# Model based co-clustering: high dimension & estimation challenges

Christophe Biernacki, Julien Jacques, Christine Keribin

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Christophe Biernacki, Julien Jacques, Christine Keribin. Model based co-clustering: high dimension & estimation challenges. 2025. hal-05442714

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Distributed under a Creative Commons CC BY 4.0 - Attribution - International License
MODEL BASED CO-CLUSTERING:
HIGH DIMENSION & ESTIMATION CHALLENGES

Christophe BIERNACKI <fnref n="1" />, Julien JACQUES <fnref n="2" />, Christine KERIBIN <fnref n="3" />

DaSSWeb - Data Science and Statistics Webinar
28 January 2025

<footnote n="1">¹Inria, CNRS, Laboratoire de Mathématiques Painlevé, U. Lille, F59650 V. d'Ascq, France</footnote>

<footnote n="2">²U. Lyon 2, ERIC, UR 3083, 5 Avenue Pierre Mendès-France, F69676 Bron Cedex, France</footnote>

<footnote n="3">³U. Paris-Saclay, CNRS, Inria, Laboratoire de mathématiques d'Orsay, F91405 Orsay, France</footnote>
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# Outline

1. Motivation

2. Latent Block Model

3. Estimation challenges

4. Co-clustering for HD

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# Clustering

## Unsupervised ML framework

* data set $\mathbf{x} = (\mathbf{x}_1, \dots, \mathbf{x}_n) \in \mathcal{X}^n$ with $dim(\mathcal{X}) = d$

* to partition into $K$ clusters $G_1, \dots, G_K$

* classification matrix $\mathbf{z} = (z_1, \dots, z_n) : z_{ik} = \mathbb{1}_{i \in G_k}$

## Model based clustering (MBC) reformulates cluster analysis in a well-posed estimation problem

* $\mathbf{x}_i$ are iid observations of a mixture pdf

$$f(\cdot; \boldsymbol{\theta}) = \sum_{k=1}^{K} \pi_k \varphi(\cdot; \alpha_k); \quad \sum_{i=1}^{K} \pi_K = 1, \pi_k \ge 0; \quad \mathbb{P}(z_{ik} = k) = \pi_k$$

* estimation with EM algorithm, partition is deduced from the conditional probability $\rho(z_i|\mathbf{x}_i; \hat{\boldsymbol{\theta}})$, typically from the MAP principle, as soon as we have an estimate $\hat{\boldsymbol{\theta}}$ of $\boldsymbol{\theta}$

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High dimension (HD) settings: $d \sim n, d \gg n$

More and more variables (d) and not so much observations (n)

► marketing: $d \sim 10^2$ for $n = 10^4 - 10^6$

► microarray gene expression: $d \sim 10^2 - 10^4$ for $n = 20 - 50$ stress conditions

► fMRI images: $d \sim 10^4 - 10^5$ voxels for $n = 50 - 100$ patients

► text mining, curve, internet logs...

Moreover, variables can be of mixed types

► different modes: qualitative, quantitative, functional

► different semantic

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Clustering in HD: curse (and blessing?)

► **curse**: density estimation quality decreases with *d* for a same *n*

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Kullback($f, \hat{f}$) for a two-component *d*-variate Gaussian mixture

$$x_j | z_j \sim \mathcal{N}_d(\mu_{z_j}, \Sigma); \pi_1 = \pi_2 = 0.5$$

Basic case: $\mu_1 = 0_d; \mu_2 = 1_d; \Sigma = I_d$

► **blessing**: but components are (in that case) more and more separated

► which impact on the **misclassification** error?

- when the variables are **correlated**, redundant, non informative?

- when $d \gg n$?

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Basic case: HD is a blessing for clustering

Each new variable is informative, sufficiently large $n \sim d$

► theoretical classification error decreases when $d$ grows: $err_{theo} = \Phi(-\sqrt{d}/2)$

basic, c= 0 eps= 1 nbobs= 30

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A two-component $d$-variate Gaussian mixture

$$x_i | z_i \sim N_d(\mu z_i, \Sigma); \pi_1 = \pi_2 = 0.5$$

Basic case: $\Sigma = I_d; \mu_1 = 0_d; \mu_2 = 1_d$

► and empirical error rate also decreases with $d$

► no model bias, classification ($\hat{z}$) variance decreases

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But HD can be less favorable for clustering

(Many) less informative variables

► theoretical error slowly decreases when *d* grows: $err_{theo} = \Phi(-||\mu_1 - \mu_2||/2)$

less informative, c=0 eps= 1 nbobs= 100

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A two-component *d*-variate Gaussian mixture

$$x_j|z_j \sim N_d(\mu_{z_j}, \Sigma); \pi_1 = \pi_2 = 0.5$$

Less informative: $\Sigma = I_d$; $\mu_1 = 0_d$.

$$\mu_2 = (1, \frac{1}{2^2}, \dots, \frac{1}{d^2})$$

► but empirical error rate does not decrease any more...

