Crowd enabled curation and querying of large and noisy text mined protein interaction data

The abundance of mined, predicted and uncertain biological data warrant massive, efficient and scalable curation efforts. The human expertise required for any successful curation enterprise is often economically prohibitive, especially for speculative end user queries that ultimately may not bear fruit. So the challenge remains in devising a low cost engine capable of delivering fast but tentative annotation and curation of a set of data items that can later be authoritatively validated by experts demanding significantly smaller investment. The aim thus is to make a large volume of predicted data available for use as early as possible with an acceptable degree of confidence in their accuracy while the curation continues. In this paper, we present a novel approach to annotation and curation of biological database contents using crowd computing. The technical contribution is in the identification and management of trust of mechanical turks, and support for ad hoc declarative queries, both of which are leveraged to enable reliable analytics using noisy predicted interactions. While the proposed approach and the CrowdCure system are designed for literature mined protein-protein interaction data curation, they are amenable to substantial generalization.     

SHadoop: Improving MapReduce performance by optimizing job execution mechanism in Hadoop clusters

As a widely-used parallel computing framework for big data processing today, the Hadoop MapReduce framework puts more emphasis on high-throughput of data than on low-latency of job execution. However, today more and more big data applications developed with MapReduce require quick response time. As a result, improving the performance of MapReduce jobs, especially for short jobs, is of great significance in practice and has attracted more and more attentions from both academia and industry. A lot of efforts have been made to improve the performance of Hadoop from job scheduling or job parameter optimization level. In this paper, we explore an approach to improve the performance of the Hadoop MapReduce framework by optimizing the job and task execution mechanism. First of all, by analyzing the job and task execution mechanism in MapReduce framework we reveal two critical limitations to job execution performance. Then we propose two major optimizations to the MapReduce job and task execution mechanisms: first, we optimize the setup and cleanup tasks of a MapReduce job to reduce the time cost during the initialization and termination stages of the job; second, instead of adopting the loose heartbeat-based communication mechanism to transmit all messages between the JobTracker and TaskTrackers, we introduce an instant messaging communication mechanism for accelerating performance-sensitive task scheduling and execution. Finally, we implement SHadoop, an optimized and fully compatible version of Hadoop that aims at shortening the execution time cost of MapReduce jobs, especially for short jobs. Experimental results show that compared to the standard Hadoop, SHadoop can achieve stable performance improvement by around 25% on average for comprehensive benchmarks without losing scalability and speedup. Our optimization work has passed a production-level test in Intel and has been integrated into the Intel Distributed Hadoop (IDH). To the best of our knowledge, this work is the first effort that explores on optimizing the execution mechanism inside map/reduce tasks of a job. The advantage is that it can complement job scheduling optimizations to further improve the job execution performance.     

Metadata for Managing Grid Resources in Data Mining Applications

The Grid is an infrastructure for resource sharing and coordinated use of those resources in dynamic heterogeneous distributed environments. The effective use of a Grid requires the definition of metadata for managing the heterogeneity of involved resources that include computers, data, network facilities, and software tools provided by different organizations. Metadata management becomes a key issue when complex applications, such as data-intensive simulations and data mining applications, are executed on a Grid. This paper discusses metadata models for heterogeneous resource management in Grid-based data mining applications. In particular, it discusses how resources are represented and managed in the Knowledge Grid, a framework for Grid-enabled distributed data mining. The paper illustrates how XML-based metadata is used to describe data mining tools, data sources, mining models, and execution plans, and how metadata is used for the design and execution of distributed knowledge discovery applications on Grids.     

An e‐Science data infrastructure for simulations within Grid computing environment: methods,approaches and practice

Grid‐based simulation usually involves large quantities of data at each stage of the simulation process. These data include simulation input and output files, intermediate results files, log and error files, associated metadata, and information capturing the processes that generate the data. The question of how to effectively store and manage data files within a Grid computing environment is increasingly becoming an important issue. This paper illustrates how we built a lightweight e‐Science infrastructure for data management within a Grid computing environment, including the integration of data curation activities into the entire Grid‐based simulation process. Rather than focusing on specific implementation details, we aim to identify the key issues and research challenges, describing how various existing technologies and tools can be best integrated to address these requirements and challenges. Although the case of quantum mechanical simulation of materials properties is used in the paper, much of the discussion is as generic as possible so that approaches, methods and practice (e.g. integrated approach, workflow taxonomy and development approach, simple but useful semantic annotation approach) can be applied to wider domains and disciplines to facilitat the digital research. A comparison between our approach and Cloud computing, and lessons learned in data management within the Grid computing environment, are also presented. Copyright © 2012 John Wiley & Sons, Ltd.     

