Articles by Year:

Why "Redefining Statistical Significance" Will Not Improve Reproducibility and Might Make the Replication Crisis Worse

Harry Crane (2017).

Abstract

A recent proposal to "redefine statistical significance" (Benjamin, et al. Nature Human Behaviour, 2017) claims that false positive rates "would immediately improve" by factors greater than two and replication rates would double simply by changing the conventional cutoff for 'statistical significance' from P<0.05 to P<0.005. I analyze the veracity of these claims, focusing especially on how Benjamin, et al neglect the effects of P-hacking in assessing the impact of their proposal. My analysis shows that once P-hacking is accounted for the perceived benefits of the lower threshold all but disappear, prompting two main conclusions: (i) The claimed improvements to false positive rate and replication rate in Benjamin, et al (2017) are exaggerated and misleading. (ii) There are plausible scenarios under which the lower cutoff will make the replication crisis worse.

Commentary by Andrew Gelman.

Response by one of the authors (E.J. Wagenmackers) Bayesian Spectacles Blog.

More discussion by Tim van der Zee.

Relational exchangeability

Harry Crane and Walter Dempsey (2016).

Abstract

We define a relationally exchangeable structure as a random combinatorial structure whose law is invariant with respect to relabeling its relations, instead of its elements. Examples of relationally exchangeable structures include edge exchangeable random graphs and hypergraphs and also exchangeable random set partitions (when viewed from a certain perspective). Relationally exchangeable models arise most naturally in certain network science applications, particularly network datasets generated processes of interactions. We prove a representation theorem for the class of relationally exchangeable structures and discuss some consequences and open problems. The representation refines Kingman's paintbox correspondence for exchangeable random partitions.

A framework for statistical network modeling

Harry Crane and Walter Dempsey (2016).

Abstract

Basic principles of statistical inference are commonly violated in network data analysis. Under the current approach, it is often impossible to identify a model that accommodates known empirical behaviors, possesses crucial inferential properties, and accurately models the data generating process. In the absence of one or more of these properties, sensible inference from network data cannot be assured. Our proposed framework decomposes every network model into a (relatively) exchangeable data generating process and a sampling mechanism that relates observed data to the population network. This framework, which encompasses all models in current use as well as many new models, such as edge exchangeable models, that lie outside the existing paradigm, offers a sound context within which to develop theory and methods for network analysis.

The structure of combinatorial Markov processes

Harry Crane and Henry Towsner (2016).

Abstract

Every exchangeable Feller process taking values in a suitably nice combinatorial state space can be constructed by a system of iterated random Lipschitz functions. In discrete time, the construction proceeds by iterated application of independent, identically distributed functions, while in continuous time the random functions occur as the atoms of a time homogeneous Poisson point process. We further show that every exchangeable Feller process projects to a Feller process in an appropriate limit space, akin to the projection of partition-valued processes into the ranked-simplex and graph-valued processes into the space of graph limits. Together, our main theorems establish common structural features shared by all exchangeable combinatorial Feller processes, regardless of the dynamics or resident state space, thereby generalizing behaviors previously observed for exchangeable coalescent and fragmentation processes as well as other combinatorial stochastic processes. If, in addition, an exchangeable Feller process evolves on a state space satisfying the n-disjoint amalgamation property for all n\geq1, then its jump measure can be decomposed explicitly in the sense of Levy-Ito-Khintchine.

Edge exchangeable models for network data

Harry Crane and Walter Dempsey. (2017). Journal of the American Statistical Association, in press.

Abstract

Exchangeable models for countable vertex-labeled graphs can- not replicate the large sample behaviors of sparsity and power law degree distribution observed in many network datasets. Out of this mathematical impossibility emerges the question of how network data can be modeled in a way that reflects known empirical behaviors and respects basic statistical principles. We address this question by observing that edges, not vertices, act as the statistical units in networks constructed from interaction data, making a theory of edge-labeled networks more natural for many applications. In this context we introduce the concept of edge exchangeability, which unlike its vertex exchangeable counterpart admits models for networks with sparse and/or power law structure. Our characterization of edge exchangeable networks gives rise to a class of nonparametric models, akin to graphon models in the vertex exchangeable setting. Within this class, we identify a tractable family of distributions with a clear interpretation and suitable theoretical properties, whose significance in estimation, prediction, and testing we demonstrate.

