Set Of Files Research Articles

Building CMU Sphinx language model for the Holy Quran using simplified Arabic phonemes

This paper investigates the use of a simplified set of Arabic phonemes in an Arabic Speech Recognition system applied to Holy Quran. The CMU Sphinx 4 was used to train and evaluate a language model for the Hafs narration of the Holy Quran. The building of the language model was done using a simplified list of Arabic phonemes instead of the mainly used Romanized set in order to simplify the process of generating the language model. The experiments resulted in very low Word Error Rate (WER) reaching 1.5% while using a very small set of audio files during the training phase when using all the audio data for both the training and the testing phases. However, when using 90% and 80% of the training data, the WER obtained was respectively 50.0% and 55.7%.

Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next-Generation Sequencing Bioinformatics and Variant Interpretation

Next-generation sequencing is becoming increasingly common in clinical laboratories worldwide and is revolutionizing clinical molecular testing. However, the large amounts of raw data produced by next-generation sequencing assays and the need for complex bioinformatics analyses present unique challenges. Proficiency testing in clinical laboratories has traditionally been designed to evaluate assays in their entirety; however, it can be alternatively applied to separate assay components. We developed and implemented a multi-institutional proficiency testing approach to directly assess custom bioinformatics and variant interpretation processes. Six clinical laboratories, all of which use the same commercial library preparation kit for next-generation sequencing analysis of tumor specimens, each submitted raw data (FASTQ files) from four samples. These 24 file sets were then deidentified and redistributed to five of the institutions for analysis and interpretation according to their clinically validated approach. Among the laboratories, there was a high rate of concordance in the calling of single-nucleotide variants, in particular those we considered clinically significant (100% concordance). However, there was significant discordance in the calling of clinically significant insertions/deletions, with only two of seven being called by all participating laboratories. Missed calls were addressed by each laboratory to improve their bioinformatics processes. Thus, through our alternative proficiency testing approach, we identified the bioinformatic detection of insertions/deletions as an area of particular concern for clinical laboratories performing next-generation sequencing testing.

Secret Sharing Approach in Multi-database System

Secret sharing schemes are ideal for storing highly sensitive data. A secret is divided into many parts and every participant gets his unique part. If we combine all of these parts and try regenerating the secret then it might be impractical, and therefore the threshold scheme is used. Shamir’s secret sharing scheme supports the same. Here, some of the parts or all of them are required to reconstruct the secret. Any threshold number of parts are sufficient to reconstruct the original secret. The Admin has a set of files which are confidentiality and availability of data. Whenever a Client requests to access the files, the Admin performs authentication of the user through an encrypted and stored on multiple databases so as to achieve Authentication module, who makes use if Shamir's secret sharing concept. This is similar to the One Time Password (OTP) mechanism. If the Client is authentic, Admin grants him the decryption key and the Client can access the file. In this paper, we shall discuss all this in detail using which we can provide security, replication of data and authentication.Â

On fair network cache allocation to content providers

In-network caching is an important solution for content offloading from content service providers. However despite a rather high maturation in the definition of caching techniques, minor attention has been given to the strategic interaction among the multiple content providers. Situations involving multiple content providers (CPs) and one Internet Service Provider (ISP) having to give them access to its caches are prone to high cache contention, in particular at the appealing topology cross-points. While available cache contention situations from the literature were solved by considering each storage as one autonomous and self managed cache, we propose in this paper to address this contention situation by segmenting the storage on a per-content provider basis (e.g., each CP receives a portion of the storage space depending on its storage demand). We propose a resource allocation and pricing framework to support the network cache provider in the cache allocation to multiple CPs, for situations where CPs have heterogeneous sets of files and untruthful demands need to be avoided. As cache imputations to CPs need to be fair and robust against overclaiming, we evaluate common proportional and max–min fairness (PF, MMF) allocation rules, as well as two coalitional game rules, the Nucleolus and the Shapley value. When comparing our cache allocation algorithm for the different allocation rules with the naive least-recently-used-based cache allocation approach, we find that the latter provides proportional fairness. Moreover, the game-theoretic rules outperform in terms of content access latency the naive cache allocation approach as well as PF and MMF approaches, while sitting in between PF and MMF in terms of fairness. Furthermore, we show that our pricing scheme encourages the CPs to declare their truthful demands by maximizing their utilities for real declarations.

