Algebraic statistics

Algebraic statistics advocates polynomial algebra as a tool for addressing problems in statistics and its applications. This connection is based on the fact that most statistical models are defined either parametrically or implicitly via polynomial equations. The idea is summarized by the phrase "Statistical models are semialgebraic sets". My tutorial will consist of a detailed study of two examples where the algebra/statistics connection has proven especially useful: in the study of phylogenetic models and in the analysis of contingency tables.

[1]  D. Madigan,et al.  A characterization of Markov equivalence classes for acyclic digraphs , 1997 .

[2]  Audrey Finkler,et al.  Goodness of fit statistics for sparse contingency tables , 2010, 1006.2620.

[3]  P. Bickel,et al.  Mathematical Statistics: Basic Ideas and Selected Topics , 1977 .

[4]  J. Peters On the Intersection Property of Conditional Independence and its Application to Causal Discovery , 2014, 1403.0408.

[5]  S. Crawford,et al.  Volume 1 , 2012, Journal of Diabetes Investigation.

[6]  Josephine Yu,et al.  On a Parametrization of Positive Semidefinite Matrices with Zeros , 2010, SIAM J. Matrix Anal. Appl..

[7]  Elsevier Sdol,et al.  Advances in Applied Mathematics , 2009 .

[8]  N. L. Johnson,et al.  Linear Statistical Inference and Its Applications , 1966 .

[9]  M. Drton,et al.  Global identifiability of linear structural equation models , 2010, 1003.1146.

[10]  Stephen E. Fienberg,et al.  Three centuries of categorical data analysis: Log-linear models and maximum likelihood estimation , 2007 .

[11]  Ezra Miller,et al.  Decompositions of commutative monoid congruences and binomial ideals , 2011, 1107.4699.

[12]  J A Lake,et al.  A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. , 1987, Molecular biology and evolution.

[13]  Caroline J. Klivans,et al.  The Bergman complex of a matroid and phylogenetic trees , 2006, J. Comb. Theory, Ser. B.

[14]  Yu. V. Vagin,et al.  Charles Robert Darwin (to the 200th Birthday and the 150th Anniversary of the publication of the book «On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life» , 2009 .

[15]  Lior Pachter,et al.  Neighbor Joining with Subtree Weights , 2004 .

[16]  Elizabeth S. Allman,et al.  The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models , 2005, J. Comput. Biol..

[17]  Michael I. Jordan Graphical Models , 2003 .

[18]  J. Neyman MOLECULAR STUDIES OF EVOLUTION: A SOURCE OF NOVEL STATISTICAL PROBLEMS* , 1971 .

[19]  Eric H. Kuo Viterbi sequences and polytopes , 2006, J. Symb. Comput..

[20]  Peter Gritzmann,et al.  Minkowski Addition of Polytopes: Computational Complexity and Applications to Gröbner Basis , 1993, SIAM J. Discret. Math..

[21]  A. Takemura,et al.  Minimal Basis for a Connected Markov Chain over 3 × 3 ×K Contingency Tables with Fixed Two‐Dimensional Marginals , 2003 .

[22]  Mateusz Michałek,et al.  Geometry of phylogenetic group-based models , 2011 .

[23]  J. N. Darroch,et al.  Additivity and interaction in three-component experiments with mixtures , 1985 .

[24]  Hidefumi Ohsugi Normality of cut polytopes of graphs is a minor closed property , 2010, Discret. Math..

[25]  H. Wynn,et al.  Algebraic Statistics: Computational Commutative Algebra in Statistics , 2000 .

[26]  Michael D. Hendy,et al.  Complete Families of Linear Invariants for Some Stochastic Models of Sequence Evolution, with and without Molecular Clock Assumption , 1996, J. Comput. Biol..

[27]  Elizabeth Gross,et al.  Goodness of fit for log-linear network models: dynamic Markov bases using hypergraphs , 2014, 1401.4896.

[28]  Stephen E. Fienberg,et al.  Algebraic Statistics for a Directed Random Graph Model with Reciprocation , 2009, 0909.0073.

[29]  Seth Sullivant,et al.  A finiteness theorem for Markov bases of hierarchical models , 2007, J. Comb. Theory, Ser. A.

[30]  Raymond Hemmecke,et al.  On the Gröbner complexity of matrices , 2009 .

[31]  Sumio Watanabe,et al.  Stochastic complexities of reduced rank regression in Bayesian estimation , 2005, Neural Networks.

[32]  J. Kruskal More factors than subjects, tests and treatments: An indeterminacy theorem for canonical decomposition and individual differences scaling , 1976 .

