Scott W. Linderman

Jimmy T. H. Smith, Andrew Warrington, Scott W. Linderman

Models using structured state space sequence (S4) layers have achieved state-of-the-art performance on long-range sequence modeling tasks. An S4 layer combines linear state space models (SSMs), the HiPPO framework, and deep learning to achieve high performance. We build on the design of the S4 layer and introduce a new state space layer, the S5 layer. Whereas an S4 layer uses many independent single-input, single-output SSMs, the S5 layer uses one multi-input, multi-output SSM. We establish a connection between S5 and S4, and use this to develop the initialization and parameterization used by the S5 model. The result is a state space layer that can leverage efficient and widely implemented parallel scans, allowing S5 to match the computational efficiency of S4, while also achieving state-of-the-art performance on several long-range sequence modeling tasks. S5 averages 87.4% on the long range arena benchmark, and 98.5% on the most difficult Path-X task.

Jimmy T. H. Smith, Shalini De Mello, Jan Kautz et al.

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.

Xavier Gonzalez, Andrew Warrington, Jimmy T. H. Smith et al.

Transformers and linear state space models can be evaluated in parallel on modern hardware, but evaluating nonlinear RNNs appears to be an inherently sequential problem. Recently, however, Lim et al. '24 developed an approach called DEER, which evaluates nonlinear RNNs in parallel by posing the states as the solution to a fixed-point problem. They derived a parallel form of Newton's method to solve the fixed-point problem and achieved significant speedups over sequential evaluation. However, the computational complexity of DEER is cubic in the state size, and the algorithm can suffer from numerical instability. We address these limitations with two novel contributions. To reduce the computational complexity, we apply quasi-Newton approximations and show they converge comparably to Newton, use less memory, and are faster. To stabilize DEER, we leverage a connection between the Levenberg-Marquardt algorithm and Kalman smoothing, which we call ELK. This connection allows us to stabilize Newton's method while using efficient parallelized Kalman smoothing algorithms to retain performance. Through several experiments, we show that these innovations allow for parallel evaluation of nonlinear RNNs at larger scales and with greater stability.

Jakub Smékal, Jimmy T. H. Smith, Michael Kleinman et al.

State space models (SSMs) have shown remarkable empirical performance on many long sequence modeling tasks, but a theoretical understanding of these models is still lacking. In this work, we study the learning dynamics of linear SSMs to understand how covariance structure in data, latent state size, and initialization affect the evolution of parameters throughout learning with gradient descent. We show that focusing on the learning dynamics in the frequency domain affords analytical solutions under mild assumptions, and we establish a link between one-dimensional SSMs and the dynamics of deep linear feed-forward networks. Finally, we analyze how latent state over-parameterization affects convergence time and describe future work in extending our results to the study of deep SSMs with nonlinear connections. This work is a step toward a theory of learning dynamics in deep state space models.

Hyun Dong Lee, Andrew Warrington, Joshua I. Glaser et al.

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.

Shizhe He, Avanika Narayan, Ishan S. Khare et al.

Agentic language model (LM) systems power modern applications like "Deep Research" and "Claude Code," and leverage multi-LM architectures to overcome context limitations. Beneath their apparent diversity lies a recurring pattern: smaller "compressor" LMs (that can even run locally) distill raw context into compact text that is then consumed by larger "predictor" LMs. Despite their popularity, the design of compressor-predictor systems remains largely ad hoc, with little guidance on how compressor and predictor choices shape downstream performance. In practice, attributing gains to compression versus prediction requires costly, task-specific pairwise sweeps. We argue that these agentic system design questions are, at root, information-theoretic. Viewing the compressor LM as a noisy channel, we introduce a simple estimator of mutual information between the context and its compression to quantify compression quality in a task-independent way. We show that mutual information strongly predicts downstream performance, independent of any specific task. Through an information-theoretic framework, we perform a comprehensive empirical analysis across five datasets and three model families. Results reveal that larger compressors not only are more accurate, but also more token-efficient, conveying more bits of information per token. A 7B Qwen-2.5 compressor, for instance, is $1.6\times$ more accurate, $4.6\times$ more concise, and conveys $5.5\times$ more bits of mutual information per token than its 1.5B sibling. Across datasets, scaling compressors is substantially more effective than scaling predictors, enabling larger on-device compressors to pair with smaller cloud predictors. Applied to a Deep Research system, these principles enable local compressors as small as 3B parameters to recover $99\%$ of frontier-LM accuracy at $26\%$ of API costs.

