Deep Interpretability Methods for Neuroimaging

Brain dynamics are highly complex and yet hold the key to understanding brain function and dysfunction. The dynamics captured by resting-state functional magnetic resonance imaging data are noisy, high-dimensional, and not readily interpretable. The typical approach of reducing this data to low-dimensional features and focusing on the most predictive features comes with strong assumptions and can miss essential aspects of the underlying dynamics. In contrast, introspection of discriminatively trained deep learning models may uncover disorder-relevant elements of the signal at the level of individual time points and spatial locations. Nevertheless, the difficulty of reliable training on high-dimensional but small-sample datasets and the unclear relevance of the resulting predictive markers prevent the widespread use of deep learning in functional neuroimaging. In this dissertation, we address these challenges by proposing a deep learning framework to learn from high-dimensional dynamical data while maintaining stable, ecologically valid interpretations. The developed model is pre-trainable and alleviates the need to collect an enormous amount of neuroimaging samples to achieve optimal training. We also provide a quantitative validation module, Retain and Retrain (RAR), that can objectively verify the higher predictability of the dynamics learned by the model. Results successfully demonstrate that the proposed framework enables learning the fMRI dynamics directly from small data and capturing compact, stable interpretations of features predictive of function and dysfunction. We also comprehensively reviewed deep interpretability literature in the neuroimaging domain. Our analysis reveals the ongoing trend of interpretability practices in neuroimaging studies and identifies the gaps that should be addressed for effective human-machine collaboration in this domain. This dissertation also proposed a post hoc interpretability method, Geometrically Guided Integrated Gradients (GGIG), that leverages geometric properties of the functional space as learned by a deep learning model. With extensive experiments and quantitative validation on MNIST and ImageNet datasets, we demonstrate that GGIG outperforms integrated gradients (IG), which is considered to be a popular interpretability method in the literature. As GGIG is able to identify the contours of the discriminative regions in the input space, GGIG may be useful in various medical imaging tasks where fine-grained localization as an explanation is beneficial

Data Augmentation for Deep-Learning-Based Electroencephalography

Background: Data augmentation (DA) has recently been demonstrated to achieve considerable performance gains for deep learning (DL)—increased accuracy and stability and reduced overfitting. Some electroencephalography (EEG) tasks suffer from low samples-to-features ratio, severely reducing DL effectiveness. DA with DL thus holds transformative promise for EEG processing, possibly like DL revolutionized computer vision, etc. New method: We review trends and approaches to DA for DL in EEG to address: Which DA approaches exist and are common for which EEG tasks? What input features are used? And, what kind of accuracy gain can be expected? Results: DA for DL on EEG begun 5 years ago and is steadily used more. We grouped DA techniques (noise addition, generative adversarial networks, sliding windows, sampling, Fourier transform, recombination of segmentation, and others) and EEG tasks (into seizure detection, sleep stages, motor imagery, mental workload, emotion recognition, motor tasks, and visual tasks). DA efficacy across techniques varied considerably. Noise addition and sliding windows provided the highest accuracy boost; mental workload most benefitted from DA. Sliding window, noise addition, and sampling methods most common for seizure detection, mental workload, and sleep stages, respectively. Comparing with existing methods: Percent of decoding accuracy explained by DA beyond unaugmented accuracy varied between 8% for recombination of segmentation and 36% for noise addition and from 14% for motor imagery to 56% for mental workload—29% on average. Conclusions: DA increasingly used and considerably improved DL decoding accuracy on EEG. Additional publications—if adhering to our reporting guidelines—will facilitate more detailed analysis

