twoblock 0.5.1

A Scikit-Learn Compatible Library for Simultaneous Two-Block Sufficient Dimension Reduction Methods

twoblock

Two-block dense and sparse simultaneous dimension reduction

The dense version is a scikit-learn compatible implementation of simultaneous two-block dimension reduction, as proposed in [1].

The sparse version is a scikit-learn compatible implementation of sparse twoblock dimension reduction, recently published by the author [2].

The robust version (rtb) extends twoblock with iterative M-estimation reweighting, providing resistance to outliers in both X and Y blocks [3].

The cellwise robust version (crtb) extends rtb with per-cell outlier weighting for both X and Y blocks, using SPADIMO to identify contaminated cells within flagged observations [4].

The diagnostic tool spadimo (SPArse DIrections of Maximal Outlyingness) identifies which variables contribute most to making an observation an outlier [5].

The crm (Cellwise Robust M-regression) method detects and handles cellwise outliers - individual contaminated cells in the data matrix rather than entire rows [6].

Optional plotly-based plot builders in twoblock.plots provide ready-made diagnostic figures (scree, scores, loadings, coefficients, predicted-vs-observed, case-weight histograms, cellwise-weight heatmaps, SPADIMO contributions).

Installation

pip install twoblock

Or install from source:

git clone https://github.com/SvenSerneels/twoblock.git
cd twoblock
pip install -e .

Dependencies

• numpy >= 1.22.0
• scikit-learn >= 1.3.0
• pandas >= 1.4.0
• scipy >= 1.8.0

Usage

twoblock — Dense and sparse two-block dimension reduction

from twoblock import twoblock
from sklearn.model_selection import GridSearchCV

# Dense twoblock
tb = twoblock(n_components_x=5, n_components_y=2, scale='std')
tb.fit(X_train, Y_train)
Y_pred = tb.predict(X_test)

# Sparse twoblock (variable selection via soft-thresholding)
tb_sparse = twoblock(n_components_x=5, n_components_y=2,
                     sparse=True, eta_x=0.7, eta_y=0, scale='std')
tb_sparse.fit(X_train, Y_train)
Y_pred = tb_sparse.predict(X_test)

# Cross-validation with scikit-learn
gcv = GridSearchCV(twoblock(),
                   {'n_components_x': range(1, 10),
                    'n_components_y': range(1, 3),
                    'scale': ['std', 'None']},
                   scoring='r2', cv=5)
gcv.fit(X_train, Y_train)

rtb — Robust twoblock with iterative reweighting

from twoblock import rtb

# Dense robust twoblock (Hampel weighting, robust centering/scaling)
r = rtb(n_components_x=5, n_components_y=2,
        centre='l1median', scale='mad',
        fun='Hampel', probp1=0.95, probp2=0.975, probp3=0.999)
r.fit(X_train, Y_train)
Y_pred = r.predict(X_test)

# Sparse robust twoblock
r_sparse = rtb(n_components_x=5, n_components_y=2,
               sparse=True, eta_x=0.5, eta_y=0,
               centre='l1median', scale='mad',
               fun='Hampel', probp1=0.95, probp2=0.975, probp3=0.999)
r_sparse.fit(X_train, Y_train)

# Inspect case weights (outliers receive low weights)
print(r_sparse.caseweights_)

# Cross-validation
gcv = GridSearchCV(rtb(verbose=False),
                   {'n_components_x': range(1, 10),
                    'n_components_y': [1, 2],
                    'scale': ['mad', 'kstepLTS'],
                    'probp1': [0.75, 0.95]},
                   scoring='r2', cv=5)
gcv.fit(X_train, Y_train)

crtb — Cellwise Robust Twoblock

CRTB extends RTB with per-cell outlier weighting. In each M-estimation iteration, SPADIMO identifies which variables drive outlyingness for flagged observations, and those individual cells are downweighted while the row continues to contribute through its case weight. An optional DDC-based pre-treatment provides cellwise-robust starting values, pushing resistance beyond the 50 % row-contamination breakdown of row-wise methods.

from twoblock import crtb
import numpy as np

# Default: fast column-wise MAD pre-filter for starting values
c = crtb(n_components_x=5, n_components_y=2,
         centre='l1median', scale='scaleTau2',
         fun='Hampel', probp1=0.95, probp2=0.975, probp3=0.999,
         start_cellwise='prefilter')
c.fit(X_train, Y_train)
Y_pred = c.predict(X_test)

