Scientific Workflows for Metabolic Flux Analysis

Metabolic engineering is a highly interdisciplinary research domain that interfaces biology, mathematics, computer science, and engineering. Metabolic flux analysis with carbon tracer experiments (13 C-MFA) is a particularly challenging metabolic engineering application that consists of several tightly interwoven building blocks such as modeling, simulation, and experimental design. While several general-purpose workflow solutions have emerged in recent years to support the realization of complex scientific applications, the transferability of these approaches are only partially applicable to 13C-MFA workflows. While problems in other research fields (e.g., bioinformatics) are primarily centered around scientific data processing, 13C-MFA workflows have more in common with business workflows. For instance, many bioinformatics workflows are designed to identify, compare, and annotate genomic sequences by "pipelining" them through standard tools like BLAST. Typically, the next workflow task in the pipeline can be automatically determined by the outcome of the previous step. Five computational challenges have been identified in the endeavor of conducting 13 C-MFA studies: organization of heterogeneous data, standardization of processes and the unification of tools and data, interactive workflow steering, distributed computing, and service orientation. The outcome of this thesis is a scientific workflow framework (SWF) that is custom-tailored for the specific requirements of 13 C-MFA applications. The proposed approach – namely, designing the SWF as a collection of loosely-coupled modules that are glued together with web services – alleviates the realization of 13C-MFA workflows by offering several features. By design, existing tools are integrated into the SWF using web service interfaces and foreign programming language bindings (e.g., Java or Python). Although the attributes "easy-to-use" and "general-purpose" are rarely associated with distributed computing software, the presented use cases show that the proposed Hadoop MapReduce framework eases the deployment of computationally demanding simulations on cloud and cluster computing resources. An important building block for allowing interactive researcher-driven workflows is the ability to track all data that is needed to understand and reproduce a workflow. The standardization of 13 C-MFA studies using a folder structure template and the corresponding services and web interfaces improves the exchange of information for a group of researchers. Finally, several auxiliary tools are developed in the course of this work to complement the SWF modules, i.e., ranging from simple helper scripts to visualization or data conversion programs. This solution distinguishes itself from other scientific workflow approaches by offering a system of loosely-coupled components that are flexibly arranged to match the typical requirements in the metabolic engineering domain. Being a modern and service-oriented software framework, new applications are easily composed by reusing existing components

Big data analytics for large-scale wireless networks: Challenges and opportunities

© 2019 Association for Computing Machinery. The wide proliferation of various wireless communication systems and wireless devices has led to the arrival of big data era in large-scale wireless networks. Big data of large-scale wireless networks has the key features of wide variety, high volume, real-time velocity, and huge value leading to the unique research challenges that are different from existing computing systems. In this article, we present a survey of the state-of-art big data analytics (BDA) approaches for large-scale wireless networks. In particular, we categorize the life cycle of BDA into four consecutive stages: Data Acquisition, Data Preprocessing, Data Storage, and Data Analytics. We then present a detailed survey of the technical solutions to the challenges in BDA for large-scale wireless networks according to each stage in the life cycle of BDA. Moreover, we discuss the open research issues and outline the future directions in this promising area

A comparison of statistical machine learning methods in heartbeat detection and classification

In health care, patients with heart problems require quick responsiveness in a clinical setting or in the operating theatre. Towards that end, automated classification of heartbeats is vital as some heartbeat irregularities are time consuming to detect. Therefore, analysis of electro-cardiogram (ECG) signals is an active area of research. The methods proposed in the literature depend on the structure of a heartbeat cycle. In this paper, we use interval and amplitude based features together with a few samples from the ECG signal as a feature vector. We studied a variety of classification algorithms focused especially on a type of arrhythmia known as the ventricular ectopic fibrillation (VEB). We compare the performance of the classifiers against algorithms proposed in the literature and make recommendations regarding features, sampling rate, and choice of the classifier to apply in a real-time clinical setting. The extensive study is based on the MIT-BIH arrhythmia database. Our main contribution is the evaluation of existing classifiers over a range sampling rates, recommendation of a detection methodology to employ in a practical setting, and extend the notion of a mixture of experts to a larger class of algorithms

Towards a more efficient and cost-sensitive extreme learning machine: A state-of-the-art review of recent trend

