arXiv subjects

Eva L. Dyer

Publications and source records attributed to Eva L. Dyer.

At least 19 recordsLinked to original sources

arXiv2025

Know Thyself by Knowing Others: Learning Neuron Identity from Population Context

Neurons process information in ways that depend on their cell type, connectivity, and the brain region in which they are embedded. However, inferring these factors from neural activity remains a significant challenge. To build general-purpose representations that allow for resolving information about a neuron's identity, we introduce NuCLR, a self-supervised framework that aims to learn representations of neural activity that allow for differentiating one neuron from the rest. NuCLR brings together views of the same neuron observed at different times and across different stimuli and uses a contrastive objective to pull these representations together. To capture population context without assuming any fixed neuron ordering, we build a spatiotemporal transformer that integrates activity in a permutation-equivariant manner. Across multiple electrophysiology and calcium imaging datasets, a linear decoding evaluation on top of NuCLR representations achieves a new state-of-the-art for both cell type and brain region decoding tasks, and demonstrates strong zero-shot generalization to unseen animals. We present the first systematic scaling analysis for neuron-level representation learning, showing that increasing the number of animals used during pretraining consistently improves downstream performance. The learned representations are also label-efficient, requiring only a small fraction of labeled samples to achieve competitive performance. These results highlight how large, diverse neural datasets enable models to recover information about neuron identity that generalize across animals. Code is available at https://github.com/nerdslab/nuclr.

cs.LG↗

arXiv2025

Generalizable, real-time neural decoding with hybrid state-space models

Real-time decoding of neural activity is central to neuroscience and neurotechnology applications, from closed-loop experiments to brain-computer interfaces, where models are subject to strict latency constraints. Traditional methods, including simple recurrent neural networks, are fast and lightweight but often struggle to generalize to unseen data. In contrast, recent Transformer-based approaches leverage large-scale pretraining for strong generalization performance, but typically have much larger computational requirements and are not always suitable for low-resource or real-time settings. To address these shortcomings, we present POSSM, a novel hybrid architecture that combines individual spike tokenization via a cross-attention module with a recurrent state-space model (SSM) backbone to enable (1) fast and causal online prediction on neural activity and (2) efficient generalization to new sessions, individuals, and tasks through multi-dataset pretraining. We evaluate POSSM's decoding performance and inference speed on intracortical decoding of monkey motor tasks, and show that it extends to clinical applications, namely handwriting and speech decoding in human subjects. Notably, we demonstrate that pretraining on monkey motor-cortical recordings improves decoding performance on the human handwriting task, highlighting the exciting potential for cross-species transfer. In all of these tasks, we find that POSSM achieves decoding accuracy comparable to state-of-the-art Transformers, at a fraction of the inference cost (up to 9x faster on GPU). These results suggest that hybrid SSMs are a promising approach to bridging the gap between accuracy, inference speed, and generalization when training neural decoders for real-time, closed-loop applications.

q-bio.NC↗

arXiv2025

Integrating Temporal and Structural Context in Graph Transformers for Relational Deep Learning

In domains such as healthcare, finance, and e-commerce, the temporal dynamics of relational data emerge from complex interactions-such as those between patients and providers, or users and products across diverse categories. To be broadly useful, models operating on these data must integrate long-range spatial and temporal dependencies across diverse types of entities, while also supporting multiple predictive tasks. However, existing graph models for relational data primarily focus on spatial structure, treating temporal information merely as a filtering constraint to exclude future events rather than a modeling signal, and are typically designed for single-task prediction. To address these gaps, we introduce a temporal subgraph sampler that enhances global context by retrieving nodes beyond the immediate neighborhood to capture temporally relevant relationships. In addition, we propose the Relational Graph Perceiver (RGP), a graph transformer architecture for relational deep learning that leverages a cross-attention-based latent bottleneck to efficiently integrate information from both structural and temporal contexts. This latent bottleneck integrates signals from different node and edge types into a common latent space, enabling the model to build global context across the entire relational system. RGP also incorporates a flexible cross-attention decoder that supports joint learning across tasks with disjoint label spaces within a single model. Experiments on RelBench, SALT, and CTU show that RGP delivers state-of-the-art performance, offering a general and scalable solution for relational deep learning with support for diverse predictive tasks.

