Analyzing the long-term behavior of high-dimensional nonlinear dynamical systems remains a significant challenge. While the Koopman operator framework provides a powerful global linearization tool, current methods for approximating its spectral components often face theoretical limitations and depend on predefined dictionaries. Residual Dynamic Mode Decomposition (ResDMD) advanced the field by introducing the \emph{spectral residual} to assess Koopman operator approximation accuracy; however, its approach of only filtering precomputed spectra prevents the discovery of the operator's complete spectral information, a limitation known as the `spectral inclusion' problem. We introduce ResKoopNet (Residual-based Koopman-learning Network), a novel method that directly addresses this by explicitly minimizing the \emph{spectral residual} to compute Koopman eigenpairs. This enables the identification of a more precise and complete Koopman operator spectrum. Using neural networks, our approach provides theoretical guarantees while maintaining computational adaptability. Experiments on a variety of physical and biological systems show that ResKoopNet achieves more accurate spectral approximations than existing methods, particularly for high-dimensional systems and those with continuous spectra, which demonstrates its effectiveness as a tool for analyzing complex dynamical systems.

Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic "field" signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings.

Time series data sets often contain heterogeneous signals, composed of both continuously changing quantities and discretely occurring events. The coupling between these measurements may provide insights into key underlying mechanisms of the systems under study. To better extract this information, we investigate the asymptotic statistical properties of coupling measures between continuous signals and point processes. We first introduce martingale stochastic integration theory as a mathematical model for a family of statistical quantities that include the phase locking value, a classical coupling measure to characterize complex dynamics. Based on the martingale central limit theorem, we can then derive the asymptotic gaussian distribution of estimates of such coupling measure that can be exploited for statistical testing. Second, based on multivariate extensions of this result and random matrix theory, we establish a principled way to analyze the low-rank coupling between a large number of point processes and continuous signals. For a null hypothesis of no coupling, we establish sufficient conditions for the empirical distribution of squared singular values of the matrix to converge, as the number of measured signals increases, to the well-known Marchenko-Pastur (MP) law, and the largest squared singular value converges to the upper end of the MP support. This justifies a simple thresholding approach to assess the significance of multivariate coupling. Finally, we illustrate with simulations the relevance of our univariate and multivariate results in the context of neural time series, addressing how to reliably quantify the interplay between multichannel local field potential signals and the spiking activity of a large population of neurons.

Many applications require the analysis of complex interactions between time series. These interactions can be non-linear and involve vector valued as well as complex data structures such as graphs or strings. Here we provide a general framework for the statistical analysis of these interactions when random variables are sampled from stationary time-series of arbitrary objects. To achieve this goal we analyze the properties of the kernel cross-spectral density operator induced by positive definite kernels on arbitrary input domains. This framework enables us to develop an independence test between time series as well as a similarity measure to compare different types of coupling. The performance of our test is compared to the HSIC test using i.i.d. assumptions, showing improvement in terms of detection errors as well as the suitability of this approach for testing dependency in complex dynamical systems. Finally, we use this approach to characterize complex interactions in electrophysiological neural time series.

Cross-spectral density (CSD), is widely used to find linear dependency between two real or complex valued time series. We define a non-linear extension of this measure by mapping the time series into two Reproducing Kernel Hilbert Spaces. The dependency is quantified by the Hilbert Schmidt norm of a cross-spectral density operator between these two spaces. We prove that, by choosing a characteristic kernel for the mapping, this quantity detects any pairwise dependency between the time series. Then we provide a fast estimator for the Hilbert-Schmidt norm based on the Fast Fourier Trans form. We demonstrate the interest of this approach to quantify non-linear dependencies between frequency bands of simulated signals and intra-cortical neural recordings.

Data recorded from multiple sources sometimes exhibit non-instantaneous couplings. For simple data sets, cross-correlograms may reveal the coupling dynamics. But when dealing with high-dimensional multivariate data there is no such measure as the cross-correlogram. We propose a simple algorithm based on Kernel Canonical Correlation Analysis (kCCA) that computes a multivariate temporal filter which links one data modality to another one. The filters can be used to compute a multivariate extension of the cross-correlogram, the canonical correlogram, between data sources that have different dimensionalities and temporal resolutions. The canonical correlogram reflects the coupling dynamics between the two sources. The temporal filter reveals which features in the data give rise to these couplings and when they do so. We present results from simulations and neuroscientific experiments showing that tkCCA yields easily interpretable temporal filters and correlograms. In the experiments, we simultaneously performed electrode recordings and functional magnetic resonance imaging (fMRI) in primary visual cortex of the non-human primate. While electrode recordings reflect brain activity directly, fMRI provides only an indirect view of neural activity via the Blood Oxygen Level Dependent (BOLD) response. Thus it is crucial for our understanding and the interpretation of fMRI signals in general to relate them to direct measures of neural activity acquired with electrodes. The results computed by tkCCA confirm recent models of the hemodynamic response to neural activity and allow for a more detailed analysis of neurovascular coupling dynamics.

