Framing Apache Spark in life sciences

Advances in high-throughput and digital technologies have required the adoption of big data for handling complex tasks in life sciences. However, the drift to big data led researchers to face technical and infrastructural challenges for storing, sharing, and analysing them. In fact, this kind of tasks requires distributed computing systems and algorithms able to ensure efficient processing. Cutting edge distributed programming frameworks allow to implement flexible algorithms able to adapt the computation to the data over on-premise HPC clusters or cloud architectures. In this context, Apache Spark is a very powerful HPC engine for large-scale data processing on clusters. Also thanks to specialised libraries for working with structured and relational data, it allows to support machine learning, graph-based computation, and stream processing. This review article is aimed at helping life sciences researchers to ascertain the features of Apache Spark and to assess whether it can be successfully used in their research activities

Distributed Computing in a Pandemic: A Review of Technologies Available for Tackling COVID-19

The current COVID-19 global pandemic caused by the SARS-CoV-2 betacoronavirus has resulted in over a million deaths and is having a grave socio-economic impact, hence there is an urgency to find solutions to key research challenges. Much of this COVID-19 research depends on distributed computing. In this article, I review distributed architectures -- various types of clusters, grids and clouds -- that can be leveraged to perform these tasks at scale, at high-throughput, with a high degree of parallelism, and which can also be used to work collaboratively. High-performance computing (HPC) clusters will be used to carry out much of this work. Several bigdata processing tasks used in reducing the spread of SARS-CoV-2 require high-throughput approaches, and a variety of tools, which Hadoop and Spark offer, even using commodity hardware. Extremely large-scale COVID-19 research has also utilised some of the world's fastest supercomputers, such as IBM's SUMMIT -- for ensemble docking high-throughput screening against SARS-CoV-2 targets for drug-repurposing, and high-throughput gene analysis -- and Sentinel, an XPE-Cray based system used to explore natural products. Grid computing has facilitated the formation of the world's first Exascale grid computer. This has accelerated COVID-19 research in molecular dynamics simulations of SARS-CoV-2 spike protein interactions through massively-parallel computation and was performed with over 1 million volunteer computing devices using the Folding@home platform. Grids and clouds both can also be used for international collaboration by enabling access to important datasets and providing services that allow researchers to focus on research rather than on time-consuming data-management tasks.Comment: 21 pages (15 excl. refs), 2 figures, 3 table

Distributed Computing in a Pandemic

The current COVID-19 global pandemic caused by the SARS-CoV-2 betacoronavirus has resulted in over a million deaths and is having a grave socio-economic impact, hence there is an urgency to find solutions to key research challenges. Much of this COVID-19 research depends on distributed computing. In this article, I review distributed architectures -- various types of clusters, grids and clouds -- that can be leveraged to perform these tasks at scale, at high-throughput, with a high degree of parallelism, and which can also be used to work collaboratively. High-performance computing (HPC) clusters will be used to carry out much of this work. Several bigdata processing tasks used in reducing the spread of SARS-CoV-2 require high-throughput approaches, and a variety of tools, which Hadoop and Spark offer, even using commodity hardware. Extremely large-scale COVID-19 research has also utilised some of the world's fastest supercomputers, such as IBM's SUMMIT -- for ensemble docking high-throughput screening against SARS-CoV-2 targets for drug-repurposing, and high-throughput gene analysis -- and Sentinel, an XPE-Cray based system used to explore natural products. Grid computing has facilitated the formation of the world's first Exascale grid computer. This has accelerated COVID-19 research in molecular dynamics simulations of SARS-CoV-2 spike protein interactions through massively-parallel computation and was performed with over 1 million volunteer computing devices using the Folding@home platform. Grids and clouds both can also be used for international collaboration by enabling access to important datasets and providing services that allow researchers to focus on research rather than on time-consuming data-management tasks

