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  • 51.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Adaptive sensor drift counteraction by a modular neural network2011Ingår i: Chemical sensors, ISSN 0379-864X, Vol. 36, nr 1, s. E41-E41Artikel i tidskrift (Övrigt vetenskapligt)
  • 52.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Adaptive sensor drift counteraction by a modular neural network2010Ingår i: Neuroscience research, ISSN 0168-0102, E-ISSN 1872-8111, Vol. 68, s. E212-E212Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    The response properties of sensors such as electronic noses vary in time due to internal or environmental factors. Recalibration is often costly or technically infeasible, which is why algorithms aimed at addressing the sensor drift problem at the data processing level have been developed. These falls in two categories: The pre-processing approaches, such as component correction [1], try to extract the direction and amount of drift in the training data and remove the drift component during operation. Adaptive algorithms, such as the self-organizing map [2], try to counteract the drift during runtime by adjusting the network to the incoming data.

    We have previously suggested a modular neural network architecture as a model of cortical layer 4 [3]. Here we show how it quite well can handle the sensor drift problem in chemosensor data. It creates a distributed and redundant code suitable for a noisy and drifting environment. A feature extraction layer governed by competitive learning allows for network adaptation during runtime. In addition, training data can be utilized to create a prediction of the underlying drift to further improve the network performance. Hence, we attempt to combine the two aforementioned methodological categories into one network model.

    The capabilities of the proposed network are demonstrated on surrogate data as well as real-world data collected from an electronic nose.

  • 53.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Extreme scaling of brain simulation on JUGENE2011Rapport (Övrigt vetenskapligt)
    Ladda ner fulltext (pdf)
    ExtremeScalingJUGENE
  • 54.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Nexa: A scalable neural simulator with integrated analysis2012Ingår i: Network, ISSN 0954-898X, E-ISSN 1361-6536, Vol. 23, nr 4, s. 254-271Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Large-scale neural simulations encompass challenges in simulator design, data handling and understanding of simulation output. As the computational power of supercomputers and the size of network models increase, these challenges become even more pronounced. Here we introduce the experimental scalable neural simulator Nexa, for parallel simulation of large-scale neural network models at a high level of biological abstraction and for exploration of the simulation methods involved. It includes firing-rate models and capabilities to build networks using machine learning inspired methods for e. g. self-organization of network architecture and for structural plasticity. We show scalability up to the size of the largest machines currently available for a number of model scenarios. We further demonstrate simulator integration with online analysis and real-time visualization as scalable solutions for the data handling challenges.

  • 55.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lundqvist, Mikael
    A model of categorization, learning of invariant representations and sequence prediction utilizing top-down activityManuskript (preprint) (Övrigt vetenskapligt)
  • 56.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Silverstein, David
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Herman, Pawel
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Melis, Paul
    Visualization Group, SARA, Amsterdam, The Netherlands.
    Slavnić, Vladimir
    Scientific Computing Laboratory, Institute of Physics Belgrade, University of Belgrade.
    Spasojević, Marko
    Scientific Computing Laboratory, Institute of Physics Belgrade, University of Belgrade.
    Alexiev, Kiril
    Department of Mathematical Methods for Sensor Information Processing, Institute of Information and Communication Technologies, Bulgaria.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Visualization of Output from Large-Scale Brain Simulations2012Rapport (Övrigt vetenskapligt)
    Abstract [en]

    This project concerned the development of tools for visualization of output from brain simulations performed on supercomputers. The project had two main parts: 1) creating visualizations using large-scale simulation output from existing neural simulation codes, and 2) making extensions to  some of the existing codes to allow interactive runtime (in-situ) visualization. In 1) simulation data was converted to HDF5 format and split over multiple files. Visualization pipelines were created for different types of visualizations, e.g. voltage and calcium. In 2) by using the VisIt visualization application and its libsim library, simulation code was instrumented so that VisIt could access simulation data directly. The simulation code was instrumented and tested on different clusters where control of simulation was demonstrated and in-situ visualization of neural unit’s and population data was achieved.

    Ladda ner fulltext (pdf)
    fulltext
  • 57.
    Berthet, Pierre
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Hällgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Action selection performance of a reconfigurable Basal Ganglia inspired model with Hebbian-Bayesian Go-NoGo connectivity2012Ingår i: Frontiers in Behavioral Neuroscience, ISSN 1662-5153, E-ISSN 1662-5153, Vol. 6, s. 65-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Several studies have shown a strong involvement of the basal ganglia (BG) in action selection and dopamine dependent learning. The dopaminergic signal to striatum, the input stage of the BG, has been commonly described as coding a reward prediction error (RPE), i.e. the difference between the predicted and actual reward. The RPE has been hypothesized to be critical in the modulation of the synaptic plasticity in cortico-striatal synapses in the direct and indirect pathway. We developed an abstract computational model of the BG, with a dual pathway structure functionally corresponding to the direct and indirect pathways, and compared its behaviour to biological data as well as other reinforcement learning models. The computations in our model are inspired by Bayesian inference, and the synaptic plasticity changes depend on a three factor Hebbian-Bayesian learning rule based on co-activation of pre- and post-synaptic units and on the value of the RPE. The model builds on a modified Actor-Critic architecture and implements the direct (Go) and the indirect (NoGo) pathway, as well as the reward prediction (RP) system, acting in a complementary fashion. We investigated the performance of the model system when different configurations of the Go, NoGo and RP system were utilized, e.g. using only the Go, NoGo, or RP system, or combinations of those. Learning performance was investigated in several types of learning paradigms, such as learning-relearning, successive learning, stochastic learning, reversal learning and a two-choice task. The RPE and the activity of the model during learning were similar to monkey electrophysiological and behavioural data. Our results, however, show that there is not a unique best way to configure this BG model to handle well all the learning paradigms tested. We thus suggest that an agent might dynamically configure its action selection mode, possibly depending on task characteristics and also on how much time is available.

  • 58.
    Berthet, Pierre
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Optogenetic Stimulation in a Computational Model of the Basal Ganglia Biases Action Selection and Reward Prediction Error2014Ingår i: PLoS ONE, E-ISSN 1932-6203, Vol. 9, nr 3, s. e90578-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Optogenetic stimulation of specific types of medium spiny neurons (MSNs) in the striatum has been shown to bias the selection of mice in a two choices task. This shift is dependent on the localisation and on the intensity of the stimulation but also on the recent reward history. We have implemented a way to simulate this increased activity produced by the optical flash in our computational model of the basal ganglia (BG). This abstract model features the direct and indirect pathways commonly described in biology, and a reward prediction pathway (RP). The framework is similar to Actor-Critic methods and to the ventral/ dorsal distinction in the striatum. We thus investigated the impact on the selection caused by an added stimulation in each of the three pathways. We were able to reproduce in our model the bias in action selection observed in mice. Our results also showed that biasing the reward prediction is sufficient to create a modification in the action selection. However, we had to increase the percentage of trials with stimulation relative to that in experiments in order to impact the selection. We found that increasing only the reward prediction had a different effect if the stimulation in RP was action dependent (only for a specific action) or not. We further looked at the evolution of the change in the weights depending on the stage of learning within a block. A bias in RP impacts the plasticity differently depending on that stage but also on the outcome. It remains to experimentally test how the dopaminergic neurons are affected by specific stimulations of neurons in the striatum and to relate data to predictions of our model.

  • 59.
    Berthet, Pierre
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. Stockholm Univ, Sweden; Karolinska Inst, Sweden.
    Lindahl, Mikael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. Karolinska Inst, Sweden.
    Tully, Philip J.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. Karolinska Inst, Sweden; Univ Edinburgh, Scotland.
    Hellgren-Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. Karolinska Inst, Sweden.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. Stockholm Univ, Sweden; Karolinska Inst, Sweden.
    Functional Relevance of Different Basal Ganglia Pathways Investigated in a Spiking Model with Reward Dependent Plasticity2016Ingår i: Frontiers in Neural Circuits, ISSN 1662-5110, E-ISSN 1662-5110, Vol. 10, artikel-id 53Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The brain enables animals to behaviorally adapt in order to survive in a complex and dynamic environment, but how reward-oriented behaviors are achieved and computed by its underlying neural circuitry is an open question. To address this concern, we have developed a spiking model of the basal ganglia (BG) that learns to dis-inhibit the action leading to a reward despite ongoing changes in the reward schedule. The architecture of the network features the two pathways commonly described in BG, the direct (denoted D1) and the indirect (denoted D2) pathway, as well as a loop involving striatum and the dopaminergic system. The activity of these dopaminergic neurons conveys the reward prediction error (RPE), which determines the magnitude of synaptic plasticity within the different pathways. All plastic connections implement a versatile four-factor learning rule derived from Bayesian inference that depends upon pre- and post-synaptic activity, receptor type, and dopamine level. Synaptic weight updates occur in the D1 or D2 pathways depending on the sign of the RPE, and an efference copy informs upstream nuclei about the action selected. We demonstrate successful performance of the system in a multiple-choice learning task with a transiently changing reward schedule. We simulate lesioning of the various pathways and show that a condition without the D2 pathway fares worse than one without D1. Additionally, we simulate the degeneration observed in Parkinson's disease (PD) by decreasing the number of dopaminergic neurons during learning. The results suggest that the D1 pathway impairment in PD might have been overlooked. Furthermore, an analysis of the alterations in the synaptic weights shows that using the absolute reward value instead of the RPE leads to a larger change in D1.

  • 60.
    Bicanski, Andrej
    et al.
    School of Engineering, École Polytechnique Fédérale de Lausanne.
    Ryczko, Dimitri
    Département de Physiologie, Université de Montréa.
    Knuesel, Jérémie
    School of Engineering, École Polytechnique Fédérale de Lausanne.
    Harischandra, Nalin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Charrier, Vanessa
    INSERM U862, Neurocentre Magendie, Université Bordeaux.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Cabelguen, Jean-Marie
    Neurocentre Magendie, Bordeaux University, Bordeaux Cedex, France.
    Ijspeert, Auke Jan
    School of Engineering, École Polytechnique Fédérale de Lausanne.
    Decoding the mechanisms of gait generation in salamanders by combining neurobiology, modeling and robotics2013Ingår i: Biological Cybernetics, ISSN 0340-1200, E-ISSN 1432-0770, Vol. 107, nr 5, s. 545-564Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Vertebrate animals exhibit impressive locomotor skills. These locomotor skills are due to the complex interactions between the environment, the musculo-skeletal system and the central nervous system, in particular the spinal locomotor circuits. We are interested in decoding these interactions in the salamander, a key animal from an evolutionary point of view. It exhibits both swimming and stepping gaits and is faced with the problem of producing efficient propulsive forces using the same musculo-skeletal system in two environments with significant physical differences in density, viscosity and gravitational load. Yet its nervous system remains comparatively simple. Our approach is based on a combination of neurophysiological experiments, numerical modeling at different levels of abstraction, and robotic validation using an amphibious salamander-like robot. This article reviews the current state of our knowledge on salamander locomotion control, and presents how our approach has allowed us to obtain a first conceptual model of the salamander spinal locomotor networks. The model suggests that the salamander locomotor circuit can be seen as a lamprey-like circuit controlling axial movements of the trunk and tail, extended by specialized oscillatory centers controlling limb movements. The interplay between the two types of circuits determines the mode of locomotion under the influence of sensory feedback and descending drive, with stepping gaits at low drive, and swimming at high drive.

  • 61. Birin, H.
    et al.
    Gal-Or, Z.
    Elias, Isaac
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Tuller, T.
    Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion2008Ingår i: Bioinformatics, ISSN 1367-4803, Vol. 24, nr 6, s. 826-832Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Motivation: The evolution of viruses is very rapid and in addition to local point mutations (insertion, deletion, substitution) it also includes frequent recombinations, genome rearrangements and horizontal transfer of genetic materials (HGTS). Evolutionary analysis of viral sequences is therefore a complicated matter for two main reasons: First, due to HGTs and recombinations, the right model of evolution is a network and not a tree. Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. These facts encourage developing methods for inferring phylogenetic networks that do not require aligned sequences as input. Results: In this work, we present the first computational approach which deals with both genome rearrangements and horizontal gene transfers and does not require a multiple alignment as input. We formalize a new set of computational problems which involve analyzing such complex models of evolution. We investigate their computational complexity, and devise algorithms for solving them. Moreover, we demonstrate the viability of our methods on several synthetic datasets as well as four biological datasets.

  • 62.
    Bo, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Skolan för elektro- och systemteknik (EES), Centra, ACCESS Linnaeus Centre.
    Eichhorn, Ralf
    KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Celani, Antonio
    Optimal stochastic transport in inhomogeneous thermal environments2013Ingår i: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 103, nr 1, s. 10010-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We consider the optimization of the average entropy production in inhomogeneous temperature environments within the framework of stochastic thermodynamics. For systems modeled by Langevin equations (e.g. a colloidal particle in a heat bath) it has been recently shown that a space-dependent temperature breaks the time reversal symmetry of the fast velocity degrees of freedom resulting in an anomalous contribution to the entropy production of the overdamped dynamics. We show that optimization of entropy production is determined by an auxiliary deterministic problem formally analogous to motion on a curved manifold in a potential. The "anomalous contribution" to entropy plays the role of the potential and the inverse of the diffusion tensor is the metric. We also find that entropy production is not minimized by adiabatically slow, quasi-static protocols but there is a finite optimal duration for the transport process. As an example we discuss the case of a linearly space-dependent diffusion coefficient.

  • 63.
    Bogdanowicz, Janusz
    et al.
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Gilbert, Matthieu
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Skolan för elektro- och systemteknik (EES), Centra, Alfvénlaboratoriet.
    Koelling, Sebastian
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Vanderheyden, Benoit
    4 Institut Montefiore, Sart-Tilman B28, B-4000 Liege, Belgium.
    Vandervorst, Wilfried
    IMEC, Kapeldreef 75, B-3000 Leuven, Belgium.
    Light absorption in conical silicon particles2013Ingår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, nr 3, s. 3891-3896Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The problem of the absorption of light by a nanoscale dielectric cone is discussed. A simplified solution based on the analytical Mie theory of scattering and absorption by cylindrical objects is proposed and supported by the experimental observation of sharply localized holes in conical silicon tips after high-fluence irradiation. This study reveals that light couples with tapered objects dominantly at specific locations, where the local radius corresponds to one of the resonant radii of a cylindrical object, as predicted by Mie theory.

  • 64.
    Brandi, Maya
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Brocke, Ekaterina
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Talukdar, Husain A.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Hanke, Michael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk analys, NA.
    Bhalla, Upinder S.
    National Centre for Biological Sciences, Bangalore, India.
    Hällgren-Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Djurfeldt, Mikael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Connecting MOOSE and NeuroRD through MUSIC: towards a communication framework for multi-scale modeling2011Ingår i: Twentieth Annual Computational Neuroscience Meeting: CNS*2011, Springer Science+Business Media B.V., 2011Konferensbidrag (Refereegranskat)
  • 65. Brette, Romain
    et al.
    Rudolph, Michelle
    Carnevale, Ted
    Hines, Michael
    Beeman, David
    Bower, James M.
    Diesmann, Markus
    Morrison, Abigail
    Goodman, Philip H.
    Harris, Frederick C., Jr.
    Zirpe, Milind
    Natschlaeger, Thomas
    Pecevski, Dejan
    Ermentrout, Bard
    Djurfeldt, Mikael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Rochel, Olivier
    Vieville, Thierry
    Muller, Eilif
    Davison, Andrew P.
    El Boustani, Sami
    Destexhe, Alain
    Simulation of networks of spiking neurons: A review of tools and strategies2007Ingår i: Journal of Computational Neuroscience, ISSN 0929-5313, E-ISSN 1573-6873, Vol. 23, nr 3, s. 349-398Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based or conductance-based synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks.

  • 66.
    Bretzner, Lars
    et al.
    KTH, Tidigare Institutioner, Numerisk analys och datalogi, NADA.
    Laptev, Ivan
    KTH, Tidigare Institutioner, Numerisk analys och datalogi, NADA.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lenman, S.
    Sundblad, Y.
    A Prototype System for Computer Vision Based Human Computer Interaction2001Rapport (Övrigt vetenskapligt)
    Ladda ner fulltext (pdf)
    fulltext
  • 67.
    Bretzner, Lars
    et al.
    KTH, Tidigare Institutioner, Numerisk analys och datalogi, NADA.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Qualitative multiscale feature hierarchies for object tracking2000Rapport (Refereegranskat)
    Abstract [en]

    This paper shows how the performance of feature trackers can be improved by building a hierarchical view-based object representation consisting of qualitative relations between image structures at different scales. The idea is to track all image features individually and to use the qualitative feature relations for avoiding mismatches, for resolving ambiguous matches, and for introducing feature hypotheses whenever image features are lost. Compared to more traditional work on view-based object tracking, this methodology has the ability to handle semirigid objects and partial occlusions. Compared to trackers based on three-dimensional object models, this approach is much simpler and of a more generic nature. A hands-on example is presented showing how an integrated application system can be constructed from conceptually very simple operations.

    Ladda ner fulltext (pdf)
    fulltext
  • 68.
    Bretzner, Lars
    et al.
    KTH, Tidigare Institutioner, Numerisk analys och datalogi, NADA.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Use your hand as a 3-D mouse or relative orientation from extended sequences of sparse point and line correspondances using the affine trifocal tensor1998Ingår i: Computer Vision — ECCV'98: 5th European Conference on Computer Vision Freiburg, Germany, June, 2–6, 1998 Proceedings, Volume I, Springer Berlin/Heidelberg, 1998, Vol. 1406, s. 141-157Konferensbidrag (Refereegranskat)
    Abstract [en]

    This paper addresses the problem of computing three-dimensional structure and motion from an unknown rigid configuration of point and lines viewed by an affine projection model. An algebraic structure, analogous to the trilinear tensor for three perspective cameras, is defined for configurations of three centered affine cameras. This centered affine trifocal tensor contains 12 coefficients and involves linear relations between point correspondences and trilinear relations between line correspondences It is shown how the affine trifocal tensor relates to the perspective trilinear tensor, and how three-dimensional motion can be computed from this tensor in a straightforward manner. A factorization approach is also developed to handle point features and line features simultaneously in image sequences.

    This theory is applied to a specific problem of human-computer interaction of capturing three-dimensional rotations from gestures of a human hand. A qualitative model is presented, in which three fingers are represented by their position and orientation, and it is shown how three point correspondences (blobs at the finger tips) and three line correspondences (ridge features at the fingers) allow the affine trifocal tensor to be determined, from which the rotation is computed. Besides the obvious application, this test problem illustrates the usefulness of the affine trifocal tensor in a situation where sufficient information is not available to compute the perspective trilinear tensor, while the geometry requires point correspondences as well as line correspondences over at least three views.

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  • 69.
    Brocke, Ekaterina
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Djurfeldt, Mikael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Efficient spike communication in the MUSIC multi-simulation framework2011Ingår i: Twentieth Annual Computational Neuroscience Meeting: CNS*2011, Springer Science+Business Media B.V., 2011Konferensbidrag (Refereegranskat)
  • 70. Brodin, L
    et al.
    Shupliakov, O
    Pieribone, V
    Hellgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Hill, R.H.
    The reticulospinal glutamate synapse in lamprey: plasticity and presynaptic variability1994Ingår i: Journal of Neurophysiology, ISSN 0022-3077, E-ISSN 1522-1598, Vol. 72, s. 592-604Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    1. The glutamatergic synapses formed between the unbranched giant reticulospinal axons onto spinal neurons in lamprey offer a central vertebrate synapse in which the presynaptic element can be impaled with one or several microelectrodes, which may be used for recording as well as microinjection of different substances. To provide a basis for the use of this synapse in studies of release mechanisms, we have examined the use-dependent modulation of the synaptic response under conditions of conventional cell body stimulation, and during direct stimulation of the presynaptic axon. 2. To examine the stability of the mixed electrotonic and chemical reticulospinal excitatory postsynaptic potential (EPSP) over time, action potentials were evoked at a rate of 1 Hz for 800-1000 trials. In three out of seven synapses the chemical component remained at a similar amplitude, while in four cases a progressive decrease (up to 35%) occurred. The electrotonic component remained at a similar amplitude in all cases. 3. During paired pulse stimulation of the reticulospinal cell body (pulse interval 65 ms) the chemical EPSP component showed a net facilitation in all cases tested [from 0.64 +/- 0.35 to 0.89 +/- 0.48 (SD) mV, n = 13], while the peak amplitude of the electrotonic component was unchanged (1.37 +/- 0.68 and 1.36 +/- 0.66 mV, respectively). Recording of the axonal action potential during paired pulse stimulation showed that the width of the first and second action potential did not differ [1/2 width (2.48 +/- 0.39 ms and 2.48 +/- 0.42 ms, respectively; n = 8)]. 4. The degree of facilitation varied markedly between different synapses, ranging from an increase of a few percent to a two-fold increase (24 +/- 16% mean change of total EPSP amplitude, corresponding to 44 +/- 26% mean change of chemical EPSP amplitude). This type of variability was also observed in synapses made from the same unbranched reticulospinal axon onto different postsynaptic cells. 5. When paired pulse stimulation was applied to the reticulospinal axon in the very vicinity of the synaptic area (0.1-1 mm) a net depression of the chemical component occurred in 11 out of 19 cases, and in the remaining cases the level of net facilitation was lower as compared with cell body stimulation (range between +17 and -23% change of total EPSP amplitude; mean -5%; n = 19). 6. To test if the change of the EPSP plasticity during local stimulation correlated with an increased transmitter release, two microelectrodes were placed in the same reticulospinal axon at different distances from the synaptic area.(ABSTRACT TRUNCATED AT 400 WORDS)

  • 71. Bruederle, Daniel
    et al.
    Petrovici, Mihai A.
    Vogginger, Bernhard
    Ehrlich, Matthias
    Pfeil, Thomas
    Millner, Sebastian
    Gruebl, Andreas
    Wendt, Karsten
    Mueller, Eric
    Schwartz, Marc-Olivier
    de Oliveira, Dan Husmann
    Jeltsch, Sebastian
    Fieres, Johannes
    Schilling, Moritz
    Mueller, Paul
    Breitwieser, Oliver
    Petkov, Venelin
    Muller, Lyle
    Davison, Andrew P.
    Krishnamurthy, Pradeep
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Kremkow, Jens
    Lundqvist, Mikael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Muller, Eilif
    Partzsch, Johannes
    Scholze, Stefan
    Zuehl, Lukas
    Mayr, Christian
    Destexhe, Alain
    Diesmann, Markus
    Potjans, Tobias C.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Schueffny, Rene
    Schemmel, Johannes
    Meier, Karlheinz
    A comprehensive workflow for general-purpose neural modeling with highly configurable neuromorphic hardware systems2011Ingår i: Biological Cybernetics, ISSN 0340-1200, E-ISSN 1432-0770, Vol. 104, nr 4-5, s. 263-296Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this article, we present a methodological framework that meets novel requirements emerging from upcoming types of accelerated and highly configurable neuromorphic hardware systems. We describe in detail a device with 45 million programmable and dynamic synapses that is currently under development, and we sketch the conceptual challenges that arise from taking this platform into operation. More specifically, we aim at the establishment of this neuromorphic system as a flexible and neuroscientifically valuable modeling tool that can be used by non-hardware experts. We consider various functional aspects to be crucial for this purpose, and we introduce a consistent workflow with detailed descriptions of all involved modules that implement the suggested steps: The integration of the hardware interface into the simulator-independent model description language PyNN; a fully automated translation between the PyNN domain and appropriate hardware configurations; an executable specification of the future neuromorphic system that can be seamlessly integrated into this biology-to-hardware mapping process as a test bench for all software layers and possible hardware design modifications; an evaluation scheme that deploys models from a dedicated benchmark library, compares the results generated by virtual or prototype hardware devices with reference software simulations and analyzes the differences. The integration of these components into one hardware-software workflow provides an ecosystem for ongoing preparative studies that support the hardware design process and represents the basis for the maturity of the model-to-hardware mapping software. The functionality and flexibility of the latter is proven with a variety of experimental results.

  • 72.
    Brunnström, Kjell
    et al.
    KTH, Tidigare Institutioner (före 2005), Numerisk analys och datalogi, NADA.
    Eklundh, Jan-Olof
    KTH, Tidigare Institutioner (före 2005), Numerisk analys och datalogi, NADA.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    On Scale and Resolution in the Analysis of Local Image Structure1990Ingår i: Proc. 1st European Conf. on Computer Vision, 1990, Vol. 427, s. 3-12Konferensbidrag (Refereegranskat)
    Abstract [en]

    Focus-of-attention is extremely important in human visual perception. If computer vision systems are to perform tasks in a complex, dynamic world they will have to be able to control processing in a way that is analogous to visual attention in humans.

    In this paper we will investigate problems in connection with foveation, that is examining selected regions of the world at high resolution. We will especially consider the problem of finding and classifying junctions from this aspect. We will show that foveation as simulated by controlled, active zooming in conjunction with scale-space techniques allows robust detection and classification of junctions.

  • 73.
    Brunnström, Kjell
    et al.
    KTH, Tidigare Institutioner, Numerisk analys och datalogi, NADA.
    Eklundh, Jan-Olof
    KTH, Tidigare Institutioner, Numerisk analys och datalogi, NADA.
    Lindeberg, Tony
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Scale and Resolution in Active Analysis of Local Image Structure1990Ingår i: Image and Vision Computing, Vol. 8, s. 289-296Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Focus-of-attention is extremely important in human visual perception. If computer vision systems are to perform tasks in a complex, dynamic world they will have to be able to control processing in a way that is analogous to visual attention in humans. Problems connected to foveation (examination of selected regions of the world at high resolution) are examined. In particular, the problem of finding and classifying junctions from this aspect is considered. It is shown that foveation as simulated by controlled, active zooming in conjunction with scale-space techniques allows for robust detection and classification of junctions.

  • 74. Bujan, Alejandro
    et al.
    Aertsen, Ad
    Kumar, Arvind
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. University of Freiburg, Freiburg, Germany .
    Role of Input Correlations in Shaping the Variability and Noise Correlations of Evoked Activity in the Neocortex2015Ingår i: Journal of Neuroscience, ISSN 0270-6474, E-ISSN 1529-2401, Vol. 35, nr 22, s. 8611-8625Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Recent analysis of evoked activity recorded across different brain regions and tasks revealed a marked decrease in noise correlations and trial-by-trial variability. Given the importance of correlations and variability for information processing within the rate coding paradigm, several mechanisms have been proposed to explain the reduction in these quantities despite an increase in firing rates. These models suggest that anatomical clusters and/or tightly balanced excitation-inhibition can generate intrinsic network dynamics that may exhibit a reduction in noise correlations and trial-by-trial variability when perturbed by an external input. Such mechanisms based on the recurrent feedback crucially ignore the contribution of feedforward input to the statistics of the evoked activity. Therefore, we investigated how statistical properties of the feedforward input shape the statistics of the evoked activity. Specifically, we focused on the effect of input correlation structure on the noise correlations and trial-by-trial variability. We show that the ability of neurons to transfer the input firing rate, correlation, and variability to the output depends on the correlations within the presynaptic pool of a neuron, and that an input with even weak within-correlations can be sufficient to reduce noise correlations and trial-by-trial variability, without requiring any specific recurrent connectivity structure. In general, depending on the ongoing activity state, feedforward input could either increase or decrease noise correlation and trial-by-trial variability. Thus, we propose that evoked activity statistics are jointly determined by the feedforward and feedback inputs.

  • 75. Celani, A.
    et al.
    Bo, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Eichhorn, Ralf
    KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Skolan för elektro- och systemteknik (EES), Centra, ACCESS Linnaeus Centre.
    Anomalous thermodynamics at the microscale2012Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 109, nr 26, s. 260603-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Particle motion at the microscale is an incessant tug-of-war between thermal fluctuations and applied forces on one side and the strong resistance exerted by fluid viscosity on the other. Friction is so strong that completely neglecting inertia - the overdamped approximation - gives an excellent effective description of the actual particle mechanics. In sharp contrast to this result, here we show that the overdamped approximation dramatically fails when thermodynamic quantities such as the entropy production in the environment are considered, in the presence of temperature gradients. In the limit of vanishingly small, yet finite, inertia, we find that the entropy production is dominated by a contribution that is anomalous, i.e., has no counterpart in the overdamped approximation. This phenomenon, which we call an entropic anomaly, is due to a symmetry breaking that occurs when moving to the small, finite inertia limit. Anomalous entropy production is traced back to futile phase-space cyclic trajectories displaying a fast downgradient sweep followed by a slow upgradient return to the original position.

  • 76. Cervenka, Simon
    et al.
    Varrone, Andrea
    Fransén, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Halldin, Christer
    Farde, Lars
    PET Studies of D2-Receptor Binding in Striatal and Extrastriatal Brain Regions: Biochemical Support In Vivo for Separate Dopaminergic Systems in Humans2010Ingår i: Synapse, ISSN 0887-4476, E-ISSN 1098-2396, Vol. 64, nr 6, s. 478-485Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Most molecular imaging studies of the dopamine (DA) system performed to date have focused on the striatum, a region receiving dense dopaminergic innervation. In clinical research on the DA D2-receptor, striatal binding has often been regarded as an index of global DA function, based on the underlying assumption of common regulatory mechanisms for receptor expression across brain regions. Recent data has challenged this view, suggesting differences in genetic regulation between striatal and extrastriatal brain regions. The relationship between binding levels in brain regions has, however, not been directly examined in the same sample. In this study, we searched for interregional correlations between DA D2-receptor availability as determined with Positron Emission Tomography in 16 control subjects. The radioligands [C-11]raclopride and [C-11]FLB 457 were used for measurements of D2-receptor binding in striatal and extrastriatal regions, respectively. No correlation was observed between D2-receptor availability in striatum and any of the extrastriatal regions, as assessed using both region of interest- and voxel-based analyses. Instead, the pattern of correlations was consistent with the model of separate dopaminergic systems as has been originally observed in rodents. These preliminary results encourage approaches searching for individual patterns of receptor binding across the whole brain volume in clinical studies on the dopamine system.

