How do we know if two systems - biological or artificial - process information in a similar way? Similarity measures such as linear regression, Centered Kernel Alignment (CKA), Normalized Bures Similarity (NBS), and angular Procrustes distance, are often used to quantify this similarity. However, it is currently unclear what drives high similarity scores and even what constitutes a "good" score. Here, we introduce a novel tool to investigate these questions by differentiating through similarity measures to directly maximize the score. Surprisingly, we find that high similarity scores do not guarantee encoding task-relevant information in a manner consistent with neural data; and this is particularly acute for CKA and even some variations of cross-validated and regularized linear regression. We find no consistent threshold for a good similarity score - it depends on both the measure and the dataset. In addition, synthetic datasets optimized to maximize similarity scores initially learn the highest variance principal component of the target dataset, but some methods like angular Procrustes capture lower variance dimensions much earlier than methods like CKA. To shed light on this, we mathematically derive the sensitivity of CKA, angular Procrustes, and NBS to the variance of principal component dimensions, and explain the emphasis CKA places on high variance components. Finally, by jointly optimizing multiple similarity measures, we characterize their allowable ranges and reveal that some similarity measures are more constraining than others. While current measures offer a seemingly straightforward way to quantify the similarity between neural systems, our work underscores the need for careful interpretation. We hope the tools we developed will be used by practitioners to better understand current and future similarity measures.

Understanding how the brain learns may be informed by studying biologically plausible learning rules. These rules, often approximating gradient descent learning to respect biological constraints such as locality, must meet two critical criteria to be considered an appropriate brain model: (1) good neuroscience task performance and (2) alignment with neural recordings. While extensive research has assessed the first criterion, the second remains underexamined. Employing methods such as Procrustes analysis on well-known neuroscience datasets, this study demonstrates the existence of a biologically plausible learning rule — namely e-prop, which is based on gradient truncation and has demonstrated versatility across a wide range of tasks — that can achieve neural data similarity comparable to Backpropagation Through Time (BPTT) when matched for task accuracy. Our findings also reveal that model architecture and initial conditions can play a more significant role in determining neural similarity than the specific learning rule. Furthermore, we observe that BPTT-trained models and their biologically plausible counterparts exhibit similar dynamical properties at comparable accuracies. These results underscore the substantial progress made in developing biologically plausible learning rules, highlighting their potential to achieve both competitive task performance and neural data similarity.

Humans and animals have a rich and flexible understanding of the physical world, which enables them to infer the underlying dynamical trajectories of objects and events, plausible future states, and use that to plan and anticipate the consequences of actions. However, the neural mechanisms underlying these computations are unclear. We combine a goal-driven modeling approach with dense neurophysiological data and high-throughput human behavioral readouts that contain thousands of comparisons to directly impinge on this question. Specifically, we construct and evaluate several classes of sensory-cognitive networks to predict the future state of rich, ethologically-relevant environments, ranging from self-supervised end-to-end models with pixel-wise or object-slot objectives, to models that future predict in the latent space of purely static image-pretrained or dynamic video-pretrained foundation models. We find that ``scale is \emph{not} all you need'', and that many state-of-the-art machine learning models fail to perform well on our neural and behavioral benchmarks for future prediction. In fact, only one class of models matches these data well overall. We find that neural responses are currently best predicted by models trained to predict the future state of their environment in the \emph{latent} space of pretrained foundation models optimized for \emph{dynamic} scenes in a self-supervised manner. These models also approach the neurons' ability to predict the environmental state variables that are visually hidden from view, despite not being explicitly trained to do so. Finally, we find that not all foundation model latents are equal. Notably, models that future predict in the latent space of video foundation models that are optimized to support a \emph{diverse} range of egocentric sensorimotor tasks, reasonably match \emph{both} human behavioral error patterns and neural dynamics across all environmental scenarios that we were able to test. Overall, these findings suggest that the neural mechanisms and behaviors of primate mental simulation have strong inductive biases associated with them, and are thus far most consistent with being optimized to future predict on \emph{reusable} visual representations that are useful for Embodied AI more generally.

A vexing problem in artificial intelligence is reasoning about events that occur in complex, changing visual stimuli such as in video analysis or game play. Inspired by a rich tradition of visual reasoning and memory in cognitive psychology and neuroscience, we developed an artificial, configurable visual question and answer dataset ( COG ) to parallel experiments in humans and animals. COG is much simpler than the general problem of video analysis, yet it addresses many of the problems relating to visual and logical reasoning and memory – problems that remain challenging for modern deep learning architectures. We additionally propose a deep learning architecture that performs competitively on other diagnostic VQA datasets (i.e. CLEVR) as well as easy settings of the COG dataset. However, several settings of COG result in datasets that are progressively more challenging to learn. After training, the network can zero-shot generalize to many new tasks. Preliminary analyses of the network architectures trained on COG demonstrate that the network accomplishes the task in a manner interpretable to humans.

The ability to simultaneously record from large numbers of neurons in behaving animals has ushered in a new era for the study of the neural circuit mechanisms underlying cognitive functions. One promising approach to uncovering the dynamical and computational principles governing population responses is to analyze model recurrent neural networks (RNNs) that have been optimized to perform the same tasks as behaving animals. Because the optimization of network parameters specifies the desired output but not the manner in which to achieve this output, "trained" networks serve as a source of mechanistic hypotheses and a testing ground for data analyses that link neural computation to behavior. Complete access to the activity and connectivity of the circuit, and the ability to manipulate them arbitrarily, make trained networks a convenient proxy for biological circuits and a valuable platform for theoretical investigation. However, existing RNNs lack basic biological features such as the distinction between excitatory and inhibitory units (Dale's principle), which are essential if RNNs are to provide insights into the operation of biological circuits. Moreover, trained networks can achieve the same behavioral performance but differ substantially in their structure and dynamics, highlighting the need for a simple and flexible framework for the exploratory training of RNNs. Here, we describe a framework for gradient descent-based training of excitatory-inhibitory RNNs that can incorporate a variety of biological knowledge. We provide an implementation based on the machine learning library Theano, whose automatic differentiation capabilities facilitate modifications and extensions. We validate this framework by applying it to well-known experimental paradigms such as perceptual decision-making, context-dependent integration, multisensory integration, parametric working memory, and motor sequence generation. Our results demonstrate the wide range of neural activity patterns and behavior that can be modeled, and suggest a unified setting in which diverse cognitive computations and mechanisms can be studied.