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Displaying results 1 to 12 of 12.

  1. An Efficient Anomaly Detection System for Crowded Scenes Using Variational Autoencoders
    Author: Ming Xu; Xiaosheng Yu; Dongyue Chen; Chengdong Wu; Yang Jiang
    Published: 2019
    Publisher:  MDPI AG

    Anomaly detection in crowded scenes is an important and challenging part of the intelligent video surveillance system. As the deep neural networks make success in feature representation, the features extracted by a deep neural network represent the... more

     

    Anomaly detection in crowded scenes is an important and challenging part of the intelligent video surveillance system. As the deep neural networks make success in feature representation, the features extracted by a deep neural network represent the appearance and motion patterns in different scenes more specifically, comparing with the hand-crafted features typically used in the traditional anomaly detection approaches. In this paper, we propose a new baseline framework of anomaly detection for complex surveillance scenes based on a variational auto-encoder with convolution kernels to learn feature representations. Firstly, the raw frames series are provided as input to our variational auto-encoder without any preprocessing to learn the appearance and motion features of the receptive fields. Then, multiple Gaussian models are used to predict the anomaly scores of the corresponding receptive fields. Our proposed two-stage anomaly detection system is evaluated on the video surveillance dataset for a large scene, UCSD pedestrian datasets, and yields competitive performance compared with state-of-the-art methods.

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: Applied Sciences, Vol 9, Iss 16, p 3337 (2019)
    Subjects: video surveillance system; anomaly detection; unsupervised learning; convolutional auto-encoder; variational auto-encoder; Technology; T; Engineering (General). Civil engineering (General); Biology (General); Physics; Chemistry
  2. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
    Author: Toh Hiroyuki; Katoh Kazutaka
    Published: 2008
    Publisher:  BMC

    Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable... more

     

    Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: BMC Bioinformatics, Vol 9, Iss 1, p 212 (2008)
    Subjects: Computer applications to medicine. Medical informatics; Biology (General)
  3. An Electric Fence-Based Intelligent Scheduling Method for Rebalancing Dockless Bike Sharing Systems
    Author: Lulu Jia; Dezhen Yang; Yi Ren; Qiang Feng; Bo Sun; Cheng Qian; Zhifeng Li; Chenchen Zeng
    Published: 2022
    Publisher:  MDPI AG

    With a new generation of bike sharing services emerging, the development of dockless bike sharing services results in considerable socioeconomic and environmental benefits but also creates new issues, such as inappropriate parking behaviors and bike... more

     

    With a new generation of bike sharing services emerging, the development of dockless bike sharing services results in considerable socioeconomic and environmental benefits but also creates new issues, such as inappropriate parking behaviors and bike imbalances. To solve the inappropriate parking problem, electric fences have been introduced to guide users to park bikes in designated zones. Considering the role of electric fences in restricting user parking behaviors, an electric fence-based intelligent scheduling method for rebalancing dockless bike sharing systems is proposed in this paper. As a dynamic method that considers the real-time usage of bike sharing systems, an electric fence adjusts its capacity based on real-time information, which guides users to return bikes to electric fences with greater urgency. Because existing approaches require prespecified models and are unable to consider all the intricacies in the dynamic optimization problem, a model-free intelligent scheduling approach based on deep Q-learning that can adapt to the changing distributions of customer arrivals, available bikes, bike locations, and user travel times is used to solve the problem. Finally, a case study involving Beihang University is employed, which shows that the method performs well in rebalancing the bike sharing system and improving the mean utilization ( MU ) and customer satisfaction ( CS ).

