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Title: Binary hidden Markov models and varieties, AS2012 Special Volume, part 2: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2013, 2013
Description: This paper closely examines HMMs in which all the hidden random variables are...
Show moreThis paper closely examines HMMs in which all the hidden random variables are binary. Its main contributions are (1) a birational parametrization for every such HMM, with an explicit inverse for recovering the hidden parameters in terms of observables, (2) a semialgebraic model membership test for every such HMM, and (3) minimal dening equations for the 4-node fully binary model, comprising 21 quadrics and 29 cubics, which were computed using Grobner bases in the cumulant coordinates of Sturmfels and Zwiernik. The new model parameters in (1) are rationally identiable in the sense of Sullivant, Garcia-Puente, and Spielvogel, and each model's Zariski closure is therefore a rational projective variety of dimension 5. Grobner basis computations for the model and its graph are found to be considerably faster using these parameters. In the case of two hidden states, item (2) supersedes a previous algorithm of Schonhuth which is only generically dened, and the dening equations (3) yield new invariants for HMMs of all lengths 4. Such invariants have been used successfully in model selection problems in phylogenetics, and one can hope for similar applications in the case of HMMs.
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Collection: Journal of Algebraic Statistics

Title: Learning Coefficient in Bayesian Estimation of Restricted Boltzmann Machine, AS2012 Special Volume, part 2: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2013, 2013
Description: We consider the real log canonical threshold for the learning model in Bayesian estimation. This threshold corresponds to a learning...
Show moreWe consider the real log canonical threshold for the learning model in Bayesian estimation. This threshold corresponds to a learning coefficient of generalization error in Bayesian estimation, which serves to measure learning efficiency in hierarchical learning models [30, 31, 33]. In this paper, we clarify the ideal which gives the log canonical threshold of the restricted Boltzmann machine and consider the learning coefficients of this model.
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Collection: Journal of Algebraic Statistics

Title: The precision space of interpolatory cubature formulæ
Date: 2015, 2015-06-11
Description: Methods from Commutative Algebra and Numerical Analysis are combined to address a problem common to many disciplines: the estimation of the...
Show moreMethods from Commutative Algebra and Numerical Analysis are combined to address a problem common to many disciplines: the estimation of the expected value of a polynomial of a random vector using a linear combination of a finite number of its values. In this work we remark on the error estimation in cubature formulæ for polynomial functions and introduce the notion of a precision space for a cubature rule.
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Collection: Journal of Algebraic Statistics

Title: The degeneration of the Grassmannian into a toric variety and the calculation of the eigenspaces of a torus action
Date: 2015, 2015-06-11
Description: Using the method of degenerating a Grassmannian into a toric variety, we calculate formulas for the dimensions of the eigenspaces of the...
Show moreUsing the method of degenerating a Grassmannian into a toric variety, we calculate formulas for the dimensions of the eigenspaces of the action of an n-dimensional torus on a Grassmannian of planes in an n-dimensional space.
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Collection: Journal of Algebraic Statistics

Title: Varieties with maximum likelihood degree one
Date: 2014, 2014-04-30
Description: We show that algebraic varieties with maximum likelihood degree one are exactly the images of reduced A-discriminantal varieties under...
Show moreWe show that algebraic varieties with maximum likelihood degree one are exactly the images of reduced A-discriminantal varieties under monomial maps with finite fibers. The maximum likelihood estimator corresponding to such a variety is Kapranov’s Horn uniformization. This extends Kapranov’s characterization of A-discriminantal hypersurfaces to varieties of arbitrary codimension.
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Collection: Journal of Algebraic Statistics

Title: Maximum Likelihood for Matrices with Rank Constraints
Date: 2014, 2014-04-30
Description: Maximum likelihood estimation is a fundamental optimization problem in statistics. We study this problem on manifolds of matrices with bounded...
Show moreMaximum likelihood estimation is a fundamental optimization problem in statistics. We study this problem on manifolds of matrices with bounded rank. These represent mixtures of distributions of two independent discrete random variables. We determine the maximum likelihood degree for a range of determinantal varieties, and we apply numerical algebraic geometry to compute all critical points of their likelihood functions. This led to the discovery of maximum likelihood duality between matrices of complementary ranks, a result proved subsequently by Draisma and Rodriguez.
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Collection: Journal of Algebraic Statistics

