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  • 101.
    Larsson, David
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik. KTH.
    Spühler, Jeannette Hiromi
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Petersson, Sven
    Karolinska Universitetssjukhuset.
    Nordenfur, Tim
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Colarieti-Tosti, Massimiliano
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Winter, Reidar
    Karolinska Institutet.
    Larsson, Matilda
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Patient-Specific Left Ventricular Flow Simulations From Transthoracic Echocardiography: Robustness Evaluation and Validation Against Ultrasound Doppler and Magnetic Resonance Imaging2017Ingår i: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 36, nr 11, s. 2261-2275Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The combination of medical imaging with computational fluid dynamics (CFD) has enabled the study of 3D blood flow on a patient-specificlevel. However, with models based on gated high-resolution data, the study of transient flows, and any model implementation into routine cardiac care, is challenging. The present paper presents a novel pathway for patient-specific CFD modelling of the left ventricle (LV), using 4D transthoracic echocardiography (TTE) as input modality. To evaluate the clinical usability, two sub-studies were performed. First, a robustness evaluation was performed where repeated models with alternating input variables were generated for 6 subjects and changes in simulated output quantified. Second, a validation study was carried out where the pathway accuracy was evaluated against pulsed-wave Doppler (100 subjects), and 2D through-plane phase-contrast magnetic resonance imaging measurements over 7 intraventricular planes (6 subjects). The robustness evaluation indicated a model deviation of <12%, with highest regional and temporal deviations at apical segments and at peak systole, respectively. The validation study showed an error of < 11% (velocities < 10 cm/s) for all subjects, with no significant regional or temporal differences observed. With the patient-specific pathway shown to provide robust output with high accuracy, and with the pathway dependent only on 4DTTE, the method has a high potential to be used within future clinical studies on 3D intraventricular flowpatterns. To this, future model developments in the form of e.g. anatomically accurate LV valves may further enhance the clinical value of the simulations.

  • 102.
    Lindahl, Mikael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Computational Dissection of the Basal Ganglia: functions and dynamics in health and disease2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The basal ganglia (BG), a group of nuclei in the forebrain of all vertebrates, are important for behavioral selection. BG receive contextual input from most cortical areas as well as from parts of the thalamus, and provide output to brain systems that are involved in the generation of behavior, i.e. the thalamus and the brain stem. Many neurological disorders such as Parkinson’s disease and Huntington’s disease, and several neuropsychiatric disorders, are related to BG. Studying BG enhances the understanding as to how behaviors are learned and modified. These insights can be used to improve treatments for several BG disorders, and to develop brain-inspired algorithms for solving special information-processing tasks.

     

    In this thesis modeling and simulations have been used to investigate function and dynamics of BG. In the first project a model was developed to explore a new hypothesis about how conflicts between competing actions are resolved in BG. It was proposed that a subsystem named the arbitration system, composed of the subthalamic nucleus (STN), pedunculopontine nucleus (PPN), the brain stem, central medial nucleus of thalamus (CM), globus pallidus interna (GPi) and globus pallidus externa (GPe), resolve basic conflicts between alternative motor programs. On top of the arbitration system there is a second subsystem named the extension systems, which involves the direct and indirect pathway of the striatum. This system can modify the output of the arbitration system to bias action selection towards outcomes dependent on contextual information.

     

    In the second project a model framework was developed in two steps, with the aim to gain a deeper understanding of how synapse dynamics, connectivity and neural excitability in the BG relate to function and dynamics in health and disease. First a spiking model of STN, GPe and substantia nigra pars reticulata (SNr), with emulated inputs from striatal medium spiny neurons (MSNs) and the cortex, was built and used to study how synaptic short-term plasticity affected action selection signaling in the direct-, hyperdirect- and indirect pathways. It was found that the functional consequences of facilitatory synapses onto SNr neurons are substantial, and only a few presynaptic MSNs can suppress postsynaptic SNr neurons. The model also predicted that STN signaling in SNr is mainly effective in a transient manner. The model was later extended with a striatal network, containing MSNs and fast spiking interneurons (FSNs), and modified to represent GPe with two types of neurons: type I, which projects downstream in BG, and type A, which have a back-projection to striatum. Furthermore, dopamine depletion dependent modification of connectivity and neuron excitability were added to the model. Using this extended BG model, it was found that FSNs and GPe type A neurons controlled excitability of striatal neurons during low cortical drive, whereas MSN collaterals have a greater impact at higher cortical drive. The indirect pathway increased the dynamical range over which two possible action commands were competing, while removing intrastriatal inhibition deteriorated action selection capabilities. Dopamine-depletion induced effects on spike synchronization and oscillations in the BG were also investigated here.

     

    For the final project, an abstract spiking BG model which included a hypothesized control of the reward signaling dopamine system was developed. This model incorporated dopamine-dependent synaptic plasticity, and used a plasticity rule based on probabilistic inference called Bayesian Confidence Propagation Neural Network (BCPNN). In this paradigm synaptic connections were controlled by gathering statistics about neural input and output activity. Synaptic weights were inferred using Bayes’ rule to estimate the confidence of future observations from the input. The model exhibits successful performance, measured as a moving average of correct selected actions, in a multiple-choice learning task with a changeable reward schedule. Furthermore, the model predicts a decreased performance upon dopamine lesioning, and suggests that removing the indirect pathway may disrupt learning in profound ways.

  • 103.
    Lindahl, Mikael
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hällgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Untangling basal ganglia network dynamics and function: role of dopamine depletion and inhibition investigated in a spiking network modelManuskript (preprint) (Övrigt vetenskapligt)
  • 104.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Discrete approximations of affine Gaussian receptive fields2017Rapport (Övrigt vetenskapligt)
    Abstract [en]

    This paper presents a theory for discretizing the affine Gaussian scale-space concept so that scale-space properties hold also for the discrete implementation.

    Two ways of discretizing spatial smoothing with affine Gaussian kernels are presented: (i) by solving semi-discretized affine diffusion equation as derived by necessity from the requirement of a semi-group structure over a continuum of scale parameters as parameterized by a family of spatial covariance matrices and obeying non-creation of new structures from any finer to any coarser scale as formalized by the requirement of non-enhancement of local extrema and (ii) a set of parameterized 3x3-kernels as derived from an additional discretization of the above theory along the scale direction and with the parameters of the kernels having a direct interpretation in terms of the covariance matrix of the composed discrete smoothing operation.

    We show how convolutions with the first family of kernels can be implemented in terms of a closed form expression for the Fourier transform and analyse how a remaining degree of freedom in the theory can be explored to ensure a positive discretization and optionally also achieve higher-order discrete approximation of the angular dependency of the shapes of the affine Gaussian kernels.

    We do also show how discrete directional derivative approximations can be efficiently implemented to approximate affine Gaussian derivatives as constituting a canonical model for receptive fields over a purely spatial image domain and with close relations to receptive fields in biological vision.

  • 105.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Discrete approximations of the affine Gaussian derivative model for visual receptive fields2017Rapport (Övrigt vetenskapligt)
    Abstract [en]

    The affine Gaussian derivative model can in several respects be regarded as a canonical model for receptive fields over a spatial image domain: (i) it can be derived by necessity from scale-space axioms that reflect structural properties of the world, (ii) it constitutes an excellent model for the receptive fields of simple cells in the primary visual cortex and (iii) it is covariant under affine image deformations, which enables more accurate modelling of image measurements under the local image deformations caused by the perspective mapping, compared to the more commonly used Gaussian derivative model based on derivatives of the rotationally symmetric Gaussian kernel.

    This paper presents a theory for discretizing the affine Gaussian scale-space concept underlying the affine Gaussian derivative model, so that scale-space properties hold also for the discrete implementation.

    Two ways of discretizing spatial smoothing with affine Gaussian kernels are presented: (i) by solving a semi-discretized affine diffusion equation, which has derived by necessity from the requirements of a semi-group structure over scale as parameterized by a family of spatial covariance matrices and obeying non-creation of new structures from any finer to any coarser scale in terms of non-enhancement of local extrema and (ii) approximating these semi-discrete affine receptive fields by parameterized families of 3x3-kernels as obtained from an additional discretization along the scale direction. The latter discrete approach can be optionally complemented by spatial subsampling at coarser scales, leading to the notion of affine hybrid pyramids.

    For the first approach, we show how the solutions can be computed from a closed form expression for the Fourier transform, and analyse how a remaining degree of freedom in the theory can be explored to ensure a positive discretization and optionally achieve higher-order discrete approximation of the angular dependency of the discrete affine Gaussian receptive fields. For the second approach, we analyse how the step length in the scale direction can be determined, given the requirements of a positive discretization.

