A Graph-Space Optimal Transport Approach Based on Kaniadakis κ-Gaussian Distribution for Inverse Problems Related to Wave Propagation.

Data-centric inverse problems are a process of inferring physical attributes from indirect measurements. Full-waveform inversion (FWI) is a non-linear inverse problem that attempts to obtain a quantitative physical model by comparing the wave equation solution with observed data, optimizing an objective function. However, the FWI is strenuously dependent on a robust objective function, especially for dealing with cycle-skipping issues and non-Gaussian noises in the dataset. In this work, we present an objective function based on the Kaniadakis κ-Gaussian distribution and the optimal transport (OT) theory to mitigate non-Gaussian noise effects and phase ambiguity concerns that cause cycle skipping. We construct the κ-objective function using the probabilistic maximum likelihood procedure and include it within a well-posed version of the original OT formulation, known as the Kantorovich-Rubinstein metric. We represent the data in the graph space to satisfy the probability axioms required by the Kantorovich-Rubinstein framework. We call our proposal the κ-Graph-Space Optimal Transport FWI (κ-GSOT-FWI). The results suggest that the κ-GSOT-FWI is an effective procedure to circumvent the effects of non-Gaussian noise and cycle-skipping problems. They also show that the Kaniadakis κ-statistics significantly improve the FWI objective function convergence, resulting in higher-resolution models than classical techniques, especially when κ=0.6.

Mutual Information as a General Measure of Structure in Interaction Networks.

Entropy-based indices are long-established measures of biological diversity, nowadays used to gauge partitioning of diversity at different spatial scales. Here, we tackle the measurement of diversity of interactions among two sets of organisms, such as plants and their pollinators. Actual interactions in ecological communities are depicted as bipartite networks or interaction matrices. Recent studies concentrate on distinctive structural patterns, such as nestedness or modularity, found in different modes of interaction. By contrast, we investigate mutual information as a general measure of structure in interactive networks. Mutual information (MI) measures the degree of reciprocal matching or specialization between interacting organisms. To ascertain its usefulness as a general measure, we explore (a) analytical solutions for different models; (b) the response of MI to network parameters, especially size and occupancy; (c) MI in nested, modular, and compound topologies. MI varies with fundamental matrix parameters: dimension and occupancy, for which it can be adjusted or normalized. Apparent differences among topologies are contingent on dimensions and occupancy, rather than on topological patterns themselves. As a general measure of interaction structure, MI is applicable to conceptually and empirically fruitful analyses, such as comparing similar ecological networks along geographical gradients or among interaction modalities in mutualistic or antagonistic networks.

Tsallis Entropy, Likelihood, and the Robust Seismic Inversion.

The nonextensive statistical mechanics proposed by Tsallis have been successfully used to model and analyze many complex phenomena. Here, we study the role of the generalized Tsallis statistics on the inverse problem theory. Most inverse problems are formulated as an optimisation problem that aims to estimate the physical parameters of a system from indirect and partial observations. In the conventional approach, the misfit function that is to be minimized is based on the least-squares distance between the observed data and the modelled data (residuals or errors), in which the residuals are assumed to follow a Gaussian distribution. However, in many real situations, the error is typically non-Gaussian, and therefore this technique tends to fail. This problem has motivated us to study misfit functions based on non-Gaussian statistics. In this work, we derive a misfit function based on the q-Gaussian distribution associated with the maximum entropy principle in the Tsallis formalism. We tested our method in a typical geophysical data inverse problem, called post-stack inversion (PSI), in which the physical parameters to be estimated are the Earth's reflectivity. Our results show that the PSI based on Tsallis statistics outperforms the conventional PSI, especially in the non-Gaussian noisy-data case.

Quantifying entropy using recurrence matrix microstates.

We conceive a new recurrence quantifier for time series based on the concept of information entropy, in which the probabilities are associated with the presence of microstates defined on the recurrence matrix as small binary submatrices. The new methodology to compute the entropy of a time series has advantages compared to the traditional entropies defined in the literature, namely, a good correlation with the maximum Lyapunov exponent of the system and a weak dependence on the vicinity threshold parameter. Furthermore, the new method works adequately even for small segments of data, bringing consistent results for short and long time series. In a case where long time series are available, the new methodology can be employed to obtain high precision results since it does not demand large computational times related to the analysis of the entire time series or recurrence matrices, as is the case of other traditional entropy quantifiers. The method is applied to discrete and continuous systems.

