136,365 research outputs found

    Phylogenetic inference's algorithms

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    Phylogenetic inference consist in the search of an evolutionary tree to explain the best way possible genealogical relationships of a set of species. Phylogenetic analysis has a large number of applications in areas such as biology, ecology, paleontology, etc. There are several criterias which has been defined in order to infer phylogenies, among which are the maximum parsimony and maximum likelihood. The first one tries to find the phylogenetic tree that minimizes the number of evolutionary steps needed to describe the evolutionary history among species, while the second tries to find the tree that has the highest probability of produce the observed data according to an evolutionary model. The search of a phylogenetic tree can be formulated as a multi-objective optimization problem, which aims to find trees which satisfy simultaneously (and as much as possible) both criteria of parsimony and likelihood. Due to the fact that these criteria are different there won't be a single optimal solution (a single tree), but a set of compromise solutions. The solutions of this set are called "Pareto Optimal". To find this solutions, evolutionary algorithms are being used with success nowadays.This algorithms are a family of techniques, which aren’t exact, inspired by the process of natural selection. They usually find great quality solutions in order to resolve convoluted optimization problems. The way this algorithms works is based on the handling of a set of trial solutions (trees in the phylogeny case) using operators, some of them exchanges information between solutions, simulating DNA crossing, and others apply aleatory modifications, simulating a mutation. The result of this algorithms is an approximation to the set of the “Pareto Optimal” which can be shown in a graph with in order that the expert in the problem (the biologist when we talk about inference) can choose the solution of the commitment which produces the higher interest. In the case of optimization multi-objective applied to phylogenetic inference, there is open source software tool, called MO-Phylogenetics, which is designed for the purpose of resolving inference problems with classic evolutionary algorithms and last generation algorithms. REFERENCES [1] C.A. Coello Coello, G.B. Lamont, D.A. van Veldhuizen. Evolutionary algorithms for solving multi-objective problems. Spring. Agosto 2007 [2] C. Zambrano-Vega, A.J. Nebro, J.F Aldana-Montes. MO-Phylogenetics: a phylogenetic inference software tool with multi-objective evolutionary metaheuristics. Methods in Ecology and Evolution. En prensa. Febrero 2016

    Multi-concentric optimal charging cordon design

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    The performance of a road pricing scheme varies greatly by its actual design and implementation. The design of the scheme is also normally constrained by several practicality requirements. One of the practicality requirements which is tackled in this paper is the topology of the charging scheme. The cordon shape of the pricing scheme is preferred due to its user-friendliness (i.e. the scheme can be understood easily). This has been the design concept for several real world cases (e.g. the schemes in London, Singapore, and Norway). The paper develops a methodology for defining an optimal location of a multi-concentric charging cordons scheme using Genetic Algorithm (GA). The branch-tree structure is developed to represent a valid charging cordon scheme which can be coded using two strings of node numbers and number of descend nodes. This branch-tree structure for a single cordon is then extended to the case with multi-concentric charging cordons. GA is then used to evolve the design of a multi-concentric charging cordons scheme encapsulated in the twostring chromosome. The algorithm developed, called GA-AS, is then tested with the network of the Edinburgh city in UK. The results suggest substantial improvements of the benefit from the optimised charging cordon schemes as compared to the judgemental ones which illustrate the potential of this algorithm

    MAA*: A Heuristic Search Algorithm for Solving Decentralized POMDPs

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    We present multi-agent A* (MAA*), the first complete and optimal heuristic search algorithm for solving decentralized partially-observable Markov decision problems (DEC-POMDPs) with finite horizon. The algorithm is suitable for computing optimal plans for a cooperative group of agents that operate in a stochastic environment such as multirobot coordination, network traffic control, `or distributed resource allocation. Solving such problems efiectively is a major challenge in the area of planning under uncertainty. Our solution is based on a synthesis of classical heuristic search and decentralized control theory. Experimental results show that MAA* has significant advantages. We introduce an anytime variant of MAA* and conclude with a discussion of promising extensions such as an approach to solving infinite horizon problems.Comment: Appears in Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence (UAI2005

    Learning optimization models in the presence of unknown relations

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    In a sequential auction with multiple bidding agents, it is highly challenging to determine the ordering of the items to sell in order to maximize the revenue due to the fact that the autonomy and private information of the agents heavily influence the outcome of the auction. The main contribution of this paper is two-fold. First, we demonstrate how to apply machine learning techniques to solve the optimal ordering problem in sequential auctions. We learn regression models from historical auctions, which are subsequently used to predict the expected value of orderings for new auctions. Given the learned models, we propose two types of optimization methods: a black-box best-first search approach, and a novel white-box approach that maps learned models to integer linear programs (ILP) which can then be solved by any ILP-solver. Although the studied auction design problem is hard, our proposed optimization methods obtain good orderings with high revenues. Our second main contribution is the insight that the internal structure of regression models can be efficiently evaluated inside an ILP solver for optimization purposes. To this end, we provide efficient encodings of regression trees and linear regression models as ILP constraints. This new way of using learned models for optimization is promising. As the experimental results show, it significantly outperforms the black-box best-first search in nearly all settings.Comment: 37 pages. Working pape
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