► no model bias, classification ($\tilde{z}$) variance increases

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# Bias/variance trade-off for clustering

## Correlated variables

* theoretical error decreases $err_{theo} = \Phi(-||\mu_1 - \mu_2||_{\Sigma} - 1/2)$

basic, c= 0.2 eps= 1 nbobs= 30

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A two-component *d*-variate Gaussian mixture

$$x_j | z_j \sim N_d(\mu_{z_j}, \Sigma); \pi_1 = \pi_2 = 0.5$$

Basic case+ correlated variables (correlation c):

$$\Sigma = \Sigma(c); \mu_1 = 0_d; \mu_2 = 1_d$$

* high error when clustered with the **real** (corr. G.) mixture model **higher** than with the **biased** (diag. G) mixture model, since corr. G. has too much variance

* error decreases with the **biased** model diag. G, which does not dammaged the separation

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Some alternatives for reducing variance

► Dimension reduction in non canonical space (PCA-like typically)

► Dimension reduction in the canonical space (variable selection)

- Gaussian mixture with 3 variable-clusters (informative, non informative, linearly dependent) [Maugis et al (2009)]

- latent class analysis [Fop et al (2018)]

► Model parsimony in the initial HD space (constraints on model parameters)

- parsimonious Gaussian mixture [Celeux and Govaert, '95]

- mixture of factor analyzers [[Ghahramani and Hinton, 97], [McLachlan et al], 03]

- HD Gaussian models [[Bouveyron et al, 07]]

↔ trade-off between “meaningful” modeling and what can be estimated in practice

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# An alternative for reducing the variance

## Main message:

* clustering is a way for dealing with large *n*

* why not also reusing this idea for large *d*?

## Co-clustering (CC)

* simultaneously clusters rows and columns

* performs parsimony of row clustering through variable clustering

* parsimonious, model-based, independent of data type, available

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From clustering to co-clustering

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(1)

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(2)

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(3)

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(4)

$$ (n = 10) \times (d = 7) $$

$$ (K = 3) \times (d = 7) $$

$$ (K = 3) \times (L = 3) $$

[Govaert (2008)]

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Interpreting LBM as an MBC dimension reduction method<fnref n="1" />

(See the Latent Block Model (LBM) definition in the next section...)

► PCA for the *i*-th data individual $\mathbf{x}_i$: acts as a dimension reduction method

$$ \mathbf{x}_i = \sum_{j=1}^{d} x_j^l \mathbf{e}^l = \sum_{j=1}^{d} a_j^l \mathbf{u}^l \approx \sum_{j=1}^{J} a_j^l \mathbf{u}^l $$

► specific CC case reduced to $K = 1$: again, acts as a dim. reduction method

$$ \mathbf{x}_i = \sum_{j=1}^{d} x_j^l \mathbf{e}^l = \sum_{j=1}^{d} (\mu_{\tilde{w}_j} + \varepsilon_j^l) \mathbf{e}^l = \sum_{\ell=1}^{L} \mu_\ell \mathbf{v}^\ell + \mathbf{r}_i \approx \sum_{\ell=1}^{L} \mu_\ell \mathbf{v}^\ell $$ 
with $\tilde{w}_j = \ell \Leftrightarrow w_j = 1$, $\varepsilon_j^l \sim \mathcal{N}(0, \sigma_{\tilde{w}_j}^2)$, $\mathbf{v}^\ell = \sum_{\{j: \tilde{w}_j = \ell\}} \mathbf{e}^l$ and $\mathbf{r}_i = \sum_{j=1}^d \varepsilon_j^l \mathbf{e}^l$

↔ return now to the clustering task:

- sequential clustering method: (1) PCA and then (2) MBC

- simultaneous clustering method: only CC, since dim. reduction is included

<footnote n="1">¹ [C. Biernacki, C. Keribin, J. Jacques, A survey on Model-Based Co-Clustering, JOC 2023] □ ▶ ◀ ▶ ◁ ▶ ◁ ▶ ▶ ▶ ▶ ▶ ▶ ▶</footnote>
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# Outline

1. Motivation

2. Latent Block Model

3. Estimation challenges

4. Co-clustering for HD

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Unsupervised block clustering framework

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► **co-clustering (CC):** to find a **block clustering** structure simultaneously on rows and columns

$H_1$: **blocks** form a **Cartesian product** of a row-partition in $K$ row-groups by a column-partition in $L$ column-groups

$z = (z_{ik})$ where $z_{ik} = 1$ if row $i$ belongs to row-group $k$

$w = (w_{j\ell})$ where $w_{j\ell} = 1$ if column $j$ belongs to column-group $\ell$

► **traditional applications:** huge data sets arising in recommendation systems (binary), genomic data analysis (Gaussian), text mining (Poisson),...

