Conflicts between short- and long-term experiences affect visual perception through modulating sensory or motor response systems: Evidence from Bayesian inference models

The independent effects of short- and long-term experiences on visual perception have been discussed for decades. However, no study has investigated whether and how these experiences simultaneously affect our visual perception. To address this question, we asked participants to estimate their self-motion directions (i.e., headings) simulated from optic flow, in which a long-term experience learned in everyday life (i.e., straight-forward motion being more common than lateral motion) plays an important role. The headings were selected from three distributions that resembled a peak, a hill, and a flat line, creating different short-term experiences. Importantly, the proportions of headings deviating from the straight-forward motion gradually increased in the peak, hill, and flat distributions, leading to a greater conflict between long- and short-term experiences. The results showed that participants biased their heading estimates towards the straight-ahead direction and previously seen headings, which increased with the growing experience conflict. This suggests that both long- and short-term experiences simultaneously affect visual perception. Finally, we developed two Bayesian models (Model 1 vs. Model 2) based on two assumptions that the experience conflict altered the likelihood distribution of sensory representation or the motor response system. The results showed that both models accurately predicted participants' estimation biases. However, Model 1 predicted a higher variance of serial dependence compared to Model 2, while Model 2 predicted a higher variance of the bias towards the straight-ahead direction compared to Model 1. This suggests that the experience conflict can influence visual perception by affecting both sensory and motor response systems. Taken together, the current study systematically revealed the effects of long- and short-term experiences on visual perception and the underlying Bayesian processing mechanisms.

Understanding anxiety through uncertainty quantification

Uncertainty has been a central concept in psychological theories of anxiety. However, this concept has been plagued by divergent connotations and operationalizations. The lack of consensus hinders the current search for cognitive and biological mechanisms of anxiety, jeopardizes theory creation and comparison, and restrains translation of basic research into improved diagnoses and interventions. Drawing upon uncertainty decomposition in Bayesian Decision Theory, we propose a well-defined conceptual structure of uncertainty in cognitive and clinical sciences, with a focus on anxiety. We discuss how this conceptual structure provides clarity and can be naturally applied to existing frameworks of psychopathology research. Furthermore, it allows formal quantification of various types of uncertainty that can benefit both research and clinical practice in the era of computational psychiatry.

Influencing factors of death in patients with MDR-TB based on Bayesian Cox regression model

OBJECTIVES

Multidrug-resistant tuberculosis (MDR-TB) has a high mortality and is always one of the major challenges in global TB prevention and control. Analyzing the factors that may impact the adverse outcomes of MDR-TB patients is helpful for improving the systematic management and optimizing the treatment strategies for MDR-TB patients. For follow-up data, the Cox proportional hazards regression model is an important multifactor analysis method. However, the method has significant limitations in its application, such as the fact that it is difficult to deal with the impacts of small sample sizes and other practical issues on the model. Therefore, Bayesian and conventional Cox regression models were both used in this study to analyze the influencing factors of death in MDR-TB patients during the anti-TB therapy, and compare the differences between these 2 methods in their application.

METHODS

Data were obtained from 388 MDR-TB patients treated at Lanzhou Pulmonary Hospital from November 1, 2017 to March 31, 2021. Survival analysis was employed to analyze the death of MDR-TB patients during the therapy and its influencing factors. Conventional and Bayesian Cox regression models were established to estimate the hazard ratios (HR) and their 95% confidence interval (95% CI) for the factors affecting the death of MDR-TB patients. The reliability of parameter estimation in these 2 models was assessed by comparing the parameter standard deviation and 95% CI of each variable. The smaller parameter standard deviation and narrower 95% CI range indicated the more reliable parameter estimation.

