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WISDoM (Wishart Distributed Matrices) is a new framework for the quantification of deviation of symmetric positive-definite matrices associated to experimental samples, like covariance or correlation matrices, from expected ones governed by the Wishart distribution WISDoM can be applied to tasks of supervised learning, like classification, in particular when such matrices are generated by data of different dimensionality (e.g. time series with same number of variables but different time sampling). We show the application of the method in two different scenarios. The first is the ranking of features associated to electro encephalogram (EEG) data with a time series design, providing a theoretically sound approach for this type of studies. The second is the classification of autistic subjects of the ABIDE study, using brain connectivity measurements., Comment: 17 pages, 6 figures, submitted to Frontiers in Neuroinformatics

MR fingerprinting (MRF) is a rapid growing approach for fast quantitave MRI. A typical drawback of dictionary-based MRF is its explosion in size as a function of the number of reconstructed parameters, according to the curse of dimensionality. Deep Neural Networks (NNs) have been proposed as a feasible alternative, but these approaches are still in their infancy. We tested different NN pipelines on simulated data: we studied optimal training procedures by including different strategies of noise addition and parameter space sampling, to achieve better accuracy and robustness to noise. Four MRF sequences were considered, two of them designed to be more specific for $B_1^+$ parameter encoding: IR-FISP, IR-FISP-$B_1$, bSSFP and IR-bSSFP-$B_1$. A comparison between NN and the dictionary approaches was performed using a numerical brain phantom. Results demonstrated that training with random sampling and different levels of noise variance yielded the best performance. NN performance was greater or equal than dictionary-based approach in reconstructing MR parameter maps: the difference in performance increased with the number of estimated parameters, because the dictionary method suffers from the coarse resolution of the MR parameter space sampling. The NN approach resulted more efficient in terms of memory and computational burden, and thus has great potential in large-scale MRF problems.

Fractional extensions of the cable equation have been proposed in the literature to describe transmembrane potential in spiny dendrites. The anomalous behavior has been related in the literature to the geometrical properties of the system, in particular, the density of spines, by experiments, computer simulations, and in comb-like models.~The same PDE can be related to more than one stochastic process leading to anomalous diffusion behavior. The time-fractional diffusion equation can be associated to a continuous time random walk (CTRW) with power-law waiting time probability or to a special case of the Erd\'ely-Kober fractional diffusion, described by the ggBm. In this work, we show that time fractional generalization of the cable equation arises naturally in the CTRW by considering a superposition of Markovian processes and in a {\it ggBm-like} construction of the random variable., Comment: 8 pages

Complex systems display anomalous diffusion, whose signature is a space/time scaling $x\sim t^\delta$ with $\delta \ne 1/2$ in the Probability Density Function (PDF). Anomalous diffusion can emerge jointly with both Gaussian, e.g., fractional Brownian motion, and power-law decaying distributions, e.g., L\'evy Flights (LFs) or L\'evy Walks (LWs). LFs get anomalous scaling, but also infinite position variance and also infinite energy and discontinuous velocity. LWs are based on random trapping events, resemble a L\'evy-type power-law distribution that is truncated in the large displacement range and have finite moments, finite energy and discontinuous velocity. However, both LFs and LWs cannot describe friction-diffusion processes. We propose and discuss a model describing a Heterogeneous Ensemble of Brownian Particles (HEBP) based on a linear Langevin equation. We show that, for proper distributions of relaxation time and velocity diffusivity, the HEBP displays features similar to LWs, in particular power-law decaying PDF, long-range correlations and anomalous diffusion, at the same time keeping finite position moments and finite energy. The main differences between the HEBP model and two LWs are investigated, finding that, even if the PDFs are similar, they differ in three main aspects: (i) LWs are biscaling, while HEBP is monoscaling; (ii) a transition from anomalous ($\delta \ne 1/2$) to normal ($\delta = 1/2$) diffusion in the long-time regime; (iii) the power-law index of the position PDF and the space/time diffusion scaling are independent in the HEBP, while they both depend on the scaling of the inter-event time PDF in LWs. The HEBP model is derived from a friction-diffusion process, it has finite energy and it satisfies the fluctuation-dissipation theorem.

The problem of biological motion is a very intriguing and topical issue. Many efforts are being focused on the development of novel modeling approaches for the description of anomalous diffusion in biological systems, such as the very complex and heterogeneous cell environment. Nevertheless, many questions are still open, such as the joint manifestation of statistical features in agreement with different models that can be also somewhat alternative to each other, e.g., Continuous Time Random Walk (CTRW) and Fractional Brownian Motion (FBM). To overcome these limitations, we propose a stochastic diffusion model with additive noise and linear friction force (linear Langevin equation), thus involving the explicit modeling of velocity dynamics. The complexity of the medium is parameterized via a population of intensity parameters (relaxation time and diffusivity of velocity), thus introducing an additional randomness, in addition to white noise, in the particle's dynamics. We prove that, for proper distributions of these parameters, we can get both Gaussian anomalous diffusion, fractional diffusion and its generalizations.

