Related papers: Heat-tree: Cross-platform software for interactive…
The technological advancements of the modern era have enabled the collection of huge amounts of data in science and beyond. Extracting useful information from such massive datasets is an ongoing challenge as traditional data visualization…
Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree…
$\textbf{Motivation:}$ Hierarchical data structures are prevalent across several fields of research, as they represent an organised and efficient approach to study complex interconnected systems. Their significance is particularly evident…
Variable trees are a new method for the exploration of discrete multivariate data. They display nested subsets and corresponding frequencies and percentages. Manual calculation of these quantities can be laborious, especially when there are…
Embedding learning transforms discrete data entities into continuous numerical representations, encoding features/properties of the entities. Despite the outstanding performance reported from different embedding learning algorithms, few…
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…
Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…
Human subject studies that map-like visualizations are as good or better than standard node-link representations of graphs, in terms of task performance, memorization and recall of the underlying data, and engagement [SSKB14, SSKB15]. With…
Summary: heatmaply is an R package for easily creating interactive cluster heatmaps that can be shared online as a stand-alone HTML file. Interactivity includes a tooltip display of values when hovering over cells, as well as the ability to…
Behavior Trees constitute a widespread AI tool which has been successfully spun out in robotics. Their advantages include simplicity, modularity, and reusability of code. However, Behavior Trees remain a high-level decision making engine;…
Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…
Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…
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…
Simulation of forest environments has applications from entertainment and art creation to commercial and scientific modelling. Due to the unique features and lighting in forests, a forest-specific simulator is desirable, however many…
Network visualization allows a quick glance at how nodes (or actors) are connected by edges (or ties). A conventional network diagram of "contact tree" maps out a root and branches that represent the structure of nodes and edges, often…
We introduce top trees as a design of a new simpler interface for data structures maintaining information in a fully-dynamic forest. We demonstrate how easy and versatile they are to use on a host of different applications. For example, we…
Analyzing large, multivariate graphs is an important problem in many domains, yet such graphs are challenging to visualize. In this paper, we introduce a novel, scalable, tree+table multivariate graph visualization technique, which makes…
PEACH Tree is an easy-to-use, online tool for displaying multiple sequence alignments and phylogenetic trees side-by-side. PEACH Tree is powerful for rapidly tracing evolutionary and transmission histories by filtering invariant sites out…
Background: Plant breeders are utilising an increasingly diverse range of data types in order to identify lines that have desirable characteristics which are suitable to be taken forward in plant breeding programmes. There are a number of…
Decision trees are flexible prediction models which are constructed to quantify outcome-covariate relationships and characterize relevant population subgroups. However, the standard graphical representation of fitted decision trees…