OpenMP Fortran and C programs for solving the time-dependent Gross–Pitaevskii equation in an anisotropic trap

We present new version of previously published Fortran and C programs for solving the Gross-Pitaevskii equation for a Bose-Einstein condensate with contact interaction in one, two and three spatial dimensions in imaginary and real time, yielding both stationary and non-stationary solutions. To reduce the execution time on multicore processors, new versions of parallelized programs are developed using Open Multi-Processing (OpenMP) interface. The input in the previous versions of programs was the mathematical quantity nonlinearity for dimensionless form of Gross-Pitaevskii equation, whereas in the present programs the inputs are quantities of experimental interest, such as, number of atoms, scattering length, oscillator length for the trap, etc. New output files for some integrated one- and two-dimensional densities of experimental interest are given. We also present speedup test results for the new programs.

Online Coded Caching

We consider a basic content distribution scenario consisting of a single origin server connected through a shared bottleneck link to a number of users each equipped with a cache of finite memory. The users issue a sequence of content requests from a set of popular files, and the goal is to operate the caches as well as the server such that these requests are satisfied with the minimum number of bits sent over the shared link. Assuming a basic Markov model for renewing the set of popular files, we characterize approximately the optimal long-term average rate of the shared link. We further prove that the optimal online scheme has approximately the same performance as the optimal offline scheme, in which the cache contents can be updated based on the entire set of popular files before each new request. To support these theoretical results, we propose an online coded caching scheme termed coded least-recently sent (LRS) and simulate it for a demand time series derived from the dataset made available by Netflix for the Netflix Prize. For this time series, we show that the proposed coded LRS algorithm significantly outperforms the popular least-recently used caching algorithm.

Fog Computing: Securing the cloud and preventing insider attacks in the cloud

Cloud computing promises to significantly change the way we use computers and access and store our personal and business information. Because of these new computing and communication paradigm there arise data security challenges. Even though existing techniques use security mechanisms, data theft attacks prevention fails. To overcome this we can use decoy technology to secure data stored in cloud. Although, Fog Computing is defined as the extension of the Cloud Computing paradigm, its distinctive characteristics in the location sensitivity, wireless connectivity, and geographical accessibility create new security and forensics issues and challenges which have not been well studied in Cloud security and Cloud forensics. We monitor data access in the cloud and detect abnormal data access patterns. When unauthorized access is suspected and then verified using challenge questions, we launch a disinformation attack by returning large amounts of decoy information to the attacker. This protects against the misuse of the user's real data. Experiments conducted in a local file setting provide evidence that this approach may provide unprecedented levels of user data security in a Cloud environment.

Fqtools: an efficient software suite for modern FASTQ file manipulation

Summary: Many Next Generation Sequencing analyses involve the basic manipulation of input sequence data before downstream processing (e.g. searching for specific sequences, format conversion or basic file statistics). The rapidly increasing data volumes involved in NGS make any dataset manipulation a time-consuming and error-prone process. I have developed fqtools; a fast and reliable FASTQ file manipulation suite that can process the full set of valid FASTQ files, including those with multi-line sequences, whilst identifying invalid files. Fqtools is faster than similar tools, and is designed for use in automatic processing pipelines.Availability and implementation: fqtools is open source and is available at: https://github.com/alastair-droop/fqtools.Supplementary information: Supplementary data are available at Bioinformatics online.Contact: a.p.droop@leeds.ac.uk

Optimising column family for OLAP queries in HBase

Apache HBase is a column-oriented NoSQL key-value store built on top of the Hadoop distributed file-system. Logically, columns in HBase are grouped into column families. Physically, all columns in one column family are stored in the same set of files. Therefore the division of column families is closely related to the response time for a specific row query. In this paper, a new evolutionary algorithm is designed and applied to group columns and find the optimum column family schema for the given user queries. The reading performance of the optimised column family schema is evaluated on a real dataset provided by ZANOX. It is shown that by using the found optimised column family schema, the reading performance while executing OLAP queries is improved with a statistical significance. Queries from a test set show that the average response time is reduced by up to 72% compared to reference column family schemas.

