Encoding DNA sequences by integer chaos game representation

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 into numerical sequences so the hidden signals can be revealed by signal processing techniques. All current transformation methods encode DNA sequences into numerical values of the same length. These representations have limitations in the applications of genomic signal compression, encryption, and steganography. We propose an integer chaos game representation (iCGR) of DNA sequences and a lossless encoding method DNA sequences by the iCGR. In the iCGR method, a DNA sequence is represented by the iterated function of the nucleotides and their positions in the sequence. Then the DNA sequence can be uniquely encoded and recovered using three integers from iCGR. One integer is the sequence length and the other two integers represent the accumulated distributions of nucleotides in the sequence. The integer encoding scheme can compress a DNA sequence by 2 bits per nucleotide. The integer representation of DNA sequences provides a prospective tool for sequence compression, encryption, and steganography. The Python programs in this study are freely available to the public at https://github.com/cyinbox/iCG

Hybrid chaos-based image encryption algorithm using Chebyshev chaotic map with deoxyribonucleic acid sequence and its performance evaluation

The media content shared on the internet has increased tremendously nowadays. The streaming service has major role in contributing to internet traffic all over the world. As the major content shared are in the form of images and rapid increase in computing power a better and complex encryption standard is needed to protect this data from being leaked to unauthorized person. Our proposed system makes use of chaotic maps, deoxyribonucleic acid (DNA) coding and ribonucleic acid (RNA) coding technique to encrypt the image. As videos are nothing but collection of images played at the rate of minimum 30 frames/images per second, this methodology can also be used to encrypt videos. The complexity and dynamic nature of chaotic systems makes decryption of content by unauthorized personal difficult. The hybrid usage of chaotic systems along with DNA and RNA sequencing improves the encryption efficiency of the algorithm and also makes it possible to decrypt the images at the same time without consuming too much of computation power

Entropy in Image Analysis II

Image analysis is a fundamental task for any application where extracting information from images is required. The analysis requires highly sophisticated numerical and analytical methods, particularly for those applications in medicine, security, and other fields where the results of the processing consist of data of vital importance. This fact is evident from all the articles composing the Special Issue "Entropy in Image Analysis II", in which the authors used widely tested methods to verify their results. In the process of reading the present volume, the reader will appreciate the richness of their methods and applications, in particular for medical imaging and image security, and a remarkable cross-fertilization among the proposed research areas

Molecular Distance Maps: An alignment-free computational tool for analyzing and visualizing DNA sequences\u27 interrelationships

In an attempt to identify and classify species based on genetic evidence, we propose a novel combination of methods to quantify and visualize the interrelationships between thousand of species. This is possible by using Chaos Game Representation (CGR) of DNA sequences to compute genomic signatures which we then compare by computing pairwise distances. In the last step, the original DNA sequences are embedded in a high dimensional space using Multi-Dimensional Scaling (MDS) before everything is projected on a Euclidean 3D space. To start with, we apply this method to a mitochondrial DNA dataset from NCBI containing over 3,000 species. The analysis shows that the oligomer composition of full mtDNA sequences can be a source of taxonomic information, suggesting that this method could be used for unclassified species and taxonomic controversies. Next, we test the hypothesis that CGR-based genomic signature is preserved along a species\u27 genome by comparing inter- and intra-genomic signatures of nuclear DNA sequences from six different organisms, one from each kingdom of life. We also compare six different distances and we assess their performance using statistical measures. Our results support the existence of a genomic signature for a species\u27 genome at the kingdom level. In addition, we test whether CGR-based genomic signatures originating only from nuclear DNA can be used to distinguish between closely-related species and we answer in the negative. To overcome this limitation, we propose the concept of ``composite signatures\u27\u27 which combine information from different types of DNA and we show that they can effectively distinguish all closely-related species under consideration. We also propose the concept of ``assembled signatures\u27\u27 which, among other advantages, do not require a long contiguous DNA sequence but can be built from smaller ones consisting of ~100-300 base pairs. Finally, we design an interactive webtool MoDMaps3D for building three-dimensional Molecular Distance Maps. The user can explore an already existing map or build his/her own using NCBI\u27s accession numbers as input. MoDMaps3D is platform independent, written in Javascript and can run in all major modern browsers

