Deep Learning in Alzheimer's Disease: Diagnostic Classification and Prognostic Prediction Using Neuroimaging Data

A 5-min Cognitive Task With Deep Learning Accurately Detects Early Alzheimer's Disease

Introduction: The goal of this study was to investigate and compare the classification performance of machine learning with behavioral data from standard neuropsychological tests, a cognitive task, or both.

Methods: A neuropsychological battery and a simple 5-min cognitive task were administered to eight individuals with mild cognitive impairment (MCI), eight individuals with mild Alzheimer's disease (AD), and 41 demographically match controls (CN). A fully connected multilayer perceptron (MLP) network and four supervised traditional machine learning algorithms were used.

Results: Traditional machine learning algorithms achieved similar classification performances with neuropsychological or cognitive data. MLP outperformed traditional algorithms with the cognitive data (either alone or together with neuropsychological data), but not neuropsychological data. In particularly, MLP with a combination of summarized scores from neuropsychological tests and the cognitive task achieved ~90% sensitivity and ~90% specificity. Applying the models to an independent dataset, in which the participants were demographically different from the ones in the main dataset, a high specificity was maintained (100%), but the sensitivity was dropped to 66.67%.

Discussion: Deep learning with data from specific cognitive task(s) holds promise for assisting in the early diagnosis of Alzheimer's disease, but future work with a large and diverse sample is necessary to validate and to improve this approach.

M 3Lung-Sys: A Deep Learning System for Multi-Class Lung Pneumonia Screening From CT Imaging

To counter the outbreak of COVID-19, the accurate diagnosis of suspected cases plays a crucial role in timely quarantine, medical treatment, and preventing the spread of the pandemic. Considering the limited training cases and resources (e.g, time and budget), we propose a Multi-task Multi-slice Deep Learning System (M 3Lung-Sys) for multi-class lung pneumonia screening from CT imaging, which only consists of two 2D CNN networks, i.e., slice- and patient-level classification networks. The former aims to seek the feature representations from abundant CT slices instead of limited CT volumes, and for the overall pneumonia screening, the latter one could recover the temporal information by feature refinement and aggregation between different slices. In addition to distinguish COVID-19 from Healthy, H1N1, and CAP cases, our M 3Lung-Sys also be able to locate the areas of relevant lesions, without any pixel-level annotation. To further demonstrate the effectiveness of our model, we conduct extensive experiments on a chest CT imaging dataset with a total of 734 patients (251 healthy people, 245 COVID-19 patients, 105 H1N1 patients, and 133 CAP patients). The quantitative results with plenty of metrics indicate the superiority of our proposed model on both slice- and patient-level classification tasks. More importantly, the generated lesion location maps make our system interpretable and more valuable to clinicians.

Application of Structural and Functional Connectome Mismatch for Classification and Individualized Therapy in Alzheimer Disease

While machine learning approaches to analyzing Alzheimer disease connectome neuroimaging data have been studied, many have limited ability to provide insight in individual patterns of disease and lack the ability to provide actionable information about where in the brain a specific patient's disease is located. We studied a cohort of patients with Alzheimer disease who underwent resting state functional magnetic resonance imaging and diffusion tractography imaging. These images were processed, and a structural and functional connectivity matrix was generated using the HCP cortical and subcortical atlas. By generating a machine learning model, individual-level structural and functional anomalies detection and characterization were explored in this study. Our study found that structural disease burden in Alzheimer's patients is mainly focused in the subcortical structures and the Default mode network (DMN). Interestingly, functional anomalies were less consistent between individuals and less common in general in these patients. More intriguing was that some structural anomalies were noted in all patients in the study, namely a reduction in fibers involving parcellations in the right anterior cingulate. Alternately, the functional consequences of connectivity loss were cortical and variable. Integrated structural/functional connectomics might provide a useful tool for assessing AD progression, while few concerns have been made for analyzing the mismatch between these two. We performed a preliminary exploration into a set of Alzheimer disease data, intending to improve a personalized approach to understanding individual connectomes in an actionable manner. Specifically, we found that there were consistent patterns of white matter fiber loss, mainly focused around the DMN and deep subcortical structures, which were present in nearly all patients with clinical AD. Functional magnetic resonance imaging shows abnormal functional connectivity different within the patients, which may be used as the individual target for further therapeutic strategies making, like non-invasive stimulation technology.