Francis R. Willett, Jingyuan Li, Trung Le et al.

Speech brain-computer interfaces aim to decipher what a person is trying to say from neural activity alone, restoring communication to people with paralysis who have lost the ability to speak intelligibly. The Brain-to-Text Benchmark '24 and associated competition was created to foster the advancement of decoding algorithms that convert neural activity to text. Here, we summarize the lessons learned from the competition ending on June 1, 2024 (the top 4 entrants also presented their experiences in a recorded webinar). The largest improvements in accuracy were achieved using an ensembling approach, where the output of multiple independent decoders was merged using a fine-tuned large language model (an approach used by all 3 top entrants). Performance gains were also found by improving how the baseline recurrent neural network (RNN) model was trained, including by optimizing learning rate scheduling and by using a diphone training objective. Improving upon the model architecture itself proved more difficult, however, with attempts to use deep state space models or transformers not yet appearing to offer a benefit over the RNN baseline. The benchmark will remain open indefinitely to support further work towards increasing the accuracy of brain-to-text algorithms.

Xavier Gonzalez, Leo Kozachkov, David M. Zoltowski et al.

The rise of parallel computing hardware has made it increasingly important to understand which nonlinear state space models can be efficiently parallelized. Recent advances like DEER (arXiv:2309.12252) or DeepPCR (arXiv:2309.16318) have shown that evaluating a state space model can be recast as solving a parallelizable optimization problem, and sometimes this approach can yield dramatic speed-ups in evaluation time. However, the factors that govern the difficulty of these optimization problems remain unclear, limiting the larger adoption of the technique. In this work, we establish a precise relationship between the dynamics of a nonlinear system and the conditioning of its corresponding optimization formulation. We show that the predictability of a system, defined as the degree to which small perturbations in state influence future behavior, impacts the number of optimization steps required for evaluation. In predictable systems, the state trajectory can be computed in $O((\log T)^2)$ time, where $T$ is the sequence length, a major improvement over the conventional sequential approach. In contrast, chaotic or unpredictable systems exhibit poor conditioning, with the consequence that parallel evaluation converges too slowly to be useful. Importantly, our theoretical analysis demonstrates that for predictable systems, the optimization problem is always well-conditioned, whereas for unpredictable systems, the conditioning degrades exponentially as a function of the sequence length. We validate our claims through extensive experiments, providing practical guidance on when nonlinear dynamical systems can be efficiently parallelized, and highlighting predictability as a key design principle for parallelizable models.

Xavier Gonzalez, E. Kelly Buchanan, Hyun Dong Lee et al.

Harnessing parallelism in seemingly sequential models is a central challenge for modern machine learning. Several approaches have been proposed for evaluating sequential processes in parallel using fixed-point methods, like Newton, Picard, and Jacobi iterations. In this work, we show that these methods can be understood within a common framework based on linear dynamical systems (LDSs), where different iteration schemes arise naturally as approximate linearizations of a nonlinear recursion. This unifying view highlights shared principles behind these techniques and clarifies when particular fixed-point methods are most likely to be effective. By bridging diverse algorithms through the language of LDSs, our framework provides a clearer theoretical foundation for parallelizing sequential models and points toward new opportunities for efficient and scalable computation.

