相关论文: Efficient Enumeration of the Directed Binary Perfe…

We propose a constructive algorithm for identifying complete data distributions in graphical models of missing data. The complete data distribution is unrestricted, while the missingness mechanism is assumed to factorize according to a…

Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…

In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…

Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…

Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…

In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex $v$ of an evolutionary tree $T$ from the states that are observed at the leaves of the tree. A simple and fast…

For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…

Given i.i.d. data from an unknown distribution, we consider the problem of predicting future items. An adaptive way to estimate the probability density is to recursively subdivide the domain to an appropriate data-dependent granularity. A…

Biclustering has proved to be a powerful data analysis technique due to its wide success in various application domains. However, the existing literature presents efficient solutions only for enumerating maximal biclusters with constant…

We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…

Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…

Dealing with datasets of very high dimension is a major challenge in machine learning. In this paper, we consider the problem of feature selection in applications where the memory is not large enough to contain all features. In this…

This paper considers structure learning from data with $n$ samples of $p$ variables, assuming that the structure is a forest, using the Chow-Liu algorithm. Specifically, for incomplete data, we construct two model selection algorithms that…

In this paper, we present a new exact algorithm for counting perfect matchings, which relies on neither inclusion-exclusion principle nor tree-decompositions. For any bipartite graph of $2n$ nodes and $\Delta n$ edges such that $\Delta \geq…

In this paper, we present new efficiently solvable cases of the Minimum Uncovering Branching problem, an optimization problem with applications in cancer genomics introduced by Hujdurovi\'c, Husi\'c, Milani\v{c}, Rizzi, and Tomescu in 2018.…

Intersection graphs are well-studied in the area of graph algorithms. Some intersection graph classes are known to have algorithms enumerating all unlabeled graphs by reverse search. Since these algorithms output graphs one by one and the…

Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…

The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…

It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…

Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…