[33]  M. Drton,et al.  Algebraic factor analysis: tetrads, pentads and beyond , 2005, math/0509390.

[34]  L. Tippett,et al.  Applied Statistics. A Journal of the Royal Statistical Society , 1952 .

[35]  Seth Sullivant Small Contingency Tables with Large Gaps , 2005, SIAM J. Discret. Math..

[36]  Alexandre Reymond,et al.  Evolutionary Discrimination of Mammalian Conserved Non-Genic Sequences (CNGs) , 2003, Science.

[37]  Stephen E. Fienberg,et al.  Discrete Multivariate Analysis: Theory and Practice , 1976 .

[38]  Ruriko Yoshida,et al.  Optimality of the Neighbor Joining Algorithm and Faces of the Balanced Minimum Evolution Polytope , 2010, Bulletin of mathematical biology.

[39]  Serkan Hosten,et al.  Least Squares Methods for Equidistant Tree Reconstruction , 2008, 0808.3979.

[40]  J. van Leeuwen,et al.  Theoretical Computer Science , 2003, Lecture Notes in Computer Science.

[41]  Sebastian Tschiatschek,et al.  Introduction to Probabilistic Graphical Models , 2014 .

[42]  Tomi Silander,et al.  A Simple Approach for Finding the Globally Optimal Bayesian Network Structure , 2006, UAI.

[43]  J. Farris A Probability Model for Inferring Evolutionary Trees , 1973 .

[44]  David Penny,et al.  Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. , 2002, Molecular biology and evolution.

[45]  G. Schwarz Estimating the Dimension of a Model , 1978 .

[46]  Thomas Lengauer,et al.  Mtreemix: a software package for learning and using mixture models of mutagenetic trees , 2005, Bioinform..

[47]  A. Geramita,et al.  Ranks of tensors, secant varieties of Segre varieties and fat points , 2002 .

[48]  J. Drife,et al.  The third edition , 2014 .

[49]  M. Gouy,et al.  Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. , 1998, Molecular biology and evolution.

[50]  F. Fisher,et al.  The Identification Problem in Econometrics. , 1967 .

[51]  Lior Pachter,et al.  The Mathematics of Phylogenomics , 2004, SIAM Rev..

[52]  David E. Speyer,et al.  The tropical Grassmannian , 2003, math/0304218.

[53]  Alexander Engstrom,et al.  Cut ideals of K4-minor free graphs are generated by quadrics , 2008, 0805.1762.

[54]  Andrew J. Viterbi,et al.  Error bounds for convolutional codes and an asymptotically optimum decoding algorithm , 1967, IEEE Trans. Inf. Theory.

[55]  Vincent Moulton,et al.  Spectronet: a package for computing spectra and median networks. , 2002, Applied bioinformatics.

[56]  June Huh,et al.  The maximum likelihood degree of a very affine variety , 2012, Compositio Mathematica.

[57]  Rekha R. Thomas Lectures in Geometric Combinatorics , 2006, Student mathematical library.

[58]  Chuong B. Do,et al.  Access the most recent version at doi: 10.1101/gr.926603 References , 2003 .

[59]  Bernd Sturmfels,et al.  Solving the Likelihood Equations , 2005, Found. Comput. Math..

[60]  M. Stanhope,et al.  Molecular Phylogenetics and Evolution , 2002 .

[61]  J. Mattick,et al.  Genome research , 1990, Nature.

[62]  Ronald Christensen,et al.  Log-Linear Models and Logistic Regression , 1997 .

[63]  David Mumford,et al.  What Can Be Computed in Algebraic Geometry , 1993, alg-geom/9304003.

[64]  A. Schäffer,et al.  Chromosome abnormalities in ovarian adenocarcinoma: III. Using breakpoint data to infer and test mathematical models for oncogenesis , 2000, Genes, chromosomes & cancer.

[65]  Arieh Iserles,et al.  On the Foundations of Computational Mathematics , 2001 .

[66]  Henry P. Wynn,et al.  Generalised confounding with Grobner bases , 1996 .

[67]  Milan Studeny,et al.  Conditional independence relations have no finite complete characterization , 1992 .

[68]  Tamio Koyama,et al.  Holonomic modules associated with multivariate normal probabilities of polyhedra , 2013, 1311.6905.

[69]  R. Nielsen,et al.  Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System , 2005, Journal of Molecular Evolution.

[70]  Seth Sullivant,et al.  Ideals of adjacent minors , 2003 .

[71]  Marco Valtorta,et al.  Parameter Identifiability of Discrete Bayesian Networks with Hidden Variables , 2014, 1406.0541.