Data Augmentation for Deep-Learning-Based Electroencephalography

Background: Data augmentation (DA) has recently been demonstrated to achieve considerable performance gains for deep learning (DL)—increased accuracy and stability and reduced overfitting. Some electroencephalography (EEG) tasks suffer from low samples-to-features ratio, severely reducing DL effectiveness. DA with DL thus holds transformative promise for EEG processing, possibly like DL revolutionized computer vision, etc. New method: We review trends and approaches to DA for DL in EEG to address: Which DA approaches exist and are common for which EEG tasks? What input features are used? And, what kind of accuracy gain can be expected? Results: DA for DL on EEG begun 5 years ago and is steadily used more. We grouped DA techniques (noise addition, generative adversarial networks, sliding windows, sampling, Fourier transform, recombination of segmentation, and others) and EEG tasks (into seizure detection, sleep stages, motor imagery, mental workload, emotion recognition, motor tasks, and visual tasks). DA efficacy across techniques varied considerably. Noise addition and sliding windows provided the highest accuracy boost; mental workload most benefitted from DA. Sliding window, noise addition, and sampling methods most common for seizure detection, mental workload, and sleep stages, respectively. Comparing with existing methods: Percent of decoding accuracy explained by DA beyond unaugmented accuracy varied between 8% for recombination of segmentation and 36% for noise addition and from 14% for motor imagery to 56% for mental workload—29% on average. Conclusions: DA increasingly used and considerably improved DL decoding accuracy on EEG. Additional publications—if adhering to our reporting guidelines—will facilitate more detailed analysis

Deep Learning Techniques for Electroencephalography Analysis

In this thesis we design deep learning techniques for training deep neural networks on electroencephalography (EEG) data and in particular on two problems, namely EEG-based motor imagery decoding and EEG-based affect recognition, addressing challenges associated with them. Regarding the problem of motor imagery (MI) decoding, we first consider the various kinds of domain shifts in the EEG signals, caused by inter-individual differences (e.g. brain anatomy, personality and cognitive profile). These domain shifts render multi-subject training a challenging task and impede robust cross-subject generalization. We build a two-stage model ensemble architecture and propose two objectives to train it, combining the strengths of curriculum learning and collaborative training. Our subject-independent experiments on the large datasets of Physionet and OpenBMI, verify the effectiveness of our approach. Next, we explore the utilization of the spatial covariance of EEG signals through alignment techniques, with the goal of learning domain-invariant representations. We introduce a Riemannian framework that concurrently performs covariance-based signal alignment and data augmentation, while training a convolutional neural network (CNN) on EEG time-series. Experiments on the BCI IV-2a dataset show that our method performs superiorly over traditional alignment, by inducing regularization to the weights of the CNN. We also study the problem of EEG-based affect recognition, inspired by works suggesting that emotions can be expressed in relative terms, i.e. through ordinal comparisons between different affective state levels. We propose treating data samples in a pairwise manner to infer the ordinal relation between their corresponding affective state labels, as an auxiliary training objective. We incorporate our objective in a deep network architecture which we jointly train on the tasks of sample-wise classification and pairwise ordinal ranking. We evaluate our method on the affective datasets of DEAP and SEED and obtain performance improvements over deep networks trained without the additional ranking objective

Shared computational principles for language processing in humans and deep language models

Departing from traditional linguistic models, advances in deep learning have resulted in a new type of predictive (autoregressive) deep language models (DLMs). Using a self-supervised next-word prediction task, these models generate appropriate linguistic responses in a given context. In the current study, nine participants listened to a 30-min podcast while their brain responses were recorded using electrocorticography (ECoG). We provide empirical evidence that the human brain and autoregressive DLMs share three fundamental computational principles as they process the same natural narrative: (1) both are engaged in continuous next-word prediction before word onset; (2) both match their pre-onset predictions to the incoming word to calculate post-onset surprise; (3) both rely on contextual embeddings to represent words in natural contexts. Together, our findings suggest that autoregressive DLMs provide a new and biologically feasible computational framework for studying the neural basis of language

Self-Supervised Pretraining and Transfer Learning on fMRI Data with Transformers

Transfer learning is a machine learning technique founded on the idea that knowledge acquired by a model during “pretraining” on a source task can be transferred to the learning of a target task. Successful transfer learning can result in improved performance, faster convergence, and reduced demand for data. This technique is particularly desirable for the task of brain decoding in the domain of functional magnetic resonance imaging (fMRI), wherein even the most modern machine learning methods can struggle to decode labelled features of brain images. This challenge is due to the highly complex underlying signal, physical and neurological differences between brains, low data collection throughput, and other factors. Transfer learning is exciting in its potential to mitigate these challenges, but with this application still in its infancy, we must begin on the ground floor. The goals of this thesis were to design, implement, and evaluate a framework for pretraining and transfer learning on arbitrary fMRI datasets, then demonstrate its performance with respect to the literature, and achieve substantive progress toward generalized pretrained models of the brain. The primary contribution is our novel framework which achieves these goals, called BEAT, which stands for Bi-directional Encoders for Auditory Tasks. The design and implementation of BEAT include adapting state-of-the-art deep learning architectures to sequences of fMRI data, as well as a novel self-supervised pretraining task called Next Thought Prediction and several novel supervised brain decoding tasks. To evaluate BEAT, we pretrained ii on Next Thought Prediction and performed transfer learning to the brain decoding tasks, which are specific to one of three fMRI datasets. To demonstrate significant benefits of transfer learning, BEAT decoded instrumental timbre from one of the fMRI datasets which standard methods failed to decode in addition to improved downstream performance. Toward generalized pretrained models of the brain, BEAT learned Next Thought Prediction on one fMRI dataset, and then successfully transferred that learning to a supervised brain decoding task on an entirely distinct dataset, with different participants and stimuli. To our knowledge this is the first instance of transfer learning across participants and stimuli–a necessity for whole-brain pretrained models

