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Piotr Zwiernik

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math.ST Statistics Theory math.AG Methodology Machine Learning math.CO math.OC math.PR

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preprint2026arXiv

Causal discovery under mean independence and linearity

Causal discovery methods such as LiNGAM identify causal structure from observational data by assuming mutually independent disturbances. This assumption is fragile: shared volatility, common scale effects, or other forms of dependence can cause the methods to recover the wrong causal order, even with infinite data. We introduce the Linear Mean-Independent Acyclic Model (LiMIAM), which replaces full independence with weaker one-sided mean-independence restrictions on the disturbances. Under finite-order consequences of these restrictions, source nodes are generically identifiable, and hence a compatible causal order can be recovered recursively. Our proof is constructive and leads to DirectLiMIAM, a sequential residual-based algorithm for causal discovery under dependent noise. In simulations with mean-independent but dependent disturbances, DirectLiMIAM outperforms LiNGAM methods. A large-scale empirical application to the oil market highlights the implausibility of the independence assumption and the ability of DirectLiMIAM to recover a realistic causal ordering, from policy to production and from prices to inflation.

preprint2026arXiv

Testing properties of trees in graphical models with covariance queries

We consider the problem of testing properties of graphs underlying high-dimensional graphical models. We adopt the model of covariance queries introduced by Lugosi, Truszkowski, Velona, and Zwiernik (2021). We study the case when the underlying graph is a tree. The main results of the paper show that, while reconstructing the entire tree may be costly, certain global structural properties can be tested efficiently. In particular, we design randomized tests for global structural properties that use a sub-quadratic number of queries. We develop testing procedures for several fundamental properties, including the number of leaves, the maximum degree, the typical distance, and the diameter of the tree. For each property, we obtain explicit query complexity bounds that depend on the target threshold and tolerance parameters.

preprint2022arXiv

Locally associated graphical models and mixed convex exponential families

The notion of multivariate total positivity has proved to be useful in finance and psychology but may be too restrictive in other applications. In this paper we propose a concept of local association, where highly connected components in a graphical model are positively associated and study its properties. Our main motivation comes from gene expression data, where graphical models have become a popular exploratory tool. The models are instances of what we term mixed convex exponential families and we show that a mixed dual likelihood estimator has simple exact properties for such families as well as asymptotic properties similar to the maximum likelihood estimator. We further relax the positivity assumption by penalizing negative partial correlations in what we term the positive graphical lasso. Finally, we develop a GOLAZO algorithm based on block-coordinate descent that applies to a number of optimization procedures that arise in the context of graphical models, including the estimation problems described above. We derive results on existence of the optimum for such problems.

preprint2021arXiv

Likelihood Geometry of Correlation Models

Correlation matrices are standardized covariance matrices. They form an affine space of symmetric matrices defined by setting the diagonal entries to one. We study the geometry of maximum likelihood estimation for this model and linear submodels that encode additional symmetries. We also consider the problem of minimizing two closely related functions of the covariance matrix: the Stein's loss and the symmetrized Stein's loss. Unlike the Gaussian log-likelihood these two functions are convex and hence admit a unique positive definite optimum. Some of our results hold for general affine covariance models.

preprint2021arXiv

Robust estimation of tree structured models

Consider the problem of learning undirected graphical models on trees from corrupted data. Recently Katiyar et al. showed that it is possible to recover trees from noisy binary data up to a small equivalence class of possible trees. Their other paper on the Gaussian case follows a similar pattern. By framing this as a special phylogenetic recovery problem we largely generalize these two settings. Using the framework of linear latent tree models we discuss tree identifiability for binary data under a continuous corruption model. For the Ising and the Gaussian tree model we also provide a characterisation of when the Chow-Liu algorithm consistently learns the underlying tree from the noisy data.

preprint2016arXiv

Maximum Likelihood Estimation for Linear Gaussian Covariance Models

We study parameter estimation in linear Gaussian covariance models, which are $p$-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill-climbing method to converge to the global maximum. Although we are primarily interested in the case in which $n>\!\!>p$, the proofs of our results utilize large-sample asymptotic theory under the scheme $n/p \to γ> 1$. Remarkably, our numerical simulations indicate that our results remain valid for $p$ as small as $2$. An important consequence of this analysis is that for sample sizes $n \simeq 14 p$, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem.