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: Applied Sciences, Vol 12, Iss 5031, p 5031 (2022)
    Subjects: bike sharing system; dockless bikes; electric fence; deep Q-learning; intelligent scheduling; Technology; T; Engineering (General). Civil engineering (General); Biology (General); Physics; Chemistry
  4. Quality control for terms and definitions in ontologies and taxonomies
    Author: Rüegg Alexander; Munn Katherine; Köhler Jacob; Skusa Andre; Smith Barry
    Published: 2006
    Publisher:  BMC

    Abstract Background Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in... more

     

    Abstract Background Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: BMC Bioinformatics, Vol 7, Iss 1, p 212 (2006)
    Subjects: Computer applications to medicine. Medical informatics; Biology (General)
  5. Thawing Frozen Robust Multi-array Analysis (fRMA)
    Author: Irizarry Rafael A; McCall Matthew N
    Published: 2011
    Publisher:  BMC

    Abstract Background A novel method of microarray preprocessing - Frozen Robust Multi-array Analysis (fRMA) - has recently been developed. This algorithm allows the user to preprocess arrays individually while retaining the advantages of multi-array... more

     

    Abstract Background A novel method of microarray preprocessing - Frozen Robust Multi-array Analysis (fRMA) - has recently been developed. This algorithm allows the user to preprocess arrays individually while retaining the advantages of multi-array preprocessing methods. The frozen parameter estimates required by this algorithm are generated using a large database of publicly available arrays. Curation of such a database and creation of the frozen parameter estimates is time-consuming; therefore, fRMA has only been implemented on the most widely used Affymetrix platforms. Results We present an R package, frmaTools, that allows the user to quickly create his or her own frozen parameter vectors. We describe how this package fits into a preprocessing workflow and explore the size of the training dataset needed to generate reliable frozen parameter estimates. This is followed by a discussion of specific situations in which one might wish to create one's own fRMA implementation. For a few specific scenarios, we demonstrate that fRMA performs well even when a large database of arrays in unavailable. Conclusions By allowing the user to easily create his or her own fRMA implementation, the frmaTools package greatly increases the applicability of the fRMA algorithm. The frmaTools package is freely available as part of the Bioconductor project.

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: BMC Bioinformatics, Vol 12, Iss 1, p 369 (2011)
    Subjects: Computer applications to medicine. Medical informatics; Biology (General)
  6. Computing paths and cycles in biological interaction graphs
    Author: von Kamp Axel; Klamt Steffen
    Published: 2009
    Publisher:  BMC

    Abstract Background Interaction graphs (signed directed graphs) provide an important qualitative modeling approach for Systems Biology. They enable the analysis of causal relationships in cellular networks and can even be useful for predicting... more

     

    Abstract Background Interaction graphs (signed directed graphs) provide an important qualitative modeling approach for Systems Biology. They enable the analysis of causal relationships in cellular networks and can even be useful for predicting qualitative aspects of systems dynamics. Fundamental issues in the analysis of interaction graphs are the enumeration of paths and cycles (feedback loops) and the calculation of shortest positive/negative paths. These computational problems have been discussed only to a minor extent in the context of Systems Biology and in particular the shortest signed paths problem requires algorithmic developments. Results We first review algorithms for the enumeration of paths and cycles and show that these algorithms are superior to a recently proposed enumeration approach based on elementary-modes computation. The main part of this work deals with the computation of shortest positive/negative paths, an NP-complete problem for which only very few algorithms are described in the literature. We propose extensions and several new algorithm variants for computing either exact results or approximations. Benchmarks with various concrete biological networks show that exact results can sometimes be obtained in networks with several hundred nodes. A class of even larger graphs can still be treated exactly by a new algorithm combining exhaustive and simple search strategies. For graphs, where the computation of exact solutions becomes time-consuming or infeasible, we devised an approximative algorithm with polynomial complexity. Strikingly, in realistic networks (where a comparison with exact results was possible) this algorithm delivered results that are very close or equal to the exact values. This phenomenon can probably be attributed to the particular topology of cellular signaling and regulatory networks which contain a relatively low number of negative feedback loops. Conclusion The calculation of shortest positive/negative paths and cycles in interaction graphs is an important method for ...

