Neuroformer: Multimodal and Multitask Generative Pretraining for Brain Data

• URL: http://arxiv.org/abs/2311.00136v4
• Date: Fri, 15 Mar 2024 22:07:06 GMT
• Title: Neuroformer: Multimodal and Multitask Generative Pretraining for Brain Data
• Authors: Antonis Antoniades, Yiyi Yu, Joseph Canzano, William Wang, Spencer LaVere Smith,
• Abstract summary: State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the analysis of large-scale, cellular-resolution neuronal spiking data into an autoregressive generation problem. We first trained Neuroformer on simulated datasets, and found that it both accurately predicted intrinsically simulated neuronal circuit activity, and also inferred the underlying neural circuit connectivity, including direction.
• Score: 3.46029409929709
• License: http://creativecommons.org/licenses/by-nc-sa/4.0/
• Abstract: State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the analysis of large-scale, cellular-resolution neuronal spiking data into an autoregressive spatiotemporal generation problem. Neuroformer is a multimodal, multitask generative pretrained transformer (GPT) model that is specifically designed to handle the intricacies of data in systems neuroscience. It scales linearly with feature size, can process an arbitrary number of modalities, and is adaptable to downstream tasks, such as predicting behavior. We first trained Neuroformer on simulated datasets, and found that it both accurately predicted simulated neuronal circuit activity, and also intrinsically inferred the underlying neural circuit connectivity, including direction. When pretrained to decode neural responses, the model predicted the behavior of a mouse with only few-shot fine-tuning, suggesting that the model begins learning how to do so directly from the neural representations themselves, without any explicit supervision. We used an ablation study to show that joint training on neuronal responses and behavior boosted performance, highlighting the model's ability to associate behavioral and neural representations in an unsupervised manner. These findings show that Neuroformer can analyze neural datasets and their emergent properties, informing the development of models and hypotheses associated with the brain.

Related papers

• BLEND: Behavior-guided Neural Population Dynamics Modeling via Privileged Knowledge Distillation [6.3559178227943764]
  We propose BLEND, a behavior-guided neural population dynamics modeling framework via privileged knowledge distillation. By considering behavior as privileged information, we train a teacher model that takes both behavior observations (privileged features) and neural activities (regular features) as inputs. A student model is then distilled using only neural activity.
  arXiv  Detail & Related papers  (2024-10-02T12:45:59Z)
• Neural Dynamics Model of Visual Decision-Making: Learning from Human Experts [28.340344705437758]
  We implement a comprehensive visual decision-making model that spans from visual input to behavioral output. Our model aligns closely with human behavior and reflects neural activities in primates. A neuroimaging-informed fine-tuning approach was introduced and applied to the model, leading to performance improvements.
  arXiv  Detail & Related papers  (2024-09-04T02:38:52Z)
• WaLiN-GUI: a graphical and auditory tool for neuron-based encoding [73.88751967207419]
  Neuromorphic computing relies on spike-based, energy-efficient communication. We develop a tool to identify suitable configurations for neuron-based encoding of sample-based data into spike trains. The WaLiN-GUI is provided open source and with documentation.
  arXiv  Detail & Related papers  (2023-10-25T20:34:08Z)
• The Expressive Leaky Memory Neuron: an Efficient and Expressive Phenomenological Neuron Model Can Solve Long-Horizon Tasks [64.08042492426992]
  We introduce the Expressive Memory (ELM) neuron model, a biologically inspired model of a cortical neuron. Our ELM neuron can accurately match the aforementioned input-output relationship with under ten thousand trainable parameters. We evaluate it on various tasks with demanding temporal structures, including the Long Range Arena (LRA) datasets.
  arXiv  Detail & Related papers  (2023-06-14T13:34:13Z)
• EINNs: Epidemiologically-Informed Neural Networks [75.34199997857341]
  We introduce a new class of physics-informed neural networks-EINN-crafted for epidemic forecasting. We investigate how to leverage both the theoretical flexibility provided by mechanistic models as well as the data-driven expressability afforded by AI models.
  arXiv  Detail & Related papers  (2022-02-21T18:59:03Z)
• Overcoming the Domain Gap in Contrastive Learning of Neural Action Representations [60.47807856873544]
  A fundamental goal in neuroscience is to understand the relationship between neural activity and behavior. We generated a new multimodal dataset consisting of the spontaneous behaviors generated by fruit flies. This dataset and our new set of augmentations promise to accelerate the application of self-supervised learning methods in neuroscience.
  arXiv  Detail & Related papers  (2021-11-29T15:27:51Z)
• Neuronal Learning Analysis using Cycle-Consistent Adversarial Networks [4.874780144224057]
  We use a variant of deep generative models called - CycleGAN, to learn the unknown mapping between pre- and post-learning neural activities. We develop an end-to-end pipeline to preprocess, train and evaluate calcium fluorescence signals, and a procedure to interpret the resulting deep learning models.
  arXiv  Detail & Related papers  (2021-11-25T13:24:19Z)
• Dynamic Neural Diversification: Path to Computationally Sustainable Neural Networks [68.8204255655161]
  Small neural networks with a constrained number of trainable parameters, can be suitable resource-efficient candidates for many simple tasks. We explore the diversity of the neurons within the hidden layer during the learning process. We analyze how the diversity of the neurons affects predictions of the model.
  arXiv  Detail & Related papers  (2021-09-20T15:12:16Z)
• The Neural Coding Framework for Learning Generative Models [91.0357317238509]
  We propose a novel neural generative model inspired by the theory of predictive processing in the brain. In a similar way, artificial neurons in our generative model predict what neighboring neurons will do, and adjust their parameters based on how well the predictions matched reality.
  arXiv  Detail & Related papers  (2020-12-07T01:20:38Z)
• Learning identifiable and interpretable latent models of high-dimensional neural activity using pi-VAE [10.529943544385585]
  We propose a method that integrates key ingredients from latent models and traditional neural encoding models. Our method, pi-VAE, is inspired by recent progress on identifiable variational auto-encoder. We validate pi-VAE using synthetic data, and apply it to analyze neurophysiological datasets from rat hippocampus and macaque motor cortex.
  arXiv  Detail & Related papers  (2020-11-09T22:00:38Z)

This list is automatically generated from the titles and abstracts of the papers in this site.

This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.