► **our proposed application:** dimension reduction for HD clustering

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Latent Block Model (LBM): a mixture model<fnref n="2" />

$H_2$: row and column labels are independently assigned :

$$z_j^{i,l,d} \sim \mathcal{M}(1, \pi) \perp w_j^{i,l,d} \sim \mathcal{M}(1, \rho)$$

$H_3$: the $n \times d$ blocks $x_{ij}$ are conditionally independent given $z$ and $w$ and follow the same conditional distribution $\varphi$ which parameter $\alpha$ only depends on the block:

$$x_{ij} | z_{ik} = 1, w_{j\ell} = 1 \sim \varphi(x_{ij}; \alpha_{k\ell})$$

Observed likelihood

$$\rho(x; \theta) = \sum_{(z,w) \in \mathcal{Z} \times \mathcal{W}} \underbrace{\prod_{i,k} \pi_k^{z_{ik}} \prod_{j,l} \rho_l^{w_{j,l}}}_{\rho(z,w;\theta)=\rho(z,\theta)\rho(w;\theta)} \underbrace{\prod_{i,j,k,l} \varphi(x_{ij}; \alpha_{k\ell})^{z_{ik}w_{j\ell}}}_{\rho(x|z,w;\theta)}$$

with $\theta = (\pi, \rho, \alpha) \in \Theta$

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<footnote n="2">²[Govaert and Nadif (2008)]</footnote>
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Parametric model

► very parsimonious model, good candidate to deal with HD settings...

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<table><thead><tr><th>Model</th><th>Number of parameters</th></tr></thead><tbody><tr><td>Binary</td><td>dim(π) + dim(ρ) + KL</td></tr><tr><td>Categorical</td><td>dim(π) + dim(ρ) + KL(m - 1)</td></tr><tr><td>Contingency</td><td>dim(π) + dim(ρ) + KL</td></tr><tr><td>Continuous</td><td>dim(π) + dim(ρ) + 2KL</td></tr></tbody></table>

$$ \text{nb. param}_{\text{HD}} = \text{nb. param}_{\text{classic}} \times \frac{L}{d} $$

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Estimation

$$ \rho(x; \theta) = \sum_{(z, w) \in \mathcal{Z} \times \mathcal{W}} \prod_{i,k} \pi_k^{z_{ik}} \prod_{j,\ell} \rho_\ell^{w_{j\ell}} \prod_{i,j,k,\ell} \varphi(x_{ij}; \alpha_{k\ell})^{z_{ik}} w_{j\ell} $$

► generic identifiability [Keribin et al., '15]

► likelihood intractable: 2 × 2 blocks and 20 × 20 matrix: ≈ 2²⁰ × 2²⁰ ≈ 10¹² terms

► E-step intractable

→ approximation with Variational EM (VEM) [Govaert and Nadif '08]

→ estimation with Stochastic EM (SEM) [Keribin et al., '10]

→ stochastic gradient descent [Baey et al., '23]

→ Bayesian versions: Gibbs and V-Bayes algorithms [Keribin, Brault, Celeux, Govaert, '15]

► consistency and asymptotic normality of ML- and V- estimators (when $log(n)/d \to 0$ and $log(d)/n \to 0$) [Brault, Keribin, Mariadassou, 20]

► model selection (ICL)

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VEM for LBM

$$ \log p(\mathbf{x}; \boldsymbol{\theta}) = \underbrace{\mathbf{E}_{q_z q_w} \left[ \log \frac{p(\mathbf{x}, \mathbf{z}, \mathbf{w}; \boldsymbol{\theta})}{q_z q_w} | \mathbf{x} \right]}_{\mathcal{F}(\boldsymbol{\theta}; q_z, q_w)} + KL(q_z q_w, \log p(\mathbf{z}, \mathbf{w}|\mathbf{x}; \boldsymbol{\theta})] $$

VEM (iteration $r$)

