: *bindingdb_features
+  - config_name: itc_seed_0
+    data_dir: data/splits/itc/seed_0
+    features: *bindingdb_features
+  - config_name: itc_seed_1
+    data_dir: data/splits/itc/seed_1
+    features: *bindingdb_features
+  - config_name: itc_seed_2
+    data_dir: data/splits/itc/seed_2
+    features: *bindingdb_features
+  - config_name: itc_seed_3
+    data_dir: data/splits/itc/seed_3
+    features: *bindingdb_features
+  - config_name: itc_seed_4
+    data_dir: data/splits/itc/seed_4
+    features: *bindingdb_features
+  - config_name: itc_seed_5
+    data_dir: data/splits/itc/seed_5
+    features: *bindingdb_features
+  - config_name: itc_seed_6
+    data_dir: data/splits/itc/seed_6
+    features: *bindingdb_features
+  - config_name: itc_seed_7
+    data_dir: data/splits/itc/seed_7
+    features: *bindingdb_features
+  - config_name: itc_seed_8
+    data_dir: data/splits/itc/seed_8
+    features: *bindingdb_features
+  - config_name: itc_seed_9
+    data_dir: data/splits/itc/seed_9
+    features: *bindingdb_features
+  - config_name: spr_seed_0
+    data_dir: data/splits/spr/seed_0
+    features: *bindingdb_features
+  - config_name: spr_seed_1
+    data_dir: data/splits/spr/seed_1
+    features: *bindingdb_features
+  - config_name: spr_seed_2
+    data_dir: data/splits/spr/seed_2
+    features: *bindingdb_features
+  - config_name: spr_seed_3
+    data_dir: data/splits/spr/seed_3
+    features: *bindingdb_features
+  - config_name: spr_seed_4
+    data_dir: data/splits/spr/seed_4
+    features: *bindingdb_features
+  - config_name: spr_seed_5
+    data_dir: data/splits/spr/seed_5
+    features: *bindingdb_features
+  - config_name: spr_seed_6
+    data_dir: data/splits/spr/seed_6
+    features: *bindingdb_features
+  - config_name: spr_seed_7
+    data_dir: data/splits/spr/seed_7
+    features: *bindingdb_features
+  - config_name: spr_seed_8
+    data_dir: data/splits/spr/seed_8
+    features: *bindingdb_features
+  - config_name: spr_seed_9
+    data_dir: data/splits/spr/seed_9
+    features: *bindingdb_features
+  - config_name: rba_seed_0
+    data_dir: data/splits/rba/seed_0
+    features: *bindingdb_features
+  - config_name: rba_seed_1
+    data_dir: data/splits/rba/seed_1
+    features: *bindingdb_features
+  - config_name: rba_seed_2
+    data_dir: data/splits/rba/seed_2
+    features: *bindingdb_features
+  - config_name: rba_seed_3
+    data_dir: data/splits/rba/seed_3
+    features: *bindingdb_features
+  - config_name: rba_seed_4
+    data_dir: data/splits/rba/seed_4
+    features: *bindingdb_features
+  - config_name: rba_seed_5
+    data_dir: data/splits/rba/seed_5
+    features: *bindingdb_features
+  - config_name: rba_seed_6
+    data_dir: data/splits/rba/seed_6
+    features: *bindingdb_features
+  - config_name: rba_seed_7
+    data_dir: data/splits/rba/seed_7
+    features: *bindingdb_features
+  - config_name: rba_seed_8
+    data_dir: data/splits/rba/seed_8
+    features: *bindingdb_features
+  - config_name: rba_seed_9
+    data_dir: data/splits/rba/seed_9
+    features: *bindingdb_features
+  - config_name: fpa_seed_0
+    data_dir: data/splits/fpa/seed_0
+    features: *bindingdb_features
+  - config_name: fpa_seed_1
+    data_dir: data/splits/fpa/seed_1
+    features: *bindingdb_features
+  - config_name: fpa_seed_2
+    data_dir: data/splits/fpa/seed_2
+    features: *bindingdb_features
+  - config_name: fpa_seed_3
+    data_dir: data/splits/fpa/seed_3
+    features: *bindingdb_features
+  - config_name: fpa_seed_4
+    data_dir: data/splits/fpa/seed_4
+    features: *bindingdb_features
+  - config_name: fpa_seed_5
+    data_dir: data/splits/fpa/seed_5
+    features: *bindingdb_features
+  - config_name: fpa_seed_6
+    data_dir: data/splits/fpa/seed_6
+    features: *bindingdb_features
+  - config_name: fpa_seed_7
+    data_dir: data/splits/fpa/seed_7
+    features: *bindingdb_features
+  - config_name: fpa_seed_8
+    data_dir: data/splits/fpa/seed_8
+    features: *bindingdb_features
+  - config_name: fpa_seed_9
+    data_dir: data/splits/fpa/seed_9
+    features: *bindingdb_features
 ---
 