[72]  Bernd Sturmfels,et al.  Marginal Likelihood Integrals for Mixtures of Independence Models , 2008, J. Mach. Learn. Res..

[73]  Inna Dubchak,et al.  Glocal alignment: finding rearrangements during alignment , 2003, ISMB.

[74]  Akimichi Takemura,et al.  On connectivity of fibers with positive marginals in multiple logistic regression , 2010, J. Multivar. Anal..

[75]  R. Laubenbacher,et al.  A computational algebra approach to the reverse engineering of gene regulatory networks. , 2003, Journal of theoretical biology.

[76]  Seth Sullivant Toric fiber products , 2006 .

[77]  P. Spirtes,et al.  Ancestral graph Markov models , 2002 .

[78]  Peter L. Hammer,et al.  Discrete Applied Mathematics , 1993 .

[79]  Journal of the Association for Computing Machinery , 1961, Nature.

[80]  David J. Buttler,et al.  Encyclopedia of Data Warehousing and Mining Second Edition , 2008 .

[81]  M. Plummer,et al.  A Bayesian information criterion for singular models , 2013, 1309.0911.

[82]  Seth Sullivant,et al.  Finite Groebner bases in infinite dimensional polynomial rings and applications , 2009, 0908.1777.

[83]  Rekha R. Thomas A Geometric Buchberger Algorithm for Integer Programming , 1995, Math. Oper. Res..

[84]  Lior Pachter,et al.  Parametric inference for biological sequence analysis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[85]  Joseph Y. Halpern,et al.  Proceedings of the Twenty-Eighth AAAI Conference on Artificial Intelligence , 2014, AAAI 2014.

[86]  Nicholas L. Bray,et al.  AVID: A global alignment program. , 2003, Genome research.

[87]  Vincent Moulton,et al.  NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks , 2002, WABI.

[88]  B. Sturmfels,et al.  Combinatorial Commutative Algebra , 2004 .

[89]  Paul T. Groth,et al.  The ENCODE (ENCyclopedia Of DNA Elements) Project , 2004, Science.

[90]  P. Holland,et al.  An Exponential Family of Probability Distributions for Directed Graphs , 1981 .

[91]  June Huh,et al.  Varieties with maximum likelihood degree one , 2013, 1301.2732.

[92]  J. Landsberg Tensors: Geometry and Applications , 2011 .

[93]  S. Sullivant,et al.  Emerging applications of algebraic geometry , 2009 .

[94]  Lior Pachter,et al.  MAVID: constrained ancestral alignment of multiple sequences. , 2003, Genome research.

[95]  S. E. Fienberg,et al.  Maximum Likelihood Estimation in Latent Class Models For Contingency Table Data , 2007, 0709.3535.

[96]  Verzekeren Naar Sparen,et al.  Cambridge , 1969, Humphrey Burton: In My Own Time.

[97]  Alexander N Gorban,et al.  The Mystery of Two Straight Lines in Bacterial Genome Statistics , 2004, Bulletin of mathematical biology.

[98]  G. Gutman,et al.  Slipped-strand mispairing: a major mechanism for DNA sequence evolution. , 1987, Molecular biology and evolution.

[99]  S. Sullivant,et al.  Toric geometry of cuts and splits , 2006, math/0606683.

[100]  R. Notari,et al.  Algebraic and Geometric Methods in Statistics: Replicated measurements and algebraic statistics , 2009 .

[101]  G. A. Miller,et al.  MATHEMATISCHE ZEITSCHRIFT. , 1920, Science.

[102]  V. Chepoi,et al.  l ∞ -approximation via subdominants , 2000 .

[103]  Serkan Hosten,et al.  Primary Decomposition of Lattice Basis Ideals , 2000, J. Symb. Comput..

[104]  G. Hardy MENDELIAN PROPORTIONS IN A MIXED POPULATION. , 1908 .

[105]  P. Diaconis Group representations in probability and statistics , 1988 .

[106]  Kai Lai Chung,et al.  A Course in Probability Theory , 1949 .

[107]  C. Matias,et al.  Identifiability of parameters in latent structure models with many observed variables , 2008, 0809.5032.

[108]  D. Gale A theorem on flows in networks , 1957 .

[109]  Seth Sullivant,et al.  A Divide-and-Conquer Algorithm for Generating Markov Bases of Multi-way Tables , 2004, Comput. Stat..

[110]  P. Diaconis,et al.  Algebraic algorithms for sampling from conditional distributions , 1998 .

