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b/src/preprocessing/generate_statistics.py |
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# coding: utf-8 |
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# Base Dependencies |
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# ------------------ |
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import numpy as np |
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from collections import Counter |
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from typing import Dict |
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from pathlib import Path |
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from os.path import join as pjoin |
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from tqdm import tqdm |
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# Local Dependencies |
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# ------------------ |
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from models.relation_collection import RelationCollection |
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# 3rd-Party Dependencies |
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# ---------------------- |
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import pandas as pd |
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from tabulate import tabulate |
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# Constants |
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# --------- |
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from constants import N2C2_REL_TYPES, DDI_ALL_TYPES, N2C2_PATH, DDI_PATH |
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TABLE_FORMAT = "latex" |
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# Main Functions |
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# --------------- |
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def generate_statistics(dataset: str, collections: Dict[str, RelationCollection]): |
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if dataset == "n2c2": |
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return generate_statistics_n2c2(collections) |
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elif dataset == "ddi": |
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return generate_statistics_ddi(collections) |
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else: |
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raise ValueError("unsupported dataset '{}'".format(dataset)) |
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def generate_statistics_n2c2(collections: Dict[str, RelationCollection]): |
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"""Generates the statistics for the n2c2 dataset""" |
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df_counts = { |
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"relation": [], |
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"train_positive": [], |
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"train_negative": [], |
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"test_positive": [], |
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"test_negative": [], |
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} |
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df_seq_lengths = { |
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"relation": [], |
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"train_min": [], |
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"train_avg": [], |
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"train_max": [], |
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"test_min": [], |
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"test_avg": [], |
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"test_max": [], |
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} |
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# number of relations per type of relation |
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for rel_type in tqdm(N2C2_REL_TYPES): |
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df_counts["relation"].append(rel_type) |
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df_seq_lengths["relation"].append(rel_type) |
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for split, collection in collections.items(): |
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subcollection = collection.type_subcollection(rel_type) |
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# add counts to data |
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count_labels = Counter(subcollection.labels) |
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df_counts[split + "_negative"].append(count_labels[0]) |
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df_counts[split + "_positive"].append(count_labels[1]) |
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# add sequence length to dataframe |
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seq_lengths = list( |
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map(lambda rel: len(rel.text.split()), subcollection.relations) |
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) |
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df_seq_lengths[split + "_min"].append(min(seq_lengths)) |
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df_seq_lengths[split + "_avg"].append(sum(seq_lengths) / len(subcollection)) |
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df_seq_lengths[split + "_max"].append(max(seq_lengths)) |
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df_counts = pd.DataFrame(df_counts) |
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df_seq_lengths = pd.DataFrame(df_seq_lengths) |
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# add totals to counts |
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df_counts["train_total"] = df_counts["train_positive"] + df_counts["train_negative"] |
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df_counts["test_total"] = df_counts["test_positive"] + df_counts["test_negative"] |
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df_counts["total_positive"] = ( |
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df_counts["train_positive"] + df_counts["test_positive"] |
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) |
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df_counts["total_negative"] = ( |
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df_counts["train_negative"] + df_counts["test_negative"] |
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) |
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df_counts["total"] = df_counts["total_positive"] + df_counts["total_negative"] |
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df_counts.loc[len(df_counts)] = ["Total"] + [ |
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df_counts[col].sum() for col in df_counts.columns[1:] |
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] |
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all_train_seq_lengths = list(map(lambda rel: len(rel.text.split()), collections["train"].relations)) |
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all_test_seq_lengths = list(map(lambda rel: len(rel.text.split()), collections["test"].relations)) |
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df_seq_lengths = df_seq_lengths.append( |
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{ |
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"relation": "Overall", |
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"train_min": min(all_train_seq_lengths), |
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"train_avg": sum(all_train_seq_lengths) / len(all_train_seq_lengths), |
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"train_max": max(all_train_seq_lengths), |