    We do also show how discrete directional derivative approximations can be efficiently implemented to approximate affine Gaussian derivatives. Using these theoretical results, we outline hybrid architectures for discrete approximations of affine covariant receptive field families, to be used as a first processing layer for affine covariant and affine invariant visual operations at higher levels.

  • 106.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Normative theory of visual receptive fields2017Rapport (Övrigt vetenskapligt)
    Abstract [en]

    This article gives an overview of a normative computational theory of visual receptive fields, by which idealized shapes of early spatial, spatio-chromatic and spatio-temporal receptive fields can be derived in an axiomatic way based on structural properties of the environment in combination with assumptions about the internal structure of a vision system to guarantee consistent handling of image representations over multiple spatial and temporal scales. Interestingly, this theory leads to predictions about visual receptive field shapes with qualitatively very good similarity to biological receptive fields measured in the retina, the LGN and the primary visual cortex (V1) of mammals.

  • 107.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Spatio-temporal scale selection in video data2017Ingår i: Scale Space and Variational Methods in Computer Vision, Springer-Verlag Tokyo Inc., 2017, Vol. 10302, s. 3-15Konferensbidrag (Refereegranskat)
    Abstract [en]

    We present a theory and a method for simultaneous detection of local spatial and temporal scales in video data. The underlying idea is that if we process video data by spatio-temporal receptive fields at multiple spatial and temporal scales, we would like to generate hypotheses about the spatial extent and the temporal duration of the underlying spatio-temporal image structures that gave rise to the feature responses.

    For two types of spatio-temporal scale-space representations, (i) a non-causal Gaussian spatio-temporal scale space for offline analysis of pre-recorded video sequences and (ii) a time-causal and time-recursive spatio-temporal scale space for online analysis of real-time video streams, we express sufficient conditions for spatio-temporal feature detectors in terms of spatio-temporal receptive fields to deliver scale covariant and scale invariant feature responses.

    A theoretical analysis is given of the scale selection properties of six types of spatio-temporal interest point detectors, showing that five of them allow for provable scale covariance and scale invariance. Then, we describe a time-causal and time-recursive algorithm for detecting sparse spatio-temporal interest points from video streams and show that it leads to intuitively reasonable results.

  • 108.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Spatio-temporal scale selection in video data2018Ingår i: Journal of Mathematical Imaging and Vision, ISSN 0924-9907, E-ISSN 1573-7683, Vol. 60, nr 4, s. 525-562Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This work presents a theory and methodology for simultaneous detection of local spatial and temporal scales in video data. The underlying idea is that if we process video data by spatio-temporal receptive fields at multiple spatial and temporal scales, we would like to generate hypotheses about the spatial extent and the temporal duration of the underlying spatio-temporal image structures that gave rise to the feature responses.

    For two types of spatio-temporal scale-space representations, (i) a non-causal Gaussian spatio-temporal scale space for offline analysis of pre-recorded video sequences and (ii) a time-causal and time-recursive spatio-temporal scale space for online analysis of real-time video streams, we express sufficient conditions for spatio-temporal feature detectors in terms of spatio-temporal receptive fields to deliver scale covariant and scale invariant feature responses.

    We present an in-depth theoretical analysis of the scale selection properties of eight types of spatio-temporal interest point detectors in terms of either: (i)-(ii) the spatial Laplacian applied to the first- and second-order temporal derivatives, (iii)-(iv) the determinant of the spatial Hessian applied to the first- and second-order temporal derivatives, (v) the determinant of the spatio-temporal Hessian matrix, (vi) the spatio-temporal Laplacian and (vii)-(viii) the first- and second-order temporal derivatives of the determinant of the spatial Hessian matrix. It is shown that seven of these spatio-temporal feature detectors allow for provable scale covariance and scale invariance. Then, we describe a time-causal and time-recursive algorithm for detecting sparse spatio-temporal interest points from video streams and show that it leads to intuitively reasonable results.

    An experimental quantification of the accuracy of the spatio-temporal scale estimates and the amount of temporal delay obtained these spatio-temporal interest point detectors is given showing that: (i) the spatial and temporal scale selection properties predicted by the continuous theory are well preserved in the discrete implementation and (ii) the spatial Laplacian or the determinant of the spatial Hessian applied to the first- and second-order temporal derivatives lead to much shorter temporal delays in a time-causal implementation compared to the determinant of the spatio-temporal Hessian or the first- and second-order temporal derivatives of the determinant of the spatial Hessian matrix.

  • 109.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Temporal scale selection in time-causal scale space2017Ingår i: Journal of Mathematical Imaging and Vision, ISSN 0924-9907, E-ISSN 1573-7683, Vol. 58, nr 1, s. 57-101Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    When designing and developing scale selection mechanisms for generating hypotheses about characteristic scales in signals, it is essential that the selected scale levels reflect the extent of the underlying structures in the signal.

    This paper presents a theory and in-depth theoretical analysis about the scale selection properties of methods for automatically selecting local temporal scales in time-dependent signals based on local extrema over temporal scales of scale-normalized temporal derivative responses. Specifically, this paper develops a novel theoretical framework for performing such temporal scale selection over a time-causal and time-recursive temporal domain as is necessary when processing continuous video or audio streams in real time or when modelling biological perception.

    For a recently developed time-causal and time-recursive scale-space concept defined by convolution with a scale-invariant limit kernel, we show that it is possible to transfer a large number of the desirable scale selection properties that hold for the Gaussian scale-space concept over a non-causal temporal domain to this temporal scale-space concept over a truly time-causal domain. Specifically, we show that for this temporal scale-space concept, it is possible to achieve true temporal scale invariance although the temporal scale levels have to be discrete, which is a novel theoretical construction.

    The analysis starts from a detailed comparison of different temporal scale-space concepts and their relative advantages and disadvantages, leading the focus to a class of recently extended time-causal and time-recursive temporal scale-space concepts based on first-order integrators or equivalently truncated exponential kernels coupled in cascade. Specifically, by the discrete nature of the temporal scale levels in this class of time-causal scale-space concepts, we study two special cases of distributing the intermediate temporal scale levels, by using either a uniform distribution in terms of the variance of the composed temporal scale-space kernel or a logarithmic distribution.

    In the case of a uniform distribution of the temporal scale levels, we show that scale selection based on local extrema of scale-normalized derivatives over temporal scales makes it possible to estimate the temporal duration of sparse local features defined in terms of temporal extrema of first- or second-order temporal derivative responses. For dense features modelled as a sine wave, the lack of temporal scale invariance does, however, constitute a major limitation for handling dense temporal structures of different temporal duration in a uniform manner.

    In the case of a logarithmic distribution of the temporal scale levels, specifically taken to the limit of a time-causal limit kernel with an infinitely dense distribution of the temporal scale levels towards zero temporal scale, we show that it is possible to achieve true temporal scale invariance to handle dense features modelled as a sine wave in a uniform manner over different temporal durations of the temporal structures as well to achieve more general temporal scale invariance for any signal over any temporal scaling transformation with a temporal scaling factor that is an integer power of the distribution parameter of the time-causal limit kernel.

    It is shown how these temporal scale selection properties developed for a pure temporal domain carry over to feature detectors defined over time-causal spatio-temporal and spectro-temporal domains.

  • 110.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Time-causal and time-recursive receptive fields for invariance and covariance under natural image transformations2016Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    Due to the huge variability of image information under natural image transformations, the receptive field responses of the local image operations that serve as input to higher level visual processes will in general be strongly dependent on the geometric and illumination conditions in the image formation process. To obtain robustness of a vision system, it is natural to require the receptive field families underlying the image operators to be either invariant or covariant under the relevant families of natural image transformations.

    This talk presents an improved model and theory for time-causal and time-recursive spatio-temporal receptive fields, obtained by a combination of Gaussian receptive fields over the spatial domain and first-order integrators or equivalently truncated exponential filters coupled in cascade over the temporal domain. This model inherits the theoretically attractive properties of the Gaussian scale-space model over a spatial domain in terms of (i) invariance or covariance of receptive field responses under scaling transformation and affine transformations over the spatial domain combined with (ii) non-creation of new image structures from finer to coarser scales. When complemented by velocity adaptation the receptive field responses can be made (iii) Galilean covariant or invariant to account for unknown or variable relative motions between objects in the world and the observer. Additionally when expressed over a logarithmic distribution of the temporal scale levels, this model allows for (iv) scale invariance and self-similarity over the temporal domain while simultaneously expressed over a time-causal and time-recursive temporal domain, which is a theoretically new type of construction.

