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arXiv 2017年

作者： Hernandez-Rosales, Maribel Hellmuth, Marc Wieseke, Nicolas Huber, Katharina T. Moulton, Vincent Stadler, Peter F. Dpt. of Mathematics and Computer Science University of Greifswald Walther- Rathenau-Strasse 47 GreifswaldD-17487 Saarland University Center for Bioinformatics Building e 2.1 P.O. Box 151150 SaarbrückenD-66041 Bioinformatics Group Department of Computer Science Interdisciplinary Center of Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany School of Computing Sciences University of East Anglia NorwichNR4 7TJ United Kingdom Max-Planck-Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Inst. F. Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Santa Fe Institute 1399 Hyde Park Rd. Santa Fe United States Parallel Computing and Complex Systems Group Department of Computer Science Leipzig University Augustusplatz 10 Leipzig04109 Germany

Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x represents a speciation or a duplication. This problem appears in the context of analyzing orthology data. Results: We show that S is a species tree for T if and only if S displays all rooted triples of T that have three distinct species as their leaves and are rooted in a speciation vertex. A valid reconciliation map can then be found in polynomial time. Simulated data shows that the event-labeled gene trees convey a large amount of information on underlying species trees, even for a large percentage of losses. Conclusions: The knowledge of event labels in a gene tree strongly constrains the possible species tree and, for a given species tree, also the possible reconciliation maps. Nevertheless, many degrees of freedom remain in the space of feasible solutions. In order to disambiguate the alternative solutions additional external constraints as well as optimization criteria could be employed. Copyright © 2017, The Authors. All rights reserved.

关键词： Polynomial approximation

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Horizons: Nuclear Astrophysics in the 2020s and Beyond

