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We have performed the comparative spectral analysis of structural connectomes for various organisms using open-access data. Our analysis indicates several new peculiar features of the human connectome. We found that the spectral density of…
Power spectra of human DNA base C+G frequency distribution in all available contiguous sections exhibit the universal inverse power law form of the statistical normal distribution for the 24 chromosomes. Inverse power law form for power…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring learning dataset of already known genes. The fact that unsupervised gene-detection is possible closely connected to…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Similarity metrics such as representational similarity analysis (RSA) and centered kernel alignment (CKA) have been used to compare layer-wise representations between neural networks. However, these metrics are confounded by the population…
Spectral clustering and co-clustering are well-known techniques in data analysis, and recent work has extended spectral clustering to square, symmetric tensors and hypermatrices derived from a network. We develop a new tensor spectral…
A numerical approach is developed for detecting the equivalence of deep learning architectures. The method is based on generating Mixed Matrix Ensembles (MMEs) out of deep neural network weight matrices and {\it conjugate circular ensemble}…
Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores we develop a maximum…
Compressed sensing (CS) is a powerful method routinely employed to accelerate image acquisition. It is particularly suited to situations when the image under consideration is sparse but can be sampled in a basis where it is non-sparse. Here…
h-BCN is an intriguing material system where the bandgap varies considerably depending on the atomic configuration, even at a fixed composition. Exploring stable atomic configurations in this system is crucial for discussing the energetic…
High-throughput material screening for the discovery and design of novel functional materials requires automatized analyses of theoretical and experimental data. Here we study the subject of human-free analyses of one-dimensional…
Principal component analysis continues to be a powerful tool in dimension reduction of high dimensional data. We assume a variance-diverging model and use the high-dimension, low-sample-size asymptotics to show that even though the…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…
In this paper, we address the problem of identifying protein functionality using the information contained in its aminoacid sequence. We propose a method to define sequence similarity relationships that can be used as input for…
Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length to locate distal enhancers, which may influence target…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the…