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  • 51.
    Ekeberg, Örjan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Fransén, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hellgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Herman, Pawel
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Kumar, Arvind
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Computational Brain Science at CST, CSC, KTH2016Övrigt (Övrigt vetenskapligt)
    Abstract [en]

    Mission and Vision - Computational Brain Science Lab at CST, CSC, KTH

    The scientific mission of the Computational Brain Science Lab at CSC is to be at the forefront of mathematical modelling, quantitative analysis and mechanistic understanding of brain function. We perform research on (i) computational modelling of biological brain function and on (ii) developing theory, algorithms and software for building computer systems that can perform brain-like functions. Our research answers scientific questions and develops methods in these fields. We integrate results from our science-driven brain research into our work on brain-like algorithms and likewise use theoretical results about artificial brain-like functions as hypotheses for biological brain research.

    Our research on biological brain function includes sensory perception (vision, hearing, olfaction, pain), cognition (action selection, memory, learning) and motor control at different levels of biological detail (molecular, cellular, network) and mathematical/functional description. Methods development for investigating biological brain function and its dynamics as well as dysfunction comprises biomechanical simulation engines for locomotion and voice, machine learning methods for analysing functional brain images, craniofacial morphology and neuronal multi-scale simulations. Projects are conducted in close collaborations with Karolinska Institutet and Karolinska Hospital in Sweden as well as other laboratories in Europe, U.S., Japan and India.

    Our research on brain-like computing concerns methods development for perceptual systems that extract information from sensory signals (images, video and audio), analysis of functional brain images and EEG data, learning for autonomous agents as well as development of computational architectures (both software and hardware) for neural information processing. Our brain-inspired approach to computing also applies more generically to other computer science problems such as pattern recognition, data analysis and intelligent systems. Recent industrial collaborations include analysis of patient brain data with MentisCura and the startup company 13 Lab bought by Facebook.

    Our long term vision is to contribute to (i) deeper understanding of the computational mechanisms underlying biological brain function and (ii) better theories, methods and algorithms for perceptual and intelligent systems that perform artificial brain-like functions by (iii) performing interdisciplinary and cross-fertilizing research on both biological and artificial brain-like functions. 

    On one hand, biological brains provide existence proofs for guiding our research on artificial perceptual and intelligent systems. On the other hand, applying Richard Feynman’s famous statement ”What I cannot create I do not understand” to brain science implies that we can only claim to fully understand the computational mechanisms underlying biological brain function if we can build and implement corresponding computational mechanisms on a computerized system that performs similar brain-like functions.

  • 52.
    Elblaus, Ludvig
    et al.
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Medieteknik och interaktionsdesign, MID.
    Tsaknaki, Vasiliki
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Medieteknik och interaktionsdesign, MID.
    Lewandowski, Vincent
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Medieteknik och interaktionsdesign, MID.
    Bresin, Roberto
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Medieteknik och interaktionsdesign, MID.
    Hwang, Sungjae
    Song, John
    Gim, Junghyeon
    Griggio, Carla
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Medieteknik och interaktionsdesign, MID.
    Leiva, Germán
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Medieteknik och interaktionsdesign, MID.
    Romero, Mario
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Georgia Institute of Technology.
    Sweeney, David
    Regan, Tim
    Helmes, John
    Vlachokyriakos, Vasillis
    Lindley, Siân
    Taylor, Alex
    Demo Hour2015Ingår i: interactions, ISSN 1072-5520, E-ISSN 1558-3449, Vol. 22, nr 5, s. 6-9Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Interactivity is a unique forum of the ACM CHI Conference that showcases hands-on demonstrations, novel interactive technologies, and artistic installations. At CHI 2015 in Seoul we hosted more than 30 exhibits, including an invited digital interactive art exhibit. Interactivity highlights the diverse group of computer scientists, sociologists, designers, psychologists, artists, and many more who make up the CHI community.

  • 53. Ercole, A.
    et al.
    Thelin, E.
    Holst, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Bellander, B.
    Nelson, D.
    BAYESIAN MODEL OF TRAUMATIC BRAIN INJURY BIOMARKER KINETICS2016Ingår i: Journal of Neurotrauma, ISSN 0897-7151, E-ISSN 1557-9042, Vol. 33, nr 3, s. A39-A39Artikel i tidskrift (Övrigt vetenskapligt)
  • 54. Ercole, A.
    et al.
    Thelin, E. P.
    Holst, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Bellander, B. M.
    Nelson, D. W.
    Kinetic modelling of serum S100b after traumatic brain injury2016Ingår i: BMC Neurology, ISSN 1471-2377, E-ISSN 1471-2377, Vol. 16, artikel-id 93Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: An understanding of the kinetics of a biomarker is essential to its interpretation. Despite this, little kinetic modelling of blood biomarkers can be found in the literature. S100b is an astrocyte related marker of brain injury used primarily in traumatic brain injury (TBI). Serum levels are expected to be the net result of a multi-compartmental process. The optimal sample times for TBI prognostication, and to follow injury development, are unclear. The purpose of this study was to develop a kinetic model to characterise the temporal course of serum S100b concentration after primary traumatic brain injury. Methods: Data of serial serum S100b samples from 154 traumatic brain injury patients in a neurointensive care unit were retrospectively analysed, including only patients without secondary peaks of this biomarker. Additionally, extra-cranial S100b can confound samples earlier than 12 h after trauma and were therefore excluded. A hierarchical, Bayesian gamma variate kinetic model was constructed and the parameters estimated by Markov chain Monte Carlo sampling. Results: We demonstrated that S100b concentration changes dramatically over timescales that are clinically important for early prognostication with a peak at 27.2 h (95 % credible interval [25.6, 28.8]). Baseline S100b levels was found to be 0.11 mu g/L (95 % credible interval [0.10, 0.12]). Conclusions: Even small differences in injury to sample time may lead to marked changes in S100b during the first days after injury. This must be taken into account in interpretation. The model offers a way to predict the peak and trajectory of S100b from 12 h post trauma in TBI patients, and to identify deviations from this, possibly indicating a secondary event. Kinetic modelling, providing an equation for the peak and projection, may offer a way to reduce the ambiguity in interpretation of, in time, randomly sampled acute biomarkers and may be generally applicable to biomarkers with, in time, well defined hits.

  • 55.
    Fiebig, Florian
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Edinburgh University, UK.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Stockholm University, Sweden.
    A Spiking Working Memory Model Based on Hebbian Short-Term Potentiation2017Ingår i: Journal of Neuroscience, ISSN 0270-6474, Vol. 37, nr 1, s. 83-96Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A dominant theory of working memory (WM), referred to as the persistent activity hypothesis, holds that recurrently connected neural networks, presumably located in the prefrontal cortex, encode and maintain WM memory items through sustained elevated activity. Reexamination of experimental data has shown that prefrontal cortex activity in single units during delay periods is much more variable than predicted by such a theory and associated computational models. Alternative models of WM maintenance based on synaptic plasticity, such as short-term nonassociative (non-Hebbian) synaptic facilitation, have been suggested but cannot account for encoding of novel associations. Here we test the hypothesis that a recently identified fast-expressing form of Hebbian synaptic plasticity (associative short-term potentiation) is a possible mechanism for WM encoding and maintenance. Our simulations using a spiking neural network model of cortex reproduce a range of cognitive memory effects in the classical multi-item WM task of encoding and immediate free recall of word lists. Memory reactivation in the model occurs in discrete oscillatory bursts rather than as sustained activity. We relate dynamic network activity as well as key synaptic characteristics to electrophysiological measurements. Our findings support the hypothesis that fast Hebbian short-term potentiation is a key WM mechanism.

