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We present an Evolutionary Placement Algorithm (EPA) for the rapid assignment of sequence fragments (short reads) to branches of a given phylogenetic tree under the Maximum Likelihood (ML) model. The accuracy of the algorithm is evaluated…

Genomics · Quantitative Biology 2009-11-17 S. A. Berger , A. Stamatakis

In recent years, many design automation methods have been developed to routinely create approximate implementations of circuits and programs that show excellent trade-offs between the quality of output and required resources. This paper…

Neural and Evolutionary Computing · Computer Science 2021-08-17 Lukas Sekanina

The Steiner tree problem is a well-known problem in network design, routing, and VLSI design. Given a graph, edge costs, and a set of dedicated vertices (terminals), the Steiner tree problem asks to output a sub-graph that connects all…

Artificial Intelligence · Computer Science 2020-11-10 Johannes K. Fichte , Markus Hecher , Andre Schidler

Given an $n$-vertex non-negatively real-weighted graph $G$, whose vertices are partitioned into a set of $k$ clusters, a \emph{clustered network design problem} on $G$ consists of solving a given network design optimization problem on $G$,…

Data Structures and Algorithms · Computer Science 2018-02-01 Mattia D'Emidio , Luca Forlizzi , Daniele Frigioni , Stefano Leucci , Guido Proietti

Bilevel optimization poses a significant computational challenge due to its nested structure, where each upper-level candidate solution requires solving a corresponding lower-level problem. While evolutionary algorithms (EAs) are effective…

Neural and Evolutionary Computing · Computer Science 2025-06-10 Dejun Xu , Jijia Chen , Gary G. Yen , Min Jiang

In the minimum $k$-edge-connected spanning subgraph ($k$-ECSS) problem the goal is to find the minimum weight subgraph resistant to up to $k-1$ edge failures. This is a central problem in network design, and a natural generalization of the…

Data Structures and Algorithms · Computer Science 2018-05-22 Michal Dory

Evolutionary algorithms (EA) have been widely accepted as efficient solvers for complex real world optimization problems, including engineering optimization. However, real world optimization problems often involve uncertain environment…

Neural and Evolutionary Computing · Computer Science 2016-11-17 Maumita Bhattacharya , R. Islam , A. Mahmood

We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…

Computational Geometry · Computer Science 2021-11-11 Ahmad Biniaz , Anil Maheshwari , Michiel Smid

Evolutionary Algorithms (EAs) are being routinely applied for a variety of optimization tasks, and real-parameter optimization in the presence of constraints is one such important area. During constrained optimization EAs often create…

Neural and Evolutionary Computing · Computer Science 2015-04-20 Nikhil Padhye , Pulkit Mittal , Kalyanmoy Deb

The minimum-cost arborescence problem is a well-studied problem in the area of graph theory, with known polynomial-time algorithms for solving it. Previous literature introduced new variations on the original problem with different…

Optimization and Control · Mathematics 2023-05-15 Xiaochen Chou , Mauro Dell'Amico , Jafar Jamal , Roberto Montemanni

Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…

Data Structures and Algorithms · Computer Science 2025-02-19 Nate Veldt , Thomas Stanley , Benjamin W. Priest , Trevor Steil , Keita Iwabuchi , T. S. Jayram , Geoffrey Sanders

In real life, it is always an urge to reach our goal in minimum effort i.e., it should have a minimum constrained path. The path may be shortest route in practical life, either physical or electronic medium. The scenario is to represents…

Neural and Evolutionary Computing · Computer Science 2014-01-14 Sounak Sadhukhan , Samar Sen Sarma

We study the NP-hard problem of approximating a Minimum Routing Cost Spanning Tree in the message passing model with limited bandwidth (CONGEST model). In this problem one tries to find a spanning tree of a graph $G$ over $n$ nodes that…

Distributed, Parallel, and Cluster Computing · Computer Science 2014-06-06 Alexandra Hochuli , Stephan Holzer , Roger Wattenhofer

It is challenging to design large and low-cost communication networks. In this paper, we formulate this challenge as the prize-collecting Steiner Tree Problem (PCSTP). The objective is to minimize the costs of transmission routes and the…

Networking and Internet Architecture · Computer Science 2019-02-07 Yahui Sun , Marcus Brazil , Doreen Thomas , Saman Halgamuge

Real-world problems are very difficult to optimize. However, many researchers have been solving benchmark problems that have been extensively investigated for the last decades even if they have very few direct applications. The Traveling…

Artificial Intelligence · Computer Science 2016-03-25 Mohamed El Yafrani , Belaïd Ahiod

Querying the shortest path between two vertexes is a fundamental operation in a variety of applications, which has been extensively studied over static road networks. However, in reality, the travel costs of road segments evolve over time,…

Databases · Computer Science 2023-03-08 Zengyang Gong , Yuxiang Zeng , Lei Chen

We present the generic Dijkstra shortest path algorithm: an efficient algorithm for finding a shortest path in an optical network, both in a wavelength-division multiplexed network, and an elastic optical network (EON). The proposed…

Networking and Internet Architecture · Computer Science 2020-01-08 Ireneusz Szcześniak , Andrzej Jajszczyk , Bożena Woźna-Szcześniak

Evolutionary strategies have recently been shown to achieve competing levels of performance for complex optimization problems in reinforcement learning. In such problems, one often needs to optimize an objective function subject to a set of…

Neural and Evolutionary Computing · Computer Science 2022-02-23 Youssef Diouane , Aurelien Lucchi , Vihang Patil

The prize-collecting Steiner tree problem PCSTP is a well-known generalization of the classical Steiner tree problem in graphs, with a large number of practical applications. It attracted particular interest during the latest (11th) DIMACS…

Optimization and Control · Mathematics 2018-11-26 Daniel Rehfeldt , Thorsten Koch

In this thesis, we present fast deterministic algorithm to find small cuts in distributed networks. Finding small min-cuts for a network is essential for ensuring the quality of service and reliability. Throughout this thesis, we use the…

Data Structures and Algorithms · Computer Science 2020-03-03 Mohit Daga