Training-free Measures Based on Algorithmic Probability Identify High Nucleosome Occupancy in DNA Sequences

We introduce and study a set of training-free methods of information-theoretic and algorithmic complexity nature applied to DNA sequences to identify their potential capabilities to determine nucleosomal binding sites. We test our measures on well-studied genomic sequences of different sizes drawn from different sources. The measures reveal the known in vivo versus in vitro predictive discrepancies and uncover their potential to pinpoint (high) nucleosome occupancy. We explore different possible signals within and beyond the nucleosome length and find that complexity indices are informative of nucleosome occupancy. We compare against the gold standard (Kaplan model) and find similar and complementary results with the main difference that our sequence complexity approach. For example, for high occupancy, complexity-based scores outperform the Kaplan model for predicting binding representing a significant advancement in predicting the highest nucleosome occupancy following a training-free approach.Comment: 8 pages main text (4 figures), 12 total with Supplementary (1 figure

Image Compression Techniques: A Survey in Lossless and Lossy algorithms

The bandwidth of the communication networks has been increased continuously as results of technological advances. However, the introduction of new services and the expansion of the existing ones have resulted in even higher demand for the bandwidth. This explains the many efforts currently being invested in the area of data compression. The primary goal of these works is to develop techniques of coding information sources such as speech, image and video to reduce the number of bits required to represent a source without significantly degrading its quality. With the large increase in the generation of digital image data, there has been a correspondingly large increase in research activity in the field of image compression. The goal is to represent an image in the fewest number of bits without losing the essential information content within. Images carry three main type of information: redundant, irrelevant, and useful. Redundant information is the deterministic part of the information, which can be reproduced without loss from other information contained in the image. Irrelevant information is the part of information that has enormous details, which are beyond the limit of perceptual significance (i.e., psychovisual redundancy). Useful information, on the other hand, is the part of information, which is neither redundant nor irrelevant. Human usually observes decompressed images. Therefore, their fidelities are subject to the capabilities and limitations of the Human Visual System. This paper provides a survey on various image compression techniques, their limitations, compression rates and highlights current research in medical image compression

Intelligent Data Storage and Retrieval for Design Optimisation – an Overview

This paper documents the findings of a literature review conducted by the Sir Lawrence Wackett Centre for Aerospace Design Technology at RMIT University. The review investigates aspects of a proposed system for intelligent design optimisation. Such a system would be capable of efficiently storing (and compressing if required) a range of types of design data into an intelligent database. This database would be accessed by the system during subsequent design processes, allowing for search of relevant design data for re-use in later designs, allowing it to become very efficient in reducing the time for later designs as the database grows in size. Extensive research has been performed, in both theoretical aspects of the project, and practical examples of current similar systems. This research covers the areas of database systems, database queries, representation and compression of design data, geometric representation and heuristic methods for design applications.

Classical-to-Quantum Sequence Encoding in Genomics

DNA sequencing allows for the determination of the genetic code of an organism, and therefore is an indispensable tool that has applications in Medicine, Life Sciences, Evolutionary Biology, Food Sciences and Technology, and Agriculture. In this paper, we present several novel methods of performing classical-to-quantum data encoding inspired by various mathematical fields, and we demonstrate these ideas within Bioinformatics. In particular, we introduce algorithms that draw inspiration from diverse fields such as Electrical and Electronic Engineering, Information Theory, Differential Geometry, and Neural Network architectures. We provide a complete overview of the existing data encoding schemes and show how to use them in Genomics. The algorithms provided utilise lossless compression, wavelet-based encoding, and information entropy. Moreover, we propose a contemporary method for testing encoded DNA sequences using Quantum Boltzmann Machines. To evaluate the effectiveness of our algorithms, we discuss a potential dataset that serves as a sandbox environment for testing against real-world scenarios. Our research contributes to developing classical-to-quantum data encoding methods in the science of Bioinformatics by introducing innovative algorithms that utilise diverse fields and advanced techniques. Our findings offer insights into the potential of Quantum Computing in Bioinformatics and have implications for future research in this area.Comment: 58 pages, 14 figure