  • 56. Frånberg, Mattias
    et al.
    Strawbridge, Rona J.
    Hamsten, Anders
    de Faire, Ulf
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Sennblad, Bengt
    Fast and general tests of genetic interaction for genome-wide association studies2017Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 13, nr 6, artikel-id e1005556Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A complex disease has, by definition, multiple genetic causes. In theory, these causes could be identified individually, but their identification will likely benefit from informed use of anticipated interactions between causes. In addition, characterizing and understanding interactions must be considered key to revealing the etiology of any complex disease. Large-scale collaborative efforts are now paving the way for comprehensive studies of interaction. As a consequence, there is a need for methods with a computational efficiency sufficient for modern data sets as well as for improvements of statistical accuracy and power. Another issue is that, currently, the relation between different methods for interaction inference is in many cases not transparent, complicating the comparison and interpretation of results between different interaction studies. In this paper we present computationally efficient tests of interaction for the complete family of generalized linear models (GLMs). The tests can be applied for inference of single or multiple interaction parameters, but we show, by simulation, that jointly testing the full set of interaction parameters yields superior power and control of false positive rate. Based on these tests we also describe how to combine results from multiple independent studies of interaction in a meta-analysis. We investigate the impact of several assumptions commonly made when modeling interactions. We also show that, across the important class of models with a full set of interaction parameters, jointly testing the interaction parameters yields identical results. Further, we apply our method to genetic data for cardiovascular disease. This allowed us to identify a putative interaction involved in Lp(a) plasma levels between two 'tag' variants in the LPA locus (p = 2.42 . 10(-09)) as well as replicate the interaction (p = 6.97 . 10(-07)). Finally, our meta-analysis method is used in a small (N = 16,181) study of interactions in myocardial infarction.

  • 57.
    Gholami, Ali
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Dowling, Jim
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Programvaruteknik och Datorsystem, SCS.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    A security framework for population-scale genomics analysis2015Ingår i: Proceedings of the 2015 International Conference on High Performance Computing and Simulation, HPCS 2015, IEEE conference proceedings, 2015, s. 106-114Konferensbidrag (Refereegranskat)
    Abstract [en]

    Biobanks store genomic material from identifiable individuals. Recently many population-based studies have started sequencing genomic data from biobank samples and cross-linking the genomic data with clinical data, with the goal of discovering new insights into disease and clinical treatments. However, the use of genomic data for research has far-reaching implications for privacy and the relations between individuals and society. In some jurisdictions, primarily in Europe, new laws are being or have been introduced to legislate for the protection of sensitive data relating to individuals, and biobank-specific laws have even been designed to legislate for the handling of genomic data and the clear definition of roles and responsibilities for the owners and processors of genomic data. This paper considers the security questions raised by these developments. We introduce a new threat model that enables the design of cloud-based systems for handling genomic data according to privacy legislation. We also describe the design and implementation of a security framework using our threat model for BiobankCloud, a platform that supports the secure storage and processing of genomic data in cloud computing environments.

  • 58.
    Griggio, Carla
    et al.
    KTH.
    Romero, Mario
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Georgia Institute of Technology.
    A real-time dance visualization framework for the design of mappings that favor user appropriation2015Konferensbidrag (Refereegranskat)
    Abstract [en]

    In this paper we present a real-time dance visualization framework with the goal of easily mapping motion data from an accelerometer and a gyroscope into visual effects that users can compose and appropriate to their own dancing style. We used this framework to design a set of dance-tovisuals mappings through a user-centered approach. As a result, we conclude with a list of factors that help users to understand how to interact with a real-time dance visualization with no prior instructions.

  • 59. Gupta, Sonali
    et al.
    Tewatia, Parul
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Misri, Jyoti
    Singh, Rajni
    Molecular Modeling of Cloned Bacillus subtilis Keratinase and Its Insinuation in Psoriasis Treatment Using Docking Studies2017Ingår i: Indian Journal of Microbiology, ISSN 0046-8991, E-ISSN 0973-7715, Vol. 57, nr 4, s. 485-491Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Present study demonstrated the expression of cloned Bacillus subtilis RSE163 keratinase gene and in silico binding affinities of deduced protein with psoriasis topical drugs for systemic absorption and permeation through skin. The ker gene expressed in E. coli showed significantly higher keratinase activity 450 +/- 10.43 U representing 1342 bp nucleotides encoding 447 amino acids with molecular weight of 46 kDa. The modeled structure was validated using ramachandran's plot showing 305 residues (84.3%) in most favoured region. Docking studies using extra precision (XP) method of Glide showed optimum binding affinities with the drugs Acitretin (- 39.62 kcal/mol), Clobetasol propionate (- 37.90 kcal/mol), Fluticasone (- 38.53 kcal/mol), Desonide (- 32.23 kcal/mol), Anthralin (- 38.04 kcal/mol), Calcipotreine (- 21.55 kcal/mol) and Mometasone (- 28.40 kcal/mol) in comparison to other psoriasis drugs. The results can further be correlated with in vitro enzymatic experiments using keratinase as an effective drug mediator through skin to serve the unmet need of industries.

  • 60. Gómez, Paula
    et al.
    Do, Ellen Yi-Luen
    Romero, Mario
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Georgia Institute of Technology.
    Activity Shapes: towards a spatiotemporal analysis in architecture2014Ingår i: DEARQ: Journal of Architecture, ISSN 2011-3188, E-ISSN 2215-969X, nr 26Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Computational spatial analyses play an important role in architectural design processes, providing feedback about spatial configurations that may inform design decisions. Current spatial analyses convey geometrical aspects of space, but aspects such as space use are not encompassed within the analyses, although they are fundamental for architectural programming. Through this study, we initiate the discussion of including human activity as an input that will change the focus of current computational spatial analyses toward a detailed understanding of activity patterns in space and time. We envision that the emergent insights will serve as guidelines for future evaluation of design intents motivated by spatial occupancy, since we –designers– mentally constructing a model of the situation and activities on it (Eastman, 2001).

  • 61. Hahn, Gerald
    et al.
    Ponce-Alvarez, Adrian
    Monier, Cyril
    Benvenuti, Giacomo
    Kumar, Arvind
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Bernstein Ctr Computat Neurosci, Germany.
    Chavane, Frederic
    Deco, Gustavo
    Fregnac, Yves
    Spontaneous cortical activity is transiently poised close to criticality2017Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 13, nr 5, artikel-id e1005543Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Brain activity displays a large repertoire of dynamics across the sleep-wake cycle and even during anesthesia. It was suggested that criticality could serve as a unifying principle underlying the diversity of dynamics. This view has been supported by the observation of spontaneous bursts of cortical activity with scale-invariant sizes and durations, known as neuronal avalanches, in recordings of mesoscopic cortical signals. However, the existence of neuronal avalanches in spiking activity has been equivocal with studies reporting both its presence and absence. Here, we show that signs of criticality in spiking activity can change between synchronized and desynchronized cortical states. We analyzed the spontaneous activity in the primary visual cortex of the anesthetized cat and the awake monkey, and found that neuronal avalanches and thermodynamic indicators of criticality strongly depend on collective synchrony among neurons, LFP fluctuations, and behavioral state. We found that synchronized states are associated to criticality, large dynamical repertoire and prolonged epochs of eye closure, while desynchronized states are associated to sub-criticality, reduced dynamical repertoire, and eyes open conditions. Our results show that criticality in cortical dynamics is not stationary, but fluctuates during anesthesia and between different vigilance states.

