Deep latent variable joint cognitive modeling of neural signals and human behavior.

As the field of computational cognitive neuroscience continues to expand and generate new theories, there is a growing need for more advanced methods to test the hypothesis of brain-behavior relationships. Recent progress in Bayesian cognitive modeling has enabled the combination of neural and behavioral models into a single unifying framework. However, these approaches require manual feature extraction, and lack the capability to discover previously unknown neural features in more complex data. Consequently, this would hinder the expressiveness of the models. To address these challenges, we propose a Neurocognitive Variational Autoencoder (NCVA) to conjoin high-dimensional EEG with a cognitive model in both generative and predictive modeling analyses. Importantly, our NCVA enables both the prediction of EEG signals given behavioral data and the estimation of cognitive model parameters from EEG signals. This novel approach can allow for a more comprehensive understanding of the triplet relationship between behavior, brain activity, and cognitive processes.

Commensurability engineering is first and foremost a theoretical exercise.

I provide a personal perspective on metastudies and emphasize lesser-known benefits. I stress the need for integrative theories to establish commensurability between experiments. I argue that mathematical social scientists should be engaged to develop integrative theories, and that likelihood functions provide a common mathematical framework across experiments. The development of quantitative theories promotes commensurability engineering on a larger scale.

Parsing memory and nonmemory contributions to age-related declines in mnemonic discrimination performance: a hierarchical Bayesian diffusion decision modeling approach.

The mnemonic discrimination task (MDT) is a widely used cognitive assessment tool. Performance in this task is believed to indicate an age-related deficit in episodic memory stemming from a decreased ability to pattern-separate among similar experiences. However, cognitive processes other than memory ability might impact task performance. In this study, we investigated whether nonmnemonic decision-making processes contribute to the age-related deficit in the MDT. We applied a hierarchical Bayesian version of the Ratcliff diffusion model to the MDT performance of 26 younger and 31 cognitively normal older adults. It allowed us to decompose decision behavior in the MDT into different underlying cognitive processes, represented by specific model parameters. Model parameters were compared between groups, and differences were evaluated using the Bayes factor. Our results suggest that the age-related decline in MDT performance indicates a predominantly mnemonic deficit rather than differences in nonmnemonic decision-making processes. In addition, this mnemonic deficit might also involve a slowing in processes related to encoding and retrieval strategies, which are relevant for successful memory as well. These findings help to better understand what cognitive processes contribute to the age-related decline in MDT performance and may help to improve the diagnostic value of this popular task.

A tutorial on fitting joint models of M/EEG and behavior to understand cognition.

We present motivation and practical steps necessary to find parameter estimates of joint models of behavior and neural electrophysiological data. This tutorial is written for researchers wishing to build joint models of human behavior and scalp and intracranial electroencephalographic (EEG) or magnetoencephalographic (MEG) data, and more specifically those researchers who seek to understand human cognition. Although these techniques could easily be applied to animal models, the focus of this tutorial is on human participants. Joint modeling of M/EEG and behavior requires some knowledge of existing computational and cognitive theories, M/EEG artifact correction, M/EEG analysis techniques, cognitive modeling, and programming for statistical modeling implementation. This paper seeks to give an introduction to these techniques as they apply to estimating parameters from neurocognitive models of M/EEG and human behavior, and to evaluate model results and compare models. Due to our research and knowledge on the subject matter, our examples in this paper will focus on testing specific hypotheses in human decision-making theory. However, most of the motivation and discussion of this paper applies across many modeling procedures and applications. We provide Python (and linked R) code examples in the tutorial and appendix. Readers are encouraged to try the exercises at the end of the document.

Quantifying Evidence for-and against-Granger Causality with Bayes Factors.

Testing for Granger causality relies on estimating the capacity of dynamics in one time series to forecast dynamics in another. The canonical test for such temporal predictive causality is based on fitting multivariate time series models and is cast in the classical null hypothesis testing framework. In this framework, we are limited to rejecting the null hypothesis or failing to reject the null - we can never validly accept the null hypothesis of no Granger causality. This is poorly suited for many common purposes, including evidence integration, feature selection, and other cases where it is useful to express evidence against, rather than for, the existence of an association. Here we derive and implement the Bayes factor for Granger causality in a multilevel modeling framework. This Bayes factor summarizes information in the data in terms of a continuously scaled evidence ratio between the presence of Granger causality and its absence. We also introduce this procedure for the multilevel generalization of Granger causality testing. This facilitates inference when information is scarce or noisy or if we are interested primarily in population-level trends. We illustrate our approach with an application on exploring causal relationships in affect using a daily life study.

