Convolutional State Space Models for Long-Range Spatiotemporal Modeling

Effectively modeling long spatiotemporal sequences is challenging due to the need to model complex spatial correlations and long-range temporal dependencies simultaneously. ConvLSTMs attempt to address this by updating tensor-valued states with recurrent neural networks, but their sequential computation makes them slow to train. In contrast, Transformers can process an entire spatiotemporal sequence, compressed into tokens, in parallel. However, the cost of attention scales quadratically in length, limiting their scalability to longer sequences. Here, we address the challenges of prior methods and introduce convolutional state space models (ConvSSM) that combine the tensor modeling ideas of ConvLSTM with the long sequence modeling approaches of state space methods such as S4 and S5. First, we demonstrate how parallel scans can be applied to convolutional recurrences to achieve subquadratic parallelization and fast autoregressive generation. We then establish an equivalence between the dynamics of ConvSSMs and SSMs, which motivates parameterization and initialization strategies for modeling long-range dependencies. The result is ConvS5, an efficient ConvSSM variant for long-range spatiotemporal modeling. ConvS5 significantly outperforms Transformers and ConvLSTM on a long horizon Moving-MNIST experiment while training 3X faster than ConvLSTM and generating samples 400X faster than Transformers. In addition, ConvS5 matches or exceeds the performance of state-of-the-art methods on challenging DMLab, Minecraft and Habitat prediction benchmarks and enables new directions for modeling long spatiotemporal sequences.

Switching Autoregressive Low-rank Tensor Models

An important problem in time-series analysis is modeling systems with time-varying dynamics. Probabilistic models with joint continuous and discrete latent states offer interpretable, efficient, and experimentally useful descriptions of such data. Commonly used models include autoregressive hidden Markov models (ARHMMs) and switching linear dynamical systems (SLDSs), each with its own advantages and disadvantages. ARHMMs permit exact inference and easy parameter estimation, but are parameter intensive when modeling long dependencies, and hence are prone to overfitting. In contrast, SLDSs can capture long-range dependencies in a parameter efficient way through Markovian latent dynamics, but present an intractable likelihood and a challenging parameter estimation task. In this paper, we propose switching autoregressive low-rank tensor (SALT) models, which retain the advantages of both approaches while ameliorating the weaknesses. SALT parameterizes the tensor of an ARHMM with a low-rank factorization to control the number of parameters and allow longer range dependencies without overfitting. We prove theoretical and discuss practical connections between SALT, linear dynamical systems, and SLDSs. We empirically demonstrate quantitative advantages of SALT models on a range of simulated and real prediction tasks, including behavioral and neural datasets. Furthermore, the learned low-rank tensor provides novel insights into temporal dependencies within each discrete state.

Revisiting Structured Variational Autoencoders

Structured variational autoencoders (SVAEs) combine probabilistic graphical model priors on latent variables, deep neural networks to link latent variables to observed data, and structure-exploiting algorithms for approximate posterior inference. These models are particularly appealing for sequential data, where the prior can capture temporal dependencies. However, despite their conceptual elegance, SVAEs have proven difficult to implement, and more general approaches have been favored in practice. Here, we revisit SVAEs using modern machine learning tools and demonstrate their advantages over more general alternatives in terms of both accuracy and efficiency. First, we develop a modern implementation for hardware acceleration, parallelization, and automatic differentiation of the message passing algorithms at the core of the SVAE. Second, we show that by exploiting structure in the prior, the SVAE learns more accurate models and posterior distributions, which translate into improved performance on prediction tasks. Third, we show how the SVAE can naturally handle missing data, and we leverage this ability to develop a novel, self-supervised training approach. Altogether, these results show that the time is ripe to revisit structured variational autoencoders.

Simplified State Space Layers for Sequence Modeling

Efficiently modeling long-range dependencies is an important goal in sequence modeling. Recently, models using structured state space sequence (S4) layers achieved state-of-the-art performance on many long-range tasks. The S4 layer combines linear state space models (SSMs) with deep learning techniques and leverages the HiPPO framework for online function approximation to achieve high performance. However, this framework led to architectural constraints and computational difficulties that make the S4 approach complicated to understand and implement. We revisit the idea that closely following the HiPPO framework is necessary for high performance. Specifically, we replace the bank of many independent single-input, single-output (SISO) SSMs the S4 layer uses with one multi-input, multi-output (MIMO) SSM with a reduced latent dimension. The reduced latent dimension of the MIMO system allows for the use of efficient parallel scans which simplify the computations required to apply the S5 layer as a sequence-to-sequence transformation. In addition, we initialize the state matrix of the S5 SSM with an approximation to the HiPPO-LegS matrix used by S4's SSMs and show that this serves as an effective initialization for the MIMO setting. S5 matches S4's performance on long-range tasks, including achieving an average of 82.46% on the suite of Long Range Arena benchmarks compared to S4's 80.48% and the best transformer variant's 61.41%.

Spatiotemporal Clustering with Neyman-Scott Processes via Connections to Bayesian Nonparametric Mixture Models

Neyman-Scott processes (NSPs) are point process models that generate clusters of points in time or space. They are natural models for a wide range of phenomena, ranging from neural spike trains to document streams. The clustering property is achieved via a doubly stochastic formulation: first, a set of latent events is drawn from a Poisson process; then, each latent event generates a set of observed data points according to another Poisson process. This construction is similar to Bayesian nonparametric mixture models like the Dirichlet process mixture model (DPMM) in that the number of latent events (i.e. clusters) is a random variable, but the point process formulation makes the NSP especially well suited to modeling spatiotemporal data. While many specialized algorithms have been developed for DPMMs, comparatively fewer works have focused on inference in NSPs. Here, we present novel connections between NSPs and DPMMs, with the key link being a third class of Bayesian mixture models called mixture of finite mixture models (MFMMs). Leveraging this connection, we adapt the standard collapsed Gibbs sampling algorithm for DPMMs to enable scalable Bayesian inference on NSP models. We demonstrate the potential of Neyman-Scott processes on a variety of applications including sequence detection in neural spike trains and event detection in document streams.