  • 62. Hahne, J.
    et al.
    Helias, M.
    Kunkel, Susanne
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Igarashi, J.
    Kitayama, I.
    Wylie, B.
    Bolten, M.
    Frommer, A.
    Diesmann, M.
    Including gap junctions into distributed neuronal network simulations2016Ingår i: 2nd International Workshop on Brain-Inspired Computing, BrainComp 2015, Springer Publishing Company, 2016, s. 43-57Konferensbidrag (Refereegranskat)
    Abstract [en]

    Contemporary simulation technology for neuronal networks enables the simulation of brain-scale networks using neuron models with a single or a few compartments. However, distributed simulations at full cell density are still lacking the electrical coupling between cells via so called gap junctions. This is due to the absence of efficient algorithms to simulate gap junctions on large parallel computers. The difficulty is that gap junctions require an instantaneous interaction between the coupled neurons, whereas the efficiency of simulation codes for spiking neurons relies on delayed communication. In a recent paper [15] we describe a technology to overcome this obstacle. Here, we give an overview of the challenges to include gap junctions into a distributed simulation scheme for neuronal networks and present an implementation of the new technology available in the NEural Simulation Tool (NEST 2.10.0). Subsequently we introduce the usage of gap junctions in model scripts as well as benchmarks assessing the performance and overhead of the technology on the supercomputers JUQUEEN and K computer.

  • 63.
    Herman, Pawel
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Benjaminsson, S.
    Lansner, A.
    Odor recognition in an attractor network model of the mammalian olfactory cortex2017Ingår i: 2017 International Joint Conference on Neural Networks (IJCNN), Institute of Electrical and Electronics Engineers (IEEE), 2017, s. 3561-3568, artikel-id 7966304Konferensbidrag (Refereegranskat)
    Abstract [en]

    Odor recognition constitutes a key functional aspect of olfaction and in real-world scenarios it requires that odorants occurring in complex chemical mixtures are identified irrespective of their concentrations. We investigate this challenging pattern recognition problem in the framework of a three-stage computational model of the mammalian olfactory system. To this end, we first synthesize odor stimuli with the primary representations in the olfactory receptor neuron (ORN) layer and the secondary representations in the output of the olfactory bulb (OB) in the model. Next, sparse olfactory codes are extracted and fed into the recurrent network model, where as a result of Hebbian-like associative learning an attractor memory storage is produced. We demonstrate the capability of the resultant olfactory cortex (OC) model to perform robust odor recognition tasks and offer computational insights into the underlying network mechanisms.

  • 64.
    Herman, Pawel
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Prasad, Girijesh
    McGinnity, Thomas Martin
    Designing an Interval Type-2 Fuzzy Logic System for Handling Uncertainty Effects in Brain-Computer Interface Classification of Motor Imagery Induced EEG Patterns2017Ingår i: IEEE transactions on fuzzy systems, ISSN 1063-6706, E-ISSN 1941-0034, Vol. 25, nr 1, s. 29-42Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    One of the urgent challenges in the automated analysis and interpretation of electrical brain activity is the effective handling of uncertainties associated with the complexity and variability of brain dynamics, reflected in the nonstationary nature of brain signals such as electroencephalogram (EEG). This poses a severe problem for existing approaches to the classification task within brain-computer interface (BCI) systems. Recently emerged type-2 fuzzy logic (T2FL) methodology has shown a remarkable potential in dealing with uncertain information given limited insight into the nature of the data-generating mechanism. The objective of this work is, thus, to examine the applicability of the T2FL approach to the problem of EEG pattern recognition. In particular, the focus is two-fold: 1) the design methodology for the interval T2FL system (IT2FLS) that can robustly deal with inter-session as well as within-session manifestations of nonstationary spectral EEG correlates of motor imagery, and 2) the comprehensive examination of the proposed fuzzy classifier in both off-line and on-line EEG classification case studies. The on-line evaluation of the IT2FLS-controlled real-time neurofeedback over multiple recording sessions holds special importance for EEG-based BCI technology. In addition, a retrospective comparative analysis accounting for other popular BCI classifiers such as linear discriminant analysis, kernel Fisher discriminant, and support vector machines as well as a conventional type-1 FLS, simulated off-line on the recorded EEGs, has demonstrated the enhanced potential of the proposed IT2FLS approach to robustly handle uncertainty effects in BCI classification.

  • 65.
    Hoffman, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Holm, Bärbel
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST).
    Richter, Thomas
    The locally adapted parametric finite element method for interface problems on triangular meshes2017Ingår i: Fluid-Structure Interaction: Modeling, Adaptive Discretizations and Solvers / [ed] Stefan Frei, Bärbel Holm, Thomas Richter, Thomas, Huidong Yang, Walter de Gruyter, 2017, s. 41-63Kapitel i bok, del av antologi (Refereegranskat)
  • 66.
    Hoffman, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC). Basque Center for Applied Mathematics (BCAM), Bilbao, Spain.
    Jansson, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Basque Center for Applied Mathematics (BCAM), Bilbao, Spain.
    Degirmenci, Niyazi Cem
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Spühler, Jeannette Hiromi
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Vilela de Abreu, Rodrigo
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Jansson, Niclas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Larcher, Aurélien
    Norwegian University of Science and Technology, Trondheim, Norway.
    FEniCS-HPC: Coupled Multiphysics in Computational Fluid Dynamics2017Ingår i: High-Performance Scientific Computing: Jülich Aachen Research Alliance (JARA) High-Performance Computing Symposium / [ed] Edoardo Di Napoli, Marc-André Hermanns, Hristo Iliev, Andreas Lintermann, Alexander Peyser, Springer, 2017, s. 58-69Konferensbidrag (Refereegranskat)
    Abstract [en]

    We present a framework for coupled multiphysics in computational fluid dynamics, targeting massively parallel systems. Our strategy is based on general problem formulations in the form of partial differential equations and the finite element method, which open for automation, and optimization of a set of fundamental algorithms. We describe these algorithms, including finite element matrix assembly, adaptive mesh refinement and mesh smoothing; and multiphysics coupling methodologies such as unified continuum fluid-structure interaction (FSI), and aeroacoustics by coupled acoustic analogies. The framework is implemented as FEniCS open source software components, optimized for massively parallel computing. Examples of applications are presented, including simulation of aeroacoustic noise generated by an airplane landing gear, simulation of the blood flow in the human heart, and simulation of the human voice organ.

  • 67.
    Hoffman, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Jansson, Niclas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Vilela de Abreu, Rodrigo
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Johnson, Claes
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Computability and Adaptivity in CFD2018Ingår i: Encyclopedia of Computational Mechanics / [ed] Erwin Stein and René de Borst and Thomas J. R. Hughes, John Wiley & Sons, 2018, 2Kapitel i bok, del av antologi (Refereegranskat)
  • 68.
    Hussain, Dena
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    The development of ICT tools for E-inclusion qualities: Work in progress2018Ingår i: 20th International Conference on Interactive Collaborative Learning, ICL 2017, Springer Verlag , 2018, s. 734-740Konferensbidrag (Refereegranskat)
    Abstract [en]

    With the diversity and increasing use of different information and communication technologies (ICT) in the educational sector, new pedagogic approaches are also being introduced and have had a major impact on the educational sector, focusing on different perspective including improved educational methods and in both schools and homes, information and communication technologies (ICT) are widely seen as enhancing learning, fulfilling their rapid diffusion and acceptance throughout developed societies. But the need to utilize ICT tools to support and guide educators in finding the right support for students with special individual needs is still a challenge, investigating different challenges that are presented to teachers in their working environment is an ongoing matter. One of these challenges that teacher face frequently is creating an inclusive environment. An “inclusive education” is a process of strengthening the capacity of the education system to reach out to all learners involved. It changes the education in content, approaches, structures and strategies, with a common vision that covers all children of the appropriate age range. Inclusion is thus seen as a process of addressing and responding to the diversity of needs of all children. Therefore an inclusive education system can only be created if schools become more inclusive, in other words, if they become better at educating all children in their communities with their individual needs. Therefore, creative forms of communication should be encouraged to promote personalized care, hence the focuses of this research is to investigate the use of data process flow map with the aim to guide the teacher towards an inclusive way of thinking. 