Randolph W. Linderman, Yiran Chen, Scott W. Linderman · stanford

Bayesian nonparametric methods are naturally suited to the problem of out-of-distribution (OOD) detection. However, these techniques have largely been eschewed in favor of simpler methods based on distances between pre-trained or learned embeddings of data points. Here we show a formal relationship between Bayesian nonparametric models and the relative Mahalanobis distance score (RMDS), a commonly used method for OOD detection. Building on this connection, we propose Bayesian nonparametric mixture models with hierarchical priors that generalize the RMDS. We evaluate these models on the OpenOOD detection benchmark and show that Bayesian nonparametric methods can improve upon existing OOD methods, especially in regimes where training classes differ in their covariance structure and where there are relatively few data points per class.

Yixiu Zhao, Scott W. Linderman

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.

Yixin Wang, Anthony Degleris, Alex H. Williams et al.

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.

Jimmy T. H. Smith, Scott W. Linderman, David Sussillo

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.

Alex H. Williams, Erin Kunz, Simon Kornblith et al.

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.

Xinwei Yu, Matthew S. Creamer, Francesco Randi et al.

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.

Alex H. Williams, Anthony Degleris, Yixin Wang et al.

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.

David M. Zoltowski, Jonathan W. Pillow, Scott W. Linderman

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.

Aaron Schein, Scott W. Linderman, Mingyuan Zhou et al.

This paper presents the Poisson-randomized gamma dynamical system (PRGDS), a model for sequentially observed count tensors that encodes a strong inductive bias toward sparsity and burstiness. The PRGDS is based on a new motif in Bayesian latent variable modeling, an alternating chain of discrete Poisson and continuous gamma latent states that is analytically convenient and computationally tractable. This motif yields closed-form complete conditionals for all variables by way of the Bessel distribution and a novel discrete distribution that we call the shifted confluent hypergeometric distribution. We draw connections to closely related models and compare the PRGDS to these models in studies of real-world count data sets of text, international events, and neural spike trains. We find that a sparse variant of the PRGDS, which allows the continuous gamma latent states to take values of exactly zero, often obtains better predictive performance than other models and is uniquely capable of inferring latent structures that are highly localized in time.

Josue Nassar, Scott W. Linderman, Monica Bugallo et al.

Many real-world systems studied are governed by complex, nonlinear dynamics. By modeling these dynamics, we can gain insight into how these systems work, make predictions about how they will behave, and develop strategies for controlling them. While there are many methods for modeling nonlinear dynamical systems, existing techniques face a trade off between offering interpretable descriptions and making accurate predictions. Here, we develop a class of models that aims to achieve both simultaneously, smoothly interpolating between simple descriptions and more complex, yet also more accurate models. Our probabilistic model achieves this multi-scale property through a hierarchy of locally linear dynamics that jointly approximate global nonlinear dynamics. We call it the tree-structured recurrent switching linear dynamical system. To fit this model, we present a fully-Bayesian sampling procedure using Polya-Gamma data augmentation to allow for fast and conjugate Gibbs sampling. Through a variety of synthetic and real examples, we show how these models outperform existing methods in both interpretability and predictive capability.

Scott W. Linderman, Gonzalo E. Mena, Hal Cooper et al.

Many matching, tracking, sorting, and ranking problems require probabilistic reasoning about possible permutations, a set that grows factorially with dimension. Combinatorial optimization algorithms may enable efficient point estimation, but fully Bayesian inference poses a severe challenge in this high-dimensional, discrete space. To surmount this challenge, we start with the usual step of relaxing a discrete set (here, of permutation matrices) to its convex hull, which here is the Birkhoff polytope: the set of all doubly-stochastic matrices. We then introduce two novel transformations: first, an invertible and differentiable stick-breaking procedure that maps unconstrained space to the Birkhoff polytope; second, a map that rounds points toward the vertices of the polytope. Both transformations include a temperature parameter that, in the limit, concentrates the densities on permutation matrices. We then exploit these transformations and reparameterization gradients to introduce variational inference over permutation matrices, and we demonstrate its utility in a series of experiments.

Christian A. Naesseth, Scott W. Linderman, Rajesh Ranganath et al.

