As a technology to read brain states from measurable brain activities, brain decoding are widely applied in industries and medical sciences. In spite of high demands in these applications for a universal decoder that can be applied to all individuals simultaneously, large variation in brain activities across individuals has limited the scope of many studies to the development of individual-specific decoders. In this study, we used deep neural network (DNN), a nonlinear hierarchical model, to construct a subject-transfer decoder. Our decoder is the first successful DNN-based subject-transfer decoder. When applied to a large-scale functional magnetic resonance imaging (fMRI) database, our DNN-based decoder achieved higher decoding accuracy than other baseline methods, including support vector machine (SVM). In order to analyze the knowledge acquired by this decoder, we applied principal sensitivity analysis (PSA) to the decoder and visualized the discriminative features that are common to all subjects in the dataset. Our PSA successfully visualized the subject-independent features contributing to the subject-transferability of the trained decoder.
Brain decoding involves the determination of a subject's cognitive state or an associated stimulus from functional neuroimaging data measuring brain activity. In this setting the cognitive state is typically characterized by an element of a finite set, and the neuroimaging data comprise voluminous amounts of spatiotemporal data measuring some aspect of the neural signal. The associated statistical problem is one of classification from high-dimensional data. We explore the use of functional principal component analysis, mutual information networks, and persistent homology for examining the data through exploratory analysis and for constructing features characterizing the neural signal for brain decoding. We review each approach from this perspective, and we incorporate the features into a classifier based on symmetric multinomial logistic regression with elastic net regularization. The approaches are illustrated in an application where the task is to infer, from brain activity measured with magnetoencephalography (MEG), the type of video stimulus shown to a subject.
The total variation (TV) penalty, as many other analysis-sparsity problems, does not lead to separable factors or a proximal operatorwith a closed-form expression, such as soft thresholding for the $\ell\_1$ penalty. As a result, in a variational formulation of an inverse problem or statisticallearning estimation, it leads to challenging non-smooth optimization problemsthat are often solved with elaborate single-step first-order methods. When thedata-fit term arises from empirical measurements, as in brain imaging, it isoften very ill-conditioned and without simple structure. In this situation, in proximal splitting methods, the computation cost of thegradient step can easily dominate each iteration. Thus it is beneficialto minimize the number of gradient steps.We present fAASTA, a variant of FISTA, that relies on an internal solver forthe TV proximal operator, and refines its tolerance to balance computationalcost of the gradient and the proximal steps. We give benchmarks andillustrations on "brain decoding": recovering brain maps from noisymeasurements to predict observed behavior. The algorithm as well as theempirical study of convergence speed are valuable for any non-exact proximaloperator, in particular analysis-sparsity problems.
We represent the sequence of fMRI (Functional Magnetic Resonance Imaging) brain volumes recorded during a cognitive stimulus by a graph which consists of a set of local meshes. The corresponding cognitive process, encoded in the brain, is then represented by these meshes each of which is estimated assuming a linear relationship among the voxel time series in a predefined locality. First, we define the concept of locality in two neighborhood systems, namely, the spatial and functional neighborhoods. Then, we construct spatially and functionally local meshes around each voxel, called seed voxel, by connecting it either to its spatial or functional p-nearest neighbors. The mesh formed around a voxel is a directed sub-graph with a star topology, where the direction of the edges is taken towards the seed voxel at the center of the mesh. We represent the time series recorded at each seed voxel in terms of linear combination of the time series of its p-nearest neighbors in the mesh. The relationships between a seed voxel and its neighbors are represented by the edge weights of each mesh, and are estimated by solving a linear regression equation. The estimated mesh edge weights lead to a better representation of information in the brain for encoding and decoding of the cognitive tasks. We test our model on a visual object recognition and emotional memory retrieval experiments using Support Vector Machines that are trained using the mesh edge weights as features. In the experimental analysis, we observe that the edge weights of the spatial and functional meshes perform better than the state-of-the-art brain decoding models.