A characterization of workflow management systems for extreme-scale applications

Automation of the execution of computational tasks is at the heart of improving scientific productivity. Over the last years, scientific workflows have been established as an important abstraction that captures data processing and computation of large and complex scientific applications. By allowing scientists to model and express entire data processing steps and their dependencies, workflow management systems relieve scientists from the details of an application and manage its execution on a computational infrastructure. As the resource requirements of today’s computational and data science applications that process vast amounts of data keep increasing, there is a compelling case for a new generation of advances in high-performance computing, commonly termed as extreme-scale computing, which will bring forth multiple challenges for the design of workflow applications and management systems. This paper presents a novel characterization of workflow management systems using features commonly associated with extreme-scale computing applications. We classify 15 popular workflow management systems in terms of workflow execution models, heterogeneous computing environments, and data access methods. The paper also surveys workflow applications and identifies gaps for future research on the road to extreme-scale workflows and management systems.     

Dr. Hadoop: an infinite scalable metadata management for Hadoop—How the baby elephant becomes immortal

In this Exa byte scale era, data increases at an exponential rate. This is in turn generating a massive amount of metadata in the file system. Hadoop is the most widely used framework to deal with big data. Due to this growth of huge amount of metadata, however, the efficiency of Hadoop is questioned numerous times by many researchers. Therefore, it is essential to create an efficient and scalable metadata management for Hadoop. Hash-based mapping and subtree partitioning are suitable in distributed metadata management schemes. Subtree partitioning does not uniformly distribute workload among the metadata servers, and metadata needs to be migrated to keep the load roughly balanced. Hash-based mapping suffers from a constraint on the locality of metadata, though it uniformly distributes the load among NameNodes, which are the metadata servers of Hadoop. In this paper, we present a circular metadata management mechanism named dynamic circular metadata splitting (DCMS). DCMS preserves metadata locality using consistent hashing and locality-preserving hashing, keeps replicated metadata for excellent reliability, and dynamically distributes metadata among the NameNodes to keep load balancing. NameNode is a centralized heart of the Hadoop. Keeping the directory tree of all files, failure of which causes the single point of failure (SPOF). DCMS removes Hadoop’s SPOF and provides an efficient and scalable metadata management. The new framework is named ‘Dr. Hadoop’ after the name of the authors.     

An intelligent,uncertainty driven aggregation scheme for streams of ordered sets

Data streams management has attracted the attention of many researchers during the recent years. The reason is that numerous devices generate huge amounts of data demanding an efficient processing scheme for delivering high quality applications. Data are reported through streams and stored into a number of partitions. Separation techniques facilitate the parallel management of data while intelligent methods are necessary to manage these multiple instances of data. Progressive analytics over huge amounts of data could be adopted to deliver partial responses and, possibly, to save time in the execution of applications. An interesting research domain is the efficient management of queries over multiple partitions. Usually, such queries demand responses in the form of ordered sets of objects (e.g., top-k queries). These ordered sets include objects in a ranked order and require novel mechanisms for deriving responses based on partial results. In this paper, we study a setting of multiple data partitions and propose an intelligent, uncertainty driven decision making mechanism that aims to respond to streams of queries. Our mechanism delivers an ordered set of objects over a number of partial ordered subsets retrieved by each partition of data. We envision that a number of query processors are placed in front of each partition and report progressive analytics to a Query Controller (QC). The QC receives queries, assigns the task to the underlying processors and decides the right time to deliver the final ordered set to the application. We propose an aggregation model for deriving the final ordered set of objects and a Fuzzy Logic (FL) inference process. We present a Type-2 FL system that decides when the QC should stop aggregating partial subsets and return the final response to the application. We report on the performance of the proposed mechanism through the execution of a large set of experiments. Our results deal with the throughput of the QC, the quality of the final ordered set of objects and the time required for delivering the final response.     

Optimizing and Tuning MapReduce Jobs to Improve the Large‐Scale Data Analysis Process

Data‐intensive applications process large volumes of data using a parallel processing method. MapReduce is a programming model designed for data‐intensive applications for massive data sets and an execution framework for large‐scale data processing on clusters of commodity servers. While fault tolerance, easy programming structure, and high scalability are considered strong points of MapReduce; however its configuration parameters must be fine‐tuned to the specific deployment, which makes it more complex in configuration and performance. This paper explains tuning of the Hadoop configuration parameters, which directly affect MapReduce's job workflow performance under various conditions to achieve maximum performance. On the basis of the empirical data we collected, it became apparent that three main methodologies can affect the execution time of MapReduce running on cluster systems. Therefore, in this paper, we present a model that consists of three main modules: (1) Extending a data redistribution technique in order to find the high‐performance nodes, (2) Utilizing the number of map/reduce slots in order to make it more efficient in terms of execution time, and (3) Developing a new hybrid routing schedule shuffle phase in order to define the scheduler task while memory management level is reduced.     