    We propose this axiomatically derived theory as the natural extension of the Gaussian scale-space paradigm for local image operations from a spatial domain to a time-causal spatio-temporal domain, to be used as a general framework for expressing spatial and spatio-temporal image operators for a computer vision system. The theory leads to (v) predictions about spatial and spatio-temporal receptive fields with good qualitative similarity to biological receptive fields measured by cell recordings in the retina, the lateral geniculate nucleus (LGN) and the primary visual cortex (V1). Specifically, this framework allows for (vi) computationally efficient real-time operations and leads to (vii) much better temporal dynamics (shorter temporal delays) compared to previously formulated time-causal temporal scale-space models.

    Reference:

    Lindeberg (2016) "Time-causal and time-recursive spatio-temporal receptive fields", Journal of Mathematical Imaging and Vision, 55(1): 50-88.

  • 111.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Time-causal and time-recursive spatio-temporal receptive fields for computer vision and computational modelling of biological vision2016Ingår i: International Workshop on Geometry, PDE’s and Lie Groups in Image Analysis, Eindhoven, The Netherlands, August 24-26, 2016., 2016Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    When operating on time-dependent image information in real time, a fundamental constraint originates from the fact that image operations must be both time-causal and time-recursive.

    In this talk, we will present an improved model and theory for time-causal and time-recursive spatio-temporal receptive fields, obtained by a combination of Gaussian filters over the spatial domain and first-order integrators or equivalently truncated exponential filters coupled in cascade over the temporal domain. This receptive field family obeys scale-space axiomatics in the sense of non-enhancement of local extrema over the spatial domain and non-creation of new local extrema over time for any purely temporal signal and does in these respects guarantee theoretically well-founded treatment of spatio-temporal image structures at different spatial and temporal scales.

    By a logarithmic distribution of the temporal scale levels in combination with the construction of a time-causal limit kernel based on an infinitely dense distribution of the temporal scale levels towards zero temporal scale, it will be shown that this family allows for temporal scale invariance although the temporal scale levels by the theory have to be discrete. Additionally, the family obeys basic invariance or covariance properties under other classes of natural image transformations including spatial scaling transformations, rotations/affine image deformations over the spatial domain, Galilean transformations of space time and local multiplicative intensity transformations. Thereby, this receptive field family allows for the formulation of multi-scale differential geometric image features with invariance or covariance properties under basic classes of natural image transformations over space-time.

    It is shown how this spatio-temporal scale-space concept (i) allows for efficient computation of different types of spatio-temporal features for purposes in computer vision and (ii) leads to predictions about biological receptive fields with good qualitative similarities to the results of cell recordings in the lateral geniculate nucleus (LGN) and the primary visual cortex (V1) in biological vision.

    References:

    T. Lindeberg (2016) ”Time-causal and time-recursive spatio-temporal receptive fields”, Journal of Mathematical Imaging and Vision, 55(1): 50-88.

    T. Lindeberg (2013) ”A computational theory of visual receptive fields”, Biological Cybernetics, 107(6): 589–635.

    T. Lindeberg (2013) ”Invariance of visual operations at the level of receptive fields”, PLOS One, 8(7): e66990.

    T. Lindeberg (2011) ”Generalized Gaussian scale-space axiomatics comprising linear scale space, affine scale space and spatio-temporal scale space”, Journal of Mathematical Imaging and Vision, 40(1): 36–81.

  • 112.
    Lindkvist, Emelie
    et al.
    Stockholm Resilience Centre, Stockholm University.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Norberg, Jon
    Stockholm Resilience Centre, Stockholm University.
    Strategies for sustainable management of renewable resources during environmental change2017Ingår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, artikel-id 20162762Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    As a consequence of global environmental change, management strategies that can deal with unexpected change in resource dynamics are becoming increasingly important. In this paper we undertake a novel approach to studying resource growth problems using a computational form of adaptive management to find optimal strategies for prevalent natural resource management dilemmas. We scrutinize adaptive management, or learning-by-doing, to better understand how to simultaneously manage and learn about a system when its dynamics are unknown. We study important trade-offs in decision-making with respect to choosing optimal actions (harvest efforts) for sustainable management during change. This is operationalized through an artificially intelligent model where we analyze how different trends and fluctuations in growth rates of a renewable resource affect the performance of different management strategies. Our results show that the optimal strategy for managing resources with declining growth is capable of managing resources with fluctuating or increasing growth at a negligible cost, creating in a management strategy that is both efficient and robust towards future unknown changes. To obtain this strategy, adaptive management should strive for: high learning rates to new knowledge, high valuation of future outcomes and modest exploration around what is perceived as the optimal action.

  • 113. Lundqvist, Mikael
    et al.
    Rose, Jonas
    Herman, Pawel
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Brincat, Scott L.
    Buschman, Timothy J.
    Miller, Earl K.
    Gamma and Beta Bursts Underlie Working Memory2016Ingår i: Neuron, ISSN 0896-6273, E-ISSN 1097-4199, Vol. 90, nr 1, s. 152-164Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Working memory is thought to result from sustained neuron spiking. However, computational models suggest complex dynamics with discrete oscillatory bursts. We analyzed local field potential (LFP) and spiking from the prefrontal cortex (PFC) of monkeys performing a working memory task. There were brief bursts of narrow-band gamma oscillations (45-100 Hz), varied in time and frequency, accompanying encoding and re-activation of sensory information. They appeared at a minority of recording sites associated with spiking reflecting the to-be-remembered items. Beta oscillations (20-35 Hz) also occurred in brief, variable bursts but reflected a default state interrupted by encoding and decoding. Only activity of neurons reflecting encoding/decoding correlated with changes in gamma burst rate. Thus, gamma bursts could gate access to, and prevent sensory interference with, working memory. This supports the hypothesis that working memory is manifested by discrete oscillatory dynamics and spiking, not sustained activity.

  • 114. Maes, Alexandre
    et al.
    Céline, Gracia
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Zhang, Kaiyang
    Aalto University, Finland .
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hajnsdorf, Eliane
    Landscape of RNA polyadenylation in E. coli2016Ingår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Polyadenylation is involved in degradation and quality control of bacterial RNAs. We used a combination of 5’-tagRACE and RNA-seq to analyse the total RNA content from wild-type strain and from mutant deficient for poly(A)polymerase. We determined that 157 mRNAs were affected as well as non-coding transcripts, up- and downregulated in the mutant when compared to the wild-type strain. Antisense RNAs were also detected and differentially affected by polyadenylation.

    Our results clearly reveal a correlation between the RNA folding energy and the requirement of polyadenylation to achieve the RNA decay. A new algorithm was developed to detect in both strains posttranscriptional modifications based on unmappable 3’-ends to analyse their position and composition. Therefore, any RNA 3'-end can be polyadenylated addressing them to the exoribonucleolytic machinery which is essential to degrade structured RNAs. Importantly, poly(A)polymerase was also upregulating the expression of genes related with the entire FliA regulon and numerous membrane transporters while downregulating the expression of the antigen 43 (flu), numerous sRNAs, antisense transcripts, REP sequences with the accumulation of numerous RNA fragments resulting from the processing of entire transcripts. Altogether we show here that polyadenylation has a broader spectrum of action than was suspected until now.

  • 115. Manzini, G.
    et al.
    Delzanno, G. L.
    Vencels, J.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    A Legendre-Fourier spectral method with exact conservation laws for the Vlasov-Poisson system2016Ingår i: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 317, s. 82-107Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present the design and implementation of an L-2-stable spectral method for the discretization of the Vlasov-Poisson model of a collisionless plasma in one space and velocity dimension. The velocity and space dependence of the Vlasov equation are resolved through a truncated spectral expansion based on Legendre and Fourier basis functions, respectively. The Poisson equation, which is coupled to the Vlasov equation, is also resolved through a Fourier expansion. The resulting system of ordinary differential equation is discretized by the implicit second-order accurate Crank-Nicolson time discretization. The non-linear dependence between the Vlasov and Poisson equations is iteratively solved at any time cycle by a Jacobian-Free Newton-Krylov method. In this work we analyze the structure of the main conservation laws of the resulting Legendre-Fourier model, e.g., mass, momentum, and energy, and prove that they are exactly satisfied in the semi-discrete and discrete setting. The L-2-stability of the method is ensured by discretizing the boundary conditions of the distribution function at the boundaries of the velocity domain by a suitable penalty term. The impact of the penalty term on the conservation properties is investigated theoretically and numerically. An implementation of the penalty term that does not affect the conservation of mass, momentum and energy, is also proposed and studied. A collisional term is introduced in the discrete model to control the filamentation effect, but does not affect the conservation properties of the system. Numerical results on a set of standard test problems illustrate the performance of the method.