Title: Uncovering Proximity of Chromosome Territories using Classical Algebraic Statistics
Date: 2015, 2015-11-09
Description: Exchange type chromosome aberrations (ETCAs) are rearrangements of the genome that occur when chromosomes break and the resulting fragments...
Show moreExchange type chromosome aberrations (ETCAs) are rearrangements of the genome that occur when chromosomes break and the resulting fragments rejoin with fragments from other chromosomes or from other regions within the same chromosome. ETCAs are commonly observed in cancer cells and in cells exposed to radiation. The frequency of these chromosome rearrangements is correlated with their spatial proximity, therefore it can be used to infer the three dimensional organization of the genome. Extracting statistical significance of spatial proximity from cancer and radiation data has remained somewhat elusive because of the sparsity of the data. We here propose a new approach to study the three dimensional organization of the genome using algebraic statistics. We test our method on a published data set of irradiated human blood lymphocyte cells. We provide a rigorous method for testing the overall organization of the genome, and in agreement with previous results we find a random relative positioning of chromosomes with the exception of the chromosome pairs {1,22} and {13,14} that have a significantly larger number of ETCAs than the rest of the chromosome pairs suggesting their spatial proximity. We conclude that algebraic methods can successfully be used to analyze genetic data and have potential applications to larger and more complex data sets.
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Collection: Journal of Algebraic Statistics

Title: A linear-algebraic tool for conditional independence inference
Date: 2015, 2015-11-09
Description: In this note, we propose a new linear-algebraic method for the implication problem among conditional independence statements, which is...
Show moreIn this note, we propose a new linear-algebraic method for the implication problem among conditional independence statements, which is inspired by the factorization characterization of conditional independence. First, we give a criterion in the case of a discrete strictly positive density and relate it to an earlier linear-algebraic approach. Then, we extend the method to the case of a discrete density that need not be strictly positive. Finally, we provide a computational result in the case of six variables.
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Collection: Journal of Algebraic Statistics

Title: A Family of Quasisymmetry Models
Date: 2015, 2015-06-11
Description: We present a one-parameter family of models for square contingency tables that interpolates between the classical quasisymmetry model and its...
Show moreWe present a one-parameter family of models for square contingency tables that interpolates between the classical quasisymmetry model and its Pearsonian analogue. Algebraically, this corresponds to deformations of toric ideals associated with graphs. Our discussion of the statistical issues centers around maximum likelihood estimation.
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Collection: Journal of Algebraic Statistics

Title: Markov degree of configurations defined by fibers of a configuration
Date: 2015, 2015-11-09
Description: We consider a series of configurations defined by fibers of a given base configuration. We prove that Markov degree of the configurations is...
Show moreWe consider a series of configurations defined by fibers of a given base configuration. We prove that Markov degree of the configurations is bounded from above by the Markov complexity of the base configuration. As important examples of base configurations we consider incidence matrices of graphs and study the maximum Markov degree of configurations defined by fibers of the incidence matrices. In particular we give a proof that the Markov degree for two-way transportation polytopes is three.
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Collection: Journal of Algebraic Statistics

Title: On Polyhedral Approximations of Polytopes for Learning Bayesian Networks, AS2012 Special Volume, part 2: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2013, 2013
Description: The motivation for this paper is the geometric approach to statistical learning Bayesiannetwork (BN) structures. We review three vector...
Show moreThe motivation for this paper is the geometric approach to statistical learning Bayesiannetwork (BN) structures. We review three vector encodings of BN structures. The first one has been used by Jaakkola et al. [9] and also by Cussens [4], the other two use special integral vectors formerly introduced, called imsets [18, 20]. The topic is the comparison of outer polyhedral approximations of the corresponding polytopes. We show how to transform the inequalities suggested by Jaakkola et al. [9] into the framework of imsets. The result of our comparison is the observation that the implicit polyhedral approximation of the standard imset polytope suggested in [21] gives a tighter approximation than the (transformed) explicit polyhedral approximation from [9]. As a consequence, we confirm a conjecture from [21] that the above-mentioned implicit polyhedral approximation of the standard imset polytope is an LP relaxation of that polytope. In the end, we review recent attempts to apply the methods of integer programming to learning BN structures and discuss the task of finding suitable explicit LP relaxation in the imset-based approach.
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Collection: Journal of Algebraic Statistics

