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/")