Adam S. Charles

Noga Mudrik, Yenho Chen, Eva Yezerets et al.

Learning interpretable representations of neural dynamics at a population level is a crucial first step to understanding how observed neural activity relates to perception and behavior. Models of neural dynamics often focus on either low-dimensional projections of neural activity, or on learning dynamical systems that explicitly relate to the neural state over time. We discuss how these two approaches are interrelated by considering dynamical systems as representative of flows on a low-dimensional manifold. Building on this concept, we propose a new decomposed dynamical system model that represents complex non-stationary and nonlinear dynamics of time series data as a sparse combination of simpler, more interpretable components. Our model is trained through a dictionary learning procedure, where we leverage recent results in tracking sparse vectors over time. The decomposed nature of the dynamics is more expressive than previous switched approaches for a given number of parameters and enables modeling of overlapping and non-stationary dynamics. In both continuous-time and discrete-time instructional examples we demonstrate that our model can well approximate the original system, learn efficient representations, and capture smooth transitions between dynamical modes, focusing on intuitive low-dimensional non-stationary linear and nonlinear systems. Furthermore, we highlight our model's ability to efficiently capture and demix population dynamics generated from multiple independent subnetworks, a task that is computationally impractical for switched models. Finally, we apply our model to neural "full brain" recordings of C. elegans data, illustrating a diversity of dynamics that is obscured when classified into discrete states.

Sai Koukuntla, Joshua B. Julian, Jesse C. Kaminsky et al.

Studying complex real-world phenomena often involves data from multiple views (e.g. sensor modalities or brain regions), each capturing different aspects of the underlying system. Within neuroscience, there is growing interest in large-scale simultaneous recordings across multiple brain regions. Understanding the relationship between views (e.g., the neural activity in each region recorded) can reveal fundamental insights into each view and the system as a whole. However, existing methods to characterize such relationships lack the expressivity required to capture nonlinear relationships, describe only shared sources of variance, or discard geometric information that is crucial to drawing insights from data. Here, we present SPLICE: a neural network-based method that infers disentangled, interpretable representations of private and shared latent variables from paired samples of high-dimensional views. Compared to competing methods, we demonstrate that SPLICE 1) disentangles shared and private representations more effectively, 2) yields more interpretable representations by preserving geometry, and 3) is more robust to incorrect a priori estimates of latent dimensionality. We propose our approach as a general-purpose method for finding succinct and interpretable descriptions of paired data sets in terms of disentangled shared and private latent variables.

Yenho Chen, Noga Mudrik, Kyle A. Johnsen et al.

Time-varying linear state-space models are powerful tools for obtaining mathematically interpretable representations of neural signals. For example, switching and decomposed models describe complex systems using latent variables that evolve according to simple locally linear dynamics. However, existing methods for latent variable estimation are not robust to dynamical noise and system nonlinearity due to noise-sensitive inference procedures and limited model formulations. This can lead to inconsistent results on signals with similar dynamics, limiting the model's ability to provide scientific insight. In this work, we address these limitations and propose a probabilistic approach to latent variable estimation in decomposed models that improves robustness against dynamical noise. Additionally, we introduce an extended latent dynamics model to improve robustness against system nonlinearities. We evaluate our approach on several synthetic dynamical systems, including an empirically-derived brain-computer interface experiment, and demonstrate more accurate latent variable inference in nonlinear systems with diverse noise conditions. Furthermore, we apply our method to a real-world clinical neurophysiology dataset, illustrating the ability to identify interpretable and coherent structure where previous models cannot.

Noga Mudrik, Gal Mishne, Adam S. Charles

Time series data across scientific domains are often collected under distinct states (e.g., tasks), wherein latent processes (e.g., biological factors) create complex inter- and intra-state variability. A key approach to capture this complexity is to uncover fundamental interpretable units within the data, Building Blocks (BBs), which modulate their activity and adjust their structure across observations. Existing methods for identifying BBs in multi-way data often overlook inter- vs. intra-state variability, produce uninterpretable components, or do not align with properties of real-world data, such as missing samples and sessions of different duration. Here, we present a framework for Similarity-driven Building Block Inference using Graphs across States (SiBBlInGS). SiBBlInGS offers a graph-based dictionary learning approach for discovering sparse BBs along with their temporal traces, based on co-activity patterns and inter- vs. intra-state relationships. Moreover, SiBBlInGS captures per-trial temporal variability and controlled cross-state structural BB adaptations, identifies state-specific vs. state-invariant components, and accommodates variability in the number and duration of observed sessions across states. We demonstrate SiBBlInGS's ability to reveal insights into complex phenomena as well as its robustness to noise and missing samples through several synthetic and real-world examples, including web search and neural data.

