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We address the problem of efficiently gathering correlated data from a wired or a wireless sensor network, with the aim of designing algorithms with provable optimality guarantees, and understanding how close we can get to the known…

Self-nested trees present a systematic form of redundancy in their subtrees and thus achieve optimal compression rates by DAG compression. A method for quantifying the degree of self-similarity of plants through self-nested trees has been…

Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…

Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…

For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…

A tree with at most $k$ leaves is called a $k$-ended tree. A spanning 2-ended tree is a Hamilton path. A Hamilton cycle can be considered as a spanning 1-ended tree. The earliest result concerning spanning trees with few leaves states that…

We revisit tree compression with top trees (Bille et al, ICALP'13) and present several improvements to the compressor and its analysis. By significantly reducing the amount of information stored and guiding the compression step using a…

Let $G$ be a simple graph on $n$ vertices. We consider the problem LIS of deciding whether there exists an induced subtree with exactly $i \leq n$ vertices and $\ell$ leaves in $G$. We study the associated optimization problem, that…

The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…

Recently proposed budding tree is a decision tree algorithm in which every node is part internal node and part leaf. This allows representing every decision tree in a continuous parameter space, and therefore a budding tree can be jointly…

We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…

In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…

Trees with many leaves have applications on broadcasting, which is a method in networks for transferring a message to all recipients simultaneously. Internal nodes of a broadcasting tree require more expensive technology, because they have…

We propose a novel method to merge convolutional neural-nets for the inference stage. Given two well-trained networks that may have different architectures that handle different tasks, our method aligns the layers of the original networks…

An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…

Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…

In this letter we present a very general method to extract information from a generic string of characters, e.g. a text, a DNA sequence or a time series. Based on data-compression techniques, its key point is the computation of a suitable…

We introduce and solve a model which considers two coupled networks growing simultaneously. The dynamics of the networks is governed by the new arrival of network elements (nodes) making preferential attachments to pre-existing nodes in…

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…