explore_dataset.py

#!/usr/bin/env python3
"""
explore_dataset.py

Exploratory Data Analysis (EDA) for the CS/ML Academic Papers Dataset.

Loads the locally-saved dataset (or downloads from HuggingFace Hub), computes
summary statistics, identifies top terms per category via TF-IDF, and saves
publication-ready visualisations as PNG files.

Usage
-----
    # Analyse the local dataset
    python explore_dataset.py

    # Load from the HuggingFace Hub instead
    python explore_dataset.py --from-hub gr8monk3ys/cs-ml-academic-papers

    # Customise the output directory for plots
    python explore_dataset.py --plots-dir ./plots
"""

from __future__ import annotations

import argparse
import logging
from pathlib import Path

import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from datasets import load_from_disk
from sklearn.feature_extraction.text import TfidfVectorizer

# Use non-interactive backend so the script works headlessly.
matplotlib.use("Agg")

LOG = logging.getLogger("explore_dataset")

DATA_DIR: Path = Path(__file__).resolve().parent / "data"
PLOTS_DIR: Path = Path(__file__).resolve().parent / "plots"

# Colour palette (colour-blind friendly, adapted from Tol's muted scheme).
PALETTE = [
    "#332288",
    "#88CCEE",
    "#44AA99",
    "#117733",
    "#999933",
    "#DDCC77",
    "#CC6677",
    "#882255",
    "#AA4499",
]

# ---------------------------------------------------------------------------
# Loading helpers
# ---------------------------------------------------------------------------


def load_local(data_dir: Path) -> pd.DataFrame:
    """Load the dataset from a local ``save_to_disk`` directory."""
    ds_path = data_dir / "hf_dataset"
    if not ds_path.exists():
        raise FileNotFoundError(
            f"No saved dataset found at {ds_path}. "
            "Run create_dataset.py first or use --from-hub."
        )
    dd = load_from_disk(str(ds_path))
    frames = [dd[split].to_pandas() for split in dd]
    return pd.concat(frames, ignore_index=True)


def load_hub(repo_id: str) -> pd.DataFrame:
    """Download the dataset from the HuggingFace Hub."""
    from datasets import load_dataset

    dd = load_dataset(repo_id)
    frames = [dd[split].to_pandas() for split in dd]
    return pd.concat(frames, ignore_index=True)


# ---------------------------------------------------------------------------
# Statistics
# ---------------------------------------------------------------------------


def print_summary(df: pd.DataFrame) -> None:
    """Print high-level summary statistics to stdout."""
    separator = "=" * 60
    print(f"\n{separator}")
    print("  CS/ML Academic Papers Dataset — Summary Statistics")
    print(separator)

    print(f"\n  Total papers           : {len(df):,}")
    print(f"  Unique arXiv IDs       : {df['arxiv_id'].nunique():,}")
    print(f"  Unique primary cats    : {df['primary_category'].nunique()}")

    # Date range
    if "published" in df.columns:
        dates = pd.to_datetime(df["published"], errors="coerce")
        valid = dates.dropna()
        if len(valid) > 0:
            print(
                f"  Published date range   : {valid.min():%Y-%m-%d} to {valid.max():%Y-%m-%d}"
            )

    # Authors
    author_counts = df["authors"].apply(len)
    print(f"\n  Authors per paper (mean): {author_counts.mean():.1f}")
    print(f"  Authors per paper (med) : {author_counts.median():.0f}")

    # Abstract lengths
    abs_len = df["abstract"].str.split().str.len()
    print("\n  Abstract length (words):")
    print(f"    mean   : {abs_len.mean():.0f}")
    print(f"    median : {abs_len.median():.0f}")
    print(f"    min    : {abs_len.min():.0f}")
    print(f"    max    : {abs_len.max():.0f}")
    print(f"    std    : {abs_len.std():.1f}")

