Sabera Talukder

Sabera Talukder, Jennifer J. Sun, Matthew Leonard et al. · uw

Neuroscientists and neuroengineers have long relied on multielectrode neural recordings to study the brain. However, in a typical experiment, many factors corrupt neural recordings from individual electrodes, including electrical noise, movement artifacts, and faulty manufacturing. Currently, common practice is to discard these corrupted recordings, reducing already limited data that is difficult to collect. To address this challenge, we propose Deep Neural Imputation (DNI), a framework to recover missing values from electrodes by learning from data collected across spatial locations, days, and participants. We explore our framework with a linear nearest-neighbor approach and two deep generative autoencoders, demonstrating DNI's flexibility. One deep autoencoder models participants individually, while the other extends this architecture to model many participants jointly. We evaluate our models across 12 human participants implanted with multielectrode intracranial electrocorticography arrays; participants had no explicit task and behaved naturally across hundreds of recording hours. We show that DNI recovers not only time series but also frequency content, and further establish DNI's practical value by recovering significant performance on a scientifically-relevant downstream neural decoding task.

Sabera Talukder, Yisong Yue, Georgia Gkioxari

This work studies the problem of time series analysis with generalist (or foundation) models, which are models trained across many data domains. Drawing inspiration from the widespread success of large language models, we consider the simple strategy of discretely tokenizing time series data drawn from a myriad of datasets via self-supervision, then using the fixed tokenization to solve a variety of tasks across many data domains. Canonically, time series models are either trained on a single dataset or built in a task-specific manner (e.g., a forecasting-only model), where many use patches of time as inputs to the model. As such, performant generalist, discrete representation time series models explored across many tasks are of value. Our method, TOkenized Time Series EMbeddings (TOTEM), produces such generalist time series models with minimal or no fine-tuning while exhibiting strong zero-shot performance. We evaluate TOTEM extensively over nearly 500 experiments on three commonly-studied time series tasks with real-world data: imputation (17 baselines, 12 datasets), anomaly detection (19 baselines, 25 datasets), and forecasting (14 baselines, 12 datasets). We conclude that TOTEM matches or outperforms existing state-of-the-art models in both the canonical specialist setting (i.e., training one model on one domain) as well as the generalist setting (i.e., training a single model on many domains), which demonstrates the efficacy of tokenization for general time series analysis. The open-source implementation is available here: https://github.com/SaberaTalukder/TOTEM; a video summary is available here: https://www.youtube.com/watch?v=OqrCpdb6MJk.

Geeling Chau, Christopher Wang, Sabera Talukder et al.

We present a self-supervised framework that learns population-level codes for arbitrary ensembles of neural recordings at scale. We address key challenges in scaling models with neural time-series data, namely, sparse and variable electrode distribution across subjects and datasets. The Population Transformer (PopT) stacks on top of pretrained temporal embeddings and enhances downstream decoding by enabling learned aggregation of multiple spatially-sparse data channels. The pretrained PopT lowers the amount of data required for downstream decoding experiments, while increasing accuracy, even on held-out subjects and tasks. Compared to end-to-end methods, this approach is computationally lightweight, while achieving similar or better decoding performance. We further show how our framework is generalizable to multiple time-series embeddings and neural data modalities. Beyond decoding, we interpret the pretrained and fine-tuned PopT models to show how they can be used to extract neuroscience insights from large amounts of data. We release our code as well as a pretrained PopT to enable off-the-shelf improvements in multi-channel intracranial data decoding and interpretability. Code is available at https://github.com/czlwang/PopulationTransformer.

Geeling Chau, Yujin An, Ahamed Raffey Iqbal et al.

A major goal in neuroscience is to discover neural data representations that generalize. This goal is challenged by variability along recording sessions (e.g. environment), subjects (e.g. varying neural structures), and sensors (e.g. sensor noise), among others. Recent work has begun to address generalization across sessions and subjects, but few study robustness to sensor failure which is highly prevalent in neuroscience experiments. In order to address these generalizability dimensions we first collect our own electroencephalography dataset with numerous sessions, subjects, and sensors, then study two time series models: EEGNet (Lawhern et al., 2018) and TOTEM (Talukder et al., 2024). EEGNet is a widely used convolutional neural network, while TOTEM is a discrete time series tokenizer and transformer model. We find that TOTEM outperforms or matches EEGNet across all generalizability cases. Finally through analysis of TOTEM's latent codebook we observe that tokenization enables generalization.

George Barnum, Sabera Talukder, Yisong Yue

Intelligently reasoning about the world often requires integrating data from multiple modalities, as any individual modality may contain unreliable or incomplete information. Prior work in multimodal learning fuses input modalities only after significant independent processing. On the other hand, the brain performs multimodal processing almost immediately. This divide between conventional multimodal learning and neuroscience suggests that a detailed study of early multimodal fusion could improve artificial multimodal representations. To facilitate the study of early multimodal fusion, we create a convolutional LSTM network architecture that simultaneously processes both audio and visual inputs, and allows us to select the layer at which audio and visual information combines. Our results demonstrate that immediate fusion of audio and visual inputs in the initial C-LSTM layer results in higher performing networks that are more robust to the addition of white noise in both audio and visual inputs.

Sabera Talukder, Guruprasad Raghavan, Yisong Yue

In this paper, we explore an alternate method for synthesizing neural network architectures, inspired by the brain's stochastic synaptic pruning. During a person's lifetime, numerous distinct neuronal architectures are responsible for performing the same tasks. This indicates that biological neural networks are, to some degree, architecture agnostic. However, artificial networks rely on their fine-tuned weights and hand-crafted architectures for their remarkable performance. This contrast begs the question: Can we build artificial architecture agnostic neural networks? To ground this study we utilize sparse, binary neural networks that parallel the brain's circuits. Within this sparse, binary paradigm we sample many binary architectures to create families of architecture agnostic neural networks not trained via backpropagation. These high-performing network families share the same sparsity, distribution of binary weights, and succeed in both static and dynamic tasks. In summation, we create an architecture manifold search procedure to discover families or architecture agnostic neural networks.