Optimizing the detection of nonstationary signals by using recurrence analysis.

Recurrence analysis and its quantifiers are strongly dependent on the evaluation of the vicinity threshold parameter, i.e., the threshold to regard two points close enough in phase space to be considered as just one. We develop a new way to optimize the evaluation of the vicinity threshold in order to assure a higher level of sensitivity to recurrence quantifiers to allow the detection of even small changes in the dynamics. It is used to promote recurrence analysis as a tool to detect nonstationary behavior of time signals or space profiles. We show that the ability to detect small changes provides information about the present status of the physical process responsible to generate the signal and offers mechanisms to predict future states. Here, a higher sensitive recurrence analysis is proposed as a precursor, a tool to predict near future states of a particular system, based on just (experimentally) obtained signals of some available variables of the system. Comparisons with traditional methods of recurrence analysis show that the optimization method developed here is more sensitive to small variations occurring in a signal. The method is applied to numerically generated time series as well as experimental data from physiology.

A quantum biochemistry investigation of willardiine partial agonism in AMPA receptors.

We employ quantum biochemistry methods based on the Density Functional Theory (DFT) approach to unveil the detailed binding energy features of willardiines co-crystallized with the AMPA receptor. Our computational results demonstrate that the total binding energies of fluorine-willardiine (FW), hydrogen-willardiine (HW), bromine-willardiine (BrW) and iodine-willardiine (IW) to the iGluR2 ligand-pocket correlate with the agonist binding energies, whose experimental sequential data match our computational counterpart, excluding the HW case. We find that the main contributions to the total willardiine-iGluR2 binding energy are due to the amino acid residues in decreasing order Glu705 > Arg485 > Ser654 > Tyr450 > T655. Furthermore, Met708, which is positioned close to the 5-substituent, attracts HW and FW, but repels BrW and IW. Our results contribute significantly to an improved understanding of the willardiine-iGluR2 binding mechanisms.

Electrophysiological damage to neuronal membrane alters ephaptic entrainment.

The brain is commonly understood as a complex network system with a particular organization and topology that can result in specific electrophysiological patterns. Among all the dynamic elements resulting from the circuits of the brain's network, ephapticity is a cellular communication mechanism that has received little attention. To understand the network's properties of ephaptic entrainment, we start investigating the ephaptic effect on a single neuron. In this study, we used numerical simulations to examine the relationship between alterations in ephaptic neuronal entrainment and impaired electrophysiological properties of the neuronal membrane, which can occur via spike field coherence (SFC). This change in frequency band amplitude is observed in some neurodegenerative diseases, such as Parkinson's or Alzheimer's. To further investigate these phenomena, we proposed a damaged model based on the impairment of both the resistance of the ion channels and the capacitance of the lipid membrane. Therefore, we simulated ephaptic entrainment with the hybrid neural model quadratic integrate-and-fire ephaptic (QIF-E), which mimics an ephaptic entrainment generated by an LFP (simulate a neuronal group). Our results indicate a link between peak entrainment (ephapticity) preference and a shift in frequency band when damage occurs mainly in ion channels. Finally, we discuss possible relationships between ephaptic entrainment and neurodegenerative diseases associated with aging factors.

Generalized statistics: Applications to data inverse problems with outlier-resistance.

The conventional approach to data-driven inversion framework is based on Gaussian statistics that presents serious difficulties, especially in the presence of outliers in the measurements. In this work, we present maximum likelihood estimators associated with generalized Gaussian distributions in the context of Rényi, Tsallis and Kaniadakis statistics. In this regard, we analytically analyze the outlier-resistance of each proposal through the so-called influence function. In this way, we formulate inverse problems by constructing objective functions linked to the maximum likelihood estimators. To demonstrate the robustness of the generalized methodologies, we consider an important geophysical inverse problem with high noisy data with spikes. The results reveal that the best data inversion performance occurs when the entropic index from each generalized statistic is associated with objective functions proportional to the inverse of the error amplitude. We argue that in such a limit the three approaches are resistant to outliers and are also equivalent, which suggests a lower computational cost for the inversion process due to the reduction of numerical simulations to be performed and the fast convergence of the optimization process.

Microseismic event detection in noisy environments with instantaneous spectral Shannon entropy.

