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Non-polynomial hard (NP-hard) problems are challenging because no polynomial-time algorithm has yet been discovered to solve them in polynomial time. The Bacteria Foraging Optimization (BFO) algorithm is one of the metaheuristics algorithms…
Sum-of-norms clustering is a clustering formulation based on convex optimization that automatically induces hierarchy. Multiple algorithms have been proposed to solve the optimization problem: subgradient descent by Hocking et al., ADMM and…
The classical comparison-based sorting problem asks us to find the underlying total order of a given set of elements, where we can only access the elements via comparisons. In this paper, we study a restricted version, where, as a hint, a…
We present a scalable approach for simplifying the stability analysis of cluster synchronization patterns on directed networks. When a network has directional couplings, decomposition of the coupling matrix into independent blocks (which in…
This paper proposes a new dimensionality reduction algorithm named branching embedding (BE). It converts a dendrogram to a two-dimensional scatter plot, and visualizes the inherent structures of the original high-dimensional data. Since the…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Balancing assembly lines, a family of optimization problems commonly known as Assembly Line Balancing Problem, is notoriously NP-Hard. They comprise a set of problems of enormous practical interest to manufacturing industry due to the…
The flawless functioning of a protein is essentially linked to its own three-dimensional structure. Therefore, the prediction of a protein structure from its amino acid sequence is a fundamental problem in many fields that draws researchers…
Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current…
In this paper, a new method for solving the power flow problem in distribution systems which is fast, parallel, as well as modular, straightforward, simplified and generic is proposed. This approach is based on a hierarchical construction…
When some 'entities' are related by the 'features' they share they are amenable to a bipartite network representation. Plant-pollinator ecological communities, co-authorship of scientific papers, customers and purchases, or answers in a…
Spectral clustering is a fundamental technique in the field of data mining and information processing. Most existing spectral clustering algorithms integrate dimensionality reduction into the clustering process assisted by manifold learning…
The Hierarchical Clustering (HC) problem consists of building a hierarchy of clusters to represent a given dataset. Motivated by the modern large-scale applications, we study the problem in the \streaming model, in which the memory is…
Finding a set of nested partitions of a dataset is useful to uncover relevant structure at different scales, and is often dealt with a data-dependent methodology. In this paper, we introduce a general two-step methodology for model-based…
An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same…
It has been widely recognized that the performance of a multi-agent system is highly affected by its organization. A large scale system may have billions of possible ways of organization, which makes it impractical to find an optimal choice…
Community detection in complex networks is a topic of considerable recent interest within the scientific community. For dealing with the problem that genetic algorithm are hardly applied to community detection, we propose a genetic…
Working with exhaustive search on large dataset is infeasible for several reasons. Recently, developed techniques that made pattern set mining feasible by a general solver with long execution time that supports heuristic search and are…
There is evidence that the self-assembly of complex molecular systems often proceeds hierarchically, by first building subunits that later assemble in larger entities, in a process that can repeat multiple times. Yet, our understanding of…