Verification of Recovered Digital Evidence on the Amazon Kindle

The Amazon Kindle is a popular e-book reader. This popularity will lead criminals to use the Kindle as an accessory to their crime. Very few Kindle publications in the digital forensics domain exist at the time of this writing. Various blogs on the Internet currently provide some of the foundation for Kindle forensics. For this research each fifth generation Kindle was populated with various types of files a typical user may introduce using one method, the USB interface. The Kindle was forensically imaged with AccessData’s Forensic Toolkit Imager before and after each Kindle was populated. Each file was deleted through the USB interface. Files were retrieved and recovered through the USB interface before and after file deletion. These two sets of files were compared to the original set of files. All files retrieved before deletion matched their original counterpart. Not all files recovered after deletion matched their original counterpart. These steps and procedures followed a similar adaptation of the NIST General Test Methodology for Computer Forensic Tools developed by Leshney (2008) for virtual machines.

Working Length Determination Using Cone-Beam Computed Tomography, Periapical Radiography and Electronic Apex Locator in Teeth with Apical Periodontitis: A Clinical Study.

Introduction:The purpose of this clinical study was to compare the accuracy of working length (WL) determination using cone-beam computed tomography (CBCT), conventional periapical radiographies and electronic apex locator. Methods and Materials: This study was conducted during root canal treatment of 19 patients with a total of 30 single-rooted teeth diagnosed with apical periodontitis. After taking the initial parallel periapical radiographies, the initial file was advanced into the canal until the WL was detected by the apex locator. Subsequently, the WL was measured and WL radiographies were taken with the file set in the canal. Afterwards, CBCT images were acquired. These three measurements were tabulated and compared and the data were analyzed using the Friedman test. The level of significance was set at 0.05. Results:The mean values for WL determination by electronic apex locator, periapical radiograph and CBCT images were 22.25, 22.43 and 22.65, respectively which was not statistically significant (P>0.05). Conclusion:Working length determination using CBCT images was precise when compared to radiographic method and electronic apex locator.

Object Relational Similarity with Semantic Similarity for User Interactive Content based Video Retrieval from Multimedia Dataset using Semantic Ontology

This chapter is about retrieval of video from large set of multimedia data set. In general the video retrieval is performed based on the contextual information. For example, if the user requests the video in which Dhoni plays football, it returns the set of video files, which contains the dhoni playing cricket or dhoni playing all games. Such irrelevancy in results is higher in the previous search mechanism. So in order to improve the efficiency of video retrieval, the object relational similarity is computed on the video content present in each class. Similarly the method computes the semantic similarity for the different class of multimedia content. Based on both the similarity measure the method ranks the results and produce to the user. The user is allowed to refine their query and based on the query provided the method refine the result or research the query. The method produces efficient result in interactive multimedia search and reduces the false ratio.

Workshop 5 – Cross Section, Nuclear Data, and Uncertainties

The Cross Section, Nuclear Data, and Uncertainties Workshop met with 30 participants. There was a lively discussion that covered several different topics. Some of the topics had resonance with topics brought up in other workshop at this symposium. One major issue was how to assign an a priori uncertainty to the trial spectrum used in spectrum adjustment techniques, or, more specifically, the need for a more rigorous and automated coupling of uncertainties into the radiation transport codes that are used to generate the a priori (trial) spectrum that is used in neutron spectrum adjustment approaches. Approaches based on discrete ordinate transport provide a means of generating sensitivity coefficients for specific variations, but fall short of the required task. While some Monte Carlo-based radiation transport codes permit the user to vary the cross sections for specific reactions or to vary material densities, a more universal and automated variation of all relevant inputs to the radiation transport code is required. One approach mentioned was a Total Monte Carlo (TMC) approach provided by a coupling into radiation transport codes of the recently generated statistical sample of random ENDF nuclear data evaluations produced by the TALYS code and incorporated into the TENDL library (for some isotopes). This would provide a set of self-consistent nuclear data files that can be sampled in a transport calculation. This variation of nuclear data would need to be coupled with a variation in material composition, density, and spatial dimensions. Another discussion topic was the need for the community to revisit the consistency of current approaches to spectrum unfolds/adjustment, i.e. a new round of the older REAL-84 and REAL-88 exercises to assess our status. While the dosimetry community has made great strides with the IRDFF library in establishing an international community consensus for dosimetry cross sections and associated nuclear data, the differences within the community in the treatment of the uncertainty in the trial spectrum and the availability of new spectrum adjustment techniques, such as Maximum Entropy codes like MAXED and the use of genetic algorithms, warrant a revisit of these international exercises to assess the current consistency (within stated uncertainty bonds) of approaches within the community to the characterization of neutron spectra and towards expressing the uncertainty in integral metrics based on these spectrum uncertainties. Since the IAEA/NDS has done such a good job in coordinating an international consensus in dosimetry cross sections and nuclear data, and since they coordinated the older REAL-8X exercises, we look to them to coordinate a new international assessment of our consistency in treating spectrum adjustments and characterizing the resulting uncertainties.

