Biology subjects

Stachenfeld, K. L.

Publications and source records attributed to Stachenfeld, K. L..

8 recordsLinked to original sources

bioRxiv2026

AI-Discovered Cognitive Models Reveal Novel Insights into Human and Animal Learning

Scientific models are widely used across the natural sciences as an interface between scientific theories and empirical data [1]. Such models play a key role, for example, in the study of human and animal learning, where they express algorithmic hypotheses and relate them to psychology and neuroscience data [2, 3]. These models are traditionally handcrafted by expert researchers based on existing theory or new insights. Such handcrafted models, however, are now known to fall short of capturing the full richness of behavior, even in their narrow domains [4-7]. An alternative data-driven approach has emerged, seeking to discover new insights by fitting and interpreting flexible models [8-11]. However, these tools require substantial human effort to derive insight from data, and it has been unclear how to discover new ideas from data efficiently. Here, we present DataDIVER, a general approach for automatically discovering computational models from data, and demonstrate that these models surface novel mechanistic insights into human and animal learning. Our approach delivers models that take the form of short computer programs, which are optimized both to fit data well and to be simple. These programs explicitly connect with existing theoretical frameworks and are readily understandable by human scientists. They can also be used to make novel predictions, some of which we show are borne out in re-analysis of existing data. General-purpose tools for surfacing new ideas from data, especially in combination with the large datasets that are increasingly available in many fields, stand to dramatically accelerate scientific discovery.

animal behavior and cognition↗

bioRxiv2026

Functional reorganization of motor cortex connectivity during learning

Learning new tasks requires the brain to reshape the flow of neural activity, but how these changes arise from dynamic neural connectivity remains unclear. Here, we used two-photon photostimulation and calcium imaging to map learning-related changes in connectivity in layer 2/3 of mouse motor cortex, induced by learning of an optical brain-computer interface (BCI) task. Mice rapidly (within minutes) learned to change activity in a conditioned neuron to earn rewards. Activity changes were sparse; the conditioned neuron increased activity more than surrounding neurons. Mapping connectivity before and after learning revealed changes in motor cortex connectivity, enriched in neurons that were active before trial initiation, analogous to motor cortex populations that are active preceding movement. Motor cortex plasticity reroutes preparatory activity to neurons that are active later and control the conditioned neuron. Our findings show how rapid learning can be achieved through structured changes in motor cortex connectivity.

neuroscience↗

bioRxiv2026

Neural representations supporting generalization under continual learning

Abstraction and generalization are essential for flexible decision-making in novel situations. Recent work in humans and monkeys has shown how abstract variables are encoded by the representational geometry of neural population activity. However, these observations--which are typically made after learning has converged--demonstrate the product of abstraction, but not the process by which abstract knowledge is learned: how are the inputs from concrete experiences transformed into abstract knowledge, and how do neural circuits perform these operations and relay this knowledge? To address these questions, we developed a factorized model of temporal abstraction that builds on the successor representation. The model disentangles the contributions of different levels of abstract learning--from stimulus-stimulus associations to a generalizable task schema--in the form of a factorized prediction error that relates the change in relational knowledge to a predicted change in representational geometry on each trial. We fit the model to the behavior of human participants performing a context-dependent decision task during fMRI. The model captured the learning dynamics at multiple timescales, including the increasing contribution of generalization as participants transferred abstracted relational knowledge between novel task instances. In fMRI, BOLD activity in hippocampus--where, in past work, abstract knowledge was represented after learning--was increasingly attributed to the acquisition of abstract knowledge based on generalization. A similar temporal pattern was observed in entorhinal cortex, a putative source of low-dimensional structural information, and orbitofrontal cortex (OFC), which may depend on relational knowledge to represent state relationships as a cognitive map that guides choices. Indeed, individual variation in the generalization signal in OFC correlated with behavioral performance on key trials that required relational knowledge. Our findings show how the brain regions previously shown to represent abstract knowledge after learning also support the process of abstraction as it evolves from learning concrete associations to a generalizable schema. Our approach offers a computational framework for disentangling the operations driving abstract learning and probing their neural correlates in the dynamics of representational geometry.