In spite of the prominence of extreme learning machine model, as well as its excellent features such as insignificant intervention for learning and model tuning, the simplicity of implementation, and high learning speed, which makes it a fascinating alternative method for Artificial Intelligence, including Big Data Analytics, it is still limited in certain aspects. These aspects must be treated to achieve an effective and cost-sensitive model. This review discussed the major drawbacks of ELM, which include difficulty in determination of hidden layer structure, prediction instability and Imbalanced data distributions, the poor capability of sample structure preserving (SSP), and difficulty in accommodating lateral inhibition by direct random feature mapping. Other drawbacks include multi-graph complexity, global memory size, one-by-one or chuck-by-chuck (a block of data), global memory size limitation, and challenges with big data. The recent trend proposed by experts for each drawback is discussed in detail towards achieving an effective and cost-sensitive mode

Proceedings of the 9th Overture Workshop

This report contains the proceedings of The 9th Overture Workshop, held in Limerick on 20th June 2011

Real-time probabilistic reasoning system using Lambda architecture

Thesis (MTech (Information Technology))--Cape Peninsula University of Technology, 2019The proliferation of data from sources like social media, and sensor devices has become overwhelming for traditional data storage and analysis technologies to handle. This has prompted a radical improvement in data management techniques, tools and technologies to meet the increasing demand for effective collection, storage and curation of large data set. Most of the technologies are open-source. Big data is usually described as very large dataset. However, a major feature of big data is its velocity. Data flow in as continuous stream and require to be actioned in real-time to enable meaningful, relevant value. Although there is an explosion of technologies to handle big data, they are usually targeted at processing large dataset (historic) and real-time big data independently. Thus, the need for a unified framework to handle high volume dataset and real-time big data. This resulted in the development of models such as the Lambda architecture. Effective decision-making requires processing of historic data as well as real-time data. Some decision-making involves complex processes, depending on the likelihood of events. To handle uncertainty, probabilistic systems were designed. Probabilistic systems use probabilistic models developed with probability theories such as hidden Markov models with inference algorithms to process data and produce probabilistic scores. However, development of these models requires extensive knowledge of statistics and machine learning, making it an uphill task to model real-life circumstances. A new research area called probabilistic programming has been introduced to alleviate this bottleneck. This research proposes the combination of modern open-source big data technologies with probabilistic programming and Lambda architecture on easy-to-get hardware to develop a highly fault-tolerant, and scalable processing tool to process both historic and real-time big data in real-time; a common solution. This system will empower decision makers with the capacity to make better informed resolutions especially in the face of uncertainty. The outcome of this research will be a technology product, built and assessed using experimental evaluation methods. This research will utilize the Design Science Research (DSR) methodology as it describes guidelines for the effective and rigorous construction and evaluation of an artefact. Probabilistic programming in the big data domain is still at its infancy, however, the developed artefact demonstrated an important potential of probabilistic programming combined with Lambda architecture in the processing of big data

Fraud detection for online banking for scalable and distributed data

Online fraud causes billions of dollars in losses for banks. Therefore, online banking fraud detection is an important field of study. However, there are many challenges in conducting research in fraud detection. One of the constraints is due to unavailability of bank datasets for research or the required characteristics of the attributes of the data are not available. Numeric data usually provides better performance for machine learning algorithms. Most transaction data however have categorical, or nominal features as well. Moreover, some platforms such as Apache Spark only recognizes numeric data. So, there is a need to use techniques e.g. One-hot encoding (OHE) to transform categorical features to numerical features, however OHE has challenges including the sparseness of transformed data and that the distinct values of an attribute are not always known in advance. Efficient feature engineering can improve the algorithm’s performance but usually requires detailed domain knowledge to identify correct features. Techniques like Ripple Down Rules (RDR) are suitable for fraud detection because of their low maintenance and incremental learning features. However, high classification accuracy on mixed datasets, especially for scalable data is challenging. Evaluation of RDR on distributed platforms is also challenging as it is not available on these platforms. The thesis proposes the following solutions to these challenges: • We developed a technique Highly Correlated Rule Based Uniformly Distribution (HCRUD) to generate highly correlated rule-based uniformly-distributed synthetic data. • We developed a technique One-hot Encoded Extended Compact (OHE-EC) to transform categorical features to numeric features by compacting sparse-data even if all distinct values are unknown. • We developed a technique Feature Engineering and Compact Unified Expressions (FECUE) to improve model efficiency through feature engineering where the domain of the data is not known in advance. • A Unified Expression RDR fraud deduction technique (UE-RDR) for Big data has been proposed and evaluated on the Spark platform. Empirical tests were executed on multi-node Hadoop cluster using well-known classifiers on bank data, synthetic bank datasets and publicly available datasets from UCI repository. These evaluations demonstrated substantial improvements in terms of classification accuracy, ruleset compactness and execution speed.Doctor of Philosoph