The probability of avoiding consecutive patterns in the Mallows distribution

Harry Crane, Stephen DeSalvo and Sergi Elizalde. (2017). Random Structures & Algorithms, accepted.

Abstract

We use various combinatorial and probabilistic techniques to study growth rates for the probability that a random permutation from the Mallows distribution avoids consecutive patterns. The Mallows distribution behaves like a q-analogue of the uniform distribution by weighting each permutation \pi by q^{inv(\pi)} , where inv(\pi) is the number of inversions in $\pi$ and q is a positive, real-valued parameter. We prove that the growth rate exists for all patterns and all q>0, and we generalize Goulden and Jackson's cluster method to keep track of the number of inversions in permutations avoiding a given consecutive pattern. Using singularity analysis, we approximate the growth rates for length-3 patterns, monotone patterns, and non-overlapping patterns starting with 1, and we compare growth rates between different patterns. We also use Stein's method to show that, under certain assumptions on q, the length of \sigma, and inv(\sigma), the number of occurrences of a given pattern \sigma is well approximated by the normal distribution.

Relative exchangeability with equivalence relations

Harry Crane and Henry Towsner. (2016). Archive of Mathematical Logic, in press.

Abstract

We describe an Aldous-Hoover-type characterization of random relational structures that are exchangeable relative to a fixed structure which may have various equivalence relations. Our main theorem gives the common generalization of the results on relative exchangeability due to Ackerman (2015) and Crane and Towsner (2015) and hierarchical exchangeability results due to Austin and Panchenko (2014).

Relatively exchangeable structures

Harry Crane and Henry Towsner. (2016). Journal of Symbolic Logic, in press.

Abstract

We study random relational structures that are relatively exchangeable---that is, whose distributions are invariant under the automorphisms of a reference structure M. When M has trivial definable closure, every relatively exchangeable structure satisfies a general Aldous-Hoover-type representation. If M satisfies the stronger properties of ultrahomogeneity and n-disjoint amalgamation property (n-DAP) for every n\geq1, then relatively exchangeable structures have a more precise description whereby each component depends locally on M.

Combinatorial Levy processes

Harry Crane. (2017). Annals of Applied Probability, in press.

Abstract

Combinatorial Levy processes evolve on general state spaces of countable combinatorial structures. In this setting, the usual Levy process properties of stationary, independent increments are defined in an unconventional way in terms of the symmetric difference operation on sets. In discrete time, the description of combinatorial Levy processes gives rise to the notion of combinatorial random walks. These processes behave differently than random walks and Levy processes on other state spaces. Standard examples include processes on sets, graphs, and n-ary relations, but the framework permits far more general possibilities. The main theorems characterize both finite and infinite state space combinatorial Levy processes by a unique sigma-finite measure. Under the additional assumption of exchangeability, we obtain a more explicit characterization by which every exchangeable combinatorial Levy process corresponds to a Poisson point process on the same state space. Associated behavior of the projection into a space of limiting objects reflects certain structural features of the covering process.

Pattern Avoidance for Random Permutations

Harry Crane and Stephen DeSalvo. (2017). Discrete Mathematics and Theoretical Computer Science (Special Issue on Pattern Avoidance), in press.

Abstract

Using techniques from Poisson approximation, we prove explicit error bounds on the number of permutations that avoid any pattern. Most generally, we bound the total variation distance between the joint distribution of pattern occurrences and a corresponding joint distribution of independent Bernoulli random variables, which as a corollary yields a Poisson approximation for the distribution of the number of occurrences of any pattern. We also investigate occurrences of consecutive patterns in random Mallows permutations, of which uniform random permutations are a special case. These bounds allow us to estimate the probability that a pattern occurs any number of times and, in particular, the probability that a random permutation avoids a given pattern.

A hidden Markov model for latent temporal clustering with application to ideological alignment in the U.S. Supreme Court

Harry Crane. (2017). Computational Statistics and Data Analysis, in press.

