Task-specific feature extraction and classification of fMRI volumes using a deep neural network initialized with a deep belief network: Evaluation using sensorimotor tasks

Data-driven models in human neuroscience and neuroengineering

Discoveries in modern human neuroscience are increasingly driven by quantitative understanding of complex data. Data-intensive approaches to modeling have promise to dramatically advance our understanding of the brain and critically enable neuroengineering capabilities. In this review, we provide an accessible primer to modern modeling approaches and highlight recent data-driven discoveries in the domains of neuroimaging, single-neuron and neuronal population responses, and device neuroengineering. Further, we suggest that meaningful progress requires the community to tackle open challenges in the realms of model interpretability and generalizability, training pipelines of data-fluent human neuroscientists, and integrated consideration of data ethics.

Classifying early and late mild cognitive impairment stages of Alzheimer's disease by fusing default mode networks extracted with multiple seeds

BACKGROUND

The default mode network (DMN) in resting state has been increasingly used in disease diagnosis since it was found in 2001. Prior work has mainly focused on extracting a single DMN with various techniques. However, by using seeding-based analysis with more than one desirable seed, we can obtain multiple DMNs, which are likely to have complementary information, and thus are more promising for disease diagnosis. In the study, we used 18 early mild cognitive impairment (EMCI) participants and 18 late mild cognitive impairment (LMCI) participants of Alzheimer's disease (AD). First, we used seeding-based analysis with four seeds to extract four DMNs for each subject. Then, we conducted fusion analysis for all different combinations of the four DMNs. Finally, we carried out nonlinear support vector machine classification based on the mixing coefficients from the fusion analysis.

RESULTS

We found that (1) the four DMNs corresponding to the four different seeds indeed capture different functional regions of each subject; (2) Maps of the four DMNs in the most different joint source from fusion analysis are centered at the regions of the corresponding seeds; (3) Classification results reveal the effectiveness of using multiple seeds to extract DMNs. When using a single seed, the regions of posterior cingulate cortex (PCC) extractions of EMCI and LMCI show the largest difference. For multiple-seed cases, the regions of PCC extraction and right lateral parietal cortex (RLP) extraction provide complementary information for each other in fusion, which improves the classification accuracy. Furthermore, the regions of left lateral parietal cortex (LLP) extraction and RLP extraction also have complementary effect in fusion. In summary, AD diagnosis can be improved by exploiting complementary information of DMNs extracted with multiple seeds.

CONCLUSIONS

In this study, we applied fusion analysis to the DMNs extracted by using different seeds for exploiting the complementary information hidden among the separately extracted DMNs, and the results supported our expectation that using the complementary information can improve classification accuracy.

Deep Belief Network for the Enhancement of Ultrasound Images with Pelvic Lesions

It is well known that ultrasound images are cost-efficient and exhibit hassle-free usage. However, very few works have focused on exploiting the ultrasound modality for lesion diagnosis. Moreover, there is no reliable contribution reported in the literature for diagnosing pelvic lesions from the pelvic portion of humans, especially females. While few contributions are found for diagnosis of lesions in the pelvic region, no effort has been made on enhancing the images. Inspired from the neural network (NN), our methodology adopts deep belief NN for enhancing the ultrasound image with pelvic lesions. The higher-order statistical characteristics of image textures, such as entropy and autocorrelation, are considered to enhance the image from its noisy environment. The alignment problem is considered using skewness. The proposed method is compared with the existing NN method to demonstrate its enhancement performance.

Deep neural network predicts emotional responses of the human brain from functional magnetic resonance imaging