[111]  Nicholas Eriksson,et al.  Polyhedral conditions for the nonexistence of the MLE for hierarchical log-linear models , 2006, J. Symb. Comput..

[112]  Bernd Sturmfels,et al.  The maximum likelihood degree , 2004, math/0406533.

[113]  M. I. Rosenberg,et al.  Naval Research Logistics Quarterly. , 1958 .

[114]  D. Penny,et al.  Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study. , 2003, Systematic biology.

[115]  David Fernández-Baca,et al.  Bounds for parametric sequence comparison , 2002, Discret. Appl. Math..

[116]  Anders Nedergaard Jensen A Non-Regular Grobner Fan , 2007, Discret. Comput. Geom..

[117]  Seth Sullivant,et al.  Distance-Based Phylogenetic Methods Around a Polytomy , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[118]  Mike A. Steel,et al.  Classifying and Counting Linear Phylogenetic Invariants for the Jukes-Cantor Model , 1995, J. Comput. Biol..

[119]  Shmuel Friedland,et al.  A proof of the set-theoretic version of the salmon conjecture , 2011, 1104.1776.

[120]  Y. Pauplin Direct Calculation of a Tree Length Using a Distance Matrix , 2000, Journal of Molecular Evolution.

[121]  A. R. Wagner Molecular Biology and Evolution , 2001 .

[122]  R. Adkins,et al.  Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. , 2001, Molecular biology and evolution.

[123]  Bruno Buchberger,et al.  The Construction of Multivariate Polynomials with Preassigned Zeros , 1982, EUROCAM.

[124]  George E. Andrews,et al.  A LOWER BOUND FOR THE VOLUME OF STRICTLY CONVEX BODIES WITH MANY BOUNDARY LATTICE POINTS , 1963 .

[125]  David A. Cox,et al.  Ideals, Varieties, and Algorithms: An Introduction to Computational Algebraic Geometry and Commutative Algebra, 3/e (Undergraduate Texts in Mathematics) , 2007 .

[126]  Seth Sullivant,et al.  Multigraded commutative algebra of graph decompositions , 2011, 1102.2601.

[127]  Sean R. Eddy,et al.  Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .

[128]  Federico Ardila A tropical morphism related to the hyperplane arrangement of the complete bipartite graph , 2004 .

[129]  Tommy Färnqvist Number Theory Meets Cache Locality – Efficient Implementation of a Small Prime FFT for the GNU Multiple Precision Arithmetic Library , 2005 .

[130]  S. Wright The Method of Path Coefficients , 1934 .

[131]  David Sankoff,et al.  Chromosome rearrangements in evolution: From gene order to genome sequence and back , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[132]  Fabio Rapallo,et al.  Markov bases and structural zeros , 2006, J. Symb. Comput..

[133]  Hans Schönemann,et al.  SINGULAR: a computer algebra system for polynomial computations , 2001, ACCA.

[134]  Federico Ardila Subdominant Matroid Ultrametrics , 2004, math/0404370.

[135]  Shmuel Onn,et al.  Entry Uniqueness in Margined Tables , 2006, Privacy in Statistical Databases.

[136]  Dan Suciu,et al.  Journal of the ACM , 2006 .

[137]  H. Ryser Combinatorial Properties of Matrices of Zeros and Ones , 1957, Canadian Journal of Mathematics.

[138]  Prasad Tetali,et al.  Simple Markov-chain algorithms for generating bipartite graphs and tournaments , 1997, SODA '97.

[139]  L. Pachter,et al.  Algebraic Statistics for Computational Biology: Preface , 2005 .

[140]  Takayuki Hibi,et al.  Distributive Lattices, Affine Semigroup Rings and Algebras with Straightening Laws , 1987 .

[141]  David P. Mindell,et al.  Ribosomal RNA in Vertebrates: Evolution and Phylogenetic Applications , 1990 .

[142]  E. Hill Journal of Theoretical Biology , 1961, Nature.

[143]  P. Buneman A Note on the Metric Properties of Trees , 1974 .

[144]  Seth Sullivant,et al.  The maximum likelihood threshold of a graph , 2014, 1404.6989.

[145]  Søren Ladegaard Buhl On the Existence of Maximum Likelihood Estimators for Graphical Gaussian Models , 1993 .

[146]  S. Sullivant,et al.  Sequential importance sampling for multiway tables , 2006, math/0605615.

[147]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[148]  Axthonv G. Oettinger,et al.  IEEE Transactions on Information Theory , 1998 .

[149]  Jesús A. De Loera,et al.  Markov bases of three-way tables are arbitrarily complicated , 2006, J. Symb. Comput..

