arXiv subjects

T. Anderson Keller

Publications and source records attributed to T. Anderson Keller.

At least 19 recordsLinked to original sources

arXiv2026

Where the Score Lives: A Wavelet View of Diffusion

Score-based generative models have had remarkable success over the last decade in generating a diverse set of visually plausible images. A variety of architectures including CNNs, U-Nets, and Transformers have been used as the score-approximation network in such diffusion modeling; however, to date, relatively little is known about how these architectural choices impact generative behavior. In this work, to provide insight into this area, we propose an analytically solvable parameterization of the score function using an expansion in a 2D orthogonal wavelet basis. In particular, we derive interpretable optimal score functions in terms of the moments of the data distribution. We use this parametrization to provide an architecture-agnostic, moment-based analysis that reveals which attributes of the data distribution tend to matter most for denoising. Our score machine is flexible enough to partially mimic the relevant inductive biases of multiple architectures, including U-Nets, and CNNs, taking a step towards understanding why different score architectures can exhibit distinct generative behavior. Since our score is solvable in terms of the moments of the data, we can begin to understand how the data distribution interacts with the score network to produce the behavior we observe in diffusion models.

cs.LG↗

arXiv2026

Spontaneous symmetry breaking and Goldstone modes for deep information propagation

In physical systems, whenever a continuous symmetry is spontaneously broken, the system possesses excitations called Goldstone modes, which allow coherent information propagation over long distances and times. In this work, we study deep neural networks whose internal layers are equivariant under a continuous symmetry and may therefore support analogous Goldstone-like degrees of freedom. We demonstrate, both analytically and empirically, that these degrees of freedom enable coherent signal propagation across depth and recurrent iterations, providing a mechanism for stable information flow without relying on architectural stabilizers such as residual connections or normalization. In feedforward networks, this results in improved trainability and representational diversity across layers. In recurrent settings, we demonstrate the same mechanism is valuable for long-term memory by propagating information over recurrent iterations, thereby improving performance of RNNs and GRUs on long-sequence modeling tasks.

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arXiv2026

Decoding Alignment without Encoding Alignment: A critique of similarity analysis in neuroscience

Decoding approaches are widely used in neuroscience and machine learning to compare stimulus representations across neural systems, such as different brain regions, organisms, and deep learning models. Popular methods include decoding (perceptual) manifolds and alignment metrics such as Representational Similarity Analysis (RSA) and Dynamic Similarity Analysis (DSA), where similarity in decoding representations is interpreted as evidence for similar computation. This paper demonstrates a fundamental weakness behind this approach: it is misleading to assume that representational geometry is representative of a neuronal population as a whole, when such representations may actually be shaped by a very small subset of neurons. We show that the complementary encoding paradigm addresses this issue directly: it characterizes how neurons are organized globally in terms of their responses to a set of data, providing insight into how the decoding representation is implemented by neurons within a population. We demonstrate across experiments in biological systems and deep learning models that (i) surprisingly, similar decoding behavior and high representational alignment can arise from small, non-representative subpopulations of neurons; and critically, (ii) alignment metrics are insensitive to encoding manifold topology (how function is distributed across neurons), despite this being a key signature of differentiation across biological systems. A controlled MNIST experiment provides causal evidence: decoding metrics remain unchanged even when encoding topology is causally manipulated via the training loss. Overall, similarity in decoding behavior, as measured by classic alignment metrics, does not imply similarity in function or computation, motivating the use of encoding manifolds as a complementary tool for comparing neural systems.