Title: Higher Connectivity of Fiber Graphs of Gröbner Bases, AS2012 Special Volume, part 2: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2013, 2013
Description: Fiber graphs of Gröbner bases from contingency tables are important in statistical hypothesis testing, where one studies random walks on these...
Show moreFiber graphs of Gröbner bases from contingency tables are important in statistical hypothesis testing, where one studies random walks on these graphs using the Metropolis-Hastings algorithm. The connectivity of the graphs has implications on how fast the algorithm converges. In this paper, we study a class of ber graphs with elementary combinatorial techniques and provide results that support a recent conjecture of Engström: the connectivity is given by the minimum vertex degree.
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Collection: Journal of Algebraic Statistics

Title: Betti Numbers of Cut Ideals of Trees, AS2012 Special Volume, part 2: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2013, 2013
Description: Cut ideals, introduced by Sturmfels and Sullivant, are used in phylogenetics and algebraic statistics. We study the minimal free resolutions...
Show moreCut ideals, introduced by Sturmfels and Sullivant, are used in phylogenetics and algebraic statistics. We study the minimal free resolutions of cut ideals of tree graphs. By employing basic methods from topological combinatorics, we obtain upper bounds for the Betti numbers of this type of ideals. These take the form of simple formulas on the number of vertices, which arise from the enumeration of induced subgraphs of certain incomparability graphs associated to the edge sets of trees.
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Collection: Journal of Algebraic Statistics

Title: Tying Up Loose Strands: Defining Equations of the Strand Symmetric Model
Date: 2015, 2015-06-11
Description: The strand symmetric model is a phylogenetic model designed to reflect the symmetry inherent in the double-stranded structure of DNA. We show...
Show moreThe strand symmetric model is a phylogenetic model designed to reflect the symmetry inherent in the double-stranded structure of DNA. We show that the set of known phylogenetic invariants for the general strand symmetric model of the three leaf claw tree entirely defines the ideal. This knowledge allows one to determine the vanishing ideal of the general strand symmetric model of any trivalent tree. Our proof of the main result is computational. We use the fact that the Zariski closure of the strand symmetric model is the secant variety of a toric variety to compute the dimension of the variety. We then show that the known equations generate a prime ideal of the correct dimension using elimination theory.
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Collection: Journal of Algebraic Statistics

Title: The maximum likelihood degree of Fermat hypersurfaces
Date: 2015, 2015-11-09
Description: We study the critical points of the likelihood function over the Fermat hypersurface. This problem is related to one of the main problems in...
Show moreWe study the critical points of the likelihood function over the Fermat hypersurface. This problem is related to one of the main problems in statistical optimization: maximum likelihood estimation. The number of critical points over a projective variety is a topological invariant of the variety and is called maximum likelihood degree. We provide closed formulas for the maximum likelihood degree of any Fermat curve in the projective plane and of Fermat hypersurfaces of degree 2 in any projective space. Algorithmic methods to compute the ML degree of a generic Fermat hypersurface are developed throughout the paper. Such algorithms heavily exploit the symmetries of the varieties we are considering. A computational comparison of the different methods and a list of the maximum likelihood degrees of several Fermat hypersurfaces are available in the last section.
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Collection: Journal of Algebraic Statistics

