Related papers: Popping Bubbles in Pangenome Graphs
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
Bloom filters are probabilistic data structures commonly used for approximate membership problems in many areas of Computer Science (networking, distributed systems, databases, etc.). With the increase in data size and distribution of data,…
Graph pebbling is the study of moving discrete pebbles from certain initial distributions on the vertices of a graph to various target distributions via pebbling moves. A pebbling move removes two pebbles from a vertex and places one pebble…
We use inelastic hard sphere molecular dynamics simulations and laboratory experiments to study patterns in vertically oscillated granular layers. The simulations and experiments reveal that {\em phase bubbles} spontaneously nucleate in the…
Graph transformation is the rule-based modification of graphs, and is a discipline dating back to the 1970s. In general, to match the left-hand graph of a fixed rule within a host graph requires polynomial time, but to improve matching…
In an experiment on a turbulent jet, we detect interfacial turbulent layers in a frame that moves, on average, along with the \tnti. This significantly prolongs the observation time of scalar and velocity structures and enables the…
The truss, a relaxation of the clique based on triangles, serves to identify clusters of actors in a way that is easy to interpret and is computationally attractive. This paper introduces the 4-cycle-based relative to the truss, called the…
In Linguistics, a grapheme is a written unit of a writing system corresponding to a phonological sound. In Natural Language Processing tasks, written language is analysed through two different mediums, word analysis, and character analysis.…
Exchangeable random graphs, which include some of the most widely studied network models, have emerged as the mainstay of statistical network analysis in recent years. Graphons, which are the central objects in graph limit theory, provide a…
Existing defects in software components is unavoidable and leads to not only a waste of time and money but also many serious consequences. To build predictive models, previous studies focus on manually extracting features or using tree…
Piecewise growth mixture models (PGMM) are a flexible and useful class of methods for analyzing segmented trends in individual growth trajectory over time, where the individuals come from a mixture of two or more latent classes. These…
The past few years have seen intensive research efforts carried out in some apparently unrelated areas of dynamic systems -- delay-tolerant networks, opportunistic-mobility networks, social networks -- obtaining closely related insights.…
We present diffusion-convolutional neural networks (DCNNs), a new model for graph-structured data. Through the introduction of a diffusion-convolution operation, we show how diffusion-based representations can be learned from…
Tangles were originally introduced as a concept to formalize regions of high connectivity in graphs. In recent years, they have also been discovered as a link between structural graph theory and data science: when interpreting similarity in…
In Bayesian structure learning, we are interested in inferring a distribution over the directed acyclic graph (DAG) structure of Bayesian networks, from data. Defining such a distribution is very challenging, due to the combinatorially…
Using neural networks to solve variational problems, and other scientific machine learning tasks, has been limited by a lack of consistency and an inability to exactly integrate expressions involving neural network architectures. We address…
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…
Agglomeration is an industrially relevant process for the production of bulk materials in which the product properties depend on the morphology of the agglomerates, e.g., on the distribution of size and shape descriptors. Thus, accurate…
Wavelet trees are widely used in the representation of sequences, permutations, text collections, binary relations, discrete points, and other succinct data structures. We show, however, that this still falls short of exploiting all of the…