Feature network models for proximity data

Feature Network Models are graphical structures that represent proximity data in a discrete space while using the same formalism that is the basis of least squares methods used in multidimensional scaling. Existing methods to derive a network model from empirical data only give the best fitting network and yield no standard errors for the parameter estimates. The additivity properties of networks make it possible to consider the model as a univariate (multiple) linear regression problem with positivity restrictions on the parameters. In the present study, both theoretical and empirical standard errors are obtained for the constrained regression parameters of a network model with known features. The performance of both types of standard errors are evaluated using Monte Carlo techniques.

[1]  W. Heiser A generalized majorization method for least souares multidimensional scaling of pseudodistances that may be negative , 1991 .

[2]  Herbert Busemann,et al.  The geometry of geodesics , 1955 .

[3]  J. W. Hutchinson,et al.  Nearest neighbor analysis of psychological spaces. , 1986 .

[4]  Willem J. Heiser,et al.  Models for asymmetric proximities , 1996 .

[5]  R. Gonzalez Applied Multivariate Statistics for the Social Sciences , 2003 .

[6]  A. Tversky,et al.  Similarity, separability, and the triangle inequality. , 1982, Psychological review.

[7]  Satoru Kawai,et al.  An Algorithm for Drawing General Undirected Graphs , 1989, Inf. Process. Lett..

[8]  R. Shepard,et al.  The internal representation of numbers , 1975, Cognitive Psychology.

[9]  Isabelle Guyon,et al.  An Introduction to Variable and Feature Selection , 2003, J. Mach. Learn. Res..

[10]  F. Tajima,et al.  Statistical method for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitution among different lineages. , 1992, Molecular biology and evolution.

[11]  R. Nosofsky Exemplars, prototypes, and similarity rules. , 1992 .

[12]  R. Shepard,et al.  Stimulus generalization in the learning of classifications. , 1963, Journal of experimental psychology.

[13]  R. Nosofsky Attention and learning processes in the identification and categorization of integral stimuli. , 1987, Journal of experimental psychology. Learning, memory, and cognition.

[14]  D. Stram,et al.  Variance components testing in the longitudinal mixed effects model. , 1994, Biometrics.

[15]  Karl Christoph Klauer,et al.  Representing proximities by network models , 1994 .

[16]  George A. Miller,et al.  A psychological method to investigate verbal concepts , 1969 .

[17]  E. Gilbert Gray codes and paths on the N-cube , 1958 .

[18]  J. Carroll,et al.  An alternating combinatorial optimization approach to fitting the INDCLUS and generalized INDCLUS models , 1994 .

[19]  Hans Joachim Werner,et al.  On Inequality Constrained Generalized Least Squares Selections in the General Possibly Singular , 1996 .

[20]  Robert L. Goldstone Influences of categorization on perceptual discrimination. , 1994, Journal of experimental psychology. General.

[21]  Yoshio Takane,et al.  Nonmetric maximum likelihood multidimensional scaling from directional rankings of similarities , 1981 .

[22]  E. E. David,et al.  Human communication : a unified view , 1972 .

[23]  S D Soli,et al.  Discrete representation of perceptual structure underlying consonant confusions. , 1986, The Journal of the Acoustical Society of America.

[24]  F. Restle A metric and an ordering on sets , 1959 .

[25]  E. Galanter,et al.  An axiomatic and experimental study of sensory order and measure. , 1956, Psychological review.

[26]  Albert Nijenhuis,et al.  Combinatorial Algorithms for Computers and Calculators , 1978 .

[27]  Willem J. Heiser,et al.  City-Block Scaling: Smoothing Strategies for Avoiding Local Minima , 1998 .

[28]  Yuhong Yang Can the Strengths of AIC and BIC Be Shared , 2005 .

[29]  O. Gascuel A note on Sattath and Tversky's, Saitou and Nei's, and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances. , 1994, Molecular biology and evolution.

[30]  Boris Mirkin,et al.  Clustering for contingency tables: boxes and partitions , 1996, Stat. Comput..

[31]  H. Künsch The Jackknife and the Bootstrap for General Stationary Observations , 1989 .

[32]  Frank A. Wolak,et al.  An Exact Test for Multiple Inequality and Equality Constraints in the Linear Regression Model , 1987 .

[33]  Richard F. Gunst,et al.  Applied Regression Analysis , 1999, Technometrics.

[34]  G. Storms,et al.  The Role of Contrast Categories in Natural Language Concepts , 2001 .