► approximated **E-step**:

$$ q_z^{(r)}, q_w^{(r)} = \arg \max_{q_z, q_w} \mathcal{F}(\boldsymbol{\theta}; q_z, q_w) $$

$$ \leftarrow s_{ik}^{(r)} \approx q_{zik}^{(r)}, t_{\ell}^{(r)} \approx q_{wj\ell}^{(r)}, e_{ijk\ell}^{(r)} \approx q_{zilk}^{(r)}, q_{wj\ell}^{(r)} $$

$$ Q(\boldsymbol{\theta}|\boldsymbol{\theta}^{(r)}) \approx \sum_{i,k} q_{zik}^{(r)} \log \pi_k + \sum_{j,\ell} q_{wj\ell}^{(r)} \log \rho_\ell + \sum_{i,j,k,\ell} q_{zilk}^{(r)} q_{wj\ell}^{(r)} \log \varphi(x_{ij}; \alpha_{k\ell}) $$

► **M-step:** $\theta^{(c+1)} = \arg \max_{\theta} \mathcal{F}(\boldsymbol{\theta}; q_z^{(r)}, q_w^{(r)})$ in $\boldsymbol{\theta}$, classical

$$ \max_{\boldsymbol{\theta}} \log p(\mathbf{x}; \boldsymbol{\theta}) \geq \max_{\boldsymbol{\theta}, q_z, q_w} \mathcal{F}(\boldsymbol{\theta}; q_z, q_w) $$

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# Outline

1 Motivation

2 Latent Block Model

3 Estimation challenges

4 Co-clustering for HD

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# Estimation challenges

## Challenges in the (classical) MBC context:

* local maxima solutions

* empty cluster solutions

* degenerate solutions

**Question to be addressed here**

What about LBM?

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Local maxima

► not just linked to the number of parameters!

► linked to the number of latent variables (here a toy two-param. Gaussian mixture)

40% of the partition is unknown

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85% of the partition is unknown

70% of the partition is unknown

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100% of the partition is unknown

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► additional order of magnitude: from $K^n$ to $K^n L^d \leftarrow$ pb for LBM?
but no way to draw a likelihood map...

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Local maxima in Gaussian LBM: illustration<fnref n="3" />

Figure: Gaussian 2 × 2 LBM (**left**) ; e.c.d.f. of ELBO values obtained from B = 100 initializations, at both standard precision (**center**) and high precision (**right**)

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► some potential slow convergence effect

► different parameters but the same partition

→ clustering is easier than estimation, no need to estimate with too much precision

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<footnote n="3">³R package blockcluster</footnote>
Empty clusters in LBM

Really frequent (and reported)!

► a component such that $\pi_K^{(r)} \approx 0$

► number of empty clusters in MBC: $\#\mathcal{Z}^0$

► number of empty clusters in LBM: $\#(\mathcal{Z} \times \mathcal{W})^0$

$$ \frac{\#(\mathcal{Z} \times \mathcal{W})^0}{\#\mathcal{Z}^0} = \frac{K^n L^d - S(n, K)S(d, L)K!L!}{K^n - S(n, K)K!} \rightarrow \infty \text{ when } n \rightarrow \infty \text{ or } d \rightarrow \infty $$

$S(n, K)$ is the Stirling number of second kind

► exponential speed even with very small sample sizes

$$ \frac{\#(\mathcal{Z} \times \mathcal{W})^0}{\#\mathcal{Z}^0} = \begin{cases} 62 & \text{when } n = d = 5 \text{ and } K = L = 2 \\ 710\,768 & \text{when } n = d = 9 \text{ and } K = L = 4 \end{cases} $$

↔ initialization often achieved by performing **independent clustering** of the rows and columns but the best initialization strategy stays **an open question**

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Degenerate and spurious solutions in MBC

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# Degenerate and spurious solutions in LBM

## No reported such problems?

* freq. of obtaining a cluster with a single element in the whole partition latent space

$$ \frac{\#Z_1^1}{\#Z} = \left(\frac{K-1}{K}\right)^{n-1} $$

* freq. of obtaining a block with a single element in the whole partition latent space

$$ \frac{\#(Z \times W)^{1,1}}{\#(Z \times W)} = \frac{\#Z_1^1}{\#Z} \left(\frac{L-1}{L}\right)^{d-1} $$

→ degeneracy situations are expected to be significantly less present in co-clustering than in clustering

Ex with $L = 4$ and $d = 50$: $(1 - 1/L)^{d-1} = 7.5510^{-7}$

* spurious case: same combinatorial arguments (but more tedious computations)