Cognitive training optimization with a closed-loop system

Les interfaces cerveau-machine (ICMs) nous offrent un moyen de fermer la boucle entre notre cerveau et le monde de la technologie numérique. Cela ouvre la porte à une pléthore de nouvelles applications où nous utilisons directement le cerveau comme entrée. S’il est facile de voir le potentiel, il est moins facile de trouver la bonne application avec les bons corrélats neuronaux pour construire un tel système en boucle fermée. Ici, nous explorons une tâche de suivi d’objets multiples en 3D, dans un contexte d’entraînement cognitif (3D-MOT). Notre capacité à suivre plusieurs objets dans un environnement dynamique nous permet d’effectuer des tâches quotidiennes telles que conduire, pratiquer des sports d’équipe et marcher dans un centre commercial achalandé. Malgré plus de trois décennies de littérature sur les tâches MOT, les mécanismes neuronaux sous- jacents restent mal compris. Ici, nous avons examiné les corrélats neuronaux via l’électroencéphalographie (EEG) et leurs changements au cours des trois phases d’une tâche de 3D-MOT, à savoir l’identification, le suivi et le rappel. Nous avons observé ce qui semble être un transfert entre l’attention et la de mémoire de travail lors du passage entre le suivi et le rappel. Nos résultats ont révélé une forte inhibition des fréquences delta et thêta de la région frontale lors du suivi, suivie d’une forte (ré)activation de ces mêmes fréquences lors du rappel. Nos résultats ont également montré une activité de retard contralatérale (CDA en anglais), une activité négative soutenue dans l’hémisphère contralatérale aux positions des éléments visuels à suivre. Afin de déterminer si le CDA est un corrélat neuronal robuste pour les tâches de mémoire de travail visuelle, nous avons reproduit huit études liées au CDA avec un ensemble de données EEG accessible au public. Nous avons utilisé les données EEG brutes de ces huit études et les avons analysées avec le même pipeline de base pour extraire le CDA. Nous avons pu reproduire les résultats de chaque étude et montrer qu’avec un pipeline automatisé de base, nous pouvons extraire le CDA. Récemment, l’apprentissage profond (deep learning / DL en anglais) s’est révélé très prometteur pour aider à donner un sens aux signaux EEG en raison de sa capacité à apprendre de bonnes représentations à partir des données brutes. La question à savoir si l’apprentissage profond présente vraiment un avantage par rapport aux approches plus traditionnelles reste une question ouverte. Afin de répondre à cette question, nous avons examiné 154 articles appliquant le DL à l’EEG, publiés entre janvier 2010 et juillet 2018, et couvrant différents domaines d’application tels que l’épilepsie, le sommeil, les interfaces cerveau-machine et la surveillance cognitive et affective. Enfin, nous explorons la possibilité de fermer la boucle et de créer un ICM passif avec une tâche 3D-MOT. Nous classifions l’activité EEG pour prédire si une telle activité se produit pendant la phase de suivi ou de rappel de la tâche 3D-MOT. Nous avons également formé un classificateur pour les essais latéralisés afin de prédire si les cibles étaient présentées dans l’hémichamp gauche ou droit en utilisant l’activité EEG. Pour la classification de phase entre le suivi et le rappel, nous avons obtenu un 80% lors de l’entraînement d’un SVM sur plusieurs sujets en utilisant la puissance des bandes de fréquences thêta et delta des électrodes frontales.Brain-computer interfaces (BCIs) offer us a way to close the loop between our brain and the digital world of technology. It opens the door for a plethora of new applications where we use the brain directly as an input. While it is easy to see the disruptive potential, it is less so easy to find the right application with the right neural correlates to build such closed-loop system. Here we explore closing the loop during a cognitive training 3D multiple object tracking task (3D-MOT). Our ability to track multiple objects in a dynamic environment enables us to perform everyday tasks such as driving, playing team sports, and walking in a crowded mall. Despite more than three decades of literature on MOT tasks, the underlying and intertwined neural mechanisms remain poorly understood. Here we looked at the electroencephalography (EEG) neural correlates and their changes across the three phases of a 3D-MOT task, namely identification, tracking and recall. We observed what seems to be a handoff between focused attention and working memory processes when going from tracking to recall. Our findings revealed a strong inhibition in delta and theta frequencies from the frontal region during tracking, followed by a strong (re)activation of these same frequencies during recall. Our results also showed contralateral delay activity (CDA), a sustained negativity over the hemisphere contralateral to the positions of visual items to be remembered. In order to investigate if the CDA is a robust neural correlate for visual working memory (VWM) tasks, we reproduced eight CDA-related studies with a publicly accessible EEG dataset. We used the raw EEG data from these eight studies and analysed all of them with the same basic pipeline to extract CDA. We were able to reproduce the results from all the studies and show that with a basic automated EEG pipeline we can extract a clear CDA signal. 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 order to address such question, we reviewed 154 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. Finally, we explore the potential for closing the loop and creating a passive BCI with a 3D-MOT task. We classify EEG activity to predict if such activity is happening during the tracking or the recall phase of the 3D-MOT task. We also trained a classifier for lateralized trials to predict if the targets were presented on the left or right hemifield using EEG brain activity. For the phase classification between tracking and recall, we obtained 80% accuracy when training a SVM across subjects using the theta and delta frequency band power from the frontal electrodes and 83% accuracy when training within subjects