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arXiv2026

Langevin Flows for Modeling Neural Latent Dynamics

Neural populations exhibit latent dynamical structures that drive time-evolving spiking activities, motivating the search for models that capture both intrinsic network dynamics and external unobserved influences. In this work, we introduce LangevinFlow, a sequential Variational Auto-Encoder where the time evolution of latent variables is governed by the underdamped Langevin equation. Our approach incorporates physical priors -- such as inertia, damping, a learned potential function, and stochastic forces -- to represent both autonomous and non-autonomous processes in neural systems. Crucially, the potential function is parameterized as a network of locally coupled oscillators, biasing the model toward oscillatory and flow-like behaviors observed in biological neural populations. Our model features a recurrent encoder, a one-layer Transformer decoder, and Langevin dynamics in the latent space. Empirically, our method outperforms state-of-the-art baselines on synthetic neural populations generated by a Lorenz attractor, closely matching ground-truth firing rates. On the Neural Latents Benchmark (NLB), the model achieves superior held-out neuron likelihoods (bits per spike) and forward prediction accuracy across four challenging datasets. It also matches or surpasses alternative methods in decoding behavioral metrics such as hand velocity. Overall, this work introduces a flexible, physics-inspired, high-performing framework for modeling complex neural population dynamics and their unobserved influences.

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arXiv2026

Kuramoto Orientation Diffusion Models

Orientation-rich images, such as fingerprints and textures, often exhibit coherent angular directional patterns that are challenging to model using standard generative approaches based on isotropic Euclidean diffusion. Motivated by the role of phase synchronization in biological systems, we propose a score-based generative model built on periodic domains by leveraging stochastic Kuramoto dynamics in the diffusion process. In neural and physical systems, Kuramoto models capture synchronization phenomena across coupled oscillators -- a behavior that we re-purpose here as an inductive bias for structured image generation. In our framework, the forward process performs \textit{synchronization} among phase variables through globally or locally coupled oscillator interactions and attraction to a global reference phase, gradually collapsing the data into a low-entropy von Mises distribution. The reverse process then performs \textit{desynchronization}, generating diverse patterns by reversing the dynamics with a learned score function. This approach enables structured destruction during forward diffusion and a hierarchical generation process that progressively refines global coherence into fine-scale details. We implement wrapped Gaussian transition kernels and periodicity-aware networks to account for the circular geometry. Our method achieves competitive results on general image benchmarks and significantly improves generation quality on orientation-dense datasets like fingerprints and textures. Ultimately, this work demonstrates the promise of biologically inspired synchronization dynamics as structured priors in generative modeling.

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arXiv2026

A Spatiotemporal Perspective on Dynamical Computation in Neural Information Processing Systems

Spatiotemporal flows of neural activity, such as traveling waves, have been observed throughout the brain since the earliest recordings; yet there is still little consensus on their functional role. Recent experiments and models have linked traveling waves to visual and physical motion, but these observations have been difficult to reconcile with standard accounts of topographically organized selectivity and feedforward receptive fields. Here, we introduce a theoretical framework that formalizes and generalizes the connection between 'motion' and flowing neural dynamics in the language of equivariant neural network theory. We consider 'motion' not only in physical or visual spaces, but also in more abstract representational spaces, and we argue that recurrent traveling-wave-like dynamics are not just useful but necessary for accurate and stable processing of any signal undergoing such motion. Formally, we show that for any non-trivial recurrent neural network to process a sequence undergoing a flow transformation (such as visual motion) in a structured equivariant manner, its hidden state dynamics must actively realize a homomorphic representation of the same flow through recurrent connectivity. In this ''spatiotemporal perspective on dynamical computation'', traveling waves and related flows are best understood as faithful dynamic representations of stimulus flows; and consequently the natural inclination of biological systems towards such dynamics may be viewed as an innate inductive bias towards efficiency and generalization in the spatiotemporally-structured dynamical world they inhabit.

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arXiv2025

Flow Equivariant Recurrent Neural Networks

Data arrives at our senses as a continuous stream, smoothly transforming from one instant to the next. These smooth transformations can be viewed as continuous symmetries of the environment that we inhabit, defining equivalence relations between stimuli over time. In machine learning, neural network architectures that respect symmetries of their data are called equivariant and have provable benefits in terms of generalization ability and sample efficiency. To date, however, equivariance has been considered only for static transformations and feed-forward networks, limiting its applicability to sequence models, such as recurrent neural networks (RNNs), and corresponding time-parameterized sequence transformations. In this work, we extend equivariant network theory to this regime of 'flows' -- one-parameter Lie subgroups capturing natural transformations over time, such as visual motion. We begin by showing that standard RNNs are generally not flow equivariant: their hidden states fail to transform in a geometrically structured manner for moving stimuli. We then show how flow equivariance can be introduced, and demonstrate that these models significantly outperform their non-equivariant counterparts in terms of training speed, length generalization, and velocity generalization, on both next step prediction and sequence classification. We present this work as a first step towards building sequence models that respect the time-parameterized symmetries which govern the world around us.

