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45 results on '"Marchiori, Elena"'

3. Multi-view Analysis of Unregistered Medical Images Using Cross-View Transformers

Author

van Tulder, Gijs, Tong, Yao, Marchiori, Elena, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, de Bruijne, Marleen, editor, Cattin, Philippe C., editor, Cotin, Stéphane, editor, Padoy, Nicolas, editor, Speidel, Stefanie, editor, Zheng, Yefeng, editor, and Essert, Caroline, editor

Published
2021
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5. Incorporating Dependencies in Spectral Kernels for Gaussian Processes

Author

Chen, Kai, van Laarhoven, Twan, Chen, Jinsong, Marchiori, Elena, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Brefeld, Ulf, editor, Fromont, Elisa, editor, Hotho, Andreas, editor, Knobbe, Arno, editor, Maathuis, Marloes, editor, and Robardet, Céline, editor

Published
2020
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6. The Representation of Speech in Deep Neural Networks

Author

Scharenborg, Odette, van der Gouw, Nikki, Larson, Martha, Marchiori, Elena, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Kompatsiaris, Ioannis, editor, Huet, Benoit, editor, Mezaris, Vasileios, editor, Gurrin, Cathal, editor, Cheng, Wen-Huang, editor, and Vrochidis, Stefanos, editor

Published
2019
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12. Transfer Learning for Domain Adaptation in MRI: Application in Brain Lesion Segmentation

Author

Ghafoorian, Mohsen, Mehrtash, Alireza, Kapur, Tina, Karssemeijer, Nico, Marchiori, Elena, Pesteie, Mehran, Guttmann, Charles R. G., de Leeuw, Frank-Erik, Tempany, Clare M., van Ginneken, Bram, Fedorov, Andriy, Abolmaesumi, Purang, Platel, Bram, Wells, William M., III, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Descoteaux, Maxime, editor, Maier-Hein, Lena, editor, Franz, Alfred, editor, Jannin, Pierre, editor, Collins, D. Louis, editor, and Duchesne, Simon, editor

Published
2017
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13. Teenagers’ Destination Website Navigation. A Comparison Among Eye-Tracking, Web Analytics, and Self-declared Investigation

Author

Cantoni, Edoardo, Marchiori, Elena, Cantoni, Lorenzo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Marcus, Aaron, editor, and Wang, Wentao, editor

Published
2017
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15. Biases of Drug–Target Interaction Network Data

Author

van Laarhoven, Twan, Marchiori, Elena, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Comin, Matteo, editor, Käll, Lukas, editor, Marchiori, Elena, editor, Ngom, Alioune, editor, and Rajapakse, Jagath, editor

Published
2014
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16. Discovering Potential Clinical Profiles of Multiple Sclerosis from Clinical and Pathological Free Text Data with Constrained Non-negative Matrix Factorization

Author

The Netherlands Brain Bank, Acquarelli, Jacopo, Bianchini, Monica, Marchiori, Elena, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Squillero, Giovanni, editor, and Burelli, Paolo, editor

Published
2016
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19. Evolutionary Methods for the Construction of Cryptographic Boolean Functions

Author

Picek, Stjepan, Jakobovic, Domagoj, Miller, Julian F., Marchiori, Elena, Batina, Lejla, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Machado, Penousal, editor, Heywood, Malcolm I., editor, McDermott, James, editor, Castelli, Mauro, editor, García-Sánchez, Pablo, editor, Burelli, Paolo, editor, Risi, Sebastian, editor, and Sim, Kevin, editor

Published
2015
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24. Combining Evolutionary Computation and Algebraic Constructions to Find Cryptography-Relevant Boolean Functions

Author

Picek, Stjepan, Marchiori, Elena, Batina, Lejla, Jakobovic, Domagoj, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Bartz-Beielstein, Thomas, editor, Branke, Jürgen, editor, Filipič, Bogdan, editor, and Smith, Jim, editor

Published
2014
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28. Transfer Learning for Domain Adaptation in MRI: Application in Brain Lesion Segmentation

Author

Ghafoorian, Mohsen, primary, Mehrtash, Alireza, additional, Kapur, Tina, additional, Karssemeijer, Nico, additional, Marchiori, Elena, additional, Pesteie, Mehran, additional, Guttmann, Charles R. G., additional, de Leeuw, Frank-Erik, additional, Tempany, Clare M., additional, van Ginneken, Bram, additional, Fedorov, Andriy, additional, Abolmaesumi, Purang, additional, Platel, Bram, additional, and Wells, William M., additional

Published
2017
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36. The Representation of Speech in Deep Neural Networks

Author

Scharenborg, O.E., van der Gouw, Nikki, Larson, M.A., Marchiori, Elena, Kompatsiaris, Ioannis, Huet, Benoit, Mezaris, Vasileios, Gurrin, Cathal, Cheng, Wen-Huang, and Vrochidis, Stefanos

Subjects
Consonant, Artificial neural network, Computer science, Place of articulation, Speech recognition, Representation (arts), 010501 environmental sciences, 01 natural sciences, Class (biology), Manner of articulation, 030507 speech-language pathology & audiology, 03 medical and health sciences, Speech representations, Vowel, Deep neural networks, Visualizations, 0305 other medical science, Cluster analysis, 0105 earth and related environmental sciences
Abstract

In this paper, we investigate the connection between how people understand speech and how speech is understood by a deep neural network. A naïve, general feed-forward deep neural network was trained for the task of vowel/consonant classification. Subsequently, the representations of the speech signal in the different hidden layers of the DNN were visualized. The visualizations allow us to study the distance between the representations of different types of input frames and observe the clustering structures formed by these representations. In the different visualizations, the input frames were labeled with different linguistic categories: sounds in the same phoneme class, sounds with the same manner of articulation, and sounds with the same place of articulation. We investigate whether the DNN clusters speech representations in a way that corresponds to these linguistic categories and observe evidence that the DNN does indeed appear to learn structures that humans use to understand speech without being explicitly trained to do so.