[35]  J. Kruschke,et al.  ALCOVE: an exemplar-based connectionist model of category learning. , 1992, Psychological review.

[36]  A. Tversky,et al.  Extended similarity trees , 1986 .

[37]  D. Freedman,et al.  Bootstrapping a Regression Equation: Some Empirical Results , 1984 .

[38]  A. Tversky,et al.  Spatial versus tree representations of proximity data , 1982 .

[39]  I. Borg,et al.  Dimensional models for the perception of rectangles , 1983, Perception & psychophysics.

[40]  Safa R. Zaki,et al.  Exemplar and prototype models revisited: response strategies, selective attention, and stimulus generalization. , 2002, Journal of experimental psychology. Learning, memory, and cognition.

[41]  M. Halle,et al.  Preliminaries to Speech Analysis: The Distinctive Features and Their Correlates , 1961 .

[42]  L. Marks,et al.  Optional processes in similarity judgments , 1992, Perception & psychophysics.

[43]  Pranab Kumar Sen,et al.  An appraisal of some aspects of statistical inference under inequality constraints , 2002 .

[44]  R. Shepard,et al.  Learning and memorization of classifications. , 1961 .

[45]  W. Li,et al.  A statistical test of phylogenies estimated from sequence data. , 1989, Molecular biology and evolution.

[46]  Geert De Soete,et al.  Tree and other network models for representing proximity data , 1996 .

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

[48]  E. Rothkopf A measure of stimulus similarity and errors in some paired-associate learning tasks. , 1957, Journal of experimental psychology.

[49]  G. Keren,et al.  Recognition models of alphanumeric characters. , 1981, Perception & psychophysics.

[50]  O. Gascuel,et al.  A reduction algorithm for approximating a (nonmetric) dissimilarity by a tree distance , 1996 .

[51]  J. Carroll,et al.  Spatial, non-spatial and hybrid models for scaling , 1976 .

[52]  M. Chasles,et al.  Aperçu historique sur l'origine et le développement des méthodes en géométrie, particulièrement de celles qui se rapportent à la géométrie moderne, suivi d'un mémoire de géométrie sur deux principes généraux de la science, la dualité et l'homographie , 1837 .

[53]  R. Nosofsky Attention, similarity, and the identification-categorization relationship. , 1986, Journal of experimental psychology. General.

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

[55]  Michael J. Brusco Integer Programming Methods for Seriation and Unidemensional Scaling of Proximity Matrices: A Review and Some Extensions , 2002, J. Classif..

[56]  J. Ramsay Some Statistical Approaches to Multidimensional Scaling Data , 1982 .

[57]  Amos Tversky,et al.  On the relation between common and distinctive feature models , 1987 .

[58]  Joseph Felsenstein,et al.  Statistical inference of phylogenies , 1983 .

[59]  J. Felsenstein CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[60]  R. Shepard Attention and the metric structure of the stimulus space. , 1964 .

[61]  J. Stephens,et al.  Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes. , 1985, Molecular biology and evolution.

[62]  Anil K. Jain,et al.  Algorithms for Clustering Data , 1988 .

[63]  W. DeSarbo,et al.  The representation of three-way proximity data by single and multiple tree structure models , 1984 .

[64]  Moonja P. Kim,et al.  The Method of Sorting as a Data-Gathering Procedure in Multivariate Research. , 1975, Multivariate behavioral research.

[65]  H. Landahl Neural mechanisms for the concepts of difference and similarity , 1945 .

[66]  P. Groenen,et al.  The tunneling method for global optimization in multidimensional scaling , 1996 .

[67]  David Krackhardt,et al.  PREDICTING WITH NETWORKS: NONPARAMETRIC MULTIPLE REGRESSION ANALYSIS OF DYADIC DATA * , 1988 .

[68]  Alain Guénoche,et al.  Trees and proximity representations , 1991, Wiley-Interscience series in discrete mathematics and optimization.

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

[70]  A. Tversky,et al.  Additive similarity trees , 1977 .

[71]  Susan J. Parault,et al.  The development of conceptual categories of attention during the elementary school years. , 2000, Journal of experimental child psychology.

[72]  A. J. Hoffman,et al.  Applications of Graph Theory to Group Structure. , 1966 .

[73]  Brian A. Davey,et al.  An Introduction to Lattices and Order , 1989 .

[74]  Hans Joachim Werner,et al.  On inequality constrained generalized least-squares estimation☆ , 1990 .