Noga Mudrik, Adam S. Charles

While recent advancements in artificial intelligence (AI) language models demonstrate cutting-edge performance when working with English texts, equivalent models do not exist in other languages or do not reach the same performance level. This undesired effect of AI advancements increases the gap between access to new technology from different populations across the world. This unsought bias mainly discriminates against individuals whose English skills are less developed, e.g., non-English speakers children. Following significant advancements in AI research in recent years, OpenAI has recently presented DALL-E: a powerful tool for creating images based on English text prompts. While DALL-E is a promising tool for many applications, its decreased performance when given input in a different language, limits its audience and deepens the gap between populations. An additional limitation of the current DALL-E model is that it only allows for the creation of a few images in response to a given input prompt, rather than a series of consecutive coherent frames that tell a story or describe a process that changes over time. Here, we present an easy-to-use automatic DALL-E storytelling framework that leverages the existing DALL-E model to enable fast and coherent visualizations of non-English songs and stories, pushing the limit of the one-step-at-a-time option DALL-E currently offers. We show that our framework is able to effectively visualize stories from non-English texts and portray the changes in the plot over time. It is also able to create a narrative and maintain interpretable changes in the description across frames. Additionally, our framework offers users the ability to specify constraints on the story elements, such as a specific location or context, and to maintain a consistent style throughout the visualization.

Scott Gigante, Adam S. Charles, Smita Krishnaswamy et al.

Understanding why and how certain neural networks outperform others is key to guiding future development of network architectures and optimization methods. To this end, we introduce a novel visualization algorithm that reveals the internal geometry of such networks: Multislice PHATE (M-PHATE), the first method designed explicitly to visualize how a neural network's hidden representations of data evolve throughout the course of training. We demonstrate that our visualization provides intuitive, detailed summaries of the learning dynamics beyond simple global measures (i.e., validation loss and accuracy), without the need to access validation data. Furthermore, M-PHATE better captures both the dynamics and community structure of the hidden units as compared to visualization based on standard dimensionality reduction methods (e.g., ISOMAP, t-SNE). We demonstrate M-PHATE with two vignettes: continual learning and generalization. In the former, the M-PHATE visualizations display the mechanism of "catastrophic forgetting" which is a major challenge for learning in task-switching contexts. In the latter, our visualizations reveal how increased heterogeneity among hidden units correlates with improved generalization performance. An implementation of M-PHATE, along with scripts to reproduce the figures in this paper, is available at https://github.com/scottgigante/M-PHATE.

Adam S. Charles

Theoretical understanding of deep learning is one of the most important tasks facing the statistics and machine learning communities. While deep neural networks (DNNs) originated as engineering methods and models of biological networks in neuroscience and psychology, they have quickly become a centerpiece of the machine learning toolbox. Unfortunately, DNN adoption powered by recent successes combined with the open-source nature of the machine learning community, has outpaced our theoretical understanding. We cannot reliably identify when and why DNNs will make mistakes. In some applications like text translation these mistakes may be comical and provide for fun fodder in research talks, a single error can be very costly in tasks like medical imaging. As we utilize DNNs in increasingly sensitive applications, a better understanding of their properties is thus imperative. Recent advances in DNN theory are numerous and include many different sources of intuition, such as learning theory, sparse signal analysis, physics, chemistry, and psychology. An interesting pattern begins to emerge in the breadth of possible interpretations. The seemingly limitless approaches are mostly constrained by the lens with which the mathematical operations are viewed. Ultimately, the interpretation of DNNs appears to mimic a type of Rorschach test --- a psychological test wherein subjects interpret a series of seemingly ambiguous ink-blots. Validation for DNN theory requires a convergence of the literature. We must distinguish between universal results that are invariant to the analysis perspective and those that are specific to a particular network configuration. Simultaneously we must deal with the fact that many standard statistical tools for quantifying generalization or empirically assessing important network features are difficult to apply to DNNs.

Noga Mudrik, Eva Yezerets, Yenho Chen et al.

Identifying latent interactions within complex systems is key to unlocking deeper insights into their operational dynamics, including how their elements affect each other and contribute to the overall system behavior. For instance, in neuroscience, discovering neuron-to-neuron interactions is essential for understanding brain function; in ecology, recognizing the interactions among populations is key for understanding complex ecosystems. Such systems, often modeled as dynamical systems, typically exhibit noisy high-dimensional and non-stationary temporal behavior that renders their identification challenging. Existing dynamical system identification methods often yield operators that accurately capture short-term behavior but fail to predict long-term trends, suggesting an incomplete capture of the underlying process. Methods that consider extended forecasts (e.g., recurrent neural networks) lack explicit representations of element-wise interactions and require substantial training data, thereby failing to capture interpretable network operators. Here we introduce Lookahead-driven Inference of Networked Operators for Continuous Stability (LINOCS), a robust learning procedure for identifying hidden dynamical interactions in noisy time-series data. LINOCS integrates several multi-step predictions with adaptive weights during training to recover dynamical operators that can yield accurate long-term predictions. We demonstrate LINOCS' ability to recover the ground truth dynamical operators underlying synthetic time-series data for multiple dynamical systems models (including linear, piece-wise linear, time-changing linear systems' decomposition, and regularized linear time-varying systems) as well as its capability to produce meaningful operators with robust reconstructions through various real-world examples.

