The Flow matrix is a novel method to describe and extrapolate transitions among categories. The Flow matrix extrapolates a constant transition size per unit of time on a time continuum with a maximum of one incident per observation during the extrapolation. The Flow matrix extrapolates linearly until the persistence of a category shrinks to zero. The Flow matrix has concepts and mathematics that are more straightforward than the Markov matrix. However, many scientists apply the Markov matrix by default because popular software packages offer no alternative to the Markov matrix, despite the conceptual and mathematical challenges that the Markov matrix poses. The Markov matrix extrapolates a constant transition proportion per time interval during wholenumber multiples of the duration of the calibration time interval. The Markov extrapolation allows at most one incident per observation during each time interval but allows repeated incidents per observation through sequential time intervals. Many Markov extrapolations approach a steady state asymptotically through time as each category size approaches a constant. We use case studies concerning land change to illustrate the characteristics of the Flow and Markov matrices. The Flow and Markov extrapolations both deviate from the reference data during a validation time interval, implying there is no reason to prefer one matrix to the other in terms of correspondence with the processes that we analyzed. The two matrices differ substantially in terms of their underlying concepts and mathematical behaviors. Scientists should consider the ease of use and interpretation for each matrix when extrapolating transitions among categories.
more » « less Award ID(s):
 1637630
 NSFPAR ID:
 10485017
 Publisher / Repository:
 MDPI
 Date Published:
 Journal Name:
 Land
 Volume:
 12
 Issue:
 7
 ISSN:
 2073445X
 Page Range / eLocation ID:
 1471
 Format(s):
 Medium: X
 Sponsoring Org:
 National Science Foundation
More Like this

Analytic perturbation theory for matrices and operators is an immensely useful mathematical technique. Most elementary introductions to this method have their background in the physics literature, and quantum mechanics in particular. In this note, we give an introduction to this method that is independent of any physics notions, and relies purely on concepts from linear algebra. An additional feature of this presentation is that matrix notation and methods are used throughout. In particular, we formulate the equations for each term of the analytic expansions of eigenvalues and eigenvectors as {\em matrix equations}, namely Sylvester equations in particular. Solvability conditions and explicit expressions for solutions of such matrix equations are given, and expressions for each term in the analytic expansions are given in terms of those solutions. This unified treatment simplifies somewhat the complex notation that is commonly seen in the literature, and in particular, provides relatively compact expressions for the nonHermitian and degenerate cases, as well as for higher order terms.more » « less

null (Ed.)Conventional methods to analyze a transition matrix do not offer indepth signals concerning land changes. The land change community needs an effective approach to visualize both the size and intensity of land transitions while considering possible map errors. We propose a framework that integrates error analysis, intensity analysis, and difference components, and then uses the framework to analyze land change in Nanchang, the capital city of Jiangxi province, China. We used remotely sensed data for six categories at four time points: 1989, 2000, 2008, and 2016. We had a confusion matrix for only 2016, which estimated that the map of 2016 had a 12% error, while the temporal difference during 2008–2016 was 22% of the spatial extent. Our tools revealed suspected errors at other years by analyzing the patterns of temporal difference. For example, the largest component of temporal difference was exchange, which could indicate map errors. Our framework identified categories that gained during one time interval then lost during the subsequent time interval, which raised the suspicion of map error. This proposed framework facilitated visualization of the size and intensity of land transitions while illustrating possible map errors that the profession routinely ignores.more » « less

Stochastic matrices are commonly used to analyze Markov chains, but revealing them can leak sensitive information. Therefore, in this paper we introduce a technique to privatize stochastic matrices in a way that (i) conceals the probabilities they contain, and (ii) still allows for accurate analyses of Markov chains. Specifically, we use differential privacy, which is a statistical framework for protecting sensitive data. To implement it, we introduce the Matrix Dirichlet Mechanism, which is a probabilistic mapping that perturbs a stochastic matrix to provide privacy. We prove that this mechanism provides differential privacy, and we quantify the error induced in private stochastic matrices as a function of the strength of privacy being provided. We then bound the distance between the stationary distribution of the underlying, sensitive stochastic matrix and the stationary distribution of its privatized form. Numerical results show that, under typical conditions, privacy introduces error as low as 5.05% in the stationary distribution of a stochastic matrix.more » « less

Abstract Cell shape is linked to cell function. The significance of cell morphodynamics, namely the temporal fluctuation of cell shape, is much less understood. Here we study the morphodynamics of MDAMB231 cells in type I collagen extracellular matrix (ECM). We systematically vary ECM physical properties by tuning collagen concentrations, alignment, and gelation temperatures. We find that morphodynamics of 3D migrating cells are externally controlled by ECM mechanics and internally modulated by Rho/ROCKsignaling. We employ machine learning to classify cell shape into four different morphological phenotypes, each corresponding to a distinct migration mode. As a result, we map cell morphodynamics at mesoscale into the temporal evolution of morphological phenotypes. We characterize the mesoscale dynamics including occurrence probability, dwell time and transition matrix at varying ECM conditions, which demonstrate the complex phenotype landscape and optimal pathways for phenotype transitions. In light of the mesoscale dynamics, we show that 3D cancer cell motility is a hidden Markov process whereby the step size distributions of cell migration are coupled with simultaneous cell morphodynamics. Morphological phenotype transitions also facilitate cancer cells to navigate nonuniform ECM such as traversing the interface between matrices of two distinct microstructures. In conclusion, we demonstrate that 3D migrating cancer cells exhibit rich morphodynamics that is controlled by ECM mechanics, Rho/ROCKsignaling, and regulate cell motility. Our results pave the way to the functional understanding and mechanical programming of cell morphodynamics as a route to predict and control 3D cell motility.

The continuoustime Markov chain (CTMC) is the mathematical workhorse of evolutionary biology. Learning CTMC model parameters using modern, gradientbased methods requires the derivative of the matrix exponential evaluated at the CTMC’s infinitesimal generator (rate) matrix. Motivated by the derivative’s extreme computational complexity as a function of state space cardinality, recent work demonstrates the surprising effectiveness of a naive, firstorder approximation for a host of problems in computational biology. In response to this empirical success, we obtain rigorous deterministic and probabilistic bounds for the error accrued by the naive approximation and establish a “blessing of dimensionality” result that is universal for a large class of rate matrices with random entries. Finally, we apply the firstorder approximation within surrogatetrajectory Hamiltonian Monte Carlo for the analysis of the early spread of Severe acute respiratory syndrome coronavirus 2 (SARSCoV2) across 44 geographic regions that comprise a state space of unprecedented dimensionality for unstructured (flexible) CTMC models within evolutionary biology.