  • 69.
    Iakymchuk, Roman
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Jordan, Herbert
    University of Innsbruck, Institute of Computer Science.
    Bo Peng, Ivy
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    A Particle-in-Cell Method for Automatic Load-Balancing with the AllScale Environment2016Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    We present an initial design and implementation of a Particle-in-Cell (PIC) method based on the work carried out in the European Exascale AllScale project. AllScale provides a unified programming system for the effective development of highly scalable, resilient and performance-portable parallel applications for Exascale systems. The AllScale approach is based on task-based nested recursive parallelism and it provides mechanisms for automatic load-balancing in the PIC simulations. We provide the preliminary results of the AllScale-based PIC implementation and draw directions for its future development. 

  • 70.
    Iakymchuk, Roman
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Quintana-Orti, E. S.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Graillat, S.
    Towards reproducible blocked lu factorization2017Ingår i: Proceedings - 2017 IEEE 31st International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2017, Institute of Electrical and Electronics Engineers (IEEE), 2017, s. 1598-1607, artikel-id 7965230Konferensbidrag (Refereegranskat)
    Abstract [en]

    In this article, we address the problem of reproducibility of the blocked LU factorization on GPUs due to cancellations and rounding errors when dealing with floating-point arithmetic. Thanks to the hierarchical structure of linear algebra libraries, the computations carried within this operation can be expressed in terms of the Level-3 BLAS routines as well as the unblocked variant of the factorization, while the latter is correspondingly built upon the Level-1/2 BLAS kernels. In addition, we strengthen numerical stability of the blocked LU factorization via partial row pivoting. Therefore, we propose a double-layer bottom-up approach for ensuring reproducibility of the blocked LUfactorization and provide experimental results for its underlying blocks.

  • 71.
    Iakymchuk, Roman
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Shakhno, S. M.
    Yarmola, H. P.
    CONVERGENCE ANALYSIS OF A TWO-STEP MODIFICATION OF THE GAUSS-NEWTON METHOD AND ITS APPLICATIONS2017Ingår i: JOURNAL OF NUMERICAL AND APPLIED MATHEMATICS, ISSN 0868-6912, Vol. 3, nr 126, s. 61-74Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We investigate the convergence of a two-step modification of the Gauss-Newton method applying the generalized Lipschitz condition for the first- and second-order derivatives. The convergence order as well as the convergence radius of the method are studied and the uniqueness ball of the solution of the nonlinear least squares problem is examined. Finally, we carry out numerical experiments on a set of well-known test problems.

  • 72. Iatropoulos, Georgios
    et al.
    Olofsson, Jonas
    Herman, Pawel
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Larsson, Maria
    Analysis of Statistics and Semantic Relations of Odor-Describing Words in Written Olfactory Versus Non- Olfactory Contexts2017Ingår i: Chemical Senses, ISSN 0379-864X, E-ISSN 1464-3553, Vol. 42, nr 2, s. E34-E35Artikel i tidskrift (Refereegranskat)
  • 73. Innocenti, M. E.
    et al.
    Cazzola, E.
    Mistry, R.
    Eastwood, J. P.
    Goldman, M. V.
    Newman, D. L.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Lapenta, G.
    Switch-off slow shock/rotational discontinuity structures in collisionless magnetic reconnection: What to look for in satellite observations2017Ingår i: Geophysical Research Letters, ISSN 0094-8276, E-ISSN 1944-8007, Vol. 44, nr 8, s. 3447-3455Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In Innocenti et al. (2015) we have observed and characterized for the first time Petschek-like switch-off slow shock/rotational discontinuity (SO-SS/RD) compound structures in a 2-D fully kinetic simulation of collisionless magnetic reconnection. Observing these structures in the solar wind or in the magnetotail would corroborate the possibility that Petschek exhausts develop in collisionless media as a result of single X point collisionless reconnection. Here we highlight their signatures in simulations with the aim of easing their identification in observations. The most notable signatures include a four-peaked ion current profile in the out-of-plane direction, associated ion distribution functions, increased electron and ion anisotropy downstream the SS, and increased electron agyrotropy downstream the RDs.

  • 74. Innocenti, M. E.
    et al.
    Johnson, A.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Amaya, J.
    Deca, J.
    Olshevsky, V.
    Lapenta, G.
    Progress towards physics-based space weather forecasting with exascale computing2017Ingår i: Advances in Engineering Software, ISSN 0965-9978, E-ISSN 1873-5339, Vol. 111, s. 3-17Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Space weather is a rapidly growing field of science which studies processes occurring in the area of space between the Sun and the Earth. The development of space weather forecasting capabilities is a task of great societal relevance: space weather effects may damage a number of technological assets, among which power and communication lines, transformers, pipelines and the telecommunication infrastructure. Exascale computing is a fundamental ingredient for space weather forecasting tools based on physical, rather than statistical, models. We describe here our recent progresses towards a physics-based space weather forecasting tool with exascale computing. We select the semi-implicit, Particle In Cell, Implicit Moment Method implemented in the parallel, object-oriented, C++ iPic3D code as a promising starting point. We analyze the structure and the performances of the current version of the iPic3D code. We describe three algorithmic developments, the fully implicit method, the Multi-Level Multi-Domain method, and the fluid-kinetic method, which can help addressing the multiple spatial and temporal scales present in space weather simulations. We then examine, in a co-design approach, which requirements - vectorization, extreme parallelism and reduced communication - an application has to satisfy to fully exploit architectures such as GPUs and Xeon Phi's. We address how to modify the iPic3D code to better satisfy these requirements. We then describe how to port the iPic3D code to the DEEP architecture currently under construction. The FP7 project DEEP (www.deep-project.eu) aims at building an exascale-ready machine composed of a cluster of Xeon nodes and of a collection of Xeon Phi coprocessors, used as boosters. The aim of the DEEP project is to enable exascale performance for codes, such as iPic3D, composed of parts which exhibit different potential for extreme scalability. Finally, we provide examples of simulations of space weather processes done with the current version of the iPic3D code. © 2016 Elsevier Ltd.

  • 75. Innocenti, M. E.
    et al.
    Norgren, C.
    Newman, D.
    Goldman, M.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Lapenta, G.
    Study of electric and magnetic field fluctuations from lower hybrid drift instability waves in the terrestrial magnetotail with the fully kinetic, semi-implicit, adaptive multi level multi domain method2016Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 23, nr 5, artikel-id 052902Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The newly developed fully kinetic, semi-implicit, adaptive multi-level multi-domain (MLMD) method is used to simulate, at realistic mass ratio, the development of the lower hybrid drift instability (LHDI) in the terrestrial magnetotail over a large wavenumber range and at a low computational cost. The power spectra of the perpendicular electric field and of the fluctuations of the parallel magnetic field are studied at wavenumbers and times that allow to appreciate the onset of the electrostatic and electromagnetic LHDI branches and of the kink instability. The coupling between electric and magnetic field fluctuations observed by Norgren et al. ["Lower hybrid drift waves: Space observations," Phys. Rev. Lett. 109, 055001 (2012)] for high wavenumber LHDI waves in the terrestrial magnetotail is verified. In the MLMD simulations presented, a domain ("coarse grid") is simulated with low resolution. A small fraction of the entire domain is then simulated with higher resolution also ("refined grid") to capture smaller scale, higher frequency processes. Initially, the MLMD method is validated for LHDI simulations. MLMD simulations with different levels of grid refinement are validated against the standard semi-implicit particle in cell simulations of domains corresponding to both the coarse and the refined grid. Precious information regarding the applicability of the MLMD method to turbulence simulations is derived. The power spectra of MLMD simulations done with different levels of refinements are then compared. They consistently show a break in the magnetic field spectra at k(perpendicular to)d(i) similar to 30, with d(i) the ion skin depth and k(perpendicular to) the perpendicular wavenumber. The break is observed at early simulated times, Omega(ci)t < 6, with Omega(ci) the ion cyclotron frequency. It is due to the initial decoupling of electric and magnetic field fluctuations at intermediate and low wavenumbers, before the development of the electromagnetic LHDI branch. Evidence of coupling between electric and magnetic field fluctuations in the wave-number range where the fast and slow LHDI branches develop is then provided for a cluster magnetotail crossing.

