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Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
The Rooted Maximum Leaf Outbranching problem consists in finding a spanning directed tree rooted at some prescribed vertex of a digraph with the maximum number of leaves. Its parameterized version asks if there exists such a tree with at…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
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…
In this paper we present a novel probabilistic sampling-based motion planning algorithm called the Fast Marching Tree algorithm (FMT*). The algorithm is specifically aimed at solving complex motion planning problems in high-dimensional…
Join ordering is the NP-hard problem of selecting the most efficient order in which to evaluate joins (conjunctive, binary operators) in a database query. Because query execution performance critically depends on this choice, join ordering…
Query workloads and database schemas in OLAP applications are becoming increasingly complex. Moreover, the queries and the schemas have to continually \textit{evolve} to address business requirements. During such repetitive transitions, the…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
We introduce a new subclass of chordal graphs that generalizes split graphs, which we call well-partitioned chordal graphs. Split graphs are graphs that admit a partition of the vertex set into cliques that can be arranged in a star…
We present several algorithms designed to learn a pattern of correspondence between two data sets in situations where it is desirable to match elements that exhibit a relationship belonging to a known parametric model. In the motivating…
An ordered binary decision diagram (OBDD) is a directed acyclic graph that represents a Boolean function. OBDDs are also known as special cases of oblivious read-once branching programs in the field of complexity theory. Since OBDDs have…
We suggest a geometrical mechanism for the ordering of slender filaments inside non-isotropic containers, using cortical microtubules in plant cells and packing of viral genetic material inside capsids as concrete examples. We show…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
This paper studies the underlying combinatorial structure of a class of object rearrangement problems, which appear frequently in applications. The problems involve multiple, similar-geometry objects placed on a flat, horizontal surface,…
We devise a polynomial-time approximation scheme for the classical geometric problem of finding an approximate short path amid weighted regions. In this problem, a triangulated region P comprising of n vertices, a positive weight associated…
The massive integration of distributed energy resources changes the operational demands of the electric power distribution system, motivating optimization-based approaches. The added computational complexities of the resulting optimal power…
Object rearrangement is a widely-applicable and challenging task for robots. Geometric constraints must be carefully examined to avoid collisions and combinatorial issues arise as the number of objects increases. This work studies the…
Let F be a set of ordered patterns, i.e., graphs whose vertices are linearly ordered. An F-free ordering of the vertices of a graph H is a linear ordering of V(H) such that none of patterns in F occurs as an induced ordered subgraph. We…
Large scale graph processing using distributed computing frameworks is becoming pervasive and efficient in the industry. In this work, we present a highly scalable and configurable distributed algorithm for building connected components,…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…