Related papers: Informed and Automated k-Mer Size Selection for Ge…
We present a new way to summarize and select mixture models via the hierarchical clustering tree (dendrogram) constructed from an overfitted latent mixing measure. Our proposed method bridges agglomerative hierarchical clustering and…
High-throughput chromatin conformation capture (Hi-C) data provide insights into the 3D structure of chromosomes, with normalization being a crucial pre-processing step. A common technique for normalization is matrix balancing, which…
In general, we can not use algebraic or enumerative methods to optimize a quality control (QC) procedure so as to detect the critical random and systematic analytical errors with stated probabilities, while the probability for false…
Uniform sampling from graphical realizations of a given degree sequence is a fundamental component in simulation-based measurements of network observables, with applications ranging from epidemics, through social networks to Internet…
Knowledge hypergraphs surpass traditional binary knowledge graphs by encapsulating complex $n$-ary atomic facts, providing a more comprehensive paradigm for semantic representation. However, constructing high-quality hypergraphs remains…
The standard evaluation protocol for measuring the quality of Knowledge Graph Completion methods - the task of inferring new links to be added to a graph - typically involves a step which ranks every entity of a Knowledge Graph to assess…
Successful material selection is critical in designing and manufacturing products for design automation. Designers leverage their knowledge and experience to create high-quality designs by selecting the most appropriate materials through…
As the multiplexing power of spectroscopic instruments increases, so does the need for automated analysis. In practice, the bottleneck for speed is the calculation of model spectra to evaluate the likelihood of candidate parameters. This…
The Boltzmann model for the random generation of "decomposable" combinatorial structures is a set of techniques that allows for efficient random sampling algorithms for a large class of families of discrete objects. The usual requirement of…
Say that a graph G has property $\mathcal{K}$ if the size of its maximum matching is equal to the order of a minimal vertex cover. We study the following process. Set $N:= \binom{n}{2}$ and let $e_1, e_2, \dots e_{N}$ be a uniformly random…
Large medical imaging data sets are becoming increasingly available, but ensuring sample quality without significant artefacts is challenging. Existing methods for identifying imperfections in medical imaging rely on data-intensive…
Strain gradient theory is an accurate model for capturing the size effect and localization phenomena. However, the challenge in identification of corresponding constitutive parameters limits the practical application of the theory. We…
Generating graphs that preserve characteristic structures while promoting sample diversity can be challenging, especially when the number of graph observations is small. Here, we tackle the problem of graph generation from only one observed…
Motivation: De Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many…
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…
The objective of this paper is to define an effective strategy for building an ensemble of Genetic Programming (GP) models. Ensemble methods are widely used in machine learning due to their features: they average out biases, they reduce the…
Automatic construction of large knowledge graphs (KG) by mining web-scale text datasets has received considerable attention recently. Estimating accuracy of such automatically constructed KGs is a challenging problem due to their size and…
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
This paper establishes formal mathematical foundations linking Chaos Game Representations (CGR) of DNA sequences to their underlying $k$-mer frequencies. We prove that the Frequency CGR (FCGR) of order $k$ is mathematically equivalent to a…