Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes

Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer

Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information, thus maximizing its value. With the already substantial and constantly expanding data generation capacity of the life sciences as well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of this information are crucial. While automated techniques certainly facilitate the process, manual annotation remains the gold standard in most domains. In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of meaningful annotations needed by modern biomedical science. We present E.D., the Entity Describer, a mashup of the Connotea social tagging system, an index of semantic web-accessible controlled vocabularies, and a new public RDF database for storing social semantic annotations

Curation of complex, context-dependent immunological data

BACKGROUND: The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data . DESCRIPTION: To identify and extract relevant data from the scientific literature in an efficient and accurate manner, novel processes were developed for manual and semi-automated annotation. CONCLUSION: Formalized curation strategies enable the processing of a large volume of context-dependent data, which are now available to the scientific community in an accessible and transparent format. The experiences described herein are applicable to other databases housing complex biological data and requiring a high level of curation expertise

Trusted resource allocation in volunteer edge-cloud computing for scientific applications

Data-intensive science applications in fields such as e.g., bioinformatics, health sciences, and material discovery are becoming increasingly dynamic and demanding with resource requirements. Researchers using these applications which are based on advanced scientific workflows frequently require a diverse set of resources that are often not available within private servers or a single Cloud Service Provider (CSP). For example, a user working with Precision Medicine applications would prefer only those CSPs who follow guidelines from HIPAA (Health Insurance Portability and Accountability Act) for implementing their data services and might want services from other CSPs for economic viability. With the generation of more and more data these workflows often require deployment and dynamic scaling of multi-cloud resources in an efficient and high-performance manner (e.g., quick setup, reduced computation time, and increased application throughput). At the same time, users seek to minimize the costs of configuring the related multi-cloud resources. While performance and cost are among the key factors to decide upon CSP resource selection, the scientific workflows often process proprietary/confidential data that introduces additional constraints of security postures. Thus, users have to make an informed decision on the selection of resources that are most suited for their applications while trading off between the key factors of resource selection which are performance, agility, cost, and security (PACS). Furthermore, even with the most efficient resource allocation across multi-cloud, the cost to solution might not be economical for all users which have led to the development of new paradigms of computing such as volunteer computing where users utilize volunteered cyber resources to meet their computing requirements. For economical and readily available resources, it is essential that such volunteered resources can integrate well with cloud resources for providing the most efficient computing infrastructure for users. In this dissertation, individual stages such as user requirement collection, user's resource preferences, resource brokering and task scheduling, in lifecycle of resource brokering for users are tackled. For collection of user requirements, a novel approach through an iterative design interface is proposed. In addition, fuzzy interference-based approach is proposed to capture users' biases and expertise for guiding their resource selection for their applications. The results showed improvement in performance i.e. time to execute in 98 percent of the studied applications. The data collected on user's requirements and preferences is later used by optimizer engine and machine learning algorithms for resource brokering. For resource brokering, a new integer linear programming based solution (OnTimeURB) is proposed which creates multi-cloud template solutions for resource allocation while also optimizing performance, agility, cost, and security. The solution was further improved by the addition of a machine learning model based on naive bayes classifier which captures the true QoS of cloud resources for guiding template solution creation. The proposed solution was able to improve the time to execute for as much as 96 percent of the largest applications. As discussed above, to fulfill necessity of economical computing resources, a new paradigm of computing viz-a-viz Volunteer Edge Computing (VEC) is proposed which reduces cost and improves performance and security by creating edge clusters comprising of volunteered computing resources close to users. The initial results have shown improved time of execution for application workflows against state-of-the-art solutions while utilizing only the most secure VEC resources. Consequently, we have utilized reinforcement learning based solutions to characterize volunteered resources for their availability and flexibility towards implementation of security policies. The characterization of volunteered resources facilitates efficient allocation of resources and scheduling of workflows tasks which improves performance and throughput of workflow executions. VEC architecture is further validated with state-of-the-art bioinformatics workflows and manufacturing workflows.Includes bibliographical references