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arXiv2025

Manifolds and Modules: How Function Develops in a Neural Foundation Model

Foundation models have shown remarkable success in fitting biological visual systems; however, their black-box nature inherently limits their utility for understanding brain function. Here, we peek inside a SOTA foundation model of neural activity (Wang et al., 2025) as a physiologist might, characterizing each 'neuron' based on its temporal response properties to parametric stimuli. We analyze how different stimuli are represented in neural activity space by building decoding manifolds, and we analyze how different neurons are represented in stimulus-response space by building neural encoding manifolds. We find that the different processing stages of the model (i.e., the feedforward encoder, recurrent, and readout modules) each exhibit qualitatively different representational structures in these manifolds. The recurrent module shows a jump in capabilities over the encoder module by 'pushing apart' the representations of different temporal stimulus patterns; while the readout module achieves biological fidelity by using numerous specialized feature maps rather than biologically plausible mechanisms. Overall, we present this work as a study of the inner workings of a prominent neural foundation model, gaining insights into the biological relevance of its internals through the novel analysis of its neurons' joint temporal response patterns.

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arXiv2025

Origins of Creativity in Attention-Based Diffusion Models

As diffusion models have become the tool of choice for image generation and as the quality of the images continues to improve, the question of how `creativity' originates in diffusion has become increasingly important. The score matching perspective on diffusion has proven particularly fruitful for understanding how and why diffusion models generate images that remain plausible while differing significantly from their training images. In particular, as explained in (Kamb \& Ganguli, 2024) and others, e.g., (Ambrogioni, 2023), theory suggests that if our score matching were optimal, we would only be able to recover training samples through our diffusion process. However, as shown by Kamb \& Ganguli, (2024), in diffusion models where the score is parametrized by a simple CNN, the inductive biases of the CNN itself (translation equivariance and locality) allow the model to generate samples that globally do not match any training samples, but are rather patch-wise `mosaics'. Notably, however, this theory does not extend to describe the role of self-attention in this process. In this work, we take a preliminary step in this direction to extend this theory to the case of diffusion models whose score is parametrized by a CNN with a final self-attention layer. We show that our theory suggests that self-attention will induce a globally image-consistent arrangement of local features beyond the patch-level in generated samples, and we verify this behavior empirically on a carefully crafted dataset.

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arXiv2025

Traveling Waves Integrate Spatial Information Through Time

Traveling waves of neural activity are widely observed in the brain, but their precise computational function remains unclear. One prominent hypothesis is that they enable the transfer and integration of spatial information across neural populations. However, few computational models have explored how traveling waves might be harnessed to perform such integrative processing. Drawing inspiration from the famous "Can one hear the shape of a drum?" problem -- which highlights how normal modes of wave dynamics encode geometric information -- we investigate whether similar principles can be leveraged in artificial neural networks. Specifically, we introduce convolutional recurrent neural networks that learn to produce traveling waves in their hidden states in response to visual stimuli, enabling spatial integration. By then treating these wave-like activation sequences as visual representations themselves, we obtain a powerful representational space that outperforms local feed-forward networks on tasks requiring global spatial context. In particular, we observe that traveling waves effectively expand the receptive field of locally connected neurons, supporting long-range encoding and communication of information. We demonstrate that models equipped with this mechanism solve visual semantic segmentation tasks demanding global integration, significantly outperforming local feed-forward models and rivaling non-local U-Net models with fewer parameters. As a first step toward traveling-wave-based communication and visual representation in artificial networks, our findings suggest wave-dynamics may provide efficiency and training stability benefits, while simultaneously offering a new framework for connecting models to biological recordings of neural activity.