High Performance Frequent Subgraph Mining on Transactional Datasets

Graph data mining has been a crucial as well as inevitable area of research. Large amounts of graph data are produced in many areas, such as Bioinformatics, Cheminformatics, Social Networks, and Web etc. Scalable graph data mining methods are getting increasingly popular and necessary due to increased graph complexities. Frequent subgraph mining is one such area where the task is to find overly recurring patterns/subgraphs. To tackle this problem, many main memory-based methods were proposed, which proved to be inefficient as the data size grew exponentially over time. In the past few years several research groups have attempted to handle the frequent subgraph mining (FSM) problem in multiple ways. Many authors have tried to achieve better performance using Graphic Processing Units (GPUs) which has multi-fold improvement over in-memory while dealing with large datasets. Later, Google\u27s MapReduce model with the Hadoop framework proved to be a major breakthrough in high performance large batch processing. Although MapReduce came with many benefits, its disk I/O and non-iterative style model could not help much for FSM domain since subgraph mining process is an iterative approach. In recent years, Spark has emerged to be the De Facto industry standard with its distributed in-memory computing capability. This is a right fit solution for iterative style of programming as well. In this work, we cover how high-performance computing has helped in improving the performance tremendously in the transactional directed and undirected aspect of graphs and performance comparisons of various FSM techniques are done based on experimental results

Concurrent software architectures for exploratory data analysis

Decades ago, increased volume of data made manual analysis obsolete and prompted the use of computational tools with interactive user interfaces and rich palette of data visualizations. Yet their classic, desktop-based architectures can no longer cope with the ever-growing size and complexity of data. Next-generation systems for explorative data analysis will be developed on client–server architectures, which already run concurrent software for data analytics but are not tailored to for an engaged, interactive analysis of data and models. In explorative data analysis, the key is the responsiveness of the system and prompt construction of interactive visualizations that can guide the users to uncover interesting data patterns. In this study, we review the current software architectures for distributed data analysis and propose a list of features to be included in the next generation frameworks for exploratory data analysis. The new generation of tools for explorative data analysis will need to address integrated data storage and processing, fast prototyping of data analysis pipelines supported by machine-proposed analysis workflows, preemptive analysis of data, interactivity, and user interfaces for intelligent data visualizations. The systems will rely on a mixture of concurrent software architectures to meet the challenge of seamless integration of explorative data interfaces at client site with management of concurrent data mining procedures on the servers

Mining Frequency of Drug Side Effects Over a Large Twitter Dataset Using Apache Spark

Despite clinical trials by pharmaceutical companies as well as current FDA reporting systems, there are still drug side effects that have not been caught. To find a larger sample of reports, a possible way is to mine online social media. With its current widespread use, social media such as Twitter has given rise to massive amounts of data, which can be used as reports for drug side effects. To process these large datasets, Apache Spark has become popular for fast, distributed batch processing. In this work, we have improved on previous pipelines in sentimental analysis-based mining, processing, and extracting tweets with drug-caused side effects. We have also added a new ensemble classifier using a combination of sentiment analysis features to increase the accuracy of identifying drug-caused side effects. In addition, the frequency count for the side effects is also provided. Furthermore, we have also implemented the same pipeline in Apache Spark to improve the speed of processing of tweets by 2.5 times, as well as to support the process of large tweet datasets. As the frequency count of drug side effects opens a wide door for further analysis, we present a preliminary study on this issue, including the side effects of simultaneously using two drugs, and the potential danger of using less-common combination of drugs. We believe the pipeline design and the results present in this work would have great implication on studying drug side effects and on big data analysis in general