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arXiv2025

RELATE: A Schema-Agnostic Perceiver Encoder for Multimodal Relational Graphs

Relational multi-table data is common in domains such as e-commerce, healthcare, and scientific research, and can be naturally represented as heterogeneous temporal graphs with multi-modal node attributes. Existing graph neural networks (GNNs) rely on schema-specific feature encoders, requiring separate modules for each node type and feature column, which hinders scalability and parameter sharing. We introduce RELATE (Relational Encoder for Latent Aggregation of Typed Entities), a schema-agnostic, plug-and-play feature encoder that can be used with any general purpose GNN. RELATE employs shared modality-specific encoders for categorical, numerical, textual, and temporal attributes, followed by a Perceiver-style cross-attention module that aggregates features into a fixed-size, permutation-invariant node representation. We evaluate RELATE on ReLGNN and HGT in the RelBench benchmark, where it achieves performance within 3% of schema-specific encoders while reducing parameter counts by up to 5x. This design supports varying schemas and enables multi-dataset pretraining for general-purpose GNNs, paving the way toward foundation models for relational graph data.

cs.AI↗

arXiv2025

A Scalable, Causal, and Energy Efficient Framework for Neural Decoding with Spiking Neural Networks

Brain-computer interfaces (BCIs) promise to enable vital functions, such as speech and prosthetic control, for individuals with neuromotor impairments. Central to their success are neural decoders, models that map neural activity to intended behavior. Current learning-based decoding approaches fall into two classes: simple, causal models that lack generalization, or complex, non-causal models that generalize and scale offline but struggle in real-time settings. Both face a common challenge, their reliance on power-hungry artificial neural network backbones, which makes integration into real-world, resource-limited systems difficult. Spiking neural networks (SNNs) offer a promising alternative. Because they operate causally these models are suitable for real-time use, and their low energy demands make them ideal for battery-constrained environments. To this end, we introduce Spikachu: a scalable, causal, and energy-efficient neural decoding framework based on SNNs. Our approach processes binned spikes directly by projecting them into a shared latent space, where spiking modules, adapted to the timing of the input, extract relevant features; these latent representations are then integrated and decoded to generate behavioral predictions. We evaluate our approach on 113 recording sessions from 6 non-human primates, totaling 43 hours of recordings. Our method outperforms causal baselines when trained on single sessions using between 2.26 and 418.81 times less energy. Furthermore, we demonstrate that scaling up training to multiple sessions and subjects improves performance and enables few-shot transfer to unseen sessions, subjects, and tasks. Overall, Spikachu introduces a scalable, online-compatible neural decoding framework based on SNNs, whose performance is competitive relative to state-of-the-art models while consuming orders of magnitude less energy.

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arXiv2024

Generalizable autoregressive modeling of time series through functional narratives

Time series data are inherently functions of time, yet current transformers often learn time series by modeling them as mere concatenations of time periods, overlooking their functional properties. In this work, we propose a novel objective for transformers that learn time series by re-interpreting them as temporal functions. We build an alternative sequence of time series by constructing degradation operators of different intensity in the functional space, creating augmented variants of the original sample that are abstracted or simplified to different degrees. Based on the new set of generated sequence, we train an autoregressive transformer that progressively recovers the original sample from the most simplified variant. Analogous to the next word prediction task in languages that learns narratives by connecting different words, our autoregressive transformer aims to learn the Narratives of Time Series (NoTS) by connecting different functions in time. Theoretically, we justify the construction of the alternative sequence through its advantages in approximating functions. When learning time series data with transformers, constructing sequences of temporal functions allows for a broader class of approximable functions (e.g., differentiation) compared to sequences of time periods, leading to a 26\% performance improvement in synthetic feature regression experiments. Experimentally, we validate NoTS in 3 different tasks across 22 real-world datasets, where we show that NoTS significantly outperforms other pre-training methods by up to 6\%. Additionally, combining NoTS on top of existing transformer architectures can consistently boost the performance. Our results demonstrate the potential of NoTS as a general-purpose dynamic learner, offering a viable alternative for developing foundation models for time series analysis.

