import datasets import csv import random class ppb_affinity(datasets.GeneratorBasedBuilder): VERSION = datasets.Version("1.0.1") BUILDER_CONFIGS = [ datasets.BuilderConfig(name="raw", description="Raw parsed PDBs dataset with critical filtrations only."), datasets.BuilderConfig(name="filtered", description="Raw dataset with additional cleaning and train/val/test splits."), datasets.BuilderConfig(name="filtered_random", description="Filtered dataset with random 80-10-10 splits."), ] def _info(self): return datasets.DatasetInfo() def _split_generators(self, dl_manager): if self.config.name == "raw": filepath = dl_manager.download_and_extract("raw.csv") return [datasets.SplitGenerator( name=datasets.Split.TRAIN, gen_kwargs={"filepath": filepath} )] elif self.config.name == "filtered": filepath = dl_manager.download_and_extract("filtered.csv") return [ datasets.SplitGenerator( name=datasets.Split.TRAIN, gen_kwargs={"filepath": filepath, "split": "train"}, ), datasets.SplitGenerator( name=datasets.Split.VALIDATION, gen_kwargs={"filepath": filepath, "split": "val"}, ), datasets.SplitGenerator( name=datasets.Split.TEST, gen_kwargs={"filepath": filepath, "split": "test"}, ), ] elif self.config.name == "filtered_random": filepath = dl_manager.download_and_extract("filtered.csv") # Read all rows to determine splits with open(filepath, encoding="utf-8") as f: reader = csv.DictReader(f) rows = list(reader) n_total = len(rows) # Generate shuffled indices with fixed seed indices = list(range(n_total)) rng = random.Random(42) # Fixed seed for reproducibility rng.shuffle(indices) # Calculate split sizes n_train = int(0.8 * n_total) n_val = int(0.1 * n_total) n_test = n_total - n_train - n_val # Handle remainder # Split indices into ranges return [ datasets.SplitGenerator( name=datasets.NamedSplit("train_rand"), gen_kwargs={ "filepath": filepath, "shuffled_indices": indices, "split_start": 0, "split_end": n_train, }, ), datasets.SplitGenerator( name=datasets.NamedSplit("validation_rand"), gen_kwargs={ "filepath": filepath, "shuffled_indices": indices, "split_start": n_train, "split_end": n_train + n_val, }, ), datasets.SplitGenerator( name=datasets.NamedSplit("test_rand"), gen_kwargs={ "filepath": filepath, "shuffled_indices": indices, "split_start": n_train + n_val, "split_end": n_total, }, ), ] def _generate_examples(self, filepath, split=None, shuffled_indices=None, split_start=None, split_end=None): with open(filepath, encoding="utf-8") as f: reader = csv.DictReader(f) rows = list(reader) if self.config.name == "raw": for idx, row in enumerate(rows): yield idx, row elif self.config.name == "filtered": for idx, row in enumerate(rows): if row["split"] == split: del row["split"] yield idx, row elif self.config.name == "filtered_random": # Iterate over the range [split_start, split_end) in shuffled_indices for global_idx in range(split_start, split_end): original_idx = shuffled_indices[global_idx] row = rows[original_idx] del row["split"] # Remove original split column yield global_idx, row # Key is global shuffled index