Gal Mishne, Adam Charles

Optical imaging of the brain has expanded dramatically in the past two decades. New optics, indicators, and experimental paradigms are now enabling in-vivo imaging from the synaptic to the cortex-wide scales. To match the resulting flood of data across scales, computational methods are continuously being developed to meet the need of extracting biologically relevant information. In this pursuit, challenges arise in some domains (e.g., SNR and resolution limits in micron-scale data) that require specialized algorithms. These algorithms can, for example, make use of state-of-the-art machine learning to maximally learn the details of a given scale to optimize the processing pipeline. In contrast, other methods, however, such as graph signal processing, seek to abstract away from some of the details that are scale-specific to provide solutions to specific sub-problems common across scales of neuroimaging. Here we discuss limitations and tradeoffs in algorithmic design with the goal of identifying how data quality and variability can hamper algorithm use and dissemination.

Jiancheng Xie, Lou C. Kohler Voinov, Noga Mudrik et al.

Recurrent neural networks (RNNs) are a widely used tool for sequential data analysis, however, they are still often seen as black boxes of computation. Understanding the functional principles of these networks is critical to developing ideal model architectures and optimization strategies. Previous studies typically only emphasize the network representation post-training, overlooking their evolution process throughout training. Here, we present Multiway Multislice PHATE (MM-PHATE), a novel method for visualizing the evolution of RNNs' hidden states. MM-PHATE is a graph-based embedding using structured kernels across the multiple dimensions spanned by RNNs: time, training epoch, and units. We demonstrate on various datasets that MM-PHATE uniquely preserves hidden representation community structure among units and identifies information processing and compression phases during training. The embedding allows users to look under the hood of RNNs across training and provides an intuitive and comprehensive strategy to understanding the network's internal dynamics and draw conclusions, e.g., on why and how one model outperforms another or how a specific architecture might impact an RNN's learning ability.

Ashwin De Silva, Rahul Ramesh, Lyle Ungar et al.

Learning is a process which can update decision rules, based on past experience, such that future performance improves. Traditionally, machine learning is often evaluated under the assumption that the future will be identical to the past in distribution or change adversarially. But these assumptions can be either too optimistic or pessimistic for many problems in the real world. Real world scenarios evolve over multiple spatiotemporal scales with partially predictable dynamics. Here we reformulate the learning problem to one that centers around this idea of dynamic futures that are partially learnable. We conjecture that certain sequences of tasks are not retrospectively learnable (in which the data distribution is fixed), but are prospectively learnable (in which distributions may be dynamic), suggesting that prospective learning is more difficult in kind than retrospective learning. We argue that prospective learning more accurately characterizes many real world problems that (1) currently stymie existing artificial intelligence solutions and/or (2) lack adequate explanations for how natural intelligences solve them. Thus, studying prospective learning will lead to deeper insights and solutions to currently vexing challenges in both natural and artificial intelligences.

Michael Shvartsman, Narayanan Sundaram, Mikio C. Aoi et al.

Multivariate analysis of fMRI data has benefited substantially from advances in machine learning. Most recently, a range of probabilistic latent variable models applied to fMRI data have been successful in a variety of tasks, including identifying similarity patterns in neural data (Representational Similarity Analysis and its empirical Bayes variant, RSA and BRSA; Intersubject Functional Connectivity, ISFC), combining multi-subject datasets (Shared Response Mapping; SRM), and mapping between brain and behavior (Joint Modeling). Although these methods share some underpinnings, they have been developed as distinct methods, with distinct algorithms and software tools. We show how the matrix-variate normal (MN) formalism can unify some of these methods into a single framework. In doing so, we gain the ability to reuse noise modeling assumptions, algorithms, and code across models. Our primary theoretical contribution shows how some of these methods can be written as instantiations of the same model, allowing us to generalize them to flexibly modeling structured noise covariances. Our formalism permits novel model variants and improved estimation strategies: in contrast to SRM, the number of parameters for MN-SRM does not scale with the number of voxels or subjects; in contrast to BRSA, the number of parameters for MN-RSA scales additively rather than multiplicatively in the number of voxels. We empirically demonstrate advantages of two new methods derived in the formalism: for MN-RSA, we show up to 10x improvement in runtime, up to 6x improvement in RMSE, and more conservative behavior under the null. For MN-SRM, our method grants a modest improvement to out-of-sample reconstruction while relaxing an orthonormality constraint of SRM. We also provide a software prototyping tool for MN models that can flexibly reuse noise covariance assumptions and algorithms across models.