    # Category distribution
    print("\n  Primary category distribution:")
    for cat, count in df["primary_category"].value_counts().items():
        pct = 100.0 * count / len(df)
        print(f"    {cat:<12s}  {count:>5,}  ({pct:5.1f}%)")

    # DOI availability
    has_doi = (df["doi"].str.len() > 0).sum()
    print(f"\n  Papers with DOI        : {has_doi:,} ({100 * has_doi / len(df):.1f}%)")

    print(f"\n{separator}\n")


# ---------------------------------------------------------------------------
# TF-IDF keyword extraction
# ---------------------------------------------------------------------------


def top_tfidf_terms(
    df: pd.DataFrame,
    text_col: str = "abstract",
    group_col: str = "primary_category",
    top_n: int = 15,
) -> dict[str, list[tuple[str, float]]]:
    """
    For each group in *group_col*, fit a TF-IDF vectoriser on the documents
    belonging to that group and return the top-*n* terms by mean TF-IDF score.
    """
    results: dict[str, list[tuple[str, float]]] = {}

    vectorizer = TfidfVectorizer(
        max_features=5000,
        stop_words="english",
        min_df=5,
        max_df=0.85,
        ngram_range=(1, 2),
        token_pattern=r"(?u)\b[a-zA-Z][a-zA-Z+#\-]{2,}\b",
    )

    for group, sub_df in df.groupby(group_col):
        texts = sub_df[text_col].tolist()
        if len(texts) < 10:
            LOG.warning(
                "Skipping group %s — too few documents (%d).", group, len(texts)
            )
            continue

        tfidf_matrix = vectorizer.fit_transform(texts)
        mean_scores = np.asarray(tfidf_matrix.mean(axis=0)).flatten()
        feature_names = vectorizer.get_feature_names_out()
        top_indices = mean_scores.argsort()[::-1][:top_n]
        results[group] = [
            (feature_names[i], float(mean_scores[i])) for i in top_indices
        ]

    return results


def print_top_terms(terms_by_cat: dict[str, list[tuple[str, float]]]) -> None:
    """Pretty-print TF-IDF top terms per category."""
    print("=" * 60)
    print("  Top TF-IDF Terms per Category")
    print("=" * 60)
    for cat in sorted(terms_by_cat):
        print(f"\n  [{cat}]")
        for rank, (term, score) in enumerate(terms_by_cat[cat], 1):
            print(f"    {rank:>2}. {term:<30s}  (score: {score:.4f})")
    print()


# ---------------------------------------------------------------------------
# Visualisations
# ---------------------------------------------------------------------------


def _savefig(fig: plt.Figure, path: Path) -> None:
    fig.savefig(str(path), dpi=150, bbox_inches="tight", facecolor="white")
    plt.close(fig)
    LOG.info("Saved plot -> %s", path)


def plot_category_distribution(df: pd.DataFrame, output_dir: Path) -> None:
    """Bar chart of primary-category counts."""
    counts = df["primary_category"].value_counts().sort_values(ascending=True)

    fig, ax = plt.subplots(figsize=(8, 5))
    bars = ax.barh(counts.index, counts.values, color=PALETTE[: len(counts)])
    ax.bar_label(bars, padding=4, fontsize=9)
    ax.set_xlabel("Number of Papers")
    ax.set_title("Papers by Primary arXiv Category")
    ax.spines[["top", "right"]].set_visible(False)
    fig.tight_layout()
    _savefig(fig, output_dir / "category_distribution.png")


def plot_abstract_length_histogram(df: pd.DataFrame, output_dir: Path) -> None:
    """Histogram of abstract word counts."""
    lengths = df["abstract"].str.split().str.len()