Semi-automatic photo annotation strategies using event based clustering and clothing based person recognition

Managing a large number of digital photos is a challenging task for casual users. Personal photos often don’t have rich metadata, or additional information associated with them. However, available metadata can play a crucial role in managing photos. Labeling the semantic content of photos (i.e., annotating them), can increase the amount of metadata and facilitate efficient management. However, manual annotation is tedious and labor intensive while automatic metadata extraction techniques often generate inaccurate and irrelevant results. This paper describes a semi-automatic annotation strategy that takes advantage of human and computer strengths. The semi-automatic approach enables users to efficiently update automatically obtained metadata interactively and incrementally. Even though automatically identified metadata are compromised with inaccurate recognition errors, the process of correcting inaccurate information can be faster and easier than manually adding new metadata from scratch. In this paper, we introduce two photo clustering algorithms for generating meaningful photo groups: (1) Hierarchical event clustering; and (2) Clothing based person recognition, which assumes that people who wear similar clothing and appear in photos taken in one day are very likely to be the same person. To explore our semi-automatic strategies, we designed and implemented a prototype called SAPHARI (Semi-Automatic PHoto Annotation and Recognition Interface). The prototype provides an annotation framework which focuses on making bulk annotations on automatically identified photo groups. The prototype automatically creates photo clusters based on events, people, and file metadata so that users can easily bulk annotation photos. We performed a series of user studies to investigate the effectiveness and usability of the semi-automatic annotation techniques when applied to personal photo collections. The results show that users were able to make annotations significantly faster with event clustering using SAPHARI. We also found that users clearly preferred the semi-automatic approaches.     

The LEMO annotation framework: weaving multimedia annotations with the web

Cultural institutions and museums have realized that annotations contribute valuable metadata for search and retrieval, which in turn can increase the visibility of the digital items they expose via their digital library systems. By exploiting annotations created by others, visitors can discover content they would not have found otherwise, which implies that annotations must be accessible and processable for humans and machines. Currently, however, there exists no widely adopted annotation standard that goes beyond specific media types. Most institutions build their own in-house annotation solution and employ proprietary annotation models, which are not interoperable with those of other systems. As a result, annotation data are usually stored in closed data silos and visible and processable only within the scope of a certain annotation system. As the main contribution of this paper, we present the LEMO Annotation Framework. It (1) provides a uniform annotation model for multimedia contents and various types of annotations, (2) can address fragments of various content-types in a uniform, interoperable manner and (3) pulls annotations out of closed data silos and makes them available as interoperable, dereferencable Web resources. With the LEMO Annotation Framework annotations become part of the Web and can be processed, linked, and referenced by other services. This in turn leads to even higher visibility and increases the potential value of annotations.     

An annotation management system for relational databases

We present an annotation management system for relational databases. In this system, every piece of data in a relation is assumed to have zero or more annotations associated with it and annotations are propagated along, from the source to the output, as data is being transformed through a query. Such an annotation management system could be used for understanding the provenance (aka lineage) of data, who has seen or edited a piece of data or the quality of data, which are useful functionalities for applications that deal with integration of scientific and biological data. We present an extension, pSQL, of a fragment of SQL that has three different types of annotation propagation schemes, each useful for different purposes. The default scheme propagates annotations according to where data is copied from. The default-all scheme propagates annotations according to where data is copied from among all equivalent formulations of a given query. The custom scheme allows a user to specify how annotations should propagate. We present a storage scheme for the annotations and describe algorithms for translating a pSQL query under each propagation scheme into one or more SQL queries that would correctly retrieve the relevant annotations according to the specified propagation scheme. For the default-all scheme, we also show how we generate finitely many queries that can simulate the annotation propagation behavior of the set of all equivalent queries, which is possibly infinite. The algorithms are implemented and the feasibility of the system is demonstrated by a set of experiments that we have conducted.     