Reverse engineering recurrent neural networks with Jacobian switching linear dynamical systems

Recurrent neural networks (RNNs) are powerful models for processing time-series data, but it remains challenging to understand how they function. Improving this understanding is of substantial interest to both the machine learning and neuroscience communities. The framework of reverse engineering a trained RNN by linearizing around its fixed points has provided insight, but the approach has significant challenges. These include difficulty choosing which fixed point to expand around when studying RNN dynamics and error accumulation when reconstructing the nonlinear dynamics with the linearized dynamics. We present a new model that overcomes these limitations by co-training an RNN with a novel switching linear dynamical system (SLDS) formulation. A first-order Taylor series expansion of the co-trained RNN and an auxiliary function trained to pick out the RNN's fixed points govern the SLDS dynamics. The results are a trained SLDS variant that closely approximates the RNN, an auxiliary function that can produce a fixed point for each point in state-space, and a trained nonlinear RNN whose dynamics have been regularized such that its first-order terms perform the computation, if possible. This model removes the post-training fixed point optimization and allows us to unambiguously study the learned dynamics of the SLDS at any point in state-space. It also generalizes SLDS models to continuous manifolds of switching points while sharing parameters across switches. We validate the utility of the model on two synthetic tasks relevant to previous work reverse engineering RNNs. We then show that our model can be used as a drop-in in more complex architectures, such as LFADS, and apply this LFADS hybrid to analyze single-trial spiking activity from the motor system of a non-human primate.

Generalized Shape Metrics on Neural Representations

Understanding the operation of biological and artificial networks remains a difficult and important challenge. To identify general principles, researchers are increasingly interested in surveying large collections of networks that are trained on, or biologically adapted to, similar tasks. A standardized set of analysis tools is now needed to identify how network-level covariates -- such as architecture, anatomical brain region, and model organism -- impact neural representations (hidden layer activations). Here, we provide a rigorous foundation for these analyses by defining a broad family of metric spaces that quantify representational dissimilarity. Using this framework we modify existing representational similarity measures based on canonical correlation analysis to satisfy the triangle inequality, formulate a novel metric that respects the inductive biases in convolutional layers, and identify approximate Euclidean embeddings that enable network representations to be incorporated into essentially any off-the-shelf machine learning method. We demonstrate these methods on large-scale datasets from biology (Allen Institute Brain Observatory) and deep learning (NAS-Bench-101). In doing so, we identify relationships between neural representations that are interpretable in terms of anatomical features and model performance.

Fast deep learning correspondence for neuron tracking and identification in C.elegans using synthetic training

We present an automated method to track and identify neurons in C. elegans, called "fast Deep Learning Correspondence" or fDLC, based on the transformer network architecture. The model is trained once on empirically derived synthetic data and then predicts neural correspondence across held-out real animals via transfer learning. The same pre-trained model both tracks neurons across time and identifies corresponding neurons across individuals. Performance is evaluated against hand-annotated datasets, including NeuroPAL [1]. Using only position information, the method achieves 80.0% accuracy at tracking neurons within an individual and 65.8% accuracy at identifying neurons across individuals. Accuracy is even higher on a published dataset [2]. Accuracy reaches 76.5% when using color information from NeuroPAL. Unlike previous methods, fDLC does not require straightening or transforming the animal into a canonical coordinate system. The method is fast and predicts correspondence in 10 ms making it suitable for future real-time applications.

Point process models for sequence detection in high-dimensional neural spike trains

Sparse sequences of neural spikes are posited to underlie aspects of working memory, motor production, and learning. Discovering these sequences in an unsupervised manner is a longstanding problem in statistical neuroscience. Promising recent work utilized a convolutive nonnegative matrix factorization model to tackle this challenge. However, this model requires spike times to be discretized, utilizes a sub-optimal least-squares criterion, and does not provide uncertainty estimates for model predictions or estimated parameters. We address each of these shortcomings by developing a point process model that characterizes fine-scale sequences at the level of individual spikes and represents sequence occurrences as a small number of marked events in continuous time. This ultra-sparse representation of sequence events opens new possibilities for spike train modeling. For example, we introduce learnable time warping parameters to model sequences of varying duration, which have been experimentally observed in neural circuits. We demonstrate these advantages on experimental recordings from songbird higher vocal center and rodent hippocampus.

Unifying and generalizing models of neural dynamics during decision-making

An open question in systems and computational neuroscience is how neural circuits accumulate evidence towards a decision. Fitting models of decision-making theory to neural activity helps answer this question, but current approaches limit the number of these models that we can fit to neural data. Here we propose a unifying framework for modeling neural activity during decision-making tasks. The framework includes the canonical drift-diffusion model and enables extensions such as multi-dimensional accumulators, variable and collapsing boundaries, and discrete jumps. Our framework is based on constraining the parameters of recurrent state-space models, for which we introduce a scalable variational Laplace-EM inference algorithm. We applied the modeling approach to spiking responses recorded from monkey parietal cortex during two decision-making tasks. We found that a two-dimensional accumulator better captured the trial-averaged responses of a set of parietal neurons than a single accumulator model. Next, we identified a variable lower boundary in the responses of an LIP neuron during a random dot motion task.