Processing and Linking Audio Events in Large Multimedia Archives: The EU inEvent Project

In the inEvent EU project [1], we aim at structuring, retrieving, and sharing large archives of networked, and dynamically changing, multimedia recordings, mainly consisting of meetings, videoconferences, and lectures. More specifically, we are developing an integrated system that performs audiovisual processing of multimedia recordings, and labels them in terms of interconnected “hyper-events ” (a notion inspired from hyper-texts). Each hyper-event is composed of simpler facets, including audio-video recordings and metadata, which are then easier to search, retrieve and share. In the present paper, we mainly cover the audio processing aspects of the system, including speech recognition, speaker diarization and linking (across recordings), the use of these features for hyper-event indexing and recommendation, and the search portal. We present initial results for feature extraction from lecture recordings using the TED talks. Index Terms: Networked multimedia events; audio processing: speech recognition; speaker diarization and linking; multimedia indexing and searching; hyper-events. 1

FAIRness and Usability for Open-access Omics Data Systems

Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the FAIRness of NASAs GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. The range of overall FAIRness scores was 6-12 (out of 14), average 10.1, and standard deviation 2.4. The range of Pass ratings for the metrics was 29-79%, Partial Pass 0-21%, and Fail 7-50%. The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. Reusability of metadata, in particular, was frequently not well supported. We relate our experiences implementing semantic integration of omics data from some of the assessed systems for federated querying and retrieval functions, given their shortcomings in data interoperability. Finally, we propose two new principles that Big Data system developers, in particular, should consider for maximizing data accessibility

Porqpine: a peer-to-peer search engine

In this paper, we present a fully distributed and collaborative search engine for web pages: Porqpine. This system uses a novel query-based model and collaborative filtering techniques in order to obtain user-customized results. All knowledge about users and profiles is stored in each user node?s application. Overall the system is a multi-agent system that runs on the computers of the user community. The nodes interact in a peer-to-peer fashion in order to create a real distributed search engine where information is completely distributed among all the nodes in the network. Moreover, the system preserves the privacy of user queries and results by maintaining the anonymity of the queries? consumers and results? producers. The knowledge required by the system to work is implicitly caught through the monitoring of users actions, not only within the system?s interface but also within one of the most popular web browsers. Thus, users are not required to explicitly feed knowledge about their interests into the system since this process is done automatically. In this manner, users obtain the benefits of a personalized search engine just by installing the application on their computer. Porqpine does not intend to shun completely conventional centralized search engines but to complement them by issuing more accurate and personalized results.Postprint (published version

CHORUS Deliverable 2.2: Second report - identification of multi-disciplinary key issues for gap analysis toward EU multimedia search engines roadmap

After addressing the state-of-the-art during the first year of Chorus and establishing the existing landscape in multimedia search engines, we have identified and analyzed gaps within European research effort during our second year. In this period we focused on three directions, notably technological issues, user-centred issues and use-cases and socio- economic and legal aspects. These were assessed by two central studies: firstly, a concerted vision of functional breakdown of generic multimedia search engine, and secondly, a representative use-cases descriptions with the related discussion on requirement for technological challenges. Both studies have been carried out in cooperation and consultation with the community at large through EC concertation meetings (multimedia search engines cluster), several meetings with our Think-Tank, presentations in international conferences, and surveys addressed to EU projects coordinators as well as National initiatives coordinators. Based on the obtained feedback we identified two types of gaps, namely core technological gaps that involve research challenges, and “enablers”, which are not necessarily technical research challenges, but have impact on innovation progress. New socio-economic trends are presented as well as emerging legal challenges

Differentiating signals to make biological sense – a guide through databases for MS-based non-targeted metabolomics

Metabolite identification is one of the most challenging steps in metabolomics studies and reflects one of the greatest bottlenecks in the entire workflow. The success of this step determines the success of the entire research, therefore the quality at which annotations are given requires special attention. A variety of tools and resources are available to aid metabolite identification or annotation, offering different and often complementary functionalities. In preparation for this article, almost 50 databases were reviewed, from which 17 were selected for discussion, chosen for their on-line ESI-MS functionality. The general characteristics and functions of each database is discussed in turn, considering the advantages and limitations of each along with recommendations for optimal use of each tool, as derived from experiences encountered at the Centre for Metabolomics and Bioanalysis (CEMBIO) in Madrid. These databases were evaluated considering their utility in non-targeted metabolomics, including aspects such as ID assignment, structural assignment and interpretation of results

Mapping the repository landscape : harnessing similarity with RepoSim and RepoSnipy

The rapid growth of scientific software development has led to the emergence of large and complex codebases, making it challenging to search, find, and compare software repositories within the scientific research community. In this paper, we propose a solution by leveraging deep learning techniques to learn embeddings that capture semantic similarities among repositories. Our approach focuses on identifying repositories with similar semantics, even when their code fragments and documentation exhibit different syntax. To address this challenge, we introduce two complementary open-source tools: RepoSim and RepoSnipy. RepoSim is a command-line toolbox designed to represent repositories at both the source code and documentation levels. It utilizes the UniXcoder pre-trained language model, which has demonstrated remarkable performance in code-related understanding tasks. RepoSnipy is a web-based neural semantic search engine that utilizes the powerful capabilities of RepoSim and offers a user-friendly search interface, allowing researchers and practitioners to query public repositories hosted on GitHub and discover semantically similar repositories. RepoSim and RepoSnipy empower researchers, developers, and practitioners by facilitating the comparison and analysis of software repositories. They not only enable efficient collaboration and code reuse but also accelerate the development of scientific software.Postprin

Closing the loop: assisting archival appraisal and information retrieval in one sweep

In this article, we examine the similarities between the concept of appraisal, a process that takes place within the archives, and the concept of relevance judgement, a process fundamental to the evaluation of information retrieval systems. More specifically, we revisit selection criteria proposed as result of archival research, and work within the digital curation communities, and, compare them to relevance criteria as discussed within information retrieval's literature based discovery. We illustrate how closely these criteria relate to each other and discuss how understanding the relationships between the these disciplines could form a basis for proposing automated selection for archival processes and initiating multi-objective learning with respect to information retrieval