QMDS: a file system metadata management service supporting a graph data model-based query language

File system metadata management has become a bottleneck for many data-intensive applications that rely on high-performance file systems. Part of the bottleneck is due to the limitations of an almost 50-year-old interface standard with metadata abstractions that were designed at a time when high-end file systems managed less than 100 MB. Today's high-performance file systems store 7–9 orders of magnitude more data, resulting in a number of data items for which these metadata abstractions are inadequate, such as directory hierarchies unable to handle complex relationships among data. Users of file systems have attempted to work around these inadequacies by moving application-specific metadata management to relational databases to make metadata searchable. Splitting file system metadata management into two separate systems introduces inefficiencies and systems management problems. To address this problem, we propose QMDS: a file system metadata management service that integrates all file system metadata and uses a graph data model with attributes on nodes and edges. Our service uses a query language interface for file identification and attribute retrieval. We present our metadata management service design and architecture and study its performance using a text analysis benchmark application. Results from our QMDS prototype show the effectiveness of this approach. Compared to the use of a file system and relational database, the QMDS prototype shows superior performance for both ingest and query workloads.     

Cross-language transfer of semantic annotation via targeted crowdsourcing: task design and evaluation

Modern data-driven spoken language systems (SLS) require manual semantic annotation for training spoken language understanding parsers. Multilingual porting of SLS demands significant manual effort and language resources, as this manual annotation has to be replicated. Crowdsourcing is an accessible and cost-effective alternative to traditional methods of collecting and annotating data. The application of crowdsourcing to simple tasks has been well investigated. However, complex tasks, like cross-language semantic annotation transfer, may generate low judgment agreement and/or poor performance. The most serious issue in cross-language porting is the absence of reference annotations in the target language; thus, crowd quality control and the evaluation of the collected annotations is difficult. In this paper we investigate targeted crowdsourcing for semantic annotation transfer that delegates to crowds a complex task such as segmenting and labeling of concepts taken from a domain ontology; and evaluation using source language annotation. To test the applicability and effectiveness of the crowdsourced annotation transfer we have considered the case of close and distant language pairs: Italian–Spanish and Italian–Greek. The corpora annotated via crowdsourcing are evaluated against source and target language expert annotations. We demonstrate that the two evaluation references (source and target) highly correlate with each other; thus, drastically reduce the need for the target language reference annotations.     

The intensive use of digital data in modern natural science

Common approaches and technologies applied to digital data storage and processing in various disciplines are analyzed. It is shown that regardless of a specific subject area, working with large data set obtained as a result of experimenting or modeling requires similar methodological support, involving data curation, metadata support, and data genesis and quality annotation. The interdisciplinary field called “The properties of materials and substances” is analyzed as an example of a discipline that actively applies digital data. New approaches to the integration of data with heterogeneous properties that take into account structural data variations by the class of substances, the state of sample, experimental conditions, and other factors are investigated.     

Para-G: Path pattern query processing on large graphs

There are plentiful and diverse applications of graph data management and mining techniques in the real-world scientific research and business activities. As one of the most basic operations, uniform path pattern query processing on graph data faces three big challenges. In this paper, we deal with these challenges by the following points. Firstly, a new query language on graph, called G-Path, is presented, which focuses on complex path pattern query processing on a very large graph. Also, the design of a system called Para-G is proposed, which is based on a BSP-like model as well as MapReduce model, and can effectively handle distributed graph data operations and queries. Secondly, the implementation of Para-G on the de facto cloud platform — Hadoop — is brought forward. Based on the concept of distributed path finite state automaton, the query processing of a G-Path statement in Para-G is detailed. In addition, as the query optimization of G-Path queries, several tricks are utilized to dramatically improve the performance of query execution. Finally, extensive experiments on several graph data sets are conducted to show the usability of the G-Path query language and the effectiveness of Para-G.     

Fast algorithms and VLSI architecture design for HEVC intra-mode decision

The emerging intra-coding tools of High Efficiency Video Coding (HEVC) standard can achieve up to 36 % bit-rate reduction compared to H.264/AVC, but with significant complexity increase. The design challenges, such as data dependency and computational complexity, make it difficult to implement a hardware encoder for real-time applications. In this paper, firstly, the data dependency in HEVC intra-mode decision is fully analyzed, which is cost by the reconstruction loop, the Most Probable Mode, the context adaption during Context-based Adaptive Binary Arithmetic Coding based rate estimation, and the Chroma derived mode. Then, several fast algorithms are proposed to remove the data dependency and to reduce the computational complexity, which include source signal based Rough Mode Decision, coarse to fine rough mode search, Prediction Mode Interlaced RDO mode decision, parallelized context adaption and Chroma-free Coding Unit (CU)/Prediction Unit (PU) decision. Finally, the parallelized VLSI architecture with CU reordering and Chroma reordering scheduling is proposed to improve the throughput. The experimental results demonstrate that the proposed intra-mode decision achieves 41.6 % complexity reduction with 4.3 % Bjontegaard Delta Rate (BDR) increase on average compared to the reference software, HM-13.0. The intra-mode decision scheme is implemented with 1571.7K gate count in 55 nm CMOS technology. The implementation results show that our design can achieve 1080p@60fps real time processing at 294 MHz operation frequency.     