Scalable Data Integration for Linked Data

Linked Data describes an extensive set of structured but heterogeneous datasources where entities are connected by formal semantic descriptions. In thevision of the Semantic Web, these semantic links are extended towards theWorld Wide Web to provide as much machine-readable data as possible forsearch queries. The resulting connections allow an automatic evaluation to findnew insights into the data. Identifying these semantic connections betweentwo data sources with automatic approaches is called link discovery. We derivecommon requirements and a generic link discovery workflow based on similaritiesbetween entity properties and associated properties of ontology concepts. Mostof the existing link discovery approaches disregard the fact that in times ofBig Data, an increasing volume of data sources poses new demands on linkdiscovery. In particular, the problem of complex and time-consuming linkdetermination escalates with an increasing number of intersecting data sources.To overcome the restriction of pairwise linking of entities, holistic clusteringapproaches are needed to link equivalent entities of multiple data sources toconstruct integrated knowledge bases. In this context, the focus on efficiencyand scalability is essential. For example, reusing existing links or backgroundinformation can help to avoid redundant calculations. However, when dealingwith multiple data sources, additional data quality problems must also be dealtwith. This dissertation addresses these comprehensive challenges by designingholistic linking and clustering approaches that enable reuse of existing links.Unlike previous systems, we execute the complete data integration workflowvia a distributed processing system. At first, the LinkLion portal will beintroduced to provide existing links for new applications. These links act asa basis for a physical data integration process to create a unified representationfor equivalent entities from many data sources. We then propose a holisticclustering approach to form consolidated clusters for same real-world entitiesfrom many different sources. At the same time, we exploit the semantic typeof entities to improve the quality of the result. The process identifies errorsin existing links and can find numerous additional links. Additionally, theentity clustering has to react to the high dynamics of the data. In particular,this requires scalable approaches for continuously growing data sources withmany entities as well as additional new sources. Previous entity clusteringapproaches are mostly static, focusing on the one-time linking and clustering ofentities from few sources. Therefore, we propose and evaluate new approaches for incremental entity clustering that supports the continuous addition of newentities and data sources. To cope with the ever-increasing number of LinkedData sources, efficient and scalable methods based on distributed processingsystems are required. Thus we propose distributed holistic approaches to linkmany data sources based on a clustering of entities that represent the samereal-world object. The implementation is realized on Apache Flink. In contrastto previous approaches, we utilize efficiency-enhancing optimizations for bothdistributed static and dynamic clustering. An extensive comparative evaluationof the proposed approaches with various distributed clustering strategies showshigh effectiveness for datasets from multiple domains as well as scalability on amulti-machine Apache Flink cluster

An Examination of How Robots, Artificial Intelligence, and Machinery Learning are Being Applied in the Medical and Healthcare Industries

Machine learning techniques are associated with diagnostics systems to apply methods that enable computers to link patient data to earlier data and give instructions to correct the disease.In recent years, researchers have promoted two or three data mining based techniques for disease diagnosis. Each function in machine learning and data mining techniques is built through characteristics and features.As a part of prognosis, information must be separated from patient data and information retrieved in stored databases and comparative records. For any disease, early diagnosis or diagnosis will determine the chances of a correct recovery. Disease prediction therefore becomes a more important task to support physicians in delivering efficient treatment to people.In health care, data is being created and disposed of at an extraordinary rate compared to the health care sectors. Data for medical profiling is often found in a variety of sources such as electronic health records, lab and imaging systems, doctor notes and accounts. The medical records database will then contain irrelevant data sourced from multiple sources. Preprocessing data and eliminating irrelevant data then immediately opening it up for predictive analysis is one of the significant difficulties of the health care industry

The Impact of Near-Duplicate Documents on Information Retrieval Evaluation

Near-duplicate documents can adversely affect the efficiency and effectiveness of search engines. Due to the pairwise nature of the comparisons required for near-duplicate detection, this process is extremely costly in terms of the time and processing power it requires. Despite the ubiquitous presence of near-duplicate detection algorithms in commercial search engines, their application and impact in research environments is not fully explored. The implementation of near-duplicate detection algorithms forces trade-offs between efficiency and effectiveness, entailing careful testing and measurement to ensure acceptable performance. In this thesis, we describe and evaluate a scalable implementation of a near-duplicate detection algorithm, based on standard shingling techniques, running under a MapReduce framework. We explore two different shingle sampling techniques and analyze their impact on the near-duplicate document detection process. In addition, we investigate the prevalence of near-duplicate documents in the runs submitted to the adhoc task of TREC 2009 web track