Related papers: Three dimensional chaos game representation of pro…
The chaos game representation (CGR) is an interesting method to visualize one-dimensional sequences. In this paper, we show how to construct a chaos game representation. The applications mentioned here are biological, in which CGR was able…
A 3D chaos game is shown to be a useful way for encoding DNA sequences. Since matching subsequences in DNA converge in space in 3D chaos game encoding, a DNA sequence's 3D chaos game representation can be used to compare DNA sequences…
DNA sequences are fundamental for encoding genetic information. The genetic information may not only be understood by symbolic sequences but also from the hidden signals inside the sequences. The symbolic sequences need to be transformed…
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…
Biological classification with interpretability remains a challenging task. For this, we introduce a novel encoding framework, Multi-Scale Reversible Chaos Game Representation (MS-RCGR), that transforms biological sequences into…
Graphs as a type of data structure have recently attracted significant attention. Representation learning of geometric graphs has achieved great success in many fields including molecular, social, and financial networks. It is natural to…
This study proposes CGRclust, a novel combination of unsupervised twin contrastive clustering of Chaos Game Representations (CGR) of DNA sequences, with convolutional neural networks (CNNs). To the best of our knowledge, CGRclust is the…
Researchers in the field of DNA-based chaotic cryptography have recently proposed a set of novel and efficient image encryption algorithms. In this paper, we present a comprehensive summary of those techniques, which are available in the…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
We present a novel information-preserving Chaos Game Representation (CGR) method, also called Reverse-CGR (R-CGR), for biological sequence analysis that addresses the fundamental limitation of traditional CGR approaches - the loss of…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
We present a three-dimensional graph convolutional network (3DGCN), which predicts molecular properties and biochemical activities, based on 3D molecular graph. In the 3DGCN, graph convolution is unified with learning operations on the…
We demonstrate the presence of chaos in stochastic simulations that are widely used to study biodiversity in nature. The investigation deals with a set of three distinct species that evolve according to the standard rules of mobility,…
Nowadays, studying introns is becoming a very promising field in the genomics. Even though they play a role in the dynamic regulation of gene and in the organism's evolution, introns have not attracted enough attention like exons did;…
In this work, we applied the Chaos Game Representation (CGR) to the complete human genomic sequence T2T-CHM13v2.0, analyzing the entire chromosome assembly and each chromosome separately, including mitochondrial DNA. Multifractal spectra…
Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D…
The analysis of sequences (e.g., protein, DNA, and SMILES string) is essential for disease diagnosis, biomaterial engineering, genetic engineering, and drug discovery domains. Conventional analytical methods focus on transforming sequences…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
Dimensionality reduction is ubiquitous in analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed…