Related papers: Fast error-tolerant quartet phylogeny algorithms
In this paper we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster…
The resiliency of a network is its ability to remain \emph{effectively} functioning also when any of its nodes or links fails. However, to reduce operational and set-up costs, a network should be small in size, and this conflicts with the…
Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and…
We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…
The authors recently gave an $n^{O(\log\log n)}$ time membership query algorithm for properly learning decision trees under the uniform distribution (Blanc et al., 2021). The previous fastest algorithm for this problem ran in $n^{O(\log…
A family of comparison-based exact pattern matching algorithms is described. They utilize multi-dimensional arrays in order to process more than one adjacent text window in each iteration of the search cycle. This approach leads to a lower…
Maximum likelihood iteration is one of the most commonly used reconstruction algorithms in quantum tomography. The main appeal of the method is that it is easy to implement and that it converges reliably to a physically meaningful density…
A likelihood-based reconstruction algorithm for arbitrary event topologies is introduced and, as an example, applied to the single-lepton decay mode of top-quark pair production. The algorithm comes with several options which further…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
The use of machine learning algorithms in finance, medicine, and criminal justice can deeply impact human lives. As a consequence, research into interpretable machine learning has rapidly grown in an attempt to better control and fix…
This paper derives a unifying theorem establishing consistency results for a broad class of tree-based algorithms. It improves current results in two aspects. First of all, it can be applied to algorithms that vary from traditional Random…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
We present the phylogenetic quartet reconstruction method SAQ (Semi-algebraic quartet reconstruction). SAQ is consistent with the most general Markov model of nucleotide substitution and, in particular, it allows for rate heterogeneity…
In an extant population, how much information do extant individuals provide on the pedigree of their ancestors? Recent work by Kim, Mossel, Ramnarayan and Turner (2020) studied this question under a number of simplifying assumptions,…
The weighted ancestor problem is a well-known generalization of the predecessor problem to trees. It is known to require $\Omega(\log\log n)$ time for queries provided $O(n\mathop{\mathrm{polylog}} n)$ space is available and weights are…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
Man-made environments typically comprise planar structures that exhibit numerous geometric relationships, such as parallelism, coplanarity, and orthogonality. Making full use of these relationships can considerably improve the robustness of…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
In this paper we present a novel probabilistic sampling-based motion planning algorithm called the Fast Marching Tree algorithm (FMT*). The algorithm is specifically aimed at solving complex motion planning problems in high-dimensional…
Time series are ubiquitous in domains ranging from medicine to marketing and finance. Frequent Pattern Mining (FPM) from a time series has thus received much attention. Recently, it has been studied under the order-preserving (OP) matching…