RESULTS

The median survival time (1st quartile, 3rd quartile) of the 388 MDR-TB patients included in the study was 10.18 (4.26, 18.13) months, with the longest survival time of 31.90 months. Among these patients, a total of 12 individuals died of MDR-TB and the mortality was 3.1%. The median survival time (1st quartile, 3rd quartile) for the deceased patients was 4.78(2.63, 6.93) months. The majority of deceased patients, accounting for 50%, experienced death within the first 5 months of anti-TB therapy, with the last mortality case occurring within the 13th month of therapy. The results of the conventional Cox regression model showed that the risk of death in MDR-TB patients with comorbidities was approximately 6.96 times higher than that of patients without complications (HR=6.96, 95% CI 2.00 to 24.24, P=0.002) and patients who received regular follow-up had a decrease in the risk of death by approximately 81% compared to those who did not receive regular follow-up (HR=0.19, 95% CI 0.05 to 0.77, P=0.020). In the results of Bayesian Cox regression model, the iterative history plot and Blue/Green/Red (BGR) plot for each parameter showed the good model convergence, and parameter estimation indicated that the risk of death in patients with a positive first sputum culture was lower than that of patients with a negative first sputum culture (HR=0.33, 95% CI 0.08 to 0.87). Additionally, compared to patients without complications, those with comorbidities had an approximately 6.80-fold increase in the risk of death (HR=7.80, 95% CI 1.90 to 21.91). Patients who received regular follow-up had a 90% reduction in the risk of death compared to those who did not receive regular follow-up (HR=0.10, 95% CI 0.01 to 0.30). The comparison between these 2 models showed that the parameter standard deviations and corresponding 95% CI ranges of other variables in the Bayesian Cox model were significantly smaller than those in the conventional model, except for parameter standard deviations of receiving regular follow-up (Bayesian model was 0.77; conventional model was 0.72) and pulmonary cavities (Bayesian model was 0.73; conventional model was 0.73).

CONCLUSIONS

The first year of anti-TB therapy is a high-risk period for mortality in MDR-TB patients. Complications are the main risk factors of death in MDR-TB patients, while patients who received regular follow-up and had positive first sputum culture presented a lower risk of death. For data with a small sample size and low incidence of outcome, the Bayesian Cox regression model provides more reliable parameter estimation than the conventional Cox model.

Research on an Optimized Evaluation Method of the Bearing Capacity of Reinforced Concrete Beam Based on the Bayesian Theory

An optimized evaluation method of the bearing capacity of reinforced concrete beam based on the Bayesian theory was proposed in this paper. This evaluation method optimized the traditional Markov Chain-Monte Carlo (MCMC) sampling method, and proposed an improved Metropolis-Hastings (MH) sampling method and a transitive MCMC (TMCMC) sampling method based on the MCMC theory. These two derived sampling methods solved the problem that the traditional MCMC algorithm makes it difficult to achieve convergence when the number of modified parameters is large. Therefore, on the basis of obtaining the measured sample information and the prior information of uncertain parameters, this paper first used multiple "model components" to form a model sample, then carried out a sensitivity analysis based on the relevant response indicators and selected the key parameters that had a great impact on the bearing capacity, carried out static load tests, and extracted and analyzed the experimental data. Then, based on a large amount of analysis data, the improved MH sampling method and TMCMC sampling method were used to establish a posterior probability distribution database. Finally, multiple posterior probability distributions were used to identify and predict the bearing capacity. The results showed that the method was feasible and effective for the evaluation of the bearing capacity of reinforced concrete beam.

Bayesian Data Selection

Insights into complex, high-dimensional data can be obtained by discovering features of the data that match or do not match a model of interest. To formalize this task, we introduce the "data selection" problem: finding a lower-dimensional statistic-such as a subset of variables-that is well fit by a given parametric model of interest. A fully Bayesian approach to data selection would be to parametrically model the value of the statistic, nonparametrically model the remaining "background" components of the data, and perform standard Bayesian model selection for the choice of statistic. However, fitting a nonparametric model to high-dimensional data tends to be highly inefficient, statistically and computationally. We propose a novel score for performing data selection, the "Stein volume criterion (SVC)", that does not require fitting a nonparametric model. The SVC takes the form of a generalized marginal likelihood with a kernelized Stein discrepancy in place of the Kullback-Leibler divergence. We prove that the SVC is consistent for data selection, and establish consistency and asymptotic normality of the corresponding generalized posterior on parameters. We apply the SVC to the analysis of single-cell RNA sequencing data sets using probabilistic principal components analysis and a spin glass model of gene regulation.

