A multi-demand operating system underlying diverse cognitive tasks.

The existence of a multiple-demand cortical system with an adaptive, domain-general, role in cognition has been proposed, but the underlying dynamic mechanisms and their links to cognitive control abilities are poorly understood. Here we use a probabilistic generative Bayesian model of brain circuit dynamics to determine dynamic brain states across multiple cognitive domains, independent datasets, and participant groups, including task fMRI data from Human Connectome Project, Dual Mechanisms of Cognitive Control study and a neurodevelopment study. We discover a shared brain state across seven distinct cognitive tasks and found that the dynamics of this shared brain state predicted cognitive control abilities in each task. Our findings reveal the flexible engagement of dynamic brain processes across multiple cognitive domains and participant groups, and uncover the generative mechanisms underlying the functioning of a domain-general cognitive operating system. Our computational framework opens promising avenues for probing neurocognitive function and dysfunction.

Bayesian analysis of Ecological Momentary Assessment (EMA) data collected in adults before and after hearing rehabilitation.

This paper presents a new Bayesian method for analyzing Ecological Momentary Assessment (EMA) data and applies this method in a re-analysis of data from a previous EMA study. The analysis method has been implemented as a freely available Python package EmaCalc, RRID:SCR 022943. The analysis model can use EMA input data including nominal categories in one or more situation dimensions, and ordinal ratings of several perceptual attributes. The analysis uses a variant of ordinal regression to estimate the statistical relation between these variables. The Bayesian method has no requirements related to the number of participants or the number of assessments by each participant. Instead, the method automatically includes measures of the statistical credibility of all analysis results, for the given amount of data. For the previously collected EMA data, the analysis results demonstrate how the new tool can handle heavily skewed, scarce, and clustered data that were collected on ordinal scales, and present results on interval scales. The new method revealed results for the population mean that were similar to those obtained in the previous analysis by an advanced regression model. The Bayesian approach automatically estimated the inter-individual variability in the population, based on the study sample, and could show some statistically credible intervention results also for an unseen random individual in the population. Such results may be interesting, for example, if the EMA methodology is used by a hearing-aid manufacturer in a study to predict the success of a new signal-processing method among future potential customers.

Development of brain state dynamics involved in working memory.

Human functional brain networks are dynamically organized to enable cognitive and behavioral flexibility to meet ever-changing environmental demands. Frontal-parietal network (FPN) and default mode network (DMN) are recognized to play an essential role in executive functions such as working memory. However, little is known about the developmental differences in the brain-state dynamics of these two networks involved in working memory from childhood to adulthood. Here, we implemented Bayesian switching dynamical systems approach to identify brain states of the FPN and DMN during working memory in 69 school-age children and 51 adults. We identified five brain states with rapid transitions, which are characterized by dynamic configurations among FPN and DMN nodes with active and inactive engagement in different task demands. Compared with adults, children exhibited less frequent brain states with the highest activity in FPN nodes dominant to high demand, and its occupancy rate increased with age. Children preferred to attain inactive brain states with low activity in both FPN and DMN nodes. Moreover, children exhibited lower transition probability from low-to-high demand states and such a transition was positively correlated with working memory performance. Notably, higher transition probability from low-to-high demand states was associated with a stronger structural connectivity across FPN and DMN, but with weaker structure-function coupling of these two networks. These findings extend our understanding of how FPN and DMN nodes are dynamically organized into a set of transient brain states to support moment-to-moment information updating during working memory and suggest immature organization of these functional brain networks in childhood, which is constrained by the structural connectivity.

Development of forecast models for COVID-19 hospital admissions using anonymized and aggregated mobile network data.

Reliable forecast of COVID-19 hospital admissions in near-term horizons can help enable effective resource management which is vital in reducing pressure from healthcare services. The use of mobile network data has come to attention in response to COVID-19 pandemic leveraged on their ability in capturing people social behavior. Crucially, we show that there are latent features in irreversibly anonymized and aggregated mobile network data that carry useful information in relation to the spread of SARS-CoV-2 virus. We describe development of the forecast models using such features for prediction of COVID-19 hospital admissions in near-term horizons (21 days). In a case study, we verified the approach for two hospitals in Sweden, Sahlgrenska University Hospital and Södra Älvsborgs Hospital, working closely with the experts engaged in the hospital resource planning. Importantly, the results of the forecast models were used in year 2021 by logisticians at the hospitals as one of the main inputs for their decisions regarding resource management.

Insights Into Multiple/Single Lower Bound Approximation for Extended Variational Inference in Non-Gaussian Structured Data Modeling.

For most of the non-Gaussian statistical models, the data being modeled represent strongly structured properties, such as scalar data with bounded support (e.g., beta distribution), vector data with unit length (e.g., Dirichlet distribution), and vector data with positive elements (e.g., generalized inverted Dirichlet distribution). In practical implementations of non-Gaussian statistical models, it is infeasible to find an analytically tractable solution to estimating the posterior distributions of the parameters. Variational inference (VI) is a widely used framework in Bayesian estimation. Recently, an improved framework, namely, the extended VI (EVI), has been introduced and applied successfully to a number of non-Gaussian statistical models. EVI derives analytically tractable solutions by introducing lower bound approximations to the variational objective function. In this paper, we compare two approximation strategies, namely, the multiple lower bounds (MLBs) approximation and the single lower bound (SLB) approximation, which can be applied to carry out the EVI. For implementation, two different conditions, the weak and the strong conditions, are discussed. Convergence of the EVI depends on the selection of the lower bound, regardless of the choice of weak or strong condition. We also discuss the convergence properties to clarify the differences between MLB and SLB. Extensive comparisons are made based on some EVI-based non-Gaussian statistical models. Theoretical analysis is conducted to demonstrate the differences between the weak and strong conditions. Experimental results based on real data show advantages of the SLB approximation over the MLB approximation.