arXiv

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arXiv 2022年

作者： Schatz, Hendrik Becerril Reyes, A.D. Best, A. Brown, E.F. Chatziioannou, K. Chipps, K.A. Deibel, C.M. Ezzeddine, R. Galloway, D.K. Hansen, C.J. Herwig, F. Ji, A.P. Lugaro, M. Meisel, Z. Norman, D. Read, J.S. Roberts, L.F. Spyrou, A. Tews, I. Timmes, F.X. Travaglio, C. Vassh, N. Abia, C. Adsley, P. Agarwal, S. Aliotta, M. Aoki, W. Arcones, A. Aryan, A. Bandyopadhyay, A. Banu, A. Bardayan, D.W. Barnes, J. Bauswein, A. Beers, T.C. Bishop, J. Boztepe, T. Côté, B. Caplan, M.E. Champagne, A.E. Clark, J.A. Couder, M. Couture, A. de Mink, S.E. Debnath, S. deBoer, R.J. den Hartogh, J. Denissenkov, P. Dexheimer, V. Dillmann, I. Escher, J.E. Famiano, M.A. Farmer, R. Fisher, R. Fröhlich, C. Frebel, A. Fryer, C. Fuller, G. Ganguly, A.K. Ghosh, S. Gibson, B.K. Gorda, T. Gourgouliatos, K.N. Graber, V. Gupta, M. Haxton, W. Heger, A. Hix, W.R. Ho, W.C.G. Holmbeck, E.M. Hood, A.A. Huth, S. Imbriani, G. Izzard, R.G. Jain, R. Jayatissa, H. Johnston, Z. Kajino, T. Kankainen, A. Kiss, G.G. Kwiatkowski, A. La Cognata, M. Laird, A.M. Lamia, L. Landry, P. Laplace, E. Launey, K.D. Leahy, D. Leckenby, G. Lennarz, A. Longfellow, B. Lovell, A.E. Lynch, W.G. Lyons, S.M. Maeda, K. Masha, E. Matei, C. Merc, J. Messer, B. Montes, F. Mukherjee, A. Mumpower, M. Neto, D. Nevins, B. Newton, W.G. Nguyen, L.Q. Nishikawa, K. Nishimura, N. Nunes, F.M. O’Connor, E. O’Shea, B.W. Ong, W.-J. Pain, S.D. Pajkos, M.A. Pignatari, M. Pizzone, R.G. Placco, V.M. Plewa, T. Pritychenko, B. Psaltis, A. Puentes, D. Qian, Y.-Z. Radice, D. Rapagnani, D. Rebeiro, B.M. Reifarth, R. Richard, A.L. Rijal, N. Roederer, I.U. Rojo, J.S. Sk, J. Saito, Y. Schwenk, A. Sergi, M.L. Sidhu, R.S. Simon, A. Sivarani, T. Skúladóttir, Á. Smith, M.S. Spiridon, A. Sprouse, T.M. Starrfield, S. Steiner, A.W. Strieder, F. Sultana, I. Surman, R. Szücs, T. Tawfik, A. Thielemann, F. Trache, L. Trappitsch, R. Department of Physics and Astronomy Michigan State University East LansingMI48824 United States Facility for Rare Isotope Beams Michigan State University East LansingMI48824 United States United States Department of Physics University of Naples"Federico II" Napoli80126 Italy INFN - Sezione di Napoli Napoli80126 Italy Department of Computational Mathematics Science and Engineering MichiganState University East LansingMI48824 United States Department of Physics California Institute of Technology PasadenaCA91125 United States LIGO Laboratory California Institute of Technology PasadenaCA91125 United States Physics Division Oak Ridge National Laboratory Oak RidgeTN37831 United States Department of Physics and Astronomy University of Tennessee Knoxville KnoxvilleTN37996 United States Department of Physics and Astronomy Louisiana State University Baton RougeLA70803 United States Department of Astronomy University of Florida GainesvilleFL32601 United States School of Physics and Astronomy Monash University VIC3800 Australia OzGRav-Monash School of Physics & Astronomy Monash University VIC3800 Australia Goethe University Frankfurt Institute for Applied Physics Max-von-Laue-Str. 12 Frankfurt am Main60438 Germany Technical University of Darmstadt Institute for Nuclear Physics Germany Max Planck Institute for Astronomy Heidelberg Germany Department of Physics and Astronomy University of Victoria VictoriaBCV8P 5C2 Canada Department of Astronomy & Astrophysics University of Chicago 5640 S Ellis Avenue ChicagoIL60637 United States Kavli Institute for Cosmological Physics University of Chicago ChicagoIL60637 United States Excellence Centre of the Hungarian Academy of Sciences Konkoly-Thege Miklós út 15-17 BudapestH-1121 Hungary ELTE Eötvös Loránd University Institute of Physics Pázmány Péter sétány 1/A Budapest1117 Hungary Institute of Nuclear & Particle Physics Department of Physics & Astronomy Ohio University AthensOH45701

Nuclear Astrophysics is a field at the intersection of nuclear physics and astrophysics, which seeks to understand the nuclear engines of astronomical objects and the origin of the chemical elements. This white paper summarizes progress and status of the field, the new open questions that have emerged, and the tremendous scientific opportunities that have opened up with major advances in capabilities across an ever growing number of disciplines and subfields that need to be integrated. We take a holistic view of the field discussing the unique challenges and opportunities in nuclear astrophysics in regards to science, diversity, education, and the interdisciplinarity and breadth of the field. Clearly nuclear astrophysics is a dynamic field with a bright future that is entering a new era of discovery opportunities. © 2022, CC BY-NC-SA.

关键词： Astrophysics

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Cograph editing: Merging modules is equivalent to editing P4s

arXiv

引用

arXiv 2017年

作者： Fritz, Adrian Hellmuth, Marc Wieseke, Nicolas Stadler, Peter F. Computational Biology of Infection Research Helmholtz Centre for Infection Research Inhoffenstraße 7 BraunschweigD-38124 Germany University of Greifswald Dpt. of Mathematics and Computer Science Walther- Rathenau-Strasse 47 GreifswaldD-17487 Germany Saarland University Center for Bioinformatics Building e 2.1 P.O. Box 151150 SaarbrückenD-66041 Germany Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Augustusplatz 10 LeipzigD-04109 Germany Bioinformatics Group Department of Computer Science Interdisciplinary Center of Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany Max-Planck-Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Inst. F. Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Santa Fe Institute 1399 Hyde Park Rd. Santa FeNM87501 United States

