Unlink previous methods, DHA is not limited by a restricted fixed kernel function.

This paper proposes Deep Hyperalignment (DHA) as a regularized, deep extension, scalable Hyperalignment (HA) method, which is well-suited for applying functional alignment to fMRI datasets with nonlinearity, high-dimensionality (broad ROI), and a large number of subjects. Unlink previous methods, DHA is not limited by a restricted fixed kernel function. Further, it uses a parametric approach, rank-m Singular Value Decomposition (SVD), and stochastic gradient descent for optimization. Therefore, DHA has a suitable time complexity for large datasets, and DHA does not require the training data when it computes the functional alignment for a new subject. Experimental studies on multi-subject fMRI analysis confirm that the DHA method achieves superior performance to other state-of-the-art HA algorithms.

In this work we introduce a self-supervised pretraining framework for transformers on functional Magnetic Resonance Imaging (fMRI) data. First, we pretrain our architecture on two self-supervised tasks simultaneously to teach the model a general understanding of the temporal and spatial dynamics of human auditory cortex during music listening. Our pretraining results are the first to suggest a synergistic effect of multitask training on fMRI data. Second, we finetune the pretrained models and train additional fresh models on a supervised fMRI classification task. We observe significantly improved accuracy on held-out runs with the finetuned models, which demonstrates the ability of our pretraining tasks to facilitate transfer learning. This work contributes to the growing body of literature on transformer architectures for pretraining and transfer learning with fMRI data, and serves as a proof of concept for our pretraining tasks and multitask pretraining on fMRI data.

Neuroimaging datasets often have a very large number of voxels and a very small number of training cases, which means that overfitting of models for this data can become a very serious problem. Working with a set of fMRI images from a study on stroke recovery, we consider a classification task for which logistic regression performs poorly, even when L1- or L2- regularized. We show that much better discrimination can be achieved by fitting a generative model to each separate condition and then seeing which model is most likely to have generated the data. We compare discriminative training of exactly the same set of models, and we also consider convex blends of generative and discriminative training.

The goal of emotional brain state classification on functional MRI (fMRI) data is to recognize brain activity patterns related to specific emotion tasks performed by subjects during an experiment. Distinguishing emotional brain states from other brain states using fMRI data has proven to be challenging due to two factors: a difficulty to generate fast yet accurate predictions in short time frames, and a difficulty to extract emotion features which generalize to unseen subjects. To address these challenges, we conducted an experiment in which 22 subjects viewed pictures designed to stimulate either negative, neutral or rest emotional responses while their brain activity was measured using fMRI. We then developed two distinct Convolution-based approaches to decode emotional brain states using only spatial information from single, minimally pre-processed (slice timing and realignment) fMRI volumes. In our first approach, we trained a 1D Convolutional Network (84.9% accuracy; chance level 33%) to classify 3 emotion conditions using One-way Analysis of Variance (ANOVA) voxel selection combined with hyperalignment. In our second approach, we trained a 3D ResNet-50 model (78.0% accuracy; chance level 50%) to classify 2 emotion conditions from single 3D fMRI volumes directly. Our Convolutional and Residual classifiers successfully learned group-level emotion features and could decode emotion conditions from fMRI volumes in milliseconds. These approaches could potentially be used in brain computer interfaces and real-time fMRI neurofeedback research.

Tensor, a multi-dimensional data structure, has been exploited recently in the machine learning community. Traditional machine learning approaches are vector- or matrix-based, and cannot handle tensorial data directly. In this paper, we propose a tensor train (TT)-based kernel technique for the first time, and apply it to the conventional support vector machine (SVM) for image classification. Specifically, we propose a kernelized support tensor train machine that accepts tensorial input and preserves the intrinsic kernel property. The main contributions are threefold. First, we propose a TT-based feature mapping procedure that maintains the TT structure in the feature space. Second, we demonstrate two ways to construct the TT-based kernel function while considering consistency with the TT inner product and preservation of information. Third, we show that it is possible to apply different kernel functions on different data modes. In principle, our method tensorizes the standard SVM on its input structure and kernel mapping scheme. Extensive experiments are performed on real-world tensor data, which demonstrates the superiority of the proposed scheme under few-sample high-dimensional inputs.

