Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals

A systematic assessment of global neural network connectivity through direct electrophysiological assays has remained technically infeasible, even in simpler systems like dissociated neuronal cultures. We introduce an improved algorithmic approach based on Transfer Entropy to reconstruct structural connectivity from network activity monitored through calcium imaging. We focus in this study on the inference of excitatory synaptic links. Based on information theory, our method requires no prior assumptions on the statistics of neuronal firing and neuronal connections. The performance of our algorithm is benchmarked on surrogate time series of calcium fluorescence generated by the simulated dynamics of a network with known ground-truth topology. We find that the functional network topology revealed by Transfer Entropy depends qualitatively on the time-dependent dynamic state of the network (bursting or non-bursting). Thus by conditioning with respect to the global mean activity, we improve the performance of our method. This allows us to focus the analysis to specific dynamical regimes of the network in which the inferred functional connectivity is shaped by monosynaptic excitatory connections, rather than by collective synchrony. Our method can discriminate between actual causal influences between neurons and spurious non-causal correlations due to light scattering artifacts, which inherently affect the quality of fluorescence imaging. Compared to other reconstruction strategies such as cross-correlation or Granger Causality methods, our method based on improved Transfer Entropy is remarkably more accurate. In particular, it provides a good estimation of the excitatory network clustering coefficient, allowing for discrimination between weakly and strongly clustered topologies. Finally, we demonstrate the applicability of our method to analyses of real recordings of in vitro disinhibited cortical cultures where we suggest that excitatory connections are characterized by an elevated level of clustering compared to a random graph (although not extreme) and can be markedly non-local.

Theory for correlation functions of processes driven by external colored noise

We study steady-state correlation functions of nonlinear stochastic processes driven by external colored noise. We present a methodology that provides explicit expressions of correlation functions approximating simultaneously short- and long-time regimes. The non-Markov nature is reduced to an effective Markovian formulation, and the nonlinearities are treated systematically by means of double expansions in high and low frequencies. We also derive some exact expressions for the coefficients of these expansions for arbitrary noise by means of a generalization of projection-operator techniques.

Processes models, environmental analyses, and cognitive architectures: Quo vadis quantum probability theory? (Commentary on Pothos and Busemeyer)

A lot of research in cognition and decision making suffers from a lack of formalism. The quantum probability program could help to improve this situation, but we wonder whether it would provide even more added value if its presumed focus on outcome models were complemented by process models that are, ideally, informed by ecological analyses and integrated into cognitive architectures.

Diffraction theory of Fresnel lenses encoded in low-resolution devices

A mathematical model that describes the behavior of low-resolution Fresnel lenses encoded in any low-resolution device (e.g., a spatial light modulator) is developed. The effects of low-resolution codification, such the appearance of new secondary lenses, are studied for a general case. General expressions for the phase of these lenses are developed, showing that each lens behaves as if it were encoded through all pixels of the low-resolution device. Simple expressions for the light distribution in the focal plane and its dependence on the encoded focal length are developed and commented on in detail. For a given codification device an optimum focal length is found for best lens performance. An optimization method for codification of a single lens with a short focal length is proposed.

Diffraction theory of optimized low-resolution Fresnel encoded lenses

A mathematical model describing the behavior of low-resolution Fresnel encoded lenses (LRFEL's) encoded in any low-resolution device (e.g., a spatial light modulator) has recently been developed. From this model, an LRFEL with a short focal length was optimized by our imposing the maximum intensity of light onto the optical axis. With this model, analytical expressions for the light-amplitude distribution, the diffraction efficiency, and the frequency response of the optimized LRFEL's are derived.

Vacuum decay in quantum field theory

We study the contribution to vacuum decay in field theory due to the interaction between the long- and short-wavelength modes of the field. The field model considered consists of a scalar field of mass M with a cubic term in the potential. The dynamics of the long-wavelength modes becomes diffusive in this interaction. The diffusive behavior is described by the reduced Wigner function that characterizes the state of the long-wavelength modes. This function is obtained from the whole Wigner function by integration of the degrees of freedom of the short-wavelength modes. The dynamical equation for the reduced Wigner function becomes a kind of Fokker-Planck equation which is solved with suitable boundary conditions enforcing an initial metastable vacuum state trapped in the potential well. As a result a finite activation rate is found, even at zero temperature, for the formation of true vacuum bubbles of size M-1. This effect makes a substantial contribution to the total decay rate.

Perturbations on domain walls and strings: A covariant theory

A covariant formalism is developed for describing perturbations on vacuum domain walls and strings. The treatment applies to arbitrary domain walls in (N+1)-dimensional flat spacetime, including the case of bubbles of a true vacuum nucleating in a false vacuum. Straight strings and planar walls in de Sitter space, as well as closed strings and walls nucleating during inflation, are also considered. Perturbations are represented by a scalar field defined on the unperturbed wall or string world sheet. In a number of interesting cases, this field has a tachyonic mass and a nonminimal coupling to the world-sheet curvature.

Perturbation theory for classical thermodynamic Green's functions

A systematic time-dependent perturbation scheme for classical canonical systems is developed based on a Wick's theorem for thermal averages of time-ordered products. The occurrence of the derivatives with respect to the canonical variables noted by Martin, Siggia, and Rose implies that two types of Green's functions have to be considered, the propagator and the response function. The diagrams resulting from Wick's theorem are "double graphs" analogous to those introduced by Dyson and also by Kawasaki, in which the response-function lines form a "tree structure" completed by propagator lines. The implication of a fluctuation-dissipation theorem on the self-energies is analyzed and compared with recent results by Deker and Haake.

On the Schoenberg transformations in data analysis: theory and illustrations

The class of Schoenberg transformations, embedding Euclidean distances into higher dimensional Euclidean spaces, is presented, and derived from theorems on positive definite and conditionally negative definite matrices. Original results on the arc lengths, angles and curvature of the transformations are proposed, and visualized on artificial data sets by classical multidimensional scaling. A distance-based discriminant algorithm and a robust multidimensional centroid estimate illustrate the theory, closely connected to the Gaussian kernels of Machine Learning.

Dissipation, noise and vacuum decay in quantum field theory

We study the process of vacuum decay in quantum field theory focusing on the stochastic aspects of the interaction between long- and short-wavelength modes. This interaction results in a diffusive behavior of the reduced Wigner function describing the state of long-wavelength modes, and thereby to a finite activation rate even at zero temperature. This effect can make a substantial contribution to the total decay rate.

Microstates of a neutral black hole in M theory

We consider vacuum solutions in M theory of the form of a five-dimensional Kaluza-Klein black hole cross T6. In a certain limit, these include the five-dimensional neutral rotating black hole (cross T6). From a type-IIA standpoint, these solutions carry D0 and D6 charges. We show that there is a simple D-brane description which precisely reproduces the Hawking-Bekenstein entropy in the extremal limit, even though supersymmetry is completely broken.