The modular decomposition of a graph G = (V;E) does not contain prime modules if and only if G is a cograph, that is, if no quadruple of vertices induces a simple connected path P4. The cograph editing problem consists in inserting into and deleting from G a set F of edges so that H = (V,EΔF) is a cograph and |F| is minimum. This NP-hard combinatorial optimization problem has recently found applications, e.g., in the context of phylogenetics. Efficient heuristics are hence of practical importance. The simple characterization of cographs in terms of their modular decomposition suggests that instead of editing G one could operate directly on the modular decomposition. We show here that editing the induced P4s is equivalent to resolving prime modules by means of a suitable defined merge operation on the submodules. Moreover, we characterize so-called module-preserving edit sets and demonstrate that optimal pairwise sequences of module-preserving edit sets exist for every non-cograph. This eventually leads to an exact algorithm for the cograph editing problem. In addition, we provide two heuristics with time complexity O(|V|3), resp., O(|V|2). Copyright © 2017, The Authors. All rights reserved.

关键词： Graph theory

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BACH: grand challenge on breast cancer histology images

arXiv

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arXiv 2018年

作者： Aresta, Guilherme Araújo, Teresa Kwok, Scotty Chennamsetty, Sai Saketh Safwan, Mohammed Alex, Varghese Marami, Bahram Prastawa, Marcel Chan, Monica Donovan, Michael Fernandez, Gerardo Zeineh, Jack Kohl, Matthias Walz, Christoph Ludwig, Florian Braunewell, Stefan Baust, Maximilian Vu, Quoc Dang Nhat To, Minh Nguyen Kim, Eal Kwak, Jin Tae Galal, Sameh Sanchez-Freire, Veronica Brancati, Nadia Frucci, Maria Riccio, Daniel Wang, Yaqi Sun, Lingling Ma, Kaiqiang Fang, Jiannan Kone, Ismael Boulmane, Lahsen Campilho, Aurélio Eloy, Catarina Polónia, António Aguiar, Paulo INESC TEC - Institute for Systems and Computer Engineering Technology and Science Porto4200-465 Portugal Faculty of Engineering of University of Porto Porto4200-465 Portugal Seek AI Limited Hong Kong Bangalore India Gurgaon India Chennai India Center for Computational and Systems Pathology Dpt. of Pathology Icahn School of Medicine at Mount Sinai Mount Sinai Hospital New York United States Konica Minolta Laboratory Europe Munich Germany Institute of Pathology Faculty of Medicine LMU Munich Munich Germany Department of Computer Science and Engineering Sejong University Seoul05006 Korea Republic of Chicago IL United States Naples Italy University of Naples "Federico II" Naples Italy Key Laboratory of RF Circuits and Systems Ministry of Education Hangzhou Dianzi University Hangzhou310018 China Zhejiang Provincial Laboratory of Integrated Circuits Design Hangzhou Dianzi University Hangzhou310018 China p2MIA Research Group LEM2A Lab Faculté des Sciences Université Moulay Ismail Meknes Morocco qLaboratório de Anatomia Patológica Ipatimup Diagnósticos Rua Júilio Amaral de Carvalho 45 Porto4200-135 Portugal Faculdade de Medicina Universidade do Porto Alameda Prof Hernâni Monteiro Porto4200-319 Portugal Universidade do Porto Rua Alfredo Allen 208 Porto4200-135 Portugal Universidade do Porto Rua Alfredo Allen 208 Porto4200-135 Portugal