Advanced ages at death in Sápmi during the eighteenth and nineteenth centuries: With special attention to longevity among the Sami population

This article examines advanced ages at death in a historical population in northern Sweden between 1780 and 1900. The source material used is a set of data files from the Demographic Data Base at Umeå University supplemented with the search tool Indiko. The belief that the Sami died at very old ages was tested, and life tables and values of remaining life expectancies at older ages were calculated. The information of the age at death was analysed using a model containing four levels of certainty. The analysis reveals that the Sami did not live to extreme ages. The analysis also reveals large differences between the parishes concerning extreme longevity and correctness of age at death.

KALAKA-3: a database for the assessment of spoken language recognition technology on YouTube audios

KALAKA-3 is a speech database specifically designed for the development and evaluation of Spoken Language Recognition (SLR) systems. The database provides TV broadcast speech for training, and audio data extracted from YouTube videos for tuning and testing. The database was created to support the Albayzin 2012 Language Recognition Evaluation (LRE), which featured two language recognition tasks, both dealing with European languages. The first one involved six target languages (Basque, Catalan, English, Galician, Portuguese and Spanish) for which there was plenty of training data, whereas the second one involved four target languages (French, German, Greek and Italian) for which no training data was provided. This second task tried to simulate the use case of low resource languages. Two separate sets of YouTube audio files were provided to test the performance of language recognition systems on both tasks. To allow open-set tests, these datasets included speech in 11 additional (Out-Of-Set) European languages. In this paper, we first discuss the design issues considered when creating the database and describe the data collection procedure. Then, we present the results attained in the Albayzin 2012 LRE, along with the performance of state-of-the-art systems on the four evaluation tracks defined on the database. Both series of results demonstrate the usefulness of KALAKA-3 as a challenging benchmark for the advancement of SLR technology. As far as we know, this is the first database specifically designed to benchmark SLR technology on YouTube audios.

Tests of PROOF-on-Demand with ATLAS Prodsys2 and first experience with HTTP federation

During the LHC Run-1, Grid resources in ATLAS have been managed by the PanDA and DQ2 systems. In order to meet the needs for the LHC Run-2, Prodsys2 and Rucio are used as the new ATLAS Workload and Data Management systems.The data are stored under various formats in ROOT files and end-user physicists have the choice to use either the ATHENA framework or directly ROOT. Within the ROOT data analysis framework it is possible to perform analysis of huge sets of ROOT files in parallel with PROOF on clusters of computers (usually organised in analysis facilities) or multi-core machines. In addition, PROOF-on-Demand (PoD) can be used to enable PROOF on top of an existing resource management system.In this work, we present the first performance obtained enabling PROOF-based analysis at CERN and in some of the Italian ATLAS Tier-2 sites within the new ATLAS workload system. Benchmark tests of data access with the httpd protocol, using also the httpd redirector, will be shown. We also present results on the startup latency tests using the new PROOF functionality of dynamic workers addition, which improves the performance of PoD using Grid resources. These new results will be compared with the expected improvements discussed in a previous work.

