40 accepted papers
Agentic language model (LM) systems have rapidly become central to modern workflows, powering applications like "Deep Research" and "Claude Code." As contexts grow beyond what even the largest frontier models can process effectively, multi-LM architectures have emerged to overcome context limitatio…
Speech brain–computer interfaces (BCIs) aim to restore communication for people with paralysis by translating neural activity into text. Most systems use cascaded frameworks that decode phonemes before assembling sentences with an n-gram language model (LM), preventing joint optimization of all stag…
Multi-compartment Hodgkin–Huxley (HH) models provide a principled framework for predicting neural dynamics and responses to electrical stimulation. However, fitting HH biophysical parameters typically requires intracellular recordings, which are invasive and low-throughput, limiting the ability to c…
We investigate an emerging setup in which a small, on-device language model (LM) with access to local data collaborates with a frontier, cloud-hosted LM to solve real-world tasks involving financial, medical, and scientific reasoning over long documents. *Can a local-remote collaboration reduce clo…
Recent work indicates that low-dimensional dynamics of neural and behavioral data are often preserved across days and subjects. However, extracting these preserved dynamics remains challenging: high-dimensional neural population activity and the recorded neuron populations vary across recording sess…
Multi-compartment Hodgkin-Huxley models are biophysical models of how electrical signals propagate throughout a neuron, and they form the basis of our knowledge of neural computation at the cellular level. However, these models have many free parameters that must be estimated for each cell, and exis…
Discrete diffusion has emerged as a powerful framework for generative modeling in discrete domains, yet efficiently sampling from these models remains challenging. Existing sampling strategies often struggle to balance computation and sample quality when the number of sampling steps is reduced, even…
Markov chain Monte Carlo (MCMC) methods are foundational algorithms for Bayesian inference and probabilistic modeling. However, most MCMC algorithms are inherently sequential and their time complexity scales linearly with the sequence length. Previous work on adapting MCMC to modern hardware has the…
The rise of parallel computing hardware has made it increasingly important to understand which nonlinear state space models can be efficiently parallelized. Recent advances have shown that evaluating a state space model can be recast as solving a parallelizable optimization problem, and sometimes th…
Latent stochastic differential equation (SDE) models are important tools for the unsupervised discovery of dynamical systems from data, with applications ranging from engineering to neuroscience. In these complex domains, exact posterior inference of the latent state path is typically intractable, m…
Verifiers can improve language model (LM) capabilities by providing feedback or selecting the best response from a pool of generated candidates. Currently, high-quality verifiers are either unscalable (e.g., humans) or limited in utility (e.g., tools like Lean for formal proofs). While LM judges and…
Understanding how the collective activity of neural populations relates to computation and ultimately behavior is a key goal in neuroscience. To this end, statistical methods which describe high-dimensional neural time series in terms of low-dimensional latent dynamics have played a fundamental role…
A core aim in theoretical and systems neuroscience is to develop models which help us better understand biological intelligence. Such models range broadly in both complexity and biological plausibility. One widely-adopted example is task-optimized recurrent neural networks (RNNs), which have been…
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 stat…
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 computa…
Sequential latent variable models (SLVMs) are essential tools in statistics and machine learning, with applications ranging from healthcare to neuroscience. As their flexibility increases, analytic inference and model learning can become challenging, necessitating approximate methods. Here we introd…
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 sequentia…
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…
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…
A core goal in systems neuroscience and neuroethology is to understand how neural circuits generate naturalistic behavior. One foundational idea is that complex naturalistic behavior may be composed of sequences of stereotyped behavioral syllables, which combine to generate rich sequences of actions…
Sequential Monte Carlo (SMC) is an inference algorithm for state space models that approximates the posterior by sampling from a sequence of target distributions. The target distributions are often chosen to be the filtering distributions, but these ignore information from future observations, leadi…
Animal pose estimation from video data is an important step in many biological studies, but current methods struggle in complex environments where occlusions are common and training data is scarce. Recent work has demonstrated improved accuracy with deep neural networks, but these methods often do n…
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 standard…
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…
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. He…
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 factorizat…
Modern recording techniques can generate large-scale measurements of multiple neural populations over extended time periods. However, it remains a challenge to model non-stationary interactions between high-dimensional populations of neurons. To tackle this challenge, we develop recurrent switching…
A fundamental goal of systems neuroscience is to understand the relationship between neural activity and behavior. Behavior has traditionally been characterized by low-dimensional, task-related variables such as movement speed or response times. More recently, there has been a growing interest in au…
Many real-world data represent sequences of interdependent events unfolding over time. They can be modeled naturally as realizations of a point process. Despite many potential applications, existing point process models are limited in their ability to capture complex patterns of interaction. Hawkes…
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 Poi…
Recent advances in optical voltage sensors have brought us closer to a critical goal in cellular neuroscience: imaging the full spatiotemporal voltage on a dendritic tree. However, current sensors and imaging approaches still face significant limitations in SNR and sampling frequency; therefore sta…
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 dyn…
Permutations and matchings are core building blocks in a variety of latent variable models, as they allow us to align, canonicalize, and sort data. Learning in such models is difficult, however, because exact marginalization over these combinatorial objects is intractable. In response, this paper in…
A fundamental goal of systems neuroscience is to understand how neural activity gives rise to natural behavior. In order to achieve this goal, we must first build comprehensive models that offer quantitative descriptions of behavior. We develop a new class of probabilistic models to tackle this ch…
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…
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…
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 o…
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…
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 p…
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.…