    fig, ax = plt.subplots(figsize=(8, 5))
    ax.hist(lengths, bins=50, color=PALETTE[0], edgecolor="white", alpha=0.85)
    ax.axvline(
        lengths.median(),
        color=PALETTE[6],
        linestyle="--",
        linewidth=1.5,
        label=f"Median ({lengths.median():.0f} words)",
    )
    ax.axvline(
        lengths.mean(),
        color=PALETTE[4],
        linestyle=":",
        linewidth=1.5,
        label=f"Mean ({lengths.mean():.0f} words)",
    )
    ax.set_xlabel("Abstract Length (words)")
    ax.set_ylabel("Frequency")
    ax.set_title("Distribution of Abstract Lengths")
    ax.legend(frameon=False)
    ax.spines[["top", "right"]].set_visible(False)
    fig.tight_layout()
    _savefig(fig, output_dir / "abstract_length_histogram.png")


def plot_abstract_length_by_category(df: pd.DataFrame, output_dir: Path) -> None:
    """Box plot of abstract lengths grouped by primary category."""
    df = df.copy()
    df["abstract_words"] = df["abstract"].str.split().str.len()

    cats = df["primary_category"].value_counts().index.tolist()
    data = [df.loc[df["primary_category"] == c, "abstract_words"].values for c in cats]

    fig, ax = plt.subplots(figsize=(8, 5))
    bp = ax.boxplot(data, labels=cats, patch_artist=True, showfliers=False)
    for patch, colour in zip(bp["boxes"], PALETTE):
        patch.set_facecolor(colour)
        patch.set_alpha(0.7)
    ax.set_ylabel("Abstract Length (words)")
    ax.set_title("Abstract Length by Primary Category")
    ax.spines[["top", "right"]].set_visible(False)
    fig.tight_layout()
    _savefig(fig, output_dir / "abstract_length_by_category.png")


def plot_authors_per_paper(df: pd.DataFrame, output_dir: Path) -> None:
    """Histogram of author counts per paper."""
    author_counts = df["authors"].apply(len)

    fig, ax = plt.subplots(figsize=(8, 5))
    max_display = int(author_counts.quantile(0.99)) + 1
    ax.hist(
        author_counts.clip(upper=max_display),
        bins=range(1, max_display + 2),
        color=PALETTE[2],
        edgecolor="white",
        alpha=0.85,
        align="left",
    )
    ax.set_xlabel("Number of Authors")
    ax.set_ylabel("Frequency")
    ax.set_title("Authors per Paper")
    ax.spines[["top", "right"]].set_visible(False)
    fig.tight_layout()
    _savefig(fig, output_dir / "authors_per_paper.png")


def plot_publication_timeline(df: pd.DataFrame, output_dir: Path) -> None:
    """Monthly publication counts over time."""
    dates = pd.to_datetime(df["published"], errors="coerce").dropna()
    monthly = dates.dt.to_period("M").value_counts().sort_index()

    fig, ax = plt.subplots(figsize=(10, 5))
    ax.bar(
        range(len(monthly)),
        monthly.values,
        color=PALETTE[1],
        edgecolor="white",
        width=1.0,
    )
    # Show a subset of tick labels to avoid crowding.
    step = max(1, len(monthly) // 12)
    tick_indices = list(range(0, len(monthly), step))
    ax.set_xticks(tick_indices)
    ax.set_xticklabels(
        [str(monthly.index[i]) for i in tick_indices],
        rotation=45,
        ha="right",
        fontsize=8,
    )
    ax.set_xlabel("Month")
    ax.set_ylabel("Number of Papers")
    ax.set_title("Publication Timeline (Monthly)")
    ax.spines[["top", "right"]].set_visible(False)
    fig.tight_layout()
    _savefig(fig, output_dir / "publication_timeline.png")


def plot_top_terms_heatmap(
    terms_by_cat: dict[str, list[tuple[str, float]]],
    output_dir: Path,
    top_n: int = 10,
) -> None:
    """Heatmap-style visualisation of top TF-IDF terms across categories."""
    # Gather the union of top terms across all categories.
    all_terms: list[str] = []
    for cat in sorted(terms_by_cat):
        for term, _ in terms_by_cat[cat][:top_n]:
            if term not in all_terms:
                all_terms.append(term)