An artificial neural network with multiple hidden layers (known as a deep neural network, or DNN) was employed as a predictive model (DNN_p) for the first time to predict emotional responses using whole-brain functional magnetic resonance imaging (fMRI) data from individual subjects. During fMRI data acquisition, 10 healthy participants listened to 80 International Affective Digital Sound stimuli and rated their own emotions generated by each sound stimulus in terms of the arousal, dominance, and valence dimensions. The whole-brain spatial patterns from a general linear model (i.e., beta-valued maps) for each sound stimulus and the emotional response ratings were used as the input and output for the DNN_P, respectively. Based on a nested five-fold cross-validation scheme, the paired input and output data were divided into training (three-fold), validation (one-fold), and test (one-fold) data. The DNN_P was trained and optimized using the training and validation data and was tested using the test data. The Pearson's correlation coefficients between the rated and predicted emotional responses from our DNN_P model with weight sparsity optimization (mean ± standard error 0.52 ± 0.02 for arousal, 0.51 ± 0.03 for dominance, and 0.51 ± 0.03 for valence, with an input denoising level of 0.3 and a mini-batch size of 1) were significantly greater than those of DNN models with conventional regularization schemes including elastic net regularization (0.15 ± 0.05, 0.15 ± 0.06, and 0.21 ± 0.04 for arousal, dominance, and valence, respectively), those of shallow models including logistic regression (0.11 ± 0.04, 0.10 ± 0.05, and 0.17 ± 0.04 for arousal, dominance, and valence, respectively; average of logistic regression and sparse logistic regression), and those of support vector machine-based predictive models (SVM_ps; 0.12 ± 0.06, 0.06 ± 0.06, and 0.10 ± 0.06 for arousal, dominance, and valence, respectively; average of linear and non-linear SVM_ps). This difference was confirmed to be significant with a Bonferroni-corrected p-value of less than 0.001 from a one-way analysis of variance (ANOVA) and subsequent paired t-test. The weights of the trained DNN_Ps were interpreted and input patterns that maximized or minimized the output of the DNN_Ps (i.e., the emotional responses) were estimated. Based on a binary classification of each emotion category (e.g., high arousal vs. low arousal), the error rates for the DNN_P (31.2% ± 1.3% for arousal, 29.0% ± 1.7% for dominance, and 28.6% ± 3.0% for valence) were significantly lower than those for the linear SVM_P (44.7% ± 2.0%, 50.7% ± 1.7%, and 47.4% ± 1.9% for arousal, dominance, and valence, respectively) and the non-linear SVM_P (48.8% ± 2.3%, 52.2% ± 1.9%, and 46.4% ± 1.3% for arousal, dominance, and valence, respectively), as confirmed by the Bonferroni-corrected p < 0.001 from the one-way ANOVA. Our study demonstrates that the DNN_p model is able to reveal neuronal circuitry associated with human emotional processing - including structures in the limbic and paralimbic areas, which include the amygdala, prefrontal areas, anterior cingulate cortex, insula, and caudate. Our DNN_p model was also able to use activation patterns in these structures to predict and classify emotional responses to stimuli.

Perspectives on Machine Learning for Classification of Schizotypy Using fMRI Data

Functional magnetic resonance imaging is capable of estimating functional activation and connectivity in the human brain, and lately there has been increased interest in the use of these functional modalities combined with machine learning for identification of psychiatric traits. While these methods bear great potential for early diagnosis and better understanding of disease processes, there are wide ranges of processing choices and pitfalls that may severely hamper interpretation and generalization performance unless carefully considered. In this perspective article, we aim to motivate the use of machine learning schizotypy research. To this end, we describe common data processing steps while commenting on best practices and procedures. First, we introduce the important role of schizotypy to motivate the importance of reliable classification, and summarize existing machine learning literature on schizotypy. Then, we describe procedures for extraction of features based on fMRI data, including statistical parametric mapping, parcellation, complex network analysis, and decomposition methods, as well as classification with a special focus on support vector classification and deep learning. We provide more detailed descriptions and software as supplementary material. Finally, we present current challenges in machine learning for classification of schizotypy and comment on future trends and perspectives.

Brain Decoding from Functional MRI Using Long Short-Term Memory Recurrent Neural Networks

Decoding brain functional states underlying different cognitive processes using multivariate pattern recognition techniques has attracted increasing interests in brain imaging studies. Promising performance has been achieved using brain functional connectivity or brain activation signatures for a variety of brain decoding tasks. However, most of existing studies have built decoding models upon features extracted from imaging data at individual time points or temporal windows with a fixed interval, which might not be optimal across different cognitive processes due to varying temporal durations and dependency of different cognitive processes. In this study, we develop a deep learning based framework for brain decoding by leveraging recent advances in sequence modeling using long short-term memory (LSTM) recurrent neural networks (RNNs). Particularly, functional profiles extracted from task functional imaging data based on their corresponding subject-specific intrinsic functional networks are used as features to build brain decoding models, and LSTM RNNs are adopted to learn decoding mappings between functional profiles and brain states. We evaluate the proposed method using task fMRI data from the HCP dataset, and experimental results have demonstrated that the proposed method could effectively distinguish brain states under different task events and obtain higher accuracy than conventional decoding models.