Many recent advances in large scale probabilistic inference rely on variational methods. The success of variational approaches depends on (i) formulating a flexible parametric family of distributions, and (ii) optimizing the parameters to find the member of this family that most closely approximates the exact posterior. In this paper we present a new approximating family of distributions, the variational sequential Monte Carlo (VSMC) family, and show how to optimize it in variational inference. VSMC melds variational inference (VI) and sequential Monte Carlo (SMC), providing practitioners with flexible, accurate, and powerful Bayesian inference. The VSMC family is a variational family that can approximate the posterior arbitrarily well, while still allowing for efficient optimization of its parameters. We demonstrate its utility on state space models, stochastic volatility models for financial data, and deep Markov models of brain neural circuits.

Scott W. Linderman, Andrew C. Miller, Ryan P. Adams et al.

Many natural systems, such as neurons firing in the brain or basketball teams traversing a court, give rise to time series data with complex, nonlinear dynamics. We can gain insight into these systems by decomposing the data into segments that are each explained by simpler dynamic units. Building on switching linear dynamical systems (SLDS), we present a new model class that not only discovers these dynamical units, but also explains how their switching behavior depends on observations or continuous latent states. These "recurrent" switching linear dynamical systems provide further insight by discovering the conditions under which each unit is deployed, something that traditional SLDS models fail to do. We leverage recent algorithmic advances in approximate inference to make Bayesian inference in these models easy, fast, and scalable.

Scott W. Linderman, Ryan P. Adams, Jonathan W. Pillow

Neural circuits contain heterogeneous groups of neurons that differ in type, location, connectivity, and basic response properties. However, traditional methods for dimensionality reduction and clustering are ill-suited to recovering the structure underlying the organization of neural circuits. In particular, they do not take advantage of the rich temporal dependencies in multi-neuron recordings and fail to account for the noise in neural spike trains. Here we describe new tools for inferring latent structure from simultaneously recorded spike train data using a hierarchical extension of a multi-neuron point process model commonly known as the generalized linear model (GLM). Our approach combines the GLM with flexible graph-theoretic priors governing the relationship between latent features and neural connectivity patterns. Fully Bayesian inference via Pólya-gamma augmentation of the resulting model allows us to classify neurons and infer latent dimensions of circuit organization from correlated spike trains. We demonstrate the effectiveness of our method with applications to synthetic data and multi-neuron recordings in primate retina, revealing latent patterns of neural types and locations from spike trains alone.

Christian A. Naesseth, Francisco J. R. Ruiz, Scott W. Linderman et al.

Variational inference using the reparameterization trick has enabled large-scale approximate Bayesian inference in complex probabilistic models, leveraging stochastic optimization to sidestep intractable expectations. The reparameterization trick is applicable when we can simulate a random variable by applying a differentiable deterministic function on an auxiliary random variable whose distribution is fixed. For many distributions of interest (such as the gamma or Dirichlet), simulation of random variables relies on acceptance-rejection sampling. The discontinuity introduced by the accept-reject step means that standard reparameterization tricks are not applicable. We propose a new method that lets us leverage reparameterization gradients even when variables are outputs of a acceptance-rejection sampling algorithm. Our approach enables reparameterization on a larger class of variational distributions. In several studies of real and synthetic data, we show that the variance of the estimator of the gradient is significantly lower than other state-of-the-art methods. This leads to faster convergence of stochastic gradient variational inference.

Scott W. Linderman, Ryan P. Adams

Networks capture our intuition about relationships in the world. They describe the friendships between Facebook users, interactions in financial markets, and synapses connecting neurons in the brain. These networks are richly structured with cliques of friends, sectors of stocks, and a smorgasbord of cell types that govern how neurons connect. Some networks, like social network friendships, can be directly observed, but in many cases we only have an indirect view of the network through the actions of its constituents and an understanding of how the network mediates that activity. In this work, we focus on the problem of latent network discovery in the case where the observable activity takes the form of a mutually-excitatory point process known as a Hawkes process. We build on previous work that has taken a Bayesian approach to this problem, specifying prior distributions over the latent network structure and a likelihood of observed activity given this network. We extend this work by proposing a discrete-time formulation and developing a computationally efficient stochastic variational inference (SVI) algorithm that allows us to scale the approach to long sequences of observations. We demonstrate our algorithm on the calcium imaging data used in the Chalearn neural connectomics challenge.