  • 116. Marino, Raffaele
    et al.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry2016Ingår i: PHYSICAL REVIEW E, ISSN 2470-0045, Vol. 93, nr 6, artikel-id 062147Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We consider coupled diffusions in n-dimensional space and on a compact manifold and the resulting effective advective-diffusive motion on large scales in space. The effective drift (advection) and effective diffusion are determined as a solvability conditions in a multiscale analysis. As an example, we consider coupled diffusions in three-dimensional space and on the group manifold SO(3) of proper rotations, generalizing results obtained by H. Brenner [J. Colloid Interface Sci. 80, 548 (1981)]. We show in detail how the analysis can be conveniently carried out using local charts and invariance arguments. As a further example, we consider coupled diffusions in two-dimensional complex space and on the group manifold SU(2). We show that although the local operators may be the same as for SO(3), due to the global nature of the solvability conditions the resulting diffusion will differ and generally be more isotropic.

  • 117. Marino, Raffaele
    et al.
    Eichhorn, Ralf
    KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Skolan för elektro- och systemteknik (EES), Centra, ACCESS Linnaeus Centre. Aalto University, Espoo, Finland.
    Entropy production of a Brownian ellipsoid in the overdamped limit2016Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 93, nr 1, artikel-id 012132Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We analyze the translational and rotational motion of an ellipsoidal Brownian particle from the viewpoint of stochastic thermodynamics. The particle's Brownian motion is driven by external forces and torques and takes place in an heterogeneous thermal environment where friction coefficients and (local) temperature depend on space and time. Our analysis of the particle's stochastic thermodynamics is based on the entropy production associated with single particle trajectories. It is motivated by the recent discovery that the overdamped limit of vanishing inertia effects (as compared to viscous fricion) produces a so-called "anomalous" contribution to the entropy production, which has no counterpart in the overdamped approximation, when inertia effects are simply discarded. Here we show that rotational Brownian motion in the overdamped limit generates an additional contribution to the "anomalous" entropy. We calculate its specific form by performing a systematic singular perturbation analysis for the generating function of the entropy production. As a side result, we also obtain the (well-known) equations of motion in the overdamped limit. We furthermore investigate the effects of particle shape and give explicit expressions of the "anomalous entropy" for prolate and oblate spheroids and for near-spherical Brownian particles.

  • 118.
    Marino, Raffaele
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Parisi, G.
    Ricci-Tersenghi, F.
    The backtracking survey propagation algorithm for solving random K-SAT problems2016Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, artikel-id 12996Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Discrete combinatorial optimization has a central role in many scientific disciplines, however, for hard problems we lack linear time algorithms that would allow us to solve very large instances. Moreover, it is still unclear what are the key features that make a discrete combinatorial optimization problem hard to solve. Here we study random K-satisfiability problems with K=3,4, which are known to be very hard close to the SAT-UNSAT threshold, where problems stop having solutions. We show that the backtracking survey propagation algorithm, in a time practically linear in the problem size, is able to find solutions very close to the threshold, in a region unreachable by any other algorithm. All solutions found have no frozen variables, thus supporting the conjecture that only unfrozen solutions can be found in linear time, and that a problem becomes impossible to solve in linear time when all solutions contain frozen variables.

  • 119.
    Markidis, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Peng, Ivy Bo
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Larsson Träff, Jesper
    Rougier, Antoine
    Bartsch, Valeria
    Machado, Rui
    Rahn, Mirko
    Hart, Alistair
    Holmes, Daniel
    Bull, Mark
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    The EPiGRAM Project: Preparing Parallel Programming Models for Exascale2016Ingår i: HIGH PERFORMANCE COMPUTING, ISC HIGH PERFORMANCE 2016 INTERNATIONAL WORKSHOPS, Springer, 2016, s. 56-68Konferensbidrag (Refereegranskat)
    Abstract [en]

    EPiGRAM is a European Commission funded project to improve existing parallel programming models to run efficiently large scale applications on exascale supercomputers. The EPiGRAM project focuses on the two current dominant petascale programming models, message-passing and PGAS, and on the improvement of two of their associated programming systems, MPI and GASPI. In EPiGRAM, we work on two major aspects of programming systems. First, we improve the performance of communication operations by decreasing the memory consumption, improving collective operations and introducing emerging computing models. Second, we enhance the interoperability of message-passing and PGAS by integrating them in one PGAS-based MPI implementation, called EMPI4Re, implementing MPI endpoints and improving GASPI interoperability with MPI. The new EPiGRAM concepts are tested in two large-scale applications, iPIC3D, a Particle-in-Cell code for space physics simulations, and Nek5000, a Computational Fluid Dynamics code.

  • 120.
    Markidis, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Peng, Ivybo
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Iakymchuk, Roman
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Kestor, G.
    Gioiosa, R.
    A performance characterization of streaming computing on supercomputers2016Ingår i: Procedia Computer Science, Elsevier, 2016, s. 98-107Konferensbidrag (Refereegranskat)
    Abstract [en]

    Streaming computing models allow for on-the-y processing of large data sets. With the increased demand for processing large amount of data in a reasonable period of time, streaming models are more and more used on supercomputers to solve data-intensive problems. Because supercomputers have been mainly used for compute-intensive workload, supercomputer performance metrics focus on the number of oating point operations in time and cannot fully characterize a streaming application performance on supercomputers. We introduce the injection and processing rates as the main metrics to characterize the performance of streaming computing on supercomputers. We analyze the dynamics of these quantities in a modi ed STREAM benchmark developed atop of an MPI streaming library in a series of di erent congurations. We show that after a brief transient the injection and processing rates converge to sustained rates. We also demonstrate that streaming computing performance strongly depends on the number of connections between data producers and consumers and on the processing task granularity.

  • 121. Mbuvha, R.
    et al.
    Jonsson, M.
    Ehn, N.
    Herman, Pawel
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Bayesian neural networks for one-hour ahead wind power forecasting2017Ingår i: 2017 6th International Conference on Renewable Energy Research and Applications, ICRERA 2017, Institute of Electrical and Electronics Engineers (IEEE), 2017, Vol. 2017, s. 591-596Konferensbidrag (Refereegranskat)
    Abstract [en]

    The greatest concern facing renewable energy sources like wind is the uncertainty in production volumes as their generation ability is inherently dependent on weather conditions. When providing forecasts for newly commissioned wind farms there is a limited amount of historical power production data, while the number of potential features from different weather forecast providers is vast. Bayesian regularization is therefore seen as a possible technique for reducing model overfitting problems that may arise. This work investigates Bayesian Neural Networks for one-hour ahead forecasting of wind power generation. Initial results show that Bayesian Neural Networks display equivalent predictive performance to Neural Networks trained by Maximum Likelihood. Further results show that Bayesian Neural Networks become superior after removing irrelevant features using Automatic Relevance Determination(ARD).

  • 122. Micallef, Luana
    et al.
    Palmas, Gregorio
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Oulasvirta, Antti
    Weinkauf, Tino
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Towards Perceptual Optimization of the Visual Design of Scatterplots2017Ingår i: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 23, nr 6, s. 1588-1599Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Designing a good scatterplot can be difficult for non-experts in visualization, because they need to decide on many parameters, such as marker size and opacity, aspect ratio, color, and rendering order. This paper contributes to research exploring the use of perceptual models and quality metrics to set such parameters automatically for enhanced visual quality of a scatterplot. A key consideration in this paper is the construction of a cost function to capture several relevant aspects of the human visual system, examining a scatterplot design for some data analysis task. We show how the cost function can be used in an optimizer to search for the optimal visual design for a user's dataset and task objectives (e.g., "reliable linear correlation estimation is more important than class separation"). The approach is extensible to different analysis tasks. To test its performance in a realistic setting, we pre-calibrated it for correlation estimation, class separation, and outlier detection. The optimizer was able to produce designs that achieved a level of speed and success comparable to that of those using human-designed presets (e.g., in R or MATLAB). Case studies demonstrate that the approach can adapt a design to the data, to reveal patterns without user intervention.

  • 123. Mirzaei, Amin
    et al.
    Kumar, Arvind
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). University of Freiburg, Germany.
    Leventhal, Daniel
    Mallet, Nicolas
    Aertsen, Ad
    Berke, Joshua
    Schmidt, Robert
    Sensorimotor Processing in the Basal Ganglia Leads to Transient Beta Oscillations during Behavior2017Ingår i: Journal of Neuroscience, ISSN 0270-6474, E-ISSN 1529-2401, Vol. 37, nr 46, s. 11220-11232Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Brief epochs of beta oscillations have been implicated in sensorimotor control in the basal ganglia of task-performing healthy animals. However, which neural processes underlie their generation and how they are affected by sensorimotor processing remains unclear. To determine the mechanisms underlying transient beta oscillations in the LFP, we combined computational modeling of the subthalamo-pallidal network for the generation of beta oscillations with realistic stimulation patterns derived from single-unit data recorded from different basal ganglia subregions in rats performing a cued choice task. In the recordings, we found distinct firing patterns in the striatum, globus pallidus, and subthalamic nucleus related to sensory and motor events during the behavioral task. Using these firing patterns to generate realistic inputs to our network model led to transient beta oscillations with the same time course as the rat LFP data. In addition, our model can account for further nonintuitive aspects of beta modulation, including beta phase resets after sensory cues and correlations with reaction time. Overall, our model can explain how the combination of temporally regulated sensory responses of the subthalamic nucleus, ramping activity of the subthalamic nucleus, and movement-related activity of the globus pallidus leads to transient beta oscillations during behavior.

