Machine learning based brain signal decoding for intelligent adaptive deep brain stimulation

Sensing enabled implantable devices and next-generation neurotechnology allow real-time adjustments of invasive neuromodulation. The identification of symptom and disease-specific biomarkers in invasive brain signal recordings has inspired the idea of demand dependent adaptive deep brain stimulation (aDBS). Expanding the clinical utility of aDBS with machine learning may hold the potential for the next breakthrough in the therapeutic success of clinical brain computer interfaces. To this end, sophisticated machine learning algorithms optimized for decoding of brain states from neural time-series must be developed. To support this venture, this review summarizes the current state of machine learning studies for invasive neurophysiology. After a brief introduction to the machine learning terminology, the transformation of brain recordings into meaningful features for decoding of symptoms and behavior is described. Commonly used machine learning models are explained and analyzed from the perspective of utility for aDBS. This is followed by a critical review on good practices for training and testing to ensure conceptual and practical generalizability for real-time adaptation in clinical settings. Finally, first studies combining machine learning with aDBS are highlighted. This review takes a glimpse into the promising future of intelligent adaptive DBS (iDBS) and concludes by identifying four key ingredients on the road for successful clinical adoption: i) multidisciplinary research teams, ii) publicly available datasets, iii) open-source algorithmic solutions and iv) strong world-wide research collaborations.Fil: Merk, Timon. Charité – Universitätsmedizin Berlin; AlemaniaFil: Peterson, Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Matemática Aplicada del Litoral. Universidad Nacional del Litoral. Instituto de Matemática Aplicada del Litoral; Argentina. Harvard Medical School; Estados UnidosFil: Köhler, Richard. Charité – Universitätsmedizin Berlin; AlemaniaFil: Haufe, Stefan. Charité – Universitätsmedizin Berlin; AlemaniaFil: Richardson, R. Mark. Harvard Medical School; Estados UnidosFil: Neumann, Wolf Julian. Charité – Universitätsmedizin Berlin; Alemani

Brain enhancement through cognitive training: A new insight from brain connectome

Owing to the recent advances in neurotechnology and the progress in understanding of brain cognitive functions, improvements of cognitive performance or acceleration of learning process with brain enhancement systems is not out of our reach anymore, on the contrary, it is a tangible target of contemporary research. Although a variety of approaches have been proposed, we will mainly focus on cognitive training interventions, in which learners repeatedly perform cognitive tasks to improve their cognitive abilities. In this review article, we propose that the learning process during the cognitive training can be facilitated by an assistive system monitoring cognitive workloads using electroencephalography (EEG) biomarkers, and the brain connectome approach can provide additional valuable biomarkers for facilitating leaners' learning processes. For the purpose, we will introduce studies on the cognitive training interventions, EEG biomarkers for cognitive workload, and human brain connectome. As cognitive overload and mental fatigue would reduce or even eliminate gains of cognitive training interventions, a real-time monitoring of cognitive workload can facilitate the learning process by flexibly adjusting difficulty levels of the training task. Moreover, cognitive training interventions should have effects on brain sub-networks, not on a single brain region, and graph theoretical network metrics quantifying topological architecture of the brain network can differentiate with respect to individual cognitive states as well as to different individuals' cognitive abilities, suggesting that the connectome is a valuable approach for tracking the learning progress. Although only a few studies have exploited the connectome approach for studying alterations of the brain network induced by cognitive training interventions so far, we believe that it would be a useful technique for capturing improvements of cognitive function

Characterizing dynamically evolving functional networks in humans with application to speech

Understanding how communication between brain areas evolves to support dynamic function remains a fundamental challenge in neuroscience. One approach to this question is functional connectivity analysis, in which statistical coupling measures are employed to detect signatures of interactions between brain regions. Because the brain uses multiple communication mechanisms at different temporal and spatial scales, and because the neuronal signatures of communication are often weak, powerful connectivity inference methodologies require continued development specific to these challenges. Here we address the challenge of inferring task-related functional connectivity in brain voltage recordings. We first develop a framework for detecting changes in statistical coupling that occur reliably in a task relative to a baseline period. The framework characterizes the dynamics of connectivity changes, allows inference on multiple spatial scales, and assesses statistical uncertainty. This general framework is modular and applicable to a wide range of tasks and research questions. We demonstrate the flexibility of the framework in the second part of this thesis, in which we refine the coupling statistics and hypothesis tests to improve statistical power and test different proposed connectivity mechanisms. In particular, we introduce frequency domain coupling measures and define test statistics that exploit theoretical properties and capture known sampling variability. The resulting test statistics use correlation, coherence, canonical correlation, and canonical coherence to infer task-related changes in coupling. Because canonical correlation and canonical coherence are not commonly used in functional connectivity analyses, we derive the theoretical values and statistical estimators for these measures. In the third part of this thesis, we present a sample application of these techniques to electrocorticography data collected during an overt reading task. We discuss the challenges that arise with task-related human data, which is often noisy and underpowered, and present functional connectivity results in the context of traditional and contemporary within-electrode analytics. In two of nine subjects we observe time-domain and frequency-domain network changes that accord with theoretical models of information routing during motor processing. Taken together, this work contributes a methodological framework for inferring task-related functional connectivity across spatial and temporal scales, and supports insight into the rapid, dynamic functional coupling of human speech