Bistable perception arises when a stimulus under continuous view is perceived as the alternation of two mutually exclusive states. Such a stimulus provides a unique opportunity for understanding the neural basis of visual perception because it dissociates the perception from the visual input. In this paper we focus on extracting the percept-related features of the induced activity from the local field potential (LFP) in monkey visual cortex for decoding its bistable structure-from-motion (SFM) perception. Because of the dissociation between the perception and the stimulus in our experimental paradigm, the stimulus-evoked activity in our data is not related to perception. Our proposed feature extraction approach consists of two stages. First, we estimate the stimulus-evoked activity via a wavelet transform based method and remove it from the single trials of each channel. Second, we use the common spatial patterns (CSP) approach to design spatial filters based on the remaining induced activity of multiple channels to extract the percept-related features. We exploit the linear discriminant analysis (LDA) classifier and the support vector machine (SVM) classifier on the extracted features to decode the reported perception on a single-trial basis. We apply the proposed approach to the multichannel intracortical LFP data collected from the middle temporal (MT) visual cortex in a macaque monkey performing a SFM task. We demonstrate that our approach is effective in extracting the discriminative features of the percept-related induced activity from LFP, which leads to excellent decoding performance. We also discover that the enhanced gamma band synchronization and reduced alpha band desynchronization may be the underpinnings of the induced activity.

The study of the neuronal correlates of the spontaneous alternation in perception elicited by bistable visual stimuli is promising for understanding the mechanism of neural information processing and the neural basis of visual perception and perceptual decision-making. In this paper we apply a sparse nonnegative tensor factorization (NTF) based method to extract features from the local field potential (LFP) in monkey visual cortex for decoding its bistable structure-from-motion (SFM) perception. We apply the feature extraction approach to the multichannel time-frequency representation of intracortical LFP data collected from the middle temporal area (MT) in a macaque monkey performing a SFM task. The advantages of the sparse NTF based feature extraction approach lies in its capability to yield components common across the space, time and frequency domains and at the same time discriminative across different conditions without prior knowledge of the discriminative frequency bands and temporal windows for a specific subject. We employ the support vector machines (SVM) classifier based on the features of the NTF components to decode the reported perception on a single-trial basis. Our results suggest that although other bands also have certain discriminability, the gamma band feature carries the most discriminative information for bistable perception, and that imposing the sparseness constraints on the nonnegative tensor factorization improves extraction of this feature.

Recordings of local field potentials (LFPs) reveal that the sensory cortex displays rhythmic activity and fluctuations over a wide range of frequencies and amplitudes. Yet, the role of this kind of activity in encoding sensory information remains largely unknown. To understand the rules of translation between the structure of sensory stimuli and the fluctuations of cortical responses, we simulated a sparsely connected network of excitatory and inhibitory neurons modeling a local cortical population, and we determined how the LFPs generated by the network encode information about input stimuli. We first considered simple static and periodic stimuli and then naturalistic input stimuli based on electrophysiological recordings from the thalamus of anesthetized monkeys watching natural movie scenes. We found that the simulated network produced stimulus-related LFP changes that were in striking agreement with the LFPs obtained from the primary visual cortex. Moreover, our results demonstrate that the network encoded static input spike rates into gamma-range oscillations generated by inhibitory-excitatory neural interactions and encoded slow dynamic features of the input into slow LFP fluctuations mediated by stimulus-neural interactions. The model cortical network processed dynamic stimuli with naturalistic temporal structure by using low and high response frequencies as independent communication channels, again in agreement with recent reports from visual cortex responses to naturalistic movies. One potential function of this frequency decomposition into independent information channels operated by the cortical network may be that of enhancing the capacity of the cortical column to encode our complex sensory environment.

We report and compare the performance of different learning algorithms based on data from cortical recordings. The task is to predict the orienta- tion of visual stimuli from the activity of a population of simultaneously recorded neurons. We compare several ways of improving the coding of the input (i.e., the spike data) as well as of the output (i.e., the orienta- tion), and report the results obtained using different kernel algorithms.