Related papers: Visualizing Co-Phylogenetic Reconciliations
Storyline visualizations are a popular way of visualizing characters and their interactions over time: Characters are drawn as x-monotone curves and interactions are visualized through close proximity of the corresponding character curves…
The Platonic Representation Hypothesis posits that neural networks trained on different modalities converge toward a shared statistical model of the world. Recent work exploits this convergence by aligning frozen pretrained vision and…
Multi-population evolutionary algorithms are, by nature, highly complex and difficult to describe. Even two populations working in concert (or opposition) present a myriad of potential configurations that are often difficult to relate using…
Decompositions of networks are useful not only for structural exploration. They also have implications and use in analysis and computational solution of processes (such as the Ising model, percolation, SIR model) running on a given network.…
This article is addressing a recurrent problem in biology: mining newly built large scale networks. Our approach consists in comparing these new networks to well known ones. The visual backbone of this comparative analysis is provided by a…
Node-link diagrams are a popular method for representing graphs that capture relationships between individuals, businesses, proteins, and telecommunication endpoints. However, node-link diagrams may fail to convey insights regarding graph…
This paper presents a co-clustering technique that, given a collection of images and their hierarchies, clusters nodes from these hierarchies to obtain a coherent multiresolution representation of the image collection. We formalize the…
For convolutional neural network models that optimize an image embedding, we propose a method to highlight the regions of images that contribute most to pairwise similarity. This work is a corollary to the visualization tools developed for…
We describe an new algorithm for visualizing an alignment of biological sequences according to a probabilistic model of evolution. The resulting data array is readily interpreted by the human eye and amenable to digital image techniques. We…
Most algorithms for computing persistent homology do so by tracking cycles that represent homology classes. There are many choices of such cycles, and specific choices have found different uses in applications. Although it is known that…
This communication describes a representation of images as a set of edges characterized by their position and orientation. This representation allows the comparison of two images and the computation of their similarity. The first step in…
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…
In numerous applications, it is required to produce forecasts for multiple time-series at different hierarchy levels. An obvious example is given by the supply chain in which demand forecasting may be needed at a store, city, or country…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
The common trade-offs of state-of-the-art methods for multi-shape representation (a single model "packing" multiple objects) involve trading modeling accuracy against memory and storage. We show how to encode multiple shapes represented as…
Vision-language model (VLM) encoders such as CLIP enable strong retrieval and zero-shot classification in a shared image-text embedding space, yet the semantic organization of this space is rarely inspected. We present a post-hoc framework…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop…
We examine visual representations of data that make use of combinations of both 2D and 3D data mappings. Combining 2D and 3D representations is a common technique that allows viewers to understand multiple facets of the data with which they…
We introduce a dynamic approach to probabilistic forecast reconciliation at scale. Our model differs from the existing literature in this area in several important ways. Firstly we explicitly allow the weights allocated to the base…