Getting aligned on representational alignment

Biological and artificial information processing systems form representations that they can use to categorize, reason, plan, navigate, and make decisions. How can we measure the extent to which the representations formed by these diverse systems agree? Do similarities in representations then translate into similar behavior? How can a system's representations be modified to better match those of another system? These questions pertaining to the study of representational alignment are at the heart of some of the most active research areas in cognitive science, neuroscience, and machine learning. For example, cognitive scientists measure the representational alignment of multiple individuals to identify shared cognitive priors, neuroscientists align fMRI responses from multiple individuals into a shared representational space for group-level analyses, and ML researchers distill knowledge from teacher models into student models by increasing their alignment. Unfortunately, there is limited knowledge transfer between research communities interested in representational alignment, so progress in one field often ends up being rediscovered independently in another. Thus, greater cross-field communication would be advantageous. To improve communication between these fields, we propose a unifying framework that can serve as a common language between researchers studying representational alignment. We survey the literature from all three fields and demonstrate how prior work fits into this framework. Finally, we lay out open problems in representational alignment where progress can benefit all three of these fields. We hope that our work can catalyze cross-disciplinary collaboration and accelerate progress for all communities studying and developing information processing systems. We note that this is a working paper and encourage readers to reach out with their suggestions for future revisions.Comment: Working paper, changes to be made in upcoming revision

Discovering Causal Relations and Equations from Data

Physics is a field of science that has traditionally used the scientific method to answer questions about why natural phenomena occur and to make testable models that explain the phenomena. Discovering equations, laws and principles that are invariant, robust and causal explanations of the world has been fundamental in physical sciences throughout the centuries. Discoveries emerge from observing the world and, when possible, performing interventional studies in the system under study. With the advent of big data and the use of data-driven methods, causal and equation discovery fields have grown and made progress in computer science, physics, statistics, philosophy, and many applied fields. All these domains are intertwined and can be used to discover causal relations, physical laws, and equations from observational data. This paper reviews the concepts, methods, and relevant works on causal and equation discovery in the broad field of Physics and outlines the most important challenges and promising future lines of research. We also provide a taxonomy for observational causal and equation discovery, point out connections, and showcase a complete set of case studies in Earth and climate sciences, fluid dynamics and mechanics, and the neurosciences. This review demonstrates that discovering fundamental laws and causal relations by observing natural phenomena is being revolutionised with the efficient exploitation of observational data, modern machine learning algorithms and the interaction with domain knowledge. Exciting times are ahead with many challenges and opportunities to improve our understanding of complex systems.Comment: 137 page