Advances in computational cognitive neuroimaging research are related to the availability of large amounts of labeled brain imaging data, but such data are scarce and expensive to generate. While powerful data generation mechanisms, such as Generative Adversarial Networks (GANs), have been designed in the last decade for computer vision, such improvements have not yet carried over to brain imaging. A likely reason is that GANs training is ill-suited to the noisy, high-dimensional and small-sample data available in functional neuroimaging. In this paper, we introduce Conditional Independent Components Analysis (Conditional ICA): a fast functional Magnetic Resonance Imaging (fMRI) data augmentation technique, that leverages abundant resting-state data to create images by sampling from an ICA decomposition. We then propose a mechanism to condition the generator on classes observed with few samples. We first show that the generative mechanism is successful at synthesizing data indistinguishable from observations, and that it yields gains in classification accuracy in brain decoding problems. In particular it outperforms GANs while being much easier to optimize and interpret. Lastly, Conditional ICA enhances classification accuracy in eight datasets without further parameters tuning.
In the past few years, significant advancements were made in reconstruction of observed natural images from fMRI brain recordings using deep-learning tools. Here, for the first time, we show that dense 3D depth maps of observed 2D natural images can also be recovered directly from fMRI brain recordings. We use an off-the-shelf method to estimate the unknown depth maps of natural images. This is applied to both: (i) the small number of images presented to subjects in an fMRI scanner (images for which we have fMRI recordings - referred to as "paired" data), and (ii) a very large number of natural images with no fMRI recordings ("unpaired data"). The estimated depth maps are then used as an auxiliary reconstruction criterion to train for depth reconstruction directly from fMRI. We propose two main approaches: Depth-only recovery and joint image-depth RGBD recovery. Because the number of available "paired" training data (images with fMRI) is small, we enrich the training data via self-supervised cycle-consistent training on many "unpaired" data (natural images & depth maps without fMRI). This is achieved using our newly defined and trained Depth-based Perceptual Similarity metric as a reconstruction criterion. We show that predicting the depth map directly from fMRI outperforms its indirect sequential recovery from the reconstructed images. We further show that activations from early cortical visual areas dominate our depth reconstruction results, and propose means to characterize fMRI voxels by their degree of depth-information tuning. This work adds an important layer of decoded information, extending the current envelope of visual brain decoding capabilities.
Addressing the question of visualising human mind could help us to find regions that are associated with observed cognition and responsible for expressing the elusive mental image, leading to a better understanding of cognitive function. The traditional approach treats brain decoding as a classification problem, reading the mind through statistical analysis of brain activity. However, human thought is rich and varied, that it is often influenced by more of a combination of object features than a specific type of category. For this reason, we propose an end-to-end brain decoding framework which translates brain activity into an image by latent space alignment. To find the correspondence from brain signal features to image features, we embedded them into two latent spaces with modality-specific encoders and then aligned the two spaces by minimising the distance between paired latent representations. The proposed framework was trained by simultaneous electroencephalogram and functional MRI data, which were recorded when the subjects were viewing or imagining a set of image stimuli. In this paper, we focused on implementing the fMRI experiment. Our experimental results demonstrated the feasibility of translating brain activity to an image. The reconstructed image matches image stimuli approximate in both shape and colour. Our framework provides a promising direction for building a direct visualisation to reveal human mind.
Dreaming is generally thought to be generated by spontaneous brain activity during sleep with patterns common to waking experience. This view is supported by a recent study demonstrating that dreamed objects can be predicted from brain activity during sleep using statistical decoders trained with stimulus-induced brain activity. However, it remains unclear whether and how visual image features associated with dreamed objects are represented in the brain. In this study, we used a deep neural network (DNN) model for object recognition as a proxy for hierarchical visual feature representation, and DNN features for dreamed objects were analyzed with brain decoding of fMRI data collected during dreaming. The decoders were first trained with stimulus-induced brain activity labeled with the feature values of the stimulus image from multiple DNN layers. The decoders were then used to decode DNN features from the dream fMRI data, and the decoded features were compared with the averaged features of each object category calculated from a large-scale image database. We found that the feature values decoded from the dream fMRI data positively correlated with those associated with dreamed object categories at mid- to high-level DNN layers. Using the decoded features, the dreamed object category could be identified at above-chance levels by matching them to the averaged features for candidate categories. The results suggest that dreaming recruits hierarchical visual feature representations associated with objects, which may support phenomenal aspects of dream experience.