    cats = sorted(terms_by_cat.keys())
    matrix = np.zeros((len(all_terms), len(cats)))
    for j, cat in enumerate(cats):
        term_map = dict(terms_by_cat[cat])
        for i, term in enumerate(all_terms):
            matrix[i, j] = term_map.get(term, 0.0)

    fig, ax = plt.subplots(figsize=(10, max(6, 0.35 * len(all_terms))))
    im = ax.imshow(matrix, aspect="auto", cmap="YlOrRd", interpolation="nearest")
    ax.set_xticks(range(len(cats)))
    ax.set_xticklabels(cats, fontsize=9)
    ax.set_yticks(range(len(all_terms)))
    ax.set_yticklabels(all_terms, fontsize=8)
    ax.set_title("Top TF-IDF Terms by Category")
    fig.colorbar(im, ax=ax, label="Mean TF-IDF Score", shrink=0.6)
    fig.tight_layout()
    _savefig(fig, output_dir / "tfidf_terms_heatmap.png")


# ---------------------------------------------------------------------------
# CLI
# ---------------------------------------------------------------------------


def parse_args() -> argparse.Namespace:
    parser = argparse.ArgumentParser(
        description="Exploratory Data Analysis for the CS/ML Academic Papers Dataset.",
    )
    parser.add_argument(
        "--data-dir",
        type=str,
        default=str(DATA_DIR),
        help=f"Local data directory (default: {DATA_DIR}).",
    )
    parser.add_argument(
        "--from-hub",
        type=str,
        default=None,
        help="Load the dataset from a HuggingFace Hub repo instead of locally.",
    )
    parser.add_argument(
        "--plots-dir",
        type=str,
        default=str(PLOTS_DIR),
        help=f"Directory for saved plots (default: {PLOTS_DIR}).",
    )
    parser.add_argument(
        "--verbose",
        action="store_true",
        help="Enable debug logging.",
    )
    return parser.parse_args()


def main() -> None:
    args = parse_args()

    logging.basicConfig(
        level=logging.DEBUG if args.verbose else logging.INFO,
        format="%(asctime)s  %(levelname)-8s  %(name)s  %(message)s",
        datefmt="%Y-%m-%d %H:%M:%S",
    )

    # ------------------------------------------------------------------
    # 1. Load data
    # ------------------------------------------------------------------
    if args.from_hub:
        LOG.info("Loading dataset from HuggingFace Hub: %s", args.from_hub)
        df = load_hub(args.from_hub)
    else:
        LOG.info("Loading dataset from local directory: %s", args.data_dir)
        df = load_local(Path(args.data_dir))

    LOG.info("Loaded %d papers.", len(df))

    # ------------------------------------------------------------------
    # 2. Summary statistics
    # ------------------------------------------------------------------
    print_summary(df)

    # ------------------------------------------------------------------
    # 3. TF-IDF keyword extraction
    # ------------------------------------------------------------------
    LOG.info("Computing TF-IDF top terms per category ...")
    terms_by_cat = top_tfidf_terms(df)
    print_top_terms(terms_by_cat)

    # ------------------------------------------------------------------
    # 4. Visualisations
    # ------------------------------------------------------------------
    plots_dir = Path(args.plots_dir)
    plots_dir.mkdir(parents=True, exist_ok=True)
    LOG.info("Generating visualisations -> %s", plots_dir)

    plot_category_distribution(df, plots_dir)
    plot_abstract_length_histogram(df, plots_dir)
    plot_abstract_length_by_category(df, plots_dir)
    plot_authors_per_paper(df, plots_dir)
    plot_publication_timeline(df, plots_dir)

    if terms_by_cat:
        plot_top_terms_heatmap(terms_by_cat, plots_dir)

    LOG.info("All plots saved to %s", plots_dir)
    print(f"Visualisations saved to: {plots_dir}")


if __name__ == "__main__":
    main()