Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Topic-based mixture language modelling

This paper describes an approach for constructing a mixture of language models based on simple statistical notions of semantics using probabilistic models developed for information retrieval. The approach encapsulates corpus-derived semantic information and is able to model varying styles of text. Using such information, the corpus texts are clustered in an unsupervised manner and a mixture of topic-specific language models is automatically created. The principal contribution of this work is to characterise the document space resulting from information retrieval techniques and to demonstrate the approach for mixture language modelling. A comparison is made between manual and automatic clustering in order to elucidate how the global content information is expressed in the space. We also compare (in terms of association with manual clustering and language modelling accuracy) alternative term-weighting schemes and the effect of singular value decomposition dimension reduction (latent semantic analysis). Test set perplexity results using the British National Corpus indicate that the approach can improve the potential of statistical language modelling. Using an adaptive procedure, the conventional model may be tuned to track text data with a slight increase in computational cost

Integration of a failure monitoring within a hybrid dynamic simulation environment

The complexity and the size of the industrial chemical processes induce the monitoring of a growing number of process variables. Their knowledge is generally based on the measurements of system variables and on the physico-chemical models of the process. Nevertheless this information is imprecise because of process and measurement noise. So the research ways aim at developing new and more powerful techniques for the detection of process fault. In this work, we present a method for the fault detection based on the comparison between the real system and the reference model evolution generated by the extended Kalman filter. The reference model is simulated by the dynamic hybrid simulator, PrODHyS. It is a general object-oriented environment which provides common and reusable components designed for the development and the management of dynamic simulation of industrial systems. The use of this method is illustrated through a didactic example relating to the field of Chemical Process System Engineering

Web Data Extraction, Applications and Techniques: A Survey

Web Data Extraction is an important problem that has been studied by means of different scientific tools and in a broad range of applications. Many approaches to extracting data from the Web have been designed to solve specific problems and operate in ad-hoc domains. Other approaches, instead, heavily reuse techniques and algorithms developed in the field of Information Extraction. This survey aims at providing a structured and comprehensive overview of the literature in the field of Web Data Extraction. We provided a simple classification framework in which existing Web Data Extraction applications are grouped into two main classes, namely applications at the Enterprise level and at the Social Web level. At the Enterprise level, Web Data Extraction techniques emerge as a key tool to perform data analysis in Business and Competitive Intelligence systems as well as for business process re-engineering. At the Social Web level, Web Data Extraction techniques allow to gather a large amount of structured data continuously generated and disseminated by Web 2.0, Social Media and Online Social Network users and this offers unprecedented opportunities to analyze human behavior at a very large scale. We discuss also the potential of cross-fertilization, i.e., on the possibility of re-using Web Data Extraction techniques originally designed to work in a given domain, in other domains.Comment: Knowledge-based System

Multi-layer Architecture For Storing Visual Data Based on WCF and Microsoft SQL Server Database

In this paper we present a novel architecture for storing visual data. Effective storing, browsing and searching collections of images is one of the most important challenges of computer science. The design of architecture for storing such data requires a set of tools and frameworks such as SQL database management systems and service-oriented frameworks. The proposed solution is based on a multi-layer architecture, which allows to replace any component without recompilation of other components. The approach contains five components, i.e. Model, Base Engine, Concrete Engine, CBIR service and Presentation. They were based on two well-known design patterns: Dependency Injection and Inverse of Control. For experimental purposes we implemented the SURF local interest point detector as a feature extractor and $K$-means clustering as indexer. The presented architecture is intended for content-based retrieval systems simulation purposes as well as for real-world CBIR tasks.Comment: Accepted for the 14th International Conference on Artificial Intelligence and Soft Computing, ICAISC, June 14-18, 2015, Zakopane, Polan

Information Extraction, Data Integration, and Uncertain Data Management: The State of The Art

Information Extraction, data Integration, and uncertain data management are different areas of research that got vast focus in the last two decades. Many researches tackled those areas of research individually. However, information extraction systems should have integrated with data integration methods to make use of the extracted information. Handling uncertainty in extraction and integration process is an important issue to enhance the quality of the data in such integrated systems. This article presents the state of the art of the mentioned areas of research and shows the common grounds and how to integrate information extraction and data integration under uncertainty management cover

On the role of pre and post-processing in environmental data mining

The quality of discovered knowledge is highly depending on data quality. Unfortunately real data use to contain noise, uncertainty, errors, redundancies or even irrelevant information. The more complex is the reality to be analyzed, the higher the risk of getting low quality data. Knowledge Discovery from Databases (KDD) offers a global framework to prepare data in the right form to perform correct analyses. On the other hand, the quality of decisions taken upon KDD results, depend not only on the quality of the results themselves, but on the capacity of the system to communicate those results in an understandable form. Environmental systems are particularly complex and environmental users particularly require clarity in their results. In this paper some details about how this can be achieved are provided. The role of the pre and post processing in the whole process of Knowledge Discovery in environmental systems is discussed