A multi-objective performance optimisation framework for video coding

Digital video technologies have become an essential part of the way visual information is created, consumed and communicated. However, due to the unprecedented growth of digital video technologies, competition for bandwidth resources has become fierce. This has highlighted a critical need for optimising the performance of video encoders. However, there is a dual optimisation problem, wherein, the objective is to reduce the buffer and memory requirements while maintaining the quality of the encoded video. Additionally, through the analysis of existing video compression techniques, it was found that the operation of video encoders requires the optimisation of numerous decision parameters to achieve the best trade-offs between factors that affect visual quality; given the resource limitations arising from operational constraints such as memory and complexity. The research in this thesis has focused on optimising the performance of the H.264/AVC video encoder, a process that involved finding solutions for multiple conflicting objectives. As part of this research, an automated tool for optimising video compression to achieve an optimal trade-off between bit rate and visual quality, given maximum allowed memory and computational complexity constraints, within a diverse range of scene environments, has been developed. Moreover, the evaluation of this optimisation framework has highlighted the effectiveness of the developed solution

Investigation of Different Video Compression Schemes Using Neural Networks

Image/Video compression has great significance in the communication of motion pictures and still images. The need for compression has resulted in the development of various techniques including transform coding, vector quantization and neural networks. this thesis neural network based methods are investigated to achieve good compression ratios while maintaining the image quality. Parts of this investigation include motion detection, and weight retraining. An adaptive technique is employed to improve the video frame quality for a given compression ratio by frequently updating the weights obtained from training. More specifically, weight retraining is performed only when the error exceeds a given threshold value. Image quality is measured objectively, using the peak signal-to-noise ratio versus performance measure. Results show the improved performance of the proposed architecture compared to existing approaches. The proposed method is implemented in MATLAB and the results obtained such as compression ratio versus signalto- noise ratio are presented

EXTRACTION AND PREDICTION OF SYSTEM PROPERTIES USING VARIABLE-N-GRAM MODELING AND COMPRESSIVE HASHING

In modern computer systems, memory accesses and power management are the two major performance limiting factors. Accesses to main memory are very slow when compared to operations within a processor chip. Hardware write buffers, caches, out-of-order execution, and prefetch logic, are commonly used to reduce the time spent waiting for main memory accesses. Compiler loop interchange and data layout transformations also can help. Unfortunately, large data structures often have access patterns for which none of the standard approaches are useful. Using smaller data structures can significantly improve performance by allowing the data to reside in higher levels of the memory hierarchy. This dissertation proposes using lossy data compression technology called ’Compressive Hashing’ to create “surrogates”, that can augment original large data structures to yield faster typical data access. One way to optimize system performance for power consumption is to provide a predictive control of system-level energy use. This dissertation creates a novel instruction-level cost model called the variable-n-gram model, which is closely related to N-Gram analysis commonly used in computational linguistics. This model does not require direct knowledge of complex architectural details, and is capable of determining performance relationships between instructions from an execution trace. Experimental measurements are used to derive a context-sensitive model for performance of each type of instruction in the context of an N-instruction sequence. Dynamic runtime power prediction mechanisms often suffer from high overhead costs. To reduce the overhead, this dissertation encodes the static instruction-level predictions into a data structure and uses compressive hashing to provide on-demand runtime access to those predictions. Genetic programming is used to evolve compressive hash functions and performance analysis of applications shows that, runtime access overhead can be reduced by a factor of ~3x-9x

Recent Advances in Steganography

Steganography is the art and science of communicating which hides the existence of the communication. Steganographic technologies are an important part of the future of Internet security and privacy on open systems such as the Internet. This book's focus is on a relatively new field of study in Steganography and it takes a look at this technology by introducing the readers various concepts of Steganography and Steganalysis. The book has a brief history of steganography and it surveys steganalysis methods considering their modeling techniques. Some new steganography techniques for hiding secret data in images are presented. Furthermore, steganography in speeches is reviewed, and a new approach for hiding data in speeches is introduced