Multivariate pattern analysis (MVPA) or brain decoding methods have become standard practice in analysing fMRI data. Although decoding methods have been extensively applied in Brain Computing Interfaces (BCI), these methods have only recently been applied to time-series neuroimaging data such as MEG and EEG to address experimental questions in Cognitive Neuroscience. In a tutorial-style review, we describe a broad set of options to inform future time-series decoding studies from a Cognitive Neuroscience perspective. Using example MEG data, we illustrate the effects that different options in the decoding analysis pipeline can have on experimental results where the aim is to 'decode' different perceptual stimuli or cognitive states over time from dynamic brain activation patterns. We show that decisions made at both preprocessing (e.g., dimensionality reduction, subsampling, trial averaging) and decoding (e.g., classifier selection, cross-validation design) stages of the analysis can significantly affect the results. In addition to standard decoding, we describe extensions to MVPA for time-varying neuroimaging data including representational similarity analysis, temporal generalisation, and the interpretation of classifier weight maps. Finally, we outline important caveats in the design and interpretation of time-series decoding experiments.
Contagion maps exploit activation times in threshold contagions to assign vectors in high-dimensional Euclidean space to the nodes of a network. A point cloud that is the image of a contagion map reflects both the structure underlying the network and the spreading behaviour of the contagion on it. Intuitively, such a point cloud exhibits features of the network's underlying structure if the contagion spreads along that structure, an observation which suggests contagion maps as a viable manifold-learning technique. We test contagion maps as a manifold-learning tool on a number of different real-world and synthetic data sets, and we compare their performance to that of Isomap, one of the most well-known manifold-learning algorithms. We find that, under certain conditions, contagion maps are able to reliably detect underlying manifold structure in noisy data, while Isomap fails due to noise-induced error. This consolidates contagion maps as a technique for manifold learning.
Multiclass classifiers are often designed and evaluated only on a sample from the classes on which they will eventually be applied. Hence, their final accuracy remains unknown. In this work we study how a classifier's performance over the initial class sample can be used to extrapolate its expected accuracy on a larger, unobserved set of classes. For this, we define a measure of separation between correct and incorrect classes that is independent of the number of classes: the "reversed ROC" (rROC), which is obtained by replacing the roles of classes and data-points in the common ROC. We show that the classification accuracy is a function of the rROC in multiclass classifiers, for which the learned representation of data from the initial class sample remains unchanged when new classes are added. Using these results we formulate a robust neural-network-based algorithm, "CleaneX", which learns to estimate the accuracy of such classifiers on arbitrarily large sets of classes. Unlike previous methods, our method uses both the observed accuracies of the classifier and densities of classification scores, and therefore achieves remarkably better predictions than current state-of-the-art methods on both simulations and real datasets of object detection, face recognition, and brain decoding.
Brain decoding, understood as the process of mapping brain activities to the stimuli that generated them, has been an active research area in the last years. In the case of language stimuli, recent studies have shown that it is possible to decode fMRI scans into an embedding of the word a subject is reading. However, such word embeddings are designed for natural language processing tasks rather than for brain decoding. Therefore, they limit our ability to recover the precise stimulus. In this work, we propose to directly classify an fMRI scan, mapping it to the corresponding word within a fixed vocabulary. Unlike existing work, we evaluate on scans from previously unseen subjects. We argue that this is a more realistic setup and we present a model that can decode fMRI data from unseen subjects. Our model achieves 5.22% Top-1 and 13.59% Top-5 accuracy in this challenging task, significantly outperforming all the considered competitive baselines. Furthermore, we use the decoded words to guide language generation with the GPT-2 model. This way, we advance the quest for a system that translates brain activities into coherent text.
Neuroimaging techniques have shown to be useful when studying the brain's activity. This paper uses Magnetoencephalography (MEG) data, provided by the Human Connectome Project (HCP), in combination with various deep artificial neural network models to perform brain decoding. More specifically, here we investigate to which extent can we infer the task performed by a subject based on its MEG data. Three models based on compact convolution, combined convolutional and long short-term architecture as well as a model based on multi-view learning that aims at fusing the outputs of the two stream networks are proposed and examined. These models exploit the spatio-temporal MEG data for learning new representations that are used to decode the relevant tasks across subjects. In order to realize the most relevant features of the input signals, two attention mechanisms, i.e. self and global attention, are incorporated in all the models. The experimental results of cross subject multi-class classification on the studied MEG dataset show that the inclusion of attention improves the generalization of the models across subjects.
What information from an act of sentence understanding is robustly represented in the human brain? We investigate this question by comparing sentence encoding models on a brain decoding task, where the sentence that an experimental participant has seen must be predicted from the fMRI signal evoked by the sentence. We take a pre-trained BERT architecture as a baseline sentence encoding model and fine-tune it on a variety of natural language understanding (NLU) tasks, asking which lead to improvements in brain-decoding performance. We find that none of the sentence encoding tasks tested yield significant increases in brain decoding performance. Through further task ablations and representational analyses, we find that tasks which produce syntax-light representations yield significant improvements in brain decoding performance. Our results constrain the space of NLU models that could best account for human neural representations of language, but also suggest limits on the possibility of decoding fine-grained syntactic information from fMRI human neuroimaging.
