Related papers: Checking Phylogenetic Decisiveness in Theory and i…
Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…
Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and…
Diagnosing an inherited disease often requires identifying the pattern of inheritance in a patient's family. We represent family trees with genetic patterns of inheritance using hypergraphs and latent state space models to provide…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Predicting the future is an important component of decision making. In most situations, however, there is not enough information to make accurate predictions. In this paper, we develop a theory of causal reasoning for predictive inference…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
It is well known that the resolution method (for propositional logic) is complete. However, completeness proofs found in the literature use an argument by contradiction showing that if a set of clauses is unsatisfiable, then it must have a…
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…
Matching cells over time has long been the most difficult step in cell tracking. In this paper, we approach this problem by recasting it as a classification problem. We construct a feature set for each cell, and compute a feature difference…
Sequential hypothesis testing asks for decision rules that update as data arrive. A natural goal is \emph{eventual correctness}: the rule may change its mind early on, but it should make only finitely many wrong decisions almost surely.…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
Consider an n-vertex graph G = (V,E) of maximum degree Delta, and suppose that each vertex v \in V hosts a processor. The processors are allowed to communicate only with their neighbors in G. The communication is synchronous, i.e., it…
We investigate data-enriched models, like Petri nets with data, where executability of a transition is conditioned by a relation between data values involved. Decidability status of various decision problems in such models may depend on the…
HyperLTL, the extension of Linear Temporal Logic by trace quantifiers, is a uniform framework for expressing information flow policies by relating multiple traces of a security-critical system. HyperLTL has been successfully applied to…
This paper provides an algorithmic framework for obtaining fast distributed algorithms for a highly-dynamic setting, in which *arbitrarily many* edge changes may occur in each round. Our algorithm significantly improves upon prior work in…
We consider a logic used to describe sets of configurations of distributed systems, whose network topologies can be changed at runtime, by reconfiguration programs. The logic uses inductive definitions to describe networks with an unbounded…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…
This paper is centered on the complexity of graph problems in the well-studied LOCAL model of distributed computing, introduced by Linial [FOCS '87]. It is widely known that for many of the classic distributed graph problems (including…