Uncovering hidden brain state dynamics that regulate performance and decision-making during cognition.

Human cognition is influenced not only by external task demands but also latent mental processes and brain states that change over time. Here, we use novel Bayesian switching dynamical systems algorithm to identify hidden brain states and determine that these states are only weakly aligned with external task conditions. We compute state transition probabilities and demonstrate how dynamic transitions between hidden states allow flexible reconfiguration of functional brain circuits. Crucially, we identify latent transient brain states and dynamic functional circuits that are optimal for cognition and show that failure to engage these states in a timely manner is associated with poorer task performance and weaker decision-making dynamics. We replicate findings in a large sample (N = 122) and reveal a robust link between cognition and flexible latent brain state dynamics. Our study demonstrates the power of switching dynamical systems models for investigating hidden dynamic brain states and functional interactions underlying human cognition.

Bayesian switching factor analysis for estimating time-varying functional connectivity in fMRI.

There is growing interest in understanding the dynamical properties of functional interactions between distributed brain regions. However, robust estimation of temporal dynamics from functional magnetic resonance imaging (fMRI) data remains challenging due to limitations in extant multivariate methods for modeling time-varying functional interactions between multiple brain areas. Here, we develop a Bayesian generative model for fMRI time-series within the framework of hidden Markov models (HMMs). The model is a dynamic variant of the static factor analysis model (Ghahramani and Beal, 2000). We refer to this model as Bayesian switching factor analysis (BSFA) as it integrates factor analysis into a generative HMM in a unified Bayesian framework. In BSFA, brain dynamic functional networks are represented by latent states which are learnt from the data. Crucially, BSFA is a generative model which estimates the temporal evolution of brain states and transition probabilities between states as a function of time. An attractive feature of BSFA is the automatic determination of the number of latent states via Bayesian model selection arising from penalization of excessively complex models. Key features of BSFA are validated using extensive simulations on carefully designed synthetic data. We further validate BSFA using fingerprint analysis of multisession resting-state fMRI data from the Human Connectome Project (HCP). Our results show that modeling temporal dependencies in the generative model of BSFA results in improved fingerprinting of individual participants. Finally, we apply BSFA to elucidate the dynamic functional organization of the salience, central-executive, and default mode networks-three core neurocognitive systems with central role in cognitive and affective information processing (Menon, 2011). Across two HCP sessions, we demonstrate a high level of dynamic interactions between these networks and determine that the salience network has the highest temporal flexibility among the three networks. Our proposed methods provide a novel and powerful generative model for investigating dynamic brain connectivity.

Variational Inference for Watson Mixture Model.

This paper addresses modelling data using the Watson distribution. The Watson distribution is one of the simplest distributions for analyzing axially symmetric data. This distribution has gained some attention in recent years due to its modeling capability. However, its Bayesian inference is fairly understudied due to difficulty in handling the normalization factor. Recent development of Markov chain Monte Carlo (MCMC) sampling methods can be applied for this purpose. However, these methods can be prohibitively slow for practical applications. A deterministic alternative is provided by variational methods that convert inference problems into optimization problems. In this paper, we present a variational inference for Watson mixture models. First, the variational framework is used to side-step the intractability arising from the coupling of latent states and parameters. Second, the variational free energy is further lower bounded in order to avoid intractable moment computation. The proposed approach provides a lower bound on the log marginal likelihood and retains distributional information over all parameters. Moreover, we show that it can regulate its own complexity by pruning unnecessary mixture components while avoiding over-fitting. We discuss potential applications of the modeling with Watson distributions in the problem of blind source separation, and clustering gene expression data sets.

Comparisons of non-Gaussian statistical models in DNA methylation analysis.

As a key regulatory mechanism of gene expression, DNA methylation patterns are widely altered in many complex genetic diseases, including cancer. DNA methylation is naturally quantified by bounded support data; therefore, it is non-Gaussian distributed. In order to capture such properties, we introduce some non-Gaussian statistical models to perform dimension reduction on DNA methylation data. Afterwards, non-Gaussian statistical model-based unsupervised clustering strategies are applied to cluster the data. Comparisons and analysis of different dimension reduction strategies and unsupervised clustering methods are presented. Experimental results show that the non-Gaussian statistical model-based methods are superior to the conventional Gaussian distribution-based method. They are meaningful tools for DNA methylation analysis. Moreover, among several non-Gaussian methods, the one that captures the bounded nature of DNA methylation data reveals the best clustering performance.

Bayesian Estimation of the von-Mises Fisher Mixture Model with Variational Inference.

This paper addresses the Bayesian estimation of the von-Mises Fisher (vMF) mixture model with variational inference (VI). The learning task in VI consists of optimization of the variational posterior distribution. However, the exact solution by VI does not lead to an analytically tractable solution due to the evaluation of intractable moments involving functional forms of the Bessel function in their arguments. To derive a closed-form solution, we further lower bound the evidence lower bound where the bound is tight at one point in the parameter distribution. While having the value of the bound guaranteed to increase during maximization, we derive an analytically tractable approximation to the posterior distribution which has the same functional form as the assigned prior distribution. The proposed algorithm requires no iterative numerical calculation in the re-estimation procedure, and it can potentially determine the model complexity and avoid the over-fitting problem associated with conventional approaches based on the expectation maximization. Moreover, we derive an analytically tractable approximation to the predictive density of the Bayesian mixture model of vMF distributions. The performance of the proposed approach is verified by experiments with both synthetic and real data.