Neural encoding and decoding, which aim to characterize the relationship between stimuli and brain activities, have emerged as an important area in cognitive neuroscience. Traditional encoding models, which focus on feature extraction and mapping, consider the brain as an input-output mapper without inner states. In this work, inspired by the fact that human brain acts like a state machine, we proposed a novel encoding framework that combines information from both the external world and the inner state to predict brain activity. The framework comprises two parts: forward encoding model that deals with visual stimuli and inner state model that captures influence from intrinsic connections in the brain. The forward model can be any traditional encoding model, making the framework flexible. The inner state model is a linear model to utilize information in the prediction residuals of the forward model. The proposed encoding framework can achieve much better performance on natural image identification from fMRI response than forwardonly models. The identification accuracy will decrease slightly with the dataset size increasing, but remain relatively stable with different identification methods. The results confirm that the new encoding framework is effective and robust when used for brain decoding.
Brain imaging data are important in brain sciences yet expensive to obtain, with big volume (i.e., large p) but small sample size (i.e., small n). To tackle this problem, transfer learning is a promising direction that leverages source data to improve performance on related, target data. Most transfer learning methods focus on minimizing data distribution mismatch. However, a big challenge in brain imaging is the large domain discrepancies in cognitive experiment designs and subject-specific structures and functions. A recent transfer learning approach minimizes domain dependence to learn common features across domains, via the Hilbert-Schmidt Independence Criterion (HSIC). Inspired by this method, we propose a new Domain Independent Support Vector Machine (DI-SVM) for transfer learning in brain condition decoding. Specifically, DI-SVM simultaneously minimizes the SVM empirical risk and the dependence on domain information via a simplified HSIC. We use public data to construct 13 transfer learning tasks in brain decoding, including three interesting multi-source transfer tasks. Experiments show that DI-SVM's superior performance over eight competing methods on these tasks, particularly an improvement of more than 24% on multi-source transfer tasks.
Electroencephalography (EEG) is a complex signal and can require several years of training to be correctly interpreted. Recently, deep learning (DL) has shown great promise in helping make sense of EEG signals due to its capacity to learn good feature representations from raw data. Whether DL truly presents advantages as compared to more traditional EEG processing approaches, however, remains an open question. In this work, we review 156 papers that apply DL to EEG, published between January 2010 and July 2018, and spanning different application domains such as epilepsy, sleep, brain-computer interfacing, and cognitive and affective monitoring. We extract trends and highlight interesting approaches in order to inform future research and formulate recommendations. Various data items were extracted for each study pertaining to 1) the data, 2) the preprocessing methodology, 3) the DL design choices, 4) the results, and 5) the reproducibility of the experiments. Our analysis reveals that the amount of EEG data used across studies varies from less than ten minutes to thousands of hours. As for the model, 40% of the studies used convolutional neural networks (CNNs), while 14% used recurrent neural networks (RNNs), most often with a total of 3 to 10 layers. Moreover, almost one-half of the studies trained their models on raw or preprocessed EEG time series. Finally, the median gain in accuracy of DL approaches over traditional baselines was 5.4% across all relevant studies. More importantly, however, we noticed studies often suffer from poor reproducibility: a majority of papers would be hard or impossible to reproduce given the unavailability of their data and code. To help the field progress, we provide a list of recommendations for future studies and we make our summary table of DL and EEG papers available and invite the community to contribute.
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.
Cognitive brain imaging is accumulating datasets about the neural substrate of many different mental processes. Yet, most studies are based on few subjects and have low statistical power. Analyzing data across studies could bring more statistical power; yet the current brain-imaging analytic framework cannot be used at scale as it requires casting all cognitive tasks in a unified theoretical framework. We introduce a new methodology to analyze brain responses across tasks without a joint model of the psychological processes. The method boosts statistical power in small studies with specific cognitive focus by analyzing them jointly with large studies that probe less focal mental processes. Our approach improves decoding performance for 80% of 35 widely-different functional-imaging studies. It finds commonalities across tasks in a data-driven way, via common brain representations that predict mental processes. These are brain networks tuned to psychological manipulations. They outline interpretable and plausible brain structures. The extracted networks have been made available; they can be readily reused in new neuro-imaging studies. We provide a multi-study decoding tool to adapt to new data.