The application of deep learning to build accurate predictive models from functional neuroimaging data is often hindered by limited dataset sizes. Though data augmentation can help mitigate such training obstacles, most data augmentation methods have been developed for natural images as in computer vision tasks such as CIF AR, not for medical images. This work helps to fills in this gap by proposing a method for generating new functional Magnetic Resonance Images (fMRI) with realistic brain morphology. This method is tested on a challenging task of predicting antidepressant treatment response from pre-treatment task-based fMRI and demonstrates a 26% improvement in performance in predicting response using augmented images. This improvement compares favorably to state-of-the-art augmentation methods for natural images. Through an ablative test, augmentation is also shown to substantively improve performance when applied before hyperparameter optimization. These results suggest the optimal order of operations and support the role of data augmentation method for improving predictive performance in tasks using fMRI.

Understanding human fetal neurodevelopment is of great clinical importance as abnormal development is linked to adverse neuropsychiatric outcomes after birth. Recent advances in functional Magnetic Resonance Imaging (fMRI) have provided new insight into development of the human brain before birth, but these studies have predominately focused on brain functional connectivity (i.e. Fisher z-score), which requires manual processing steps for feature extraction from fMRI images. Deep learning approaches (i.e., Convolutional Neural Networks) have achieved remarkable success on learning directly from image data, yet have not been applied on fetal fMRI for understanding fetal neurodevelopment. Here, we bridge this gap by applying a novel application of deep 3D CNN to fetal blood oxygen-level dependence (BOLD) resting-state fMRI data. Specifically, we test a supervised CNN framework as a data-driven approach to isolate variation in fMRI signals that relate to younger v.s. older fetal age groups. Based on the learned CNN, we further perform sensitivity analysis to identify brain regions in which changes in BOLD signal are strongly associated with fetal brain age. The findings demonstrate that deep CNNs are a promising approach for identifying spontaneous functional patterns in fetal brain activity that discriminate age groups. Further, we discovered that regions that most strongly differentiate groups are largely bilateral, share similar distribution in older and younger age groups, and are areas of heightened metabolic activity in early human development.

This paper proposes Deep Hyperalignment (DHA) as a regularized, deep extension, scalable Hyperalignment (HA) method, which is well-suited for applying functional alignment to fMRI datasets with nonlinearity, high-dimensionality (broad ROI), and a large number of subjects. Unlink previous methods, DHA is not limited by a restricted fixed kernel function. Further, it uses a parametric approach, rank-m Singular Value Decomposition (SVD), and stochastic gradient descent for optimization. Therefore, DHA has a suitable time complexity for large datasets, and DHA does not require the training data when it computes the functional alignment for a new subject. Experimental studies on multi-subject fMRI analysis confirm that the DHA method achieves superior performance to other state-of-the-art HA algorithms.

Accurate diagnosis of psychiatric disorders plays a critical role in improving quality of life for patients and potentially supports the development of new treatments. Many studies have been conducted on machine learning techniques that seek brain imaging data for specific biomarkers of disorders. These studies have encountered the following dilemma: An end-to-end classification overfits to a small number of high-dimensional samples but unsupervised feature-extraction has the risk of extracting a signal of no interest. In addition, such studies often provided only diagnoses for patients without presenting the reasons for these diagnoses. This study proposed a deep neural generative model of resting-state functional magnetic resonance imaging (fMRI) data. The proposed model is conditioned by the assumption of the subject's state and estimates the posterior probability of the subject's state given the imaging data, using Bayes' rule. This study applied the proposed model to diagnose schizophrenia and bipolar disorders. Diagnosis accuracy was improved by a large margin over competitive approaches, namely a support vector machine, logistic regression, and multilayer perceptron with or without unsupervised feature-extractors in addition to a Gaussian mixture model. The proposed model visualizes brain regions largely related to the disorders, thus motivating further biological investigation.