 # Assay-aware BindingDB
@@ -69,10 +209,27 @@ records organized by experimental assay type. Each row represents a BindingDB
 reactant set and includes its measured affinity, source publication, original
 experimental context, and an assay-specific structured description.
 
-The dataset is provided as one unsplit `full` split. It is intended for
-assay-aware binding-affinity analysis, information extraction, retrieval, and
-dataset curation. It does not include predefined training, validation, or test
-partitions.
+The complete dataset remains available as the `full` split. Four assay
+configurations provide direct access to ITC, SPR, FPA, or RBA records, and 40
+training-compatible configurations provide predefined training, validation,
+and test partitions for seeds 0 through 9.
+
+## Configurations and splits
+
+The `default` configuration contains all four assays in one `full` split.
+The `itc`, `spr`, `rba`, and `fpa` configurations each expose one complete
+assay as `full` without applying training eligibility filters.
+
+Configurations named `<assay>_seed_<seed>` reproduce the data used in single-assay binding-affinity experiments for seeds 0–9 and expose `train`, `validation`, and `test` splits.
+
+Eligible records require:
+
+- A precomputed Boltz-2 affinity representation.
+- A Qwen3 assay-context embedding.
+- Exactly one positive numeric Kd, Ki, or IC50 value.
+- No `<` or `>` qualifier.
+
+Unique PMIDs are shuffled with NumPy `RandomState(seed)`. Using integer truncation, 20% are assigned to test, 10% to validation, and the remainder to train, preventing PMID leakage.
 
 
 ## Data schema
@@ -124,6 +281,22 @@ print(dataset)
 print(f"Number of records: {len(dataset):,}")
 ```
 
+### Load one complete assay
+
+Pass the assay configuration name as the second argument:
+
+```python
+from datasets import load_dataset
+
+dataset = load_dataset(
+    "anonymousapple/Assay-aware-BindingDB",
+    "itc",
+    split="full",
+)
+
+print(f"ITC records: {len(dataset)}")
+```
+
 ### Read an individual record
 
 ```python
@@ -200,9 +373,30 @@ if value is not None:
     print(json.dumps(original_paragraph, indent=2, ensure_ascii=False))
 ```
 
-### Filter by assay
+### Load a training-compatible seeded split
+
+Combine the assay and split seed in the configuration name, then select a
+normal Hugging Face split:
 
 ```python
-itc = dataset.filter(lambda row: row["assay_type"] == "itc")
-print(f"ITC records: {len(itc):,}")
-```
+from datasets import load_dataset
+
+itc_train_seed_1 = load_dataset(
+    "anonymousapple/Assay-aware-BindingDB",
+    "itc_seed_1",
+    split="train",
+)
+
+itc_validation_seed_1 = load_dataset(
+    "anonymousapple/Assay-aware-BindingDB",
+    "itc_seed_1",
+    split="validation",
+)
+
+itc_test_seed_1 = load_dataset(
+    "anonymousapple/Assay-aware-BindingDB",
+    "itc_seed_1",
+    split="test",
+)
+```
+

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