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: BMC Bioinformatics, Vol 10, Iss 1, p 181 (2009)
    Subjects: Computer applications to medicine. Medical informatics; Biology (General)
  7. LinkedImm: a linked data graph database for integrating immunological data
    Author: Syed Ahmad Chan Bukhari; Shrikant Pawar; Jeff Mandell; Steven H. Kleinstein; Kei-Hoi Cheung
    Published: 2021
    Publisher:  BMC

    Abstract Background Many systems biology studies leverage the integration of multiple data types (across different data sources) to offer a more comprehensive view of the biological system being studied. While SQL (Structured Query Language)... more

     

    Abstract Background Many systems biology studies leverage the integration of multiple data types (across different data sources) to offer a more comprehensive view of the biological system being studied. While SQL (Structured Query Language) databases are popular in the biomedical domain, NoSQL database technologies have been used as a more relationship-based, flexible and scalable method of data integration. Results We have created a graph database integrating data from multiple sources. In addition to using a graph-based query language (Cypher) for data retrieval, we have developed a web-based dashboard that allows users to easily browse and plot data without the need to learn Cypher. We have also implemented a visual graph query interface for users to browse graph data. Finally, we have built a prototype to allow the user to query the graph database in natural language. Conclusion We have demonstrated the feasibility and flexibility of using a graph database for storing and querying immunological data with complex biological relationships. Querying a graph database through such relationships has the potential to discover novel relationships among heterogeneous biological data and metadata.

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: BMC Bioinformatics, Vol 22, Iss S9, Pp 1-14 (2021)
    Subjects: Ontology; Knowledgebase; Graph database; Immunology; Influenza vaccine; Computer applications to medicine. Medical informatics; Biology (General)
  8. Multi‐modal meta‐analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor
    Author: Alok Jaiswal; Prson Gautam; Elina A Pietilä; Sanna Timonen; Nora Nordström; Yevhen Akimov; Nina Sipari; Ziaurrehman Tanoli; Thomas Fleischer; Kaisa Lehti; Krister Wennerberg; Tero Aittokallio
    Published: 2021
    Publisher:  Wiley

    Abstract Molecular and functional profiling of cancer cell lines is subject to laboratory‐specific experimental practices and data analysis protocols. The current challenge therefore is how to make an integrated use of the omics profiles of cancer... more

     

    Abstract Molecular and functional profiling of cancer cell lines is subject to laboratory‐specific experimental practices and data analysis protocols. The current challenge therefore is how to make an integrated use of the omics profiles of cancer cell lines for reliable biological discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta‐analysis of 53 omics studies across 12 research laboratories for 2,018 cell lines. To account for a relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. The multi‐modal meta‐analysis approach also identified synthetic lethal partners of cancer drivers, including a co‐dependency of PTEN deficient endometrial cancer cells on RNA helicases.

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: Molecular Systems Biology, Vol 17, Iss 3, Pp n/a-n/a (2021)
    Subjects: cancer driver; data integration; multi‐omics data; reproducibility; synthetic lethality; Biology (General); Medicine (General)
  9. Graph of graphs analysis for multiplexed data with application to imaging mass cytometry.
    Author: Ya-Wei Eileen Lin; Tal Shnitzer; Ronen Talmon; Franz Villarroel-Espindola; Shruti Desai; Kurt Schalper; Yuval Kluger
    Published: 2021
    Publisher:  Public Library of Science (PLoS)

    Imaging Mass Cytometry (IMC) combines laser ablation and mass spectrometry to quantitate metal-conjugated primary antibodies incubated in intact tumor tissue slides. This strategy allows spatially-resolved multiplexing of dozens of simultaneous... more

     