  • 124. Molnos, Sonja
    et al.
    Mamdouh, Tarek
    Petri, Stefan
    Nocke, Thomas
    Weinkauf, Tino
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Coumou, Dim
    A network-based detection scheme for the jet stream core2017Ingår i: Earth System Dynamics, ISSN 2190-4979, E-ISSN 2190-4987, Vol. 8, nr 1, s. 75-89Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The polar and subtropical jet streams are strong upper-level winds with a crucial influence on weather throughout the Northern Hemisphere midlatitudes. In particular, the polar jet is located between cold arctic air to the north and warmer subtropical air to the south. Strongly meandering states therefore often lead to extreme surface weather. Some algorithms exist which can detect the 2-D (latitude and longitude) jets' core around the hemisphere, but all of them use a minimal threshold to determine the subtropical and polar jet stream. This is particularly problematic for the polar jet stream, whose wind velocities can change rapidly from very weak to very high values and vice versa. We develop a network-based scheme using Dijkstra's shortest-path algorithm to detect the polar and subtropical jet stream core. This algorithm not only considers the commonly used wind strength for core detection but also takes wind direction and climatological latitudinal position into account. Furthermore, it distinguishes between polar and subtropical jet, and between separate and merged jet states. The parameter values of the detection scheme are optimized using simulated annealing and a skill function that accounts for the zonal-mean jet stream position (Rikus, 2015). After the successful optimization process, we apply our scheme to reanalysis data covering 1979-2015 and calculate seasonal-mean probabilistic maps and trends in wind strength and position of jet streams. We present longitudinally defined probability distributions of the positions for both jets for all on the Northern Hemisphere seasons. This shows that winter is characterized by two well-separated jets over Europe and Asia (ca. 20 degrees W to 140 degrees E). In contrast, summer normally has a single merged jet over the western hemisphere but can have both merged and separated jet states in the eastern hemisphere. With this algorithm it is possible to investigate the position of the jets' cores around the hemisphere and it is therefore very suitable to analyze jet stream patterns in observations and models, enabling more advanced model-validation.

  • 125.
    Muhammad, Sayyed Auwn
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Probabilistic Modelling of Domain and Gene Evolution2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Phylogenetic inference relies heavily on statistical models that have been extended and refined over the past years into complex hierarchical models to capture the intricacies of evolutionary processes. The wealth of information in the form of fully sequenced genomes has led to the development of methods that are used to reconstruct the gene and species evolutionary histories in greater and more accurate detail. However, genes are composed of evolutionary conserved sequence segments called domains, and domains can also be affected by duplications, losses, and bifurcations implied by gene or species evolution. This thesis proposes an extension of evolutionary models, such as duplication-loss, rate, and substitution, that have previously been used to model gene evolution, to model the domain evolution.

    In this thesis, I am proposing DomainDLRS: a comprehensive, hierarchical Bayesian method, based on the DLRS model by Åkerborg et al., 2009, that models domain evolution as occurring inside the gene and species tree. The method incorporates a birth-death process to model the domain duplications and losses along with a domain sequence evolution model with a relaxed molecular clock assumption. The method employs a variant of Markov Chain Monte Carlo technique called, Grouped Independence Metropolis-Hastings for the estimation of posterior distribution over domain and gene trees. By using this method, we performed analyses of Zinc-Finger and PRDM9 gene families, which provides an interesting insight of domain evolution.

    Finally, a synteny-aware approach for gene homology inference, called GenFamClust, is proposed that uses similarity and gene neighbourhood conservation to improve the homology inference. We evaluated the accuracy of our method on synthetic and two biological datasets consisting of Eukaryotes and Fungal species. Our results show that the use of synteny with similarity is providing a significant improvement in homology inference.

  • 126.
    Muhammad, Sayyed Auwn
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Sennblad, Bengt
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Species tree aware simultaneous reconstruction of gene and domain evolutionManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Most genes are composed of multiple domains with a common evolutionary history that typically perform a specific function in the resulting protein. As witnessed by many studies of key gene families, it is important to understand how domains have been duplicated, lost, transferred between genes, and rearranged. Similarly to the case of evolutionary events affecting entire genes, these domain events have large consequences for phylogenetic reconstruction and, in addition, they create considerable obstacles for gene sequence alignment algorithms, a prerequisite for phylogenetic reconstruction.

    We introduce the Domain-DLRS model, a hierarchical, generative probabilistic model containing three levels corresponding to species, genes, and domains, respectively. From a dated species tree, a gene tree is generated according to the DL model, which is a birth-death model generalized to occur in a dated tree. Then, from the dated gene tree, a pre-specified number of dated domain trees are generated using the DL model and the molecular clock is relaxed, effectively converting edge times to edge lengths. Finally, for each domain tree and its lengths, domain sequences are generated for the leaves based on a selected model of sequence evolution.

    For this model, we present a MCMC based inference framework called Domain-DLRS that as input takes a dates species tree together with a multiple sequence alignment for each domain family, while it as output provids an estimated posterior distribution over reconciled gene and domain trees. By requiring aligned domains rather than genes, our framework evades the problem of aligning genes that have been exposed to domain duplications, in particular non-tandem domain duplications. We show that Domain-DLRS performs better than MrBayes on synthetic data and that it outperforms MrBayes on biological data. We analyse several zinc-finger genes and show that most domain duplications have been tandem duplications, of which some have involved two or more domains, but non-tandem duplications have also been common, in particular in gene families of complex evolutionary history such as PRDM9.

  • 127. Munteanu, C.
    et al.
    Molyneaux, H.
    Moncur, W.
    Romero, Mario
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Georgia Institute of Technology.
    O'Donnell, S.
    Vines, J.
    Situational ethics: Re-thinking approaches to formal ethics requirements for human-computer interaction2015Ingår i: Conference on Human Factors in Computing Systems - Proceedings, Association for Computing Machinery (ACM), 2015, s. 105-114Konferensbidrag (Refereegranskat)
    Abstract [en]

    Most Human-Computer Interaction (HCI) researchers are accustomed to the process of formal ethics review for their evaluation or field trial protocol. Although this process varies by country, the underlying principles are universal. While this process is often a formality, for field research or lab-based studies with vulnerable users, formal ethics requirements can be challenging to navigate - A common occurrence in the social sciences; yet, in many cases, foreign to HCI researchers. Nevertheless, with the increase in new areas of research such as mobile technologies for marginalized populations or assistive technologies, this is a current reality. In this paper we present our experiences and challenges in conducting several studies that evaluate interactive systems in difficult settings, from the perspective of the ethics process. Based on these, we draft recommendations for mitigating the effect of such challenges to the ethical conduct of research. We then issue a call for interaction researchers, together with policy makers, to refine existing ethics guidelines and protocols in order to more accurately capture the particularities of such field-based evaluations, qualitative studies, challenging labbased evaluations, and ethnographic observations.

  • 128. Mushtaq, M.
    et al.
    Ali, Raja Hashim
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Kashuba, V.
    Klein, G.
    Kashuba, E.
    S18 family of mitochondrial ribosomal proteins: Evolutionary history and Gly132 polymorphism in colon carcinoma2016Ingår i: OncoTarget, ISSN 1949-2553, E-ISSN 1949-2553, Vol. 7, nr 34, s. 55649-55662Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    S18 family of mitochondrial ribosomal proteins (MRPS18, S18) consists of three members, S18-1 to -3. Earlier, we found that overexpression of S18-2 protein resulted in immortalization and eventual transformation of primary rat fibroblasts. The S18-1 and -3 have not exhibited such abilities. To understand the differences in protein properties, the evolutionary history of S18 family was analyzed. The S18-3, followed by S18-1 and S18-2 emerged as a result of ancient gene duplication in the root of eukaryotic species tree, followed by two metazoan-specific gene duplications. However, the most conserved metazoan S18 homolog is the S18-1; it shares the most sequence similarity with S18 proteins of bacteria and of other eukaryotic clades. Evolutionarily conserved residues of S18 proteins were analyzed in various cancers. S18-2 is mutated at a higher rate, compared with S18-1 and -3 proteins. Moreover, the evolutionarily conserved residue, Gly132 of S18-2, shows genetic polymorphism in colon adenocarcinomas that was confirmed by direct DNA sequencing. Concluding, S18 family represents the yet unexplored important mitochondrial ribosomal proteins.

