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Functional neuroimaging is sometimes criticized as showing only where in the brain things happen, not how they happen, and thus being unable to inform us about questions of mental and neural representation. Novel analytical methods increasingly make clear that imaging can give us access to constructs of interest to psychology. In this paper I argue that neuroimaging can give us an important, if limited, window into the large-scale structure of neural representation. I describe Representational Similarity Analysis, increasingly used in neuroimaging studies, and lay out desiderata for representations in general. In that context I discuss what RSA can and cannot tell us about neural representation. I compare RSA with fMRI to a different experimental paradigm which has been embraced as being indicative of representation in psychology, and argue that it compares favorably.

Although there is a substantial philosophical literature on dynamical systems theory in the cognitive sciences, the same is not the case for neuroscience. This paper attempts to motivate increased discussion via a set of overlapping issues. The first aim is primarily historical and is to demonstrate that dynamical systems theory is currently experiencing a renaissance in neuroscience. Although dynamical concepts and methods are becoming increasingly popular in contemporary neuroscience, the general approach should not be viewed as something entirely new to neuroscience. Instead, it is more appropriate to view the current developments as making central again approaches that facilitated some of neuroscience’s most significant early achievements, namely, the Hodgkin–Huxley and FitzHugh–Nagumo models. The second aim is primarily critical and defends a version of the “dynamical hypothesis” in neuroscience. Whereas the original version centered on defending a noncomputational and nonrepresentational account of cognition, the version I have in mind is broader and includes both cognition and the neural systems that realize it as well. In view of that, I discuss research on motor control as a paradigmatic example demonstrating that the concepts and methods of dynamical systems theory are increasingly and successfully being applied to neural systems in contemporary neuroscience. More significantly, such applications are motivating a stronger metaphysical claim, that is, understanding neural systems as being dynamical systems, which includes not requiring appeal to representations to explain or understand those phenomena. Taken together, the historical claim and the critical claim demonstrate that the dynamical hypothesis is undergoing a renaissance in contemporary neuroscience.

The concept of “representation” is used broadly and uncontroversially throughout neuroscience, in contrast to its highly controversial status within the philosophy of mind and cognitive science. In this paper I first discuss the way that the term is used within neuroscience, in particular describing the strategies by which representations are characterized empirically. I then relate the concept of representation within neuroscience to one that has developed within the field of machine learning (in particular through recent work in deep learning or “representation learning”). I argue that the recent success of artificial neural networks on certain tasks such as visual object recognition reflects the degree to which those systems (like biological brains) exhibit inherent inductive biases that reflect the structure of the physical world. I further argue that any system that is going to behave intelligently in the world must contain representations that reflect the structure of the world; otherwise, the system must perform unconstrained function approximation which is destined to fail due to the curse of dimensionality, in which the number of possible states of the world grows exponentially with the number of dimensions in the space of possible inputs. An analysis of these concepts in light of philosophical debates regarding the ontological status of representations suggests that the representations identified within both biological and artificial neural networks qualify as legitimate representations in the philosophical sense.

High-resolution functional imaging is providing increasingly rich measurements of brain activity in animals and humans. A major challenge is to leverage such data to gain insight into the brain's computational mechanisms. The first step is to define candidate brain-computational models (BCMs) that can perform the behavioural task in question. We would then like to infer which of the candidate BCMs best accounts for measured brain-activity data. Here we describe a method that complements each BCM by a measurement model (MM), which simulates the way the brain-activity measurements reflect neuronal activity (e.g. local averaging in functional magnetic resonance imaging (fMRI) voxels or sparse sampling in array recordings). The resulting generative model (BCM-MM) produces simulated measurements. To avoid having to fit the MM to predict each individual measurement channel of the brain-activity data, we compare the measured and predicted data at the level of summary statistics. We describe a novel particular implementation of this approach, called probabilistic representational similarity analysis (pRSA) with MMs, which uses representational dissimilarity matrices (RDMs) as the summary statistics. We validate this method by simulations of fMRI measurements (locally averaging voxels) based on a deep convolutional neural network for visual object recognition. Results indicate that the way the measurements sample the activity patterns strongly affects the apparent representational dissimilarities. However, modelling of the measurement process can account for these effects, and different BCMs remain distinguishable even under substantial noise. The pRSA method enables us to perform Bayesian inference on the set of BCMs and to recognize the data-generating model in each case. This article is part of the themed issue ‘Interpreting BOLD: a dialogue between cognitive and cellular neuroscience’.