Cognitive Impairment and Dementia in Primary Care: Current Knowledge and Future Directions Based on Findings From a Large Cross-Sectional Study in Crete, Greece

Introduction: Dementia severely affects the quality of life of patients and their caregivers; however, it is often not adequately addressed in the context of a primary care consultation, especially in patients with multi-morbidity. Study Population and Methods: A cross-sectional study was conducted between March-2013 and December-2014 among 3,140 consecutive patients aged >60 years visiting 14 primary health care practices in Crete, Greece. The Mini-Mental-State-Examination [MMSE] was used to measure cognitive status using the conventional 24-point cut-off. Participants who scored low on MMSE were matched with a group of elders scoring >24 points, according to age and education; both groups underwent comprehensive neuropsychiatric and neuropsychological assessment. For the diagnosis of dementia and Mild-Cognitive-Impairment (MCI), the Diagnostic and Statistical Manual-of-Mental-Disorders (DSM-IV) criteria and the International-Working-Group (IWG) criteria were used. Chronic conditions were categorized according to ICD-10 categories. Logistic regression was used to provide associations between chronic illnesses and cognitive impairment according to MMSE scores. Generalized Linear Model Lasso Regularization was used for feature selection in MMSE items. A two-layer artificial neural network model was used to classify participants as impaired (dementia/MCI) vs. non-impaired. Results: In the total sample of 3,140 participants (42.1% men; mean age 73.7 SD = 7.8 years), low MMSE scores were identified in 645 (20.5%) participants. Among participants with low MMSE scores 344 (54.1%) underwent comprehensive neuropsychiatric evaluation and 185 (53.8%) were diagnosed with Mild-Cognitive-Impairment (MCI) and 118 (34.3%) with dementia. Mental and behavioral disorders (F00-F99) and diseases of the nervous system (G00-G99) increased the odds of low MMSE scores in both genders. Generalized linear model lasso regularization indicated that 7/30 MMSE questions contributed the most to the classification of patients as impaired (dementia/MCI) vs. non-impaired with a combined accuracy of 82.0%. These MMSE items were questions 5, 13, 19, 20, 22, 23, and 26 of the Greek version of MMSE assessing orientation in time, repetition, calculation, registration, and visuo-constructive ability. Conclusions: Our study identified certain chronic illness-complexes that were associated with low MMSE scores within the context of primary care consultation. Also, our analysis indicated that seven MMSE items provide strong evidence for the presence of dementia or MCI.

Denouements of machine learning and multimodal diagnostic classification of Alzheimer's disease

Alzheimer's disease (AD) is the most common type of dementia. The exact cause and treatment of the disease are still unknown. Different neuroimaging modalities, such as magnetic resonance imaging (MRI), positron emission tomography, and single-photon emission computed tomography, have played a significant role in the study of AD. However, the effective diagnosis of AD, as well as mild cognitive impairment (MCI), has recently drawn large attention. Various technological advancements, such as robots, global positioning system technology, sensors, and machine learning (ML) algorithms, have helped improve the diagnostic process of AD. This study aimed to determine the influence of implementing different ML classifiers in MRI and analyze the use of support vector machines with various multimodal scans for classifying patients with AD/MCI and healthy controls. Conclusions have been drawn in terms of employing different classifier techniques and presenting the optimal multimodal paradigm for the classification of AD.

Functional connectivity of white matter as a biomarker of cognitive decline in Alzheimer's disease

OBJECTIVE

In vivo functional changes in white matter during the progression of Alzheimer's disease (AD) have not been previously reported. Our objectives are to measure changes in white matter functional connectivity (FC) in an elderly population undergoing cognitive decline as AD develops, to establish their relationship to neuropsychological scores of cognitive abilities, and to assess the performance in prediction of AD using white matter FC measures as features.

METHODS

Analyses were conducted using resting state functional MRI and neuropsychological data from 383 ADNI participants, including 136 cognitive normal (CN) controls, 46 with significant memory concern, 83 with early mild cognitive impairment (MCI), 37 with MCI, 46 with late MCI, and 35 with AD dementia. FC metrics between segregated white matter tracts and discrete gray matter volumes or between white matter tracts were quantitatively analyzed and characterized, along with their relationships to 6 cognitive measures. Finally, supervised machine learning was implemented on white matter FCs to classify the participants and performance of the classification was evaluated.

RESULTS

Significant decreases in FC measures were found in white matter with prominent, specific, regional deficits appearing in late MCI and AD dementia patients from CN. These changes significantly correlated with neuropsychological measurements of impairments in cognition and memory. The sensitivity and specificity of distinguishing AD dementia and CN using white matter FCs were 0.83 and 0.81 respectively.

CONCLUSIONS AND RELEVANCE

The white matter FC decreased in late MCI and AD dementia patients compared to CN participants, and this decrease was correlated with cognitive measures. White matter FC is valuable in the prediction of AD. All these findings suggest that white matter FC may be a promising avenue for understanding functional impairments in white matter tracts during AD progression.