The detection of information-bearing signals in a time series is very important for describing and analyzing a wide variety of complex physical systems. However, identifying events in low signal-to-noise ratio circumstances remains a challenge once heavy data preprocessing is usually required. In this work, we propose a robust methodology based on the instantaneous-spectral Shannon entropy for capturing microseismic events in noisy environments without the requirement of data preprocessing. We call our proposal the instantaneous spectral entropy detection (ISED) method. We tested the ISED in a couple of real empirical seismic records to detect microseismic events. Our methodology detects microseismic patterns even without any preprocessing, in contrast to usual methods in the literature which need appreciable data preprocessing.

Ephaptic entrainment in hybrid neuronal model.

In recent decades, there has been a growing interest in the impact of electric fields generated in the brain. Transmembrane ionic currents originate electric fields in the extracellular space and are capable of affecting nearby neurons, a phenomenon called ephaptic neuronal communication. In the present work, the Quadratic Integrated-and-Fire model (QIF-E) underwent an adjustment/improvement to include the ephaptic entrainment behavior between neurons and electric fields. Indeed, the aim of our study is to validate the QIF-E model, which is a model to estimate the influence of electric fields on neurons. For this purpose, we evaluated whether the main properties observed in an experiment by Anastassiou et al. (Nat Neurosci 14:217-223, 2011), which analyzed the effect of an electric field on cortical pyramidal neurons, are reproduced with the QIF-E model. In this way, the analysis tools are employed according to the neuronal activity regime: (i) for the subthreshold regime, the circular statistic is used to describe the phase differences between the input stimulus signal (electrode) and the modeled membrane response; (ii) in the suprathreshold regime, the Population Vector and the Spike Field Coherence are used to estimate phase preferences and the entrainment intensity between the input stimulus and Action Potentials. The results observed are (i) in the subthreshold regime the values of the phase differences change with distinct frequencies of the input stimulus; (ii) in the supra-threshold regime the preferential phase of Action Potentials changes for different frequencies. In addition, we explore other parameters of the model, such as noise and membrane characteristic-time, in order to understand different types of neurons and extracellular environment related to ephaptic communication. Such results are consistent with results observed in empirical experiments based on ephaptic phenomenon. In addition, the QIF-E model allows further studies on the physiological importance of ephaptic communication in the brain, and its simplicity may open a door to simulate the ephaptic response in neuronal networks and assess the impact of ephaptic communication in such scenarios.

Scale-free distribution of silences.

Soundscape studies help us understand ecological processes, biodiversity distribution, anthropic influences, and even urban quality, across a wide variety of places and time periods. In this work, instead of looking for differences, we ask if there are common characteristics shared by all soundscapes. Based on our results, we propose a universal distribution of quiet-time (background noise) and sound-time (acoustic energy bursts) in audio recordings. We analyzed one continuous hour during daylight and one at night, from ten randomly selected days in each environment: urban, dry forest, savanna, rupestrian field, Atlantic forest, marine, and freshwater. We found that the histograms of the quiet-time followed a power law for all scenarios analyzed, they present fractal events or scale-free distributions. This distribution covers up to four orders of magnitude, with an exponent of 1.6≤α≤2.0 for all soundscapes. By contrast, the sound-time distribution in all environments followed a log-normal or timescale dependence, with a typical time for the duration of sounds (0.06-0.12 s). Such time duration limitation can be related to the physiology of sound emission in animals.

An objective function for full-waveform inversion based on frequency-dependent offset-preconditioning.

Full-waveform inversion (FWI) is a powerful technique to obtain high-resolution subsurface models, from seismic data. However, FWI is an ill-posed problem, which means that the solution is not unique, and therefore the expert use of the information is required to mitigate the FWI ill-posedness, especially when wide-aperture seismic acquisitions are considered. In this way, we investigate the multiscale frequency-domain FWI by using a weighting operator according to the distances between each source-receiver pair. In this work, we propose a weighting operator that acts on the data misfit as preconditioning of the objective function that depends on the source-receiver distance (offset) and the frequency used during the inversion. The proposed operator emphasizes information from long offsets, especially at low frequencies, and as a consequence improves the update of deep geological structures. To demonstrate the effectiveness of our proposal, we perform numerical simulations on 2D acoustic Marmousi2 case study, which is widely used in seismic imaging tests, considering three different scenarios. In the first two ones, we have used an acquisition geometry with a maximum offset of 4 and 8 km, respectively. In the last one, we have considered all-offsets. The results show that our proposal outperforms similar strategies, for all scenarios, providing more reliable quantitative subsurface models. In fact, our inversion result has the lowest error and the highest similarity to the true model than similar approaches.