preprint2016arXiv

The correlation space of Gaussian latent tree models and model selection without fitting

We provide a complete description of possible covariance matrices consistent with a Gaussian latent tree model for any tree. We then present techniques for utilising these constraints to assess whether observed data is compatible with that Gaussian latent tree model. Our method does not require us first to fit such a tree. We demonstrate the usefulness of the inverse-Wishart distribution for performing preliminary assessments of tree-compatibility using semialgebraic constraints. Using results from Drton et al. (2008) we then provide the appropriate moments required for test statistics for assessing adherence to these equality constraints. These are shown to be effective even for small sample sizes and can be easily adjusted to test either the entire model or only certain macrostructures hypothesized within the tree. We illustrate our exploratory tetrad analysis using a linguistic application and our confirmatory tetrad analysis using a biological application.

preprint2016arXiv

Total positivity in Markov structures

We discuss properties of distributions that are multivariate totally positive of order two (MTP2) related to conditional independence. In particular, we show that any independence model generated by an MTP2 distribution is a compositional semigraphoid which is upward-stable and singleton-transitive. In addition, we prove that any MTP2 distribution satisfying an appropriate support condition is faithful to its concentration graph. Finally, we analyze factorization properties of MTP2 distributions and discuss ways of constructing MTP2 distributions; in particular we give conditions on the log-linear parameters of a discrete distribution which ensure MTP2 and characterize conditional Gaussian distributions which satisfy MTP2.

preprint2015arXiv

Automorphism groups of Gaussian chain graph models

In this paper we extend earlier work on groups acting on Gaussian graphical models to Gaussian Bayesian networks and more general Gaussian models defined by chain graphs. We discuss the maximal group which leaves a given model invariant and provide basic statistical applications of this result. This includes equivariant estimation, maximal invariants and robustness. The computation of the group requires finding the essential graph. However, by applying Studeny's theory of imsets we show that computations for DAGs can be performed efficiently without building the essential graph. In our proof we derive simple necessary and sufficient conditions on vanishing sub-minors of the concentration matrix in the model.

preprint2014arXiv

Cremona linearizations of some classical varieties

In this paper we present an effective method for linearizing rational varieties of codimension at least two under Cremona transformations, starting from a given parametrization. Using these linearizing Cremonas, we simplify the equations of secant and tangential varieties of some classical examples, including Veronese, Segre and Grassmann varieties. We end the paper by treating the special case of the Segre embedding of the n-fold product of projective spaces, where cumulant Cremonas, arising from algebraic statistics, appear as specific cases of our general construction.

preprint2013arXiv

Groups acting on Gaussian graphical models

Gaussian graphical models have become a well-recognized tool for the analysis of conditional independencies within a set of continuous random variables. From an inferential point of view, it is important to realize that they are composite exponential transformation families. We reveal this structure by explicitly describing, for any undirected graph, the (maximal) matrix group acting on the space of concentration matrices in the model. The continuous part of this group is captured by a poset naturally associated to the graph, while automorphisms of the graph account for the discrete part of the group. We compute the dimension of the space of orbits of this group on concentration matrices, in terms of the combinatorics of the graph; and for dimension zero we recover the characterization by Letac and Massam of models that are transformation families. Furthermore, we describe the maximal invariant of this group on the sample space, and we give a sharp lower bound on the sample size needed for the existence of equivariant estimators of the concentration matrix. Finally, we address the issue of robustness of these estimators by computing upper bounds on finite sample breakdown points.

preprint2013arXiv

Secant cumulants and toric geometry

We study the secant line variety of the Segre product of projective spaces using special cumulant coordinates adapted for secant varieties. We show that the secant variety is covered by open normal toric varieties. We prove that in cumulant coordinates its ideal is generated by binomial quadrics. We present new results on the local structure of the secant variety. In particular, we show that it has rational singularities and we give a description of the singular locus. We also classify all secant varieties that are Gorenstein. Moreover, generalizing (Sturmfels and Zwiernik 2012), we obtain analogous results for the tangential variety.

