Applying Automatic Translation for Optical Music Recognition’s Encoding Step

Optical music recognition is a research field whose efforts have been mainly focused, due to the difficulties involved in its processes, on document and image recognition. However, there is a final step after the recognition phase that has not been properly addressed or discussed, and which is relevant to obtaining a standard digital score from the recognition process: the step of encoding data into a standard file format. In this paper, we address this task by proposing and evaluating the feasibility of using machine translation techniques, using statistical approaches and neural systems, to automatically convert the results of graphical encoding recognition into a standard semantic format, which can be exported as a digital score. We also discuss the implications, challenges and details to be taken into account when applying machine translation techniques to music languages, which are very different from natural human languages. This needs to be addressed prior to performing experiments and has not been reported in previous works. We also describe and detail experimental results, and conclude that applying machine translation techniques is a suitable solution for this task, as they have proven to obtain robust results.

RaViS: Real-time accelerated View Synthesizer for immersive video 6DoF VR

MPEG-I, the upcoming standard for immersive video, has steadily explored immersive video technology for free navigation applications, where any virtual viewpoint to the scene is created using Depth Image-Based Rendering (DIBR) from any number of stationary cameras positioned around the scene. This exploration has recently evolved towards a rendering pipeline using camera feeds, as well as a standard file format, containing all information for synthesizing a virtual viewpoint to a scene. We present an acceleration of our Reference View Synthesis software (RVS) that enables the rendering in real-time of novel views in a head mounted display, hence supporting virtual reality (VR) with 6 Degrees of Freedom (6DoF) including motion parallax within a restricted viewing volume. In this paper, we explain its main engineering challenges.

dsCleaner: A Python Library to Clean, Preprocess and Convert Non-Instrusive Load Monitoring Datasets

Datasets play a vital role in data science and machine learning research as they serve as the basis for the development, evaluation, and benchmark of new algorithms. Non-Intrusive Load Monitoring is one of the fields that has been benefiting from the recent increase in the number of publicly available datasets. However, there is a lack of consensus concerning how dataset should be made available to the community, thus resulting in considerable structural differences between the publicly available datasets. This technical note presents the DSCleaner, a Python library to clean, preprocess, and convert time series datasets to a standard file format. Two application examples using real-world datasets are also presented to show the technical validity of the proposed library.

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analysed per experiment, as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elastic compute resources such as Linux-based cluster environments and cloud infrastructures. Unfortunately, the vast majority of cross-platform proteomics tools are not able to operate directly on the proprietary formats generated by the diverse mass spectrometers. Here, we presented ThermoRawFileParser, an open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML. To ensure the broadest possible availability, and to increase integration capabilities with popular workflow systems such as Galaxy or Nextflow, we have also built Conda and BioContainers containers around ThermoRawFileParser. In addition, we implemented a user-friendly interface (ThermoRawFileParserGUI) for those users not familiar with command-line tools. Finally, we performed a benchmark of ThermoRawFileParser and msconvert to verify that the converted mzML files contain reliable quantitative results.

A Systematic Review of the Three-Dimensional Portable Document Format (3D PDF) in Clinical Communication and Biomedical Sciences: Applications, Tools, and Protocols (Preprint)

BACKGROUND The Portable Document Format (PDF) is the standard file format for the communication of biomedical information via the Internet and for electronic scholarly publishing. Although PDF allows for the embedding of three-dimensional (3D) objects and although this technology has great potential for the communication of such data, it is not broadly used by the scientific community or by clinicians. OBJECTIVE The objective of this review was to provide an overview of existing publications that apply 3D PDF technology and the protocols and tools for the creation of model files and 3D PDFs for scholarly purposes to demonstrate the possibilities and the ways to use this technology. METHODS A systematic literature review was performed using PubMed and Google Scholar. Articles searched for were in English, peer-reviewed with biomedical reference, published since 2005 in a journal or presented at a conference or scientific meeting. Ineligible articles were removed after screening. The found literature was categorized into articles that (1) applied 3D PDF for visualization, (2) showed ways to use 3D PDF, and (3) provided tools or protocols for the creation of 3D PDFs or necessary models. Finally, the latter category was analyzed in detail to provide an overview of the state of the art. RESULTS The search retrieved a total of 902 items. Screening identified 200 in-scope publications, 13 covering the use of 3D PDF for medical purposes. Only one article described a clinical routine use case; all others were pure research articles. The disciplines that were covered beside medicine were many. In most cases, either animal or human anatomies were visualized. A method, protocol, software, library, or other tool for the creation of 3D PDFs or model files was described in 19 articles. Most of these tools required advanced programming skills and/or the installation of further software packages. Only one software application presented an all-in-one solution with a graphical user interface. CONCLUSIONS The use of 3D PDF for visualization purposes in clinical communication and in biomedical publications is still not in common use, although both the necessary technique and suitable tools are available, and there are many arguments in favor of this technique. The potential of 3D PDF usage should be disseminated in the clinical and biomedical community. Furthermore, easy-to-use, standalone, and free-of-charge software tools for the creation of 3D PDFs should be developed.