Fake Malware Generation Using HMM and GAN

In the past decade, the number of malware attacks have grown considerably and, more importantly, evolved. Many researchers have successfully integrated state-of-the-art machine learning techniques to combat this ever present and rising threat to information security. However, the lack of enough data to appropriately train these machine learning models is one big challenge that is still present. Generative modelling has proven to be very efficient at generating image-like synthesized data that can match the actual data distribution. In this paper, we aim to generate malware samples as opcode sequences and attempt to differentiate them from the real ones with the goal to build fake malware data that can be used to effectively train the machine learning models. We use and compare different Generative Adversarial Networks (GAN) algorithms and Hidden Markov Models (HMM) to generate such fake samples obtaining promising results

Crowdfunding Non-fungible Tokens on the Blockchain

Non-fungible tokens (NFTs) have been used as a way of rewarding content creators. Artists publish their works on the blockchain as NFTs, which they can then sell. The buyer of an NFT then holds ownership of a unique digital asset, which can be resold in much the same way that real-world art collectors might trade paintings. However, while a deal of effort has been spent on selling works of art on the blockchain, very little attention has been paid to using the blockchain as a means of fundraising to help finance the artist’s work in the first place. Additionally, while blockchains like Ethereum are ideal for smaller works of art, additional support is needed when the artwork is larger than is feasible to store on the blockchain. In this paper, we propose a fundraising mechanism that will help artists to gain financial support for their initiatives, and where the backers can receive a share of the profits in exchange for their support. We discuss our prototype implementation using the SpartanGold framework. We then discuss how this system could be expanded to support large NFTs with the 0Chain blockchain, and describe how we could provide support for ongoing storage of these NFTs

Entropy in Image Analysis III

Image analysis can be applied to rich and assorted scenarios; therefore, the aim of this recent research field is not only to mimic the human vision system. Image analysis is the main methods that computers are using today, and there is body of knowledge that they will be able to manage in a totally unsupervised manner in future, thanks to their artificial intelligence. The articles published in the book clearly show such a future

Undecidability and novelty generation in RNA automata

As today, the evolution of the earliest life was an exploration of adaptive forms. The earliest life also undertook great leaps in the overall complexity of the molecular dynamic system. A theoretical framework for this form of evolution has not been resolved. This thesis builds upon the discoveries of early life chemistry and seeks to move towards understanding the organising principles that allowed life to evolve. In computer science novelty generation is often linked to universal computation, as the boundaries of complexity are found at the edge of undecidability where self-referential incomputable statements can be generated. At the intersection of early life chemistry and computer science, this thesis draws from the dominant RNA-world model and incorporates this into the constructions of automata theory to investigate the computational properties of a system of single-stranded RNA molecules. Limited to the plausible RNA-world operations of ligation and cleavage, RNA automata are constructed of increasing complexity; from the Finite Automaton (RNA-FA) to the Turing machine equivalent 2-stack Pushdown Automaton (RNA-2PDA) and ultimately a universal RNA-UPDA with the capacity to generate undecidability. A path forward from undecidable computation in RNA automata to novelty generation is mapped. The coupled phenotype-environment space is presented as a framework for biological system expansion. The framework draws on the discoveries of Alan Turing and Emil Post on the continual expansion of computational systems overcoming their undecidable boundaries. An analogue of these extensions, from the perspective of ecological developmental biology, offers a self-referential model of the organism coupled with its environment, which is capable of novelty generation. This thesis concludes by outlining future avenues of research to develop the coupled phenotype-environment space framework as well as identifying biological computational constructions in extant organisms