User-centered visual analysis using a hybrid reasoning architecture for intensive care units

One problem pertaining to Intensive Care Unit information systems is that, in some cases, a very dense display of data can result. To ensure the overview and readability of the increasing volumes of data, some special features are required (e.g., data prioritization, clustering, and selection mechanisms) with the application of analytical methods (e.g., temporal data abstraction, principal component analysis, and detection of events). This paper addresses the problem of improving the integration of the visual and analytical methods applied to medical monitoring systems. We present a knowledge- and machine learning-based approach to support the knowledge discovery process with appropriate analytical and visual methods. Its potential benefit to the development of user interfaces for intelligent monitors that can assist with the detection and explanation of new, potentially threatening medical events. The proposed hybrid reasoning architecture provides an interactive graphical user interface to adjust the parameters of the analytical methods based on the users' task at hand. The action sequences performed on the graphical user interface by the user are consolidated in a dynamic knowledge base with specific hybrid reasoning that integrates symbolic and connectionist approaches. These sequences of expert knowledge acquisition can be very efficient for making easier knowledge emergence during a similar experience and positively impact the monitoring of critical situations. The provided graphical user interface incorporating a user-centered visual analysis is exploited to facilitate the natural and effective representation of clinical information for patient care

Charting a new frontier of science by integrating mathematical modeling to understand and predict complex biological systems

Biological systems are staggeringly complex. To untangle this complexity and make predictions about biological systems is a continuous goal of biological research. One approach to achieve these goals is to emphasize the use of quantitative measures of biological processes. Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, ecological) has transformed how we understand, categorize, and predict complex biological systems. Simultaneously, thanks to increased computational power, mathematicians, engineers and physical scientists -- collectively termed theoreticians -- have developed sophisticated models of biological systems at different scales. But there is still a disconnect between the two fields. This surge of quantitative data creates an opportunity to apply, develop, and evaluate mathematical models of biological systems and explore novel methods of analysis. The novel modeling schemes can also offer deeper understanding of principles in biology. In the context of this paper, we use “models” to refer to mathematical representations of biological systems. This data revolution puts scientists in a unique position to leverage information-rich datasets to improve descriptive modeling. Moreover, advances in technology allow inclusion of heterogeneity and variability within these datasets and mathematical models. This inclusion may lead to identifying previously undetermined variables driving or maintaining heterogeneity and diversity. Improved inclusion of variation may even improve biologically meaningful predictions about how systems will respond to perturbations. Although some of these practices are mainstream in specific sub-fields of biology, such practices are not widespread across all fields of biological sciences. With resources dedicated to better integrating biology and mathematical modeling, we envision a transformational improvement in the ability to describe and predict complex biological systems

Unveiling the frontiers of deep learning: innovations shaping diverse domains

Deep learning (DL) enables the development of computer models that are capable of learning, visualizing, optimizing, refining, and predicting data. In recent years, DL has been applied in a range of fields, including audio-visual data processing, agriculture, transportation prediction, natural language, biomedicine, disaster management, bioinformatics, drug design, genomics, face recognition, and ecology. To explore the current state of deep learning, it is necessary to investigate the latest developments and applications of deep learning in these disciplines. However, the literature is lacking in exploring the applications of deep learning in all potential sectors. This paper thus extensively investigates the potential applications of deep learning across all major fields of study as well as the associated benefits and challenges. As evidenced in the literature, DL exhibits accuracy in prediction and analysis, makes it a powerful computational tool, and has the ability to articulate itself and optimize, making it effective in processing data with no prior training. Given its independence from training data, deep learning necessitates massive amounts of data for effective analysis and processing, much like data volume. To handle the challenge of compiling huge amounts of medical, scientific, healthcare, and environmental data for use in deep learning, gated architectures like LSTMs and GRUs can be utilized. For multimodal learning, shared neurons in the neural network for all activities and specialized neurons for particular tasks are necessary.Comment: 64 pages, 3 figures, 3 table