    Imaging Mass Cytometry (IMC) combines laser ablation and mass spectrometry to quantitate metal-conjugated primary antibodies incubated in intact tumor tissue slides. This strategy allows spatially-resolved multiplexing of dozens of simultaneous protein targets with 1μm resolution. Each slide is a spatial assay consisting of high-dimensional multivariate observations (m-dimensional feature space) collected at different spatial positions and capturing data from a single biological sample or even representative spots from multiple samples when using tissue microarrays. Often, each of these spatial assays could be characterized by several regions of interest (ROIs). To extract meaningful information from the multi-dimensional observations recorded at different ROIs across different assays, we propose to analyze such datasets using a two-step graph-based approach. We first construct for each ROI a graph representing the interactions between the m covariates and compute an m dimensional vector characterizing the steady state distribution among features. We then use all these m-dimensional vectors to construct a graph between the ROIs from all assays. This second graph is subjected to a nonlinear dimension reduction analysis, retrieving the intrinsic geometric representation of the ROIs. Such a representation provides the foundation for efficient and accurate organization of the different ROIs that correlates with their phenotypes. Theoretically, we show that when the ROIs have a particular bi-modal distribution, the new representation gives rise to a better distinction between the two modalities compared to the maximum a posteriori (MAP) estimator. We applied our method to predict the sensitivity to PD-1 axis blockers treatment of lung cancer subjects based on IMC data, achieving 97.3% average accuracy on two IMC datasets. This serves as empirical evidence that the graph of graphs approach enables us to integrate multiple ROIs and the intra-relationships between the features at each ROI, giving rise to an informative ...

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: PLoS Computational Biology, Vol 17, Iss 3, p e1008741 (2021)
    Subjects: Biology (General)
  10. Extraction of transcript diversity from scientific literature.
    Author: Parantu K Shah; Lars J Jensen; Stéphanie Boué; Peer Bork
    Published: 2005
    Publisher:  Public Library of Science (PLoS)

    Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered... more

     

    Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term "alternative splicing" to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at www.bork.embl.de/LSAT/.

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: PLoS Computational Biology, Vol 1, Iss 1, p e10 (2005)
    Subjects: Biology (General)
  11. A (fire)cloud-based DNA methylation data preprocessing and quality control platform
    Author: Divy Kangeyan; Andrew Dunford; Sowmya Iyer; Chip Stewart; Megan Hanna; Gad Getz; Martin J. Aryee
    Published: 2019
    Publisher:  BMC

    Abstract Background Bisulfite sequencing allows base-pair resolution profiling of DNA methylation and has recently been adapted for use in single-cells. Analyzing these data, including making comparisons with existing data, remains challenging due to... more

     

    Abstract Background Bisulfite sequencing allows base-pair resolution profiling of DNA methylation and has recently been adapted for use in single-cells. Analyzing these data, including making comparisons with existing data, remains challenging due to the scale of the data and differences in preprocessing methods between published datasets. Results We present a set of preprocessing pipelines for bisulfite sequencing DNA methylation data that include a new R/Bioconductor package, scmeth, for a series of efficient QC analyses of large datasets. The pipelines go from raw data to CpG-level methylation estimates and can be run, with identical results, either on a single computer, in an HPC cluster or on Google Cloud Compute resources. These pipelines are designed to allow users to 1) ensure reproducibility of analyses, 2) achieve scalability to large whole genome datasets with 100 GB+ of raw data per sample and to single-cell datasets with thousands of cells, 3) enable integration and comparison between user-provided data and publicly available data, as all samples can be processed through the same pipeline, and 4) access to best-practice analysis pipelines. Pipelines are provided for whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS) and hybrid selection (capture) bisulfite sequencing (HSBS). Conclusions The workflows produce data quality metrics, visualization tracks, and aggregated output for further downstream analysis. Optional use of cloud computing resources facilitates analysis of large datasets, and integration with existing methylome profiles. The workflow design principles are applicable to other genomic data types.