  • 129. Nadadhur, A. G.
    et al.
    Melero, J. E.
    Meijer, M.
    Schut, D.
    Jacobs, G.
    Wan Li, K.
    Hjorth, Johannes
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab. Vrije Universiteit, Netherlands.
    Meredith, R. M.
    Toonen, R. F.
    Van Kesteren, R. E.
    Smit, A. B.
    Verhage, M.
    Heine, V. M.
    Multi-level characterization of balanced inhibitory-excitatory cortical neuron network derived from human pluripotent stem cells2017Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, nr 6, artikel-id 0178533Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Generation of neuronal cultures from induced pluripotent stem cells (hiPSCs) serve the studies of human brain disorders. However we lack neuronal networks with balanced excitatory- inhibitory activities, which are suitable for single cell analysis. We generated low-density networks of hPSC-derived GABAergic and glutamatergic cortical neurons. We used two different co-culture models with astrocytes. We show that these cultures have balanced excitatory-inhibitory synaptic identities using confocal microscopy, electrophysiological recordings, calcium imaging and mRNA analysis. These simple and robust protocols offer the opportunity for single-cell to multi-level analysis of patient hiPSC-derived cortical excitatory- inhibitory networks; thereby creating advanced tools to study disease mechanisms underlying neurodevelopmental disorders.

  • 130.
    Nair, Anu G.
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Bhalla, Upinder S
    Kotaleski, Jeanette Hellgren
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Role of DARPP-32 and ARPP-21 in the Emergence of Temporal Constraints on Striatal Calcium and Dopamine Integration2016Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 12, nr 9, artikel-id e1005080Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In reward learning, the integration of NMDA-dependent calcium and dopamine by striatal projection neurons leads to potentiation of corticostriatal synapses through CaMKII/PP1 signaling. In order to elicit the CaMKII/PP1-dependent response, the calcium and dopamine inputs should arrive in temporal proximity and must follow a specific (dopamine after calcium) order. However, little is known about the cellular mechanism which enforces these temporal constraints on the signal integration. In this computational study, we propose that these temporal requirements emerge as a result of the coordinated signaling via two striatal phosphoproteins, DARPP-32 and ARPP-21. Specifically, DARPP-32-mediated signaling could implement an input-interval dependent gating function, via transient PP1 inhibition, thus enforcing the requirement for temporal proximity. Furthermore, ARPP-21 signaling could impose the additional input-order requirement of calcium and dopamine, due to its Ca2+/calmodulin sequestering property when dopamine arrives first. This highlights the possible role of phosphoproteins in the temporal aspects of striatal signal transduction.

  • 131.
    Nair, Anu G.
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hällgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Detection of phasic dopamine by D1 and D2 striatal medium spiny neuronsIngår i: Journal of Physiology, ISSN 0022-3751, E-ISSN 1469-7793Artikel i tidskrift (Refereegranskat)
  • 132. Natesan, D.
    et al.
    Saxena, N.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Sane, S. P.
    Airflow mediated antennal positioning in flying hawkmoths2016Ingår i: Integrative and Comparative Biology, ISSN 1540-7063, E-ISSN 1557-7023, Vol. 56, s. E159-E159Artikel i tidskrift (Övrigt vetenskapligt)
  • 133.
    Nguyen, Van Dang
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    A FENICS-HPC framework for multi-compartment Bloch-Torrey models2016Konferensbidrag (Refereegranskat)
  • 134.
    Nguyen, Van Dang
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Implementation of MPI-based conjugate gradient methodfor solving the Poisson equation on Cartesian grid2015Rapport (Övrigt vetenskapligt)
    Abstract [en]

    In this project, we develop an MPI-based conjugate gradient method (CG) to solve the Poisson equation on Cartesian grids. The finite difference method will be used for space discretization. Thanks to the funtionalities of the MPI virtual topology, the computational domain is decomposed into subdomains and then each subdomain is assigned to an MPI process. The performance analysis will also be taken into account in this project.

  • 135.
    Nguyen, Van Dang
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Jansson, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Li, Jing-Rebecca
    A partition of unity finite element method for computational diffusion MRIManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    The Bloch-Torrey equation describes the evolution of the spin (usually water proton) magnetization under the influence of applied magnetic field gradients and is commonly used in numerical simulations for diffusion MRI and NMR. Microscopic heterogeneity inside the imaging voxel is modeled by interfaces inside the simulation domain, where a discontinuity in the magnetization across the interfaces is produced via a permeability coefficient on the interfaces. To avoid having to simulate on a computational domain that is the size of an entire imaging voxel, which is often much larger than the scale of the microscopic heterogeneity as well as the mean spin diffusion displacement, smaller representative volumes of the imaging medium can be used as the simulation domain. In this case, the exterior boundaries of a representative volume either must be far away from the initial positions of the spins or suitable boundary conditions must be found to allow the movement of spins across these exterior boundaries. Many efforts have been made to solve the equation but there is still missing an efficient high performance computing framework. In this work, we present formulations of the interface as well as the exterior boundary conditions that are computationally efficient and suitable for arbitrary order finite elements and parallelization. In particular, the formulations use extended finite elements with weak enforcement of real (in the case of interior interfaces) and artificial (in the case of exterior boundaries) permeability conditions as well as operator splitting for the exterior boundary conditions. The method appears to be straightforward to implement and it is implemented in the FEniCS for moderate-scale simulations and in the FEniCS-HPC for the large-scale simulations. The accuracy of the resulting method is validated numerically and a good scalability is shown for the parallel implementation. We show that the simulated dMRI signals offer good approximations to reference signals in cases where the latter are available. Finally, we do simulations on a complex neuron to study how the signals decay under the effect of the permeable membrane and to show that the method can be used to simulate for complex geometries that we have not done before.

    Highlights:

    • The discontinuity in the magnetization across the interior interfaces of the medium is weakly imposed, allowing generalization to arbitrary order finite elements.
    • Spin exchange across the external boundaries is implemented by weakly imposing an artificial, high permeability, condition, allowing generalization to non-matching meshes.
    • Thus, optimal convergence with respect to the space discretization is achieved.
    • The second-order Crank-Nicolson method is chosen for the time discretization to reduce oscillations at high gradient strengths and allows for larger time-step sizes.
    • The method is of a high level of simplicity and suitable for parallelization.
    • An efficient open-source code is implemented in the FEniCS and FEniCS-HPC platforms.
  • 136.
    Nguyen, Van Dang
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Jansson, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Leoni, Massimiliano
    Janssen, Barbel
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Goude, Anders
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Modelling of rotating vertical axis turbines using a multiphase finite element method2017Ingår i: MARINE 2017: Computational Methods in Marine Engineering VII15 - 17 May 2017, Nantes, France, 2017, s. 950-960Konferensbidrag (Övrigt vetenskapligt)
  • 137. Olshevsky, Vyacheslav
    et al.
    Deca, Jan
    Divin, Andrey
    Peng, Ivy 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).
    Innocenti, Maria Elena
    Cazzola, Emanuele
    Lapenta, Giovanni
    Magnetic Null Points In Kinetic Simulations of Space Plasmas2016Ingår i: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 819, nr 1, artikel-id 52Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a systematic attempt to study magnetic null points and the associated magnetic energy conversion in kinetic particle-in-cell simulations of various plasma configurations. We address three-dimensional simulations performed with the semi-implicit kinetic electromagnetic code iPic3D in different setups: variations of a Harris current sheet, dipolar and quadrupolar magnetospheres interacting with the solar wind,. and a relaxing turbulent configuration with multiple null points. Spiral nulls are more likely created in space plasmas: in all our simulations except lunar magnetic anomaly (LMA) and quadrupolar mini-magnetosphere the number of spiral nulls prevails over the number of radial nulls by a factor of 3-9. We show that often magnetic nulls do not indicate the regions of intensive energy dissipation. Energy dissipation events caused by topological bifurcations at radial nulls are rather rare and short-lived. The so-called X-lines formed by the radial nulls in the Harris current sheet and LMA simulations are rather stable and do not exhibit any energy dissipation. Energy dissipation is more powerful in the vicinity of spiral nulls enclosed by magnetic flux ropes with strong currents at their axes (their cross. sections resemble 2D magnetic islands). These null lines reminiscent of Z-pinches efficiently dissipate magnetic energy due to secondary instabilities such as the two-stream or kinking instability, accompanied by changes in magnetic topology. Current enhancements accompanied by spiral nulls may signal magnetic energy conversion sites in the observational data.