Waiting-time statistics in magnetic systems.

Many complex systems, from earthquakes and financial markets to Barkhausen effect in ferromagnetic materials, respond with a noise consisting of discrete avalanche-like events with broad range of sizes and durations, separated by waiting times. Here we focus on the waiting-time statistics in magnetic systems. By investigating the Barkhausen noise in amorphous and polycrystalline ferromagnetic films having different thicknesses, we uncover the form of the waiting-time distribution in time series recorded from the irregular and irreversible motion of magnetic domain walls. Further, we address the question of if the waiting-time distribution evolves with the threshold level, as well as with the film thickness and structural character of the materials. Our results, besides informing on the temporal avalanche correlations, disclose the waiting-time statistics in magnetic systems also bring fingerprints of the universality classes of Barkhausen avalanches and a dimensional crossover in the domain wall dynamics.

Full-waveform inversion based on Kaniadakis statistics.

Full-waveform inversion (FWI) is a wave-equation-based methodology to estimate the subsurface physical parameters that honor the geologic structures. Classically, FWI is formulated as a local optimization problem, in which the misfit function, to be minimized, is based on the least-squares distance between the observed data and the modeled data (residuals or errors). From a probabilistic maximum-likelihood viewpoint, the minimization of the least-squares distance assumes a Gaussian distribution for the residuals, which obeys Gauss's error law. However, in real situations, the error is seldom Gaussian and therefore it is necessary to explore alternative misfit functions based on non-Gaussian error laws. In this way, starting from the κ-generalized exponential function, we propose a misfit function based on the κ-generalized Gaussian probability distribution, associated with the Kaniadakis statistics (or κ-statistics), which we call κ-FWI. In this study, we perform numerical simulations on a realistic acoustic velocity model, considering two noisy data scenarios. In the first one, we considered Gaussian noisy data, while in the second one, we considered realistic noisy data with outliers. The results show that the κ-FWI outperforms the least-squares FWI, providing better parameter estimation of the subsurface, especially in situations where the seismic data are very noisy and with outliers, independently of the κ-parameter. Although the κ-parameter does not affect the quality of the results, it is important for the fast convergence of FWI.

Using fish lateral line sensing to improve seismic acquisition and processing.

Bioengineering, which studies the principles and design of biological systems, is a field that has inspired the development of several technologies that are currently in use. In this work, we use concepts from the fish lateral line sensing mechanism and apply them to seismic imaging processing. The lateral line is a sensory system composed of an integrated array of mechanical sensors spanning along the fish body. We compare the array of sensors along body fish with the seismic acquisition, which employs an array of equally spaced identical mechanical sensors to image the Earth's subsurface. In both situations, the mechanical sensors capture and process mechanical vibrations from the environment to produce useful information. We explore the strategy of using the low-pass and high-pass sensors schema of fish lateral line to improve the seismic technique. We use the full-wave inversion method to compare the conventional acquisition procedure of identical sensors with alternative sets of different sensors, which mimics the fish lateral line. Our results show that the alternate sensors arrangement surpasses the performance of the conventional acquisition method, using just half of the input information. The results point at an image processing technique that is computationally more efficient and economical than the usual seismic processing method.

Hippocampal and cortical communication around micro-arousals in slow-wave sleep.

Sleep plays a crucial role in the regulation of body homeostasis and rhythmicity in mammals. Recently, a specific component of the sleep structure has been proposed as part of its homeostatic mechanism, named micro-arousal. Here, we studied the unique progression of the dynamic behavior of cortical and hippocampal local field potentials (LFPs) during slow-wave sleep-related to motor-bursts (micro-arousals) in mice. Our main results comprised: (i) an abrupt drop in hippocampal LFP amplitude preceding micro-arousals which persisted until the end of motor-bursts (we defined as t interval, around 4s) and a similar, but delayed amplitude reduction in cortical (S1/M1) LFP activity occurring at micro-arousal onset; (ii) two abrupt frequency jumps in hippocampal LFP activity: from Theta (6-12 Hz) to Delta (2-4 Hz), also t seconds before the micro-arousal onset, and followed by another frequency jump from Delta to Theta range (5-7 Hz), now occurring at micro-arousal onset; (iii) a pattern of cortico-hippocampal frequency communication precedes micro-arousals: the analysis between hippocampal and cortical LFP fluctuations reveal high coherence during τ interval in a broader frequency band (2-12 Hz), while at a lower frequency band (0.5-2 Hz) the coherence reaches its maximum after the onset of micro-arousals. In conclusion, these novel findings indicate that oscillatory dynamics pattern of cortical and hippocampal LFPs preceding micro-arousals could be part of the regulatory processes in sleep architecture.