Extraordinary claims, extraordinary evidence? A discussion.

Roberts (2020, Learning & Behavior, 48[2], 191-192) discussed research claiming honeybees can do arithmetic. Some readers of this research might regard such claims as unlikely. The present authors used this example as a basis for a debate on the criterion that ought to be used for publication of results or conclusions that could be viewed as unlikely by a significant number of readers, editors, or reviewers.

Metastudies for robust tests of theory.

We describe and demonstrate an empirical strategy useful for discovering and replicating empirical effects in psychological science. The method involves the design of a metastudy, in which many independent experimental variables-that may be moderators of an empirical effect-are indiscriminately randomized. Radical randomization yields rich datasets that can be used to test the robustness of an empirical claim to some of the vagaries and idiosyncrasies of experimental protocols and enhances the generalizability of these claims. The strategy is made feasible by advances in hierarchical Bayesian modeling that allow for the pooling of information across unlike experiments and designs and is proposed here as a gold standard for replication research and exploratory research. The practical feasibility of the strategy is demonstrated with a replication of a study on subliminal priming.

The latency of a visual evoked potential tracks the onset of decision making.

Encoding of a sensory stimulus is believed to be the first step in perceptual decision making. Previous research has shown that electrical signals recorded from the human brain track evidence accumulation during perceptual decision making (Gold and Shadlen, 2007; O'Connell et al., 2012; Philiastides et al., 2014). In this study we directly tested the hypothesis that the latency of the N200 recorded by EEG (a negative peak occurring between 150 and 275 ms after stimulus presentation in human participants) reflects the visual encoding time (VET) required for completion of figure-ground segregation before evidence accumulation. We show that N200 latencies vary across individuals, are modulated by external visual noise, and increase response time by x milliseconds when they increase by x milliseconds, reflecting a linear regression slope of 1. Simulations of cognitive decision-making theory show that variation in human response times not related to evidence accumulation (non-decision time; NDT), including VET, are tracked by the fastest response times. Evidence that VET is tracked by N200 latencies was found by fitting a linear model between trial-averaged N200 latencies and the 10th percentiles of response times, a model-independent estimate of NDT. Fitting a novel neuro-cognitive model of decision making also yielded a slope of 1 between N200 latency and model-estimated NDT in multiple visual noise conditions, indicating that N200 latencies track the completion of visual encoding and the onset of evidence accumulation. The N200 waveforms were localized to the cortical surface at distributed temporal and extrastriate locations, consistent with a distributed network engaged in figure-ground segregation of the target stimulus.

Modeling when people quit: Bayesian censored geometric models with hierarchical and latent-mixture extensions.

People often interact with environments that can provide only a finite number of items as resources. Eventually a book contains no more chapters, there are no more albums available from a band, and every Pokémon has been caught. When interacting with these sorts of environments, people either actively choose to quit collecting new items, or they are forced to quit when the items are exhausted. Modeling the distribution of how many items people collect before they quit involves untangling these two possibilities, We propose that censored geometric models are a useful basic technique for modeling the quitting distribution, and, show how, by implementing these models in a hierarchical and latent-mixture framework through Bayesian methods, they can be extended to capture the additional features of specific situations. We demonstrate this approach by developing and testing a series of models in two case studies involving real-world data. One case study deals with people choosing jokes from a recommender system, and the other deals with people completing items in a personality survey.

Bayesian Data Analysis with the Bivariate Hierarchical Ornstein-Uhlenbeck Process Model.

In this paper, we propose a multilevel process modeling approach to describing individual differences in within-person changes over time. To characterize changes within an individual, repeated measures over time are modeled in terms of three person-specific parameters: a baseline level, intraindividual variation around the baseline, and regulatory mechanisms adjusting toward baseline. Variation due to measurement error is separated from meaningful intraindividual variation. The proposed model allows for the simultaneous analysis of longitudinal measurements of two linked variables (bivariate longitudinal modeling) and captures their relationship via two person-specific parameters. Relationships between explanatory variables and model parameters can be studied in a one-stage analysis, meaning that model parameters and regression coefficients are estimated simultaneously. Mathematical details of the approach, including a description of the core process model-the Ornstein-Uhlenbeck model-are provided. We also describe a user friendly, freely accessible software program that provides a straightforward graphical interface to carry out parameter estimation and inference. The proposed approach is illustrated by analyzing data collected via self-reports on affective states.

Pupil-linked arousal determines variability in perceptual decision making.

