Matminer

matminer

What this library is for

matminer is a materials-informatics library for converting compositions, structures, band structures, density of states objects, and materials data tables into features suitable for machine learning. It is most useful when a materials-aware featurizer should replace ad hoc elemental-property code.

When to use this vs. alternatives

• Use matminer for composition, structure, site, DOS, and band-structure featurization with documented feature names and citations.
• Use pymatgen for representing and transforming structures/compositions before featurization.
• Use scikit-learn for model fitting and validation after matminer has created features.
• Do not hand-roll mean atomic number, electronegativity, or radius features unless the user explicitly wants a custom descriptor; matminer already standardizes many of these and records labels/citations.

Canonical workflow

Start from formulas or pymatgen objects, featurize before fitting, and keep the featurizer object with the model artifacts.

import pandas as pd
from pymatgen.core import Composition
from matminer.featurizers.composition import ElementProperty
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.metrics import mean_absolute_error

df = pd.read_csv("band_gaps.csv")  # columns: formula, band_gap
df["composition"] = df["formula"].map(Composition)

featurizer = ElementProperty.from_preset("magpie")
feature_labels = featurizer.feature_labels()
df = featurizer.featurize_dataframe(df, "composition", ignore_errors=False)

X = df[feature_labels]
y = df["band_gap"]
X_train, X_test, y_train, y_test = train_test_split(
    X, y, test_size=0.2, random_state=42
)

model = RandomForestRegressor(random_state=42)
model.fit(X_train, y_train)
pred = model.predict(X_test)
print("MAE:", mean_absolute_error(y_test, pred))

print(featurizer.citations())

For deeper examples, use the official matminer tutorials and the matminer examples repository.

Key conventions and gotchas

• featurize_dataframe mutates/returns a DataFrame with feature columns; use feature_labels() to select only generated feature columns for modeling.
• Many featurizers expect pymatgen Composition or Structure objects, not raw strings. Convert formulas with pymatgen.core.Composition.
• ignore_errors=True can silently insert NaNs. Use it only when you also log which rows failed and drop/impute deliberately.
• Fit train/test splits before any target-aware preprocessing. Featurization is usually target-free, but imputation, scaling, feature selection, and model selection must be fit on training data only.
• Keep citations from featurizer.citations() and record presets such as "magpie" because features can encode specific data sources.
• Structure featurizers need physically meaningful structures: oxidation states, disorder handling, primitive/conventional choices, and neighbor cutoffs can change features materially.

Anti-patterns

• Do not scrape periodic-table values into custom pandas columns when ElementProperty, Stoichiometry, ValenceOrbital, or related matminer featurizers cover the descriptor.
• Do not use formula strings directly with composition featurizers.
• Do not report a model score without logging featurizer class, preset, feature labels, dropped rows, random seed, and train/test split.
• Do not fill missing generated features with zeros unless zero has a physical meaning for that feature; prefer explicit imputation and report it.

Diagnostic checks

Before trusting outputs, the agent should:

• Print the generated feature count and inspect a few feature labels.
• Check NaN/inf counts after featurization and identify failed formulas or structures.
• Verify train/test split grouping if multiple rows come from the same material family, polymorph, or composition.
• Record featurizer citations, preset, matminer version, and source data date.
• Compare against a simple baseline model to make sure descriptors add value.

Pointers to deeper material

• Documentation: https://hackingmaterials.lbl.gov/matminer/
• Tutorials: https://hackingmaterials.lbl.gov/matminer/tutorials.html
• Featurizer summary: https://hackingmaterials.lbl.gov/matminer/featurizer_summary.html
• Examples repository: https://github.com/hackingmaterials/matminer_examples
• Paper: Ward et al. (2018), "Matminer: An open source toolkit for materials data mining", Computational Materials Science 152, 60-69.