Predictability of arousal in mouse slow wave sleep by accelerometer data.

Arousals can be roughly characterized by punctual intrusions of wakefulness into sleep. In a standard perspective, using human electroencephalography (EEG) data, arousals are associated to slow-wave rhythms and K-complex brain activity. The physiological mechanisms that give rise to arousals during sleep are not yet fully understood. Moreover, subtle body movement patterns, which may characterize arousals both in human and in animals, are usually not detectable by eye perception and are not in general present in sleep studies. In this paper, we focus attention on accelerometer records (AR) to characterize and predict arousal during slow wave sleep (SWS) stage of mice. Furthermore, we recorded the local field potentials (LFP) from the CA1 region in the hippocampus and paired with accelerometer data. The hippocampus signal was also used here to identify the SWS stage. We analyzed the AR dynamics of consecutive arousals using recurrence technique and the determinism (DET) quantifier. Recurrence is a fundamental property of dynamical systems, which can be exploited to characterize time series properties. The DET index evaluates how similar are the evolution of close trajectories: in this sense, it computes how accurate are predictions based on past trajectories. For all analyzed mice in this work, we observed, for the first time, the occurrence of a universal dynamic pattern a few seconds that precedes the arousals during SWS sleep stage based only on the AR signal. The predictability success of an arousal using DET from AR is nearly 90%, while similar analysis using LFP of hippocampus brain region reveal 88% of success. Noteworthy, our findings suggest an unique dynamical behavior pattern preceding an arousal of AR data during sleep. Thus, the employment of this technique applied to AR data may provide useful information about the dynamics of neuronal activities that control sleep-waking switch during SWS sleep period. We argue that the predictability of arousals observed through DET(AR) can be functionally explained by a respiratory-driven modification of neural states. Finally, we believe that the method associating AR data with other physiologic events such as neural rhythms can become an accurate, convenient and non-invasive way of studying the physiology and physiopathology of movement and respiratory processes during sleep.

Families and clustering in a natural numbers network.

We develop a network in which the natural numbers are the vertices. The decomposition of natural numbers by prime numbers is used to establish the connections. We perform data collapse and show that the degree distribution of these networks scales linearly with the number of vertices. We explore the families of vertices in connection with prime numbers decomposition. We compare the average distance of the network and the clustering coefficient with the distance and clustering coefficient of the corresponding random graph. In case we set connections among vertices each time the numbers share a common prime number the network has properties similar to a random graph. If the criterion for establishing links becomes more selective, only prime numbers greater than p(l) are used to establish links, where the network has high clustering coefficient.

Modeling habitat split: landscape and life history traits determine amphibian extinction thresholds.

Habitat split is a major force behind the worldwide decline of amphibian populations, causing community change in richness and species composition. In fragmented landscapes, natural remnants, the terrestrial habitat of the adults, are frequently separated from streams, the aquatic habitat of the larvae. An important question is how this landscape configuration affects population levels and if it can drive species to extinction locally. Here, we put forward the first theoretical model on habitat split which is particularly concerned on how split distance - the distance between the two required habitats - affects population size and persistence in isolated fragments. Our diffusive model shows that habitat split alone is able to generate extinction thresholds. Fragments occurring between the aquatic habitat and a given critical split distance are expected to hold viable populations, while fragments located farther away are expected to be unoccupied. Species with higher reproductive success and higher diffusion rate of post-metamorphic youngs are expected to have farther critical split distances. Furthermore, the model indicates that negative effects of habitat split are poorly compensated by positive effects of fragment size. The habitat split model improves our understanding about spatially structured populations and has relevant implications for landscape design for conservation. It puts on a firm theoretical basis the relation between habitat split and the decline of amphibian populations.