Abstract

An alternative approach to modeling latent time-varying sequences of clusters demonstrates certain benefits over existing methods for analyzing Supreme Court voting data. The family of Markov chains presented satisfies important statistical properties, including exchangeability, consistency under subsampling, and reversibility with respect to a tractable class of two-parameter partition models. These properties make the model robust to missing data, choice of labels, and changes in the sample over time. When combined with an appropriate model for the response, exchangeability and consistency give rise to the stronger model properties of label equivariance and non-interference, respectively, which together make inferences readily interpretable. These and other aspects of the approach are illustrated with a detailed analysis of voting data in the Supreme Court over the period 1946--2012. The results of this analysis agree with what is known about the Court's behavior during this period of time. In some cases, this approach detects aspects of the Court that other quantitative analyses, such as Martin--Quinn scores, do not.

Exchangeable graph-valued Feller processes

Harry Crane. (2017). Probability Theory and Related Fields, in press.

Abstract

The transition law of every exchangeable Feller process on the space of countable graphs is determined by a sigma-finite measure on the space of {0,1}x{0,1}-valued arrays. In discrete-time, this characterization amounts to a construction from an independent, identically distributed sequence of exchangeable random functions. In continuous-time, the behavior is enriched by a Levy--Ito-type decomposition of the jump measure into mutually singular components that govern global, vertex-level, and edge-level dynamics. Furthermore, every such process almost surely projects to a Feller process in the space of graph limits.

Generalized Markov branching trees

Harry Crane. (2017). Advances in Applied Probability, in press.

Abstract

Motivated by the gene tree/species tree problem from statistical phylogenetics, we extend the class of Markov branching trees to a parametric family of distributions on fragmentation trees that satisfies a generalized Markov branching property. The main theorems establish important statistical properties of this model, specifically necessary and sufficient conditions under which a family of trees can be constructed consistently as sample size grows. We also consider the question of attaching random edge lengths to these trees.

The ubiquitous Ewens sampling formula (with discussion and a rejoinder by the author)

Harry Crane. (2016). Statistical Science, 31(1):1-39.

Abstract

Ewens's sampling formula exemplifies the harmony of mathematical theory, statistical application, and scientific discovery. The formula not only contributes to the foundations of evolutionary molecular genetics, the neutral theory of biodiversity, Bayesian nonparametrics, combinatorial stochastic processes, and inductive inference but also emerges from fundamental concepts in probability theory, algebra, and number theory. With an emphasis on its far-reaching influence throughout statistics and probability, we highlight these and many other consequences of Ewens's seminal discovery.

Dynamic random networks and their graph limits

Harry Crane. (2016). Annals of Applied Probability 26(2):691-721.

Abstract

We study a broad class of stochastic process models for dynamic networks that satisfy the minimal regularity conditions of (i) exchangeability and (ii) cadlag sample paths. Our main theorems characterize these processes through their induced behavior in the space of graph limits. Under the assumption of time-homogeneous Markovian dependence, we classify the discontinuities of these processes into three types, prove bounded variation of the sample paths in graph limit space and express the process as a mixture of time-inhomogeneous, exchangeable Markov processes with cadlag sample paths.

Exchangeable Markov processes on [k]^N with cadlag sample paths

Harry Crane and Stephen P. Lalley. (2016). Journal of Theoretical Probability, 29:206-230

Abstract

Any exchangeable, time-homogeneous Markov processes on [k]^{\mathbb {N}} with cadlag sample paths projects to a Markov process on the simplex whose sample paths are cadlag and of locally bounded variation. Furthermore, any such process has a de Finetti-type description as a mixture of independent, identically distributed copies of time-inhomogeneous Markov processes on [k] . In the Feller case, these time-inhomogeneous Markov processes have a relatively simple structure; however, in the non-Feller case, a greater variety of behaviors is possible since the transition law of the underlying Markov process on [k]^{\mathbb N} can depend in a nontrivial way on its exchangeable sigma-algebra.

Clustering from categorical data sequences

Harry Crane. (2015). Journal of the American Statistical Association, 110(510):810-823.

