Related papers: Visualizing Multispecies Coalescent Trees: Drawing…
A graph is geometric 1-planar if it admits a straight-line drawing where each edge is crossed at most once. We provide the first systematic study of the parameterized complexity of recognizing geometric 1-planar graphs. By substantially…
The past few years have witnessed growth in the computational requirements for training deep convolutional neural networks. Current approaches parallelize training onto multiple devices by applying a single parallelization strategy (e.g.,…
The analysis of the internal structure of trees is highly important for both forest experts, biological scientists, and the wood industry. Traditionally, CT-scanners are considered as the most efficient way to get an accurate inner…
Working with exhaustive search on large dataset is infeasible for several reasons. Recently, developed techniques that made pattern set mining feasible by a general solver with long execution time that supports heuristic search and are…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common…
Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic…
Neural codes are binary codes in $\{0,1\}^n$; here we focus on the ones which represent the firing patterns of a type of neurons called place cells. There is much interest in determining which neural codes can be realized by a collection of…
Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between species trees obtained using different methods or data…
We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can…
Optimal path planning involves finding a feasible state sequence between a start and a goal that optimizes an objective. This process relies on heuristic functions to guide the search direction. While a robust function can improve search…
This paper describes structuring data and constructing plots to explore forest classification models interactively. A forest classifier is an example of an ensemble, produced by bagging multiple trees. The process of bagging and combining…
This paper studies constructive heuristics for the minimum labelling spanning tree (MLST) problem. The purpose is to find a spanning tree that uses edges that are as similar as possible. Given an undirected labeled connected graph (i.e.,…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
The crossing resolution of a non-planar drawing of a graph is the value of the minimum angle formed by any pair of crossing edges. Recent experiments have shown that the larger the crossing resolution is, the easier it is to read and…
Recently, multiple formulations of vision problems as probabilistic inversions of generative models based on computer graphics have been proposed. However, applications to 3D perception from natural images have focused on low-dimensional…
Motivated by interpretability and reliability, we investigate whether large language models (LLMs) deploy universal geometric structures to encode discrete, graph-structured knowledge. To this end, we present two complementary experimental…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…