De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space

Sequencing technologies allow for an in-depth analysis of biological species but the size of the generated datasets introduce a number of analytical challenges. Recently, we demonstrated the application of numerical sequence representations and data transformations for the alignment of short reads to a reference genome. Here, we expand out approach for de novo assembly of short reads. Our results demonstrate that highly compressed data can encapsulate the signal suffi- ciently to accurately assemble reads to big contigs or complete genomes

On the pricing and hedging of volatility derivatives

We consider the pricing of a range of volatility derivatives, including volatility and variance swaps and swaptions. Under risk-neutral valuation we provide closed-form formulae for volatility-average and variance swaps for a variety of diffusion and jump-diffusion models for volatility. We describe a general partial differential equation framework for derivatives that have an extra dependence on an average of the volatility. We give approximate solutions of this equation for volatility products written on assets for which the volatility process fluctuates on a time-scale that is fast compared with the lifetime of the contracts, analysing both the ``outer'' region and, by matched asymptotic expansions, the ``inner'' boundary layer near expiry

Knowledge Base Reuse With Frame Representation In Artificial Intelligence Applications

The creation and upkeep of knowledge bases have emerged as the primary issue in artificial intelligence development. The knowledge domain is expanding, and application interoperability is urgently demanded. To accommodate this modification, the knowledge base, which serves as the foundation of the artificial intelligence architecture, must be updated. XML (extensible markup language), RDF (resources description framework), DAML (DARPA agent markup language), OIL (ontology inference layer), and OKBC are just a few of the standards that have been introduced as a result of the development of the internet (Open Knowledge-Base Connectivity). One type of knowledge representation that can store information and facts about a subject is frame-based representation. The OKBC, which can help with knowledge base interoperability, supports this approach. In this work, the main issues covered are the comprehension and fundamentals of knowledge base creation with frame representation. To better understand how frame representation functions as a reusable component, a case study from a news publication were used as an example

Local Binary Patterns as a Feature Descriptor in Alignment-free Visualisation of Metagenomic Data

Shotgun sequencing has facilitated the analysis of complex microbial communities. However, clustering and visualising these communities without prior taxonomic information is a major challenge. Feature descriptor methods can be utilised to extract these taxonomic relations from the data. Here, we present a novel approach consisting of local binary patterns (LBP) coupled with randomised singular value decomposition (RSVD) and Barnes-Hut t-stochastic neighbor embedding (BH-tSNE) to highlight the underlying taxonomic structure of the metagenomic data. The effectiveness of our approach is demonstrated using several simulated and a real metagenomic datasets

Factors influencing the distribution of charge in polar nanocrystals

We perform first-principles calculations of wurtzite GaAs nanorods to explore the factors determining charge distributions in polar nanostructures. We show that both the direction and magnitude of the dipole moment $\mathbf{d}$ of a nanorod, and its electic field, depend sensitively on how its surfaces are terminated and do not depend strongly on the spontaneous polarization of the underlying lattice. We identify two physical mechanisms by which $\mathbf{d}$ is controlled by the surface termination, and we show that the excess charge on the nanorod ends is not strongly localized. We discuss the implications of these results for tuning nanocrystal properties, and for their growth and assembly.Comment: Accepted for publication in Phys. Rev. B Rapid Communication