[75]  P. Groenen,et al.  Global Optimization in Least-Squares Multidimensional Scaling by Distance Smoothing , 1999 .

[76]  R. Shepard Integrality versus separability of stimulus dimensions: From an early convergence of evidence to a p , 1991 .

[77]  Boris G. Mirkin,et al.  Least-Squares Structuring, Clustering and Data Processing Issues , 1998, Comput. J..

[78]  J. Durbin,et al.  Testing for serial correlation in least squares regression. I. , 1950, Biometrika.

[79]  R. Shepard Representation of structure in similarity data: Problems and prospects , 1974 .

[80]  C. L. Mallows Some comments on C_p , 1973 .

[81]  M. Nei,et al.  A Simple Method for Estimating and Testing Minimum-Evolution Trees , 1992 .

[82]  Regina Y. Liu,et al.  Efficiency and robustness in resampling , 1992 .

[83]  Hannes Eisler THE ALGEBRAIC AND STATISTICAL TRACTABILITY OF THE CITY BLOCK METRIC , 1973 .

[84]  G. Box,et al.  A general distribution theory for a class of likelihood criteria. , 1949, Biometrika.

[85]  F ATTNEAVE,et al.  Dimensions of similarity. , 1950, The American journal of psychology.

[86]  B. Rannala,et al.  Phylogenetic methods come of age: testing hypotheses in an evolutionary context. , 1997, Science.

[87]  M. Bulmer Use of the Method of Generalized Least Squares in Reconstructing Phylogenies from Sequence Data , 1991 .

[88]  A. Tversky,et al.  Representations of qualitative and quantitative dimensions. , 1982, Journal of experimental psychology. Human perception and performance.

[89]  Won-Chan Lee,et al.  Bootstrapping correlation coefficients using univariate and bivariate sampling. , 1998 .

[90]  B. Mirkin A sequential fitting procedure for linear data analysis models , 1990 .

[91]  Charles L. Lawson,et al.  Solving least squares problems , 1976, Classics in applied mathematics.

[92]  M. Lee,et al.  Extending the ALCOVE model of category learning to featural stimulus domains , 2002, Psychonomic bulletin & review.

[93]  Mårten Gulliksson,et al.  Perturbation theory for generalized and constrained linear least squares , 2000, Numer. Linear Algebra Appl..

[94]  J. Corter,et al.  An Efficient Metric Combinatorial Algorithm for Fitting Additive Trees. , 1998, Multivariate behavioral research.

[95]  H Kishino,et al.  Converting distance to time: application to human evolution. , 1990, Methods in enzymology.

[96]  Phipps Arabie,et al.  Combinatorial Data Analysis: Optimization by Dynamic Programming , 1987 .

[97]  J. Ramsay,et al.  Analysis of pairwise preference data using integrated B-splines , 1981 .

[98]  Roberta L. Klatzky,et al.  Human navigation ability: Tests of the encoding-error model of path integration , 1999, Spatial Cogn. Comput..

[99]  Regina Y. Liu Moving blocks jackknife and bootstrap capture weak dependence , 1992 .

[100]  R. Shepard,et al.  Toward a universal law of generalization for psychological science. , 1987, Science.

[101]  J. Fox Bootstrapping Regression Models , 2002 .

[102]  James E. Corter,et al.  A graph-theoretic method for organizing overlapping clusters into trees, multiple trees, or extended trees , 1995 .

[103]  Phipps Arabie,et al.  Was euclid an unnecessarily sophisticated psychologist? , 1991 .

[104]  P. Buneman The Recovery of Trees from Measures of Dissimilarity , 1971 .

[105]  Joseph L. Zinnes,et al.  Theory and Methods of Scaling. , 1958 .

[106]  T. Micceri The unicorn, the normal curve, and other improbable creatures. , 1989 .

[107]  P. Arabie,et al.  Mapclus: A mathematical programming approach to fitting the adclus model , 1980 .

[108]  C. K. Liew,et al.  Inequality Constrained Least-Squares Estimation , 1976 .

[109]  P. Arabie,et al.  Indclus: An individual differences generalization of the adclus model and the mapclus algorithm , 1983 .

[110]  Yoshio Takane,et al.  Multidimensional successive categories scaling: A maximum likelihood method , 1981 .

[111]  W. Fischer,et al.  The metric of multidimensional psychological spaces as a function of the differential attention to subjective attributes , 1970 .

[112]  L. Hubert,et al.  Multidimensional scaling in the city-block metric: A combinatorial approach , 1992 .

