Related papers: Spectral concepts in genome informational analysis
Understanding the spectral properties of kernels offers a principled perspective on generalization and representation quality. While deep models achieve state-of-the-art accuracy in molecular property prediction, kernel methods remain…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
In this paper, we propose a new spectral-based approach to hypothesis testing for populations of networks. The primary goal is to develop a test to determine whether two given samples of networks come from the same random model or…
We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from…
Large-scale statistical analysis of data sets associated with genome sequences plays an important role in modern biology. A key component of such statistical analyses is the computation of $p$-values and confidence bounds for statistics…
In this study, we present a novel approach for predicting genomic information from medical imaging modalities using a transformer-based model. We aim to bridge the gap between imaging and genomics data by leveraging transformer networks,…
Despite the availability of various sequence analysis models, comparative genomic analysis remains a challenge in genomics, genetics, and phylogenetics. Commutative algebra, a fundamental tool in algebraic geometry and number theory, has…
Basic quantum information measures involved in the information analysis of quantum systems are considered. It is shown that the main quantum information measurement methods depend on whether the corresponding quantum events are compatible…
The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a…
Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and…
Spectrograms visualize the frequency components of a given signal which may be an audio signal or even a time-series signal. Audio signals have higher sampling rate and high variability of frequency with time. Spectrograms can capture such…
k-mers (nucleotide strings of length k) form the basis of several algorithms in computational genomics. In particular, k-mer abundance information in sequence data is useful in read error correction, parameter estimation for genome…
We review the field of Quantum Optical Information from elementary considerations through to quantum computation schemes. We illustrate our discussion with descriptions of experimental demonstrations of key communication and processing…
We describe some aspects of spectral theory that involve algebraic considerations but need no analysis. Some of the important applications of the results are to the algebra of $n\times n$ matrices with entries that are polynomials or more…
The coherent information concept is used to analyze a variety of simple quantum systems. Coherent information was calculated for the information decay in a two-level atom in the presence of an external resonant field, for the information…
We derive a message passing method for computing the spectra of locally tree-like networks and an approximation to it that allows us to compute closed-form expressions or fast numerical approximates for the spectral density of random graphs…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
A spectrograph is an optical instrument that disperses photons of different energies into distinct directions and space locations, and images photon spectra on a position-sensitive detector. Spectrographs consist of collimating, angular…
We propose a new kernel for biological sequences which borrows ideas and techniques from information theory and data compression. This kernel can be used in combination with any kernel method, in particular Support Vector Machines for…