Brain decoding is a popular multivariate approach for hypothesis testing in neuroimaging. It is well known that the brain maps derived from weights of linear classifiers are hard to interpret because of high correlations between predictors, low signal to noise ratios, and the high dimensionality of neuroimaging data. Therefore, improving the interpretability of brain decoding approaches is of primary interest in many neuroimaging studies. Despite extensive studies of this type, at present, there is no formal definition for interpretability of multivariate brain maps. As a consequence, there is no quantitative measure for evaluating the interpretability of different brain decoding methods. In this paper, first, we present a theoretical definition of interpretability in brain decoding; we show that the interpretability of multivariate brain maps can be decomposed into their reproducibility and representativeness. Second, as an application of the proposed theoretical definition, we formalize a heuristic method for approximating the interpretability of multivariate brain maps in a binary magnetoencephalography (MEG) decoding scenario. Third, we propose to combine the approximated interpretability and the performance of the brain decoding model into a new multi-objective criterion for model selection. Our results for the MEG data show that optimizing the hyper-parameters of the regularized linear classifier based on the proposed criterion results in more informative multivariate brain maps. More importantly, the presented definition provides the theoretical background for quantitative evaluation of interpretability, and hence, facilitates the development of more effective brain decoding algorithms in the future.
Spatially-sparse predictors are good models for brain decoding: they give accurate predictions and their weight maps are interpretable as they focus on a small number of regions. However, the state of the art, based on total variation or graph-net, is computationally costly. Here we introduce sparsity in the local neighborhood of each voxel with social-sparsity, a structured shrinkage operator. We find that, on brain imaging classification problems, social-sparsity performs almost as well as total-variation models and better than graph-net, for a fraction of the computational cost. It also very clearly outlines predictive regions. We give details of the model and the algorithm.
Improving the interpretability of brain decoding approaches is of primary interest in many neuroimaging studies. Despite extensive studies of this type, at present, there is no formal definition for interpretability of brain decoding models. As a consequence, there is no quantitative measure for evaluating the interpretability of different brain decoding methods. In this paper, we present a simple definition for interpretability of linear brain decoding models. Then, we propose to combine the interpretability and the performance of the brain decoding into a new multi-objective criterion for model selection. Our preliminary results on the toy data show that optimizing the hyper-parameters of the regularized linear classifier based on the proposed criterion results in more informative linear models. The presented definition provides the theoretical background for quantitative evaluation of interpretability in linear brain decoding.
The study of neurocognitive tasks requiring accurate localisation of activity often rely on functional Magnetic Resonance Imaging, a widely adopted technique that makes use of a pipeline of data processing modules, each involving a variety of parameters. These parameters are frequently set according to the local goal of each specific module, not accounting for the rest of the pipeline. Given recent success of neural network research in many different domains, we propose to convert the whole data pipeline into a deep neural network, where the parameters involved are jointly optimised by the network to best serve a common global goal. As a proof of concept, we develop a module able to adaptively apply the most suitable spatial smoothing to every brain volume for each specific neuroimaging task, and we validate its results in a standard brain decoding experiment.
We propose a new framework, called Hierarchical Multi-resolution Mesh Networks (HMMNs), which establishes a set of brain networks at multiple time resolutions of fMRI signal to represent the underlying cognitive process. The suggested framework, first, decomposes the fMRI signal into various frequency subbands using wavelet transforms. Then, a brain network, called mesh network, is formed at each subband by ensembling a set of local meshes. The locality around each anatomic region is defined with respect to a neighborhood system based on functional connectivity. The arc weights of a mesh are estimated by ridge regression formed among the average region time series. In the final step, the adjacency matrices of mesh networks obtained at different subbands are ensembled for brain decoding under a hierarchical learning architecture, called, fuzzy stacked generalization (FSG). Our results on Human Connectome Project task-fMRI dataset reflect that the suggested HMMN model can successfully discriminate tasks by extracting complementary information obtained from mesh arc weights of multiple subbands. We study the topological properties of the mesh networks at different resolutions using the network measures, namely, node degree, node strength, betweenness centrality and global efficiency; and investigate the connectivity of anatomic regions, during a cognitive task. We observe significant variations among the network topologies obtained for different subbands. We, also, analyze the diversity properties of classifier ensemble, trained by the mesh networks in multiple subbands and observe that the classifiers in the ensemble collaborate with each other to fuse the complementary information freed at each subband. We conclude that the fMRI data, recorded during a cognitive task, embed diverse information across the anatomic regions at each resolution.