Published
2018
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37. Supervised Selective Kernel Fusion for Membrane Protein Prediction

Author

Tatarchuk, Alexander, Sulimova, Valentina, Torshin, Ivan, Mottl, Vadim, Windridge, David, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Comin, Matteo, editor, Käll, Lukas, editor, Marchiori, Elena, editor, Ngom, Alioune, editor, and Rajapakse, Jagath, editor

Published
2014
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38. CytomicsDB: A Metadata-Based Storage and Retrieval Approach for High-Throughput Screening Experiments

Author

Larios, E., Zhang, Y., Cao, L., Verbeek, F. J., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Comin, Matteo, editor, Käll, Lukas, editor, Marchiori, Elena, editor, Ngom, Alioune, editor, and Rajapakse, Jagath, editor

Published
2014
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39. CUDAGRN: Parallel Speedup of Inferring Large Gene Regulatory Networks from Expression Data Using Random Forest

Author

Alborzi, Seyed Ziaeddin, Maduranga, D. A. K., Fan, Rui, Rajapakse, Jagath C., Zheng, Jie, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Comin, Matteo, editor, Käll, Lukas, editor, Marchiori, Elena, editor, Ngom, Alioune, editor, and Rajapakse, Jagath, editor

Published
2014
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40. SFFS-SW: A Feature Selection Algorithm Exploring the Small-World Properties of GNs

Author

da Rocha Vicente, Fábio Fernandes, Lopes, Fabrício Martins, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Comin, Matteo, editor, Käll, Lukas, editor, Marchiori, Elena, editor, Ngom, Alioune, editor, and Rajapakse, Jagath, editor

Published
2014
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41. Logol: Expressive Pattern Matching in Sequences. Application to Ribosomal Frameshift Modeling

Author

Belleannée, Catherine, Sallou, Olivier, Nicolas, Jacques, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Comin, Matteo, editor, Käll, Lukas, editor, Marchiori, Elena, editor, Ngom, Alioune, editor, and Rajapakse, Jagath, editor

Published
2014
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42. Acquiring Decision Rules for Predicting Ames-Negative Hepatocarcinogens Using Chemical-Chemical Interactions

Author

Tung, Chun-Wei, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Comin, Matteo, editor, Käll, Lukas, editor, Marchiori, Elena, editor, Ngom, Alioune, editor, and Rajapakse, Jagath, editor

Published
2014
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43. Evolutionary Algorithm Based on New Crossover for the Biclustering of Gene Expression Data

Author

Maâtouk, Ons, Ayadi, Wassim, Bouziri, Hend, Duval, Beatrice, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Comin, Matteo, editor, Käll, Lukas, editor, Marchiori, Elena, editor, Ngom, Alioune, editor, and Rajapakse, Jagath, editor

Published
2014
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44. Using Topology Information for Protein-Protein Interaction Prediction

Author

Birlutiu, Adriana, Heskes, Tom, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Comin, Matteo, editor, Käll, Lukas, editor, Marchiori, Elena, editor, Ngom, Alioune, editor, and Rajapakse, Jagath, editor

Published
2014
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45. Logol: Expressive Pattern Matching in Sequences. Application to Ribosomal Frameshift Modeling

Author

Catherine Belleannée, Jacques Nicolas, Olivier Sallou, Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Plateforme bioinformatique GenOuest [Rennes], Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Lukas KALL, Comin, Matteo, Kall, Lukas, Marchiori, Elena, Ngom, Alioune, Rajapakse, Jagath, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes)

Subjects
Translational frameshift, Parsing, business.industry, Computer science, Suite, Complex pattern, Linguistic analysis, String Variable Grammar, computer.software_genre, Machine learning, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Pattern search, Ribosomal frameshift, Living systems, Sequence modeling, Pseudo-knot, Current practice, Pattern matching, Artificial intelligence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, Natural language processing, Frameshift event
Abstract

Most of the current practice of pattern matching tools is oriented towards finding efficient ways to compare sequences. This is useful but insufficient: as the knowledge and understanding of some functional or structural aspects of living systems improve, analysts in molecular biology progressively shift from mere classification tasks to modeling tasks. People need to be able to express global sequence architectures and check various hypotheses on the way their sequences are structured. It appears necessary to offer generic tools for this task, allowing to build more expressive models of biological sequence families, on the basis of their content and structure. This article introduces Logol, a new application designed to achieve pattern matching in possibly large sequences with customized biological patterns. Logol consists in both a language for describing patterns, and the associated parser for effective pattern search in sequences (RNA, DNA or protein) with such patterns. The Logol language, based on an high level grammatical formalism, allows to express flexible patterns (with mispairings and indels) composed of both sequential elements (such as motifs) and structural elements (such as repeats or pseudoknots). Its expressive power is presented through an application using the main components of the language : the identification of -1 programmed ribosomal frameshifting (PRF) events in messenger RNA sequences. Logol allows the design of sophisticated patterns, and their search in large nucleic or amino acid sequences. It is available on the GenOuest bioinformatics platform at http://logol.genouest.org. The core application is a command-line application, available for different operating systems. The Logol suite also includes interfaces, e.g. an interface for graphically drawing the pattern.

Published
2014
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