Autonomy is a hallmark of animal intelligence, enabling adaptive and intelligent behavior in complex environments without relying on external reward or task structure. Existing reinforcement learning approaches to exploration in reward-free environments, including a class of methods known as *model-based intrinsic motivation*, exhibit inconsistent exploration patterns and do not converge to an exploratory policy, thus failing to capture robust autonomous behaviors observed in animals. Moreover, systems neuroscience has largely overlooked the neural basis of autonomy, focusing instead on experimental paradigms where animals are motivated by external reward rather than engaging in ethological, naturalistic and task-independent behavior. To bridge these gaps, we introduce a novel model-based intrinsic drive explicitly designed after the principles of autonomous exploration in animals. Our method (3M-Progress) achieves animal-like exploration by tracking divergence between an online world model and a fixed prior learned from an ecological niche. To the best of our knowledge, we introduce the first autonomous embodied agent that predicts brain data entirely from self-supervised optimization of an intrinsic goal—without any behavioral or neural training data—demonstrating that 3M-Progress agents capture the explainable variance in behavioral patterns and whole-brain neural-glial dynamics recorded from autonomously behaving larval zebrafish, thereby providing the first goal-driven, population-level model of neural-glial computation. Our findings establish a computational framework connecting model-based intrinsic motivation to naturalistic behavior, providing a foundation for building artificial agents with animal-like autonomy.

Machine learning models have difficulty generalizing to data outside of the distribution they were trained on. In particular, vision models are usually vulnerable to adversarial attacks or common corruptions, to which the human visual system is robust. Recent studies have found that regularizing machine learning models to favor brain-like representations can improve model robustness, but it is unclear why. We hypothesize that the increased model robustness is partly due to the low spatial frequency preference inherited from the neural representation. We tested this simple hypothesis with several frequency-oriented analyses, including the design and use of hybrid images to probe model frequency sensitivity directly. We also examined many other publicly available robust models that were trained on adversarial images or with data augmentation, and found that all these robust models showed a greater preference to low spatial frequency information. We show that preprocessing by blurring can serve as a defense mechanism against both adversarial attacks and common corruptions, further confirming our hypothesis and demonstrating the utility of low spatial frequency information in robust object recognition.

Sensory observations about the world are invariably ambiguous. Inference about the world's latent variables is thus an important computation for the brain. However, computational constraints limit the performance of these computations. These constraints include energetic costs for neural activity and noise on every channel. Efficient coding is one prominent theory that describes how such limited resources can best be used. In one incarnation, this leads to a theory of predictive coding, where predictions are subtracted from signals, reducing the cost of sending something that is already known. This theory does not, however, account for the costs or noise associated with those predictions. Here we offer a theory that accounts for both feedforward and feedback costs, and noise in all computations. We formulate this inference problem as message-passing on a graph whereby feedback serves as an internal control signal aiming to maximize how well an inference tracks a target state while minimizing the costs of computation. We apply this novel formulation of inference as control to the canonical problem of inferring the hidden scalar state of a linear dynamical system with Gaussian variability. The best solution depends on architectural constraints, such as Dale's law, the ubiquitous law that each neuron makes solely excitatory or inhibitory postsynaptic connections. This biological structure can create asymmetric costs for feedforward and feedback channels. Under such conditions, our theory predicts the gain of optimal predictive feedback and how it is incorporated into the inference computation. We show that there is a non-monotonic dependence of optimal feedback gain as a function of both the computational parameters and the world dynamics, leading to phase transitions in whether feedback provides any utility in optimal inference under computational constraints.

Sampling and Variational Inference (VI) are two large families of methods for approximate inference that have complementary strengths. Sampling methods excel at approximating arbitrary probability distributions, but can be inefficient. VI methods are efficient, but may misrepresent the true distribution. Here, we develop a general framework where approximations are stochastic mixtures of simple component distributions. Both sampling and VI can be seen as special cases: in sampling, each mixture component is a delta-function and is chosen stochastically, while in standard VI a single component is chosen to minimize divergence. We derive a practical method that interpolates between sampling and VI by analytically solving an optimization problem over a mixing distribution. Intermediate inference methods then arise by varying a single parameter. Our method provably improves on sampling (reducing variance) and on VI (reducing bias+variance despite increasing variance). We demonstrate our method’s bias/variance trade-off in practice on reference problems, and we compare outcomes to commonly used sampling and VI methods. This work takes a step towards a highly flexible yet simple family of inference methods that combines the complementary strengths of sampling and VI.

