Related papers: Parking functions, labeled trees and DCJ sorting s…
Multi-label classification is a challenging task, particularly in domains where the number of labels to be predicted is large. Deep neural networks are often effective at multi-label classification of images and textual data. When dealing…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Object rearrangement is a fundamental problem in robotics with various practical applications ranging from managing warehouses to cleaning and organizing home kitchens. While existing research has primarily focused on single-agent…
Tandem-duplication-random-loss (TDRL) is an important genome rearrangement operation studied in evolutionary biology. This paper investigates some of the formal properties of TDRL operations on the symmetric group (the space of permutations…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
Industrial robots can solve very complex tasks in controlled environments, but modern applications require robots able to operate in unpredictable surroundings as well. An increasingly popular reactive policy architecture in robotics is…
We introduce the class of bilateral parking procedures on the integer line. While cars try to park in the nearest available spot to their right in the classical case, we consider more general parking rules that allow cars to use the nearest…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
Finding tumour genetic markers is essential to biomedicine due to their relevance for cancer detection and therapy development. In this paper, we explore a recently released dataset of chromosome rearrangements in 2,586 cancer patients,…
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…
The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the…
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
Breakpoint graphs are ubiquitous structures in the field of genome rearrangements. Their cycle decomposition has proved useful in computing and bounding many measures of (dis)similarity between genomes, and studying the distribution of…
Probabilistic programming is becoming increasingly popular thanks to its ability to specify problems with a certain degree of uncertainty. In this work, we focus on term rewriting, a well-known computational formalism. In particular, we…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
We apply the concept of parking functions to rooted labelled trees and functional digraphs of mappings (i.e., functions $f : [n] \to [n]$) by considering the nodes as parking spaces and the directed edges as one-way streets: Each driver has…