  • 76. Innocenti, M. E.
    et al.
    Tronci, C.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Lapenta, G.
    Grid coupling mechanism in the semi-implicit adaptive Multi-Level Multi-Domain method2016Ingår i: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 719, nr 1, artikel-id 12019Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Multi-Level Multi-Domain (MLMD) method is a semi-implicit adaptive method for Particle-In-Cell plasma simulations. It has been demonstrated in the past in simulations of Maxwellian plasmas, electrostatic and electromagnetic instabilities, plasma expansion in vacuum, magnetic reconnection [1, 2, 3]. In multiple occasions, it has been commented on the coupling between the coarse and the refined grid solutions. The coupling mechanism itself, however, has never been explored in depth. Here, we investigate the theoretical bases of grid coupling in the MLMD system. We obtain an evolution law for the electric field solution in the overlap area of the MLMD system which highlights a dependance on the densities and currents from both the coarse and the refined grid, rather than from the coarse grid alone: grid coupling is obtained via densities and currents.

  • 77.
    Ivanov, Ilya
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Machado, Rui
    Rahn, Mirko
    Akhmetova, Dana
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Gong, Jing
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Henningson, Dan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Fischer, Paul
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Evaluating New Communication Models in the Nek5000 Code for Exascale2015Konferensbidrag (Övrigt vetenskapligt)
  • 78.
    Janssen, Bärbel
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Wihler, Thomas P.
    Computational Comparison of Continuous and Discontinuous Galerkin Time-Stepping Methods for Nonlinear Initial Value Problems2015Ingår i: SPECTRAL AND HIGH ORDER METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS ICOSAHOM 2014, Springer Berlin/Heidelberg, 2015, s. 103-114Konferensbidrag (Refereegranskat)
    Abstract [en]

    This article centers on the computational performance of the continuous and discontinuous Galerkin time stepping schemes for general first-order initial value problems in R-n, with continuous nonlinearities. We briefly review a recent existence result for discrete solutions from Janssen and Wihler (Existence results for the continuous and discontinuous Galerkin time stepping methods for nonlinear initial value problems, 2014, Submitted), and provide a numerical comparison of the two time discretization methods.

  • 79.
    Jansson, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Degirmenci, N. C.
    KTH, Skolan för datavetenskap och kommunikation (CSC).
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem2017Ingår i: International Journal for Numerical Methods in Biomedical Engineering, ISSN 2040-7939, E-ISSN 2040-7947, Vol. 33, nr 9, artikel-id e2851Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this paper, we address a 3D fluid-structure interaction benchmark problem that represents important characteristics of biomedical modeling. We present a goal-oriented adaptive finite element methodology for incompressible fluid-structure interaction based on a streamline diffusion–type stabilization of the balance equations for mass and momentum for the entire continuum in the domain, which is implemented in the Unicorn/FEniCS software framework. A phase marker function and its corresponding transport equation are introduced to select the constitutive law, where the mesh tracks the discontinuous fluid-structure interface. This results in a unified simulation method for fluids and structures. We present detailed results for the benchmark problem compared with experiments, together with a mesh convergence study.

  • 80.
    Jansson, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Direct FEM parallel-in-time computation of turbulent flowManuskript (preprint) (Övrigt vetenskapligt)
  • 81.
    Jansson, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Krishnasamy, Ezhilmathi
    Leoni, Massimiliano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Jansson, Niclas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Time-resolved Adaptive Direct FEM Simulation of High-lift Aircraft Configurations: Chapter in "Numerical Simulation of the Aerodynamics of High-Lift Configurations'", Springer2018Ingår i: Numerical Simulation of the Aerodynamics of High-Lift Configurations / [ed] Omar Darío López Mejia andJaime A. Escobar Gomez, Springer, 2018, s. 67-92Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    We present an adaptive finite element method for time-resolved simulation of aerodynamics without any turbulence-model parameters, which is applied to a benchmark problem from the HiLiftPW-3workshop to compute the flowpast a JAXA Standard Model (JSM) aircraft model at realistic Reynolds numbers. The mesh is automatically constructed by the method as part of an adaptive algorithm based on a posteriori error estimation using adjoint techniques. No explicit turbulence model is used, and the effect of unresolved turbulent boundary layers is modeled by a simple parametrization of the wall shear stress in terms of a skin friction. In the case of very high Reynolds numbers, we approximate the small skin friction by zero skin friction, corresponding to a free-slip boundary condition, which results in a computational model without any model parameter to be tuned, and without the need for costly boundary-layer resolution. We introduce a numerical tripping-noise term to act as a seed for growth of perturbations; the results support that this triggers the correct physical separation at stall and has no significant pre-stall effect. We show that the methodology quantitavely and qualitatively captures the main features of the JSM experiment-aerodynamic forces and the stall mechanism-with a much coarser mesh resolution and lower computational cost than the state-of-the-art methods in the field, with convergence under mesh refinement by the adaptive method. Thus, the simulation methodology appears to be a possible answer to the challenge of reliably predicting turbulent-separated flows for a complete air vehicle.

  • 82.
    Jansson, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Basque Center for Applied Mathematics, Bilbao, Spain.
    Nguyen, Dang
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Margarida, Moragues
    BCAM - Basque Center for Applied Mathematics.
    Castanon, Daniel
    BCAM - Basque Center for Applied Mathematics.
    Saavedra, Laura
    Universidad Politécnica de Madrid.
    Krishnasamy, Ezhilmathi
    BCAM - Basque Center for Applied Mathematics.
    Goude, Anders
    Uppsala University.
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Basque Center for Applied Mathematics, Bilbao, Spain.
    Direct finite element simulation of turbulent flow for marine based renewable energyManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    In this article we present a computational framework for simulation ofturbulent flow in marine based renewable energy applications. Inparticular, we focus on floating structures and rotatingturbines. This work is an extension to multiphase turbulent flow, ofour existing framework of residual based turbulence modeling forsingle phase turbulent incompressible flow. We illustrate theframework in four examples: a regular wave test where we compareagainst an exact solution, the standard MARIN wave impact benchmarkwith experimental validation data, a vertical axis turbine withcomplex geometry from an existing turbine, and finally a prototypesimulation of decay test in a coupled moving boundary rigid-body andtwo-phase fluid simulation.

  • 83.
    Jansson, Ylva
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Dynamic texture recognition using time-causal and time-recursive spatio-temporal receptive fields2017Rapport (Övrigt vetenskapligt)
    Abstract [en]

    This work presents a first evaluation of using spatiotemporal receptive fields from a recently proposed time-causal spatio-temporal scale-space framework as primitives for video analysis. We propose a new family of video descriptors based on regional statistics of spatio-temporal receptive field responses and evaluate this approach on the problem of dynamic texture recognition. Our approach generalises a previously used method, based on joint histograms of receptive field responses, from the spatial to the spatio-temporal domain and from object recognition to dynamic texture recognition. The time-recursive formulation enables computationally efficient time-causal recognition.