Scott W. Linderman, Matthew J. Johnson, Ryan P. Adams

Many practical modeling problems involve discrete data that are best represented as draws from multinomial or categorical distributions. For example, nucleotides in a DNA sequence, children's names in a given state and year, and text documents are all commonly modeled with multinomial distributions. In all of these cases, we expect some form of dependency between the draws: the nucleotide at one position in the DNA strand may depend on the preceding nucleotides, children's names are highly correlated from year to year, and topics in text may be correlated and dynamic. These dependencies are not naturally captured by the typical Dirichlet-multinomial formulation. Here, we leverage a logistic stick-breaking representation and recent innovations in Pólya-gamma augmentation to reformulate the multinomial distribution in terms of latent variables with jointly Gaussian likelihoods, enabling us to take advantage of a host of Bayesian inference techniques for Gaussian models with minimal overhead.

Scott W. Linderman, Matthew J. Johnson, Matthew A. Wilson et al.

Rodent hippocampal population codes represent important spatial information about the environment during navigation. Several computational methods have been developed to uncover the neural representation of spatial topology embedded in rodent hippocampal ensemble spike activity. Here we extend our previous work and propose a nonparametric Bayesian approach to infer rat hippocampal population codes during spatial navigation. To tackle the model selection problem, we leverage a nonparametric Bayesian model. Specifically, to analyze rat hippocampal ensemble spiking activity, we apply a hierarchical Dirichlet process-hidden Markov model (HDP-HMM) using two Bayesian inference methods, one based on Markov chain Monte Carlo (MCMC) and the other based on variational Bayes (VB). We demonstrate the effectiveness of our Bayesian approaches on recordings from a freely-behaving rat navigating in an open field environment. We find that MCMC-based inference with Hamiltonian Monte Carlo (HMC) hyperparameter sampling is flexible and efficient, and outperforms VB and MCMC approaches with hyperparameters set by empirical Bayes.

Scott W. Linderman, Christopher H. Stock, Ryan P. Adams

Learning and memory in the brain are implemented by complex, time-varying changes in neural circuitry. The computational rules according to which synaptic weights change over time are the subject of much research, and are not precisely understood. Until recently, limitations in experimental methods have made it challenging to test hypotheses about synaptic plasticity on a large scale. However, as such data become available and these barriers are lifted, it becomes necessary to develop analysis techniques to validate plasticity models. Here, we present a highly extensible framework for modeling arbitrary synaptic plasticity rules on spike train data in populations of interconnected neurons. We treat synaptic weights as a (potentially nonlinear) dynamical system embedded in a fully-Bayesian generalized linear model (GLM). In addition, we provide an algorithm for inferring synaptic weight trajectories alongside the parameters of the GLM and of the learning rules. Using this method, we perform model comparison of two proposed variants of the well-known spike-timing-dependent plasticity (STDP) rule, where nonlinear effects play a substantial role. On synthetic data generated from the biophysical simulator NEURON, we show that we can recover the weight trajectories, the pattern of connectivity, and the underlying learning rules.

Scott W. Linderman, Ryan P. Adams

Networks play a central role in modern data analysis, enabling us to reason about systems by studying the relationships between their parts. Most often in network analysis, the edges are given. However, in many systems it is difficult or impossible to measure the network directly. Examples of latent networks include economic interactions linking financial instruments and patterns of reciprocity in gang violence. In these cases, we are limited to noisy observations of events associated with each node. To enable analysis of these implicit networks, we develop a probabilistic model that combines mutually-exciting point processes with random graph models. We show how the Poisson superposition principle enables an elegant auxiliary variable formulation and a fully-Bayesian, parallel inference algorithm. We evaluate this new model empirically on several datasets.