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Register a new userUsing a Big Data Database to Identify Pathogens in Protein Data Space
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Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper explores using big data database technologies to characterize very large metagenomic DNA sequences in protein space, with the ultimate goal of rapid pathogen identification in patient samples. Our approach uses the abilities of a big data databases to hold large sparse associative array representations of genetic data to extract statistical patterns about the data that can be used in a variety of ways to improve identification algorithms.
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Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the validation is typically limited to individual modes for a single protein. We use anisotropic displacement parameters from crystallography to test the quality of prediction of both the magnitude and directionality of conformational variance. Normal modes from four simple elastic network model potentials and from the CHARMM forcefield are calculated for a data set of 83 diverse, ultrahigh resolution crystal structures. While all five potentials provide good predictions of the magnitude of flexibility, the methods that consider all atoms have a clear edge at prediction of directionality, and the CHARMM potential produces the best agreement. The low-frequency modes from different potentials are similar, but those computed from the CHARMM potential show the greatest difference from the elastic network models. This was illustrated by computing the dynamic correlation matrices from different potentials for a PDZ domain structure. Comparison of normal mode results with anisotropic temperature factors opens the possibility of using ultrahigh resolution crystallographic data as a quantitative measure of molecular flexibility. The comprehensive evaluation demonstrates the costs and benefits of using normal mode potentials of varying complexity. Comparison of the dynamic correlation matrices suggests that a combination of topological and chemical potentials may help identify residues in which chemical forces make large contributions to intramolecular coupling.
In any knowledge discovery process the value of extracted knowledge is directly related to the quality of the data used. Big Data problems, generated by massive growth in the scale of data observed in recent years, also follow the same dictate. A common problem affecting data quality is the presence of noise, particularly in classification problems, where label noise refers to the incorrect labeling of training instances, and is known to be a very disruptive feature of data. However, in this Big Data era, the massive growth in the scale of the data poses a challenge to traditional proposals created to tackle noise, as they have difficulties coping with such a large amount of data. New algorithms need to be proposed to treat the noise in Big Data problems, providing high quality and clean data, also known as Smart Data. In this paper, two Big Data preprocessing approaches to remove noisy examples are proposed: an homogeneous ensemble and an heterogeneous ensemble filter, with special emphasis in their scalability and performance traits. The obtained results show that these proposals enable the practitioner to efficiently obtain a Smart Dataset from any Big Data classification problem.
Next Generation Sequencing (NGS) technology has resulted in massive amounts of proteomics and genomics data. This data is of no use if it is not properly analyzed. ETL (Extraction, Transformation, Loading) is an important step in designing data analytics applications. ETL requires proper understanding of features of data. Data format plays a key role in understanding of data, representation of data, space required to store data, data I/O during processing of data, intermediate results of processing, in-memory analysis of data and overall time required to process data. Different data mining and machine learning algorithms require input data in specific types and formats. This paper explores the data formats used by different tools and algorithms and also presents modern data formats that are used on Big Data Platform. It will help researchers and developers in choosing appropriate data format to be used for a particular tool or algorithm.
In Big data era, information integration often requires abundant data extracted from massive data sources. Due to a large number of data sources, data source selection plays a crucial role in information integration, since it is costly and even impossible to access all data sources. Data Source selection should consider both efficiency and effectiveness issues. For efficiency, the approach should achieve high performance and be scalability to fit large data source amount. From effectiveness aspect, data quality and overlapping of sources are to be considered, since data quality varies much from data sources, with significant differences in the accuracy and coverage of the data provided, and the overlapping of sources can even lower the quality of data integrated from selected data sources. In this paper, we study source selection problem in textit{Big Data Era} and propose methods which can scale to datasets with up to millions of data sources and guarantee the quality of results. Motivated by this, we propose a new object function taking the expected number of true values a source can provide as a criteria to evaluate the contribution of a data source. Based on our proposed index we present a scalable algorithm and two pruning strategies to improve the efficiency without sacrificing precision. Experimental results on both real world and synthetic data sets show that our methods can select sources providing a large proportion of true values efficiently and can scale to massive data sources.
We introduce an improved unsupervised clustering protocol specially suited for large-scale structured data. The protocol follows three steps: a dimensionality reduction of the data, a density estimation over the low dimensional representation of the data, and a final segmentation of the density landscape. For the dimensionality reduction step we introduce a parallelized implementation of the well-known t-Stochastic Neighbouring Embedding (t-SNE) algorithm that significantly alleviates some inherent limitations, while improving its suitability for large datasets. We also introduce a new adaptive Kernel Density Estimation particularly coupled with the t-SNE framework in order to get accurate density estimates out of the embedded data, and a variant of the rainfalling watershed algorithm to identify clusters within the density landscape. The whole mapping protocol is wrapped in the bigMap R package, together with visualization and analysis tools to ease the qualitative and quantitative assessment of the clustering.
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