    The experimental evaluation demonstrates competitive performance compared to state-of-the-art. Especially, it is shown that binary versions of our dynamic texture descriptors achieve improved performance compared to a large range of similar methods using different primitives either handcrafted or learned from data. Further, our qualitative and quantitative investigation into parameter choices and the use of different sets of receptive fields highlights the robustness and flexibility of our approach. Together, these results support the descriptive power of this family of time-causal spatio-temporal receptive fields, validate our approach for dynamic texture recognition and point towards the possibility of designing a range of video analysis methods based on these new time-causal spatio-temporal primitives.

  • 84.
    Jansson, Ylva
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Dynamic texture recognition using time-causal spatio-temporal scale-space filters2017Ingår i: Scale Space and Variational Methods in Computer Vision, Springer, 2017, Vol. 10302, s. 16-28Konferensbidrag (Refereegranskat)
    Abstract [en]

    This work presents an evaluation of using time-causal scale-space filters as primitives for video analysis. For this purpose, we present a new family of video descriptors based on regional statistics of spatiotemporal scale-space filter responses and evaluate this approach on the problem of dynamic texture recognition. Our approach generalises a previously used method, based on joint histograms of receptive field responses, from the spatial to the spatio-temporal domain. We evaluate one member in this family, constituting a joint binary histogram, on two widely used dynamic texture databases. The experimental evaluation shows competitive performance compared to previous methods for dynamic texture recognition, especially on the more complex DynTex database. These results support the descriptive power of time-causal spatio-temporal scale-space filters as primitives for video analysis.

  • 85. Johlander, A.
    et al.
    Schwartz, S. J.
    Vaivads, Andris
    Khotyaintsev, Yu. V.
    Gingell, I.
    Peng, Bo
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Lindqvist, Per-Arne
    KTH, Skolan för elektro- och systemteknik (EES), Rymd- och plasmafysik.
    Ergun, R. E.
    Marklund, G. T.
    Plaschke, F.
    Magnes, W.
    Strangeway, R. J.
    Russell, C. T.
    Wei, H.
    Torbert, R. B.
    Paterson, W. R.
    Gershman, D. J.
    Dorelli, J. C.
    Avanov, L. A.
    Lavraud, B.
    Saito, Y.
    Giles, B. L.
    Pollock, C. J.
    Burch, J. L.
    Rippled Quasiperpendicular Shock Observed by the Magnetospheric Multiscale Spacecraft2016Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 117, nr 16, artikel-id 165101Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Collisionless shock nonstationarity arising from microscale physics influences shock structure and particle acceleration mechanisms. Nonstationarity has been difficult to quantify due to the small spatial and temporal scales. We use the closely spaced (subgyroscale), high-time-resolution measurements from one rapid crossing of Earth's quasiperpendicular bow shock by the Magnetospheric Multiscale (MMS) spacecraft to compare competing nonstationarity processes. Using MMS's high-cadence kinetic plasma measurements, we show that the shock exhibits nonstationarity in the form of ripples.

  • 86. Jordan, Jakob
    et al.
    Ippen, Tammo
    Helias, Moritz
    Kitayama, Itaru
    Sato, Mitsuhisa
    Igarashi, Jun
    Diesmann, Markus
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Julich Res Ctr, Inst Neurosci & Med INM 6, Julich, Germany; Julich Res Ctr, Inst Adv Simulat IAS 6, Julich, Germany; ulich Res Ctr, JARA Inst Brain Struct Funct Relationships INM 10, Julich, Germany; Rhein Westfal TH Aachen, Fac 1, Dept Phys, Aachen, Germany; Julich Res Ctr, Simulat Lab Neurosci, Bernstein Facil Simulat & Da, Julich, Germany.
    Kunkel, Susanne
    Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers2018Ingår i: Frontiers in Neuroinformatics, ISSN 1662-5196, E-ISSN 1662-5196, Vol. 12, artikel-id 2Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    State-of-the-art software tools for neuronal network simulations scale to the largest computing systems available today and enable investigations of large-scale networks of up to 10 % of the human cortex at a resolution of individual neurons and synapses. Due to an upper limit on the number of incoming connections of a single neuron, network connectivity becomes extremely sparse at this scale. To manage computational costs, simulation software ultimately targeting the brain scale needs to fully exploit this sparsity. Here we present a two-tier connection infrastructure and a framework for directed communication among compute nodes accounting for the sparsity of brain-scale networks. We demonstrate the feasibility of this approach by implementing the technology in the NEST simulation code and we investigate its performance in different scaling scenarios of typical network simulations. Our results show that the new data structures and communication scheme prepare the simulation kernel for post-petascale high-performance computing facilities without sacrificing performance in smaller systems.

  • 87.
    Jovanovic, Stojan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Correlations of Higher Order in Networks of Spiking Neurons2016Doktorsavhandling, monografi (Övrigt vetenskapligt)
    Abstract [en]

    The topic of this dissertation is the study of the emergence of higher-order correlations in recurrentlyconnected populations of brain cells.Neurons have been experimentally shown to form vast networks in the brain. In these networks, eachbrain cell communicates with tens of thousands of its neighbors by sending out and receiving electricalsignals, known as action potentials or spikes. The effect of a single action potential can propagate throughthe network and cause additional spikes to be generated. Thus, the connectivity of the neuronal networkgreatly influences the network's spiking dynamics. However, while the methods of action potentialgeneration are very well studied, many dynamical features of neuronal networks are still only vaguelyunderstood.The reasons for this mostly have to do with the difficulties of keeping track of the collective, non-linearbehavior of hundreds of millions of brain cells. Even when one focuses on small groups of neurons, all butthe most trivial questions about coordinated activity remain unanswered, due to the combinatorialexplosion that arises in all questions of this sort. In theoretical neuroscience one often needs to resort tomathematical models that try to explain the most important dynamical phenomena while abstractingaway many of the morphological features of real neurons.On the other hand, advances in experimental methods are making simultaneous recording of largeneuronal populations possible. Datasets consisting of collective spike trains of thousands of neurons arebecoming available. With these new developments comes the possibility of finally understanding the wayin which connectivity gives rise to the many interesting dynamical aspects of spiking networks.The main research question, addressed in this thesis, is how connectivity between neurons influences thedegree of synchrony between their respective spike trains. Using a linear model of spiking neurondynamics, we show that there is a mathematical relationship between the network's connectivity and theso-called higher-order cumulants, which quantify beyond-chance-level coordinated activity of groups ofneurons. Our equations describe the specific connectivity patterns that give rise to higher-ordercorrelations. In addition, we explore the special case of correlations of third-order and find that, in large,regular networks, it is the presence of a single subtree that is responsible for third-order synchrony.In summary, the results presented in this dissertation advance our understanding of how higher-ordercorrelations between spike trains of neurons are affected by certain patterns in synaptic connectivity.Our hope is that a better understanding of such complicated neuronal dynamics can lead to a consistenttheory of the network's functional properties.

