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dataset/AptaBench_dataset.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:6f8b01685137cc495b35b50681eccf6e1fd4ade476b13067462ea5f2d6cc4459
+size 112730

dataset/make_splits.py

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+import os
+import sys
+import json
+import numpy as np
+import pandas as pd
+
+# make src/ available
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "src")))
+
+from data.split import (
+    stratified_group_splits,
+    disjoint_aptamer_splits,
+    disjoint_molecule_splits,
+)
+
+# ======================================================
+# CONFIG
+# ======================================================
+DATASET_PATH = os.path.join(os.path.dirname(__file__), "AptaBench_dataset_v3.csv")
+N_SPLITS = 5
+RANDOM_STATE = 42
+FRAC_TOLERANCE = 0.02  # acceptable abs deviation from expected test fraction
+MAX_TRIES = 200  # retry different seeds to meet ratio
+
+# ======================================================
+# LOAD DATA
+# ======================================================
+df = pd.read_csv(DATASET_PATH)
+
+# ======================================================
+# MAKE OUTPUT DIR
+# ======================================================
+outdir = os.path.join(os.path.dirname(__file__), "splits")
+os.makedirs(outdir, exist_ok=True)
+
+# ======================================================
+# HELPER TO SAVE SPLITS
+# ======================================================
+def save_splits(name, splits):
+    outpath = os.path.join(outdir, f"{name}.json")
+    data = []
+    for i, (tr, va) in enumerate(splits):
+        data.append({
+            "fold": i,
+            "train_idx": tr.tolist(),
+            "val_idx": va.tolist(),
+        })
+    with open(outpath, "w") as f:
+        json.dump(data, f, indent=2)
+    print(f"Saved {name} splits -> {outpath}")
+
+
+# ======================================================
+# STRATIFIED
+# ======================================================
+splits = stratified_group_splits(
+    df,
+    n_splits=N_SPLITS,
+    random_state=RANDOM_STATE,
+    frac_tolerance=FRAC_TOLERANCE,
+    max_tries=MAX_TRIES,
+)
+save_splits("stratified", splits)
+
+# ======================================================
+# DISJOINT APTAMER
+# ======================================================
+splits = disjoint_aptamer_splits(
+    df,
+    n_splits=N_SPLITS,
+    random_state=RANDOM_STATE,
+    frac_tolerance=FRAC_TOLERANCE,
+    max_tries=MAX_TRIES,
+)
+save_splits("disjoint_aptamer", splits)
+
+# ======================================================
+# DISJOINT MOLECULE
+# ======================================================
+splits = disjoint_molecule_splits(
+    df,
+    n_splits=N_SPLITS,
+    random_state=RANDOM_STATE,
+    scaffold_missing="separate",
+    frac_tolerance=FRAC_TOLERANCE,
+    max_tries=MAX_TRIES,
+)
+save_splits("disjoint_molecule", splits)
+
+print("All splits successfully saved in dataset/splits/")