Rethinking Rationality

We seek to understand rational decision making and if it exists whether finite (bounded) agents may be able to achieve its principles. This aim has been a singular objective throughout much of human science and philosophy, with early discussions identified since antiquity. More recently, there has been a thriving debate based on differing perspectives on rationality, including adaptive heuristics, Bayesian theory, quantum theory, resource rationality, and probabilistic language of thought. Are these perspectives on rationality mutually exclusive? Are they all needed? Do they undermine an aim to have rational standards in decision situations like politics, medicine, legal proceedings, and others, where there is an expectation and need for decision making as close to "optimal" as possible? This special issue brings together representative contributions from the currently predominant views on rationality, with a view to evaluate progress on these and related questions.

Groundwater contamination source identification using improved differential evolution Markov chain algorithm

The groundwater contamination source identification (GCSI) can provide important bases for the design of pollution remediation plans. The Bayesian theory is commonly used in the GCSI problem. Usually, we use the Markov chain Monte Carlo (MCMC) method to realize the Bayesian framework. However, due to the ill-posed nature of the GCSI and the system model's complexity, the conventional MCMC algorithm is time-consuming and has low accuracy. In this study, we proposed an adaptive mutation differential evolution Markov chain (AM-DEMC) algorithm. In this algorithm, the Kent mapping chaotic sequence method, combined with differential evolution (DE) algorithm, was used to generate the initial population. In the iteration process, we introduced a hybrid mutation strategy to generate the candidate vectors. Moreover, we adaptively adjust the essential parameter F of the AM-DEMC algorithm according to the individual fitness value. For further improving the efficiency of solving the GCSI problem, the Kriging method was used to establish a surrogate model to avoid the enormous computational load associated with the numerical simulation model. Finally, a hypothetical groundwater contamination case was given to verify the effectiveness of the AM-DEMC algorithm. The results indicated that the proposed AM-DEMC algorithm successfully identified the contamination sources' characteristics and simulation model's parameters. It also exhibited stronger search-ability and higher accuracy than the MCMC and DE-MC algorithms.

Certainty and integration of options in animal movement

Physical energy defines the energy landscape and determines the species-specific cost of movement, thus influencing movement decisions. In unpredictable and dynamic environments, observing the locomotion of others increases individual certainty in the distribution of physical energy to increase movement efficiency. Beyond the physical energy landscape, social sampling increases certainty in all ecological landscapes that influence animal movement (including fear and resource landscapes), and individuals use energy to express each of these. We call for the development of an 'optimal movement theory' (OMT) that integrates the multidimensional reality of movement decisions by combining ecological landscapes according to a single expectation of energy cost-benefit, where social sampling provides up-to-date information under uncertain conditions. This mechanistic framework has implications for predicting individual movement patterns and for investigating the emergence of aggregations.

Performance of Bayesian outbreak detection algorithm in the syndromic surveillance of influenza-like illness in small region

Early warning for Infectious disease outbreak is an important public health policy concern, and finding a reliable method for early warning remains one of the active fields for researchers. The purpose of this study was to evaluate the performance of the Bayesian outbreak detection algorithm in the surveillance of influenza-like illness in small regions. The Bayesian outbreak detection algorithm (BODA) and modified cumulative sum control chart algorithm (CUSUM) were applied to daily counts of influenza-like illness in Tehran, Iran. We used data from September 2016 through August 2017 to provide background counts for the algorithms, and data from September 2017 through August 2018 used for testing the algorithms. The performances of the BODA and modified CUSUM algorithms were compared with the results coming from experts' signal inspections. The data of syndromic surveillance of influenza-like illness in Tehran had a median daily counts of 7 (IQR = 3-14). The data showed significant seasonal trends and holiday and day-of-the-week effects. The utility of the BODA algorithm in real-time detection of the influenza outbreak was better than the modified CUSUM algorithm. Moreover, the best performance was when a trend included in the analysis. The BODA algorithm was able to detect the influenza outbreaks with 4-5 days delay, with the least false-positive alarm. Applying the BODA algorithm as an outbreak detection method in influenza-like syndromic surveillance might be useful in early detection of the outbreaks in small regions.

