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The experimenter must perform a legitimate search in the entire set of feasible censoring schemes to identify the optimal type II progressive censoring scheme, when applied to a life-testing experiment. Current recommendations are limited…

Motivation: Optimizing seed selection is an important problem in read mapping. The number of non-overlapping seeds a mapper selects determines the sensitivity of the mapper while the total frequency of all selected seeds determines the…

Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…

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…

A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…

It is common to encounter situations where one must solve a sequence of similar computational problems. Running a standard algorithm with worst-case runtime guarantees on each instance will fail to take advantage of valuable structure…

A fundamental problem arising in many applications in Web science and social network analysis is, given an arbitrary approximation factor $c>1$, to output a set $S$ of nodes that with high probability contains all nodes of PageRank at least…

Colonies of ants can collectively choose the best of several nests, even when many of the active ants who organize the move visit only one site. Understanding such a behavior can help us design efficient distributed decision making…

The community structure of a complex network can be determined by finding the partitioning of its nodes that maximizes modularity. Many of the proposed algorithms for doing this work by recursively bisecting the network. We show that this…

Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…

When analysing binary data, the ease at which one can interpret results is very important. Many existing methods, however, discover either models that are difficult to read, or return so many results interpretation becomes impossible. Here,…

It was recently shown that almost all solutions in the symmetric binary perceptron are isolated, even at low constraint densities, suggesting that finding typical solutions is hard. In contrast, some algorithms have been shown empirically…

This work examines the expected computational cost to determine an approximate global minimum of a class of cost functions characterized by the variance of coefficients. The cost function takes $N$-dimensional binary states as arguments and…

In this article we provide a comprehensive review of the different evolutionary algorithm techniques used to address multimodal optimization problems, classifying them according to the nature of their approach. On the one hand there are…

We study the min-cost seed selection problem in online social networks, where the goal is to select a set of seed nodes with the minimum total cost such that the expected number of influenced nodes in the network exceeds a predefined…

The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the…

We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…

Inferring probabilistic networks from data is a notoriously difficult task. Under various goodness-of-fit measures, finding an optimal network is NP-hard, even if restricted to polytrees of bounded in-degree. Polynomial-time algorithms are…

We study the problem of set discovery where given a few example tuples of a desired set, we want to find the set in a collection of sets. A challenge is that the example tuples may not uniquely identify a set, and a large number of…

Computationally efficient and automated generation of convex hulls is desirable for high throughput materials discovery of thermodynamically stable multi-species crystal structures. A convex hull genetic algorithm is proposed that uses…