Reconstructing multisets over commutative groupoids and affine functions over nonassociative semirings

A reconstruction problem is formulated for multisets over commutative groupoids. The cards of a multiset are obtained by replacing a pair of its elements by their sum. Necessary and sufficient conditions for the reconstructibility of multisets are determined. These results find an application in a different kind of reconstruction problem for functions of several arguments and identification minors: classes of linear or affine functions over nonassociative semirings are shown to be weakly reconstructible. Moreover, affine functions of sufficiently large arity over finite fields are reconstructible.Comment: 18 pages. Int. J. Algebra Comput. (2014

Input Reconstructibility for Linear Dynamics. Ordinary Differential Equations

The paper deals with the standard input-output observation scheme for a dynamic system governed by a linear ordinary differential equation. The initial problem is to reconstruct the actually working time-varying input, given a state observation result. Normally, the problem has no solution: observation is too poor to select the real input from the collection of "possible" ones. It is proposed to turn the problem as follows: what information of the real input is reconstructible precisely? The dual setting: what information of the real input is totally non-reconstructible? The question of aftereffect arises naturally: does accumulation of observation results lead to the informational jump -- from nonreconstructibility to complete reconstructibility -- in the past? Posing and answering these questions is the goal of the present study

Reconstruction of functions from minors

The central notion of this thesis is the minor relation on functions of several arguments. A function f: A^n→B is called a minor of another function g: A^m→B if f can be obtained from g by permutation of arguments, identification of arguments, and introduction of inessential arguments. We first provide some general background and context to this work by presenting a brief survey of basic facts and results concerning different aspects of the minor relation, placing some emphasis on the author’s contributions to the field. The notions of functions of several arguments and minors give immediately rise to the following reconstruction problem: Is a function f: A^n→B uniquely determined, up to permutation of arguments, by its identification minors, i.e., the minors obtained by identifying a pair of arguments? We review known results – both positive and negative – about the reconstructibility of functions from identification minors, and we outline the main ideas of the proofs, which often amount to formulating and solving reconstruction problems for other kinds of mathematical objects. We then turn our attention to functions determined by the order of first occurrence, and we are interested in the reconstructibility of such functions. One of the main results of this thesis states that the class of functions determined by the order of first occurrence is weakly reconstructible. Some reconstructible subclasses are identified; in particular, pseudo-Boolean functions determined by the order of first occurrence are reconstructible. As our main tool, we introduce the notion of minor of permutation. This is a quotient-like construction for permutations that parallels minors of functions and has some similarities to permutation patterns. We develop the theory of minors of permutations, focusing on Galois connections induced by the minor relation and on the interplay between permutation groups and minors of permutations. Our results will then find applications in the analysis of the reconstruction problem of functions determined by the order of first occurrence

Polytopes close to being simple

It is known that polytopes with at most two nonsimple vertices are reconstructible from their graphs, and that d-polytopes with at most d- 2 nonsimple vertices are reconstructible from their 2-skeletons. Here we close the gap between 2 and d- 2 , showing that certain polytopes with more than two nonsimple vertices are reconstructible from their graphs. In particular, we prove that reconstructibility from graphs also holds for d-polytopes with d+ k vertices and at most d- k+ 3 nonsimple vertices, provided

What May Visualization Processes Optimize?

In this paper, we present an abstract model of visualization and inference processes and describe an information-theoretic measure for optimizing such processes. In order to obtain such an abstraction, we first examined six classes of workflows in data analysis and visualization, and identified four levels of typical visualization components, namely disseminative, observational, analytical and model-developmental visualization. We noticed a common phenomenon at different levels of visualization, that is, the transformation of data spaces (referred to as alphabets) usually corresponds to the reduction of maximal entropy along a workflow. Based on this observation, we establish an information-theoretic measure of cost-benefit ratio that may be used as a cost function for optimizing a data visualization process. To demonstrate the validity of this measure, we examined a number of successful visualization processes in the literature, and showed that the information-theoretic measure can mathematically explain the advantages of such processes over possible alternatives.Comment: 10 page

Reconstructing binary images from discrete X-rays

We present a new algorithm for reconstructing binary images from their projections along a small number of directions. Our algorithm performs a sequence of related reconstructions, each using only two projections. The algorithm makes extensive use of network flow algorithms for solving the two-projection subproblems. Our experimental results demonstrate that the algorithm can compute reconstructions which resemble the original images very closely from a small number of projections, even in the presence of noise. Although the effectiveness of the algorithm is based on certain smoothness assumptions about the image, even tiny, non-smooth details are reconstructed exactly. The class of images for which the algorithm is most effective includes images of convex objects, but images of objects that contain holes or consist of multiple components can also be reconstructed with great accurac

Multi-level Decomposition of Probalistic Relations

Two methods of decomposition of probabilistic relations are presented in this paper. They consist of splitting relations (blocks) into pairs of smaller blocks related to each other by new variables generated in such a way so as to minimize a cost function which depends on the size and structure of the result. The decomposition is repeated iteratively until a stopping criterion is met. Topology and contents of the resulting structure develop dynamically in the decomposition process and reflect relationships hidden in the data

Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions

Prokaryotic organisms share genetic material across species boundaries by means of a process known as horizontal gene transfer (HGT). This process has great significance for understanding prokaryotic genome diversification and unraveling their complexities. Phylogeny-based detection of HGT is one of the most commonly used methods for this task, and is based on the fundamental fact that HGT may cause gene trees to disagree with one another, as well as with the species phylogeny. Using these methods, we can compare gene and species trees, and infer a set of HGT events to reconcile the differences among these trees. In this paper, we address three factors that confound the detection of the true HGT events, including the donors and recipients of horizontally transferred genes. First, we study experimentally the effects of error in the estimated gene trees (statistical error) on the accuracy of inferred HGT events. Our results indicate that statistical error leads to overestimation of the number of HGT events, and that HGT detection methods should be designed with unresolved gene trees in mind. Second, we demonstrate, both theoretically and empirically, that based on topological comparison alone, the number of HGT scenarios that reconcile a pair of species/gene trees may be exponential. This number may be reduced when branch lengths in both trees are estimated correctly. This set of results implies that in the absence of additional biological information, and/or a biological model of how HGT occurs, multiple HGT scenarios must be sought, and efficient strategies for how to enumerate such solutions must be developed. Third, we address the issue of lineage sorting, how it confounds HGT detection, and how to incorporate it with HGT into a single stochastic framework that distinguishes between the two events by extending population genetics theories. This result is very important, particularly when analyzing closely related organisms, where coalescent effects may not be ignored when reconciling gene trees. In addition to these three confounding factors, we consider the problem of enumerating all valid coalescent scenarios that constitute plausible species/gene tree reconciliations, and develop a polynomial-time dynamic programming algorithm for solving it. This result bears great significance on reducing the search space for heuristics that seek reconciliation scenarios. Finally, we show, empirically, that the locality of incongruence between a pair of trees has an impact on the numbers of HGT and coalescent reconciliation scenarios