Cognitive Processes Unfold in a Social Context: A Review and Extension of Social Baseline Theory

Psychologists often assume that social and cognitive processes operate independently, an assumption that prompts research into how social context influences cognitive processes. We propose that social and cognitive processes are not necessarily separate, and that social context is innate to resource dependent cognitive processes. We review the research supporting social baseline theory, which argues that our default state in physiological, cognitive, and neural processing is to incorporate the relative costs and benefits of acting in our social environment. The review extends social baseline theory by applying social baseline theory to basic cognitive processes such as vision, memory, and attention, incorporating individual differences into the theory, reviewing environmental influences on social baselines, and exploring the dynamic effects of social interactions. The theoretical and methodological implications of social baseline theory are discussed, and future research endeavors into social cognition should consider that cognitive processes are situated within our social environments.

Underwater Bearing-Only and Bearing-Doppler Target Tracking Based on Square Root Unscented Kalman Filter

Underwater target tracking system can be kept covert using the bearing-only or the bearing-Doppler measurements (passive measurements), which will reduce the risk of been detected. According to the characteristics of underwater target tracking, the square root unscented Kalman filter (SRUKF) algorithm, which is based on the Bayesian theory, was applied to the underwater bearing-only and bearing-Doppler non-maneuverable target tracking problem. Aiming at the shortcomings of the unscented Kalman filter (UKF), the SRUKF uses the QR decomposition and the Cholesky factor updating, in order to avoid that the process noise covariance matrix loses its positive definiteness during the target tracking period. The SRUKF uses sigma sampling to avoid the linearization of the nonlinear bearing-only and the bearing-Doppler measurements. To ensure the target state observability in underwater target tracking, the paper uses single maneuvering observer to track the single non-maneuverable target. The simulation results show that the SRUKF has better tracking performance than the extended Kalman filter (EKF) and the UKF in tracking accuracy and stability, and the computational complexity of the SRUKF algorithm is low.

Sensorimotor priors are effector dependent

During sensorimotor tasks, subjects use sensory feedback but also prior information. It is often assumed that the sensorimotor prior is just given by the experiment and that the details for acquiring this prior (e.g., the effector) are irrelevant. However, recent research has suggested that the construction of priors is nontrivial. To test if the sensorimotor details matter for the construction of a prior, we designed two tasks that differ only in the effectors that subjects use to indicate their estimate. For both a typical reaching setting and an atypical wrist rotation setting, prior and feedback uncertainty matter as quantitatively predicted by Bayesian statistics. However, in violation of simple Bayesian models, the importance of the prior differs across effectors. Subjects overly rely on their prior in the typical reaching case compared with the wrist case. The brain is not naively Bayesian with a single and veridical prior. NEW & NOTEWORTHY Traditional Bayesian models often assume that we learn statistics of movements and use the information as a prior to guide subsequent movements. The effector is merely a reporting modality for information processing. We asked subjects to perform a visuomotor learning task with different effectors (finger or wrist). Surprisingly, we found that prior information is used differently between the effectors, suggesting that learning of the prior is related to the movement context such as the effector involved or that naive models of Bayesian behavior need to be extended.

Establishment of optimal regulatory network of colorectal cancer based on p42.3 protein

