3,222 research outputs found
A Unified Multi-Functional Dynamic Spectrum Access Framework: Tutorial, Theory and Multi-GHz Wideband Testbed
Dynamic spectrum access is a must-have ingredient for future sensors that are ideally cognitive. The goal of this paper is a tutorial treatment of wideband cognitive radio and radarâa convergence of (1) algorithms survey, (2) hardware platforms survey, (3) challenges for multi-function (radar/communications) multi-GHz front end, (4) compressed sensing for multi-GHz waveformsârevolutionary A/D, (5) machine learning for cognitive radio/radar, (6) quickest detection, and (7) overlay/underlay cognitive radio waveforms. One focus of this paper is to address the multi-GHz front end, which is the challenge for the next-generation cognitive sensors. The unifying theme of this paper is to spell out the convergence for cognitive radio, radar, and anti-jamming. Mooreâs law drives the system functions into digital parts. From a system viewpoint, this paper gives the first comprehensive treatment for the functions and the challenges of this multi-function (wideband) system. This paper brings together the inter-disciplinary knowledge
Thirty Years of Machine Learning: The Road to Pareto-Optimal Wireless Networks
Future wireless networks have a substantial potential in terms of supporting
a broad range of complex compelling applications both in military and civilian
fields, where the users are able to enjoy high-rate, low-latency, low-cost and
reliable information services. Achieving this ambitious goal requires new radio
techniques for adaptive learning and intelligent decision making because of the
complex heterogeneous nature of the network structures and wireless services.
Machine learning (ML) algorithms have great success in supporting big data
analytics, efficient parameter estimation and interactive decision making.
Hence, in this article, we review the thirty-year history of ML by elaborating
on supervised learning, unsupervised learning, reinforcement learning and deep
learning. Furthermore, we investigate their employment in the compelling
applications of wireless networks, including heterogeneous networks (HetNets),
cognitive radios (CR), Internet of things (IoT), machine to machine networks
(M2M), and so on. This article aims for assisting the readers in clarifying the
motivation and methodology of the various ML algorithms, so as to invoke them
for hitherto unexplored services as well as scenarios of future wireless
networks.Comment: 46 pages, 22 fig
Automated Protein Subfamily Identification and Classification
Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in function prediction but has been difficult to automate for high-throughput application. To address this limitation, we present a computationally efficient pipeline for phylogenomic classification of proteins. This pipeline uses the SCI-PHY (Subfamily Classification in Phylogenomics) algorithm for automatic subfamily identification, followed by subfamily hidden Markov model (HMM) construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs enables classification of novel sequences to protein families and subfamilies. Sequences representing entirely novel subfamilies are differentiated from those that can be classified to subfamilies in the input training set using logistic regression. Subfamily HMM parameters are estimated using an information-sharing protocol, enabling subfamilies containing even a single sequence to benefit from conservation patterns defining the family as a whole or in related subfamilies. SCI-PHY subfamilies correspond closely to functional subtypes defined by experts and to conserved clades found by phylogenetic analysis. Extensive comparisons of subfamily and family HMM performances show that subfamily HMMs dramatically improve the separation between homologous and non-homologous proteins in sequence database searches. Subfamily HMMs also provide extremely high specificity of classification and can be used to predict entirely novel subtypes. The SCI-PHY Web server at http://phylogenomics.berkeley.edu/SCI-PHY/ allows users to upload a multiple sequence alignment for subfamily identification and subfamily HMM construction. Biologists wishing to provide their own subfamily definitions can do so. Source code is available on the Web page. The Berkeley Phylogenomics Group PhyloFacts resource contains pre-calculated subfamily predictions and subfamily HMMs for more than 40,000 protein families and domains at http://phylogenomics.berkeley.edu/phylofacts/
AlbayzĂn-2014 evaluation: audio segmentation and classification in broadcast news domains