To extract the voice of a target speaker when mixed with a variety of other sounds, such as white and ambient noises or the voices of interfering speakers, we extend the Transformer network to attend the most relevant information with respect to the target speaker given the characteristics of his or her voices as a form of contextual information. The idea has a natural interpretation in terms of the selective attention theory. Specifically, we propose two models to incorporate the voice characteristics in Transformer based on different insights of where the feature selection should take place. Both models yield excellent performance, on par or better than published state-of-the-art models on the speaker extraction task, including separating speech of novel speakers not seen during training.

A fundamental question in neuroscience is how the brain creates an internal model of the world to guide actions using sequences of ambiguous sensory information. This is naturally formulated as a reinforcement learning problem under partial observations, where an agent must estimate relevant latent variables in the world from its evidence, anticipate possible future states, and choose actions that optimize total expected reward. This problem can be solved by control theory, which allows us to find the optimal actions for a given system dynamics and objective function. However, animals often appear to behave suboptimally. Why? We hypothesize that animals have their own flawed internal model of the world, and choose actions with the highest expected subjective reward according to that flawed model. We describe this behavior as {\it rational} but not optimal. The problem of Inverse Rational Control (IRC) aims to identify which internal model would best explain an agent's actions. Our contribution here generalizes past work on Inverse Rational Control which solved this problem for discrete control in partially observable Markov decision processes. Here we accommodate continuous nonlinear dynamics and continuous actions, and impute sensory observations corrupted by unknown noise that is private to the animal. We first build an optimal Bayesian agent that learns an optimal policy generalized over the entire model space of dynamics and subjective rewards using deep reinforcement learning. Crucially, this allows us to compute a likelihood over models for experimentally observable action trajectories acquired from a suboptimal agent. We then find the model parameters that maximize the likelihood using gradient ascent. Our method successfully recovers the true model of rational agents. This approach provides a foundation for interpreting the behavioral and neural dynamics of animal brains during complex tasks.

Despite impressive performance on numerous visual tasks, Convolutional Neural Networks (CNNs) --- unlike brains --- are often highly sensitive to small perturbations of their input, e.g. adversarial noise leading to erroneous decisions. We propose to regularize CNNs using large-scale neuroscience data to learn more robust neural features in terms of representational similarity. We presented natural images to mice and measured the responses of thousands of neurons from cortical visual areas. Next, we denoised the notoriously variable neural activity using strong predictive models trained on this large corpus of responses from the mouse visual system, and calculated the representational similarity for millions of pairs of images from the model's predictions. We then used the neural representation similarity to regularize CNNs trained on image classification by penalizing intermediate representations that deviated from neural ones. This preserved performance of baseline models when classifying images under standard benchmarks, while maintaining substantially higher performance compared to baseline or control models when classifying noisy images. Moreover, the models regularized with cortical representations also improved model robustness in terms of adversarial attacks. This demonstrates that regularizing with neural data can be an effective tool to create an inductive bias towards more robust inference.

In this paper, we revisit the recurrent back-propagation (RBP) algorithm, discuss the conditions under which it applies as well as how to satisfy them in deep neural networks. We show that RBP can be unstable and propose two variants based on conjugate gradient on the normal equations (CG-RBP) and Neumann series (Neumann-RBP). We further investigate the relationship between Neumann-RBP and back propagation through time (BPTT) and its truncated version (TBPTT). Our Neumann-RBP has the same time complexity as TBPTT but only requires constant memory, whereas TBPTT’s memory cost scales linearly with the number of truncation steps. We examine all RBP variants along with BPTT and TBPTT in three different application domains: associative memory with continuous Hopfield networks, document classification in citation networks using graph neural networks and hyperparameter optimization for fully connected networks. All experiments demonstrate that RBPs, especially the Neumann-RBP variant, are efficient and effective for optimizing convergent recurrent neural networks.

