Global Continuous Optimization with Error Bound and Fast Convergence

This paper considers global optimization with a black-box unknown objective function that can be non-convex and non-differentiable. Such a difficult optimization problem arises in many real-world applications, such as parameter tuning in machine learning, engineering design problem, and planning with a complex physics simulator. This paper proposes a new global optimization algorithm, called Locally Oriented Global Optimization (LOGO), to aim for both fast convergence in practice and finite-time error bound in theory. The advantage and usage of the new algorithm are illustrated via theoretical analysis and an experiment conducted with 11 benchmark test functions. Further, we modify the LOGO algorithm to specifically solve a planning problem via policy search with continuous state/action space and long time horizon while maintaining its finite-time error bound. We apply the proposed planning method to accident management of a nuclear power plant. The result of the application study demonstrates the practical utility of our method

Mathematical modeling of evolutionary changes of oligonucleotide frequency patterns of bacterial genomes for genome-scale phylogenetic inferences

Modern phylogenetic studies from the advancement of next generation sequencing can benefit from an analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome scale analysis were believed to be more accurate than gene-based ones. However, the computational complexity of current phylogenomic procedures and lack of reliable annotation and alignment free evolutionary models keep microbiologists from wider use of these opportunities. For example, the super-matrix approach of phylogenomics requires identification of clusters of orthologous genes in compared genomes followed by alignment of numerous sequences to proceed with reconciliation of multiple trees inferred by traditional phylogenetic tools. In fact, the approach potentially multiplies the problems of gene annotation and sequence alignment, not mentioning the computational difficulties and laboriousness of the methods. For this research, we identified that the alignment and annotation-free method based on comparison of oligonucleotide usage patterns (OUP) calculated for genome-scale DNA sequences allowed fast inferring of phylogenetic trees. These were also congruent with the corresponding whole genome supermatrix trees in terms of tree topology and branch lengths. Validation and benchmarking tests for OUP phylogenomics were done based on comparisons to current literature and artificially created sequences with known phylogeny. It was demonstrated that the OUP diversification between taxa was driven by global adjustments of codon usage to fit fluctuating tRNA concentrations that were well aligned to the species evolution. A web-based program to perform OUP-based phylogenomics was released on http://swphylo.bi.up.ac.za/. Applicability of the tool was proven for different taxa from species to family levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, e.g. gyrA.Thesis (PhD)--University of Pretoria, 2018.BiochemistryPhDUnrestricte

PIANO: Proximity-based User Authentication on Voice-Powered Internet-of-Things Devices

Voice is envisioned to be a popular way for humans to interact with Internet-of-Things (IoT) devices. We propose a proximity-based user authentication method (called PIANO) for access control on such voice-powered IoT devices. PIANO leverages the built-in speaker, microphone, and Bluetooth that voice-powered IoT devices often already have. Specifically, we assume that a user carries a personal voice-powered device (e.g., smartphone, smartwatch, or smartglass), which serves as the user's identity. When another voice-powered IoT device of the user requires authentication, PIANO estimates the distance between the two devices by playing and detecting certain acoustic signals; PIANO grants access if the estimated distance is no larger than a user-selected threshold. We implemented a proof-of-concept prototype of PIANO. Through theoretical and empirical evaluations, we find that PIANO is secure, reliable, personalizable, and efficient.Comment: To appear in ICDCS'1

Comparative mitogenomic analyses of three scallops (Bivalvia: Pectinidae) reveal high level variation of genomic organization and a diversity of transfer RNA gene sets

<p>Abstract</p> <p>Background</p> <p>It can be seen from the available mollusk mitogenomes that the family Pectinidae exhibits the most variation in genome organization. In this study, comparative mitogenomic analyses were performed for three scallops from the subfamily Chlamydinae (Pectinidae), with the goal of characterizing the degree of variability of mitogenome organization and other characteristics among species from the same subfamily and exploring their possible evolution route.</p> <p>Findings</p> <p>The complete or nearly complete mtDNA sequences of scallop <it>Mimachlamys nobilis </it>(17 935 bp), <it>Mizuhopecten yessoensis </it>(20 964 bp) and <it>Chlamys farreri </it>(17 035 bp) were determined using long PCR amplification and primer walking sequencing strategy. Highly variable size difference of the three genomes resulted primarily from length and number variations of non-coding regions, and the major difference in gene content of the three scallop species are due to varying tRNA gene sets. Only 21, 16, and 17 tRNA genes were detected in the mitogenomes of <it>M. nobilis</it>, <it>M. yessoensis </it>and <it>C. farreri</it>, respectively. Remarkably, no <it>trnS </it>gene could be identified in any of the three scallops. A newly-detected <it>trnA</it>-like sequence within the mitogenome of <it>M. yessoensis </it>seems to exemplify the functional loss of a tRNA gene, and the duplication of <it>trnD </it>in <it>M. yessoensis </it>raises a fundamental question of whether the retention of the tRNA gene copy of 2-tRNAs is easier than that of 4-tRNAs. Analysis of putative evolutionary pathways of gene rearrangement indicates that transposition of neighboring gene blocks may play an important role in the evolution of mitogenomes in scallops. Parsimonious analysis of the genomic variations implies that the mitogenomes of <it>M. yessoensis </it>and <it>C. farreri </it>are likely to derive independently from a common ancestor that was closely related to <it>M. nobilis</it>.</p> <p>Conclusion</p> <p>Comparative mitogenomic analyses among three species from the subfamily Chlamydinae show that the three genomes exhibit a high level of genomic variation and a diversity of tRNA gene sets, characterized by extensive translocation of genes. These features provide useful clues and information for evolutionary analysis of scallop mitogenomes.</p