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

A novel approach for structural feature extraction: contour vs. direction

In this study, an investigation was undertaken to determine whether the predictive accuracy of an indirect, multiwavelength spectroscopic technique for rapidly determining oxygen demand (OD) values is affected by the use of unfiltered and turbid samples, as well as by the use of absorbance values measured below 200 nm. The rapid OD technique was developed that uses UV–Vis spectroscopy and artificial neural networks (ANNs) to indirectly determine chemical oxygen demand (COD) levels. It was found that the most accurate results were obtained when a spectral range of 190–350 nm was provided as data input to the ANN, and when using unfiltered samples below a turbidity range of 150 NTU. This is because high correlations of above 0.90 were obtained with the data using the standard COD method. This indicates that samples can be measured directly without the additional need for preprocessing by filtering. Samples with turbidity values higher than 150 NTU were found to produce poor correlations with the standard COD method, which made them unsuitable for accurate, real-time, on-line monitoring of OD levels.

A rapid analytical method for predicting the oxygen demand of wastewater

To date, identifying cracks in bridges and determining bridge conditions primarily involve manual labour. Bridge inspection by human experts has some drawbacks such as the inability to physically examine all parts of the bridge, sole dependency on the expert knowledge of the bridge inspector. Moreover it requires proper training of the human resource and overall it is not cost effective. This article proposes an automatic bridge inspection approach exploiting wavelet-based image features along with Support Vector Machines for automatic detection of cracks in bridge images. A two-stage approach is followed, where in the first stage a decision is made as whether an image should undergo a pre-processing step (depending on image characteristics), and later in the second stage, wavelet features are extracted from the image using a sliding window-based technique. We obtained an overall accuracy of 92.11% while conducting experiments even on noisy and complex bridge images.

/pdf/automatic-bridge-crack-detection-a-texture-analysis-based-1xtukzpkbu.pdf

Automatic Bridge Crack Detection A Texture Analysis-Based Approach

Texture feature is an important feature descriptor for many image analysis applications. The objectives of this research are to determine distinctive texture features for crowd density estimation and counting. In this paper, we have comprehensively reviewed different texture features and their different possible combinations to evaluate their performance on pedestrian crowds. A two-stage classification and regression based framework have been proposed for performance evaluation of all the texture features for crowd density estimation and counting. According to the framework, input images are divided into blocks and blocks into cells of different sizes, having varying crowd density levels. Due to perspective distortion, people appearing close to the camera contribute more to the feature vector than people far away. Therefore, features extracted are normalized using a perspective normalization map of the scene. At the first stage, image blocks are classified using multi-class SVM into different density level. At the second stage Gaussian Process Regression is used to re gress low-level features to count. Various texture features and their possible combinations are evaluated on publicly available dataset.

Texture-based feature mining for crowd density estimation: A study

A bridge-deterioration approach is to predict the condition ratings and the deterioration pattern of bridge elements for determining optimal maintenance strategies and estimating future funding requirements. To effectively predict long-term bridge performance, an advanced integrated deterioration approach has been developed that incorporates a time-based model, a state-based model with the Elman neural network (ENN) and a backward prediction model (BPM). The proposed approach involves the categorization of the selected inspection records by bridge components, material types, traffic volume, and the construction era. The primary advantage of such categorization is to group similar components together, thereby identifying the common deterioration patterns. A selection process embedded in the proposed approach offers the ability to automatically select the most appropriate model for predicting future bridge condition ratings. To demonstrate the advantage of the proposed approach in predicting long-te...

/pdf/prediction-of-long-term-bridge-performance-integrated-vuq0y90z3v.pdf

Michael Blumenstein

Papers

A novel approach for structural feature extraction: contour vs. direction

A rapid analytical method for predicting the oxygen demand of wastewater

Automatic Bridge Crack Detection A Texture Analysis-Based Approach

Texture-based feature mining for crowd density estimation: A study

Prediction of Long-Term Bridge Performance: Integrated Deterioration Approach with Case Studies