WHIDE—a web tool for visual data mining colocation patterns in multivariate bioimages

Motivation: Bioimaging techniques rapidly develop toward higher resolution and dimension. The increase in dimension is achieved by different techniques such as multitag fluorescence imaging, Matrix Assisted Laser Desorption / Ionization (MALDI) imaging or Raman imaging, which record for each pixel an N-dimensional intensity array, representing local abundances of molecules, residues or interaction patterns. The analysis of such multivariate bioimages (MBIs) calls for new approaches to support users in the analysis of both feature domains: space (i.e. sample morphology) and molecular colocation or interaction. In this article, we present our approach WHIDE (Web-based Hyperbolic Image Data Explorer) that combines principles from computational learning, dimension reduction and visualization in a free web application

Bioinformatics Solutions for Image Data Processing

In recent years, the increasing use of medical devices has led to the generation of large amounts of data, including image data. Bioinformatics solutions provide an effective approach for image data processing in order to retrieve information of interest and to integrate several data sources for knowledge extraction; furthermore, images processing techniques support scientists and physicians in diagnosis and therapies. In addition, bioinformatics image analysis may be extended to support several scenarios, for instance, in cyber-security the biometric recognition systems are applied to unlock devices and restricted areas, as well as to access sensitive data. In medicine, computational platforms generate high amount of data from medical devices such as Computed Tomography (CT), and Magnetic Resonance Imaging (MRI); this chapter will survey on bioinformatics solutions and toolkits for medical imaging in order to suggest an overview of techniques and methods that can be applied for the imaging analysis in medicine

AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization

Langenkämper D, Goesmann A, Nattkemper TW. AKE - The Accelerated k-mer Exploration Web-Tool for Rapid Taxonomic Classification and Visualization. BMC Bioinformatics. 2014;15(1): 384.Background: With the advent of low cost, fast sequencing technologies metagenomic analyses are made possible. The large data volumes gathered by these techniques and the unpredictable diversity captured in them are still, however, a challenge for computational biology. Results: In this paper we address the problem of rapid taxonomic assignment with small and adaptive data models (< 5 MB) and present the accelerated k-mer explorer (AKE). Acceleration in AKE's taxonomic assignments is achieved by a special machine learning architecture, which is well suited to model data collections that are intrinsically hierarchical. We report classification accuracy reasonably well for ranks down to order, observed on a study on real world data (Acid Mine Drainage, Cow Rumen). Conclusion: We show that the execution time of this approach is orders of magnitude shorter than competitive approaches and that accuracy is comparable. The tool is presented to the public as a web application

Nonsmooth optimization models and algorithms for data clustering and visualization

Cluster analysis deals with the problem of organization of a collection of patterns into clusters based on a similarity measure. Various distance functions can be used to define this measure. Clustering problems with the similarity measure defined by the squared Euclidean distance have been studied extensively over the last five decades. However, problems with other Minkowski norms have attracted significantly less attention. The use of different similarity measures may help to identify different cluster structures of a data set. This in turn may help to significantly improve the decision making process. High dimensional data visualization is another important task in the field of data mining and pattern recognition. To date, the principal component analysis and the self-organizing maps techniques have been used to solve such problems. In this thesis we develop algorithms for solving clustering problems in large data sets using various similarity measures. Such similarity measures are based on the squared LDoctor of Philosoph

Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging

Gorzolka K, Kölling J, Nattkemper TW, Niehaus K. Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging. PLOS ONE. 2016;11(3): e0150208.MALDI mass spectrometry imaging was performed to localize metabolites during the first seven days of the barley germination. Up to 100 mass signals were detected of which 85 signals were identified as 48 different metabolites with highly tissue-specific localizations. Oligosaccharides were observed in the endosperm and in parts of the developed embryo. Lipids in the endosperm co-localized in dependency on their fatty acid compositions with changes in the distributions of diacyl phosphatidylcholines during germination. 26 potentially antifungal hordatines were detected in the embryo with tissue-specific localizations of their glycosylated, hydroxylated, and O-methylated derivates. In order to reveal spatio-temporal patterns in local metabolite compositions, multiple MSI data sets from a time series were analyzed in one batch. This requires a new preprocessing strategy to achieve comparability between data sets as well as a new strategy for unsupervised clustering. The resulting spatial segmentation for each time point sample is visualized in an interactive cluster map and enables simultaneous interactive exploration of all time points. Using this new analysis approach and visualization tool germination-dependent developments of metabolite patterns with single MS position accuracy were discovered. This is the first study that presents metabolite profiling of a cereals’ germination process over time by MALDI MSI with the identification of a large number of peaks of agronomically and industrially important compounds such as oligosaccharides, lipids and antifungal agents. Their detailed localization as well as the MS cluster analyses for on-tissue metabolite profile mapping revealed important information for the understanding of the germination process, which is of high scientific interest