[113]  Michael J. Brusco A Simulated Annealing Heuristic for Unidimensional and Multidimensional (City-Block) Scaling of Symmetric Proximity Matrices , 2001, J. Classif..

[114]  C. Mallows More comments on C p , 1995 .

[115]  Carla Savage,et al.  A Survey of Combinatorial Gray Codes , 1997, SIAM Rev..

[116]  H. Colonius,et al.  Tree structures for proximity data , 1981 .

[117]  Roger N. Shepard,et al.  Additive clustering: Representation of similarities as combinations of discrete overlapping properties. , 1979 .

[118]  R N Shepard,et al.  Multidimensional Scaling, Tree-Fitting, and Clustering , 1980, Science.

[119]  J. Cunningham,et al.  Free trees and bidirectional trees as representations of psychological distance , 1978 .

[120]  Nonmetric Method for Extended Indscal Model , 1980 .

[121]  F. Restle Psychology of judgment and choice , 1961 .

[122]  R. Dykstra,et al.  Minimizing linear inequality constrained mahalanobis distances , 1987 .

[123]  A. Tversky,et al.  Weighting common and distinctive features in perceptual and conceptual judgments , 1984, Cognitive Psychology.

[124]  Yoshio Takane,et al.  Multidimensional scaling models for reaction times and same-different judgments , 1983 .

[125]  Ronald Christensen,et al.  Linear and Log-Linear Models , 2000 .

[126]  W. Torgerson Multidimensional scaling: I. Theory and method , 1952 .

[127]  Andreas Buja,et al.  Visualization Methodology for Multidimensional Scaling , 2002, J. Classif..

[128]  K. C. Klauer Ordinal network representation: Representing proximities by graphs , 1989 .

[129]  Peter G. M. van der Heijden,et al.  A least squares algorithm for a mixture model for compositional data , 1999 .

[130]  G. A. Miller,et al.  An Analysis of Perceptual Confusions Among Some English Consonants , 1955 .

[131]  H Kishino,et al.  Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. , 2000, Molecular biology and evolution.

[132]  Safa R. Zaki,et al.  Prototype and exemplar accounts of category learning and attentional allocation: a reassessment. , 2003, Journal of experimental psychology. Learning, memory, and cognition.

[133]  W. R. Garner The Processing of Information and Structure , 1974 .

[134]  W. Heiser Fitting Graphs and Trees with Multidimensional Scaling Methods , 1998 .

[135]  K. Liang,et al.  Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests under Nonstandard Conditions , 1987 .

[136]  D. B. MacKay Probabilistic Multidimensional Scaling Using a City-Block Metric. , 2001, Journal of mathematical psychology.

[137]  J. Navarro-Pedreño Numerical Methods for Least Squares Problems , 1996 .

[138]  Angel R. Martinez,et al.  Computational Statistics Handbook with MATLAB , 2001 .

[139]  Hannes Eisler,et al.  Multidimensional similarity: an experimental and theoretical comparison of vector, distance, and set theoretical models: I. Models and internal consistency of data , 1977 .

[140]  J. Lackner,et al.  The Psychological Representation of Speech Sounds , 1975, The Quarterly journal of experimental psychology.

[141]  R. Nosofsky American Psychological Association, Inc. Choice, Similarity, and the Context Theory of Classification , 2022 .

[142]  A. Tversky Features of Similarity , 1977 .

[143]  M. Lee,et al.  Clustering Using the Contrast Model , 2001 .

[144]  Bernhard Ronacher,et al.  Pattern recognition in honeybees: Multidimensional scaling reveals a city-block metric , 1992, Vision Research.

[145]  G. Soete A least squares algorithm for fitting additive trees to proximity data , 1983 .

[146]  Karl Christoph Klauer,et al.  A mathematical programming approach to fitting general graphs , 1989 .

[147]  Kikumi K. Tatsuoka,et al.  Architecture of knowledge structures and cognitive diagnosis: A statistical pattern recognition and classification approach. , 1995 .

[148]  A Rzhetsky,et al.  Interior-branch and bootstrap tests of phylogenetic trees. , 1995, Molecular biology and evolution.

[149]  R. Tibshirani Regression Shrinkage and Selection via the Lasso , 1996 .

[150]  M. Lee On the Complexity of Additive Clustering Models. , 2001, Journal of mathematical psychology.

[151]  B. Mirkin Additive clustering and qualitative factor analysis methods for similarity matrices , 1989 .