# DDC-based cellwise starting values (requires robpy)
c_ddc = crtb(n_components_x=5, n_components_y=2,
             centre='l1median', scale='scaleTau2',
             start_cellwise='DDC', crit_cellwise=0.99)
c_ddc.fit(X_train, Y_train)

# Inspect row- and cell-level diagnostics
print(f"Row case weights: {c.caseweights_}")
print(f"X cellwise outliers: {np.sum(c.x_cellwise_outliers_)}")
print(f"Y cellwise outliers: {np.sum(c.y_cellwise_outliers_)}")

# Sparse CRTB — variable selection + cellwise robustness
c_sparse = crtb(n_components_x=5, n_components_y=2,
                sparse=True, eta_x=0.5, eta_y=0,
                centre='l1median', scale='scaleTau2')
c_sparse.fit(X_train, Y_train)

# Impute outlying cells from the fitted model
X_imputed, Y_imputed = c.impute(X_train, Y_train)

Key parameters:

• start_cellwise: Cellwise starting-value strategy ('prefilter', 'DDC', or False)
• crit_cellwise: Chi-squared quantile used to flag cells and observations for SPADIMO (default 0.99)
• spadieta: Sparsity sequence passed to SPADIMO (default np.arange(0.9, 0.05, -0.1))
• Inherits fun, probp1/2/3, centre, scale, sparse, eta_x/y from rtb

Key attributes (in addition to those from rtb):

• x_cellwise_outliers_, y_cellwise_outliers_: Boolean cell-outlier maps
• x_cellweights_, y_cellweights_: Cellwise weights (0 = flagged, 1 = clean)
• ddc_x_outliers_, ddc_y_outliers_: Cellwise outliers from DDC initialisation (if start_cellwise='DDC')

spadimo — Sparse directions of maximal outlyingness

SPADIMO identifies which variables contribute most to making an observation an outlier. Given case weights from a robust estimator (e.g., rtb), it computes a sparse direction of maximal outlyingness and flags the contributing variables.

from twoblock import rtb, spadimo

# First, fit a robust model to get case weights
r = rtb(n_components_x=5, n_components_y=2,
        centre='l1median', scale='mad', fun='Hampel')
r.fit(X, Y)

# Find observations with low weights (potential outliers)
outlier_indices = np.where(r.caseweights_ < 0.5)[0]

# Analyze an outlier to find contributing variables
sp = spadimo(scale='Qn', stop_early=True)
sp.fit(X, r.caseweights_, obs=outlier_indices[0])

# Get the flagged variables
print(f"Outlying variables: {sp.outlvars_}")
print(f"Outlyingness before: {sp.outlyingness_before_:.2f}")
print(f"Outlyingness after removing flagged vars: {sp.outlyingness_after_:.2f}")

# With a DataFrame, get variable names directly
sp.fit(X_df, r.caseweights_, obs=outlier_indices[0])
print(f"Outlying variable names: {sp.get_outlying_variables(names=True)}")

# Print a summary
sp.summary()

Key parameters:

• scale: Robust scale estimator ('Qn', 'mad', 'scaleTau2')
• etas: Sparsity parameters (default: sequence from 0.9 to 0.1)
• stop_early: Stop at first eta where observation becomes non-outlying
• csq_critv: Chi-squared quantile for outlyingness threshold (default: 0.975)

crm — Cellwise Robust M-regression

CRM detects and handles cellwise outliers - individual contaminated cells rather than entire rows. It provides regression coefficients robust against both vertical outliers and leverage points, a map of cellwise outliers, and an imputed dataset with outlying cells replaced.

from twoblock import crm
import numpy as np

# Fit CRM model with casewise robust starting values (default)
model = crm(center='median', scale='Qn', fun='Hampel')
model.fit(X, y)

# Fit CRM with cellwise robust starting values via DDC
# (requires robpy: pip install robpy)
model_ddc = crm(start_cellwise=True, center='median', scale='Qn')
model_ddc.fit(X, y)

# Predictions
y_pred = model.predict(X_new)

# View cellwise outlier map
print(f"Cellwise outliers detected: {np.sum(model.cellwise_outliers_)}")
print(f"Casewise outliers: {model.get_casewise_outliers()}")

# Get imputed data (outlying cells replaced)
X_imputed = model.X_imputed_

# Inspect which cells are outliers for a specific row
row_outliers = model.get_cellwise_outliers(row=0)
print(f"Outlying variables in row 0: {row_outliers}")

