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Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the…
The objective of clustering is to discover natural groups in datasets and to identify geometrical structures which might reside there, without assuming any prior knowledge on the characteristics of the data. The problem can be seen as…
We study the electrical distribution network reconfiguration problem, defined as follows. We are given an undirected graph with a root vertex, demand at each non-root vertex, and resistance on each edge. Then, we want to find a spanning…
In this paper we consider alignment of sparse graphs, for which we introduce the Neighborhood Tree Matching Algorithm (NTMA). For correlated Erd\H{o}s-R\'{e}nyi random graphs, we prove that the algorithm returns -- in polynomial time -- a…
The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view…
The minimum linear arrangement problem on a network consists of finding the minimum sum of edge lengths that can be achieved when the vertices are arranged linearly. Although there are algorithms to solve this problem on trees in polynomial…
The graph invariant EPT-sum has cropped up in several unrelated fields in later years: As an objective function for hierarchical clustering, as a more fine-grained version of the classical edge ranking problem, and, specifically when the…
Moss and Rabani[12] study constrained node-weighted Steiner tree problems with two independent weight values associated with each node, namely, cost and prize (or penalty). They give an O(log n)-approximation algorithm for the…
This work focuses on a class of general decentralized constraint-coupled optimization problems. We propose a novel nested primal-dual gradient algorithm (NPGA), which can achieve linear convergence under the weakest known condition, and its…
We study the problem of optimal power allocation in a single-hop ad hoc wireless network. In solving this problem, we depart from classical purely model-based approaches and propose a hybrid method that retains key modeling elements in…
Rank aggregation seeks a representative permutation for a collection of rankings and plays a central role in areas such as social choice, information retrieval, and computational biology. Two fundamental aggregation tasks are the center and…
It is required to find an optimal order of constructing the edges of a network so as to minimize the sum of the weighted connection times of relevant pairs of vertices. Construction can be performed anytime anywhere in the network, with a…
We propose NEP_MiniMax, a novel computational method for solving nonlinear eigenvalue problems (NEPs) $T(\lambda)\mathbf{u}= 0$ on compact continua $\Omega \subset \mathbb{C}$. The method combines two key components: (1) a rational minimax…
The neighbor-joining algorithm is a popular phylogenetics method for constructing trees from dissimilarity maps. The neighbor-net algorithm is an extension of the neighbor-joining algorithm and is used for constructing split networks. We…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
We study the complexity of finding an optimal hierarchical clustering of an unweighted similarity graph under the recently introduced Dasgupta objective function. We introduce a proof technique, called the normalization procedure, that…
The Minimum Spanning Tree problem (abbr. MSTP) is a well-known combinatorial optimization problem that has been extensively studied by the researchers in the field of evolutionary computing to theoretically analyze the optimization…
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…
We consider the problems of finding a maximum clique in a graph and finding a maximum-edge biclique in a bipartite graph. Both problems are NP-hard. We write both problems as matrix-rank minimization and then relax them using the nuclear…