Related papers: Popping Bubbles in Pangenome Graphs
Recent theoretical work has implicated fast bar formation modes and subsequent evolution as the creation mechanism for the observed peanut-shaped bulges in some edge-on disk galaxies. We demonstrate an N-body simulation of a disk undergoing…
The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconstructing this tree from genomic sequences is challenging due…
Brambles were introduced as the dual notion to treewidth, one of the most central concepts of the graph minor theory of Robertson and Seymour. Recently, Grohe and Marx showed that there are graphs G, in which every bramble of order larger…
We introduce a comprehensive data structure, tangle structure trees, which simultaneously displays all the $\mathcal{F}$-tangles of an abstract separation system for very general obstruction sets $\mathcal{F}$. It simultaneously also…
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify…
Polynomial functors model systems with interfaces: each polynomial specifies the outputs a system can produce and, for each output, the inputs it accepts. The bicategory $\mathbb{O}\mathbf{rg}$ of dynamic organizations…
Heavy and light particles are commonly found in many natural phenomena and industrial processes, such as suspensions of bubbles, dust, and droplets in incompressible turbulent flows. Based on a recent machine learning approach using a…
Graph theory has successfully used to solve a wide range of problems encountered in diverse fields such as medical sciences, neural networks, control theory, transportation, clustering analysis, expert systems, image capturing, and network…
We present a theory for slicing probabilistic imperative programs -- containing random assignments, and ``observe'' statements (for conditioning) -- represented as probabilistic control-flow graphs (pCFGs) whose nodes modify probability…
Provenance is a record that describes how entities, activities, and agents have influenced a piece of data; it is commonly represented as graphs with relevant labels on both their nodes and edges. With the growing adoption of provenance in…
Convolution trees, loopy belief propagation, and fast numerical p-convolution are combined for the first time to efficiently solve networks with several additive constraints between random variables. An implementation of this "convolution…
Uncovering rationales behind predictions of graph neural networks (GNNs) has received increasing attention over the years. Existing literature mainly focus on selecting a subgraph, through combinatorial optimization, to provide faithful…
Time series data across scientific domains are often collected under distinct states (e.g., tasks), wherein latent processes (e.g., biological factors) create complex inter- and intra-state variability. A key approach to capture this…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
Innovation and its complement exnovation describe the progression of realized possibilities from the past to the future, and the process depends on the structure of the underlying graph. For example, the phylogenetic tree represents the…
Graph pebbling is a problem in which pebbles are distributed across the vertices of a graph and moved according to a specific rule: two pebbles are removed from a vertex to place one on an adjacent vertex. The goal is to determine the…
Probabilistic graphical models (PGMs) provide a compact and flexible framework to model very complex real-life phenomena. They combine the probability theory which deals with uncertainty and logical structure represented by a graph which…
A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…
Physarum polycephalum is a single-celled, multi-nucleated slime mold whose body constitutes a network of veins. As it explores its environment, it adapts and optimizes its network to external stimuli. It has been shown to exhibit complex…
We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary…