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  • 1.
    Hertz, John A.
    et al.
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). University of Copenhagen, Denmark.
    Roudi, Yasser
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway; Institute for Advanced Study, Princeton, NJ, USA.
    Sollich, Peter
    Path integral methods for the dynamics of stochastic and disordered systems2017Inngår i: Journal of Physics A: Mathematical and Theoretical, ISSN 1751-8113, E-ISSN 1751-8121, Vol. 50, nr 3, artikkel-id 033001Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    We review some of the techniques used to study the dynamics of disordered systems subject to both quenched and fast (thermal) noise. Starting from the Martin-Siggia-Rose/Janssen-De Dominicis-Peliti path integral formalism for a single variable stochastic dynamics, we provide a pedagogical survey of the perturbative, i.e. diagrammatic, approach to dynamics and how this formalism can be used for studying soft spin models. We review the supersymmetric formulation of the Langevin dynamics of these models and discuss the physical implications of the supersymmetry. We also describe the key steps involved in studying the disorder-averaged dynamics. Finally, we discuss the path integral approach for the case of hard Ising spins and review some recent developments in the dynamics of such kinetic Ising models.

  • 2.
    Hertz, John
    et al.
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    Roudi, Yasser
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    Thorning, Andreas
    Niels Bohr Institute, Copenhagen University, 2100 Copenhagen Ø, Denmark .
    Tyrcha, Joanna
    Stockholms universitet, Naturvetenskapliga fakulteten, Matematiska institutionen.
    Aurell, Erik
    Department of Computational Biology, Royal Institute of Technology, 106 91 Stockholm, Sweden .
    Zeng, Hong-Li
    Department of Applied Physics, Helsinki University of Technology, 02015 TKK Espoo, Finland .
    Inferring network connectivity using kinetic Ising models2010Inngår i: BMC neuroscience (Online), ISSN 1471-2202, E-ISSN 1471-2202, Vol. 11, nr Suppl 1, s. P51-Artikkel i tidsskrift (Fagfellevurdert)
  • 3. Jovanovic, Stojan
    et al.
    Hertz, John
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). University of Copenhagen, Denmark.
    Rotter, Stefan
    Cumulants of Hawkes point processes2015Inngår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 91, nr 4, artikkel-id 042802Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We derive explicit, closed-form expressions for the cumulant densities of a multivariate, self-exciting Hawkes point process, generalizing a result of Hawkes in his earlier work on the covariance density and Bartlett spectrum of such processes. To do this, we represent the Hawkes process in terms of a Poisson cluster process and show how the cumulant density formulas can be derived by enumerating all possible family trees, representing complex interactions between point events. We also consider the problem of computing the integrated cumulants, characterizing the average measure of correlated activity between events of different types, and derive the relevant equations.

  • 4.
    Roudi, Yasser
    et al.
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    Tyrcha, Joanna
    Stockholms universitet, Naturvetenskapliga fakulteten, Matematiska institutionen.
    Hertz, John
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    Fast and realiable methods for extracting functional connectivity in large populations2009Inngår i: BMC neuroscience (Online), ISSN 1471-2202, E-ISSN 1471-2202, BMC Neuroscience, ISSN 1471-2202, Vol. 10, nr Suppl 1, s. 09-Artikkel i tidsskrift (Fagfellevurdert)
  • 5.
    Tyrcha, Joanna
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Matematiska institutionen.
    Hertz, John
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). Niels Bohr Institute, Copenhagen, Denmark.
    NETWORK INFERENCE WITH HIDDEN UNITS2014Inngår i: Mathematical Biosciences and Engineering, ISSN 1547-1063, E-ISSN 1551-0018, Vol. 11, nr 1, s. 149-165Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We derive learning rules for finding the connections between units in stochastic dynamical networks from the recorded history of a visible subset of the units. We consider two models. In both of them, the visible units are binary and stochastic. In one model the hidden units are continuous-valued, with sigmoidal activation functions, and in the other they are binary and stochastic like the visible ones. We derive exact learning rules for both cases. For the stochastic case, performing the exact calculation requires, in general, repeated summations over an number of configurations that grows exponentially with the size of the system and the data length, which is not feasible for large systems. We derive a mean field theory, based on a factorized ansatz for the distribution of hidden-unit states, which offers an attractive alternative for large systems. We present the results of some numerical calculations that illustrate key features of the two models and, for the stochastic case, the exact and approximate calculations.

  • 6.
    Tyrcha, Joanna
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Matematiska institutionen.
    Roudi, Yasser
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). Kavli Institute for Systems Neuroscience, NTNU, Norway.
    Marsili, Matteo
    Hertz, John
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). Niels Bohr Institute, Denmark.
    The effect of nonstationarity on models inferred from neural data2013Inngår i: Journal of Statistical Mechanics: Theory and Experiment, ISSN 1742-5468, E-ISSN 1742-5468, artikkel-id P03005Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Neurons subject to a common nonstationary input may exhibit a correlated firing behavior. Correlations in the statistics of neural spike trains also arise as the effect of interaction between neurons. Here we show that these two situations can be distinguished with machine learning techniques, provided that the data are rich enough. In order to do this, we study the problem of inferring a kinetic Ising model, stationary or nonstationary, from the available data. We apply the inference procedure to two data sets: one from salamander retinal ganglion cells and the other from a realistic computational cortical network model. We show that many aspects of the concerted activity of the salamander retinal neurons can be traced simply to the external input. A model of non-interacting neurons subject to a nonstationary external field outperforms a model with stationary input with couplings between neurons, even accounting for the differences in the number of model parameters. When couplings are added to the nonstationary model, for the retinal data, little is gained: the inferred couplings are generally not significant. Likewise, the distribution of the sizes of sets of neurons that spike simultaneously and the frequency of spike patterns as a function of their rank (Zipf plots) are well explained by an independent-neuron model with time-dependent external input, and adding connections to such a model does not offer significant improvement. For the cortical model data, robust couplings, well correlated with the real connections, can be inferred using the nonstationary model. Adding connections to this model slightly improves the agreement with the data for the probability of synchronous spikes but hardly affects the Zipf plot.

  • 7. Zeng, Hong-Li
    et al.
    Alava, Mikko
    Aurell, Erik
    Hertz, John
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    Roudi, Yasser
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    Maximum Likelihood Reconstruction for Ising Models with Asynchronous Updates2013Inngår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 110, nr 21, s. 210601-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We describe how the couplings in an asynchronous kinetic Ising model can be inferred. We consider two cases: one in which we know both the spin history and the update times and one in which we know only the spin history. For the first case, we show that one can average over all possible choices of update times to obtain a learning rule that depends only on spin correlations and can also be derived from the equations of motion for the correlations. For the second case, the same rule can be derived within a further decoupling approximation. We study all methods numerically for fully asymmetric Sherrington-Kirkpatrick models, varying the data length, system size, temperature, and external field. Good convergence is observed in accordance with the theoretical expectations.

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