[150]  Robert M Thrall,et al.  Mathematics of Operations Research. , 1978 .

[151]  Takuya Kon-no,et al.  Transactions of the American Mathematical Society , 1996 .

[152]  J. Felsenstein Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[153]  H. Scheffé Experiments with Mixtures , 1958 .

[154]  G. D,et al.  American Naturalist , 1867, Nature.

[155]  Charles R. Johnson,et al.  The Real Positive Definite Completion Problem: Cycle Completability , 1996 .

[156]  Narendra Karmarkar,et al.  A new polynomial-time algorithm for linear programming , 1984, Comb..

[157]  L. Pachter,et al.  Tropical geometry of statistical models. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[158]  Ronald D. Snee,et al.  Screening Concepts and Designs for Experiments with Mixtures , 1976 .

[159]  J. Tukey,et al.  An algorithm for the machine calculation of complex Fourier series , 1965 .

[160]  A. Neumaier Interval methods for systems of equations , 1990 .

[161]  Piotr Zwiernik,et al.  Tree cumulants and the geometry of binary tree models , 2010, 1004.4360.

[162]  E. Lander,et al.  Genomic mapping by fingerprinting random clones: a mathematical analysis. , 1988, Genomics.

[163]  J. Felsenstein,et al.  Invariants of phylogenies in a simple case with discrete states , 1987 .

[164]  Zoubin Ghahramani,et al.  Optimization with EM and Expectation-Conjugate-Gradient , 2003, ICML.

[165]  Diane Maclagan,et al.  Antichains of monomial ideals are finite , 1999, math/9909168.

[166]  P. Pevzner,et al.  Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. , 2004, Genome research.

[167]  A. Dobra Statistical tools for disclosure limitation in multi-way contingency tables , 2002 .

[168]  H. Busemann Advances in mathematics , 1961 .

[169]  Seth Sullivant,et al.  Toric Ideals of Phylogenetic Invariants , 2004, J. Comput. Biol..

[170]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[171]  D. Eisenbud Commutative Algebra: with a View Toward Algebraic Geometry , 1995 .

[172]  I. G. BONNER CLAPPISON Editor , 1960, The Electric Power Engineering Handbook - Five Volume Set.

[173]  Hardy-Weinberg ProportionsThe Hardy-Weinberg Monte Carlo Algorithms for Hardy-Weinberg Proportions , 2003 .

[174]  Ross Ihaka,et al.  Gentleman R: R: A language for data analysis and graphics , 1996 .

[175]  Matthias Wolfrum,et al.  Bernstein's second theorem and Viro's method for sparse polynomial systems in chemistry , 2005, Adv. Appl. Math..

[176]  Raazesh Sainudiin,et al.  Enclosing the Maximum Likelihood of the Simplest DNA Model Evolving on Fixed Topologies: Towards a Rigorous Framework for Phylogenetic Inference , 2004 .

[177]  Andrew P. Robinson,et al.  Randomization, Bootstrap and Monte Carlo Methods in Biology , 2007 .

[178]  D. Rubin,et al.  Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .

[179]  Daniel H. Huson,et al.  Estimating phylogenetic trees and networks using SplitsTree 4 , 2004 .

[180]  Seth Sullivant,et al.  Polyhedral combinatorics of UPGMA cones , 2013, Adv. Appl. Math..

[181]  Tandy J. Warnow,et al.  Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining , 2001, SODA '01.

[182]  John J. Cannon,et al.  The Magma Algebra System I: The User Language , 1997, J. Symb. Comput..

[183]  Hisayuki Hara,et al.  Graver basis for an undirected graph and its application to testing the beta model of random graphs , 2011, 1102.2583.

[184]  D. Geiger,et al.  Stratified exponential families: Graphical models and model selection , 2001 .

[185]  H. Kishino,et al.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.

[186]  D. Steinley Journal of Classification , 2004, Vegetatio.

[187]  Henry P. Wynn,et al.  Algebraic and geometric methods in statistics , 2009 .

[188]  M. Drton Likelihood ratio tests and singularities , 2007, math/0703360.

[189]  Fatemeh Mohammadi,et al.  Divisors on graphs, orientations, syzygies, and system reliability , 2014, 1405.7972.

[190]  Alex Fink The binomial ideal of the intersection axiom for conditional probabilities , 2009, 0902.1495.

[191]  Bernd Sturmfels,et al.  Resultants in genetic linkage analysis , 2004, J. Symb. Comput..

[192]  J. Pearl,et al.  A New Identification Condition for Recursive Models With Correlated Errors , 2002 .

