The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Data Mining Practical Machine Learning Tools and Techniques

The PASCAL Visual Object Classes Challenge

IEEE Transactions on Pattern Analysis and Machine Intelligence

Artificial neural networks (ANNs) constitute a class of flexible nonlinear models designed to mimic biological neural systems. In this entry, we introduce ANN using familiar econometric terminology and provide an overview of ANN modeling approach and its implementation methods. † Correspondence: Chung-Ming Kuan, Institute of Economics, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115, Taiwan; ckuan@econ.sinica.edu.tw. †† I would like to express my sincere gratitude to the editor, Professor Steven Durlauf, for his patience and constructive comments on early drafts of this entry. I also thank Shih-Hsun Hsu and Yu-Lieh Huang for very helpful suggestions. The remaining errors are all mine.

Artificial neural networks

Local Resultant Gradient Vector Difference and Inpainting for 3D Text Detection in the Wild

The latest sequencing technologies such as the Pacific Biosciences (PacBio) and Oxford Nanopore machines can generate long reads at the length of thousands of nucleic bases which is much longer than the reads at the length of hundreds generated by Illumina machines. However, these long reads are prone to much higher error rates, for example, 15 percent, making downstream analysis and applications very difficult. Error correction is a process to improve the quality of sequencing data. Hybrid correction strategies have been recently proposed to combine Illumina reads of low error rates to fix sequencing errors in the noisy long reads with good performance. In this paper, we propose a new method named Bicolor, a bi-level framework of hybrid error correction for further improving the quality of PacBio long reads. At the first level, our method uses a de Bruijn graph-based error correction idea to search paths in pairs of solid $k$ k -mers iteratively with an increasing length of $k$ k -mer. At the second level, we combine the processed results under different parameters from the first level. In particular, a multiple sequence alignment algorithm is used to align those similar long reads, followed by a voting algorithm which determines the final base at each position of the reads. We compare the superior performance of Bicolor with three state-of-the-art methods on three real data sets. Results demonstrate that Bicolor always achieves the highest identity ratio. Bicolor also achieves a higher alignment ratio ( $> 1.3\%$ > 1 . 3 % ) and a higher number of aligned reads than the current methods on two data sets. On the third data set, our method is closely competitive to the current methods in terms of number of aligned reads and genome coverage. The C++ source codes of our algorithm are freely available at https://github.com/yuansliu/Bicolor .

/pdf/bi-level-error-correction-for-pacbio-long-reads-h5q3vrsyiu.pdf

Bi-Level Error Correction for PacBio Long Reads

Writer age estimation through handwriting

We propose a data-driven approach for context-aware person image generation. Specifically, we attempt to generate a person image such that the synthesized instance can blend into a complex scene. In our method, the position, scale, and appearance of the generated person are semantically conditioned on the existing persons in the scene. The proposed technique is divided into three sequential steps. At first, we employ a Pix2PixHD model to infer a coarse semantic mask that represents the new person's spatial location, scale, and potential pose. Next, we use a data-centric approach to select the closest representation from a precomputed cluster of fine semantic masks. Finally, we adopt a multi-scale, attention-guided architecture to transfer the appearance attributes from an exemplar image. The proposed strategy enables us to synthesize semantically coherent realistic persons that can blend into an existing scene without altering the global context. We conclude our findings with relevant qualitative and quantitative evaluations.

Michael Blumenstein

Papers

Local Resultant Gradient Vector Difference and Inpainting for 3D Text Detection in the Wild

Bi-Level Error Correction for PacBio Long Reads

Writer age estimation through handwriting

Global Context-Aware Person Image Generation

Classification of aesthetic natural scene images using statistical and semantic features