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ShapeRotator
(2018)
The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate into modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures. While there are existing methods for analyzing shape variation in articulated structures in two-dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research. Here, we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space, so it can be applied to any morphometric problem that also uses 3D coordinates (e.g., spherical harmonics). We demonstrate the method by applying it to a landmark-based dataset for analyzing shape variation using geometric morphometrics. We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.
Particle filters contain the promise of fully nonlinear data assimilation. They have been applied in numerous science areas, including the geosciences, but their application to high-dimensional geoscience systems has been limited due to their inefficiency in high-dimensional systems in standard settings. However, huge progress has been made, and this limitation is disappearing fast due to recent developments in proposal densities, the use of ideas from (optimal) transportation, the use of localization and intelligent adaptive resampling strategies. Furthermore, powerful hybrids between particle filters and ensemble Kalman filters and variational methods have been developed. We present a state-of-the-art discussion of present efforts of developing particle filters for high-dimensional nonlinear geoscience state-estimation problems, with an emphasis on atmospheric and oceanic applications, including many new ideas, derivations and unifications, highlighting hidden connections, including pseudo-code, and generating a valuable tool and guide for the community. Initial experiments show that particle filters can be competitive with present-day methods for numerical weather prediction, suggesting that they will become mainstream soon.
Nonlinear data assimilation
(2015)
This book contains two review articles on nonlinear data assimilation that deal with closely related topics but were written and can be read independently. Both contributions focus on so-called particle filters.
The first contribution by Jan van Leeuwen focuses on the potential of proposal densities. It discusses the issues with present-day particle filters and explorers new ideas for proposal densities to solve them, converging to particle filters that work well in systems of any dimension, closing the contribution with a high-dimensional example. The second contribution by Cheng and Reich discusses a unified framework for ensemble-transform particle filters. This allows one to bridge successful ensemble Kalman filters with fully nonlinear particle filters, and allows a proper introduction of localization in particle filters, which has been lacking up to now.
The interdisciplinary workshop STOCHASTIC PROCESSES WITH APPLICATIONS IN THE NATURAL SCIENCES was held in Bogotá, at Universidad de los Andes from December 5 to December 9, 2016. It brought together researchers from Colombia, Germany, France, Italy, Ukraine, who communicated recent progress in the mathematical research related to stochastic processes with application in biophysics.
The present volume collects three of the four courses held at this meeting by Angelo Valleriani, Sylvie Rœlly and Alexei Kulik.
A particular aim of this collection is to inspire young scientists in setting up research goals within the wide scope of fields represented in this volume.
Angelo Valleriani, PhD in high energy physics, is group leader of the team "Stochastic processes in complex and biological systems" from the Max-Planck-Institute of Colloids and Interfaces, Potsdam.
Sylvie Rœlly, Docteur en Mathématiques, is the head of the chair of Probability at the University of Potsdam.
Alexei Kulik, Doctor of Sciences, is a Leading researcher at the Institute of Mathematics of Ukrainian National Academy of Sciences.
Tasking machine learning to predict segments of a time series requires estimating the parameters of a ML model with input/output pairs from the time series. We borrow two techniques used in statistical data assimilation in order to accomplish this task: time-delay embedding to prepare our input data and precision annealing as a training method. The precision annealing approach identifies the global minimum of the action (-log[P]). In this way, we are able to identify the number of training pairs required to produce good generalizations (predictions) for the time series. We proceed from a scalar time series s(tn);tn=t0+n Delta t and, using methods of nonlinear time series analysis, show how to produce a DE>1-dimensional time-delay embedding space in which the time series has no false neighbors as does the observed s(tn) time series. In that DE-dimensional space, we explore the use of feedforward multilayer perceptrons as network models operating on DE-dimensional input and producing DE-dimensional outputs.
This thesis aims at presenting in an organized fashion the required basics to understand the Glauber dynamics as a way of simulating configurations according to the Gibbs distribution of the Curie-Weiss Potts model. Therefore, essential aspects of discrete-time Markov chains on a finite state space are examined, especially their convergence behavior and related mixing times. Furthermore, special emphasis is placed on a consistent and comprehensive presentation of the Curie-Weiss Potts model and its analysis. Finally, the Glauber dynamics is studied in general and applied afterwards in an exemplary way to the Curie-Weiss model as well as the Curie-Weiss Potts model. The associated considerations are supplemented with two computer simulations aiming to show the cutoff phenomenon and the temperature dependence of the convergence behavior.
The overall program "arborescent numbers" is to similarly perform the constructions from the natural numbers (N) to the positive fractional numbers (Q+) to positive real numbers (R+) beginning with (specific) binary trees instead of natural numbers. N can be regarded as the associative binary trees. The binary trees B and the left-commutative binary trees P allow the hassle-free definition of arbitrary high arithmetic operations (hyper ... hyperpowers). To construct the division trees the algebraic structure "coppice" is introduced which is a group with an addition over which the multiplication is right-distributive. Q+ is the initial associative coppice. The present work accomplishes one step in the program "arborescent numbers". That is the construction of the arborescent equivalent(s) of the positive fractional numbers. These equivalents are the "division binary trees" and the "fractional trees". A representation with decidable word problem for each of them is given. The set of functions f:R1->R1 generated from identity by taking powers is isomorphic to P and can be embedded into a coppice by taking inverses.
Students of computer science studies enter university education with very different competencies, experience and knowledge. 145 datasets collected of freshmen computer science students by learning management systems in relation to exam outcomes and learning dispositions data (e. g. student dispositions, previous experiences and attitudes measured through self-reported surveys) has been exploited to identify indicators as predictors of academic success and hence make effective interventions to deal with an extremely heterogeneous group of students.