OzFlux data: network integration from collection to curation

Measurement of the exchange of energy and mass between the surface and the atmospheric boundary-layer by the eddy covariance technique has undergone great change in the last 2 decades. Early studies of these exchanges were confined to brief field campaigns in carefully controlled conditions followed by months of data analysis. Current practice is to run tower-based eddy covariance systems continuously over several years due to the need for continuous monitoring as part of a global effort to develop local-, regional-, continental- and global-scale budgets of carbon, water and energy. Efficient methods of processing the increased quantities of data are needed to maximise the time available for analysis and interpretation. Standardised methods are needed to remove differences in data processing as possible contributors to observed spatial variability. Furthermore, public availability of these data sets assists with undertaking global research efforts. The OzFlux data path has been developed (i) to provide a standard set of quality control and post-processing tools across the network, thereby facilitating inter-site integration and spatial comparisons; (ii) to increase the time available to researchers for analysis and interpretation by reducing the time spent collecting and processing data; (iii) to propagate both data and metadata to the final product; and (iv) to facilitate the use of the OzFlux data by adopting a standard file format and making the data available from web-based portals. Discovery of the OzFlux data set is facilitated through incorporation in FLUXNET data syntheses and the publication of collection metadata via the RIF-CS format. This paper serves two purposes. The first is to describe the data sets, along with their quality control and post-processing, for the other papers of this Special Issue. The second is to provide an example of one solution to the data collection and curation challenges that are encountered by similar flux tower networks worldwide.

veraPDF: building an open source, industry supported PDF/A validator for cultural heritage institutions

Purpose This paper describes the development of the veraPDF validator. The objective of veraPDF is to build an industry supported, open source validator for all parts and conformance levels of the PDF/A specification for archival PDF documents. The project is led by the Open Preservation Foundation and the PDF Association and is funded by the EU PREFORMA project. Design/methodology/approach veraPDF is designed to meet the needs of the digital preservation community and the PDF industry alike. The technology is subject to the review of and acceptance by the PDF Association’s PDF Validation Technical Working Group, including many participants of the relevant ISO working groups. Cultural heritage institutions are collecting ever-increasing volumes of digital information, which they have a mandate to preserve for the long term. However, in many cases, they need to ensure their content has been produced to the specifications of a standard file format, as well as any acceptance criteria stated in their institutional policy. Findings With increasing knowledge and experience of processes and policies, cultural heritage institutions are influencing the production and development of digital preservation software. The product development funded by the PREFORMA project shows how such cooperation can benefit the community as a whole. Originality/value This paper describes the value of an open source approach to developing a PDF/A validator for cultural heritage organisations.

OzFlux Data: Network integration from collection to curation

Measurement of the exchange of energy and mass between the surface and the atmospheric boundary-layer by the eddy covariance technique has undergone great change in the last two decades. Early studies of these exchanges were confined to brief field campaigns in carefully controlled conditions followed by months of data analysis. Current practice is to run tower-based eddy covariance systems continuously over several years due to the need for continuous monitoring as part of a global effort to develop local-, regional-, continental- and global-scale budgets of carbon, water and energy. Efficient methods of processing the increased quantities of data are needed to maximise the time available for analysis and interpretation. Standardised methods are needed to remove differences in data processing as possible contributors to observed spatial variability. Furthermore, public availability of these datasets assists with undertaking global research efforts. The OzFlux data path has been developed (i) to provide a standard set of quality control and post-processing tools across the network, thereby facilitating inter-site integration and spatial comparisons; (ii) to increase the time available to researchers for analysis and interpretation by reducing the time spent collecting and processing data; (iii) to propagate both data and metadata to the final product; and (iv) to facilitate the use of the OzFlux data by adopting a standard file format and making the data available from web-based portals. The fundamentals of the OzFlux data path include the adoption of netCDF as the underlying file format to integrate data and metadata, a suite of Python scripts to provide a standard quality control, post-processing, gap filling and partitioning environment, a portal from which data can be downloaded and an OPeNDAP server offering internet access to the latest version of the OzFlux data set. Discovery of the OzFlux data set is facilitated through incorporation in FluxNet data syntheses and the publication of collection metadata via the RIF-CS format. This paper serves two purposes. The first is to describe the datasets, along with their quality control and post-processing, for the other papers of this Special Issue. The second is to provide an example of one solution to the data collection and curation challenges that are encountered by similar flux tower networks worldwide.

Maftools: Efficient analysis, visualization and summarization of MAF files from large-scale cohort based cancer studies

Mutation Annotation Format (MAF) has become a standard file format for storing somatic/germline variants derived from sequencing of large cohort of cancer samples. MAF files contain a list of all variants detected in a sample along with various annotations associated with the putative variant. MAF file forms the basis for many downstream analyses and provides complete landscape of the cohort. Here we introduce maftools–an R package that provides rich source of functions for performing various analyses, visualizations and summarization of MAF files. Maftools uses data.table library for faster processing/summarization and ggplot2 for generating rich and publication quality visualizations. Maftools also takes advantages of S4 class system for better data representation, with easy to use and flexible functions.Availability and Implementationmaftools is implemented as an R package available at https://github.com/PoisonAlien/[email protected]