The rise of precision medicine is being augmented by greater use of deep learning technologies that provide predictive analytics for earlier diagnosis of a range of debilitating diseases. The latest example comes from researchers at Michigan-based Beaumont Health who used deep learning to analyze genomic DNA. The resulting simple blood test could be used to detect earlier onset of Alzheimer's disease. In a study published this week in the peer-reviewed scientific journal PLOS ONE, the researchers said their analysis discovered 152 "significant" genetic differences among Alzheimer's and healthy patients. Those biomarkers could be used to provide diagnoses before Alzheimer's symptoms develop and a patient's brain is irreversibly damaged.
A study published in the Journal of Medical Imaging unveils the use of machine learning to detect the early stages of Alzheimer's disease (AD) by functional magnetic resonance imaging. Alzheimer's disease is a neurodegenerative condition primarily occurring in late-adulthood and begins with symptoms of cognitive decline. Researchers from Texas Tech University developed a deep-learning algorithm called a convolutional neural network able to distinguish between the fMRI signals of healthy individuals, patients with mild cognitive impairment (MCI), and patients with Alzheimer's. "We present one such synergy of fMRI and deep learning, where we apply a simplified yet accurate method using a modified 3D convolutional neural networks to resting-state fMRI data for feature extraction and classification of Alzheimer's disease," the co-authors explained in their findings. "The convolutional neural network is designed in such a way that it uses the fMRI data with much less preprocessing, preserving both spatial and temporal information."
Functional magnetic resonance imaging (fMRI) is a noninvasive diagnostic technique for brain disorders, such as Alzheimer's disease (AD). It measures minute changes in blood oxygen levels within the brain over time, giving insight into the local activity of neurons; however, fMRI has not been widely used in clinical diagnosis. Their limited use is due to the fact fMRI data are highly susceptible to noise, and the fMRI data structure is very complicated compared to a traditional x-ray or MRI scan. Scientists from Texas Tech University now report they developed a type of deep-learning algorithm known as a convolutional neural network (CNN) that can differentiate among the fMRI signals of healthy people, people with mild cognitive impairment, and people with AD. Their findings, "Spatiotemporal feature extraction and classification of Alzheimer's disease using deep learning 3D-CNN for fMRI data," is published in the Journal of Medical Imaging and led by Harshit Parmar, doctoral student at Texas Tech University.
This paper revisits spectral graph convolutional neural networks (graph-CNNs) given in Defferrard (2016) and develops the Laplace-Beltrami CNN (LB-CNN) by replacing the graph Laplacian with the LB operator. We then define spectral filters via the LB operator on a graph. We explore the feasibility of Chebyshev, Laguerre, and Hermite polynomials to approximate LB-based spectral filters and define an update of the LB operator for pooling in the LBCNN. We employ the brain image data from Alzheimer's Disease Neuroimaging Initiative (ADNI) and demonstrate the use of the proposed LB-CNN. Based on the cortical thickness of the ADNI dataset, we showed that the LB-CNN didn't improve classification accuracy compared to the spectral graph-CNN. The three polynomials had a similar computational cost and showed comparable classification accuracy in the LB-CNN or spectral graph-CNN. Our findings suggest that even though the shapes of the three polynomials are different, deep learning architecture allows us to learn spectral filters such that the classification performance is not dependent on the type of the polynomials or the operators (graph Laplacian and LB operator).
Language is a valuable source of clinical information in Alzheimer's Disease, as it declines concurrently with neurodegeneration. Consequently, speech and language data have been extensively studied in connection with its diagnosis. This paper summarises current findings on the use of artificial intelligence, speech and language processing to predict cognitive decline in the context of Alzheimer's Disease, detailing current research procedures, highlighting their limitations and suggesting strategies to address them. We conducted a systematic review of original research between 2000 and 2019, registered in PROSPERO (reference CRD42018116606). An interdisciplinary search covered six databases on engineering (ACM and IEEE), psychology (PsycINFO), medicine (PubMed and Embase) and Web of Science. Bibliographies of relevant papers were screened until December 2019. From 3,654 search results 51 articles were selected against the eligibility criteria. Four tables summarise their findings: study details (aim, population, interventions, comparisons, methods and outcomes), data details (size, type, modalities, annotation, balance, availability and language of study), methodology (pre-processing, feature generation, machine learning, evaluation and results) and clinical applicability (research implications, clinical potential, risk of bias and strengths/limitations). While promising results are reported across nearly all 51 studies, very few have been implemented in clinical research or practice. We concluded that the main limitations of the field are poor standardisation, limited comparability of results, and a degree of disconnect between study aims and clinical applications. Attempts to close these gaps should support translation of future research into clinical practice.
