Related papers: Exact reconciliation of undated trees
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
Integer Linear Programming (ILP) can be seen as the archetypical problem for NP-complete optimization problems, and a wide range of problems in artificial intelligence are solved in practice via a translation to ILP. Despite its huge range…
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…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
In this article, we introduce a new technique for precision tuning. This problem consists of finding the least data types for numerical values such that the result of the computation satisfies some accuracy requirement. State of the art…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Resilience is one of the key algorithmic problems underlying various forms of reverse data management (such as view maintenance, deletion propagation, and various interventions for fairness): What is the minimal number of tuples to delete…
Answering science questions posed in natural language is an important AI challenge. Answering such questions often requires non-trivial inference and knowledge that goes beyond factoid retrieval. Yet, most systems for this task are based on…
Many probabilistic inference tasks involve summations over exponentially large sets. Recently, it has been shown that these problems can be reduced to solving a polynomial number of MAP inference queries for a model augmented with randomly…
Joint object matching, also known as multi-image matching, namely, the problem of finding consistent partial maps among all pairs of objects within a collection, is a crucial task in many areas of computer vision. This problem subsumes…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
We consider the problem of drawing multiple gene trees inside a single species tree in order to visualize multispecies coalescent trees. Specifically, the drawing of the species tree fills a rectangle in which each of its edges is…
Linear programming (LP) is an extremely useful tool and has been successfully applied to solve various problems in a wide range of areas, including operations research, engineering, economics, or even more abstract mathematical areas such…
Integer linear programming (ILP) is an elegant approach to solve linear optimization problems, naturally described using integer decision variables. Within the context of physics-inspired machine learning applied to chemistry, we…
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…
We consider a set reconciliation setting in which two parties hold similar sets which they would like to reconcile In particular, we focus on set reconciliation based on invertible Bloom lookup tables (IBLTs), a probabilistic data structure…
The history of gene families - which are equivalent to \emph{event-labeled} gene trees - can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The…
We study integer linear programs (ILP) of the form $\min\{c^\top x\ \vert\ Ax=b,l\le x\le u,x\in\mathbb Z^n\}$ and analyze their parameterized complexity with respect to their distance to the generalized matching problem, following the…
Nomadic applications create replicas of shared objects that evolve independently while they are disconnected. When reconnecting, the system has to reconcile the divergent replicas. In the log-based approach to reconciliation, such as in the…
Integer Linear Programs (ILPs) are powerful tools for modeling and solving a large number of combinatorial optimization problems. Recently, it has been shown that Large Neighborhood Search (LNS), as a heuristic algorithm, can find high…