  • 88. Karlsson, A.
    et al.
    Olofsson, N.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Clements, M.
    A parallel microsimulation package for modelling cancer screening policies2017Ingår i: Proceedings of the 2016 IEEE 12th International Conference on e-Science, e-Science 2016, IEEE, 2017, s. 323-330Konferensbidrag (Refereegranskat)
    Abstract [en]

    Microsimulation with stochastic life histories is an important tool in the development of public policies. In this article, we use microsimulation to evaluate policies for prostate cancer testing. We implemented the microsimulations as an R package, with pre- and post-processing in R and with the simulations written in C++. Calibrating a microsimulation model with a large population can be computationally expensive. To address this issue, we investigated four forms of parallelism: (i) shared memory parallelism using R; (ii) shared memory parallelism using OpenMP at the C++ level; (iii) distributed memory parallelism using R; and (iv) a hybrid shared/distributed memory parallelism using OpenMP at the C++ level and MPI at the R level. The close coupling between R and C++ offered advantages for ease of software dissemination and the use of high-level R parallelisation methods. However, this combination brought challenges when trying to use shared memory parallelism at the C++ level: the performance gained by hybrid OpenMP/MPI came at the cost of significant re-factoring of the existing code. As a case study, we implemented a prostate cancer model in the microsimulation package. We used this model to investigate whether prostate cancer testing with specific re-testing protocols would reduce harms and maintain any mortality benefit from prostate-specific antigen testing. We showed that four-yearly testing would have a comparable effectiveness and a marked decrease in costs compared with two-yearly testing and current testing. In summary, we developed a microsimulation package in R and assessed the cost-effectiveness of prostate cancer testing. We were able to scale up the microsimulations using a combination of R and C++, however care was required when using shared memory parallelism at the C++ level.

  • 89.
    Karlsson, Vide
    et al.
    KTH. Gavagai, Sweden.
    Herman, Pawel
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Gavagai, Sweden.
    Karlgren, Jussi
    KTH, Skolan för datavetenskap och kommunikation (CSC), Teoretisk datalogi, TCS.
    Evaluating Categorisation in Real Life: An argument against simple but impractical metrics2016Ingår i: 7th CLEF Conference and Labs of the Evaluation Forum, Springer, 2016Konferensbidrag (Refereegranskat)
    Abstract [en]

    Text categorisation in commercial application poses several limiting constraints on the technology solutions to be employed. This paper describes how a method with some potential improvements is eval- uated for practical purposes and argues for a richer and more expressive evaluation procedure. In this paper one such method is exemplified by a precision-recall matrix which sacrifices convenience for expressiveness. 

  • 90.
    Kasperi, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC).
    Picha Edwardsson, Malin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Medieteknik och interaktionsdesign, MID.
    Romero, Mario
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Occlusion in outdoor Augmented Reality using geospatial building data2017Ingår i: VRST '17 Proceedings of the 23rd ACM Symposium on Virtual Reality Software and Technology, Association for Computing Machinery (ACM), 2017, Vol. Part F131944, artikel-id a30Konferensbidrag (Refereegranskat)
    Abstract [en]

    Aligning virtual and real objects in Augmented Reality (AR) is essential for the user experience. Without alignment, the user loses suspension of disbelief and the sense of depth, distance, and size. Occlusion is a key feature to be aligned. Virtual content should be partially or fully occluded if real world objects are in its line-of-sight. The challenge for simulating occlusion is to construct the geometric model of the environment. Earlier studies have aimed to create realistic occlusions, yet most have either required depth-sensing hardware or a static predened environment. is paper proposes and evaluates an alternative model-based method for dynamic outdoor AR of virtual buildings rendered on non depth-sensing smartphones. It uses geospatial data to construct the geometric model of real buildings surrounding the virtual building. The method removes the target regions from the virtual building using masks constructed from real buildings. While the method is not pixel-perfect, meaning that the simulated occlusion is not fully realistic, results from the user study indicate that it fullled its goal. A majority of the participants expressed that their experience and depth perception improved with the method activated. The result from this study has applications to mobile AR since the majority of smartphones are not equipped with depth sensors. Using geospatial data for simulating occlusions is a suciently eective solution until depth-sensing AR devices are more widely available.

  • 91.
    Kastemaa, Juho
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Recognizing Compound Facial Expressions of Virtual Characters in Augmented Reality2017Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Hur är det möjligt att designa virtuella karaktärer som kan uttrycka olika känslor, till exempel blandade känslor som är en blandning av grundläggande känslor? Augmented Reality (AR) kan skapa engagerande upplevelser för deltagarna, och de senaste åren har virtuella ansikten och virtuella karaktärer blivit alltmer realistiska och uttrycksfulla, till exempel då kostnaderna minskas med hjälp av terapeutiska tillämpningar. Giltigheten av virtuellt uttryck har visats i studier på stationära datorer, men mindre i AR. I denna rapport studerades de grundläggande känslorna och hur de blandade känslorna av virtuella karaktären kan konstrueras för att fungera med Microsoft HoloLens i AR. Processen att skapa blandade känslor till en mänsklig virtuell karaktär konstruerades och animationerna modifierades med hjälp av Unity3D-spelmotor. Deltagarna (n = 24) upplevde den virtuella karaktären i en jobbintervju med Microsofts HoloLens. Den virtuella karaktären gjorde grundläggande och sammansatta ansiktsuttryck och deltagarna ombads kategorisera dom. Resultatet visar att alla deltagare framgångsrikt erkänt sju grundläggande känslor och sju blandade känslor från en virtuell karaktär i AR med hjälp av HoloLens; disgust var ihopblandad med sad, och angry var ibland ihopblandad med disgust. Fearfully surprised blev också ofta felaktig ihopblandad med awed. Studiens resultat visar att de blandade känslorna var lätta att känna igen och resultaten antyder på att den uppfattade valens förändras beroende på ansiktsuttryck. Studien ger insikter om hur blandade känslouttryck för virtuella karaktärer har konstruerats och uppfattats.

  • 92.
    Khan, Mehmood Alam
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Computational Problems in Modeling Evolution and Inferring Gene Families.2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Over the last few decades, phylogenetics has emerged as a very promising field, facilitating a comparative framework to explain the genetic relationships among all the living organisms on earth. These genetic relationships are typically represented by a bifurcating phylogenetic tree — the tree of life. Reconstructing a phylogenetic tree is one of the central tasks in evolutionary biology. The different evolutionary processes, such as gene duplications, gene losses, speciation, and lateral gene transfer events, make the phylogeny reconstruction task more difficult. However, with the rapid developments in sequencing technologies and availability of genome-scale sequencing data, give us the opportunity to understand these evolutionary processes in a more informed manner, and ultimately, enable us to reconstruct genes and species phylogenies more accurately. This thesis is an attempt to provide computational methods for phylogenetic inference and give tools to conduct genome-scale comparative evolutionary studies, such as detecting homologous sequences and inferring gene families.

    In the first project, we present FastPhylo as a software package containing fast tools for reconstructing distance-based phylogenies. It implements the previously published efficient algorithms for estimating a distance matrix from the input sequences and reconstructing an un-rooted Neighbour Joining tree from a given distance matrix. Results on simulated datasets reveal that FastPhylo can handles hundred of thousands of sequences in a minimum time and memory efficient manner. The easy to use, well-defined interfaces, and the modular structure of FastPhylo allows it to be used in very large Bioinformatic pipelines.

    In the second project, we present a synteny-aware gene homology method, called GenFamClust (GFC) that uses gene content and gene order conservation to detect homology. Results on simulated and biological datasets suggest that local synteny information combined with the sequence similarity improves the detection of homologs.

    In the third project, we introduce a novel phylogeny-based clustering method, PhyloGenClust, which partitions a very large gene family into smaller subfamilies. ROC (receiver operating characteristics) analysis on synthetic datasets show that PhyloGenClust identify subfamilies more accurately. PhyloGenClust can be used as a middle tier clustering method between raw clustering methods, such as sequence similarity methods, and more sophisticated Bayesian-based phylogeny methods.

    Finally, we introduce a novel probabilistic Bayesian method based on the DLTRS model, to sample reconciliations of a gene tree inside a species tree. The method uses MCMC framework to integrate LGTs, gene duplications, gene losses and sequence evolution under a relaxed molecular clock for substitution rates. The proposed sampling method estimates the posterior distribution of gene trees and provides the temporal information of LGT events over the lineages of a species tree. Analysis on simulated datasets reveal that our method performs well in identifying the true temporal estimates of LGT events. We applied our method to the genome-wide gene families for mollicutes and cyanobacteria, which gave an interesting insight into the potential LGTs highways. 

