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MD-JEEP: a New Release for Discretizable Distance Geometry Problems with Interval Data

Abstract : With the most recent releases of MD-JEEP, new relevant features have been included to our software tool. MD-JEEP solves instances of the class of Discretizable Distance Geometry Problems (DDGPs), which ask to find possible realizations, in a Euclidean space, of a simple weighted undirected graph for which distance constraints between vertices are given, and for which a discretization of the search space can be supplied. Since its version 0.3.0, MD-JEEP is able to deal with instances containing interval data. We focus in this short paper on the most recent release MD-JEEP 0.3.2: among the new implemented features, we will focus our attention on three features: (i) an improved procedure for the generation and update of the boxes used in the coarse-grained representation (necessary to deal with instances containing interval data); (ii) a new procedure for the selection of the so-called discretization vertices (necessary to perform the discretization of the search space); (iii) the implementation of a general parser which allows the user to easily load DDGP instances in a given specified format. The source code of MD-JEEP 0.3.2 is available on GitHub, where the reader can find all additional details about the implementation of such new features, as well as verify the effectiveness of such features by comparing MD-JEEP 0.3.2 with its previous releases.
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https://hal.inria.fr/hal-03030154
Contributor : Leo Liberti Connect in order to contact the contributor
Submitted on : Sunday, November 29, 2020 - 7:52:08 PM
Last modification on : Wednesday, November 3, 2021 - 8:01:47 AM

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  • HAL Id : hal-03030154, version 1

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Antonio Mucherino, Douglas Gonçalves, Leo Liberti, Jung-Hsin Lin, Carlile Lavor, et al.. MD-JEEP: a New Release for Discretizable Distance Geometry Problems with Interval Data. FedCSIS 2020 - 15th Conference on Computer Science and Information Systems, Sep 2020, Sofia, Bulgaria. pp.1-6. ⟨hal-03030154⟩

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