Learning Linear Non-Gaussian Polytree Models

In the context of graphical causal discovery, we adapt the versatile framework of linear non-Gaussian acyclic models (LiNGAMs) to propose new algorithms to efficiently learn graphs that are polytrees. Our approach combines the Chow--Liu algorithm, which first learns the undirected tree structure, with novel schemes to orient the edges. The orientation schemes assess algebraic relations among moments of the data-generating distribution and are computationally inexpensive. We establish high-dimensional consistency results for our approach and compare different algorithmic versions in numerical experiments

An efficiency upper bound for inverse covariance estimation

We derive an upper bound for the efficiency of estimating entries in the inverse covariance matrix of a high dimensional distribution. We show that in order to approximate an off-diagonal entry of the density matrix of a $d$-dimensional Gaussian random vector, one needs at least a number of samples proportional to $d$. Furthermore, we show that with $n \ll d$ samples, the hypothesis that two given coordinates are fully correlated, when all other coordinates are conditioned to be zero, cannot be told apart from the hypothesis that the two are uncorrelated.Comment: 7 Page

A Mutagenetic Tree Hidden Markov Model for Longitudinal Clonal HIV Sequence Data

RNA viruses provide prominent examples of measurably evolving populations. In HIV infection, the development of drug resistance is of particular interest, because precise predictions of the outcome of this evolutionary process are a prerequisite for the rational design of antiretroviral treatment protocols. We present a mutagenetic tree hidden Markov model for the analysis of longitudinal clonal sequence data. Using HIV mutation data from clinical trials, we estimate the order and rate of occurrence of seven amino acid changes that are associated with resistance to the reverse transcriptase inhibitor efavirenz.Comment: 20 pages, 6 figure

Generalized Permutohedra from Probabilistic Graphical Models

A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. There is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models and also for mixed graphical models containing undirected, directed and bidirected edges, we give a construction of this polytope, up to equivalence of normal fans, as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models.Comment: Appendix B is expanded. Final version to appear in SIAM J. Discrete Mat

A new method for the estimation of variance matrix with prescribed zeros in nonlinear mixed effects models

We propose a new method for the Maximum Likelihood Estimator (MLE) of nonlinear mixed effects models when the variance matrix of Gaussian random effects has a prescribed pattern of zeros (PPZ). The method consists in coupling the recently developed Iterative Conditional Fitting (ICF) algorithm with the Expectation Maximization (EM) algorithm. It provides positive definite estimates for any sample size, and does not rely on any structural assumption on the PPZ. It can be easily adapted to many versions of EM.Comment: Accepted for publication in Statistics and Computin

A Localization Approach to Improve Iterative Proportional Scaling in Gaussian Graphical Models

We discuss an efficient implementation of the iterative proportional scaling procedure in the multivariate Gaussian graphical models. We show that the computational cost can be reduced by localization of the update procedure in each iterative step by using the structure of a decomposable model obtained by triangulation of the graph associated with the model. Some numerical experiments demonstrate the competitive performance of the proposed algorithm.Comment: 12 page

Separability problem for multipartite states of rank at most four

One of the most important problems in quantum information is the separability problem, which asks whether a given quantum state is separable. We investigate multipartite states of rank at most four which are PPT (i.e., all their partial transposes are positive semidefinite). We show that any PPT state of rank two or three is separable and has length at most four. For separable states of rank four, we show that they have length at most six. It is six only for some qubit-qutrit or multiqubit states. It turns out that any PPT entangled state of rank four is necessarily supported on a 3x3 or a 2x2x2 subsystem. We obtain a very simple criterion for the separability problem of the PPT states of rank at most four: such a state is entangled if and only if its range contains no product vectors. This criterion can be easily applied since a four-dimensional subspace in the 3x3 or 2x2x2 system contains a product vector if and only if its Pluecker coordinates satisfy a homogeneous polynomial equation (the Chow form of the corresponding Segre variety). We have computed an explicit determinantal expression for the Chow form in the former case, while such expression was already known in the latter case.Comment: 19 page

Dynamic Gaussian graphical models for modelling genomic networks

After sequencing the entire DNA for various organisms, the challenge has become understanding the functional interrelatedness of the genome. Only by understanding the pathways for various complex diseases can we begin to make sense of any type of treatment. Unfortu- nately, decyphering the genomic network structure is an enormous task. Even with a small number of genes the number of possible networks is very large. This problem becomes even more difficult, when we consider dynamical networks. We consider the problem of estimating a sparse dy- namic Gaussian graphical model with L1 penalized maximum likelihood of structured precision matrix. The structure can consist of specific time dynamics, known presence or absence of links in the graphical model or equality constraints on the parameters. The model is defined on the basis of partial correlations, which results in a specific class precision matrices. A priori L1 penalized maximum likelihood estimation in this class is extremely difficult, because of the above mentioned constraints, the computational complexity of the L1 constraint on the side of the usual positive-definite constraint. The implementation is non-trivial, but we show that the computation can be done effectively by taking advan- tage of an efficient maximum determinant algorithm developed in convex optimization

Binary Models for Marginal Independence

Log-linear models are a classical tool for the analysis of contingency tables. In particular, the subclass of graphical log-linear models provides a general framework for modelling conditional independences. However, with the exception of special structures, marginal independence hypotheses cannot be accommodated by these traditional models. Focusing on binary variables, we present a model class that provides a framework for modelling marginal independences in contingency tables. The approach taken is graphical and draws on analogies to multivariate Gaussian models for marginal independence. For the graphical model representation we use bi-directed graphs, which are in the tradition of path diagrams. We show how the models can be parameterized in a simple fashion, and how maximum likelihood estimation can be performed using a version of the Iterated Conditional Fitting algorithm. Finally we consider combining these models with symmetry restrictions