# With a DataFrame, get variable names
model.fit(X_df, y)
print(model.get_cellwise_outliers(row=0, names=True))

# Print summary
model.summary()

Key parameters:

• start_cellwise: If True, use DDC for cellwise robust starting values (default: False, requires robpy)
• center: Centering method ('median', 'mean', 'l1median')
• scale: Scale estimator ('Qn', 'mad', 'scaleTau2')
• regtype: Initial regression type ('MM', 'LTS')
• fun: M-estimation psi-function ('Hampel', 'Huber', 'Fair')
• crit_cellwise: Chi-squared quantile for cellwise outlier detection (default: 0.99)
• maxiter: Maximum IRLS iterations (default: 100)
• tolerance: Convergence threshold (default: 0.01)

Key attributes:

• coef_: Regression coefficients
• cellwise_outliers_: Boolean matrix of cell outliers (n, p)
• casewise_outliers_: Boolean array of row outliers (n,)
• X_imputed_: Imputed X matrix with outliers replaced
• caseweights_: Case weights from M-estimation
• ddc_outliers_: Cellwise outliers from DDC initialization (if start_cellwise=True)

plots — Plotly diagnostic builders

twoblock.plots provides a small set of plotly-based builders that accept plain numpy arrays (e.g. est.x_scores_, est.coef_, est.caseweights_) and return a plotly.graph_objects.Figure. Because the API is array-first, the same builders work with any fitted twoblock estimator and with sklearn's PLSRegression.

Install the optional dependency:

pip install "twoblock[plots]"

from twoblock import crtb
from twoblock.plots import (
    scree, score_scatter, loadings_bar, coefficients_bar,
    y_pred_vs_obs, caseweight_hist, cellweight_heatmap,
    spadimo_contributions,
)

c = crtb(n_components_x=3, n_components_y=1).fit(X, Y)

# Latent-space diagnostics
score_scatter(c.x_scores_, comp_x=0, comp_y=1,
              case_weights=c.caseweights_).show()
loadings_bar(c.x_loadings_, component=0,
             feature_names=X.columns).show()

# Regression diagnostics
coefficients_bar(c.coef_, feature_names=X.columns).show()
y_pred_vs_obs(Y, c.predict(X)).show()

# Outlier diagnostics
caseweight_hist(c.caseweights_).show()
cellweight_heatmap(c.x_cellweights_, feature_names=X.columns).show()

# SPADIMO contributions for a flagged observation
import numpy as np
from twoblock import spadimo
sp = spadimo(scale='scaleTau2', stop_early=True).fit(
    X, c.caseweights_, obs=int(np.argmin(c.caseweights_)))
spadimo_contributions(sp.contributions_,
                      feature_names=X.columns,
                      flagged_indices=sp.outlvars_).show()

Examples

Example notebooks are provided in the examples/ folder:

• cookie_example.ipynb — Cookie dough NIR spectroscopy
• gas_turbine_example.ipynb — Gas turbine CO/NOx emissions
• simulation_rtb.ipynb — Simulation study comparing twoblock, sparse twoblock, rtb, and sparse rtb
• crm_simulation.ipynb — CRM simulation under cellwise contamination with normal and Cauchy noise
• cookie_example_crtb.ipynb, gas_turbine_example_crtb.ipynb, voc_example_crtb.ipynb — CRTB applied to real datasets
• simulation_crtb.py — CRTB simulation study under cellwise contamination

References

[1] R.D. Cook, L. Forzani, L. Liu. "Partial least squares for simultaneous reduction of response and predictor vectors in regression." Journal of Multivariate Analysis 196 (2023): 105163.

[2] S. Serneels. "Sparse Twoblock Dimension Reduction: A Versatile Alternative to Sparse PLS2 and CCA." Journal of Chemometrics, 39 (2025): e70051.

[3] S. Serneels. "Robust Twoblock Dimension Reduction." (2026, submitted). Preprint available at arXiv.org, arXiv: 2603.24820.

[4] S. Serneels. "Cellwise Robust Twoblock Dimension Reduction." (2026, submitted). Preprint available at arXiv.org, arXiv: 2604.15106.

[5] M. Debruyne, S. Höppner, S. Serneels, T. Verdonck. "Outlyingness: which variables contribute most?" Statistics and Computing 29 (4), 707-723.

[6] P. Filzmoser, S. Höppner, I. Ortner, S. Serneels, T. Verdonck. "Cellwise Robust M regression." Computational Statistics & Data Analysis 147 (2020): 106944.