Objective: to establish regulatory network of colorectal cancer involving p42.3 protein and to provide theoretical evidence for deep functional exploration of p42.3 protein in the onset and development of colorectal cancer. Methods: with protein similarity algorithm, reference protein set of p42.3 cell apoptosis was built according to structural features of p42.3. GO and KEGG databases were used to establish regulatory network of tumor cell apoptosis involving p42.3; meanwhile, the largest possible working pathway that involves p42.3 protein was screened out based on Bayesian network theory. Besides, GO and KEGG were used to build regulatory network on early diagnosis gene markers for colorectal cancer including WWOX, K-ras, COX-2, p53, APC, DCC and PTEN, at the same time, a regulatory network of colorectal cancer cell apoptosis which involves p42.3 was established. Results: cell apoptotic regulatory network that p42.3 participates in primarily consists of Bcl-2 family genes and the largest possible pathway is p42.3 → FKBP → Bcl-2 centered as FKBP protein. Combined with colorectal cancer regulatory network that involves early diagnosis gene markers, it can be predicted that p42.3 is most likely to regulate the colorectal cancer cell apoptosis through FKBP → Bcl-2 → Bax → caspase-9 → caspase-3 pathway. Conclusion: the colorectal cancer apoptosis network based on p42.3 established in the study provides theoretical evidence for deep exploration of p42.3 regulatory mechanism and molecular targeting treatment of colorectal cancer.

The Vector Matching Method in Geomagnetic Aiding Navigation

In this paper, a geomagnetic matching navigation method that utilizes the geomagnetic vector is developed, which can greatly improve the matching probability and positioning precision, even when the geomagnetic entropy information in the matching region is small or the geomagnetic contour line's variety is obscure. The vector iterative closest contour point (VICCP) algorithm that is proposed here has better adaptability with the positioning error characteristics of the inertial navigation system (INS), where the rigid transformation in ordinary ICCP is replaced with affine transformation. In a subsequent step, a geomagnetic vector information fusion algorithm based on Bayesian statistical analysis is introduced into VICCP to improve matching performance further. Simulations based on the actual geomagnetic reference map have been performed for the validation of the proposed algorithm.

What can we learn from Plausible Values?

In this paper, we show that the marginal distribution of plausible values is a consistent estimator of the true latent variable distribution, and, furthermore, that convergence is monotone in an embedding in which the number of items tends to infinity. We use this result to clarify some of the misconceptions that exist about plausible values, and also show how they can be used in the analyses of educational surveys.

Spatial-Temporal Epidemiology of Tuberculosis in Mainland China: An Analysis Based on Bayesian Theory

OBJECTIVE

To explore the spatial-temporal interaction effect within a Bayesian framework and to probe the ecological influential factors for tuberculosis.

METHODS

Six different statistical models containing parameters of time, space, spatial-temporal interaction and their combination were constructed based on a Bayesian framework. The optimum model was selected according to the deviance information criterion (DIC) value. Coefficients of climate variables were then estimated using the best fitting model.

RESULTS

The model containing spatial-temporal interaction parameter was the best fitting one, with the smallest DIC value (-4,508,660). Ecological analysis results showed the relative risks (RRs) of average temperature, rainfall, wind speed, humidity, and air pressure were 1.00324 (95% CI, 1.00150-1.00550), 1.01010 (95% CI, 1.01007-1.01013), 0.83518 (95% CI, 0.93732-0.96138), 0.97496 (95% CI, 0.97181-1.01386), and 1.01007 (95% CI, 1.01003-1.01011), respectively.

CONCLUSIONS

The spatial-temporal interaction was statistically meaningful and the prevalence of tuberculosis was influenced by the time and space interaction effect. Average temperature, rainfall, wind speed, and air pressure influenced tuberculosis. Average humidity had no influence on tuberculosis.

Probabilistic inference in discrete spaces can be implemented into networks of LIF neurons

The means by which cortical neural networks are able to efficiently solve inference problems remains an open question in computational neuroscience. Recently, abstract models of Bayesian computation in neural circuits have been proposed, but they lack a mechanistic interpretation at the single-cell level. In this article, we describe a complete theoretical framework for building networks of leaky integrate-and-fire neurons that can sample from arbitrary probability distributions over binary random variables. We test our framework for a model inference task based on a psychophysical phenomenon (the Knill-Kersten optical illusion) and further assess its performance when applied to randomly generated distributions. As the local computations performed by the network strongly depend on the interaction between neurons, we compare several types of couplings mediated by either single synapses or interneuron chains. Due to its robustness to substrate imperfections such as parameter noise and background noise correlations, our model is particularly interesting for implementation on novel, neuro-inspired computing architectures, which can thereby serve as a fast, low-power substrate for solving real-world inference problems.