cs.CV↗

arXiv2024

Learning Artistic Signatures: Symmetry Discovery and Style Transfer

Despite nearly a decade of literature on style transfer, there is no undisputed definition of artistic style. State-of-the-art models produce impressive results but are difficult to interpret since, without a coherent definition of style, the problem of style transfer is inherently ill-posed. Early work framed style-transfer as an optimization problem but treated style as a measure only of texture. This led to artifacts in the outputs of early models where content features from the style image sometimes bled into the output image. Conversely, more recent work with diffusion models offers compelling empirical results but provides little theoretical grounding. To address these issues, we propose an alternative definition of artistic style. We suggest that style should be thought of as a set of global symmetries that dictate the arrangement of local textures. We validate this perspective empirically by learning the symmetries of a large dataset of paintings and showing that symmetries are predictive of the artistic movement to which each painting belongs. Finally, we show that by considering both local and global features, using both Lie generators and traditional measures of texture, we can quantitatively capture the stylistic similarity between artists better than with either set of features alone. This approach not only aligns well with art historians' consensus but also offers a robust framework for distinguishing nuanced stylistic differences, allowing for a more interpretable, theoretically grounded approach to style transfer.

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arXiv2024

Traveling Waves Encode the Recent Past and Enhance Sequence Learning

Traveling waves of neural activity have been observed throughout the brain at a diversity of regions and scales; however, their precise computational role is still debated. One physically inspired hypothesis suggests that the cortical sheet may act like a wave-propagating system capable of invertibly storing a short-term memory of sequential stimuli through induced waves traveling across the cortical surface, and indeed many experimental results from neuroscience correlate wave activity with memory tasks. To date, however, the computational implications of this idea have remained hypothetical due to the lack of a simple recurrent neural network architecture capable of exhibiting such waves. In this work, we introduce a model to fill this gap, which we denote the Wave-RNN (wRNN), and demonstrate how such an architecture indeed efficiently encodes the recent past through a suite of synthetic memory tasks where wRNNs learn faster and reach significantly lower error than wave-free counterparts. We further explore the implications of this memory storage system on more complex sequence modeling tasks such as sequential image classification and find that wave-based models not only again outperform comparable wave-free RNNs while using significantly fewer parameters, but additionally perform comparably to more complex gated architectures such as LSTMs and GRUs.

cs.NE↗

arXiv2023

DUET: 2D Structured and Approximately Equivariant Representations

Multiview Self-Supervised Learning (MSSL) is based on learning invariances with respect to a set of input transformations. However, invariance partially or totally removes transformation-related information from the representations, which might harm performance for specific downstream tasks that require such information. We propose 2D strUctured and EquivarianT representations (coined DUET), which are 2d representations organized in a matrix structure, and equivariant with respect to transformations acting on the input data. DUET representations maintain information about an input transformation, while remaining semantically expressive. Compared to SimCLR (Chen et al., 2020) (unstructured and invariant) and ESSL (Dangovski et al., 2022) (unstructured and equivariant), the structured and equivariant nature of DUET representations enables controlled generation with lower reconstruction error, while controllability is not possible with SimCLR or ESSL. DUET also achieves higher accuracy for several discriminative tasks, and improves transfer learning.

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arXiv2023

Deep Generative Models of Music Expectation

A prominent theory of affective response to music revolves around the concepts of surprisal and expectation. In prior work, this idea has been operationalized in the form of probabilistic models of music which allow for precise computation of song (or note-by-note) probabilities, conditioned on a 'training set' of prior musical or cultural experiences. To date, however, these models have been limited to compute exact probabilities through hand-crafted features or restricted to linear models which are likely not sufficient to represent the complex conditional distributions present in music. In this work, we propose to use modern deep probabilistic generative models in the form of a Diffusion Model to compute an approximate likelihood of a musical input sequence. Unlike prior work, such a generative model parameterized by deep neural networks is able to learn complex non-linear features directly from a training set itself. In doing so, we expect to find that such models are able to more accurately represent the 'surprisal' of music for human listeners. From the literature, it is known that there is an inverted U-shaped relationship between surprisal and the amount human subjects 'like' a given song. In this work we show that pre-trained diffusion models indeed yield musical surprisal values which exhibit a negative quadratic relationship with measured subject 'liking' ratings, and that the quality of this relationship is competitive with state of the art methods such as IDyOM. We therefore present this model a preliminary step in developing modern deep generative models of music expectation and subjective likability.