BCI applications based on artificial intelligence oriented to deep learning techniques

A Brain-Computer Interface, BCI, can decode the brain signals corresponding to the intentions of individuals who have lost neuromuscular connection, to reestablish communication to control external devices. To this aim, BCI acquires brain signals as Electroencephalography (EEG) or Electrocorticography (ECoG), uses signal processing techniques and extracts features to train classifiers for providing proper control instructions. BCI development has increased in the last decades, improving its performance through the use of different signal processing techniques for feature extraction and artificial intelligence approaches for classification, such as deep learning-oriented classifiers. All of these can assure more accurate assistive systems but also can enable an analysis of the learning process of signal characteristics for the classification task. Initially, this work proposes the use of a priori knowledge and a correlation measure to select the most discriminative ECoG signal electrodes. Then, signals are processed using spatial filtering and three different types of temporal filtering, followed by a classifier made of stacked autoencoders and a softmax layer to discriminate between ECoG signals from two types of visual stimuli. Results show that the average accuracy obtained is 97% (+/- 0.02%), which is similar to state-of-the-art techniques, nevertheless, this method uses minimal prior physiological and an automated statistical technique to select some electrodes to train the classifier. Also, this work presents classifier analysis, figuring out which are the most relevant signal features useful for visual stimuli classification. The features and physiological information such as the brain areas involved are compared. Finally, this research uses Convolutional Neural Networks (CNN) or Convnets to classify 5 categories of motor tasks EEG signals. Movement-related cortical potentials (MRCPs) are used as a priori information to improve the processing of time-frequency representation of EEG signals. Results show an increase of more than 25% in average accuracy compared to a state-of-the-art method that uses the same database. In addition, an analysis of CNN or ConvNets filters and feature maps is done to and the most relevant signal characteristics that can help classify the five types of motor tasks.DoctoradoDoctor en Ingeniería Eléctrica y Electrónic

ECoG correlates of visuomotor transformation, neural plasticity, and application to a force-based brain computer interface

Electrocorticography: ECoG) has gained increased notoriety over the past decade as a possible recording modality for Brain-Computer Interface: BCI) applications that offers a balance of minimal invasiveness to the patient in addition to robust spectral information over time. More recently, the scale of ECoG devices has begun to shrink to the order of micrometer diameter contacts and millimeter spacings with the intent of extracting more independent signals for BCI control within less cortical real-estate. However, most control signals to date, whether within the field of ECoG or any of the more seasoned recording techniques, have translated their control signals to kinematic control parameters: i.e. position or velocity of an object) which may not be practical for certain BCI applications such as functional neuromuscular stimulation: FNS). Thus, the purpose of this dissertation was to present a novel application of ECoG signals to a force-based control algorithm and address its feasibility for such a BCI system. Micro-ECoG arrays constructed from thin-film polyimide were implanted epidurally over areas spanning premotor, primary motor, and parietal cortical areas of two monkeys: three hemispheres, three arrays). Monkeys first learned to perform a classic center-out task using a brain signal-to-velocity mapping for control of a computer cursor. The BCI algorithm utilized day-to-day adaptation of the decoding model to match the task intention of the monkeys with no need for pre-screeening of movement-related ECoG signals. Using this strategy, subjects showed notable 2-D task profiency and increased task-related modulation of ECoG features within five training sessions. After fixing the last model trained for velocity control of the cursor, the monkeys then utilized this decoding model to control the acceleration of the cursor in the same center-out task. Cursor movement profiles under this mapping paralleled those demonstrated using velocity control, and neural control signal profiles revealed the monkeys actively accelerated and decelerated the cursor within a limited time window: 1-1.5 seconds). The fixed BCI decoding model was recast once again to control the force on a virtual cursor in a novel mass-grab task. This task required targets not only to reach to peripheral targets but also account for an additional virtual mass as they grabbed each target and moved it to a second target location in the presence of the external force of gravity. Examination of the ensemble control signals showed neural adaptation to variations in the perceived mass of the target as well as the presence or absence of gravity. Finally, short rest periods were interleaved within blocks of each task type to elucidate differences between active BCI intention and rest. Using a post-hoc state-decoder model, periods of active BCI task control could be distinguished from periods of rest with a very high degree of accuracy: ~99%). Taken together, the results from these experiments present a first step toward the design of a dynamics-based BCI system suitable for FNS applications as well as a framework for implementation of an asyncrhonous ECoG BCI