The electronic version of this article is the complete one and can be found online at: http://dx.doi.org/10.1186/s13636-015-0076-3Audio segmentation is important as a pre-processing task to improve the performance of many speech technology tasks and, therefore, it has an undoubted research interest. This paper describes the database, the metric, the systems and the results for the AlbayzĂn-2014 audio segmentation campaign. In contrast to previous evaluations where the task was the segmentation of non-overlapping classes, AlbayzĂn-2014 evaluation proposes the delimitation of the presence of speech, music and/or noise that can be found simultaneously. The database used in the evaluation was created by fusing different media and noises in order to increase the difficulty of the task. Seven segmentation systems from four different research groups were evaluated and combined. Their experimental results were analyzed and compared with the aim of providing a benchmark and showing up the promising directions in this field.This work has been partially funded by the Spanish Government and the European Union (FEDER) under the project TIN2011-28169-C05-02 and supported by the European Regional Development Fund and the Spanish
Government (âSpeechTech4All Projectâ TEC2012-38939-C03
Ecosystemic Evolution Feeded by Smart Systems
Information Society is advancing along a route of ecosystemic evolution. ICT and Internet advancements, together with the progression of the systemic approach for enhancement and application of Smart Systems, are grounding such an evolution. The needed approach is therefore expected to evolve by increasingly fitting into the basic requirements of a significant general enhancement of human and social well-being, within all spheres of life (public, private, professional). This implies enhancing and exploiting the net-living virtual space, to make it a virtuous beneficial integration of the real-life space. Meanwhile, contextual evolution of smart cities is aiming at strongly empowering that ecosystemic approach by enhancing and diffusing net-living benefits over our own lived territory, while also incisively targeting a new stable socio-economic local development, according to social, ecological, and economic sustainability requirements. This territorial focus matches with a new glocal vision, which enables a more effective diffusion of benefits in terms of well-being, thus moderating the current global vision primarily fed by a global-scale market development view. Basic technological advancements have thus to be pursued at the system-level. They include system architecting for virtualization of functions, data integration and sharing, flexible basic service composition, and end-service personalization viability, for the operation and interoperation of smart systems, supporting effective net-living advancements in all application fields. Increasing and basically mandatory importance must also be increasingly reserved for humanâtechnical and socialâtechnical factors, as well as to the associated need of empowering the cross-disciplinary approach for related research and innovation. The prospected eco-systemic impact also implies a social pro-active participation, as well as coping with possible negative effects of net-living in terms of social exclusion and isolation, which require incisive actions for a conformal socio-cultural development. In this concern, speed, continuity, and expected long-term duration of innovation processes, pushed by basic technological advancements, make ecosystemic requirements stricter. This evolution requires also a new approach, targeting development of the needed basic and vocational education for net-living, which is to be considered as an engine for the development of the related ânew living know-howâ, as well as of the conformal ânew making know-howâ
VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes
Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists, and have been demonstrated to increase host virulence. The increasing ease of bacterial genome se- quencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES, a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bac- terial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster, and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab separated format and generates intuitive and interactive visualizations for data exploration. De- spite VIBESâ primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1,072 Pseudomonas spp. genomes
On-premise containerized, light-weight software solutions for Biomedicine
Bioinformatics software systems are critical tools for analysing large-scale biological
data, but their design and implementation can be challenging due to the need for reliability, scalability, and performance. This thesis investigates the impact of several
software approaches on the design and implementation of bioinformatics software
systems. These approaches include software patterns, microservices, distributed
computing, containerisation and container orchestration. The research focuses on
understanding how these techniques affect bioinformatics software systemsâ reliability, scalability, performance, and efficiency. Furthermore, this research highlights
the challenges and considerations involved in their implementation. This study also
examines potential solutions for implementing container orchestration in bioinformatics research teams with limited resources and the challenges of using container
orchestration. Additionally, the thesis considers microservices and distributed computing and how these can be optimised in the design and implementation process to