[193]  E. Hansen Global optimization using interval analysis — the multi-dimensional case , 1980 .

[194]  John Aitchison,et al.  The Statistical Analysis of Compositional Data , 1986 .

[195]  Paul D. Seymour,et al.  Matroids and Multicommodity Flows , 1981, Eur. J. Comb..

[196]  Charles R. Johnson,et al.  Positive definite completions of partial Hermitian matrices , 1984 .

[197]  Jotun Hein,et al.  Statistical Methods in Bioinformatics: An Introduction , 2002 .

[198]  Yuguo Chen,et al.  Sequential Monte Carlo Methods for Statistical Analysis of Tables , 2005 .

[199]  Robert J. McEliece,et al.  The generalized distributive law , 2000, IEEE Trans. Inf. Theory.

[200]  Michael Ian Shamos,et al.  Computational geometry: an introduction , 1985 .

[201]  K. Strimmer,et al.  Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies , 1996 .

[202]  Aldo Conca,et al.  Gröbner Bases of Ideals of Minors of a Symmetric Matrix , 1994 .

[203]  Michel Deza,et al.  Geometry of cuts and metrics , 2009, Algorithms and combinatorics.

[204]  Michael Joswig,et al.  Polymake: an approach to modular software design in computational geometry , 2001, SCG '01.

[205]  S. Fienberg,et al.  Bounds for cell entries in contingency tables induced by fixed marginal totals with applications to disclosure limitation , 2001 .

[206]  Vladimir Kolmogorov,et al.  Multi-camera Scene Reconstruction via Graph Cuts , 2002, ECCV.

[207]  M. Panella Associate Editor of the Journal of Computer and System Sciences , 2014 .

[208]  E. Susko Confidence regions and hypothesis tests for topologies using generalized least squares. , 2003, Molecular biology and evolution.

[209]  W. Bowen,et al.  Philadelphia , 1892 .

[210]  Monte Carlo Goodness of Fit Tests , 2014 .

[211]  A. Dobra Markov bases for decomposable graphical models , 2003 .

[212]  Seth Sullivant,et al.  Gröbner Bases and Polyhedral Geometry of Reducible and Cyclic Models , 2002, J. Comb. Theory, Ser. A.

[213]  P. Steerenberg,et al.  Targeting pathophysiological rhythms: prednisone chronotherapy shows sustained efficacy in rheumatoid arthritis. , 2010, Annals of the rheumatic diseases.

[214]  Wen-Hsiung Li,et al.  NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods. , 2000, Molecular biology and evolution.

[215]  H. Scheffé The Simplex‐Centroid Design for Experiments with Mixtures , 1963 .

[216]  Akimichi Takemura,et al.  Calculation of orthant probabilities by the holonomic gradient method , 2012, ArXiv.

[217]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[218]  Journal of Molecular Biology , 1959, Nature.

[219]  Amelia Taylor,et al.  A Semialgebraic Description of the General Markov Model on Phylogenetic Trees , 2012, SIAM J. Discret. Math..

[220]  Persi Diaconis,et al.  A Sequential Importance Sampling Algorithm for Generating Random Graphs with Prescribed Degrees , 2011, Internet Math..

[221]  K. Roberts,et al.  Thesis , 2002 .

[222]  Lennart Ljung,et al.  On global identifiability for arbitrary model parametrizations , 1994, Autom..

[223]  I. Csiszár,et al.  Generalized maximum likelihood estimates for exponential families , 2008 .

[224]  B. Sturmfels Gröbner bases and convex polytopes , 1995 .

[225]  Joel E. Cohen,et al.  Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better , 2004, PLoS biology.

[226]  R. Salakhutdinov,et al.  Relationship between gradient and EM steps in latent variable models , 2003 .

[227]  Norman R. Draper,et al.  Mixture models based on homogeneous polynomials , 1998 .

[228]  E. Chong,et al.  Wiley‐Interscience Series in Discrete Mathematics and Optimization , 2011 .

[229]  Abdul Salam Jarrah,et al.  A Gröbner fan method for biochemical network modeling , 2007, ISSAC '07.

[230]  David E Speyer Tropical Linear Spaces , 2008, SIAM J. Discret. Math..

[231]  Teo Mora,et al.  The Gröbner Fan of an Ideal , 1988, J. Symb. Comput..

[232]  Seth Sullivant,et al.  Identifiability of Large Phylogenetic Mixture Models , 2010, Bulletin of mathematical biology.

[233]  P G Mezey,et al.  Fractional Simplex Designs for Interaction Screening in Complex Mixtures , 2000, Biometrics.

