4,175 research outputs found

    Inference in particle tracking experiments by passing messages between images

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    Methods to extract information from the tracking of mobile objects/particles have broad interest in biological and physical sciences. Techniques based on simple criteria of proximity in time-consecutive snapshots are useful to identify the trajectories of the particles. However, they become problematic as the motility and/or the density of the particles increases due to uncertainties on the trajectories that particles followed during the images' acquisition time. Here, we report an efficient method for learning parameters of the dynamics of the particles from their positions in time-consecutive images. Our algorithm belongs to the class of message-passing algorithms, known in computer science, information theory and statistical physics as Belief Propagation (BP). The algorithm is distributed, thus allowing parallel implementation suitable for computations on multiple machines without significant inter-machine overhead. We test our method on the model example of particle tracking in turbulent flows, which is particularly challenging due to the strong transport that those flows produce. Our numerical experiments show that the BP algorithm compares in quality with exact Markov Chain Monte-Carlo algorithms, yet BP is far superior in speed. We also suggest and analyze a random-distance model that provides theoretical justification for BP accuracy. Methods developed here systematically formulate the problem of particle tracking and provide fast and reliable tools for its extensive range of applications.Comment: 18 pages, 9 figure

    Attacking Shortest Paths by Cutting Edges

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    Identifying shortest paths between nodes in a network is a common graph analysis problem that is important for many applications involving routing of resources. An adversary that can manipulate the graph structure could alter traffic patterns to gain some benefit (e.g., make more money by directing traffic to a toll road). This paper presents the Force Path Cut problem, in which an adversary removes edges from a graph to make a particular path the shortest between its terminal nodes. We prove that this problem is APX-hard, but introduce PATHATTACK, a polynomial-time approximation algorithm that guarantees a solution within a logarithmic factor of the optimal value. In addition, we introduce the Force Edge Cut and Force Node Cut problems, in which the adversary targets a particular edge or node, respectively, rather than an entire path. We derive a nonconvex optimization formulation for these problems, and derive a heuristic algorithm that uses PATHATTACK as a subroutine. We demonstrate all of these algorithms on a diverse set of real and synthetic networks, illustrating the network types that benefit most from the proposed algorithms.Comment: 37 pages, 11 figures; Extended version of arXiv:2104.0376

    Penalized Likelihood Methods for Estimation of Sparse High Dimensional Directed Acyclic Graphs

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    Directed acyclic graphs (DAGs) are commonly used to represent causal relationships among random variables in graphical models. Applications of these models arise in the study of physical, as well as biological systems, where directed edges between nodes represent the influence of components of the system on each other. The general problem of estimating DAGs from observed data is computationally NP-hard, Moreover two directed graphs may be observationally equivalent. When the nodes exhibit a natural ordering, the problem of estimating directed graphs reduces to the problem of estimating the structure of the network. In this paper, we propose a penalized likelihood approach that directly estimates the adjacency matrix of DAGs. Both lasso and adaptive lasso penalties are considered and an efficient algorithm is proposed for estimation of high dimensional DAGs. We study variable selection consistency of the two penalties when the number of variables grows to infinity with the sample size. We show that although lasso can only consistently estimate the true network under stringent assumptions, adaptive lasso achieves this task under mild regularity conditions. The performance of the proposed methods is compared to alternative methods in simulated, as well as real, data examples.Comment: 19 pages, 8 figure

    The Inverse 1-Median Problem on Tree Networks with Variable Real Edge Lengths

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    Location problems exist in the real world and they mainly deal with finding optimal locations for facilities in a network, such as net servers, hospitals, and shopping centers. The inverse location problem is also often met in practice and has been intensively investigated in the literature. As a typical inverse location problem, the inverse 1-median problem on tree networks with variable real edge lengths is discussed in this paper, which is to modify the edge lengths at minimum total cost such that a given vertex becomes a 1-median of the tree network with respect to the new edge lengths. First, this problem is shown to be solvable in linear time with variable nonnegative edge lengths. For the case when negative edge lengths are allowable, the NP-hardness is proved under Hamming distance, and strongly polynomial time algorithms are presented under l1 and l∞ norms, respectively

    A New Measure for Analyzing and Fusing Sequences of Objects

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    This work is related to the combinatorial data analysis problem of seriation used for data visualization and exploratory analysis. Seriation re-sequences the data, so that more similar samples or objects appear closer together, whereas dissimilar ones are further apart. Despite the large number of current algorithms to realize such re-sequencing, there has not been a systematic way for analyzing the resulting sequences, comparing them, or fusing them to obtain a single unifying one. We propose a new positional proximity measure that evaluates the similarity of two arbitrary sequences based on their agreement on pairwise positional information of the sequenced objects. Furthermore, we present various statistical properties of this measure as well as its normalized version modeled as an instance of the generalized correlation coefficient. Based on this measure, we define a new procedure for consensus seriation that fuses multiple arbitrary sequences based on a quadratic assignment problem formulation and an efficient way of approximating its solution. We also derive theoretical links with other permutation distance functions and present their associated combinatorial optimization forms for consensus tasks. The utility of the proposed contributions is demonstrated through the comparison and fusion of multiple seriation algorithms we have implemented, using many real-world datasets from different application domains
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