Response to commentaries on our paper: Critical comments on dynamic causal modelling

Causality in Cognitive Neuroscience: Concepts, Challenges, and Distributional Robustness

Whereas probabilistic models describe the dependence structure between observed variables, causal models go one step further: They predict, for example, how cognitive functions are affected by external interventions that perturb neuronal activity. In this review and perspective article, we introduce the concept of causality in the context of cognitive neuroscience and review existing methods for inferring causal relationships from data. Causal inference is an ambitious task that is particularly challenging in cognitive neuroscience. We discuss two difficulties in more detail: the scarcity of interventional data and the challenge of finding the right variables. We argue for distributional robustness as a guiding principle to tackle these problems. Robustness (or invariance) is a fundamental principle underlying causal methodology. A (correctly specified) causal model of a target variable generalizes across environments or subjects as long as these environments leave the causal mechanisms of the target intact. Consequently, if a candidate model does not generalize, then either it does not consist of the target variable's causes or the underlying variables do not represent the correct granularity of the problem. In this sense, assessing generalizability may be useful when defining relevant variables and can be used to partially compensate for the lack of interventional data.

A study of problems encountered in Granger causality analysis from a neuroscience perspective

Granger causality methods were developed to analyze the flow of information between time series. These methods have become more widely applied in neuroscience. Frequency-domain causality measures, such as those of Geweke, as well as multivariate methods, have particular appeal in neuroscience due to the prevalence of oscillatory phenomena and highly multivariate experimental recordings. Despite its widespread application in many fields, there are ongoing concerns regarding the applicability of Granger causality methods in neuroscience. When are these methods appropriate? How reliably do they recover the system structure underlying the observed data? What do frequency-domain causality measures tell us about the functional properties of oscillatory neural systems? In this paper, we analyze fundamental properties of Granger-Geweke (GG) causality, both computational and conceptual. Specifically, we show that (i) GG causality estimates can be either severely biased or of high variance, both leading to spurious results; (ii) even if estimated correctly, GG causality estimates alone are not interpretable without examining the component behaviors of the system model; and (iii) GG causality ignores critical components of a system's dynamics. Based on this analysis, we find that the notion of causality quantified is incompatible with the objectives of many neuroscience investigations, leading to highly counterintuitive and potentially misleading results. Through the analysis of these problems, we provide important conceptual clarification of GG causality, with implications for other related causality approaches and for the role of causality analyses in neuroscience as a whole.

Deficient approaches to human neuroimaging

Functional magnetic resonance imaging (fMRI) is the workhorse of imaging-based human cognitive neuroscience. The use of fMRI is ever-increasing; within the last 4 years more fMRI studies have been published than in the previous 17 years. This large body of research has mainly focused on the functional localization of condition- or stimulus-dependent changes in the blood-oxygenation-level dependent signal. In recent years, however, many aspects of the commonly practiced analysis frameworks and methodologies have been critically reassessed. Here we summarize these critiques, providing an overview of the major conceptual and practical deficiencies in widely used brain-mapping approaches, and exemplify some of these issues by the use of imaging data and simulations. In particular, we discuss the inherent pitfalls and shortcomings of methodologies for statistical parametric mapping. Our critique emphasizes recent reports of excessively high numbers of both false positive and false negative findings in fMRI brain mapping. We outline our view regarding the broader scientific implications of these methodological considerations and briefly discuss possible solutions.

Reliability of Dynamic Causal Modeling using the Statistical Parametric Mapping Toolbox

Dynamic causal modeling (DCM) is a recently developed approach for effective connectivity measurement in the brain. It has attracted considerable attention in recent years and quite widespread used to investigate brain connectivity in response to different tasks as well as auditory, visual, and somatosensory stimulation. This method uses complex algorithms, and currently the only implementation available is the Statistical Parametric Mapping (SPM8) toolbox with functionality for use on EEG and fMRI. The objective of the current work is to test the robustness of the toolbox when applied to EEG, by comparing results obtained from various versions of the software and operating systems when using identical datasets. Contrary to expectations, it was found that estimated connectivities were not consistent between different operating systems, the version of SPM8, or the version of MATLAB being used. The exact cause of this problem is not clear, but may relate to the high number of parameters in the model. Caution is thus recommended when interpreting the results of DCM estimated with the SPM8 software.

Neural and behavioral investigations into timbre perception

Timbre is the attribute that distinguishes sounds of equal pitch, loudness and duration. It contributes to our perception and discrimination of different vowels and consonants in speech, instruments in music and environmental sounds. Here we begin by reviewing human timbre perception and the spectral and temporal acoustic features that give rise to timbre in speech, musical and environmental sounds. We also consider the perception of timbre by animals, both in the case of human vowels and non-human vocalizations. We then explore the neural representation of timbre, first within the peripheral auditory system and later at the level of the auditory cortex. We examine the neural networks that are implicated in timbre perception and the computations that may be performed in auditory cortex to enable listeners to extract information about timbre. We consider whether single neurons in auditory cortex are capable of representing spectral timbre independently of changes in other perceptual attributes and the mechanisms that may shape neural sensitivity to timbre. Finally, we conclude by outlining some of the questions that remain about the role of neural mechanisms in behavior and consider some potentially fruitful avenues for future research.