  • 77.
    Chatterjee, Saikat
    et al.
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    Koslicki, David
    Dept of Mathematics, Oregon State University, Corvallis, USA.
    Dong, Siyuan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Cheng, Lu
    Dept of Mathematics and Statistics, University of Helsinki, Finland.
    Lan, Yueheng
    Dept of Physics, Tsinghua University, Beijing, China.
    Vehkaperä, Mikko
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    Skoglund, Mikael
    KTH, Skolan för elektro- och systemteknik (EES), Centra, ACCESS Linnaeus Centre. KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    K. Rasmussen, Lars
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Corander, Jukka
    Dept of Signal Processing, Aalto University, Finland.
    SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition2014Ingår i: Bioinformatics, ISSN 1460-2059, Vol. 30, nr 17, s. 2423-2431Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment.

    Results: Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method.

    Availability and implementation: A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.

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  • 78. Chen, Fu
    et al.
    Werner, Maria
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Gish, Gerald
    Ernberg, Ingemar
    Integrin β4 Interacts with Syk: Effects on Migration of Epithelial CellsManuskript (preprint) (Övrigt vetenskapligt)
  • 79. Chiel, Hillel J.
    et al.
    Ting, Lena H.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Hartmann, Mitra J. Z.
    The Brain in Its Body: Motor Control and Sensing in a Biomechanical Context2009Ingår i: Journal of Neuroscience, ISSN 0270-6474, E-ISSN 1529-2401, Vol. 29, nr 41, s. 12807-12814Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Although it is widely recognized that adaptive behavior emerges from the ongoing interactions among the nervous system, the body, and the environment, it has only become possible in recent years to experimentally study and to simulate these interacting systems. We briefly review work on molluscan feeding, maintenance of postural control in cats and humans, simulations of locomotion in lamprey, insect, cat and salamander, and active vibrissal sensing in rats to illustrate the insights that can be derived from studies of neural control and sensing within a biomechanical context. These studies illustrate that control may be shared between the nervous system and the periphery, that neural activity organizes degrees of freedom into biomechanically meaningful subsets, that mechanics alone may play crucial roles in enforcing gait patterns, and that mechanics of sensors is crucial for their function.

  • 80.
    Cürüclü, Baran
    et al.
    Mälardalens högskola.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Quantitative Assessment of the Local and Long-Range Horizontal Connections within the Striate Cortex2003Konferensbidrag (Övrigt vetenskapligt)
  • 81. Daniel, C.
    et al.
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Öhman, M.
    RNA editing of non-coding RNA and its role in gene regulation2015Ingår i: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 117, s. 22-27Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    It has for a long time been known that repetitive elements, particularly Alu sequences in human, are edited by the adenosine deaminases acting on RNA, ADAR, family. The functional interpretation of these events has been even more difficult than that of editing events in coding sequences, but today there is an emerging understanding of their downstream effects. A surprisingly large fraction of the human transcriptome contains inverted Alu repeats, often forming long double stranded structures in RNA transcripts, typically occurring in introns and UTRs of protein coding genes. Alu repeats are also common in other primates, and similar inverted repeats can frequently be found in non-primates, although the latter are less prone to duplex formation. In human, as many as 700,000 Alu elements have been identified as substrates for RNA editing, of which many are edited at several sites. In fact, recent advancements in transcriptome sequencing techniques and bioinformatics have revealed that the human editome comprises at least a hundred million adenosine to inosine (A-to-I) editing sites in Alu sequences. Although substantial additional efforts are required in order to map the editome, already present knowledge provides an excellent starting point for studying cis-regulation of editing. In this review, we will focus on editing of long stem loop structures in the human transcriptome and how it can effect gene expression.

  • 82. De Schutter, E.
    et al.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Hellgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Achard, P.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Biophysically detailed modelling of microcircuits and beyond2005Ingår i: TINS - Trends in Neurosciences, ISSN 0166-2236, E-ISSN 1878-108X, Vol. 28, nr 10, s. 562-569Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Realistic bottom-up modelling has been seminal to understanding which properties of microcircuits control their dynamic behaviour, such as the locomotor rhythms generated by central pattern generators. In this article of the TINS Microcircuits Special Feature, we review recent modelling work on the leech-heartbeat and lamprey-swimming pattern generators as examples. Top-down mathematical modelling also has an important role in analyzing microcircuit properties but it has not always been easy to reconcile results from the two modelling approaches. Most realistic microcircuit models are relatively simple and need to be made more detailed to represent complex processes more accurately. We review methods to add neuromechanical feedback, biochemical pathways or full dendritic morphologies to microcircuit models. Finally, we consider the advantages and challenges of full-scale simulation of networks of microcircuits.

  • 83.
    Del Ferraro, Gino
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Skolan för elektro- och systemteknik (EES), Centra, ACCESS Linnaeus Centre. Aalto University, Finland.
    Dynamic message-passing approach for kinetic spin models with reversible dynamics2015Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 92, nr 1, artikel-id 010102Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A method to approximately close the dynamic cavity equations for synchronous reversible dynamics on a locally treelike topology is presented. The method builds on (a) a graph expansion to eliminate loops from the normalizations of each step in the dynamics and (b) an assumption that a set of auxilary probability distributions on histories of pairs of spins mainly have dependencies that are local in time. The closure is then effectuated by projecting these probability distributions on n-step Markov processes. The method is shown in detail on the level of ordinary Markov processes (n = 1) and outlined for higher-order approximations (n > 1). Numerical validations of the technique are provided for the reconstruction of the transient and equilibrium dynamics of the kinetic Ising model on a random graph with arbitrary connectivity symmetry.

  • 84.
    Del Ferraro, Gino
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Perturbative large deviation analysis of non-equilibrium dynamics2014Ingår i: Journal of the Physical Society of Japan, ISSN 0031-9015, E-ISSN 1347-4073, Vol. 83, nr 8Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Macroscopic fluctuation theory has shown that a wide class of non-equilibrium stochastic dynamical systems obey a large deviation principle, but except for a few one-dimensional examples these large deviation principles are in general not known in closed form. We consider the problem of constructing successive approximations to an (unknown) large deviation functional and show that the non-equilibrium probability distribution the takes a Gibbs-Boltzmann form with a set of auxiliary (non-physical) energy functions. The expectation values of these auxiliary energy functions and their conjugate quantities satisfy a closed system of equations which can imply a considerable reduction of dimensionality of the dynamics. We show that the accuracy of the approximations can be tested self-consistently without solving the full non- equilibrium equations. We test the general procedure on the simple model problem of a relaxing 1D Ising chain. 