preprint2013arXiv

Tensors of Nonnegative Rank Two

A nonnegative tensor has nonnegative rank at most 2 if and only if it is supermodular and has flattening rank at most 2. We prove this result, then explore the semialgebraic geometry of the general Markov model on phylogenetic trees with binary states, and comment on possible extensions to tensors of higher rank.

preprint2012arXiv

L-cumulants, L-cumulant embeddings and algebraic statistics

Focusing on the discrete probabilistic setting we generalize the combinatorial definition of cumulants to L-cumulants. This generalization keeps all the desired properties of the classical cumulants like semi-invariance and vanishing for independent blocks of random variables. These properties make L-cumulants useful for the algebraic analysis of statistical models. We illustrate this for general Markov models and hidden Markov processes in the case when the hidden process is binary. The main motivation of this work is to understand cumulant-like coordinates in algebraic statistics and to give a more insightful explanation why tree cumulants give such an elegant description of binary hidden tree models. Moreover, we argue that L-cumulants can be used in the analysis of certain classical algebraic varieties.

preprint2012arXiv

The Dependence of Routine Bayesian Model Selection Methods on Irrelevant Alternatives

Bayesian methods - either based on Bayes Factors or BIC - are now widely used for model selection. One property that might reasonably be demanded of any model selection method is that if a model ${M}_{1}$ is preferred to a model ${M}_{0}$, when these two models are expressed as members of one model class $\mathbb{M}$, this preference is preserved when they are embedded in a different class $\mathbb{M}'$. However, we illustrate in this paper that with the usual implementation of these common Bayesian procedures this property does not hold true even approximately. We therefore contend that to use these methods it is first necessary for there to exist a "natural" embedding class. We argue that in any context like the one illustrated in our running example of Bayesian model selection of binary phylogenetic trees there is no such embedding.

preprint2012arXiv

Tree cumulants and the geometry of binary tree models

In this paper we investigate undirected discrete graphical tree models when all the variables in the system are binary, where leaves represent the observable variables and where all the inner nodes are unobserved. A novel approach based on the theory of partially ordered sets allows us to obtain a convenient parametrization of this model class. The construction of the proposed coordinate system mirrors the combinatorial definition of cumulants. A simple product-like form of the resulting parametrization gives insight into identifiability issues associated with this model class. In particular, we provide necessary and sufficient conditions for such a model to be identified up to the switching of labels of the inner nodes. When these conditions hold, we give explicit formulas for the parameters of the model. Whenever the model fails to be identified, we use the new parametrization to describe the geometry of the unidentified parameter space. We illustrate these results using a simple example.

preprint2011arXiv

Binary Cumulant Varieties

Algebraic statistics for binary random variables is concerned with highly structured algebraic varieties in the space of 2x2x...x2-tensors. We demonstrate the advantages of representing such varieties in the coordinate system of binary cumulants. Our primary focus lies on hidden subset models. Parametrizations and implicit equations in cumulants are derived for hyperdeterminants, for secant and tangential varieties of Segre varieties, and for certain context-specific independence models. Extending work of Rota and collaborators, we explore the polynomial inequalities satisfied by cumulants.

preprint2011arXiv

Implicit inequality constraints in a binary tree model

In this paper we investigate the geometry of a discrete Bayesian network whose graph is a tree all of whose variables are binary and the only observed variables are those labeling its leaves. We provide the full geometric description of these models which is given by a set of polynomial equations together with a set of complementary implied inequalities induced by the positivity of probabilities on hidden variables. The phylogenetic invariants given by the equations can be useful in the construction of simple diagnostic tests. However, in this paper we point out the importance of also incorporating the associated inequalities into any statistical analysis. The full characterization of these inequality constraints derived in this paper helps us determine how and why routine statistical methods can break down for this model class.

preprint2010arXiv

An asymptotic approximation of the marginal likelihood for general Markov models

The standard Bayesian Information Criterion (BIC) is derived under regularity conditions which are not always satisfied by the graphical models with hidden variables. In this paper we derive the BIC score for Bayesian networks in the case of binary data and when the underlying graph is a rooted tree and all the inner nodes represent hidden variables. This provides a direct generalization of a similar formula given by Rusakov and Geiger for naive Bayes models. The main tool used in this paper is a connection between asymptotic approximation of Laplace integrals and the real log-canonical threshold.

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