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Ancestral mixture model, proposed by Chen and Lindsay (2006), is an important model to build a hierarchical tree from high dimensional binary sequences. Mixture trees created from ancestral mixture models involve in the inferred…

We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known…

Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…

Ancestry and genealogy tree are proven tools to determine the lineage of any person and establish dependencies among individuals. Genealogy tree can be exploited further to gain information about the researcher and his scholastic lineage…

An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…

Fruit tree image segmentation is an essential problem in automating a variety of agricultural tasks such as phenotyping, harvesting, spraying, and pruning. Many research papers have proposed a diverse spectrum of solutions suitable to…

Keeping track of the ever-increasing body of scientific literature is an escalating challenge. We present PubTree a hierarchical search tool that efficiently searches the PubMed/MEDLINE dataset based upon a decision tree constructed using…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

Up-to-date catalogs of the urban tree population are important for municipalities to monitor and improve quality of life in cities. Despite much research on automation of tree mapping, mainly relying on dedicated airborne LiDAR or…

Survival analysis studies and predicts the time of death, or other singular unrepeated events, based on historical data, while the true time of death for some instances is unknown. Survival trees enable the discovery of complex nonlinear…

We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…

This paper presents an asynchronous distributed algorithm to manage multiple trees for peer-to-peer streaming in a flow level model. It is assumed that videos are cut into substreams, with or without source coding, to be distributed to all…

In this work, we propose trait-based merge trees a generalization of merge trees to feature level sets, targeting the analysis of tensor field or general multi-variate data. For this, we employ the notion of traits defined in attribute…

Inferring who infected whom in an outbreak is essential for characterising transmission dynamics and guiding public health interventions. However, this task is challenging due to limited surveillance data and the complexity of immunological…

Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…

Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…

Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume…

In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…

Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…

Mathematical models of infectious diseases, which are in principle analytically tractable, use two general approaches. The first approach, generally known as compartmental modeling, addresses the time evolution of disease propagation at the…