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Will This Snail Choose to Mate?

Given the species, populations, shell sizes and trial conditions, will a male periwinkle snail mount the female he's paired with? Who mates with whom is how new species begin to split.

Use caseBiologyPredictionModel evaluation

The table

940 mating trials between Littoraria snails, with species, populations, sizes and conditions, and whether mounting happened. It's in Welt's research catalogue as Assortative Mating and Genital Divergence in Littoraria, 940 rows by 23 columns, licensed CC0. The catalogue measures its signal at 0.35. At 940 rows and 22 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="assortative mating Littoraria", 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 mating probabilityFor any pairing in the trials.
Size or speciesCompare models to see what drives choice.
An honest signalThe catalogue measures a modest signal.

Try it

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