Related papers: LvD: A New Algorithm for Computing the Likelihood …
The treedepth of a graph $G$ is the least possible depth of an elimination forest of $G$: a rooted forest on the same vertex set where every pair of vertices adjacent in $G$ is bound by the ancestor/descendant relation. We propose an…
The goal of image oversegmentation is to divide an image into several pieces, each of which should ideally be part of an object. One of the simplest and yet most effective oversegmentation algorithms is known as local variation (LV)…
We present a randomized algorithm that computes a constant approximation of a graph's arboricity, using $\tilde{O}(n/\lambda)$ queries to adjacency lists and in the same time bound. Here, $n$ and $\lambda$ denote the number of nodes and the…
Inference of the marginal likelihood of sample allele configurations using backward algorithms yields identical results with the Kingman coalescent, the Moran model, and the diffusion model (up to a scaling of time). For inference of…
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…
The rapid growth in genomic pathogen data spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
Forward gradient descent (FGD) has been proposed as a biologically more plausible alternative of gradient descent as it can be computed without backward pass. Considering the linear model with $d$ parameters, previous work has found that…
We present an algorithm that, with high probability, generates a random spanning tree from an edge-weighted undirected graph in $\tilde{O}(n^{4/3}m^{1/2}+n^{2})$ time (The $\tilde{O}(\cdot)$ notation hides $\operatorname{polylog}(n)$…
This paper is concerned with the ordered statistic decoding with local constraints (LC-OSD) of binary linear block codes, which is a near maximum-likelihood decoding algorithm. Compared with the conventional OSD, the LC-OSD significantly…
We consider LSTD($\lambda$), the least-squares temporal-difference algorithm with eligibility traces algorithm proposed by Boyan (2002). It computes a linear approximation of the value function of a fixed policy in a large Markov Decision…
Densest Subgraph Problem (DSP) is an important primitive problem with a wide range of applications, including fraud detection, community detection and DNA motif discovery. Edge-based density is one of the most common metrics in DSP.…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
A central task in the study of molecular sequence data from present-day species is the reconstruction of the ancestral relationships. The most established approach to tree reconstruction is the maximum likelihood (ML) method. In this…
We consider the problem of making nonparametric inference in a class of multi-dimensional diffusions in divergence form, from low-frequency data. Statistical analysis in this setting is notoriously challenging due to the intractability of…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…