Related papers: p-Adic numbers in bioinformatics: from genetic cod…

In phylogenetics it is of interest for rate matrix sets to satisfy closure under matrix multiplication as this makes finding the set of corresponding transition matrices possible without having to compute matrix exponentials. It is also…

This paper presents a memory-optimized metadata-based data structure for implementation of binary chromosome in Genetic Algorithm. In GA different types of genotypes are used depending on the problem domain. Among these, binary genotype is…

Poor DRAM technology scaling over the course of many years has caused DRAM-based main memory to increasingly become a larger system bottleneck. A major reason for the bottleneck is that data stored within DRAM must be moved across a…

Matrix multiplications between asymmetric bit-width operands, especially between 8- and 4-bit operands are likely to become a fundamental kernel of many important workloads including neural networks and machine learning. While existing SIMD…

Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…

We propose the use of sparse grids to accelerate particle-in-cell (PIC) schemes. By using the so-called `combination technique' from the sparse grids literature, we are able to dramatically increase the size of the spatial cells in…

Statistics in ranked lists is important in analyzing molecular biology measurement data, such as ChIP-seq, which yields ranked lists of genomic sequences. State of the art methods study fixed motifs in ranked lists. More flexible models…

Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…

Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prevision for the not yet measured thermodynamical…

In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably…

Pattern matching is commonly required in many application areas and bioinformatics is a major area of interest that requires both exact and approximate pattern matching. Much work has been done in this area, yet there is still a significant…

Various studies have shown an association between single nucleotide polymorphisms (SNPs) and common disease. We hypothesize that information encoded in the structure of SNP haploblock variation illumines molecular pathways and cellular…

This paper introduces a novel approach to multi-parameter persistence using 2-categorical structures. We develop a framework that captures hierarchical interactions between filter parameters, overcoming fundamental limitations of…

Upon a matrix representation of a binary bipartite network, via the permutation invariance, a coupling geometry is computed to approximate the minimum energy macrostate of a network's system. Such a macrostate is supposed to constitute the…

We present the extention and application of a new unsupervised statistical learning technique--the Partition Decoupling Method--to gene expression data. Because it has the ability to reveal non-linear and non-convex geometries present in…

Over fields of characteristic unequal to $2$, we can identify symmetric matrices with homogeneous polynomials of degree $2$. This allows us to view symmetric rank-metric codes as living inside the space of such polynomials. In this paper,…

In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…

Distributed quantum computing offers a potential solution to the complexity of superconducting chip hardware layouts and error correction algorithms. High-quality gates between distributed chips enable the simplification of existing error…

We introduce a Parametric Information Maximization (PIM) model for the Generalized Category Discovery (GCD) problem. Specifically, we propose a bi-level optimization formulation, which explores a parameterized family of objective functions,…

One of the major problems in modeling natural signals is that signals with very similar structure may locally have completely different measurements, e.g., images taken under different illumination conditions, or the speech signal captured…