Brain gender differences have been known for a long time and are the possible reason for many psychological, psychiatric and behavioral differences between males and females. Predicting genders from brain functional connectivity (FC) can build the relationship between brain activities and gender, and extracting important gender related FC features from the prediction model offers a way to investigate the brain gender difference. Current predictive models applied to gender prediction demonstrate good accuracies, but usually extract individual functional connections instead of connectivity patterns in the whole connectivity matrix as features. In addition, current models often omit the effect of the input brain FC scale on prediction and cannot give any model uncertainty information. Hence, in this study we propose to predict gender from multiple scales of brain FC with deep learning, which can extract full FC patterns as features. We further develop the understanding of the feature extraction mechanism in deep neural network (DNN) and propose a DNN feature ranking method to extract the highly important features based on their contributions to the prediction. Moreover, we apply Bayesian deep learning to the brain FC gender prediction, which as a probabilistic model can not only make accurate predictions but also generate model uncertainty for each prediction. Experiments were done on the high-quality Human Connectome Project S1200 release dataset comprising the resting state functional MRI data of 1003 healthy adults. First, DNN reaches 83.0%, 87.6%, 92.0%, 93.5% and 94.1% accuracies respectively with the FC input derived from 25, 50, 100, 200, 300 independent component analysis (ICA) components. DNN outperforms the conventional machine learning methods on the 25-ICA-component scale FC, but the linear machine learning method catches up as the number of ICA components increases...
Characterizing the subtle changes of functional brain networks associated with the pathological cascade of Alzheimer's disease (AD) is important for early diagnosis and prediction of disease progression prior to clinical symptoms. We developed a new deep learning method, termed multiple graph Gaussian embedding model (MG2G), which can learn highly informative network features by mapping high-dimensional resting-state brain networks into a low-dimensional latent space. These latent distribution-based embeddings enable a quantitative characterization of subtle and heterogeneous brain connectivity patterns at different regions and can be used as input to traditional classifiers for various downstream graph analytic tasks, such as AD early stage prediction, and statistical evaluation of between-group significant alterations across brain regions. We used MG2G to detect the intrinsic latent dimensionality of MEG brain networks, predict the progression of patients with mild cognitive impairment (MCI) to AD, and identify brain regions with network alterations related to MCI.
Objective: Deriving disease subtypes from electronic health records (EHRs) can guide next-generation personalized medicine. However, challenges in summarizing and representing patient data prevent widespread practice of scalable EHR-based stratification analysis. Here, we present a novel unsupervised framework based on deep learning to process heterogeneous EHRs and derive patient representations that can efficiently and effectively enable patient stratification at scale. Materials and methods: We considered EHRs of $1,608,741$ patients from a diverse hospital cohort comprising of a total of $57,464$ clinical concepts. We introduce a representation learning model based on word embeddings, convolutional neural networks and autoencoders (i.e., "ConvAE") to transform patient trajectories into low-dimensional latent vectors. We evaluated these representations as broadly enabling patient stratification by applying hierarchical clustering to different multi-disease and disease-specific patient cohorts. Results: ConvAE significantly outperformed several common baselines in a clustering task to identify patients with different complex conditions, with $2.61$ entropy and $0.31$ purity average scores. When applied to stratify patients within a certain condition, ConvAE led to various clinically relevant subtypes for different disorders, including type 2 diabetes, Parkinson's disease and Alzheimer's disease, largely related to comorbidities, disease progression, and symptom severity. Conclusions: Patient representations derived from modeling EHRs with ConvAE can help develop personalized medicine therapeutic strategies and better understand varying etiologies in heterogeneous sub-populations.
Brain-Computer Interface (BCI) is a powerful communication tool between users and systems, which enhances the capability of the human brain in communicating and interacting with the environment directly. Advances in neuroscience and computer science in the past decades have led to exciting developments in BCI, thereby making BCI a top interdisciplinary research area in computational neuroscience and intelligence. Recent technological advances such as wearable sensing devices, real-time data streaming, machine learning, and deep learning approaches have increased interest in electroencephalographic (EEG) based BCI for translational and healthcare applications. Many people benefit from EEG-based BCIs, which facilitate continuous monitoring of fluctuations in cognitive states under monotonous tasks in the workplace or at home. In this study, we survey the recent literature of EEG signal sensing technologies and computational intelligence approaches in BCI applications, compensated for the gaps in the systematic summary of the past five years (2015-2019). In specific, we first review the current status of BCI and its significant obstacles. Then, we present advanced signal sensing and enhancement technologies to collect and clean EEG signals, respectively. Furthermore, we demonstrate state-of-art computational intelligence techniques, including interpretable fuzzy models, transfer learning, deep learning, and combinations, to monitor, maintain, or track human cognitive states and operating performance in prevalent applications. Finally, we deliver a couple of innovative BCI-inspired healthcare applications and discuss some future research directions in EEG-based BCIs.
Early detection is a crucial goal in the study of Alzheimer's Disease (AD). In this work, we describe several techniques to boost the performance of 3D convolutional neural networks trained to detect AD using structural brain MRI scans. Specifically, we provide evidence that (1) instance normalization outperforms batch normalization, (2) early spatial downsampling negatively affects performance, (3) widening the model brings consistent gains while increasing the depth does not, and (4) incorporating age information yields moderate improvement. Together, these insights yield an increment of approximately 14% in test accuracy over existing models when distinguishing between patients with AD, mild cognitive impairment, and controls in the ADNI dataset. Similar performance is achieved on an independent dataset.