enhance the productivity and performance of bioinformatics software systems. The
research was conducted using a combination of software development, experimentation, and evaluation. The results show that implementing software patterns can
significantly improve the code accessibility and structure of bioinformatics software
systems. Specifically, microservices and containerisation also enhanced system reliability, scalability, and performance. Additionally, the study indicates that adopting
advanced software engineering practices, such as model-driven design and container
orchestration, can facilitate efficient and productive deployment and management of
bioinformatics software systems, even for researchers with limited resources. Overall, we develop a software system integrating all our findings. Our proposed system
demonstrated the ability to address challenges in bioinformatics. The thesis makes
several key contributions in addressing the research questions surrounding the design,
implementation, and optimisation of bioinformatics software systems using software
patterns, microservices, containerisation, and advanced software engineering principles and practices. Our findings suggest that incorporating these technologies can
significantly improve bioinformatics software systemsâ reliability, scalability, performance, efficiency, and productivity.Bioinformatische Software-Systeme stellen bedeutende Werkzeuge fĂŒr die Analyse
umfangreicher biologischer Daten dar. Ihre Entwicklung und Implementierung kann
jedoch aufgrund der erforderlichen ZuverlÀssigkeit, Skalierbarkeit und LeistungsfÀhigkeit eine Herausforderung darstellen. Das Ziel dieser Arbeit ist es, die Auswirkungen von Software-Mustern, Microservices, verteilten Systemen, Containerisierung
und Container-Orchestrierung auf die Architektur und Implementierung von bioinformatischen Software-Systemen zu untersuchen. Die Forschung konzentriert sich
darauf, zu verstehen, wie sich diese Techniken auf die ZuverlÀssigkeit, Skalierbarkeit,
LeistungsfÀhigkeit und Effizienz von bioinformatischen Software-Systemen auswirken
und welche Herausforderungen mit ihrer Konzeptualisierungen und Implementierung
verbunden sind. Diese Arbeit untersucht auch potenzielle Lösungen zur Implementierung von Container-Orchestrierung in bioinformatischen Forschungsteams mit begrenzten Ressourcen und die EinschrĂ€nkungen bei deren Verwendung in diesem Kontext. Des Weiteren werden die SchlĂŒsselfaktoren, die den Erfolg von bioinformatischen Software-Systemen mit Containerisierung, Microservices und verteiltem Computing beeinflussen, untersucht und wie diese im Design- und Implementierungsprozess optimiert werden können, um die ProduktivitĂ€t und Leistung bioinformatischer
Software-Systeme zu steigern. Die vorliegende Arbeit wurde mittels einer Kombination aus Software-Entwicklung, Experimenten und Evaluation durchgefĂŒhrt. Die
erzielten Ergebnisse zeigen, dass die Implementierung von Software-Mustern, die ZuverlÀssigkeit und Skalierbarkeit von bioinformatischen Software-Systemen erheblich
verbessern kann. Der Einsatz von Microservices und Containerisierung trug ebenfalls zur Steigerung der ZuverlÀssigkeit, Skalierbarkeit und LeistungsfÀhigkeit des
Systems bei. DarĂŒber hinaus legt die Arbeit dar, dass die Anwendung von SoftwareEngineering-Praktiken, wie modellgesteuertem Design und Container-Orchestrierung,
die effiziente und produktive Bereitstellung und Verwaltung von bioinformatischen
Software-Systemen erleichtern kann. Zudem löst die Implementierung dieses SoftwareSystems, Herausforderungen fĂŒr Forschungsgruppen mit begrenzten Ressourcen. Insgesamt hat das System gezeigt, dass es in der Lage ist, Herausforderungen im Bereich
der Bioinformatik zu bewĂ€ltigen und stellt somit ein wertvolles Werkzeug fĂŒr Forscher in diesem Bereich dar. Die vorliegende Arbeit leistet mehrere wichtige BeitrĂ€ge
zur Beantwortung von Forschungsfragen im Zusammenhang mit dem Entwurf, der
Implementierung und der Optimierung von Software-Systemen fĂŒr die Bioinformatik unter Verwendung von Prinzipien und Praktiken der Softwaretechnik. Unsere
Ergebnisse deuten darauf hin, dass die Einbindung dieser Technologien die ZuverlÀssigkeit, Skalierbarkeit, LeistungsfÀhigkeit, Effizienz und ProduktivitÀt bioinformatischer Software-Systeme erheblich verbessern kann
Speech Recognition
Chapters in the first part of the book cover all the essential speech processing techniques for building robust, automatic speech recognition systems: the representation for speech signals and the methods for speech-features extraction, acoustic and language modeling, efficient algorithms for searching the hypothesis space, and multimodal approaches to speech recognition. The last part of the book is devoted to other speech processing applications that can use the information from automatic speech recognition for speaker identification and tracking, for prosody modeling in emotion-detection systems and in other speech processing applications that are able to operate in real-world environments, like mobile communication services and smart homes
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