Related papers: Visualizing Multispecies Coalescent Trees: Drawing…

Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…

In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

Cutting planes (cuts) are crucial for solving Mixed Integer Linear Programming (MILP) problems. Advanced MILP solvers typically rely on manually designed heuristic algorithms for cut selection, which require much expert experience and…

To increase the interpretability and prediction accuracy of the Machine Learning (ML) models, visualization of ML models is a key part of the ML process. Decision Trees (DTs) are essential in machine learning (ML) because they are used to…

Many computer vision pipelines involve dynamic programming primitives such as finding a shortest path or the minimum energy solution in a tree-shaped probabilistic graphical model. In such cases, extracting not merely the best, but the set…

Algorithms for learning decision trees often include heuristic local-search operations such as (1) adjusting the threshold of a cut or (2) also exchanging the feature of that cut. We study minimizing the number of classification errors by…

Given the increasing interest in interpretable machine learning, classification trees have again attracted the attention of the scientific community because of their glass-box structure. These models are usually built using greedy…

The problem of inferring unknown graph edges from numerical data at a graph's nodes appears in many forms across machine learning. We study a version of this problem that arises in the field of \emph{landscape genetics}, where genetic…

The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…

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,…

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…

Kernelization is a theoretical formalization of efficient preprocessing for NP-hard problems. Empirically, preprocessing is highly successful in practice, for example in state-of-the-art ILP-solvers like CPLEX. Motivated by this, previous…

While the algorithmic drawing of static trees is well-understood and well-supported by software tools, creating animations depicting how a tree changes over time is currently difficult: software support, if available at all, is not…

Using evolutionary computation algorithms to solve multiple tasks with knowledge sharing is a promising approach. Image feature learning can be considered as a multitask problem because different tasks may have a similar feature space.…

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In…

Automatic detection and segmentation of overlapping leaves in dense foliage can be a difficult task, particularly for leaves with strong textures and high occlusions. We present Dense-Leaves, an image dataset with ground truth segmentation…

The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on…

To introduce selection into a model of coalescence, I explore the use of modified integer partitions that allow the identification of a preferred lineage. I show that a partition-partition transition matrix, along with Monte Carlo discrete…

We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…