Related papers: A short note on the tractability of constructing p…

Hierarchical structure is ubiquitous in data across many domains. There are many hierarchical clustering methods, frequently used by domain experts, which strive to discover this structure. However, most of these methods limit discoverable…

Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

The 0/1 knapsack problem is weakly NP-hard in that there exist pseudo-polynomial time algorithms based on dynamic programming that can solve it exactly. There are also the core branch and bound algorithms that can solve large randomly…

In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…

Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…

Designing algorithms that generate networks with a given degree sequence while varying both subgraph composition and distribution of subgraphs around nodes is an important but challenging research problem. Current algorithms lack control of…

We study feature selection for $k$-means clustering. Although the literature contains many methods with good empirical performance, algorithms with provable theoretical behavior have only recently been developed. Unfortunately, these…

We design a recursive algorithm to compute the partition function of the Ising model, summed over cubic maps with fixed size and genus. The algorithm runs in polynomial time, which is much faster than methods based on a Tutte-like, or…

Clustering algorithms are often used to find subpopulations in exploratory data analysis workflows. Not only the clusters themselves, but also their shape can represent meaningful subpopulations. In this paper, we present FLASC, an…

Performing efficient inference on Bayesian Networks (BNs), with large numbers of densely connected variables is challenging. With exact inference methods, such as the Junction Tree algorithm, clustering complexity can grow exponentially…

Recently it was shown that a certain class of phylogenetic networks, called level-$2$ networks, cannot be reconstructed from their associated distance matrices. In this paper, we show that they can be reconstructed from their induced…

This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…

This paper characterizes hierarchical clustering methods that abide by two previously introduced axioms -- thus, denominated admissible methods -- and proposes tractable algorithms for their implementation. We leverage the fact that, for…

Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…

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…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

We present and discuss the results of an experimental analysis in the design of Boolean networks by means of genetic algorithms. A population of networks is evolved with the aim of finding a network such that the attractor it reaches is of…

We study the problem of recovering a known cluster structure in a sparse network, also known as the planted partitioning problem, by means of statistical mechanics. We find a sharp transition from un-recoverable to recoverable structure as…

This paper presents two new deterministic algorithms for constructing consensus trees. Given an input of k phylogenetic trees with identical leaf label sets and n leaves each, the first algorithm constructs the majority rule (+) consensus…