To better understand the representations in visual cortex, we need to generate better predictions of neural activity in awake animals presented with their ecological input: natural video. Despite recent advances in models for static images, models for predicting responses to natural video are scarce and standard linear-nonlinear models perform poorly. We developed a new deep recurrent network architecture that predicts inferred spiking activity of thousands of mouse V1 neurons simultaneously recorded with two-photon microscopy, while accounting for confounding factors such as the animal's gaze position and brain state changes related to running state and pupil dilation. Powerful system identification models provide an opportunity to gain insight into cortical functions through in silico experiments that can subsequently be tested in the brain. However, in many cases this approach requires that the model is able to generalize to stimulus statistics that it was not trained on, such as band-limited noise and other parameterized stimuli. We investigated these domain transfer properties in our model and find that our model trained on natural images is able to correctly predict the orientation tuning of neurons in responses to artificial noise stimuli. Finally, we show that we can fully generalize from movies to noise and maintain high predictive performance on both stimulus domains by fine-tuning only the final layer's weights on a network otherwise trained on natural movies. The converse, however, is not true.

Studies of neuron-behaviour correlation and causal manipulation have long been used separately to understand the neural basis of perception. Yet these approaches sometimes lead to drastically conflicting conclusions about the functional role of brain areas. Theories that focus only on choice-related neuronal activity cannot reconcile those findings without additional experiments involving large-scale recordings to measure interneuronal correlations. By expanding current theories of neural coding and incorporating results from inactivation experiments, we demonstrate here that it is possible to infer decoding weights of different brain areas at a coarse scale without precise knowledge of the correlation structure. We apply this technique to neural data collected from two different cortical areas in macaque monkeys trained to perform a heading discrimination task. We identify two opposing decoding schemes, each consistent with data depending on the nature of correlated noise. Our theory makes specific testable predictions to distinguish these scenarios experimentally without requiring measurement of the underlying noise correlations.

Behavioral experiments on humans and animals suggest that the brain performs probabilistic inference to interpret its environment. Here we present a new general-purpose, biologically-plausible neural implementation of approximate inference. The neural network represents uncertainty using Probabilistic Population Codes (PPCs), which are distributed neural representations that naturally encode probability distributions, and support marginalization and evidence integration in a biologically-plausible manner. By connecting multiple PPCs together as a probabilistic graphical model, we represent multivariate probability distributions. Approximate inference in graphical models can be accomplished by message-passing algorithms that disseminate local information throughout the graph. An attractive and often accurate example of such an algorithm is Loopy Belief Propagation (LBP), which uses local marginalization and evidence integration operations to perform approximate inference efficiently even for complex models. Unfortunately, a subtle feature of LBP renders it neurally implausible. However, LBP can be elegantly reformulated as a sequence of Tree-based Reparameterizations (TRP) of the graphical model. We re-express the TRP updates as a nonlinear dynamical system with both fast and slow timescales, and show that this produces a neurally plausible solution. By combining all of these ideas, we show that a network of PPCs can represent multivariate probability distributions and implement the TRP updates to perform probabilistic inference. Simulations with Gaussian graphical models demonstrate that the neural network inference quality is comparable to the direct evaluation of LBP and robust to noise, and thus provides a promising mechanism for general probabilistic inference in the population codes of the brain.

This paper shows how sparse, high-dimensional probability distributions could be represented by neurons with exponential compression. The representation is a novel application of compressive sensing to sparse probability distributions rather than to the usual sparse signals. The compressive measurements correspond to expected values of nonlinear functions of the probabilistically distributed variables. When these expected values are estimated by sampling, the quality of the compressed representation is limited only by the quality of sampling. Since the compression preserves the geometric structure of the space of sparse probability distributions, probabilistic computation can be performed in the compressed domain. Interestingly, functions satisfying the requirements of compressive sensing can be implemented as simple perceptrons. If we use perceptrons as a simple model of feedforward computation by neurons, these results show that the mean activity of a relatively small number of neurons can accurately represent a high-dimensional joint distribution implicitly, even without accounting for any noise correlations. This comprises a novel hypothesis for how neurons could encode probabilities in the brain.

Loopy belief propagation performs approximate inference on graphical models with loops. One might hope to compensate for the approximation by adjusting model parameters. Learning algorithms for this purpose have been explored previously, and the claim has been made that every set of locally consistent marginals can arise from belief propagation run on a graphical model. On the contrary, here we show that many probability distributions have marginals that cannot be reached by belief propagation using any set of model parameters or any learning algorithm. We call such marginals `unbelievable.' This problem occurs whenever the Hessian of the Bethe free energy is not positive-definite at the target marginals. All learning algorithms for belief propagation necessarily fail in these cases, producing beliefs or sets of beliefs that may even be worse than the pre-learning approximation. We then show that averaging inaccurate beliefs, each obtained from belief propagation using model parameters perturbed about some learned mean values, can achieve the unbelievable marginals.