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arXiv2024

The good, the bad and the ugly sides of data augmentation: An implicit spectral regularization perspective

Data augmentation (DA) is a powerful workhorse for bolstering performance in modern machine learning. Specific augmentations like translations and scaling in computer vision are traditionally believed to improve generalization by generating new (artificial) data from the same distribution. However, this traditional viewpoint does not explain the success of prevalent augmentations in modern machine learning (e.g. randomized masking, cutout, mixup), that greatly alter the training data distribution. In this work, we develop a new theoretical framework to characterize the impact of a general class of DA on underparameterized and overparameterized linear model generalization. Our framework reveals that DA induces implicit spectral regularization through a combination of two distinct effects: a) manipulating the relative proportion of eigenvalues of the data covariance matrix in a training-data-dependent manner, and b) uniformly boosting the entire spectrum of the data covariance matrix through ridge regression. These effects, when applied to popular augmentations, give rise to a wide variety of phenomena, including discrepancies in generalization between over-parameterized and under-parameterized regimes and differences between regression and classification tasks. Our framework highlights the nuanced and sometimes surprising impacts of DA on generalization, and serves as a testbed for novel augmentation design.

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arXiv2023

A Unified, Scalable Framework for Neural Population Decoding

Our ability to use deep learning approaches to decipher neural activity would likely benefit from greater scale, in terms of both model size and datasets. However, the integration of many neural recordings into one unified model is challenging, as each recording contains the activity of different neurons from different individual animals. In this paper, we introduce a training framework and architecture designed to model the population dynamics of neural activity across diverse, large-scale neural recordings. Our method first tokenizes individual spikes within the dataset to build an efficient representation of neural events that captures the fine temporal structure of neural activity. We then employ cross-attention and a PerceiverIO backbone to further construct a latent tokenization of neural population activities. Utilizing this architecture and training framework, we construct a large-scale multi-session model trained on large datasets from seven nonhuman primates, spanning over 158 different sessions of recording from over 27,373 neural units and over 100 hours of recordings. In a number of different tasks, we demonstrate that our pretrained model can be rapidly adapted to new, unseen sessions with unspecified neuron correspondence, enabling few-shot performance with minimal labels. This work presents a powerful new approach for building deep learning tools to analyze neural data and stakes out a clear path to training at scale.

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arXiv2023

LatentDR: Improving Model Generalization Through Sample-Aware Latent Degradation and Restoration

Despite significant advances in deep learning, models often struggle to generalize well to new, unseen domains, especially when training data is limited. To address this challenge, we propose a novel approach for distribution-aware latent augmentation that leverages the relationships across samples to guide the augmentation procedure. Our approach first degrades the samples stochastically in the latent space, mapping them to augmented labels, and then restores the samples from their corrupted versions during training. This process confuses the classifier in the degradation step and restores the overall class distribution of the original samples, promoting diverse intra-class/cross-domain variability. We extensively evaluate our approach on a diverse set of datasets and tasks, including domain generalization benchmarks and medical imaging datasets with strong domain shift, where we show our approach achieves significant improvements over existing methods for latent space augmentation. We further show that our method can be flexibly adapted to long-tail recognition tasks, demonstrating its versatility in building more generalizable models. Code is available at https://github.com/nerdslab/LatentDR.

cs.CV↗

arXiv2023

Half-Hop: A graph upsampling approach for slowing down message passing

Message passing neural networks have shown a lot of success on graph-structured data. However, there are many instances where message passing can lead to over-smoothing or fail when neighboring nodes belong to different classes. In this work, we introduce a simple yet general framework for improving learning in message passing neural networks. Our approach essentially upsamples edges in the original graph by adding "slow nodes" at each edge that can mediate communication between a source and a target node. Our method only modifies the input graph, making it plug-and-play and easy to use with existing models. To understand the benefits of slowing down message passing, we provide theoretical and empirical analyses. We report results on several supervised and self-supervised benchmarks, and show improvements across the board, notably in heterophilic conditions where adjacent nodes are more likely to have different labels. Finally, we show how our approach can be used to generate augmentations for self-supervised learning, where slow nodes are randomly introduced into different edges in the graph to generate multi-scale views with variable path lengths.