Despite the rapid advances in Brain-computer Interfacing (BCI) and continuous effort to improve the accuracy of brain decoding systems, the urge for the systems to reconstruct the experiences of the users has been widely acknowledged. This urge has been investigated by some researchers during the past years in terms of reconstruction of the naturalistic images, abstract images, video and audio. In this study, we try to tackle this issue by regressing the stimuli spectrogram using the spectrogram analysis of the brain signals. The results of our regression-based method suggest the feasibility of such reconstructions using the neuroimaging techniques that are appropriate for out-of-lab scenarios.
Brain decoding is a hot spot in cognitive science, which focuses on reconstructing perceptual images from brain activities. Analyzing the correlations of collected data from human brain activities and representing activity patterns are two problems in brain decoding based on functional magnetic resonance imaging (fMRI) signals. However, existing correlation analysis methods mainly focus on the strength information of voxel, which reveals functional connectivity in the cerebral cortex. They tend to neglect the structural information that implies the intracortical or intrinsic connections; that is, structural connectivity. Hence, the effective connectivity inferred by these methods is relatively unilateral. Therefore, we proposed a correlation network (CorrNet) framework that could be flexibly combined with diverse pattern representation models. In the CorrNet framework, the topological correlation was introduced to reveal structural information. Rich correlations were obtained, which contributed to specifying the underlying effective connectivity. We also combined the CorrNet framework with a linear support vector machine (SVM) and a dynamic evolving spike neuron network (SNN) for pattern representation separately, thus providing a novel method for decoding cognitive activity patterns. Experimental results verified the reliability and robustness of our CorrNet framework and demonstrated that the new method achieved significant improvement in brain decoding over comparable methods.
Language decoding studies have identified word representations which can be used to predict brain activity in response to novel words and sentences (Anderson et al., 2016; Pereira et al., 2018). The unspoken assumption of these studies is that, during processing, linguistic information is transformed into some shared semantic space, and those semantic representations are then used for a variety of linguistic and non-linguistic tasks. We claim that current studies vastly underdetermine the content of these representations, the algorithms which the brain deploys to produce and consume them, and the computational tasks which they are designed to solve. We illustrate this indeterminacy with an extension of the sentence-decoding experiment of Pereira et al. (2018), showing how standard evaluations fail to distinguish between language processing models which deploy different mechanisms and which are optimized to solve very different tasks. We conclude by suggesting changes to the brain decoding paradigm which can support stronger claims of neural representation.
Simultaneous modeling of the spatio-temporal variation patterns of brain functional network from 4D fMRI data has been an important yet challenging problem for the field of cognitive neuroscience and medical image analysis. Inspired by the recent success in applying deep learning for functional brain decoding and encoding, in this work we propose a spatio-temporal convolutional neural network (ST-CNN)to jointly learn the spatial and temporal patterns of targeted network from the training data and perform automatic, pin-pointing functional network identification. The proposed ST-CNN is evaluated by the task of identifying the Default Mode Network (DMN) from fMRI data. Results show that while the framework is only trained on one fMRI dataset,it has the sufficient generalizability to identify the DMN from different populations of data as well as different cognitive tasks. Further investigation into the results show that the superior performance of ST-CNN is driven by the jointly-learning scheme, which capture the intrinsic relationship between the spatial and temporal characteristic of DMN and ensures the accurate identification.