[234]  Seth Sullivant,et al.  POSITIVE MARGINS AND PRIMARY DECOMPOSITION , 2012, 1201.2591.

[235]  Robert R. Sokal,et al.  A statistical method for evaluating systematic relationships , 1958 .

[236]  J. Cavanaugh Biostatistics , 2005, Definitions.

[237]  Cynthia Vinzant Lower bounds for optimal alignments of binary sequences , 2009, Discret. Appl. Math..

[238]  Eva Riccomagno,et al.  Minimal average degree aberration and the state polytope for experimental designs , 2008, 0808.3055.

[239]  P. Stolley,et al.  When genius errs: R.A. Fisher and the lung cancer controversy. , 1991, American journal of epidemiology.

[240]  E V Dunn,et al.  Snoring as a risk factor for disease: an epidemiological survey. , 1985, British medical journal.

[241]  Andrew Rambaut,et al.  Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees , 1997, Comput. Appl. Biosci..

[242]  Bernd Sturmfels,et al.  Algebraic geometry of Bayesian networks , 2005, J. Symb. Comput..

[243]  Claudiu Raicu Secant varieties of Segre–Veronese varieties , 2010, 1011.5867.

[244]  M. Mišík,et al.  Oxford University Press , 1968, PMLA/Publications of the Modern Language Association of America.

[245]  D. Geiger,et al.  On the toric algebra of graphical models , 2006, math/0608054.

[246]  Sergi Elizalde,et al.  BOUNDS ON THE NUMBER OF INFERENCE FUNCTIONS OF A GRAPHICAL MODEL , 2006 .

[247]  Alexander Varchenko,et al.  Critical Points of the Product of Powers of Linear Functions and Families of Bases of Singular Vectors , 1993, hep-th/9312119.

[248]  渡邊 澄夫 Algebraic geometry and statistical learning theory , 2009 .

[249]  A. Louis,et al.  Documenta Mathematica , 1996 .

[250]  採編典藏組 Society for Industrial and Applied Mathematics(SIAM) , 2008 .

[251]  V. Strassen Rank and optimal computation of generic tensors , 1983 .

[252]  G. William Walster,et al.  Rump's Example Revisited , 2002, Reliab. Comput..

[253]  Aleksandra Slavkovic,et al.  Synthetic two-way contingency tables that preserve conditional frequencies , 2010 .

[254]  Jan Draisma,et al.  On the ideals of equivariant tree models , 2007, 0712.3230.

[255]  J. Darroch,et al.  Generalized Iterative Scaling for Log-Linear Models , 1972 .

[256]  Michael Joswig,et al.  polymake: a Framework for Analyzing Convex Polytopes , 2000 .

[257]  P. Diaconis Finite forms of de Finetti's theorem on exchangeability , 1977, Synthese.

[258]  Thomas Lengauer,et al.  Estimating cancer survival and clinical outcome based on genetic tumor progression scores , 2005, Bioinform..

[259]  Stephen E. Fienberg,et al.  Algebraic Statistics for p1 Random Graph Models: Markov Bases and Their Uses , 2011 .

[260]  J. Besag Spatial Interaction and the Statistical Analysis of Lattice Systems , 1974 .

[261]  David R. Cox,et al.  A note on polynomial response functions for mixtures , 1971 .

[262]  A. Karimi,et al.  Master‟s thesis , 2011 .

[263]  D. Haughton On the Choice of a Model to Fit Data from an Exponential Family , 1988 .

[264]  F J Ayala,et al.  Tempo and mode in evolution. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[265]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[266]  B. Bainbridge,et al.  Genetics , 1981, Experientia.

[267]  Walter Zucchini,et al.  Series of Seminars: Hidden Markov Models for Time Series , 2013 .

[268]  K. Zang,et al.  Meningioma: a cytogenetic model of a complex benign human tumor, including data on 394 karyotyped cases , 2001, Cytogenetic and Genome Research.

[269]  M. Kimura A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[270]  George A. Kirkup Random variables with completely independent subcollections , 2004 .

[271]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[272]  L. Kedes,et al.  Evolution of the functional human beta-actin gene and its multi-pseudogene family: conservation of noncoding regions and chromosomal dispersion of pseudogenes , 1985, Molecular and cellular biology.

[273]  H. Akaike A new look at the statistical model identification , 1974 .

[274]  Stephen E. Fienberg,et al.  Β Models for Random Hypergraphs with a given Degree Sequence , 2014, ArXiv.

[275]  D. Freedman,et al.  Finite Exchangeable Sequences , 1980 .

