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Is This Rice Grain Cammeo or Osmancik?

From seven measurements of its shape in a photograph, which of two Turkish rice varieties is this grain? Mixed lots sell for less, so buyers want a quick check.

Use caseBiologyPredictionModel evaluation

The table

3,810 rice grains measured from images for area, perimeter, axis lengths, eccentricity, convex area and extent, labelled by variety. It's in Welt's research catalogue as Rice Grain Varieties Cammeo and Osmancik, 3,810 rows by 8 columns, licensed CC BY 4.0. The catalogue measures its signal at 0.82. At 3,810 rows and 7 features, TabICLv2, Kumo Tabular Medium and Mitra-v2 take the table as it is. The others can't take a table this size, so the walkthrough leaves them out.

Walkthrough

  1. Load it from the catalogue

    Find the table, read its recorded target and print the column names.

    import pandas as pd
    from welt import Client
    
    with Client() as client:
        item = client.research_datasets(q="rice Cammeo Osmancik", limit=1)["items"][0]
        info = client.research_dataset(item["id"])
        data = client.load_research_dataset(item["id"])
    
    target = info["targets"][0]
    target = target["name"] if isinstance(target, dict) else target
    print([column["name"] for column in info["schema"]], target)
  2. Pick the rows

    Set aside 20 rows to predict at the end, and keep the rest for the models to learn from.

    known = data.dropna(subset=[target])
    new_rows = known.sample(20, random_state=1)
    table = known.drop(new_rows.index)
  3. Compare the models and predict

    The models compete on the same folds against a simple guess, then the top-ranked one is fitted on the whole table. ROC AUC runs from 0.5, a coin toss, to 1, a perfect ranking, and a lower Brier score means the probabilities can be trusted more. The last table puts each prediction next to the real answer.

    with Client() as client:
        evaluation = client.evaluate(table, target, task="classification", seed=7,
                                     models=["tabicl-v2", "kumo-medium", "mitra-v2"])
        model = evaluation.fit()
    
    print(evaluation.summary()[["name", "rank", "roc_auc_mean", "brier_mean"]])
    features = new_rows.drop(columns=target)
    print(pd.DataFrame({"actual": new_rows[target].values, "predicted": model.predict(features),
                        "probability": model.predict_proba(features).max(axis=1)}))

What you get

A variety per grainWith a probability.
A purity checkEstimate how mixed a lot is from a sample.
A strong signalThe catalogue measures a high signal.

Try it

Use Open with to run the research datasets notebook in Colab, Kaggle or Jupyter and search for "rice Cammeo Osmancik", or run the code above after pip install "welt-client[parquet]".