Classification and Prediction of Brain Disorders Using Functional Connectivity: Promising but Challenging

Brain functional imaging data, especially functional magnetic resonance imaging (fMRI) data, have been employed to reflect functional integration of the brain. Alteration in brain functional connectivity (FC) is expected to provide potential biomarkers for classifying or predicting brain disorders. In this paper, we present a comprehensive review in order to provide guidance about the available brain FC measures and typical classification strategies. We survey the state-of-the-art FC analysis methods including widely used static functional connectivity (SFC) and more recently proposed dynamic functional connectivity (DFC). Temporal correlations among regions of interest (ROIs), data-driven spatial network and functional network connectivity (FNC) are often computed to reflect SFC from different angles. SFC can be extended to DFC using a sliding-window framework, and intrinsic connectivity states along the time-varying connectivity patterns are typically extracted using clustering or decomposition approaches. We also briefly summarize window-less DFC approaches. Subsequently, we highlight various strategies for feature selection including the filter, wrapper and embedded methods. In terms of model building, we include traditional classifiers as well as more recently applied deep learning methods. Moreover, we review representative applications with remarkable classification accuracy for psychosis and mood disorders, neurodevelopmental disorder, and neurological disorders using fMRI data. Schizophrenia, bipolar disorder, autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), Alzheimer's disease and mild cognitive impairment (MCI) are discussed. Finally, challenges in the field are pointed out with respect to the inaccurate diagnosis labeling, the abundant number of possible features and the difficulty in validation. Some suggestions for future work are also provided.

Brain State Decoding Based on fMRI Using Semisupervised Sparse Representation Classifications

Multivariate classification techniques have been widely applied to decode brain states using functional magnetic resonance imaging (fMRI). Due to variabilities in fMRI data and the limitation of the collection of human fMRI data, it is not easy to train an efficient and robust supervised-learning classifier for fMRI data. Among various classification techniques, sparse representation classifier (SRC) exhibits a state-of-the-art classification performance in image classification. However, SRC has rarely been applied to fMRI-based decoding. This study aimed to improve SRC using unlabeled testing samples to allow it to be effectively applied to fMRI-based decoding. We proposed a semisupervised-learning SRC with an average coefficient (semiSRC-AVE) method that performed the classification using the average coefficient of each class instead of the reconstruction error and selectively updated the training dataset using new testing data with high confidence to improve the performance of SRC. Simulated and real fMRI experiments were performed to investigate the feasibility and robustness of semiSRC-AVE. The results of the simulated and real fMRI experiments showed that semiSRC-AVE significantly outperformed supervised learning SRC with an average coefficient (SRC-AVE) method and showed better performance than the other three semisupervised learning methods.

Latent source mining in FMRI via restricted Boltzmann machine

Blind source separation (BSS) is commonly used in functional magnetic resonance imaging (fMRI) data analysis. Recently, BSS models based on restricted Boltzmann machine (RBM), one of the building blocks of deep learning models, have been shown to improve brain network identification compared to conventional single matrix factorization models such as independent component analysis (ICA). These models, however, trained RBM on fMRI volumes, and are hence challenged by model complexity and limited training set. In this article, we propose to apply RBM to fMRI time courses instead of volumes for BSS. The proposed method not only interprets fMRI time courses explicitly to take advantages of deep learning models in latent feature learning but also substantially reduces model complexity and increases the scale of training set to improve training efficiency. Our experimental results based on Human Connectome Project (HCP) datasets demonstrated the superiority of the proposed method over ICA and the one that applied RBM to fMRI volumes in identifying task-related components, resulted in more accurate and specific representations of task-related activations. Moreover, our method separated out components representing intermixed effects between task events, which could reflect inherent interactions among functionally connected brain regions. Our study demonstrates the value of RBM in mining complex structures embedded in large-scale fMRI data and its potential as a building block for deeper models in fMRI data analysis.

