Which Variety Is This Dry Bean?
From the size and shape measured in a photograph, which of seven varieties is this bean? Sorting by camera keeps seed lots pure without anyone checking beans by eye.
The table
13,611 beans photographed and measured for area, perimeter, axis lengths, roundness and other shape features, labelled with their variety. It's in Welt's research catalogue as Dry Bean Grain Shape Dataset, 13,611 rows by 17 columns, licensed CC BY 4.0. The catalogue measures its signal at 0.92. At 13,611 rows and 16 features the table is larger than the model limits allow, so the walkthrough evaluates and fits on a seeded sample of 8,000 rows. TabICLv2 and Kumo Tabular Medium compete.
Walkthrough
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="dry bean", 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)Pick the rows
Set aside 20 rows to predict at the end. The models learn from a seeded sample of 8,000 of the rest, the most this table's width allows.
known = data.dropna(subset=[target]) new_rows = known.sample(20, random_state=1) table = known.drop(new_rows.index).sample(8000, random_state=7)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"]) 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
Try it
Use Open with to run the research datasets notebook in Colab, Kaggle or Jupyter and search for "dry bean", or run the code above after pip install "welt-client[parquet]".
Open with
- Type
- Use case
- Area
- Biology
- Question
- Which Variety Is This Dry Bean?
- Model
- TabICLv2, Kumo Tabular Medium
- Data
- Dry Bean Grain Shape Dataset, 13,611 rows
- For
- Seed producers and food-processing engineers
- Licence
- CC BY 4.0