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  • 85.
    Del Ferraro, Gino
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Wang, Chuang
    Zhou, Hai-Jun
    Aurell, Erik
    KTH, Skolan för elektro- och systemteknik (EES), Centra, ACCESS Linnaeus Centre. Aalto University, Finland.
    On one-step replica symmetry breaking in the Edwards-Anderson spin glass model2016Ingår i: Journal of statistical physics, ISSN 0022-4715, E-ISSN 1572-9613, artikel-id 073305Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We consider a one-step replica symmetry breaking description of the Edwards–Anderson spin glass model in 2D. The ingredients of this description are a Kikuchi approximation to the free energy and a second-level statistical model built on the extremal points of the Kikuchi approximation, which are also fixed points of a generalized belief propagation (GBP) scheme. We show that a generalized free energy can be constructed where these extremal points are exponentially weighted by their Kikuchi free energy and a Parisi parameter y, and that the Kikuchi approximation of this generalized free energy leads to second-level, one-step replica symmetry breaking (1RSB), GBP equations. We then proceed analogously to the Bethe approximation case for tree-like graphs, where it has been shown that 1RSB belief propagation equations admit a survey propagation solution. We discuss when and how the one-step-replica symmetry breaking GBP equations that we obtain also allow a simpler class of solutions which can be interpreted as a class of generalized survey propagation equations for the single instance graph case.

  • 86.
    Djurfeldt, Mikael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Large-scale simulation of neuronal systems2009Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Biologically detailed computational models of large-scale neuronal networks have now become feasible due to the development of increasingly powerful massively parallel supercomputers. We report here about the methodology involved in simulation of very large neuronal networks. Using conductance-based multicompartmental model neurons based on Hodgkin-Huxley formalism, we simulate a neuronal network model of layers II/III of the neocortex. These simulations, the largest of this type ever performed, were made on the Blue Gene/L supercomputer and comprised up to 8 million neurons and 4 billion synapses. Such model sizes correspond to the cortex of a small mammal. After a series of optimization steps, performance measurements show linear scaling behavior both on the Blue Gene/L supercomputer and on a more conventional cluster computer. Results from the simulation of a model based on more abstract formalism, and of considerably larger size, also shows linear scaling behavior on both computer architectures.

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  • 87.
    Djurfeldt, Mikael
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Large-scale modeling - a tool for conquering the complexity of the brain2008Ingår i: Frontiers in Neuroinformatics, ISSN 1662-5196, E-ISSN 1662-5196, Vol. 2, s. 1-4Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Is there any hope of achieving a thorough understanding of higher functions such as perception, memory, thought and emotion or is the stunning complexity of the brain a barrier which will limit such efforts for the foreseeable future? In this perspective we discuss methods to handle complexity, approaches to model building, and point to detailed large-scale models as a new contribution to the toolbox of the computational neuroscientist. We elucidate some aspects which distinguishes large-scale models and some of the technological challenges which they entail.

  • 88.
    Djurfeldt, Mikael
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Hjorth, Johannes
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Eppler, Jochen
    Honda Research Institute.
    Dudani, Niraj
    Helias, Moritz
    University of Freiburg, Germany.
    Potjans, Tobias
    Bhalla, Upinder
    Diesmann, Markus
    Hellgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Run-Time Interoperability Between Neuronal Network Simulators Based on the MUSIC Framework2010Ingår i: Neuroinformatics, ISSN 1539-2791, E-ISSN 1559-0089, Vol. 8, nr 1, s. 43-60Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    MUSIC is an API allowing large scale neuron simulators using MPI internally to exchange data during runtime. We provide experiences from the adaptation of two neuronal network simulators of different kinds, NEST and MOOSE, to this API. A multi-simulation of a cortico-striatal network model involving both simulators is performed, demonstrating how MUSIC can promote inter-operability between models written for different simulators and how these can be re-used to build a larger model system. We conclude that MUSIC fulfills the design goals of being portable and simple to adapt to existing simulators. In addition, since the MUSIC API enforces independence between the applications, the multi-simulationcould be built from pluggable component modules without adaptation of the components to each other in terms of simulation time-step or topology of connections between the modules.

  • 89.
    Djurfeldt, Mikael
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Johansson, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk Analys och Datalogi, NADA.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Rehn, Martin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lundqvist, Mikael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Massively parallel simulation of brain-scale neuronal network models2005Rapport (Övrigt vetenskapligt)
    Ladda ner fulltext (pdf)
    FULLTEXT01
  • 90.
    Djurfeldt, Mikael
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    1st INCF Workshop on Large-scale Modeling of the Nervous System2007Rapport (Övrigt vetenskapligt)
  • 91.
    Djurfeldt, Mikael
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Memory capacity in a model of cortical layers II/III2008Konferensbidrag (Refereegranskat)
  • 92.
    Djurfeldt, Mikael
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lundqvist, Mikael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Johansson, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Rehn, Martin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Brain-scale simulation of the neocortex on the IBM Blue Gene/L  supercomputer2008Ingår i: IBM Journal of Research and Development, ISSN 0018-8646, E-ISSN 2151-8556, Vol. 52, nr 1-2, s. 31-41Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Biologically detailed large-scale models of the brain can now be simulated thanks to increasingly powerful massively parallel supercomputers. We present an overview, for the general technical reader, of a neuronal network model of layers II/III of the neocortex built with biophysical model neurons. These simulations, carried out on an IBM Blue Gene/Le supercomputer, comprise up to 22 million neurons and 11 billion synapses, which makes them the largest simulations of this type ever performed. Such model sizes correspond to the cortex of a small mammal. The SPLIT library, used for these simulations, runs on single-processor as well as massively parallel machines. Performance measurements show good scaling behavior on the Blue Gene/L supercomputer up to 8,192 processors. Several key phenomena seen in the living brain appear as emergent phenomena in the simulations. We discuss the role of this kind of model in neuroscience and note that full-scale models may be necessary to preserve natural dynamics. We also discuss the need for software tools for the specification of models as well as for analysis and visualization of output data. Combining models that range from abstract connectionist type to biophysically detailed will help us unravel the basic principles underlying neocortical function.