Abstract

The three parameter cluster model is a combinatorial stochastic process that generates categorical response sequences by randomly perturbing a fixed clustering param-eter. This clear relationship between the observed data and the underlying clustering is particularly attractive in cluster analysis, in which supervised learning is a common goal and missing data is a familiar issue. The model is well-equipped for this task, as it can handle missing data, perform out-of-sample inference, and accommodate both independent and dependent data sequences. Moreover, its clustering parameter lies in the unrestricted space of partitions, so that the number of clusters need not be specified beforehand. We establish these and other theoretical properties and also demonstrate the model on data sets from epidemiology, genetics, political science, and legal studies.

Generalized Ewens-Pitman model for Bayesian clustering

Harry Crane. (2015). Biometrika, 102(1), 231-238.

Abstract

We propose a Bayesian method for clustering from discrete data structures that commonly arise in genetics and other applications. This method is equivariant with respect to relabeling units; unsampled units do not interfere with sampled data; and missing data do not hinder inference. Cluster inference using the posterior mode performs well on simulated and real data sets, and the posterior predictive distribution enables supervised learning based on a partial clustering of the sample.

Time-varying network models

Harry Crane. (2015). Bernoulli, 21(3):1670-1696.

Abstract

We introduce the exchangeable rewiring process for modeling time-varying networks. The process fulfills fundamental mathematical and statistical properties and can be easily constructed from the novel operation of random rewiring. We derive basic properties of the model, including consistency under subsampling, exchangeability, and the Feller property. A reversible sub-family related to the Erdos-Renyi model arises as a special case.

Lipschitz partition processes

Harry Crane. (2015). Bernoulli, 21(3):1386-1411.

Abstract

We introduce a family of Markov processes on set partitions with a bounded number of blocks, called Lipschitz partition processes. We construct these processes explicitly by a Poisson point process on the space of Lipschitz continuous maps on partitions. By this construction, the Markovian consistency property is readily satisfied; that is, the finite restrictions of any Lipschitz partition process comprise a compatible collection of finite state space Markov chains. We further characterize the class of exchangeable Lipschitz partition processes by a novel set-valued matrix operation.

Poisson superposition processes

Harry Crane and Peter McCullagh. (2015). Journal of Applied Probability, 52(4):1013-1027.

Abstract

Superposition is a mapping on point configurations that sends the n-tuple (x1, . . . , xn) ∈ X n into the n-point configuration {x1, . . . , xn} ⊂ X , counted with multiplicity. It is an additive set operation such the superposition of a k-point configuration in X n is a kn-point configuration in X . A Poisson superposition process is the superposition in X of a Poisson process in the space of finite-length X -valued sequences. From properties of Poisson processes as well as some algebraic properties of formal power series, we obtain an explicit expression for the Janossy measure of Poisson superposition processes, and we study their law under domain restriction. Examples of well-known Poisson superposition processes include compound Poisson, negative binomial, and permanental (boson) processes.

Reversible Markov structures on divisible set partitions

Harry Crane and Peter McCullagh. (2015). Journal of Applied Probability, 52(3):622-635.

Abstract

We study k-divisible partition structures, which are families of random set partitions whose block sizes are divisible by an integer k = 1, 2, . . .. In this setting, exchangeability corresponds to the usual invariance under relabeling by arbitrary permutations; however, for k > 1, the ordinary deletion maps on partitions no longer preserve divisibility, and so a random deletion procedure is needed to obtain a partition structure. We describe explicit Chinese restaurant-type seating rules for generating families of exchangeable k-divisible partitions that are consistent under random deletion. We further introduce the notion of Markovian partition structures, which are ensembles of exchangeable Markov chains on k-divisible partitions that are consistent under a random process of Markovian deletion. The Markov chains we study are reversible and refine the class of Markov chains introduced in J. Appl. Probab. 48(3):778–791.

Left-right arrangements, set partitions, and pattern avoidance

Harry Crane. (2015). Australasian Journal of Combinatorics, 61(1):57-72.

Abstract

We show structural properties of the system of ordered partitions of [n] := {1, . . . , n} all of whose left-to-right minima occur in odd locations, called left-to-right arrange-ments. Our main objectives are (i) to show that the set of all finite left-to-right arrangements is a projective system under a natural choice of restriction operation, (ii) to establish a non-trivial embedding of set partitions of [n] into the set of left-to-right arrangements of [n], and (iii) to illustrate how this embedding can be used to easily enumerate certain sets of pattern-avoiding set partitions.