Multi-subject fMRI data analysis is an interesting and challenging problem in human brain decoding studies. The inherent anatomical and functional variability across subjects make it necessary to do both anatomical and functional alignment before classification analysis. Besides, when it comes to big data, time complexity becomes a problem that cannot be ignored. This paper proposes Gradient Hyperalignment (Gradient-HA) as a gradient-based functional alignment method that is suitable for multi-subject fMRI datasets with large amounts of samples and voxels. The advantage of Gradient-HA is that it can solve independence and high dimension problems by using Independent Component Analysis (ICA) and Stochastic Gradient Ascent (SGA). Validation using multi-classification tasks on big data demonstrates that Gradient-HA method has less time complexity and better or comparable performance compared with other state-of-the-art functional alignment methods.
We propose a statistical learning model for classifying cognitive processes based on distributed patterns of neural activation in the brain, acquired via functional magnetic resonance imaging (fMRI). In the proposed learning method, local meshes are formed around each voxel. The distance between voxels in the mesh is determined by using a functional neighbourhood concept. In order to define the functional neighbourhood, the similarities between the time series recorded for voxels are measured and functional connectivity matrices are constructed. Then, the local mesh for each voxel is formed by including the functionally closest neighbouring voxels in the mesh. The relationship between the voxels within a mesh is estimated by using a linear regression model. These relationship vectors, called Functional Connectivity aware Local Relational Features (FC-LRF) are then used to train a statistical learning machine. The proposed method was tested on a recognition memory experiment, including data pertaining to encoding and retrieval of words belonging to ten different semantic categories. Two popular classifiers, namely k-nearest neighbour (k-nn) and Support Vector Machine (SVM), are trained in order to predict the semantic category of the item being retrieved, based on activation patterns during encoding. The classification performance of the Functional Mesh Learning model, which range in 62%-71% is superior to the classical multi-voxel pattern analysis (MVPA) methods, which range in 40%-48%, for ten semantic categories.
This work investigates the use of mixed-norm regularization for sensor selection in Event-Related Potential (ERP) based Brain-Computer Interfaces (BCI). The classification problem is cast as a discriminative optimization framework where sensor selection is induced through the use of mixed-norms. This framework is extended to the multi-task learning situation where several similar classification tasks related to different subjects are learned simultaneously. In this case, multi-task learning helps in leveraging data scarcity issue yielding to more robust classifiers. For this purpose, we have introduced a regularizer that induces both sensor selection and classifier similarities. The different regularization approaches are compared on three ERP datasets showing the interest of mixed-norm regularization in terms of sensor selection. The multi-task approaches are evaluated when a small number of learning examples are available yielding to significant performance improvements especially for subjects performing poorly.
Brain decoding is a data analysis paradigm for neuroimaging experiments that is based on predicting the stimulus presented to the subject from the concurrent brain activity. In order to make inference at the group level, a straightforward but sometimes unsuccessful approach is to train a classifier on the trials of a group of subjects and then to test it on unseen trials from new subjects. The extreme difficulty is related to the structural and functional variability across the subjects. We call this approach "decoding across subjects". In this work, we address the problem of decoding across subjects for magnetoencephalographic (MEG) experiments and we provide the following contributions: first, we formally describe the problem and show that it belongs to a machine learning sub-field called transductive transfer learning (TTL). Second, we propose to use a simple TTL technique that accounts for the differences between train data and test data. Third, we propose the use of ensemble learning, and specifically of stacked generalization, to address the variability across subjects within train data, with the aim of producing more stable classifiers. On a face vs. scramble task MEG dataset of 16 subjects, we compare the standard approach of not modelling the differences across subjects, to the proposed one of combining TTL and ensemble learning. We show that the proposed approach is consistently more accurate than the standard one.
Functional magnetic resonance imaging produces high dimensional data, with a less then ideal number of labelled samples for brain decoding tasks (predicting brain states). In this study, we propose a new deep temporal convolutional neural network architecture with spatial pooling for brain decoding which aims to reduce dimensionality of feature space along with improved classification performance. Temporal representations (filters) for each layer of the convolutional model are learned by leveraging unlabelled fMRI data in an unsupervised fashion with regularized autoencoders. Learned temporal representations in multiple levels capture the regularities in the temporal domain and are observed to be a rich bank of activation patterns which also exhibit similarities to the actual hemodynamic responses. Further, spatial pooling layers in the convolutional architecture reduce the dimensionality without losing excessive information. By employing the proposed temporal convolutional architecture with spatial pooling, raw input fMRI data is mapped to a non-linear, highly-expressive and low-dimensional feature space where the final classification is conducted. In addition, we propose a simple heuristic approach for hyper-parameter tuning when no validation data is available. Proposed method is tested on a ten class recognition memory experiment with nine subjects. The results support the efficiency and potential of the proposed model, compared to the baseline multi-voxel pattern analysis techniques.