Breast cancer is the most common invasive cancer in women, affecting more than 10% of women worldwide. Microscopic analysis of a biopsy remains one of the most important methods to diagnose the type of breast cancer. This requires specialized analysis by pathologists, in a task that i) is highly time- and cost-consuming and ii) often leads to nonconsensual results. The relevance and potential of automatic classification algorithms using hematoxylin-eosin stained histopathological images has already been demonstrated, but the reported results are still sub-optimal for clinical use. With the goal of advancing the state-of-the-art in automatic classification, the Grand Challenge on BreAst Cancer Histology images (BACH) was organized in conjunction with the 15th International Conference on Image Analysis and Recognition (ICIAR 2018). BACH aimed at the classification and localization of clinically relevant histopathological classes in microscopy and whole-slide images from a large annotated dataset, specifically compiled and made publicly available for the challenge. Following a positive response from the scientific community, a total of 64 submissions, out of 677 registrations, effectively entered the competition. The submitted algorithms improved the state-of-the-art in automatic classification of breast cancer with microscopy images to an accuracy of 87%. Convolutional neuronal networks were the most successful methodology in the BACH challenge. Detailed analysis of the collective results allowed the identification of remaining challenges in the field and recommendations for future developments. The BACH dataset remains publicly available as to promote further improvements to the field of automatic classification in digital pathology. Copyright © 2018, The Authors. All rights reserved.

关键词： Neurons

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Mesh Generation for Atmospheric Boundary Layer Simulation in Wind Farm Design and Management

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Procedia Engineering 2015年 124卷 239-251页

作者： A. Gargallo-Peiró M. Avila H. Owen L. Prieto A. Folch Dpt. Computer Applications in Science and Engineering Barcelona Supercomputing Center C/ Gran Capitán 2-4 08034 Barcelona Spain Energy Resource Dpt. Iberdrola Renovables Energía C/ Tomás Redondo 1 28033 Madrid Spain

We propose a new automatic procedure to generate hybrid meshes to simulate turbulent flows for wind farm design and management. In particular, numerical modeling of wind farms involves a RANS simulation of the Atmospheric Boundary Layer (ABL) flow and modeling the turbines using the actuator disc theory. Therefore, the generated meshes have to fulfill several geometrical requirements to answer to the different modeling features. They must: capture the topography features that can influence the wind flow; have a boundary layer close to the terrain to resolve the ABL; be conformally adapted to the disc (turbine) to simulate the turbine effects on the wind flow; be adapted around the disc to capture the wake effect; and present a smooth mesh size transition around the disc to conform the mesh size of the ABL mesh, in which the turbines are immersed. We highlight that the mesh generation procedure is fully automatic once given the mesh size, a topography description, the wind inflow direction, a list of turbine insertion points, and the turbine models. To illustrate the applicability of the proposed procedure, we present two wind farm cases: an offshore wind farm mesh where we illustrate the computed wind deficit, and an onshore farm assimilating real topography data.

关键词： hybrid meshes hexahedral meshes quadrilateral meshes mesh optimization wind farm wind turbine atmospheric boundary layer

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LGHD: A feature descriptor for matching across non-linear intensity variations

LGHD: A feature descriptor for matching across non-linear in...

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IEEE International Conference on Image Processing

作者： Cristhian A. Aguilera Angel D. Sappa Ricardo Toledo Computer Science Dpt. Universitat Autònoma de Barcelona Bellaterra Spain Campus Gustavo Galindo Escuela Superior Politécnica del Litoral Guayaquil Ecuador Campus UAB Computer Vision Center Bellaterra Spain

This paper presents a new feature descriptor suitable to the task of matching features points between images with nonlinear intensity variations. This includes image pairs with significant illuminations changes, multi-modal image pairs and multi-spectral image pairs. The proposed method describes the neighbourhood of feature points combining frequency and spatial information using multi-scale and multi-oriented Log-Gabor filters. Experimental results show the validity of the proposed approach and also the improvements with respect to the state of the art.

关键词： Histograms Feature extraction Robustness Detectors computer vision Three-dimensional displays

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Aspects of quality evaluation in Linguistic Descriptions of Data

Aspects of quality evaluation in Linguistic Descriptions of ...

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IEEE International Conference on Fuzzy Systems

作者： Alberto Bugarin Nicolas Marin Daniel Sanchez Gracian Trivino Research Center on Information Technologies University of Santiago de Compostela Dpt. Computer Science and AI University of Granada European Centre for Soft Computing

ISBN: (纸本)9781467374293

Quality evaluation is a fundamental problem in the field of linguistic description of data. In this work, we analyze the concept of quality and study different approaches to measure quality. Although most of the approaches considered focused on time series data, that are one of the most frequent datasets in real application domains, they can be used for quality assessment of linguistic descriptions generated for any type of data.