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arXiv2023

Relax, it doesn't matter how you get there: A new self-supervised approach for multi-timescale behavior analysis

Natural behavior consists of dynamics that are complex and unpredictable, especially when trying to predict many steps into the future. While some success has been found in building representations of behavior under constrained or simplified task-based conditions, many of these models cannot be applied to free and naturalistic settings where behavior becomes increasingly hard to model. In this work, we develop a multi-task representation learning model for behavior that combines two novel components: (i) An action prediction objective that aims to predict the distribution of actions over future timesteps, and (ii) A multi-scale architecture that builds separate latent spaces to accommodate short- and long-term dynamics. After demonstrating the ability of the method to build representations of both local and global dynamics in realistic robots in varying environments and terrains, we apply our method to the MABe 2022 Multi-agent behavior challenge, where our model ranks 1st overall and on all global tasks, and 1st or 2nd on 7 out of 9 frame-level tasks. In all of these cases, we show that our model can build representations that capture the many different factors that drive behavior and solve a wide range of downstream tasks.

cs.LG↗

arXiv2023

Learning signatures of decision making from many individuals playing the same game

Human behavior is incredibly complex and the factors that drive decision making--from instinct, to strategy, to biases between individuals--often vary over multiple timescales. In this paper, we design a predictive framework that learns representations to encode an individual's 'behavioral style', i.e. long-term behavioral trends, while simultaneously predicting future actions and choices. The model explicitly separates representations into three latent spaces: the recent past space, the short-term space, and the long-term space where we hope to capture individual differences. To simultaneously extract both global and local variables from complex human behavior, our method combines a multi-scale temporal convolutional network with latent prediction tasks, where we encourage embeddings across the entire sequence, as well as subsets of the sequence, to be mapped to similar points in the latent space. We develop and apply our method to a large-scale behavioral dataset from 1,000 humans playing a 3-armed bandit task, and analyze what our model's resulting embeddings reveal about the human decision making process. In addition to predicting future choices, we show that our model can learn rich representations of human behavior over multiple timescales and provide signatures of differences in individuals.

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arXiv2023

Large-Scale Representation Learning on Graphs via Bootstrapping

Self-supervised learning provides a promising path towards eliminating the need for costly label information in representation learning on graphs. However, to achieve state-of-the-art performance, methods often need large numbers of negative examples and rely on complex augmentations. This can be prohibitively expensive, especially for large graphs. To address these challenges, we introduce Bootstrapped Graph Latents (BGRL) - a graph representation learning method that learns by predicting alternative augmentations of the input. BGRL uses only simple augmentations and alleviates the need for contrasting with negative examples, and is thus scalable by design. BGRL outperforms or matches prior methods on several established benchmarks, while achieving a 2-10x reduction in memory costs. Furthermore, we show that BGRL can be scaled up to extremely large graphs with hundreds of millions of nodes in the semi-supervised regime - achieving state-of-the-art performance and improving over supervised baselines where representations are shaped only through label information. In particular, our solution centered on BGRL constituted one of the winning entries to the Open Graph Benchmark - Large Scale Challenge at KDD Cup 2021, on a graph orders of magnitudes larger than all previously available benchmarks, thus demonstrating the scalability and effectiveness of our approach.

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arXiv2023

MTNeuro: A Benchmark for Evaluating Representations of Brain Structure Across Multiple Levels of Abstraction

There are multiple scales of abstraction from which we can describe the same image, depending on whether we are focusing on fine-grained details or a more global attribute of the image. In brain mapping, learning to automatically parse images to build representations of both small-scale features (e.g., the presence of cells or blood vessels) and global properties of an image (e.g., which brain region the image comes from) is a crucial and open challenge. However, most existing datasets and benchmarks for neuroanatomy consider only a single downstream task at a time. To bridge this gap, we introduce a new dataset, annotations, and multiple downstream tasks that provide diverse ways to readout information about brain structure and architecture from the same image. Our multi-task neuroimaging benchmark (MTNeuro) is built on volumetric, micrometer-resolution X-ray microtomography images spanning a large thalamocortical section of mouse brain, encompassing multiple cortical and subcortical regions. We generated a number of different prediction challenges and evaluated several supervised and self-supervised models for brain-region prediction and pixel-level semantic segmentation of microstructures. Our experiments not only highlight the rich heterogeneity of this dataset, but also provide insights into how self-supervised approaches can be used to learn representations that capture multiple attributes of a single image and perform well on a variety of downstream tasks. Datasets, code, and pre-trained baseline models are provided at: https://mtneuro.github.io/ .

