Dynamic Decomposition of Spatiotemporal Neural Signals

Neural signals are characterized by rich temporal and spatiotemporal dynamics that reflect the organization of cortical networks. Theoretical research has shown how neural networks can operate at different dynamic ranges that correspond to specific types of information processing. Here we present a data analysis framework that uses a linearized model of these dynamic states in order to decompose the measured neural signal into a series of components that capture both rhythmic and non-rhythmic neural activity. The method is based on stochastic differential equations and Gaussian process regression. Through computer simulations and analysis of magnetoencephalographic data, we demonstrate the efficacy of the method in identifying meaningful modulations of oscillatory signals corrupted by structured temporal and spatiotemporal noise. These results suggest that the method is particularly suitable for the analysis and interpretation of complex temporal and spatiotemporal neural signals

Application of new probabilistic graphical models in the genetic regulatory networks studies

This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an Independence Graph (IG) model with either a forward or a backward search algorithm and the other one is a Gaussian Network (GN) model with a novel greedy search method. The performances of both models were evaluated on four MAPK pathways in yeast and three simulated data sets. Generally, an IG model provides a sparse graph but a GN model produces a dense graph where more information about gene-gene interactions is preserved. Additionally, we found two key limitations in the prediction of genetic regulatory networks using DNA microarray data, the first is the sufficiency of sample size and the second is the complexity of network structures may not be captured without additional data at the protein level. Those limitations are present in all prediction methods which used only DNA microarray data.Comment: 38 pages, 3 figure

Segmentation of Fault Networks Determined from Spatial Clustering of Earthquakes

We present a new method of data clustering applied to earthquake catalogs, with the goal of reconstructing the seismically active part of fault networks. We first use an original method to separate clustered events from uncorrelated seismicity using the distribution of volumes of tetrahedra defined by closest neighbor events in the original and randomized seismic catalogs. The spatial disorder of the complex geometry of fault networks is then taken into account by defining faults as probabilistic anisotropic kernels, whose structures are motivated by properties of discontinuous tectonic deformation and previous empirical observations of the geometry of faults and of earthquake clusters at many spatial and temporal scales. Combining this a priori knowledge with information theoretical arguments, we propose the Gaussian mixture approach implemented in an Expectation-Maximization (EM) procedure. A cross-validation scheme is then used and allows the determination of the number of kernels that should be used to provide an optimal data clustering of the catalog. This three-steps approach is applied to a high quality relocated catalog of the seismicity following the 1986 Mount Lewis ($M_l=5.7$) event in California and reveals that events cluster along planar patches of about 2 km$^2$, i.e. comparable to the size of the main event. The finite thickness of those clusters (about 290 m) suggests that events do not occur on well-defined euclidean fault core surfaces, but rather that the damage zone surrounding faults may be seismically active at depth. Finally, we propose a connection between our methodology and multi-scale spatial analysis, based on the derivation of spatial fractal dimension of about 1.8 for the set of hypocenters in the Mnt Lewis area, consistent with recent observations on relocated catalogs

Past and present cosmic structure in the SDSS DR7 main sample

We present a chrono-cosmography project, aiming at the inference of the four dimensional formation history of the observed large scale structure from its origin to the present epoch. To do so, we perform a full-scale Bayesian analysis of the northern galactic cap of the Sloan Digital Sky Survey (SDSS) Data Release 7 main galaxy sample, relying on a fully probabilistic, physical model of the non-linearly evolved density field. Besides inferring initial conditions from observations, our methodology naturally and accurately reconstructs non-linear features at the present epoch, such as walls and filaments, corresponding to high-order correlation functions generated by late-time structure formation. Our inference framework self-consistently accounts for typical observational systematic and statistical uncertainties such as noise, survey geometry and selection effects. We further account for luminosity dependent galaxy biases and automatic noise calibration within a fully Bayesian approach. As a result, this analysis provides highly-detailed and accurate reconstructions of the present density field on scales larger than $\sim~3$ Mpc$/h$, constrained by SDSS observations. This approach also leads to the first quantitative inference of plausible formation histories of the dynamic large scale structure underlying the observed galaxy distribution. The results described in this work constitute the first full Bayesian non-linear analysis of the cosmic large scale structure with the demonstrated capability of uncertainty quantification. Some of these results will be made publicly available along with this work. The level of detail of inferred results and the high degree of control on observational uncertainties pave the path towards high precision chrono-cosmography, the subject of simultaneously studying the dynamics and the morphology of the inhomogeneous Universe.Comment: 27 pages, 9 figure

Gene Regulatory Network Analysis and Web-based Application Development

Microarray data is a valuable source for gene regulatory network analysis. Using earthworm microarray data analysis as an example, this dissertation demonstrates that a bioinformatics-guided reverse engineering approach can be applied to analyze time-series data to uncover the underlying molecular mechanism. My network reconstruction results reinforce previous findings that certain neurotransmitter pathways are the target of two chemicals - carbaryl and RDX. This study also concludes that perturbations to these pathways by sublethal concentrations of these two chemicals were temporary, and earthworms were capable of fully recovering. Moreover, differential networks (DNs) analysis indicates that many pathways other than those related to synaptic and neuronal activities were altered during the exposure phase. A novel differential networks (DNs) approach is developed in this dissertation to connect pathway perturbation with toxicity threshold setting from Live Cell Array (LCA) data. Findings from this proof-of-concept study suggest that this DNs approach has a great potential to provide a novel and sensitive tool for threshold setting in chemical risk assessment. In addition, a web-based tool “Web-BLOM” was developed for the reconstruction of gene regulatory networks from time-series gene expression profiles including microarray and LCA data. This tool consists of several modular components: a database, the gene network reconstruction model and a user interface. The Bayesian Learning and Optimization Model (BLOM), originally implemented in MATLAB, was adopted by Web-BLOM to provide an online reconstruction of large-scale gene regulation networks. Compared to other network reconstruction models, BLOM can infer larger networks with compatible accuracy, identify hub genes and is much more computationally efficient

End-to-End Kernel Learning with Supervised Convolutional Kernel Networks

In this paper, we introduce a new image representation based on a multilayer kernel machine. Unlike traditional kernel methods where data representation is decoupled from the prediction task, we learn how to shape the kernel with supervision. We proceed by first proposing improvements of the recently-introduced convolutional kernel networks (CKNs) in the context of unsupervised learning; then, we derive backpropagation rules to take advantage of labeled training data. The resulting model is a new type of convolutional neural network, where optimizing the filters at each layer is equivalent to learning a linear subspace in a reproducing kernel Hilbert space (RKHS). We show that our method achieves reasonably competitive performance for image classification on some standard "deep learning" datasets such as CIFAR-10 and SVHN, and also for image super-resolution, demonstrating the applicability of our approach to a large variety of image-related tasks.Comment: to appear in Advances in Neural Information Processing Systems (NIPS