Title: On the Connectivity of Fiber Graphs
Date: 2015, 2015-06-11
Description: We consider the connectivity of fiber graphs with respect to Gröbner basis and Graver basis moves. First, we present a sequence of fiber...
Show moreWe consider the connectivity of fiber graphs with respect to Gröbner basis and Graver basis moves. First, we present a sequence of fiber graphs using moves from a Gröbner basis and prove that their edge-connectivity is lowest possible and can have an arbitrarily large distance from the minimal degree. We then show that graph-theoretic properties of fiber graphs do not depend on the size of the right-hand side. This provides a counterexample to a conjecture of Engström on the node-connectivity of fiber graphs. Our main result shows that the edge-connectivity in all fiber graphs of this counterexample is best possible if we use moves from Graver basis instead.
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Collection: Journal of Algebraic Statistics

Title: Geometry of Higher-Order Markov Chains, AS2012 Special Volume, part 1: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2012, 2012
Description: We determine an explicit Gr ?obner basis, consisting of linear forms and determinantal quadrics, for the prime ideal of Raftery’s mixture...
Show moreWe determine an explicit Gr ?obner basis, consisting of linear forms and determinantal quadrics, for the prime ideal of Raftery’s mixture transition distribution model for Markov chains. When the states are binary, the corresponding projective variety is a linear space, the model itself consists of two simplices in a cross-polytope, and the likelihood function typically has two local maxima. In the general non-binary case, the model corresponds to a cone over a Segre variety.
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Collection: Journal of Algebraic Statistics

Title: Phylogenetic invariants for group-based models, AS2012 Special Volume, part 1: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2012, 2012
Description: In this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating...
Show moreIn this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating many phylogenetic invariants. We prove that we obtain all invariants for any tree for the two-state Jukes-Cantor model. We conjecture that for a large class of models our method can give all phylogenetic invariants for any tree. We show that for 3-Kimura our conjecture is equivalent to the conjecture of Sturmfels and Sullivant [22, Conjecture 2]. This, combined with the results in [22], would make it possible to determine all phylogenetic invariants for any tree for 3-Kimura model, and also other phylogenetic models. Next we give the (first) examples of non-normal varieties associated to general group-based model for an abelian group. Following Kubjas [17] we prove that for many group-based models varieties associated to trees with the same number of leaves do not have to be deformation equivalent.
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Collection: Journal of Algebraic Statistics

Title: Properties of semi-elementary imsets as sums of elementary imsets
Date: 2011, 2011
Description: We study properties of semi-elementary imsets and elementary imsets introduced by Studeny [10]. The rules of the semi-graphoid axiom ...
Show moreWe study properties of semi-elementary imsets and elementary imsets introduced by Studeny [10]. The rules of the semi-graphoid axiom (decomposition, weak union and contraction) for conditional independence statements can be translated into a simple identity among three semi-elementary imsets. By recursively applying the identity, any semi-elementary imset can be written as a sum of elementary imsets, which we call a representation of the semi-elementary imset. A semi-elementary imset has many representations. We study properties of the set of possible representations of a semi-elementary imset and prove that all representations are connected by relations among four elementary imsets.
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Collection: Journal of Algebraic Statistics

Title: Connectivity for 3 x 3 x K contingency tables
Description: We consider an exact sequential conditional test for three-way conditional test of no interaction. At each time τ, the test uses as the...
Show moreWe consider an exact sequential conditional test for three-way conditional test of no interaction. At each time τ, the test uses as the conditional inference frame the set F(Hτ) of all tables with the same three two-way marginal tables as the obtained table Hτ . For 3 × 3 × K tables, we propose a method to construct F(Hτ) from F(Hτ−1). This enables us to perform efficiently the sequential exact conditional test. The subset Sτ of F (Hτ ) consisting of s + Hτ − Hτ −1 for s ∈ F(Hτ−1) contains Hτ , where the operations + and − are defined elementwise. Our argument is based on the minimal Markov basis for 3 × 3 × K contingency tables and we give a minimal subset M of some Markov basis which has the property that F (Hτ ) = {s − m | s ∈ Sτ , m ∈ M}.
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Collection: Journal of Algebraic Statistics

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