     
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    Source: BASE Selection for Comparative Literature
    Language: English
    Media type: Article (journal)
    Format: Online
    Parent title: BMC Bioinformatics, Vol 20, Iss 1, Pp 1-5 (2019)
    Subjects: DNA methylation; Cloud computing; Bioinformatics workflows; Quality control analysis; Computer applications to medicine. Medical informatics; Biology (General)
  12. Natur und Gesellschaft - Perspektiven der interdisziplinären Umweltgeschichte
    Author: Jakubowski-Tiessen, Manfred; Sprenger, Jana
    Published: 2014
    Publisher:  Universitätsverlag Göttingen, s.l.

    Umweltgeschichte hat sich zu einem bedeutenden Themenfeld historischer Forschung entwickelt. Die Betrachtung vergangener Mensch-Umwelt-Interaktionen kann zum Verständnis heutiger Wechselwirkungen beitragen und Orientierungswissen für aktuelle... more

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    Max-Planck-Institut für ethnologische Forschung, Bibliothek
    Inter-library loan:
    No inter-library loan

     

    Umweltgeschichte hat sich zu einem bedeutenden Themenfeld historischer Forschung entwickelt. Die Betrachtung vergangener Mensch-Umwelt-Interaktionen kann zum Verständnis heutiger Wechselwirkungen beitragen und Orientierungswissen für aktuelle gesellschaftliche und politische Umwelt-Debatten bereitstellen. Die Einrichtung des DFG-Graduiertenkollegs 1024 „Interdisziplinäre Umweltgeschichte. Naturale Umwelt und gesellschaftliches Handeln in Mitteleuropa“ an der Georg-August-Universität Göttingen 2004 war ein wichtiger Schritt zur Etablierung der Umweltgeschichte in der deutschen Forschungslandschaft. Kennzeichnend für die Göttinger Forschungen war stets der interdisziplinäre Ansatz, welcher naturwissenschaftliche und kulturwissenschaftliche Forschungsmethoden und Forschungsfragen zu verbinden versucht. Nach neunjähriger Förderzeit beendete das Kolleg im Jahr 2013 seine Arbeit. Der vorliegende Band enthält Beiträge des Abschlussworkshops. Unter den Themenkomplexen „Die Umwelt erfassen“, „Die Umwelt planen“ und „Der Umwelt widerstehen“ geben die Autoren anhand ausgewählter Fallstudien Einblicke in einige der erreichten Forschungsergebnisse des Graduiertenkollegs.

    Umweltgeschichte hat sich zu einem bedeutenden Themenfeld historischer Forschung entwickelt. Die Betrachtung vergangener Mensch-Umwelt-Interaktionen kann zum Verständnis heutiger Wechselwirkungen beitragen und Orientierungswissen für aktuelle gesellschaftliche und politische Umwelt-Debatten bereitstellen. Die Einrichtung des DFG-Graduiertenkollegs 1024 „Interdisziplinäre Umweltgeschichte. Naturale Umwelt und gesellschaftliches Handeln in Mitteleuropa“ an der Georg-August-Universität Göttingen 2004 war ein wichtiger Schritt zur Etablierung der Umweltgeschichte in der deutschen Forschungslandschaft. Kennzeichnend für die Göttinger Forschungen war stets der interdisziplinäre Ansatz, welcher naturwissenschaftliche und kulturwissenschaftliche Forschungsmethoden und Forschungsfragen zu verbinden versucht. Nach neunjähriger Förderzeit beendete das Kolleg im Jahr 2013 seine Arbeit. Der vorliegende Band enthält Beiträge des Abschlussworkshops. Unter den Themenkomplexen „Die Umwelt erfassen“, „Die Umwelt planen“ und „Der Umwelt widerstehen“ geben die Autoren anhand ausgewä ...

     
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    Content information
    Volltext (Description of rights in Directory of Open Access Books (DOAB): Attribution Share Alike (CC by-sa))
    Source: Union catalogues
    Media type: Ebook
    Format: Online
    ISBN: 9783863951528
    RVK Categories: AR 11900
    Subjects: History (General); Biology (General); History (General); Biology (General)
    Scope: 1 Online-Ressource (1 electronic resource ( p.))