neuroscience data analysts

Abstract: State inference and parameter learning for nonlinear filters is a core computation for scientific machine learning with varied applications in engineering and neuroscience. The unnormalized filtering distribution is governed by the Zakai equation, a stochastic partial differential equation (SPDE) that combines the forward Kolmogorov operator (known as the Fokker-Planck equation) with observed likelihood updates. Although solving these high-dimensional SPDEs is often impossible analytically and intractable numerically, advances in operator learning and physics-informed machine learning have made it feasible. Harnessing these advances, we introduce the Zakai Equation Neural Operator (ZENO), a model that optimizes a neural operator against a Zakai Equation based physics-informed loss to approximate the exact unnormalized filtering distribution for latent stochastic dynamical systems. We use this ZENO-inferred posterior distribution in an expectation-maximization (EM) framework to perform parameter learning and state inference. We demonstrate ZENO's ability to accurately infer the posterior distribution and learn its corresponding SDE parameters in three simulated stochastic dynamical systems (Double-Well bistable system, Van Der Pol (VDP) oscillator, and Lorenz system) and compare its performance against established methods for latent SDE inference and learning. We show that ZENO recovers previously observed limit cycles representing forward and backward locomotion from a whole-brain imaging dataset of immobilized \textit{C. elegans} nematodes. ZENO is a novel approach to the problem of nonlinear filtering and dynamical inference through the lens of partial differential equations and operator theory.

Abstract: We encounter a system through its responses, yet its state concerns how the system is. Predicting further responses promises knowledge beyond what is immediately observed. What that knowledge tells us about the system's state depends on what we mean by a state in the first place. We give this notion a model-relative meaning: a state is the complete response profile over a specified query universe, and configurations agreeing on every query are regarded as the same state. From this perspective, a learned state is understood through the distinctions between these profiles that it retains. Prediction concerns selected observations; recovery concerns the profile as a whole. We examine their relationship through query ambiguity, state-space geometry, and the choice of prediction targets. Synthetic systems with known response laws and neural recordings provide complementary settings for this investigation. The aim is to clarify how prediction can become a way of knowing a system, and what it would mean for a learned state to preserve the state being studied.

Abstract: Neural networks routinely develop representations in which individual neurons contribute to multiple distinct functions, leading to the widespread view that such networks lack modular organization. We challenge this conclusion by introducing a formally nested hierarchy of modularity: unit-level, which requires distinct computations to occupy disjoint neurons; orthogonal, which asks whether a rotation reveals functionally independent subspaces; and linear, which asks whether a bounded linear map can separate task-relevant computations into independent subspaces. We develop a unified framework for learning decompositions at each level and evaluating them causally through selective ablation. Across vision models, language models and multi-task Recurrent Neural Networks (RNNs), we find that networks which lack unit-level modularity nonetheless often exhibit clear functional modularity at the subspace level. In vision and language models, content versus style and syntax versus semantics respectively dissociate under subspace ablation despite sharing overlapping populations of neurons. These learned subspaces also align differentially with brain data, with content and style subspaces predicting higher and lower visual cortex respectively, and semantic subspaces outperforming syntactic ones in predicting language cortex activity. In RNNs trained on multiple cognitive tasks and previously shown to lack modular structure, our decomposition recovers sharp double dissociations between tasks. The absence of unit-level modularity frequently coexists with clear subspace-level modularity across domains, enabling targeted intervention on specific computations even in networks where no individual neuron is specialized, with broad implications for mechanistic interpretability and for understanding functional organization in both biological and artificial neural systems.

Abstract: The term "linear representation hypothesis" (LRH) has appeared across diverse subfields of artificial intelligence, neuroscience, and cognitive science. But previous works have not consistently treated the LRH as a falsifiable scientific hypothesis; we analyze these inconsistencies and examine their implications for how prior theoretical and methodological results should be interpreted. Based on this analysis, we argue that claims regarding linear representations become well-defined only through careful examination of the model, representation location, feature definition, and evaluation dataset. We therefore propose a more rigorous formalization of the LRH that makes these dependencies explicit and allows the hypothesis to be evaluated as a falsifiable scientific claim. Finally, we identify some non-trivial open problems that warrant further attention from the research community.