Decision making between several alternatives is thought to involve the gradual accumulation of evidence in favor of each available choice. This process is profoundly variable even for nominally identical stimuli, yet the neuro-cognitive substrates that determine the magnitude of this variability are poorly understood. Here, we demonstrate that arousal state is a powerful determinant of variability in perceptual decision making. We measured pupil size, a highly sensitive index of arousal, while human subjects performed a motion-discrimination task, and decomposed task behavior into latent decision making parameters using an established computational model of the decision process. In direct contrast to previous theoretical accounts specifying a role for arousal in several discrete aspects of decision making, we found that pupil diameter was uniquely related to a model parameter representing variability in the rate of decision evidence accumulation: Periods of increased pupil size, reflecting heightened arousal, were characterized by greater variability in accumulation rate. Pupil diameter also correlated trial-by-trial with specific patterns of behavior that collectively are diagnostic of changing accumulation rate variability, and explained substantial individual differences in this computational quantity. These findings provide a uniquely clear account of how arousal state impacts decision making, and may point to a relationship between pupil-linked neuromodulation and behavioral variability. They also pave the way for future studies aimed at augmenting the precision with which people make decisions.

Extending JAGS: a tutorial on adding custom distributions to JAGS (with a diffusion model example).

We demonstrate how to add a custom distribution into the general-purpose, open-source, cross-platform graphical modeling package JAGS ("Just Another Gibbs Sampler"). JAGS is intended to be modular and extensible, and modules written in the way laid out here can be loaded at runtime as needed and do not interfere with regular JAGS functionality when not loaded. Writing custom extensions requires knowledge of C++, but installing a new module can be highly automatic, depending on the operating system. As a basic example, we implement a Bernoulli distribution in JAGS. We further present our implementation of the Wiener diffusion first-passage time distribution, which is freely available at https://sourceforge.net/projects/jags-wiener/ .

The HDI + ROPE decision rule is logically incoherent but we can fix it.

The Bayesian highest-density interval plus region of practical equivalence (HDI + ROPE) decision rule is an increasingly common approach to testing null parameter values. The decision procedure involves a comparison between a posterior highest-density interval (HDI) and a prespecified region of practical equivalence. One then accepts or rejects the null parameter value depending on the overlap (or lack thereof) between these intervals. Here, we demonstrate, both theoretically and through examples, that this procedure is logically incoherent. Because the HDI is not transformation invariant, the ultimate inferential decision depends on statistically arbitrary and scientifically irrelevant properties of the statistical model. The incoherence arises from a common confusion between probability density and probability proper. The HDI + ROPE procedure relies on characterizing posterior densities as opposed to being based directly on probability. We conclude with recommendations for alternative Bayesian testing procedures that do not exhibit this pathology and provide a "quick fix" in the form of quantile intervals. This article is the work of the authors and is reformatted from the original, which was published under a CC-BY Attribution 4.0 International license and is available at https://psyarxiv.com/5p2qt/. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Cortico-Brainstem Mechanisms of Biased Perceptual Decision-Making in the Context of Pain.

Prior expectations can bias how we perceive pain. Using a drift diffusion model, we recently showed that this influence is primarily based on changes in perceptual decision-making (indexed as shift in starting point). Only during unexpected application of high-intensity noxious stimuli, altered information processing (indexed as increase in drift rate) explained the expectancy effect on pain processing. Here, we employed functional magnetic resonance imaging to investigate the neural basis of both these processes in healthy volunteers. On each trial, visual cues induced the expectation of high- or low-intensity noxious stimulation or signaled equal probability for both intensities. Participants categorized a subsequently applied electrical stimulus as either low- or high-intensity pain. A shift in starting point towards high pain correlated negatively with right dorsolateral prefrontal cortex activity during cue presentation underscoring its proposed role of "keeping pain out of mind". This anticipatory right dorsolateral prefrontal cortex signal increase was positively correlated with periaqueductal gray (PAG) activity when the expected high-intensity stimulation was applied. A drift rate increase during unexpected high-intensity pain was reflected in amygdala engagement and increased functional connectivity between amygdala and PAG. Our findings suggest involvement of the PAG in both decision-making bias and altered information processing to implement expectancy effects on pain. PERSPECTIVE: Modulation of pain through expectations has been linked to changes in perceptual decision-making and altered processing of afferent information. Our results suggest involvement of the dorsolateral prefrontal cortex, amygdala, and periaqueductal gray in these processes.

A pre-registered, multi-lab non-replication of the action-sentence compatibility effect (ACE).

