Nonlocal operator learning for fMRI encoding and decoding tasks
Authors: Andreas Kramer, Saugat Acharya, Alice Giola, Emanuele Zappala
Organizations: Department of Computer Science, Idaho State University 921 S. 8th Ave Mail Stop 8060, Pocatello, ID 83209-8023 · Department of Mathematics and Statistics, Idaho State University Physical Science Complex, 921 S. 8th Ave., Stop 8085, Pocatello, ID 83209
Abstract
Functional MRI data exhibit high-dimensional spatiotemporal structure, making both prediction and decoding challenging. In this work, we investigate neural integral-operator-based models for encoding and decoding tasks in fMRI, with particular emphasis on the role of nonlocal spatiotemporal context. We implement a latent neural integral operator framework that performs fixed point iterations in an auxiliary space from which classification and stimuli prediction is performed via a decoder. We evaluate our model on two open-source fMRI datasets. Our experiments examine both decoding of stimuli from fMRI recordings and encoding of fMRI dynamics from stimulus representations. A main focus is the effect of spatiotemporal context: we systematically compare short and long temporal windows, as well as the use of visual cortex vs whole brain recordings, and analyze their influence on performance and latent-space geometry. Across tasks and datasets, larger temporal windows generally improve results and produce more structured learned representations. In decoding experiments, the learned latent space often provides clearer class separation than the raw data. In encoding experiments, although absolute performance remains moderate due to the difficulty of the task, longer temporal windows still yield consistent gains. These findings suggest that neural integral operators provide a promising framework for modeling fMRI dynamics and that broader spatiotemporal context can be beneficial for both prediction and representation learning. More broadly, the results indicate that exploiting distributed nonlocal structure in brain dynamics requires model architectures specifically designed to capture such dependencies.
Accelerated acquisition of fMRI enables enhanced detection of neurovascular (BOLD) activity in the brain, but image reconstruction becomes challenging with high k-space undersampling: Task-evoked BOLD signals are small in magnitude, which traditional anatomical MRI reconstruction methods fail to recover, as they favor spatial accuracy over temporal fidelity. We present DD-INR, a Dynamics-Driven Implicit Neural Representation framework tailored for accelerated fMRI that benefits from incoherent time-varying sampling and a tailored spatiotemporal prior, outperforming traditional methods, demonstrated in simulation and in-vivo acquisition, both in terms of image quality and retrieval of activation patterns. DD-INR achieves this by splitting the fMRI data into a static background and a temporally varying dynamic component, representing only the dynamics with a dedicated INR, thereby focusing the model's capacity on activation-relevant changes while remaining compact. In general, DD-INR provides a promising framework for accelerated fMRI reconstruction, with the potential to improve the sensitivity and robustness of fMRI studies within practical scan time limits. The source code is available at https://github.com/JoosenLi/DD-INR.
Learning meaningful latent representations from nonlinear fMRI data remains a fundamental challenge in neuroimaging analysis. Traditional independent component analysis, widely used due to its ability to estimate interpretable functional brain networks, relies on a linear mixing assumption for latent sources, limiting its ability to capture the inherently nonlinear and complex organization of brain dynamics. More recently, deep representation learning methods have emerged as promising alternatives for modeling nonlinear latent structure. However, many of these approaches have been evaluated primarily on simulated datasets or natural image benchmarks, with comparatively limited validation on real-world neuroimaging data such as fMRI. In this work, we are motivated by the β-TCVAE (Total Correlation Variational Autoencoder), a refinement of the β-VAE framework for learning latent representations without introducing additional hyperparameters during training. We adapt and modify this model to fMRI data for nonlinear source disentanglement, aiming to separate mixed spatial and temporal brain signals into interpretable components. We show that the β-TCVAE framework can recover meaningful nonlinear spatial components with biological relevance, including well-established intrinsic connectivity networks such as the default mode network. Furthermore, we evaluate the learned representations using functional network connectivity, showing that the latent structure captures coherent and interpretable brain organization patterns. This study provides a pilot investigation that bridges nonlinear representation learning and fMRI analysis.
Neuroscientists have recently turned to intracranial brain recording methods, like electrocorticography (ECoG), for human experiments because of the fine spatial and temporal resolution that they afford. Models trained on this data, however, are fundamentally restricted by the patient populations that can receive the implants necessary for recording. We propose using non-invasive fMRI to bridge the gap in training data. Using spoken language representations fine-tuned on fMRI, we build encoding models of ECoG. These representations showed improved prediction performance in ECoG, even though the temporal resolution of fMRI is two orders of magnitude worse. Prediction improved in frequency bands well beyond what is directly measured in fMRI. Next, to test the procedure's generalization ability, we fine-tuned models on fMRI responses that were temporally downsampled by a factor of 2. Despite the loss in resolution, these models were able to predict fMRI and ECoG responses at levels comparable to the original fMRI-tuned models. Finally, we showed that ECoG performance steadily scales with the amount of fMRI-tuning data. Our results show that "slow" data like fMRI can be a valuable resource for building better models of "fast" brain data like ECoG. In the future, integrating across multiple recording methods may further improve performance in other applications, like decoding.
Aditya R. Vaidya, Richard J. Antonello, Alexander G. Huth