[276]  Alan Agresti,et al.  Categorical Data Analysis , 2003 .

[277]  S E Fienberg,et al.  INAUGURAL ARTICLE by a Recently Elected Academy Member:Bounds for cell entries in contingency tables given marginal totals and decomposable graphs , 2000 .

[278]  Peter H. A. Sneath,et al.  Numerical Taxonomy: The Principles and Practice of Numerical Classification , 1973 .

[279]  P. Pevzner,et al.  Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. , 2003, Genome research.

[280]  D. Haussler,et al.  Human-mouse alignments with BLASTZ. , 2003, Genome research.

[281]  J. Quadrat,et al.  The Maslov Dequantization, Idempotent and Tropical Mathematics: a Very Brief Introduction , 2005 .

[282]  Valerie Hower,et al.  Parametric Analysis of RNA Branching Configurations , 2011, Bulletin of mathematical biology.

[283]  H. W. Parker,et al.  Systematic Zoology , 1896, Nature.

[284]  Leland H. Hartwell,et al.  Genetics: From Genes to Genomes , 1999 .

[285]  J. A. Salvato John wiley & sons. , 1994, Environmental science & technology.

[286]  Elizabeth S. Allman,et al.  Phylogenetic ideals and varieties for the general Markov model , 2004, Adv. Appl. Math..

[287]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[288]  Daniel H. Huson,et al.  Constructing splits graphs , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[289]  O. H. Lowry Academic press. , 1972, Analytical chemistry.

[290]  Lior Pachter,et al.  Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models , 2004, q-bio/0410008.

[291]  J. Garland THE NEW ENGLAND JOURNAL OF MEDICINE , 1977, The Lancet.

[292]  J. Rhodes A concise proof of Kruskal’s theorem on tensor decomposition , 2009, 0901.1796.

[293]  Martin Feinberg,et al.  Multiple Equilibria in Complex Chemical Reaction Networks: I. the Injectivity Property * , 2006 .

[294]  David Mond,et al.  Stochastic factorizations, sandwiched simplices and the topology of the space of explanations , 2003, Proceedings of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[295]  Pavel A. Pevzner,et al.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals , 1995, JACM.

[296]  Judea Pearl,et al.  Reverend Bayes on Inference Engines: A Distributed Hierarchical Approach , 1982, AAAI.

[297]  P. J. Claringbold USE OF THE SIMPLEX DESIGN IN THE STUDY OF JOINT ACTION OF RELATED HORMONES , 1955 .

[298]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[299]  John N. Tsitsiklis,et al.  Introduction to linear optimization , 1997, Athena scientific optimization and computation series.

[300]  F. N. Cole THE AMERICAN MATHEMATICAL SOCIETY. , 1910, Science.

[301]  W. H. Day Computational complexity of inferring phylogenies from dissimilarity matrices. , 1987, Bulletin of mathematical biology.

[302]  M. Ziegler Volume 152 of Graduate Texts in Mathematics , 1995 .

[303]  Thomas Lengauer,et al.  Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. , 2005, The Journal of infectious diseases.

[304]  W. Marsden I and J , 2012 .

[305]  O. Barndorff-Nielsen Information and Exponential Families in Statistical Theory , 1980 .

[306]  James M. Dickey,et al.  Discussion: Testing for Independence in a Two-Way Table: New Interpretations of the Chi-Square Statistic , 1985 .

[307]  S. Sullivant,et al.  Trek separation for Gaussian graphical models , 2008, 0812.1938.

[308]  Thomas S. Richardson,et al.  Graphical Methods for Efficient Likelihood Inference in Gaussian Covariance Models , 2007, J. Mach. Learn. Res..

[309]  Aleksandra B. Slavkovic,et al.  Algebraic Statistics , 2011, International Encyclopedia of Statistical Science.

[310]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[311]  G. Shorack Probability for Statisticians , 2000 .

[312]  Greg F Piepel,et al.  Methods for Assessing Curvature and Interaction in Mixture Experiments , 2002, Technometrics.

[313]  D. S. Arnon,et al.  Algorithms in real algebraic geometry , 1988 .

[314]  Caroline Uhler,et al.  Geometry of maximum likelihood estimation in Gaussian graphical models , 2010, 1012.2643.

[315]  David Kahle mpoly: Multivariate Polynomials in R , 2013, R J..

[316]  P. Cochat,et al.  Et al , 2008, Archives de pediatrie : organe officiel de la Societe francaise de pediatrie.

[317]  S. Sullivant Gaussian conditional independence relations have no finite complete characterization , 2007, 0704.2847.