Novel Computational Approaches For Multidimensional Brain Image Analysis

The overall goal of this dissertation is focused on addressing challenging problems in 1D, 2D/3D and 4D neuroimaging by developing novel algorithms that combine signal processing and machine learning techniques. One of these challenging tasks is the accurate localization of the eloquent language cortex in brain resection pre-surgery patients. This is especially important since inaccurate localization can lead to diminshed functionalities and thus, a poor quality of life for the patient. The first part of this dissertation addresses this problem in the case of drug-resistant epileptic patients. We propose a novel machine learning based algorithm to establish an alternate electrical stimulation-free approach, electro-corticography (ECoG) as a viable technique for localization of the eloqeunt language cortex. We process the 1D signals in frequency domain to train a classifier and identify language responsive electrodes from the surface of the brain. We then enhance the proposed approach by developing novel multi-modal deep learning algorithms. We test different aspects of the experimental paradigm and identify the best features and models for classification. Another difficult neuroimaging task is that of identifying biomarkers of a disease. This is even more challenging considering that skill acquisition leads to neurological changes. We propose to help understand these changes in the brain of chess masters via a multi-modal approach that combines 3D and 4D imaging modalities in a novel way. The proposed approaches may help narrow the regions to be tested in pre-surgical localization tasks and in better surgery planning. The proposed work may also pave the way for a holistic view of the human brain by combining several modalities into one. Finally, we deal with the problem of learning strong signal representations/features by proposing a novel capsule based variational autoencoder, B-Caps. The proposed B-Caps helps in learning a strong feature representation that can be used with multi-dimensional data

The Electrophysiology of Resting State fMRI Networks

Traditional research in neuroscience has studied the topography of specific brain functions largely by presenting stimuli or imposing tasks and measuring evoked brain activity. This paradigm has dominated neuroscience for 50 years. Recently, investigations of brain activity in the resting state, most frequently using functional magnetic resonance imaging (fMRI), have revealed spontaneous correlations within widely distributed brain regions known as resting state networks (RSNs). Variability in RSNs across individuals has found to systematically relate to numerous diseases as well as differences in cognitive performance within specific domains. However, the relationship between spontaneous fMRI activity and the underlying neurophysiology is not well understood. This thesis aims to combine invasive electrophysiology and resting state fMRI in human subjects to better understand the nature of spontaneous brain activity. First, we establish an approach to precisely coregister intra-cranial electrodes to fMRI data (Chapter 2). We then created a novel machine learning approach to define resting state networks in individual subjects (Chapter 3). This approach is validated with cortical stimulation in clinical electrocorticography (ECoG) patients (Chapter 4). Spontaneous ECoG data are then analyzed with respect to fMRI time-series and fMRI-defined RSNs in order to illustrate novel ECoG correlates of fMRI for both local field potentials and band-limited power (BLP) envelopes (Chapter 5). In Chapter 6, we show that the spectral specificity of these resting state ECoG correlates link classic brain rhythms with large-scale functional domains. Finally, in Chapter 7 we show that the frequencies and topographies of spontaneous ECoG correlations specifically recapitulate the spectral and spatial structure of task responses within individual subjects

Machine learning reveals interhemispheric somatosensory coherence as indicator of anesthetic depth

The goal of this study was to identify features in mouse electrocorticogram recordings that indicate the depth of anesthesia as approximated by the administered anesthetic dosage. Anesthetic depth in laboratory animals must be precisely monitored and controlled. However, for the most common lab species (mice) few indicators useful for monitoring anesthetic depth have been established. We used electrocorticogram recordings in mice, coupled with peripheral stimulation, in order to identify features of brain activity modulated by isoflurane anesthesia and explored their usefulness in monitoring anesthetic depth through machine learning techniques. Using a gradient boosting regressor framework we identified interhemispheric somatosensory coherence as the most informative and reliable electrocorticogram feature for determining anesthetic depth, yielding good generalization and performance over many subjects. Knowing that interhemispheric somatosensory coherence indicates the effectively administered isoflurane concentration is an important step for establishing better anesthetic monitoring protocols and closed-loop systems for animal surgeries