Adam Charles, Dong Yin, Christopher Rozell

Recurrent neural networks (RNNs) have drawn interest from machine learning researchers because of their effectiveness at preserving past inputs for time-varying data processing tasks. To understand the success and limitations of RNNs, it is critical that we advance our analysis of their fundamental memory properties. We focus on echo state networks (ESNs), which are RNNs with simple memoryless nodes and random connectivity. In most existing analyses, the short-term memory (STM) capacity results conclude that the ESN network size must scale linearly with the input size for unstructured inputs. The main contribution of this paper is to provide general results characterizing the STM capacity for linear ESNs with multidimensional input streams when the inputs have common low-dimensional structure: sparsity in a basis or significant statistical dependence between inputs. In both cases, we show that the number of nodes in the network must scale linearly with the information rate and poly-logarithmically with the ambient input dimension. The analysis relies on advanced applications of random matrix theory and results in explicit non-asymptotic bounds on the recovery error. Taken together, this analysis provides a significant step forward in our understanding of the STM properties in RNNs.

Qi She, Xiaoli Wu, Beth Jelfs et al.

Accurate statistical models of neural spike responses can characterize the information carried by neural populations. But the limited samples of spike counts during recording usually result in model overfitting. Besides, current models assume spike counts to be Poisson-distributed, which ignores the fact that many neurons demonstrate over-dispersed spiking behaviour. Although the Negative Binomial Generalized Linear Model (NB-GLM) provides a powerful tool for modeling over-dispersed spike counts, the maximum likelihood-based standard NB-GLM leads to highly variable and inaccurate parameter estimates. Thus, we propose a hierarchical parametric empirical Bayes method to estimate the neural spike responses among neuronal population. Our method integrates both Generalized Linear Models (GLMs) and empirical Bayes theory, which aims to (1) improve the accuracy and reliability of parameter estimation, compared to the maximum likelihood-based method for NB-GLM and Poisson-GLM; (2) effectively capture the over-dispersion nature of spike counts from both simulated data and experimental data; and (3) provide insight into both neural interactions and spiking behaviours of the neuronal populations. We apply our approach to study both simulated data and experimental neural data. The estimation of simulation data indicates that the new framework can accurately predict mean spike counts simulated from different models and recover the connectivity weights among neural populations. The estimation based on retinal neurons demonstrate the proposed method outperforms both NB-GLM and Poisson-GLM in terms of the predictive log-likelihood of held-out data. Codes are available in https://doi.org/10.5281/zenodo.4704423

Adam Charles, Aurele Balavoine, Christopher Rozell

Despite the importance of sparsity signal models and the increasing prevalence of high-dimensional streaming data, there are relatively few algorithms for dynamic filtering of time-varying sparse signals. Of the existing algorithms, fewer still provide strong performance guarantees. This paper examines two algorithms for dynamic filtering of sparse signals that are based on efficient l1 optimization methods. We first present an analysis for one simple algorithm (BPDN-DF) that works well when the system dynamics are known exactly. We then introduce a novel second algorithm (RWL1-DF) that is more computationally complex than BPDN-DF but performs better in practice, especially in the case where the system dynamics model is inaccurate. Robustness to model inaccuracy is achieved by using a hierarchical probabilistic data model and propagating higher-order statistics from the previous estimate (akin to Kalman filtering) in the sparse inference process. We demonstrate the properties of these algorithms on both simulated data as well as natural video sequences. Taken together, the algorithms presented in this paper represent the first strong performance analysis of dynamic filtering algorithms for time-varying sparse signals as well as state-of-the-art performance in this emerging application.

Adam S. Charles, Han Lun Yap, Christopher J. Rozell

Cortical networks are hypothesized to rely on transient network activity to support short term memory (STM). In this paper we study the capacity of randomly connected recurrent linear networks for performing STM when the input signals are approximately sparse in some basis. We leverage results from compressed sensing to provide rigorous non asymptotic recovery guarantees, quantifying the impact of the input sparsity level, the input sparsity basis, and the network characteristics on the system capacity. Our analysis demonstrates that network memory capacities can scale superlinearly with the number of nodes, and in some situations can achieve STM capacities that are much larger than the network size. We provide perfect recovery guarantees for finite sequences and recovery bounds for infinite sequences. The latter analysis predicts that network STM systems may have an optimal recovery length that balances errors due to omission and recall mistakes. Furthermore, we show that the conditions yielding optimal STM capacity can be embodied in several network topologies, including networks with sparse or dense connectivities.