关键词： Pragmatics Measurement Time series analysis Quality assessment Context Electronic mail Proposals

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Copenhagen-Malmö: Tree Approximations of Semantic Parsing Problems 8

Copenhagen-Malmö: Tree Approximations of Semantic Parsing P...

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8th International Workshop on Semantic Evaluation, SemEval 2014

作者： Schluter, Natalie Elming, Jakob Klerke, Sigrid Alonso, Héctor Martínez Hovy, Dirk Plank, Barbara Johannsen, Anders Søgaard, Anders Dpt. of Computer Science Malmö University Sweden Center for Language Technology University of Copenhagen Denmark

ISBN: (纸本)9781941643242

In this shared task paper for SemEval-2014 Task 8, we show that most semantic structures can be approximated by trees through a series of almost bijective graph transformations. We transform input graphs, apply off-the-shelf methods from syntactic parsing on the resulting trees, and retrieve output graphs. Using tree approximations, we obtain good results across three semantic formalisms, with a 15.9% error reduction over a state-of-the-art semantic role labeling system on development data. Our system came in 3/6 in the shared task closed track. © 8th International Workshop on Semantic Evaluation, SemEval 2014 - co-located with the 25th International Conference on Computational Linguistics, COLING 2014, Proceedings. All rights reserved.

关键词： Semantics

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DISTRIBUTION OF GLACIAL AND PERIGLACIAL FEATURES WITHIN ICE-FREE AREAS SURROUNDING MAXWELL BAY (SOUTH SHETLAND ISLANDS) USING POLARIMETRIC RADARSAT-2 DATA

DISTRIBUTION OF GLACIAL AND PERIGLACIAL FEATURES WITHIN ICE-...

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IEEE International Geoscience and Remote Sensing Symposium

作者： T. Schmid J. Lopez-Martinez S. Guillaso O. D'Hondt M. Koch S. Mink A. Nieto E. Serrano CIEMAT Dpto. Geologia y Geoquimica Facultad de Ciencias Universidad Autonoma de Madrid Computer Vision and Remote Sensing Group Technische Universitat Berlin Center for Remote Sensing Boston University Instituto Geologico y Minero de Espana Rios Rosas Dpt. Geografia Universidad de Valladolid

ISBN: (纸本)9781479979301

Active periglacial processes and landforms are common within the Northern Antarctic Peninsula region and are becoming the focus of interest for studying changes occurring to permafrost. The objective of this study was to identify and characterize glacial and periglacial surface features with fully polarimetric SAR C band RADARSAT-2 data in ice-free regions surrounding Maxwell Bay, South Shetland Islands. Extraction of polarimetric parameters, a selection of field based training sites and a supervised classification approach, were chosen to determine the spatial distribution of the different geomorphological surface features. These results show the identification of complex and relatively small scale geomorphological features such as periglacial landforms that are an important indicator of the presence of permafrost.

关键词： Periglacial RADARSAT-2 Polarimetry Antarctic ice-free areas South Shetland Islands

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Cost-Sensitive Structured SVM for Multi-category Domain Adaptation

Cost-Sensitive Structured SVM for Multi-category Domain Adap...

引用

International Conference on Pattern Recognition

作者： Jiaolong Xu Sebastian Ramos David Vázquez Antonio M. López Computer Vision Center C. Sc. Dpt. Univ. Autonoma de Barcelona Spain

ISBN: (纸本)9781479952106

Domain adaptation addresses the problem of accuracy drop that a classifier may suffer when the training data (source domain) and the testing data (target domain) are drawn from different distributions. In this work, we focus on domain adaptation for structured SVM (SSVM). We propose a cost-sensitive domain adaptation method for SSVM, namely COSS-SSVM. In particular, during the re-training of an adapted classifier based on target and source data, the idea that we explore consists in introducing a non-zero cost even for correctly classified source domain samples. Eventually, we aim to learn a more target-oriented classifier by not rewarding (zero loss) properly classified source-domain training samples. We assess the effectiveness of COSS-SSVM on multi-category object recognition.

关键词： Support vector machines Accuracy Training Adaptation models Object recognition Linear programming Vectors

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