cs.CV↗

arXiv2022

Seeing the forest and the tree: Building representations of both individual and collective dynamics with transformers

Complex time-varying systems are often studied by abstracting away from the dynamics of individual components to build a model of the population-level dynamics from the start. However, when building a population-level description, it can be easy to lose sight of each individual and how they contribute to the larger picture. In this paper, we present a novel transformer architecture for learning from time-varying data that builds descriptions of both the individual as well as the collective population dynamics. Rather than combining all of our data into our model at the onset, we develop a separable architecture that operates on individual time-series first before passing them forward; this induces a permutation-invariance property and can be used to transfer across systems of different size and order. After demonstrating that our model can be applied to successfully recover complex interactions and dynamics in many-body systems, we apply our approach to populations of neurons in the nervous system. On neural activity datasets, we show that our model not only yields robust decoding performance, but also provides impressive performance in transfer across recordings of different animals without any neuron-level correspondence. By enabling flexible pre-training that can be transferred to neural recordings of different size and order, our work provides a first step towards creating a foundation model for neural decoding.

q-bio.NC↗

arXiv2022

Learning Behavior Representations Through Multi-Timescale Bootstrapping

Natural behavior consists of dynamics that are both unpredictable, can switch suddenly, and unfold over many different timescales. While some success has been found in building representations of behavior under constrained or simplified task-based conditions, many of these models cannot be applied to free and naturalistic settings due to the fact that they assume a single scale of temporal dynamics. In this work, we introduce Bootstrap Across Multiple Scales (BAMS), a multi-scale representation learning model for behavior: we combine a pooling module that aggregates features extracted over encoders with different temporal receptive fields, and design a set of latent objectives to bootstrap the representations in each respective space to encourage disentanglement across different timescales. We first apply our method on a dataset of quadrupeds navigating in different terrain types, and show that our model captures the temporal complexity of behavior. We then apply our method to the MABe 2022 Multi-agent behavior challenge, where our model ranks 3rd overall and 1st on two subtasks, and show the importance of incorporating multi-timescales when analyzing behavior.

cs.LG↗

arXiv2022

Learning Sinkhorn divergences for supervised change point detection

Many modern applications require detecting change points in complex sequential data. Most existing methods for change point detection are unsupervised and, as a consequence, lack any information regarding what kind of changes we want to detect or if some kinds of changes are safe to ignore. This often results in poor change detection performance. We present a novel change point detection framework that uses true change point instances as supervision for learning a ground metric such that Sinkhorn divergences can be then used in two-sample tests on sliding windows to detect change points in an online manner. Our method can be used to learn a sparse metric which can be useful for both feature selection and interpretation in high-dimensional change point detection settings. Experiments on simulated as well as real world sequences show that our proposed method can substantially improve change point detection performance over existing unsupervised change point detection methods using only few labeled change point instances.

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arXiv2022

Neural Latents Benchmark '21: Evaluating latent variable models of neural population activity

Advances in neural recording present increasing opportunities to study neural activity in unprecedented detail. Latent variable models (LVMs) are promising tools for analyzing this rich activity across diverse neural systems and behaviors, as LVMs do not depend on known relationships between the activity and external experimental variables. However, progress with LVMs for neuronal population activity is currently impeded by a lack of standardization, resulting in methods being developed and compared in an ad hoc manner. To coordinate these modeling efforts, we introduce a benchmark suite for latent variable modeling of neural population activity. We curate four datasets of neural spiking activity from cognitive, sensory, and motor areas to promote models that apply to the wide variety of activity seen across these areas. We identify unsupervised evaluation as a common framework for evaluating models across datasets, and apply several baselines that demonstrate benchmark diversity. We release this benchmark through EvalAI. http://neurallatents.github.io

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