  • 138.
    Onishi, Keiji
    et al.
    RIKEN Advanced Institute for Computational Science.
    Jansson, Niclas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). RIKEN Advanced Institute for Computational Science.
    Bale, Rahul
    RIKEN Advanced Institute for Computational Science.
    Wang, Wei-Hsiang
    RIKEN Advanced Institute for Computational Science.
    Li, Chung-Gang
    Kobe University and RIKEN Advanced Institute for Computational Science.
    Tsubokura, Makoto
    Kobe University and RIKEN Advanced Institute for Computational Science.
    A Deployment of HPC Algorithm into Pre/Post-Processing for Industrial CFD on K-Computer2017Konferensbidrag (Refereegranskat)
    Abstract [en]

    Pre- and post-processing is still a major problem in industrial computational fluid dynamics (CFD). With the rapid development of computers, physical solvers are getting faster, while pre- remains slow because it's mainly a serial process. A methodology using MPI+OpenMP hybrid parallelization has been proposed to eliminate the manual work required during pre-processing for correcting the surface imperfections of CAD data. Compared to the rapidly increasing amount of data in recent years, the speed-up of visualization is insufficient. We address this limitation of post- by adapting the in-situ visualization to parallelize the post-processing using libsim (Visit) library. The performance of pre-/post- processing is investigated in this work, and we show that the pre-processing time has been reduced from several days in the conventional framework to order of minutes. The post-processing time has been reduced seconds order per frame, and approximately 30% increase of computational time was observed in vehicle aerodynamics cases. 

  • 139. Paetzel, M.
    et al.
    Hupont, I.
    Varni, G.
    Chetouani, M.
    Peters, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Castellano, G.
    Exploring the link between self-assessed mimicry and embodiment in HRI2017Ingår i: ACM/IEEE International Conference on Human-Robot Interaction, IEEE Computer Society , 2017, s. 245-246Konferensbidrag (Refereegranskat)
    Abstract [en]

    This work explores the relationship between a robot's embodiment and people's ability to mimic its behavior. It presents a study in which participants were asked to mimic a 3D mixed-embodied robotic head and a 2D version of the same character. Quantitative and qualitative analysis were performed from questionnaires. Quantitative results show no significant influence of the character's embodiment on the self-assessed ability to mimic it, while qualitative ones indicate a preference for mimicking the robotic head.

  • 140. Paetzel, Maike
    et al.
    Peters, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Nystrom, Ingela
    Castellano, Ginevra
    Effects of Multimodal Cues on Children's Perception of Uncanniness in a Social Robot2016Ingår i: ICMI'16: PROCEEDINGS OF THE 18TH ACM INTERNATIONAL CONFERENCE ON MULTIMODAL INTERACTION, ASSOC COMPUTING MACHINERY , 2016, s. 297-301Konferensbidrag (Refereegranskat)
    Abstract [en]

    This paper investigates the influence of multimodal incongruent gender cues on the perception of a robot's uncanniness and gender in children. The back-projected robot head Furhat was equipped with a female and male face texture and voice synthesizer and the voice and facial cues were tested in congruent and incongruent combinations. 106 children between the age of 8 and 13 participated in the study. Results show that multimodal incongruent cues do not trigger the feeling of uncanniness in children. These results are significant as they support other recent research showing that the perception of uncanniness cannot be triggered by a categorical ambiguity in the robot. In addition, we found that children rely on auditory cues much stronger than on the facial cues when assigning a gender to the robot if presented with incongruent cues. These findings have implications for the robot design, as it seems possible to change the gender of a robot by only changing its voice without creating a feeling of uncanniness in a child.

  • 141. Paetzel, Maike
    et al.
    Peters, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Nyström, Ingela
    Castellano, Ginevra
    Congruency Matters: How Ambiguous Gender Cues Increase a Robot's Uncanniness2016Ingår i: SOCIAL ROBOTICS, (ICSR 2016), Springer, 2016, s. 402-412Konferensbidrag (Refereegranskat)
    Abstract [en]

    Most research on the uncanny valley effect is concerned with the influence of human-likeness and realism as a trigger of an uncanny feeling in humans. There has been a lack of investigation on the effect of other dimensions, for example, gender. Back-projected robotic heads allow us to alter visual cues in the appearance of the robot in order to investigate how the perception of it changes. In this paper, we study the influence of gender on the perceived uncanniness. We conducted an experiment with 48 participants in which we used different modalities of interaction to change the strength of the gender cues in the robot. Results show that incongruence in the gender cues of the robot, and not its specific gender, influences the uncanniness of the back-projected robotic head. This finding has potential implications for both the perceptual mismatch and categorization ambiguity theory as a general explanation of the uncanny valley effect.

  • 142. Paetzel, Maike
    et al.
    Varni, Giovanna
    Hupont, Isabelle
    Chetouani, Mohamed
    Peters, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Castellano, Ginevra
    Investigating the Influence of Embodiment on Facial Mimicry in HRI Using Computer Vision-Based Measures2017Ingår i: 2017 26TH IEEE INTERNATIONAL SYMPOSIUM ON ROBOT AND HUMAN INTERACTIVE COMMUNICATION (RO-MAN) / [ed] Howard, A Suzuki, K Zollo, L, IEEE , 2017, s. 579-586Konferensbidrag (Refereegranskat)
    Abstract [en]

    Mimicry plays an important role in social interaction. In human communication, it is used to establish rapport and bonding both with other humans, as well as robots and virtual characters. However, little is known about the underlying factors that elicit mimicry in humans when interacting with a robot. In this work, we study the influence of embodiment on participants' ability to mimic a social character. Participants were asked to intentionally mimic the laughing behavior of the Furhat mixed embodied robotic head and a 2D virtual version of the same character. To explore the effect of embodiment, we present two novel approaches to automatically assess people's ability to mimic based solely on videos of their facial expressions. In contrast to participants' self-assessment, the analysis of video recordings suggests a better ability to mimic when people interact with the 2D embodiment.

  • 143.
    Palmas, Gregorio
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Visual Analysis of Multidimensional Data for Biomechanics and HCI2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Multidimensional analysis is performed in many scientific fields.Its main tasks involve the identification of correlations between data dimensions,the investigation of data clusters, and the identification of outliers. Visualization techniques often help in getting a better understanding. In this thesis, we present our work on improving visual multidimensional analysis by exploiting the semantics of the data and enhancing the perception of existing visualizations. Firstly, we exploit the semantics of the data by creating new visualizations which present visual encodings specifically tailoredto the analyzed dimensions. We consider the resulting visual analysis to be more intuitive for the user asit provides a more easily understandable idea of the data. In this thesis we concentrate on the visual analysis of multidimensional biomechanical data for Human-Computer Interaction (HCI).To this end, we present new visualizations tackling the specific features of different aspectsof biomechanical data such as movement ergonomics, leading to a more intuitive analysis. Moreover, by integrating drawings or sketches of the physical setup of a case study as new visualizations, we allow for a fast and effective case-specific analysis. The creation of additional visualizations for communicating trends of clusters of movements enables a cluster-specific analysis which improves our understanding of postures and muscular co-activation.Moreover, we create a new visualization which addresses the specificity of the multidimensional data related to permutation-based optimization problems. Each permutation of a given set of n elements represents a point defined in an n-dimensional space. Our method approximates the topologyof the problem-related optimization landscape inferring the minima basins and their properties and visualizing them organized in a quasi-landscape. We show the variability of the solutions in a basin using heat maps generated from permutation matrices.Furthermore, we continue improving our visual multidimensional analysis by enhancing the perceptual encoding of existing well-known multidimensional visualizations. We focus on Parallel Coordinates Plots (PCP) and its derivative Continuous Parallel Coordinates (CPC). The main perceptual issues of PCP are visual clutter and overplotting which hamper the recognition of patterns in large data sets. In this thesis, we present an edge-bundling method for PCP which uses density-based clustering for each dimension. This reduces clutter and provides a faster overview of clusters and trends. Moreover, it allows for a fast rendering of the clustered lines using polygons. Furthermore, we present the first bundling approach for Continuous Parallel Coordinates where classic edge-bundling fails due to the absence of lines. Our method performs a deformation of the visualization space of CPC leading to similar results as those obtained through classic edge-bundling.Our work involved 10 HCI case studies and helped to establisha new research methodology in this field. This led to publications in internationally peer-reviewed journals and conference proceedings.