The cut-and-paste process

Harry Crane. (2014). Annals of Probability, 42(5):1952-1979.

Abstract

We characterize the class of exchangeable Feller processes evolving on partitions with boundedly many blocks. In continuous-time, the jump measure decomposes into two parts: a $\sigma$-finite measure on stochastic matrices and a collection of nonnegative real constants. This decomposition prompts a Levy-Ito representation. In discrete-time, the evolution is described more simply by a product of independent, identically distributed random matrices.

Permanental partition models and Markovian Gibbs structures

Harry Crane. (2013). Journal of Statistical Physics, 153:698-726.

Abstract

We study both time-invariant and time-varying Gibbs distributions for configurations of particles into disjoint clusters. Specifically, we introduce and give some fundamental properties for a class of partition models, called permanental partition models, whose distributions are expressed in terms of the α-permanent of a similarity matrix parameter. We show that, in the time-invariant case, the permanental partition model is a refinement of the celebrated Pitman–Ewens distribution; whereas, in the time-varying case, the permanental model refines the Ewens cut-and-paste Markov chains (J. Appl. Probab. 43(3):778–791, 2011). By a special property of the α-permanent, the partition function can be computed exactly, allowing us to make several precise statements about this general model, including a characterization of exchangeable and consistent permanental models.

Some algebraic identities for the alpha-permanent

Harry Crane (2013). Linear Algebra and Its Applications, 439(11):3445-3459.

Abstract

We show that the permanent of a matrix is a linear combination of determinants of block diagonal matrices which are simple functions of the original matrix. To prove this, we first show a more general identity involving \alpha-permanents: for arbitrary complex numbers \alpha and \beta, we show that the \alpha-permanent of any matrix can be expressed as a linear combination of \beta-permanents of related matrices. Some other identities for the \alpha-permanent of sums and products of matrices are shown, as well as a relationship between the \alpha-permanent and general immanants. We conclude with a discussion of the computational complexity of the \alpha-permanent and provide some numerical illustrations.

Consistent Markov branching trees with discrete edge lengths

Harry Crane. (2013). Electronic Communications in Probability, 18(paper no. 73):1-14.

Abstract

We study consistent collections of random fragmentation trees with random integer-valued edge lengths. We prove several equivalent necessary and sufficient conditions under which Geometrically distributed edge lengths can be consistently assigned to a Markov branching tree. Among these conditions is a characterization by a unique probability measure, which plays a role similar to the dislocation measure for homogeneous fragmentation processes. We discuss this and other connections to previous work on Markov branching trees and homogeneous fragmentation processes.

Convergence rates of Markov chains on spaces of partitions

Harry Crane and Stephen P. Lalley. (2013). Electronic Journal of Probability, 18(paper no. 61):1-22.

Abstract

We study the convergence rate to stationarity for a class of exchangeable partition-valued Markov chains called cut-and-paste chains. The law governing the transitions of a cut-and-paste chain are determined by products of i.i.d. stochastic matrices, which describe the chain induced on the simplex by taking asymptotic frequencies. Using this representation, we establish upper bounds for the mixing times of ergodic cut-and-paste chains, and under certain conditions on the distribution of the governing random matrices we show that the "cutoff phenomenon" holds.

A consistent Markov partition process generated from the paintbox process

Harry Crane (2011). Journal of Applied Probability, 23(3):778-791.

Abstract

We study a family of Markov processes on \mathcal{P}^{(k)}, the space of partitions of the natural numbers with at most k blocks. The process can be constructed from a Poisson point process on $\mathbb{R}^+\times\prod_{i=1}^k\mathcal{P}^{(k)}$ with intensity $dt\otimes\varrho_{\nu}^{(k)}$, where $\varrho_{\nu}$ is the distribution of the paintbox based on the probability measure \nu on the set of ranked-mass partitions of 1 and $\varrho_{\nu}^{(k)}$ is the product measure on $\prod_{i=1}^k\mathcal{P}^{(k)}$. We show that these processes possess a unique stationary measure, and we discuss a particular set of reversible processes for which transition probabilities can be written down explicitly.