Sublinear Computation Paradigm

This open access book gives an overview of cutting-edge work on a new paradigm called the “sublinear computation paradigm,” which was proposed in the large multiyear academic research project “Foundations of Innovative Algorithms for Big Data.” That project ran from October 2014 to March 2020, in Japan. To handle the unprecedented explosion of big data sets in research, industry, and other areas of society, there is an urgent need to develop novel methods and approaches for big data analysis. To meet this need, innovative changes in algorithm theory for big data are being pursued. For example, polynomial-time algorithms have thus far been regarded as “fast,” but if a quadratic-time algorithm is applied to a petabyte-scale or larger big data set, problems are encountered in terms of computational resources or running time. To deal with this critical computational and algorithmic bottleneck, linear, sublinear, and constant time algorithms are required. The sublinear computation paradigm is proposed here in order to support innovation in the big data era. A foundation of innovative algorithms has been created by developing computational procedures, data structures, and modelling techniques for big data. The project is organized into three teams that focus on sublinear algorithms, sublinear data structures, and sublinear modelling. The work has provided high-level academic research results of strong computational and algorithmic interest, which are presented in this book. The book consists of five parts: Part I, which consists of a single chapter on the concept of the sublinear computation paradigm; Parts II, III, and IV review results on sublinear algorithms, sublinear data structures, and sublinear modelling, respectively; Part V presents application results. The information presented here will inspire the researchers who work in the field of modern algorithms

The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure

Energy efficient enabling technologies for semantic video processing on mobile devices

Semantic object-based processing will play an increasingly important role in future multimedia systems due to the ubiquity of digital multimedia capture/playback technologies and increasing storage capacity. Although the object based paradigm has many undeniable benefits, numerous technical challenges remain before the applications becomes pervasive, particularly on computational constrained mobile devices. A fundamental issue is the ill-posed problem of semantic object segmentation. Furthermore, on battery powered mobile computing devices, the additional algorithmic complexity of semantic object based processing compared to conventional video processing is highly undesirable both from a real-time operation and battery life perspective. This thesis attempts to tackle these issues by firstly constraining the solution space and focusing on the human face as a primary semantic concept of use to users of mobile devices. A novel face detection algorithm is proposed, which from the outset was designed to be amenable to be offloaded from the host microprocessor to dedicated hardware, thereby providing real-time performance and reducing power consumption. The algorithm uses an Artificial Neural Network (ANN), whose topology and weights are evolved via a genetic algorithm (GA). The computational burden of the ANN evaluation is offloaded to a dedicated hardware accelerator, which is capable of processing any evolved network topology. Efficient arithmetic circuitry, which leverages modified Booth recoding, column compressors and carry save adders, is adopted throughout the design. To tackle the increased computational costs associated with object tracking or object based shape encoding, a novel energy efficient binary motion estimation architecture is proposed. Energy is reduced in the proposed motion estimation architecture by minimising the redundant operations inherent in the binary data. Both architectures are shown to compare favourable with the relevant prior art

Forensic Ancestry Analysis with Autosomal Polymorphisms

The inference of ancestry from biological material left at a crimescene has been a longstanding but specialised forensic technique, often lacking sufficient detail to make a reliable inference of ancestr y. This thesis describes the key steps in developing a forensic ancestry test that can be adopted by any laboratory using capillary electrophoresis equipment: optimisation of a PCR multiplex to detect DNA markers from contact traces; compilation of population data from which to infer the likely pop ulation of origin of the person; detection of coancestry patterns in an individual with admixed backgr ounds; and development of online statistical tools that calculate the probability of an individual’s an cestry from a submitted SNP profile. Additional types of autosomal markers were compiled from Ind el polymorphisms; short tandem repeats (STRs); multiple allele SNPs; and Microhaplotype markers