The Action-sentence Compatibility Effect (ACE) is a well-known demonstration of the role of motor activity in the comprehension of language. Participants are asked to make sensibility judgments on sentences by producing movements toward the body or away from the body. The ACE is the finding that movements are faster when the direction of the movement (e.g., toward) matches the direction of the action in the to-be-judged sentence (e.g., Art gave you the pen describes action toward you). We report on a pre-registered, multi-lab replication of one version of the ACE. The results show that none of the 18 labs involved in the study observed a reliable ACE, and that the meta-analytic estimate of the size of the ACE was essentially zero.

The case for formal methodology in scientific reform.

Current attempts at methodological reform in sciences come in response to an overall lack of rigor in methodological and scientific practices in experimental sciences. However, most methodological reform attempts suffer from similar mistakes and over-generalizations to the ones they aim to address. We argue that this can be attributed in part to lack of formalism and first principles. Considering the costs of allowing false claims to become canonized, we argue for formal statistical rigor and scientific nuance in methodological reform. To attain this rigor and nuance, we propose a five-step formal approach for solving methodological problems. To illustrate the use and benefits of such formalism, we present a formal statistical analysis of three popular claims in the metascientific literature: (i) that reproducibility is the cornerstone of science; (ii) that data must not be used twice in any analysis; and (iii) that exploratory projects imply poor statistical practice. We show how our formal approach can inform and shape debates about such methodological claims.

Timing of readiness potentials reflect a decision-making process in the human brain.

Decision-making in two-alternative forced choice tasks has several underlying components including stimulus encoding, perceptual categorization, response selection, and response execution. Sequential sampling models of decision-making are based on an evidence accumulation process to a decision boundary. Animal and human studies have focused on perceptual categorization and provide evidence linking brain signals in parietal cortex to the evidence accumulation process. In this exploratory study, we use a task where the dominant contribution to response time is response selection and model the response time data with the drift-diffusion model. EEG measurement during the task show that the Readiness Potential (RP) recorded over motor areas has timing consistent with the evidence accumulation process. The duration of the RP predicts decision-making time, the duration of evidence accumulation, suggesting that the RP partly reflects an evidence accumulation process for response selection in the motor system. Thus, evidence accumulation may be a neural implementation of decision-making processes in both perceptual and motor systems. The contributions of perceptual categorization and response selection to evidence accumulation processes in decision-making tasks can be potentially evaluated by examining the timing of perceptual and motor EEG signals.

The Quality of Response Time Data Inference: A Blinded, Collaborative Assessment of the Validity of Cognitive Models.

Most data analyses rely on models. To complement statistical models, psychologists have developed cognitive models, which translate observed variables into psychologically interesting constructs. Response time models, in particular, assume that response time and accuracy are the observed expression of latent variables including 1) ease of processing, 2) response caution, 3) response bias, and 4) non-decision time. Inferences about these psychological factors, hinge upon the validity of the models' parameters. Here, we use a blinded, collaborative approach to assess the validity of such model-based inferences. Seventeen teams of researchers analyzed the same 14 data sets. In each of these two-condition data sets, we manipulated properties of participants' behavior in a two-alternative forced choice task. The contributing teams were blind to the manipulations, and had to infer what aspect of behavior was changed using their method of choice. The contributors chose to employ a variety of models, estimation methods, and inference procedures. Our results show that, although conclusions were similar across different methods, these "modeler's degrees of freedom" did affect their inferences. Interestingly, many of the simpler approaches yielded as robust and accurate inferences as the more complex methods. We recommend that, in general, cognitive models become a typical analysis tool for response time data. In particular, we argue that the simpler models and procedures are sufficient for standard experimental designs. We finish by outlining situations in which more complicated models and methods may be necessary, and discuss potential pitfalls when interpreting the output from response time models.

Introduction to Bayesian Inference for Psychology.

We introduce the fundamental tenets of Bayesian inference, which derive from two basic laws of probability theory. We cover the interpretation of probabilities, discrete and continuous versions of Bayes' rule, parameter estimation, and model comparison. Using seven worked examples, we illustrate these principles and set up some of the technical background for the rest of this special issue of Psychonomic Bulletin & Review. Supplemental material is available via https://osf.io/wskex/ .

Bayesian inference for psychology, part III: Parameter estimation in nonstandard models.

We demonstrate the use of three popular Bayesian software packages that enable researchers to estimate parameters in a broad class of models that are commonly used in psychological research. We focus on WinBUGS, JAGS, and Stan, and show how they can be interfaced from R and MATLAB. We illustrate the use of the packages through two fully worked examples; the examples involve a simple univariate linear regression and fitting a multinomial processing tree model to data from a classic false-memory experiment. We conclude with a comparison of the strengths and weaknesses of the packages. Our example code, data, and this text are available via https://osf.io/ucmaz/ .