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"test_min": min(all_test_seq_lengths), |
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"test_avg": sum(all_test_seq_lengths) / len(all_test_seq_lengths), |
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"test_max": max(all_test_seq_lengths), |
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}, |
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ignore_index=True, |
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) |
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# select and reorder columns |
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df_counts = df_counts.loc[:, ["relation", "train_positive", "train_negative", "train_total", "test_positive", "test_negative", "test_total", "total"]] |
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# save data to csv |
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df_counts.to_csv(Path(pjoin(N2C2_PATH, "counts.csv")), index=False) |
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df_seq_lengths.to_csv(Path(pjoin(N2C2_PATH, "seq_length.csv")), index=False) |
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# print statistics |
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print("\n **** Statistics of the N2C2 Dataset ****") |
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print("Counts:") |
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print(tabulate(df_counts, headers="keys", tablefmt=TABLE_FORMAT)) |
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print("Seq Length:") |
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print(tabulate(df_seq_lengths, headers="keys", tablefmt=TABLE_FORMAT)) |
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def generate_statistics_ddi(collections: Dict[str, RelationCollection]) -> None: |
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"""Generates the statistics of the DDI dataset""" |
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df_counts = {"relation": [], "train": [], "test": []} |
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df_seq_lengths = { |
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"relation": [], |
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"train_min": [], |
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"train_avg": [], |
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"train_max": [], |
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"test_min": [], |
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"test_avg": [], |
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"test_max": [], |
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} |
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for rel_type in DDI_ALL_TYPES: |
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df_counts["relation"].append(rel_type) |
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df_seq_lengths["relation"].append(rel_type) |
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for split, collection in collections.items(): |
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subcollection = collection.type_subcollection(rel_type) |
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df_counts[split].append(len(subcollection)) |
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seq_lengths = list( |
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map(lambda rel: len(rel.text.split()), subcollection.relations) |
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) |
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df_seq_lengths[split + "_min"].append(min(seq_lengths)) |
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df_seq_lengths[split + "_avg"].append(sum(seq_lengths) / len(subcollection)) |
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df_seq_lengths[split + "_max"].append(max(seq_lengths)) |
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# convert to dataframes |
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df_counts = pd.DataFrame(df_counts) |
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df_seq_lengths = pd.DataFrame(df_seq_lengths) |
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# add totals |
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train_negative = df_counts.loc[(df_counts["relation"] == "NO-REL"), "train"].values[ |
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0 |
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] |
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train_positive = df_counts.loc[(df_counts["relation"] != "NO-REL"), "train"].sum() |
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test_negative = df_counts.loc[(df_counts["relation"] == "NO-REL"), "test"].values[0] |
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test_positive = df_counts.loc[(df_counts["relation"] != "NO-REL"), "test"].sum() |
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train_total = train_positive + train_negative |
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test_total = test_positive + test_negative |
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total = train_total + test_total |
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# add positive row |
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df_counts.loc[len(df_counts)] = ["Total Positive", train_positive, test_positive] |
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# add totals |
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df_counts["total"] = df_counts["train"] + df_counts["test"] |
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df_counts.loc[len(df_counts)] = [" Total", train_total, test_total, total] |
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all_train_seq_lengths = list(map(lambda rel: len(rel.text.split()), collections["train"].relations)) |
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all_test_seq_lengths = list(map(lambda rel: len(rel.text.split()), collections["test"].relations)) |
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df_seq_lengths = df_seq_lengths.append( |
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{ |
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"relation": "Overall", |
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"train_min": min(all_train_seq_lengths), |
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"train_avg": sum(all_train_seq_lengths) / len(all_train_seq_lengths), |
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"train_max": max(all_train_seq_lengths), |
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"test_min": min(all_test_seq_lengths), |
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"test_avg": sum(all_test_seq_lengths) / len(all_test_seq_lengths), |
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"test_max": max(all_test_seq_lengths), |
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}, |
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ignore_index=True, |
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) |
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# save data to csv |
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df_counts.to_csv(Path(pjoin(DDI_PATH, "counts.csv")), index=False) |
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df_seq_lengths.to_csv(Path(pjoin(DDI_PATH, "seq_length.csv")), index=False) |
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# print statistics |
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print("\n **** Statistics of the DDI Dataset ****") |
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print("Counts:") |
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print(tabulate(df_counts, headers="keys", tablefmt=TABLE_FORMAT)) |
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print("Seq Length:") |
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print(tabulate(df_seq_lengths, headers="keys", tablefmt=TABLE_FORMAT)) |