Related papers: Visualizing Multispecies Coalescent Trees: Drawing…
This work addresses the uniform parallel machine scheduling problem within an optimistic bilevel optimization framework. The leader seeks to minimize the weighted number of tardy jobs, while the follower aims to minimize the total…
Isotonic regression is a nonparametric approach for fitting monotonic models to data that has been widely studied from both theoretical and practical perspectives. However, this approach encounters computational and statistical overfitting…
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…
Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories…
A witness drawing of a graph is a visualization that clearly shows a given property of a graph. We study and implement various drawing paradigms for witness drawings to clearly show that graphs have bounded pathwidth or treewidth. Our…
Trees corresponding to $\Lambda$- and $\Xi$-$n$-coalescents can be both quite similar and fundamentally different compared to bifurcating tree models based on Kingman's $n$-coalescent. This has consequences for inference of a well-fitting…
Geometric trees are characterized by their tree-structured layout and spatially constrained nodes and edges, which significantly impacts their topological attributes. This inherent hierarchical structure plays a crucial role in domains such…
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…
Graph neural networks have been successful in many learning problems and real-world applications. A recent line of research explores the power of graph neural networks to solve combinatorial and graph algorithmic problems such as subgraph…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
We study the compressed representation of a ranked tree by a (string) straight-line program (SLP) for its preorder traversal, and compare it with the well-studied representation by straight-line context free tree grammars (which are also…
The visualization of argumentation frameworks (AFs) is crucial for enabling a wide applicability of argumentative tools. However, their visualization is often considered only as an accompanying part of tools for computing semantics and…
This paper presents a Genetic Programming (GP) approach to solving multi-robot path planning (MRPP) problems in single-lane workspaces, specifically those easily mapped to graph representations. GP's versatility enables this approach to…
There is a warning light for the loss of plant habitats worldwide that entails concerted efforts to conserve plant biodiversity. Thus, plant species classification is of crucial importance to address this environmental challenge. In recent…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Given a graph, we can form a spanning forest by first sorting the edges in some order, and then only keep edges incident to a vertex which is not incident to any previous edge. The resulting forest is dependent on the ordering of the edges,…
We study the problem of sampling a uniformly random directed rooted spanning tree, also known as an arborescence, from a possibly weighted directed graph. Classically, this problem has long been known to be polynomial-time solvable; the…
Motivated by evacuation scenarios arising in extreme events such as flooding or forest fires, we study the problem of smoothly scheduling a set of paths in graphs where connections become impassable at some point in time. A schedule is…
Graph-level representations are crucial tools for characterising structural differences between graphs. However, comparing graphs with different cardinalities, even when sampled from the same underlying distribution, remains challenging.…
Linear Genetic Programming (LGP) is a powerful technique that allows for a variety of problems to be solved using a linear representation of programs. However, there still exists some limitations to the technique, such as the need for…