History & Mathematics: Trends and Cycles

The present yearbook (which is the fourth in the series) is subtitled Trends & Cycles. It is devoted to cyclical and trend dynamics in society and nature; special attention is paid to economic and demographic aspects, in particular to the mathematical modeling of the Malthusian and post-Malthusian traps' dynamics. An increasingly important role is played by new directions in historical research that study long-term dynamic processes and quantitative changes. This kind of history can hardly develop without the application of mathematical methods. There is a tendency to study history as a system of various processes, within which one can detect waves and cycles of different lengths – from a few years to several centuries, or even millennia. The contributions to this yearbook present a qualitative and quantitative analysis of global historical, political, economic and demographic processes, as well as their mathematical models. This issue of the yearbook consists of three main sections: (I) Long-Term Trends in Nature and Society; (II) Cyclical Processes in Pre-industrial Societies; (III) Contemporary History and Processes. We hope that this issue of the yearbook will be interesting and useful both for historians and mathematicians, as well as for all those dealing with various social and natural science

Hydrocarbon quantification using neural networks and deep learning based hyperspectral unmixing

Hydrocarbon (HC) spills are a global issue, which can seriously impact human life and the environment, therefore early identification and remedial measures taken at an early stage are important. Thus, current research efforts aim at remotely quantifying incipient quantities of HC mixed with soils. The increased spectral and spatial resolution of hyperspectral sensors has opened ground-breaking perspectives in many industries including remote inspection of large areas and the environment. The use of subpixel detection algorithms, and in particular the use of the mixture models, has been identified as a future advance that needs to be incorporated in remote sensing. However, there are some challenging tasks since the spectral signatures of the targets of interest may not be immediately available. Moreover, real time processing and analysis is required to support fast decision-making. Progressing in this direction, this thesis pioneers and researches novel methodologies for HC quantification capable of exceeding the limitations of existing systems in terms of reduced cost and processing time with improved accuracy. Therefore the goal of this research is to develop, implement and test different methods for improving HC detection and quantification using spectral unmixing and machine learning. An efficient hybrid switch method employing neural networks and hyperspectral is proposed and investigated. This robust method switches between state of the art hyperspectral unmixing linear and nonlinear models, respectively. This procedure is well suited for the quantification of small quantities of substances within a pixel with high accuracy as the most appropriate model is employed. Central to the proposed approach is a novel method for extracting parameters to characterise the non-linearity of the data. These parameters are fed into a feedforward neural network which decides in a pixel by pixel fashion which model is more suitable. The quantification process is fully automated by applying further classification techniques to the acquired hyperspectral images. A deep learning neural network model is designed for the quantification of HC quantities mixed with soils. A three-term backpropagation algorithm with dropout is proposed to avoid overfitting and reduce the computational complexity of the model. The above methods have been evaluated using classical repository datasets from the literature and a laboratory controlled dataset. For that, an experimental procedure has been designed to produce a labelled dataset. The data was obtained by mixing and homogenizing different soil types with HC substances, respectively and measuring the reflectance with a hyperspectral sensor. Findings from the research study reveal that the two proposed models have high performance, they are suitable for the detection and quantification of HC mixed with soils, and surpass existing methods. Improvements in sensitivity, accuracy, computational time are achieved. Thus, the proposed approaches can be used to detect HC spills at an early stage in order to mitigate significant pollution from the spill areas