Correctly understood, teleosemantics is the claim that “representation” is a function term. Things are called “representations” if they have a certain kind of function or telos and perform it in a certain kind of way. This claim is supported with a discussion and proposals about the function of a representation and of how representations perform that function. These proposals have been retrieved by putting together current descriptions from the literature on neural representations with earlier explorations of the features common to most things we are inclined to call representations (… maps, graphs, human language, signals between animals, stop signs … etc.) as these were assessed in Millikan (Language, thought and other biological categories. MIT Press, Cambridge, 1984 and following). Of interest is the degree to which these independent sources converge. I conclude that there is no need to employ any new or technical sense of the term “representation” for it to play an important role in neuroscience.

The notion of representation in neuroscience has largely been predicated on localizing the components of computational processes that explain cognitive function. On this view, which I call “algorithmic homuncularism,” individual, spatially and temporally distinct parts of the brain serve as vehicles for distinct contents, and the causal relationships between them implement the transformations specified by an algorithm. This view has a widespread influence in philosophy and cognitive neuroscience, and has recently been ably articulated and defended by Shea (2018). Still, I am skeptical about algorithmic homuncularism, and I argue against it by focusing on recent methods for complex data analysis in systems neuroscience. I claim that analyses such as principle components analysis and linear discriminant analysis prevent individuating vehicles as algorithmic homuncularism recommends. Rather, each individual part contributes to a global state space, trajectories of which vary with important task parameters. I argue that, while homuncularism is false, this view still supports a kind of “vehicle realism,” and I apply this view to debates about the explanatory role of representation.

Neuroscientists have located brain activity that prepares or encodes action plans before agents are aware of intending to act. On the basis of these findings and broader agency research, activity in these regions has been proposed as the neural realizers of practical intention. My aim in this paper is to evaluate the case for taking these neural states to be neural representations of intention. I draw on work in philosophy of action on the role and nature of practical intentions to construct a framework of the functional profile of intentions fit for empirical investigation. With this framework, I turn to the broader empirical neuroscience literature on agency to assess these proposed neural representations of intention. I argue that while these neural states in some respects satisfy the functions of intention in planning agency prospective of action, their fit with the role of intention in action execution is not well supported. I close by offering a sketch of which experimental task features could aid in the search for the neural realizer of intention in action.

Healthy aging affects several domains of cognitive and motor performance and is further associated with multiple structural and functional neural reorganization patterns. However, gap of knowledge exists, referring to the impact of these age-related alterations on the neural basis of tool use – an important, complex action involved in everyday life throughout the entire lifespan. The current fMRI study aims to investigate age-related changes of neural correlates involved in planning and executing a complex object manipulation task, further providing a better understanding of impaired tool use performance in apraxia patients. A balanced number of sixteen older and younger healthy adults repeatedly manipulated everyday tools in an event-related Go-No-Go fMRI paradigm. Our data indicates that the left-lateralized network, including widely distributed frontal, temporal, parietal and occipital regions, involved in tool use performance is not subjected to age-related functional reorganization processes. However, age-related changes regarding the applied strategical procedure can be detected, indicating stronger investment into the planning, preparatory phase of such an action in older participants. Key Words: tool use, brain representation, apraxia, healthy aging, fMRI

Finding links between genes and structural connectivity is of the utmost importance for unravelling the underlying mechanism of the brain connectome. In this study we identify links between the gene expression and the axonal projection density in the mouse brain, by applying a modified version of the Linked ICA method to volumetric data from the Allen Institute for Brain Science for identifying independent sources of information that link both modalities at the voxel level. We performed separate analyses on sets of projections from the visual cortex, the caudoputamen and the midbrain reticular nucleus, and we determined those brain areas, injections and genes that were most involved in independent components that link both gene expression and projection density data, while we validated their biological context through enrichment analysis. We identified representative and literature-validated cortico-midbrain and cortico-striatal projections, whose gene subsets were enriched with annotations for neuronal and synaptic function and related developmental and metabolic processes. The results were highly reproducible when including all available projections, as well as consistent with factorisations obtained using the Dictionary Learning and Sparse Coding technique. Hence, Linked ICA yielded reproducible independent components that were preserved under increasing data variance. Taken together, we have developed and validated a novel paradigm for linking gene expression and structural projection patterns in the mouse mesoconnectome, which can power future studies aiming to relate genes to brain function.