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# Outline

1. Motivation

2. Latent Block Model

3. Estimation challenges

4. Co-clustering for HD

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## Properties of LBM in view of HD clustering

* parsimonious model

* the true partition is recovered when there is a consistent estimator [Mariadassou and Matias, '15]

$$ \hat{\theta}^{n,d \to \infty} \theta^* \Rightarrow p(\hat{\mathbf{z}} = \mathbf{z}^*, \hat{\mathbf{w}} = \mathbf{w}^* | \mathbf{x}; \hat{\theta})^{n,d \to \infty} 1, $$

* non asymptotic properties (binary case) [Braault, '14]

$$ \mathbb{P}(\hat{\mathbf{z}} \neq \mathbf{z}^*) \leq 2n \exp \left\{ -\frac{1}{8} d \left[ \min_{k \neq k'} |\tau_k - \tau_{k'}| \right] \right\} + K(1 - \min_k \pi_k)^n $$

→ LBM is a natural regularized candidate for HD clustering

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Numerical illustrations: experimental design

Generating models, with two balanced ($\pi_1 = \pi_2$) row clusters in $\mathbb{R}^d$

<table><thead><tr><th></th><th><i>I</i><sub>d</sub></th><th><i>Σ</i>(<i>c</i>)</th></tr></thead><tbody><tr><td><i>μ</i><sub>1</sub> = <b>0</b><sub>d</sub>, <i>μ</i><sub>2</sub> = <b>1</b><sub>d</sub></td><td>(<i>M</i><sub>1</sub>)</td><td>(<i>M</i><sub>2</sub>)</td></tr><tr><td><i>μ</i><sub>1</sub> = <b>0</b><sub>d</sub>, <i>μ</i><sub>2</sub> = (1, 2<sup>-2</sup>, ..., <i>d</i><sup>-2</sup>)</td><td>(<i>M</i><sub>3</sub>)</td><td>(<i>M</i><sub>6</sub>)</td></tr><tr><td>(<i>M</i><sub>1</sub>) of size <i>n</i> × <i>d</i>/2 duplicated twice</td><td>(<i>M</i><sub>4</sub>)</td><td></td></tr><tr><td><i>μ</i><sub>1</sub> ~ <i>N</i><sub>d</sub>(<b>0</b>, <b>I</b><sub>d</sub>), <i>μ</i><sub>2</sub> ~ <i>N</i><sub>d</sub>((1, ..., <b>1</b>, 0, ..., 0), <b>I</b><sub>d</sub>)</td><td>(<i>M</i><sub>5</sub>)</td><td></td></tr></tbody></table>

↔ only (<i>M</i><sub>1</sub>) is a nominal LBM (2x1)

Row clustering is performed using four different methods

* clustering with a mixture of two spherical *d*-dim. Gaussian distributions

* clustering with a mixture of two full-covariance *d*-dim. Gaussian distr.

* co-clustering with a Gaussian (2 × 1) LBM

* co-clustering with a Gaussian (2 × 2) LBM

Classification error averaged over 30 samples of size *n* = 30

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LBM resists to HD

LBM performs better than simple
mixture, although the underlying
model overrides the co-clustering
conditional independence
assumptions

<figure><img src="image_155.png" /></figure>
Numerical illustrations: results (cont'd)

<figure><img src="image_156.png" /></figure>

non informative variables

redundancy: duplicated variables

Same conclusion for LBM, which resists to such HD scenarios

<figure><img src="image_157.png" /></figure>
Numerical illustrations: results (cont'd)

<figure><img src="image_158.png" /></figure>

too many noninformative variables

* too much bias, classification error with CC no longer lines up with Bayes risk

* but CC methods still perform better than simple mixture

<figure><img src="image_159.png" /></figure>
# Take home message

* in HD clustering, accept model bias to reduce variance on the classification

* CC acts as a **regularized tool** to perform clustering
  → very parsimonious model, with model bias but often offers better classification error

* LBM also offers a level of **flexibility** despite its parsimony
  → using LBM for HD clustering should be more emphasized
  → estimation is challenging, but there are solutions
  → less cases of spurious / degenerate solutions than in simple mixture models

## For further research...

* interpret the groups of variables in co-clustering

* extend the empirical results by theoretical guidelines

* robust estimation

* model selection: to be fixed by theoretical results

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# A Survey on Model-Based Co-Clustering: High Dimension and Estimation Challenges

C. Biernacki¹ · J. Jacques² · C. Keribin³

Accepted: 9 May 2023

© The Author(s) under exclusive licence to The Classification Society 2023

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