  • 144.
    Palmas, Gregorio
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Oulasvirta, Antti
    Aalto University.
    Weinkauf, Tino
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Optimization Landscapes: A Topological Approach to Understanding Permutation-based Optimization ProblemsManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Permutation-based optimization problemsare a class of NP-hard combinatorial problemsrepresenting many challenges in theory and practice.Their solution spaceconsists of all permutations $n!$of a given set of $n$ elements.Hence, for many real-world problemsthe solution spaceis too largeto even just visit every solution.The quality of a solutionis described by an objective function.A good understandingof the structures and symmetriesin this data is requiredto develop and steer heuristic algorithmsand other approaches to solving the underlying problem.We present a novel topological approachto exploring the objective functionsof permutation-based optimization problems.We infer the minima basinsand their propertiesfrom descending optimization paths.To deal with noise and general oversegmentation,we introduce an approachinspired by topological simplification of scalar fields.Based on this,we construct an edge-weighted graphapproximating the distances between basins,and visualize it using a force-directed layout,which shows the basins of local and global optimaorganized in a quasi-landscape.We show the variabilityof the solutions in a basinusing heat maps generated from permutation matrices.Our method is designed to be interactiveand read its input data as a streamfrom a simultaneously running simulation.We evaluate our method using different optimization problemsfrom both theory and practice.

  • 145.
    Palmas, Gregorio
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Weinkauf, Tino
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Space Bundling for Continuous Parallel Coordinates2016Ingår i: Eurographics Proceedings, The Eurographics Association , 2016Konferensbidrag (Refereegranskat)
    Abstract [en]

    Continuous Parallel Coordinates (CPC) are a visualization technique used to perform multivariate analysis of different scalar fields defined on thesame domain.While classic Parallel Coordinatesdraws a line for each sample point,a CPC visualization uses a density-based representation.An interesting possibility for the classic methodis to highlight higher-dimensional clustersusing edge bundling,where each line becomes a spline bent towards the centroid of the cluster.This often leads to expressive, illustrative visualizations.Unfortunately, bundling lines is not possible for CPC,as they are not involved in this method.In this paper,we propose a deformation of the visualization space for Continuous Parallel Coordinatesthat leads to similar results as those obtained through classic edge bundling.We achieve this by performing a curved-profile transformation in image space.The approach lends itself to a computationally lightweight GPU implementation.Furthermore, we provide intuitive interactionswith the bundled clusters.We show several examples of our technique applied to a commonly available data set.

  • 146.
    Palmberg, Robin
    et al.
    KTH, Skolan för arkitektur och samhällsbyggnad (ABE), Samhällsplanering och miljö.
    Peters, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Qureshi, Adam
    When Facial Expressions Dominate Emotion Perception in Groups of Virtual Characters2017Ingår i: 2017 9th International Conference on Virtual Worlds and Games for Serious Applications, VS-Games 2017 - Proceedings, IEEE, 2017, s. 157-160Konferensbidrag (Refereegranskat)
    Abstract [en]

    Virtual characters play a central role in populating virtual worlds, whether they act as conduits for human expressions as avatars or are automatically controlled by a machine as agents. In modern game-related scenarios, it is economical to assemble virtual characters from varying sources of appearances and motions. However, doing so may have unintended consequences with respect to how people perceive their expressions. This paper presents an initial study investigating the impact of facial expressions and full body motions from varying sources on the perception of intense positive and negative emotional expressions in small groups of virtual characters. 21 participants views a small group of three virtual characters engaged in intense animated behaviours as their face and body motions were varied between positive, neutral and negative valence expressions. While emotion perception was based on both the bodies and the faces of the characters, we found a strong impact of the valence of facial expressions on the perception of emotions in the group. We discuss these findings in relation to the combination of manually created and automatically defined motion sources, highlighting implications for the animation of virtual characters.

  • 147.
    Peng, I. B.
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Gioiosa, R.
    Kestor, G.
    Cicotti, P.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Exploring the performance benefit of hybrid memory system on HPC environments2017Ingår i: Proceedings - 2017 IEEE 31st International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2017, Institute of Electrical and Electronics Engineers (IEEE), 2017, s. 683-692, artikel-id 7965110Konferensbidrag (Refereegranskat)
    Abstract [en]

    Hardware accelerators have become a de-facto standard to achieve high performance on current supercomputers and there are indications that this trend will increase in the future. Modern accelerators feature high-bandwidth memory next to the computing cores. For example, the Intel Knights Landing (KNL) processor is equipped with 16 GB of high-bandwidth memory (HBM) that works together with conventional DRAM memory. Theoretically, HBM can provide ∼4× higher bandwidth than conventional DRAM. However, many factors impact the effective performance achieved by applications, including the application memory access pattern, the problem size, the threading level and the actual memory configuration. In this paper, we analyze the Intel KNL system and quantify the impact of the most important factors on the application performance by using a set of applications that are representative of scientific and data-analytics workloads. Our results show that applications with regular memory access benefit from MCDRAM, achieving up to 3× performance when compared to the performance obtained using only DRAM. On the contrary, applications with random memory access pattern are latency-bound and may suffer from performance degradation when using only MCDRAM. For those applications, the use of additional hardware threads may help hide latency and achieve higher aggregated bandwidth when using HBM.

  • 148.
    Peng, I. B.
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    The cost of synchronizing imbalanced processes in message passing systems2015Ingår i: Proceedings - IEEE International Conference on Cluster Computing, ICCC, Institute of Electrical and Electronics Engineers (IEEE), 2015, s. 408-417Konferensbidrag (Refereegranskat)
    Abstract [en]

    Synchronization in message passing systems is achieved by communication among processes. System and architectural noise and different workloads cause processes to be imbalanced and to reach synchronization points at different time. Thus, both communication and imbalance impact the synchronization performance. In this paper, we study the algorithmic properties that allow the communication in synchronization to absorb the initial imbalance among processes. We quantify the imbalance absorption properties of different barrier algorithms using a LogP Monte Carlo simulator. We found that linear and f-way tournament barriers can absorb up to 95% of random exponential imbalance with the standard deviation equal to the communication time for one message. Dissemination, butterfly and pairwise exchange barriers, on the other hand, do not absorb imbalance but can effectively bound the post-barrier imbalance. We identify that synchronization transits from communication-dominated to imbalance-dominated when the standard deviation of imbalance distribution is more than twice the communication time for one message. In our study, f-way tournament barriers provided the best imbalance absorption rate and convenient communication time.

  • 149.
    Peng, I. Bo
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Kestor, G.
    Gioiosa, R.
    Exploring Application Performance on Emerging Hybrid-Memory Supercomputers2017Ingår i: Proceedings - 18th IEEE International Conference on High Performance Computing and Communications, 14th IEEE International Conference on Smart City and 2nd IEEE International Conference on Data Science and Systems, HPCC/SmartCity/DSS 2016, Institute of Electrical and Electronics Engineers (IEEE), 2017, s. 473-480, artikel-id 7828415Konferensbidrag (Refereegranskat)
    Abstract [en]

    Next-generation supercomputers will feature more hierarchical and heterogeneous memory systems with different memory technologies working side-by-side. A critical question is whether at large scale existing HPC applications and emerging data-analytics workloads will have performance improvement or degradation on these systems. We propose a systematic and fair methodology to identify the trend of application performance on emerging hybrid-memory systems. We model the memory system of next-generation supercomputers as a combination of 'fast' and 'slow' memories. We then analyze performance and dynamic execution characteristics of a variety of workloads, from traditional scientific applications to emerging data analytics to compare traditional and hybrid-memory systems. Our results show that data analytics applications can clearly benefit from the new system design, especially at large scale. Moreover, hybrid-memory systems do not penalize traditional scientific applications, which may also show performance improvement.

  • 150.
    Peng, I. Bo
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Kestor, G.
    Gioiosa, R.
    Idle period propagation in message-passing applications2017Ingår i: Proceedings - 18th IEEE International Conference on High Performance Computing and Communications, 14th IEEE International Conference on Smart City and 2nd IEEE International Conference on Data Science and Systems, HPCC/SmartCity/DSS 2016, Institute of Electrical and Electronics Engineers (IEEE), 2017, s. 937-944, artikel-id 7828475Konferensbidrag (Refereegranskat)
    Abstract [en]

    Idle periods on different processes of Message Passing applications are unavoidable. While the origin of idle periods on a single process is well understood as the effect of system and architectural random delays, yet it is unclear how these idle periods propagate from one process to another. It is important to understand idle period propagation in Message Passing applications as it allows application developers to design communication patterns avoiding idle period propagation and the consequent performance degradation in their applications. To understand idle period propagation, we introduce a methodology to trace idle periods when a process is waiting for data from a remote delayed process in MPI applications. We apply this technique in an MPI application that solves the heat equation to study idle period propagation on three different systems. We confirm that idle periods move between processes in the form of waves and that there are different stages in idle period propagation. Our methodology enables us to identify a self-synchronization phenomenon that occurs on two systems where some processes run slower than the other processes.

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