Related papers: Towards a Data Reduction for the Minimum Flip Supe…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
With the rapid popularization of big data, the dichotomy between tractable and intractable problems in big data computing has been shifted. Sublinear time, rather than polynomial time, has recently been regarded as the new standard of…
Query evaluation in an XML database requires reconstructing XML subtrees rooted at nodes found by an XML query. Since XML subtree reconstruction can be expensive, one approach to improve query response time is to use reconstruction views -…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
A MapReduce algorithm can be described by a mapping schema, which assigns inputs to a set of reducers, such that for each required output there exists a reducer that receives all the inputs that participate in the computation of this…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
When, in terms of the number of data points, the size of a dataset exceeds available computing resources, or when labeling is expensive, an attractive solution consists of selecting only some of the data points (subdata) for further…
In this paper, we consider the problem of distributed inference in tree based networks. In the framework considered in this paper, distributed nodes make a 1-bit local decision regarding a phenomenon before sending it to the fusion center…
We resolve a long-standing open question, about the existence of a constant-factor approximation algorithm for the average-case \textsc{Decision Tree} problem with uniform probability distribution over the hypotheses. We answer the question…
The independence number of a tree decomposition is the size of a largest independent set contained in a single bag. The tree-independence number of a graph $G$ is the minimum independence number of a tree decomposition of $G$. As shown…
This paper presents a general framework for generating greedy algorithms for solving convex constraint satisfaction problems for sparse solutions by mapping the satisfaction problem into one of graph traversal on a rooted tree of unknown…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
We address the problem of configuring a power distribution network with reliability and resilience objectives by satisfying the demands of the consumers and saturating each production source as little as possible. We consider power…
Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Motivated by the philosophy and phenomenal success of compressed sensing, the problem of reconstructing a matrix from a sampling of its entries has attracted much attention recently. Such a problem can be viewed as an information-theoretic…
We present a new universal source code for distributions of unlabeled binary and ordinal trees that achieves optimal compression to within lower order terms for all tree sources covered by existing universal codes. At the same time, it…
Given a rooted tree and a ranking of its leaves, what is the minimum number of inversions of the leaves that can be attained by ordering the tree? This variation of the problem of counting inversions in arrays originated in mathematical…