  • 93.
    Khan, Mehmood Alam
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Arvestad, Lars
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Phylogenetic Partitioning of Gene FamiliesManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Clustering and organizing molecular sequences is one of the central tasks in Bioinformatics. It is a common first step in, for example, phylogenomic analysis. For some tasks, a large gene family needs to be partitioned into more manageable subfamilies. In particular, Bayesian phylogenetic analysis can be very expensive. There is a need for easy and natural means of breaking up a gene family, with moderate computational requirements, to enable careful analysis of subfamilies with computationally expensive tools. We devised and implemented a method that infer and reconcile gene trees to species trees and identifies putative orthogroups as subfamilies. To achieve reasonable speed, approximate ML phylogenies are inferred using the FastTree method and combined with a subfamily-centered bootstrapping procedure to ensure robustness. Using the new method, very large clusters of sequences are now easier to manage in pipelines containing computationally expensive steps. The implementation of PhyloGenClust is available at a public repository, https://github.com/malagori/PhyloGenClust, under the GNU General Public License version 3. 

  • 94.
    Khan, Mehmood Alam
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Mahmudi, Owais
    KTH, Skolan för datavetenskap och kommunikation (CSC). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ulah, Ikram
    KTH, Skolan för datavetenskap och kommunikation (CSC). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Sweden.
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Probabilistic inference of lateral gene transfer events2016Ingår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 17, artikel-id 431Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge. Results: In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify "highways" of LGT. Conclusions: Based on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples.

  • 95. Khotyaintsev, Yu. V.
    et al.
    Divin, A.
    Vaivads, A.
    Andre, M.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Energy conversion at dipolarization fronts2017Ingår i: Geophysical Research Letters, ISSN 0094-8276, E-ISSN 1944-8007, Vol. 44, nr 3, s. 1234-1242Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We use multispacecraft observations by Cluster in the Earth's magnetotail and 3-D particle-in-cell simulations to investigate conversion of electromagnetic energy at the front of a fast plasma jet. We find that the major energy conversion is happening in the Earth (laboratory) frame, where the electromagnetic energy is being transferred from the electromagnetic field to particles. This process operates in a region with size of the order several ion inertial lengths across the jet front, and the primary contribution to E . j is coming from the motional electric field and the ion current. In the frame of the front we find fluctuating energy conversion with localized loads and generators at sub-ion scales which are primarily related to the lower hybrid drift instability excited at the front; however, these provide relatively small net energy conversion.

  • 96. Knight, James C.
    et al.
    Tully, Philip J.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Kaplan, Bernhard A.
    Lansner, Anders
    Furber, Steve B.
    Large-Scale Simulations of Plastic Neural Networks on Neuromorphic Hardware2016Ingår i: Frontiers in Neuroanatomy, ISSN 1662-5129, E-ISSN 1662-5129, Vol. 10, artikel-id 37Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Rather than using bespoke analog or digital hardware, the basic computational unit of a SpiNNaker system is a general-purpose ARM processor, allowing it to be programmed to simulate a wide variety of neuron and synapse models. This flexibility is particularly valuable in the study of biological plasticity phenomena. A recently proposed learning rule based on the Bayesian Confidence Propagation Neural Network (BCPNN) paradigm offers a generic framework for modeling the interaction of different plasticity mechanisms using spiking neurons. However, it can be computationally expensive to simulate large networks with BCPNN learning since it requires multiple state variables for each synapse, each of which needs to be updated every simulation time-step. We discuss the trade-offs in efficiency and accuracy involved in developing an event-based BCPNN implementation for SpiNNaker based on an analytical solution to the BCPNN equations, and detail the steps taken to fit this within the limited computational and memory resources of the SpiNNaker architecture. We demonstrate this learning rule by learning temporal sequences of neural activity within a recurrent attractor network which we simulate at scales of up to 2.0 x 10(4) neurons and 5.1 x 10(7) plastic synapses: the largest plastic neural network ever to be simulated on neuromorphic hardware. We also run a comparable simulation on a Cray XC-30 supercomputer system and find that, if it is to match the run-time of our SpiNNaker simulation, the super computer system uses approximately 45x more power. This suggests that cheaper, more power efficient neuromorphic systems are becoming useful discovery tools in the study of plasticity in large-scale brain models.

  • 97. Krishnasamy, E.
    et al.
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). BCAM - Basque Center for Applied Mathematics, Spain.
    Jansson, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). BCAM - Basque Center for Applied Mathematics, Spain.
    Direct FEM large scale computation of turbulent multiphase flow in urban water systems and marine energy2016Ingår i: ECCOMAS Congress 2016 - Proceedings of the 7th European Congress on Computational Methods in Applied Sciences and Engineering, National Technical University of Athens , 2016, s. 1339-1351Konferensbidrag (Refereegranskat)
    Abstract [en]

    High-Reynolds number turbulent incompressible multiphase flow represents a large class of engineering problems of key relevance to society. Here we describe our work on modeling two such problems: 1. The Consorcio de Aguas Bilbao Bizkaia is constructing a new storm tank system with an automatic cleaning system, based on periodically pushing tank water out in a tunnel 2. In the framework of the collaboration between BCAM - Basque Center for Applied Mathematics and Tecnalia R & I, the interaction of the sea flow with a semi submersible floating offshore wind platform is computationally investigated. We study the MARIA' benchmark modeling breaking waves over objects in marine environments. Both of these problems are modeled in the the Direct FEM/General Galerkin methodology for turbulent incompressible variable-densitv flow 1,2 in the FEniCS software framework.

  • 98.
    Kumar, Arvind
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Reprogramming the striatal stars: A new treatment option for Parkinson's disease2017Ingår i: Movement Disorders, ISSN 0885-3185, E-ISSN 1531-8257, Vol. 32, nr 7, s. 991-991Artikel i tidskrift (Refereegranskat)
  • 99. Lapenta, G.
    et al.
    Goldman, M.
    Newman, D.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Where should MMS look for electron diffusion regions?2016Ingår i: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 719, nr 1, artikel-id 12011Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A great possible achievement for the MMS mission would be crossing electron diffusion regions (EDR). EDR are regions in proximity of reconnection sites where electrons decouple from field lines, breaking the frozen in condition. Decades of research on reconnection have produced a widely shared map of where EDRs are. We expect reconnection to take place around a so called x-point formed by the intersection of the separatrices dividing inflowing from outflowing plasma. The EDR forms around this x-point as a small electron scale box nested inside a larger ion diffusion region. But this point of view is based on a 2D mentality. We have recently proposed that once the problem is considered in full 3D, secondary reconnection events can form [Lapenta et al., Nature Physics, 11, 690, 2015] in the outflow regions even far downstream from the primary reconnection site. We revisit here this new idea confirming that even using additional indicators of reconnection and even considering longer periods and wider distances the conclusion remains true: secondary reconnection sites form downstream of a reconnection outflow causing a sort of chain reaction of cascading reconnection sites. If we are right, MMS will have an interesting journey even when not crossing necessarily the primary site. The chances are greatly increased that even if missing a primary site during an orbit, MMS could stumble instead on one of these secondary sites.

  • 100. Lara, Pedro Valero
    et al.
    Pelayo, Fernando L.
    Jansson, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Basque Center for Applied Mathematics (BCAM), Spain.
    Introduction to the special issue on high performance computing solutions for complex problems2016Ingår i: Scalable Computing: Practice and Experience, ISSN 1895-1767, E-ISSN 1895-1767, Vol. 17, nr 1, s. III-IIIArtikel i tidskrift (Övrigt vetenskapligt)
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