NScale: neighborhood-centric large-scale graph analytics in the cloud

There is an increasing interest in executing complex analyses over large graphs, many of which require processing a large number of multi-hop neighborhoods or subgraphs. Examples include ego network analysis, motif counting, finding social circles, personalized recommendations, link prediction, anomaly detection, analyzing influence cascades, and others. These tasks are not well served by existing vertex-centric graph processing frameworks, where user programs are only able to directly access the state of a single vertex at a time, resulting in high communication, scheduling, and memory overheads in executing such tasks. Further, most existing graph processing frameworks ignore the challenges in extracting the relevant portions of the graph that an analysis task is interested in, and loading those onto distributed memory. This paper introduces NScale, a novel end-to-end graph processing framework that enables the distributed execution of complex subgraph-centric analytics over large-scale graphs in the cloud. NScale enables users to write programs at the level of subgraphs rather than at the level of vertices. Unlike most previous graph processing frameworks, which apply the user program to the entire graph, NScale allows users to declaratively specify subgraphs of interest. Our framework includes a novel graph extraction and packing (GEP) module that utilizes a cost-based optimizer to partition and pack the subgraphs of interest into memory on as few machines as possible. The distributed execution engine then takes over and runs the user program in parallel on those subgraphs, restricting the scope of the execution appropriately, and utilizes novel techniques to minimize memory consumption by exploiting overlaps among the subgraphs. We present a comprehensive empirical evaluation comparing against three state-of-the-art systems, namely Giraph, GraphLab, and GraphX, on several real-world datasets and a variety of analysis tasks. Our experimental results show orders-of-magnitude improvements in performance and drastic reductions in the cost of analytics compared to vertex-centric approaches.     

An asynchronous traversal engine for graph-based rich metadata management

Rich metadata in high-performance computing (HPC) systems contains extended information about users, jobs, data files, and their relationships. Property graphs are a promising data model to represent heterogeneous rich metadata flexibly. Specifically, a property graph can use vertices to represent different entities and edges to record the relationships between vertices with unique annotations. The high-volume HPC use case, with millions of entities and relationships, naturally requires an out-of-core distributed property graph database, which must support live updates (to ingest production information in real time), low-latency point queries (for frequent metadata operations such as permission checking), and large-scale traversals (for provenance data mining).Among these needs, large-scale property graph traversals are particularly challenging for distributed graph storage systems. Most existing graph systems implement a “level-synchronous” breadth-first search algorithm that relies on global synchronization in each traversal step. This performs well in many problem domains; but a rich metadata management system is characterized by imbalanced graphs, long traversal lengths, and concurrent workloads, each of which has the potential to introduce or exacerbate stragglers (i.e., abnormally slow steps or servers in a graph traversal) that lead to low overall throughput for synchronous traversal algorithms. Previous research indicated that the straggler problem can be mitigated by using asynchronous traversal algorithms, and many graph-processing frameworks have successfully demonstrated this approach. Such systems require the graph to be loaded into a separate batch-processing framework instead of being iteratively accessed, however.In this work, we investigate a general asynchronous graph traversal engine that can operate atop a rich metadata graph in its native format. We outline a traversal-aware query language and key optimizations (traversal-affiliate caching and execution merging) necessary for efficient performance. We further explore the effect of different graph partitioning strategies on the traversal performance for both synchronous and asynchronous traversal engines. Our experiments show that the asynchronous graph traversal engine is more efficient than its synchronous counterpart in the case of HPC rich metadata processing, where more servers are involved and larger traversals are needed. Moreover, the asynchronous traversal engine is more adaptive to different graph partitioning strategies.     

Data Flow Analysis as a General Concept for the Transport of Verifiable Program Annotations

Just-in-Time (JIT) compilation is frequently employed in order to speed-up the execution of platform-independent and dynamically extensible mobile code applications. Since the time required for dynamic compilation directly influences a program's execution time, JIT compilers usually utilize only simple and fast techniques for program analysis and optimization. To improve further the analysis and optimization process of such compilers program annotations can be used.However, mostly all current annotation approaches suffer from the fact that the verification of transmitted program information is time consuming and therefore will not be carried out on the consumer side of a mobile code system. In this paper, we present a verifiable annotation technique that is based on a well known iterative data flow algorithm and which can be used for the transmission of all program information that can be derived through data flow analysis. Preliminary measurements of compilation and verification time indicate that the presented technique seems to be implementable and therefore could be used as an all-purpose transportation technique for safe program annotations.