Engineering the CernVM-Filesystem as a High Bandwidth Distributed Filesystem for Auxiliary Physics Data

A common use pattern in the computing models of particle physics experiments is running many distributed applications that read from a shared set of data files. We refer to this data is auxiliary data, to distinguish it from (a) event data from the detector (which tends to be different for every job), and (b) conditions data about the detector (which tends to be the same for each job in a batch of jobs). Relatively speaking, conditions data also tends to be relatively small per job where both event data and auxiliary data are larger per job. Unlike event data, auxiliary data comes from a limited working set of shared files. Since there is spatial locality of the auxiliary data access, the use case appears to be identical to that of the CernVM- Filesystem (CVMFS). However, we show that distributing auxiliary data through CVMFS causes the existing CVMFS infrastructure to perform poorly. We utilize a CVMFS client feature called "alien cache" to cache data on existing local high-bandwidth data servers that were engineered for storing event data. This cache is shared between the worker nodes at a site and replaces caching CVMFS files on both the worker node local disks and on the site's local squids. We have tested this alien cache with the dCache NFSv4.1 interface, Lustre, and the Hadoop Distributed File System (HDFS) FUSE interface, and measured performance. In addition, we use high-bandwidth data servers at central sites to perform the CVMFS Stratum 1 function instead of the low-bandwidth web servers deployed for the CVMFS software distribution function. We have tested this using the dCache HTTP interface. As a result, we have a design for an end-to-end high-bandwidth distributed caching read-only filesystem, using existing client software already widely deployed to grid worker nodes and existing file servers already widely installed at grid sites. Files are published in a central place and are soon available on demand throughout the grid and cached locally on the site with a convenient POSIX interface. This paper discusses the details of the architecture and reports performance measurements.

FTS3: Quantitative Monitoring

The overall success of LHC data processing depends heavily on stable, reliable and fast data distribution. The Worldwide LHC Computing Grid (WLCG) relies on the File Transfer Service (FTS) as the data movement middleware for moving sets of files from one site to another. This paper describes the components of FTS3 monitoring infrastructure and how they are built to satisfy the common and particular requirements of the LHC experiments. We show how the system provides a complete and detailed cross-virtual organization (VO) picture of transfers for sites, operators and VOs. This information has proven critical due to the shared nature of the infrastructure, allowing a complete view of all transfers on shared network links between various workflows and VOs using the same FTS transfer manager. We also report on the performance of the FTS service itself, using data generated by the aforementioned monitoring infrastructure both during the commissioning and the first phase of production. We also explain how this monitoring information and network metrics produced can be used both as a starting point for troubleshooting data transfer issues, but also as a mechanism to collect information such as transfer efficiency between sites, achieved throughput and its evolution over time, most common errors, etc, and take decision upon them to further optimize transfer workflows. The service setup is subject to sites policies to control the network resource usage, as well as all the VOs making use of the Grid resources at the site to satisfy their requirements. FTS3 is the new version of FTS and has been deployed in production in August 2014.

Transparent handling of small files with dCache to optimize tape access

We introduce a service for dCache that allows automatic and transparent packing and extracting of file sets into large container files. This is motivated by the adoption of dCache by new communities that often work with rather small data files which causes large time overheads on reads and writes by the underlying tape systems. Our service can be attached to existing dCache instances and we were show that it is able to optimize average access times to tape access.

The S-Lab’s Lab in a Box: A Potential Game Changer for Rural Schools in the Developing World

The S-Lab’s Lab-in-a-Box features a computer lab hosting a rich set of educational resources (the GSAP Portal) for internet- and electricity deprived- schools. The first version of the portal prototyped in Ghana includes the Rachel initiative on a 32 GB file set. The portal has been expanded to a 64 GB drive hosted on a Raspberry Pi server, on a local dedicated file server or directly on a PC or Laptop and its elements have been mapped to the Ghana school curriculum. The original powering option which consisted of solar collector and lead-acid battery was re-designed to eliminate the 12v-to-5v conversion making use of LiPo battery packs with significant improvements in energy, costs, weight and size. The system was also extended to bring science activities to the schools using available (Android) tablet sensors and instrument- analysis- reference- simulation- APPs plus a few inexpensive instruments and components. Eighty-two schools, the most recent of the 158 recipient schools, were reviewed; seventy-two of these had connection to the grid and 4 of the remaining 10 were provided with the solar powered Lab-in-a-Box . Several challenges were encountered ranging from equipment theft (1 school) and interveners replacing the computer OS resulting in erasure of the drive (several schools) to staff turnover. The latter is the biggest challenge as staff trained on the systems are replaced every two years at most schools; several schools failed to train replacements. Dramatic results were realized in one district, Birim North, which moved from the lowest performing school in the region and 117th in the country prior to the intervention to 1st in the region and 17th in the country over two years following the intervention. The results demonstrate the need for commitments of the district as well as the individual schools.