neuroscience↗

bioRxiv2025

Discovering Symbolic Cognitive Models from Human and Animal Behavior

Symbolic models play a key role in cognitive science, expressing computationally precise hypotheses about how the brain implements a cognitive process. Identifying an appropriate model typically requires a great deal of effort and ingenuity on the part of a human scientist. Here, we adapt FunSearch Romera-Paredes et al. (2024), a recently developed tool that uses Large Language Models (LLMs) in an evolutionary algorithm, to automatically discover symbolic cognitive models that accurately capture human and animal behavior. We consider datasets from three species performing a classic reward-learning task that has been the focus of substantial modeling effort, and find that the discovered programs outperform state-of-the-art cognitive models for each. The discovered programs can readily be interpreted as hypotheses about human and animal cognition, instantiating interpretable symbolic learning and decision-making algorithms. Broadly, these results demonstrate the viability of using LLM-powered program synthesis to propose novel scientific hypotheses regarding mechanisms of human and animal cognition.

animal behavior and cognition↗

bioRxiv2023

A generative model of the hippocampal formation trained with theta driven local learning rules

Advances in generative models have recently revolutionised machine learning. Meanwhile, in neuroscience, generative models have long been thought fundamental to animal intelligence. Understanding the biological mechanisms that support these processes promises to shed light on the relationship between biological and artificial intelligence. In animals, the hippocampal formation is thought to learn and use a generative model to support its role in spatial and non-spatial memory. Here we introduce a biologically plausible model of the hippocampal formation tantamount to a Helmholtz machine that we apply to a temporal stream of inputs. A novel component of our model is that fast theta-band oscillations (5-10 Hz) gate the direction of information flow throughout the network, training it akin to a high-frequency wake-sleep algorithm. Our model accurately infers the latent state of high-dimensional sensory environments and generates realistic sensory predictions. Furthermore, it can learn to path integrate by developing a ring attractor connectivity structure matching previous theoretical proposals and flexibly transfer this structure between environments. Whereas many models trade-off biological plausibility with generality, our model captures a variety of hippocampal cognitive functions under one biologically plausible local learning rule.

neuroscience↗

bioRxiv2022

A probabilistic successor representation for context-dependent prediction

The different strategies that animals use for predicting reward are often classified as model-based or model-free reinforcement learning (RL) algorithms. Model-based RL involves explicit simulation the future to make decisions while model-free strategies rely on learning associations between stimuli and predicted reward by trial and error. An alternative, intermediate strategy for RL is based on the "successor representation" (SR), an encoding of environmental states in terms of predicted future states. A recent theoretical proposal suggests that the hippocampus encodes the SR in order to facilitate prediction of future reward. However, this proposal does not take into account how learning should adapt under uncertainty and switches of context. Here, we introduce a theory of learning SRs using prediction errors which includes optimally balancing uncertainty in new observations versus existing knowledge. We then generalise that approach to a multi-context setting, allowing the model to learn and maintain multiple task-specific SRs and infer which one to use at any moment based on the accuracy of its predictions. Thus, the context used for predictions can be determined by both the contents of the states themselves and the distribution of transitions between them. This probabilistic SR model captures animal behaviour in tasks which require contextual memory and generalisation, and unifies previous SR theory with hippocampal-dependent contextual decision making.

animal behavior and cognition↗

bioRxiv2018

What is a cognitive map? Organising knowledge for flexible behaviour

It is proposed that a cognitive map encoding the relationships between entities in the world supports flexible behaviour, but the majority of the neural evidence for such a system comes from studies of spatial navigation. Recent work describing neuronal parallels between spatial and non-spatial behaviours has rekindled the notion of a systematic organisation of knowledge across multiple domains. We review experimental evidence and theoretical frameworks that point to principles unifying these apparently disparate functions. These principles describe how to learn and use abstract, generalisable knowledge and suggest map-like representations observed in a spatial context may be an instance of general coding mechanisms capable of organising knowledge of all kinds. We highlight how artificial agents endowed with such principles exhibit flexible behaviour and learn map-like representations observed in the brain. Finally, we speculate on how these principles may offer insight into the extreme generalisations, abstractions and inferences that characterise human cognition.

neuroscience↗

bioRxiv2016

The hippocampus as a predictive map

A cognitive map has long been the dominant metaphor for hippocampal function, embracing the idea that place cells encode a geometric representation of space. However, evidence for predictive coding, reward sensitivity, and policy dependence in place cells suggests that the representation is not purely spatial. We approach this puzzle from a reinforcement learning perspective: what kind of spatial representation is most useful for maximizing future reward? We show that the answer takes the form of a predictive representation. This representation captures many aspects of place cell responses that fall outside the traditional view of a cognitive map. Furthermore, we argue that entorhinal grid cells encode a low-dimensional basis set for the predictive representation, useful for suppressing noise in predictions and extracting multiscale structure for hierarchical planning.

neuroscience↗