Unlike the case for text--wherein every document written in a given language shares a basic lexicon for tokenization--there is no one-to-one correspondence between neurons in different individuals.

Modern neural interfaces allow access to the activity of up to a million neurons withinbraincircuits.

Brain stimulation has the potential to create desired neural population activity states. However, it is challenging to search the large space of stimulation parameters, for example, selecting which subset of electrodes to be used for stimulation. In this scenario, creating a model that maps the configuration of stimulation parameters to the brain's response can be beneficial. Training such an expansive model usually requires more stimulation-response samples than can be collected in a given experimental session. Furthermore, changes in the properties of the recorded activity over time can make it challenging to merge stimulation-response samples across sessions.

Neural datasets often contain measurements of neural activity across multiple trials of a repeated stimulus or behavior. An important problem in the analysis of such datasets is to characterize systematic aspects of neural activity that carry information about the repeated stimulus or behavior of interest, which can be considered noise''. Gaussian Process factor models provide a powerful tool for identifying shared structure in high-dimensional neural data. However, they have not yet been adapted to the problem of characterizing signal and noise in multi-trial datasets. Here we address this shortcoming by proposing ``signal-noise'' Poisson-spiking Gaussian Process Factor Analysis (SNP-GPFA), a flexible latent variable model that resolves signal and noise latent structure in neural population spiking activity. To learn the parameters of our model, we introduce a Fourier-domain black box variational inference method that quickly identifies smooth latent structure.

Neural networks are often described as black boxes, reflecting the significant challenge of understanding their internal workings and interactions. We propose a different perspective that challenges the prevailing view: rather than being inscrutable, neural networks exhibit patterns in their raw population activity that mirror regularities in the training data. We refer to this as the Reflection Hypothesis and provide evidence for this phenomenon in both simple recurrent neural networks (RNNs) and complex large language models (LLMs). Building on this insight, we propose to leverage our cognitive tendency of chunking to segment high-dimensional neural population dynamics into interpretable units that reflect underlying concepts. We propose three methods to extract recurring chunks on a neural population level, complementing each other based on label availability and neural data dimensionality. Discrete sequence chunking (DSC) learns a dictionary of entities in a lower-dimensional neural space; population averaging (PA) extracts recurring entities that correspond to known labels; and unsupervised chunk discovery (UCD) can be used when labels are absent. We demonstrate the effectiveness of these methods in extracting concept-encoding entities agnostic to model architectures. These concepts can be both concrete (words), abstract (POS tags), or structural (narrative schema). Additionally, we show that extracted chunks play a causal role in network behavior, as grafting them leads to controlled and predictable changes in the model's behavior. Our work points to a new direction for interpretability, one that harnesses both cognitive principles and the structure of naturalistic data to reveal the hidden computations of complex learning systems, gradually transforming them from black boxes into systems we can begin to understand.

Unlike the case for text--wherein every document written in a given language shares a basic lexicon for tokenization--there is no one-to-one correspondence between neurons in different individuals.

Neural population activity in cortical circuits is not solely driven by external inputs, but is also modulated by endogenous states which vary on multiple time-scales. To understand information processing in cortical circuits, we need to understand the statistical structure of internal states and their interaction with sensory inputs. Here, we present a statistical model for extracting hierarchically organised neural population states from multi-channel recordings of neural spiking activity. Population states are modelled using a hidden Markov decision tree with state-dependent tuning parameters and a generalised linear observation model. We present a varia-tional Bayesian inference algorithm for estimating the posterior distribution over parameters from neural population recordings. On simulated data, we show that we can identify the underlying sequence of population states and reconstruct the ground truth parameters. Using population recordings from visual cortex, we find that a model with two levels of population states outperforms both a one-state and a two-state generalised linear model. Finally, we find that modelling of state-dependence also improves the accuracy with which sensory stimuli can be decoded from the population response.

Neural responses in visual cortex are influenced by visual stimuli and by ongoing spiking activity in local circuits. An important challenge in computational neuroscience is to develop models that can account for both of these features in large multi-neuron recordings and to reveal how stimulus representations interact with and depend on cortical dynamics. Here we introduce a statistical model of neural population activity that integrates a nonlinear receptive field model with a latent dynamical model of ongoing cortical activity. This model captures temporal dynamics and correlations due to shared stimulus drive as well as common noise. Moreover, because the nonlinear stimulus inputs are mixed by the ongoing dynamics, the model can account for a multiple idiosyncratic receptive field shapes with a small number of nonlinear inputs to a low-dimensional dynamical model. We introduce a fast estimation method using online expectation maximization with Laplace approximations, for which inference scales linearly in both population size and recording duration. We test this model to multi-channel recordings from primary visual cortex and show that it accounts for neural tuning properties as well as cross-neural correlations.