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We extend biologically-informed neural networks (BINNs) for genomic prediction (GP) and selection (GS) in crops by integrating thousands of single-nucleotide polymorphisms (SNPs) with multi-omics measurements and prior biological knowledge.…
Several modern applications require the integration of multiple large data matrices that have shared rows and/or columns. For example, cancer studies that integrate multiple omics platforms across multiple types of cancer, pan-omics…
A linear code with parameters $[n, k, n - k + 1]$ is called maximum distance separable (MDS), and one with parameters $[n, k, n - k]$ is called almost MDS (AMDS). A code is near-MDS (NMDS) if both it and its dual are AMDS. NMDS codes…
This paper examines the Arithmetically Cohen-Macaulay (ACM) property for certain codimension 2 varieties in $\mathbb P^1\times \mathbb P^2$ called sets of lines in $\mathbb P^1\times \mathbb P^2$ (not necessarily reduced). We discuss some…
We describe a framework for random pairwise comparisons matrices, inspired by selected constructions releted to the so called inconsistency reduction of pairwise comparisons (PC) matrices. In to build up structures on random pairwise…
The topology, the symmetry involving the shape of dielectric cylinders, and the lattice structure are among the most important ingredients in the architecture of photonic crystals. In this paper, we present a systematic derivation of the…
This thesis investigates the use of problem-specific knowledge to enhance a genetic algorithm approach to multiple-choice optimisation problems.It shows that such information can significantly enhance performance, but that the choice of…
The characteristics and determinants of health and disease are often organised in space, reflecting our spatially extended nature. Understanding the influence of such factors requires models capable of capturing spatial relations. Though a…
Motivated by the important problem of detecting association between genetic markers and binary traits in genome-wide association studies, we present a novel Bayesian model that establishes a hierarchy between markers and genes by defining…
This paper presents an efficient optimization technique for super-resolution two-dimensional (2D) direction of arrival (DOA) estimation by introducing a new formulation of atomic norm minimization (ANM). ANM allows gridless angle estimation…
Distributed approaches based on the map-reduce programming paradigm have started to be proposed in the bioinformatics domain, due to the large amount of data produced by the next-generation sequencing techniques. However, the use of…
Spectral clustering is one of the most popular clustering approaches with the capability to handle some challenging clustering problems. Most spectral clustering methods provide a nonlinear map from the data manifold to a subspace. Only a…
Recent publications have described and applied a novel metric that quantifies the genetic distance of an individual with respect to two population samples, and have suggested that the metric makes it possible to infer the presence of an…
We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the…
End-to-end topological learning using 1-parameter persistence is well-known. We show that the framework can be enhanced using 2-parameter persistence by adopting a recently introduced 2-parameter persistence based vectorization technique…
In this paper, we propose a novel construction for secure distributed matrix multiplication (SDMM) based on algebraic geometry (AG) codes, which we call the PoleGap SDMM scheme. The proposed construction is inspired by the GASP code, where…
The statistics of gap ratios between consecutive energy levels is a widely used tool, in particular in the context of many-body physics, to distinguish between chaotic and integrable systems, described respectively by Gaussian ensembles of…
The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has…
The applications of additive codes mainly lie in quantum error correction and quantum computing. Due to their applications in quantum codes, additive codes have grown in importance. In addition to this, additive codes allow the…
Exploiting geometric structure to improve the asymptotic complexity of discrete assignment problems is a well-studied subject. In contrast, the practical advantages of using geometry for such problems have not been explored. We implement…