We consider an ensemble of Ornstein-Uhlenbeck processes featuring a population of relaxation times and a population of noise amplitudes that characterize the heterogeneity of the ensemble. We show that the centre-of-mass like variable corresponding to this ensemble is statistically equivalent to a process driven by a non-autonomous stochastic differential equation with time- dependent drift and a white noise. In particular, the time scaling and the density function of such variable are driven by the population of timescales and of noise amplitudes, respectively. Moreover, we show that this variable is equivalent in distribution to a randomly-scaled Gaussian process, i.e., a process built by the product of a Gaussian process times a non-negative independent random variable. This last result establishes a connection with the so-called generalized gray Brownian motion and suggests application to model fractional anomalous diffusion in biological systems.

We propose an extension of the cable equation by introducing a Caputo time fractional derivative. The fundamental solutions of the most common boundary problems are derived analitically via Laplace Transform, and result be written in terms of known special functions. This generalization could be useful to describe anomalous diffusion phenomena with leakage as signal conduction in spiny dendrites. The presented solutions are computed in Matlab and plotted., Comment: 10 figures. arXiv admin note: substantial text overlap with arXiv:1702.05325

We perform a statistical study of the distances between successive occurrencies of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the dinucleotide CG distribution in mammalian DNA, pointing towards a connection with the role of such dinucleotide in DNA methylation. While the CG distributions of mammals exhibit exponential tails with comparable parameters, the picture for the other organisms studied (e.g., fish, insects, bacteria and viruses) is more heterogeneous, possibly because in these organisms DNA methylation has different functional roles. Our analysis suggests that the distribution of the distances between dinucleotides CG provides useful insights in characterizing and classifying organisms in terms of methylation functionalities., Comment: 13 pages, 5 figures. To be published in the Philosophical Transactions A theme issue "DNA as information"

In this paper we study noise-induced bistability in a specific circuit with many biological implications, namely a single-step enzymatic cycle described by Michaelis Menten equations with quasi-steady state assumption. We study the system both with a Master Equation formalism, and with the Fokker-Planck continuous approximation, characterizing the conditions in which the continuous approach is a good approximation of the exact discrete model. An analysis of the stationary distribution in both cases shows that bimodality can not occur in such a system. We discuss which additional requirements can generate stochastic bimodality, by coupling the system with a chemical reaction involving enzyme production and turnover. This extended system shows a bistable behaviour only in specific parameter windows depending on the number of molecules involved, providing hints about which should be a feasible system size in order that such a phenomenon could be exploited in real biological systems., Comment: 6 pages, 4 figures

We analyze the effects of noise correlations in the input to, or among, BCM neurons using the Wigner semicircular law to construct random, positive-definite symmetric correlation matrices and compute their eigenvalue distributions. In the finite dimensional case, we compare our analytic results with numerical simulations and show the effects of correlations on the lifetimes of synaptic strengths in various visual environments. These correlations can be due either to correlations in the noise from the input LGN neurons, or correlations in the variability of lateral connections in a network of neurons. In particular, we find that for fixed dimensionality, a large noise variance can give rise to long lifetimes of synaptic strengths. This may be of physiological significance., Comment: 7 pages, 7 figures

In the study of the basic properties observed in the immune system and, in a broader view, in biological systems, several concepts have already been mathematically formulated or treated in an analytical perspective, such as degeneracy, robustness, noise, and bow tie architecture. These properties, among others, seem to rule many aspects of the system functioning, and share among themselvesseveral characteristics, intersecting each other, and often becoming one the indivisible part of the other. According to Kitano, systems biology needs solid theoretical and methodological foundation of principles and properties, able to lead towards a unified perspective. An effort in unifying the formalization and analysis of these principles can be now timely attempted., Comment: 3 pages, abstract of the poster and oral presentation at SBH2007 SysBioHealth Symposium, Systems Biology for Health, Milano, 17-19 October 2007

Immune cells coordinate their efforts for the correct and efficient functioning of the immune system (IS). Each cell type plays a distinct role and communicates with other cell types through mediators such as cytokines, chemokines and hormones, among others, that are crucial for the functioning of the IS and its fine tuning. Nevertheless, a quantitative analysis of the topological properties of an immunological network involving this complex interchange of mediators among immune cells is still lacking. Here we present a method for quantifying the relevance of different mediators in the immune network, which exploits a definition of centrality based on the concept of efficient communication. The analysis, applied to the human immune system, indicates that its mediators significantly differ in their network relevance. We found that cytokines involved in innate immunity and inflammation and some hormones rank highest in the network, revealing that the most prominent mediators of the IS are molecules involved in these ancestral types of defence mechanisms highly integrated with the adaptive immune response, and at the interplay among the nervous, the endocrine and the immune systems., Comment: 10 pages, 3 figures

The influx of calcium ions into the dendritic spines through the N-metyl-D-aspartate (NMDA) channels is believed to be the primary trigger for various forms of synaptic plasticity. In this paper, the authors calculate analytically the mean values of the calcium transients elicited by a spiking neuron undergoing a simple model of ionic currents and back-propagating action potentials. The relative variability of these transients, due to the stochastic nature of synaptic transmission, is further considered using a simple Markov model of NMDA receptos. One finds that both the mean value and the variability depend on the timing between pre- and postsynaptic action-potentials. These results could have implications on the expected form of synaptic-plasticity curve and can form a basis for a unified theory of spike time-dependent, and rate based plasticity., Comment: 14 pages, 10 figures. A few changes in section IV and addition of a new figure