  • 93. Dominguez, Eduardo
    et al.
    Del Ferraro, Gino
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Ricci-Tersenghi, Federico
    A simple approach to the dynamics of Ising spin systemsManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    We study a novel variational approach to solve the dynamics of Ising-like discrete spin systems. The equations are derived under mean-field approximations based on the cluster variational method. Comparison with the actual Glauber dynamics of models defined on Erdos-R\'enyi random graphs show that some of these approximations are extremely accurate, both at equilibrium and in the off-equilibrium regime, providing the same result of the Monte Carlo simulation in a much shorter time. The models studied are the ferromagnetic kinetic Ising model (both with symmetric and partially asymmetric interactions), the random field Ising model and the Viana-Bray model. Only for the latter model we find some small discrepancies in the very low temperature phase, probably due to the existence of a large number of metastable states.

    Ladda ner fulltext (pdf)
    fulltext
  • 94.
    DONG, SIYUAN
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. Aalto University.
    A time dependent adaptive learning process for estimating drug exposure from register data - applied to insulin and its analogues2013Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Ladda ner fulltext (pdf)
    My_thesis
  • 95.
    Dong, Siyuan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    A time dependent adaptive learning process for estimating drug exposure from register data - applied to insulin and its analogues2013Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Ladda ner fulltext (pdf)
    fulltext
  • 96.
    Edin, Fredrik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Alpha synchronization after training of visuospatial working memory in patients with epilepsyManuskript (Övrigt vetenskapligt)
  • 97.
    Edin, Fredrik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Flexible Prefrontal Bias Signals Regulate Capacity and Access to Working Memory2008Manuskript (preprint) (Övrigt vetenskapligt)
  • 98.
    Edin, Fredrik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Scaling errors in measures of brain activity cause erroneous estimates of effective connectivity2010Ingår i: NeuroImage, ISSN 1053-8119, E-ISSN 1095-9572, Vol. 49, nr 1, s. 621-630Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Effective connectivity (EC) is the collective term for various measures of the interaction between the nodes in a network of neurons or neural populations during a certain experimental condition. Here, I investigated three types of EC that differ with respect to signal normalization, and therefore measure different aspects of neural interactions. Unnormalized EC measures pure connection strength. Amplitude-scaled EC measures the combined influence of signal amplitude and connection strength on neural activity. Finally, normalized EC measures the influence of one node on the activity of another relative to all influences on that node. With a theoretical analysis, I investigated the sensitivity of EC to signal scaling (the ratio of the amplitude of the measured signal and the underlying neural activity) and found that scaling affects the conclusions of the analysis of unnormalized EC severely, whereas normalized EC is not affected by the scaling problem. In an analysis of previously published hemodynamic response functions (Handwerker, D. A., Ollinger, J. M., D'Esposito, M., 2004. Variation of BOLD hemodynamic responses across subjects and brain regions and their effects on statistical analyses. Neuroimage 21, 1639-1651), I tested the predictions of the theoretical analysis. The empirical analysis indicated that signal scaling contributes to a large extent to measurement errors of unnormalized EC, although hemodynamic response function shape variability also contributed. Normalized EC, on the other hand, was only affected by shape differences and not by scaling. In addition to being more accurate, normalized EC is also an appropriate type of measure of neural interactivity if one is interested in the relative influence of one node on another, rather than absolute connection strengths per se.

  • 99.
    Edin, Fredrik
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Klingberg, T.
    Karolinska Institutet, Stockholm.
    Stödberg, T.
    Karolinska Institutet, Stockholm.
    Tegnér, J.
    Karolinska Institutet, Stockholm.
    Fronto-Pariatal connection asymmetry regulates working memory distractibility2007Ingår i: Journal of Integrative Neuroscience, ISSN 0219-6352, E-ISSN 1757-448X, Vol. 6, nr 4, s. 567-596Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Recent functional magnetic resonance imaging studies demonstrate that increased task-related neural activity in parietal and frontal cortex during development and training is positively correlated with improved visuospatial working memory (vsWM) performance. Yet, the analysis of the corresponding underlying functional reorganization of the fronto-parietal network has received little attention. Here, we perform an integrative experimental and computational analysis to determine the effective balance between the superior frontal sulcus (SFS) and intraparietal sulcus (IPS) and their putative role(s) in protecting against distracters. To this end, we performed electroencephalographic (EEG) recordings during a vsWM task. We utilized a biophysically based computational cortical network model to analyze the effects of different neural changes in the underlying cortical networks on the directed transfer function (DTF) and spiking activity. Combining a DTF analysis of our EEG data with the DTF analysis of the computational model, a directed strong SFS → IPS network was revealed. Such a configuration offers protection against distracters, whereas the opposite is true for strong IPS → SFS connections. Our results therefore suggest that the previously demonstrated improvement of vsWM performance during development could be due to a shift in the control of the effective balance between the SFS-IPS networks.

  • 100.
    Edin, Fredrik
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Klingberg, Torkel
    Johansson, Par
    McNab, Fiona
    Tegner, Jesper
    Compte, Albert
    Mechanism for top-down control of working memory capacity2009Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, nr 16, s. 6802-6807Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Working memory capacity, the maximum number of items that we can transiently store in working memory, is a good predictor of our general cognitive abilities. Neural activity in both dorsolateral prefrontal cortex and posterior parietal cortex has been associated with memory retention during visuospatial working memory tasks. The parietal cortex is thought to store the memories. However, the role of the dorsolateral prefrontal cortex, a top-down control area, during pure information retention is debated, and the mechanisms regulating capacity are unknown. Here, we propose that a major role of the dorsolateral prefrontal cortex in working memory is to boost parietal memory capacity. Furthermore, we formulate the boosting mechanism computationally in a biophysical cortical microcircuit model and derive a simple, explicit mathematical formula relating memory capacity to prefrontal and parietal model parameters. For physiologically realistic parameter values, lateral inhibition in the parietal cortex limits mnemonic capacity to a maximum of 2-7 items. However, at high loads inhibition can be counteracted by excitatory prefrontal input, thus boosting parietal capacity. Predictions from the model were confirmed in an fMRI study. Our results show that although memories are stored in the parietal cortex, interindividual differences in memory capacity are partly determined by the strength of prefrontal top-down control. The model provides a mechanistic framework for understanding top-down control of working memory and specifies two different contributions of prefrontal and parietal cortex to working memory capacity.

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