Multivariate Pattern Classification of Facial Expressions Based on Large-Scale Functional Connectivity

It is an important question how human beings achieve efficient recognition of others’ facial expressions in cognitive neuroscience, and it has been identified that specific cortical regions show preferential activation to facial expressions in previous studies. However, the potential contributions of the connectivity patterns in the processing of facial expressions remained unclear. The present functional magnetic resonance imaging (fMRI) study explored whether facial expressions could be decoded from the functional connectivity (FC) patterns using multivariate pattern analysis combined with machine learning algorithms (fcMVPA). We employed a block design experiment and collected neural activities while participants viewed facial expressions of six basic emotions (anger, disgust, fear, joy, sadness, and surprise). Both static and dynamic expression stimuli were included in our study. A behavioral experiment after scanning confirmed the validity of the facial stimuli presented during the fMRI experiment with classification accuracies and emotional intensities. We obtained whole-brain FC patterns for each facial expression and found that both static and dynamic facial expressions could be successfully decoded from the FC patterns. Moreover, we identified the expression-discriminative networks for the static and dynamic facial expressions, which span beyond the conventional face-selective areas. Overall, these results reveal that large-scale FC patterns may also contain rich expression information to accurately decode facial expressions, suggesting a novel mechanism, which includes general interactions between distributed brain regions, and that contributes to the human facial expression recognition.

Resting State fMRI Functional Connectivity-Based Classification Using a Convolutional Neural Network Architecture

Machine learning techniques have become increasingly popular in the field of resting state fMRI (functional magnetic resonance imaging) network based classification. However, the application of convolutional networks has been proposed only very recently and has remained largely unexplored. In this paper we describe a convolutional neural network architecture for functional connectome classification called connectome-convolutional neural network (CCNN). Our results on simulated datasets and a publicly available dataset for amnestic mild cognitive impairment classification demonstrate that our CCNN model can efficiently distinguish between subject groups. We also show that the connectome-convolutional network is capable to combine information from diverse functional connectivity metrics and that models using a combination of different connectivity descriptors are able to outperform classifiers using only one metric. From this flexibility follows that our proposed CCNN model can be easily adapted to a wide range of connectome based classification or regression tasks, by varying which connectivity descriptor combinations are used to train the network.

Euler Elastica Regularized Logistic Regression for Whole-Brain Decoding of fMRI Data

OBJECTIVE

Multivariate pattern analysis methods have been widely applied to functional magnetic resonance imaging (fMRI) data to decode brain states. Due to the "high features, low samples" in fMRI data, machine learning methods have been widely regularized using various regularizations to avoid overfitting. Both total variation (TV) using the gradients of images and Euler's elastica (EE) using the gradient and the curvature of images are the two popular regulations with spatial structures. In contrast to TV, EE regulation is able to overcome the disadvantage of TV regulation that favored piecewise constant images over piecewise smooth images. In this study, we introduced EE to fMRI-based decoding for the first time and proposed the EE regularized multinomial logistic regression (EELR) algorithm for multi-class classification.

METHODS

We performed experimental tests on both simulated and real fMRI data to investigate the feasibility and robustness of EELR. The performance of EELR was compared with sparse logistic regression (SLR) and TV regularized LR (TVLR).

RESULTS

The results showed that EELR was more robustness to noises and showed significantly higher classification performance than TVLR and SLR. Moreover, the forward models and weights patterns revealed that EELR detected larger brain regions that were discriminative to each task and activated by each task than TVLR.

CONCLUSION

The results suggest that EELR not only performs well in brain decoding but also reveals meaningful discriminative and activation patterns.

SIGNIFICANCE

This study demonstrated that EELR showed promising potential in brain decoding and discriminative/activation pattern detection.

Inference in the age of big data: Future perspectives on neuroscience

Neuroscience is undergoing faster changes than ever before. Over 100 years our field qualitatively described and invasively manipulated single or few organisms to gain anatomical, physiological, and pharmacological insights. In the last 10 years neuroscience spawned quantitative datasets of unprecedented breadth (e.g., microanatomy, synaptic connections, and optogenetic brain-behavior assays) and size (e.g., cognition, brain imaging, and genetics). While growing data availability and information granularity have been amply discussed, we direct attention to a less explored question: How will the unprecedented data richness shape data analysis practices? Statistical reasoning is becoming more important to distill neurobiological knowledge from healthy and pathological brain measurements. We argue that large-scale data analysis will use more statistical models that are non-parametric, generative, and mixing frequentist and Bayesian aspects, while supplementing classical hypothesis testing with out-of-sample predictions.