cs.SD↗

arXiv2023

Flow Factorized Representation Learning

A prominent goal of representation learning research is to achieve representations which are factorized in a useful manner with respect to the ground truth factors of variation. The fields of disentangled and equivariant representation learning have approached this ideal from a range of complimentary perspectives; however, to date, most approaches have proven to either be ill-specified or insufficiently flexible to effectively separate all realistic factors of interest in a learned latent space. In this work, we propose an alternative viewpoint on such structured representation learning which we call Flow Factorized Representation Learning, and demonstrate it to learn both more efficient and more usefully structured representations than existing frameworks. Specifically, we introduce a generative model which specifies a distinct set of latent probability paths that define different input transformations. Each latent flow is generated by the gradient field of a learned potential following dynamic optimal transport. Our novel setup brings new understandings to both \textit{disentanglement} and \textit{equivariance}. We show that our model achieves higher likelihoods on standard representation learning benchmarks while simultaneously being closer to approximately equivariant models. Furthermore, we demonstrate that the transformations learned by our model are flexibly composable and can also extrapolate to new data, implying a degree of robustness and generalizability approaching the ultimate goal of usefully factorized representation learning.

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arXiv2023

Latent Traversals in Generative Models as Potential Flows

Despite the significant recent progress in deep generative models, the underlying structure of their latent spaces is still poorly understood, thereby making the task of performing semantically meaningful latent traversals an open research challenge. Most prior work has aimed to solve this challenge by modeling latent structures linearly, and finding corresponding linear directions which result in `disentangled' generations. In this work, we instead propose to model latent structures with a learned dynamic potential landscape, thereby performing latent traversals as the flow of samples down the landscape's gradient. Inspired by physics, optimal transport, and neuroscience, these potential landscapes are learned as physically realistic partial differential equations, thereby allowing them to flexibly vary over both space and time. To achieve disentanglement, multiple potentials are learned simultaneously, and are constrained by a classifier to be distinct and semantically self-consistent. Experimentally, we demonstrate that our method achieves both more qualitatively and quantitatively disentangled trajectories than state-of-the-art baselines. Further, we demonstrate that our method can be integrated as a regularization term during training, thereby acting as an inductive bias towards the learning of structured representations, ultimately improving model likelihood on similarly structured data.

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arXiv2022

Homomorphic Self-Supervised Learning

In this work, we observe that many existing self-supervised learning algorithms can be both unified and generalized when seen through the lens of equivariant representations. Specifically, we introduce a general framework we call Homomorphic Self-Supervised Learning, and theoretically show how it may subsume the use of input-augmentations provided an augmentation-homomorphic feature extractor. We validate this theory experimentally for simple augmentations, demonstrate how the framework fails when representational structure is removed, and further empirically explore how the parameters of this framework relate to those of traditional augmentation-based self-supervised learning. We conclude with a discussion of the potential benefits afforded by this new perspective on self-supervised learning.

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arXiv2022

As easy as APC: overcoming missing data and class imbalance in time series with self-supervised learning

High levels of missing data and strong class imbalance are ubiquitous challenges that are often presented simultaneously in real-world time series data. Existing methods approach these problems separately, frequently making significant assumptions about the underlying data generation process in order to lessen the impact of missing information. In this work, we instead demonstrate how a general self-supervised training method, namely Autoregressive Predictive Coding (APC), can be leveraged to overcome both missing data and class imbalance simultaneously without strong assumptions. Specifically, on a synthetic dataset, we show that standard baselines are substantially improved upon through the use of APC, yielding the greatest gains in the combined setting of high missingness and severe class imbalance. We further apply APC on two real-world medical time-series datasets, and show that APC improves the classification performance in all settings, ultimately achieving state-of-the-art AUPRC results on the Physionet benchmark.

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