The Future of Skull Base Surgery: A View Through Tinted Glasses

In the present report, we have broadly outlined the potential advances in the field of skull base surgery, which might occur within the next 20 years based on the many areas of current research in biology and technology. Many of these advances will also be broadly applicable to other areas of neurosurgery. We have grounded our predictions for future developments in an exploration of what patients and surgeons most desire as outcomes for care. We next examined the recent developments in the field and outlined several promising areas of future improvement in skull base surgery, per se, as well as identifying the new hospital support systems needed to accommodate these changes. These include, but are not limited to, advances in imaging, Raman spectroscopy and microscopy, 3-dimensional printing and rapid prototyping, master-slave and semiautonomous robots, artificial intelligence applications in all areas of medicine, telemedicine, and green technologies in hospitals. In addition, we have reviewed the therapeutic approaches using nanotechnology, genetic engineering, antitumor antibodies, and stem cell technologies to repair damage caused by traumatic injuries, tumors, and iatrogenic injuries to the brain and cranial nerves. Additionally, we have discussed the training requirements for future skull base surgeons and stressed the need for adaptability and change. However, the essential requirements for skull base surgeons will remain unchanged, including knowledge, attention to detail, technical skill, innovation, judgment, and compassion. We believe that active involvement in these rapidly evolving technologies will enable us to shape some of the future of our discipline to address the needs of both patients and our profession.

Deep learning of brain magnetic resonance images: A brief review

Magnetic resonance imaging (MRI) is one of the most popular techniques in brain science and is important for understanding brain function and neuropsychiatric disorders. However, the processing and analysis of MRI is not a trivial task with lots of challenges. Recently, deep learning has shown superior performance over traditional machine learning approaches in image analysis. In this survey, we give a brief review of the recent popular deep learning approaches and their applications in brain MRI analysis. Furthermore, popular brain MRI databases and deep learning tools are also introduced. The strength and weaknesses of different approaches are addressed, and challenges as well as future directions are also discussed.

Possible Neuroprotective Mechanisms of Physical Exercise in Neurodegeneration

Physical exercise (PE) improves physical performance, mental status, general health, and well-being. It does so by affecting many mechanisms at the cellular and molecular level. PE is beneficial for people suffering from neuro-degenerative diseases because it improves the production of neurotrophic factors, neurotransmitters, and hormones. PE promotes neuronal survival and neuroplasticity and also optimizes neuroendocrine and physiological responses to psychosocial and physical stress. PE sensitizes the parasympathetic nervous system (PNS), Autonomic Nervous System (ANS) and central nervous system (CNS) by promoting many processes such as synaptic plasticity, neurogenesis, angiogenesis, and autophagy. Overall, it carries out many protective and preventive activities such as improvements in memory, cognition, sleep and mood; growth of new blood vessels in nervous system; and the reduction of stress, anxiety, neuro-inflammation, and insulin resistance. In the present work, the protective effects of PE were overviewed. Suitable examples from the current research work in this context are also given in the article.

Neurological update: neuroimaging in dementia

Neuroimaging for dementia has made remarkable progress in recent years, shedding light on diagnostic subtypes of dementia, predicting prognosis and monitoring pathology. This review covers some updates in the understanding of dementia using structural imaging, positron emission tomography (PET), structural and functional connectivity, and using big data and artificial intelligence. Progress with neuroimaging methods allows neuropathology to be examined in vivo, providing a suite of biomarkers for understanding neurodegeneration and for application in clinical trials. In addition, we highlight quantitative susceptibility imaging as an exciting new technique that may prove to be a sensitive biomarker for a range of neurodegenerative diseases. There are challenges in translating novel imaging techniques to clinical practice, particularly in developing standard methodologies and overcoming regulatory issues. It is likely that clinicians will need to lead the way if these obstacles are to be overcome. Continued efforts applying neuroimaging to understand mechanisms of neurodegeneration and translating them to clinical practice will complete a revolution in neuroimaging.

Explainable Deep Learning Models in Medical Image Analysis

Deep learning methods have been very effective for a variety of medical diagnostic tasks and have even outperformed human experts on some of those. However, the black-box nature of the algorithms has restricted their clinical use. Recent explainability studies aim to show the features that influence the decision of a model the most. The majority of literature reviews of this area have focused on taxonomy, ethics, and the need for explanations. A review of the current applications of explainable deep learning for different medical imaging tasks is presented here. The various approaches, challenges for clinical deployment, and the areas requiring further research are discussed here from a practical standpoint of a deep learning researcher designing a system for the clinical end-users.

A survey on machine and statistical learning for longitudinal analysis of neuroimaging data in Alzheimer's disease

BACKGROUND AND OBJECTIVES

Recently, longitudinal studies of Alzheimer's disease have gathered a substantial amount of neuroimaging data. New methods are needed to successfully leverage and distill meaningful information on the progression of the disease from the deluge of available data. Machine learning has been used successfully for many different tasks, including neuroimaging related problems. In this paper, we review recent statistical and machine learning applications in Alzheimer's disease using longitudinal neuroimaging.

METHODS

We search for papers using longitudinal imaging data, focused on Alzheimer's Disease and published between 2007 and 2019 on four different search engines.

RESULTS

After the search, we obtain 104 relevant papers. We analyze their approach to typical challenges in longitudinal data analysis, such as missing data and variability in the number and extent of acquisitions.

CONCLUSIONS

Reviewed works show that machine learning methods using longitudinal data have potential for disease progression modelling and computer-aided diagnosis. We compare results and models, and propose future research directions in the field.

Prediction of conversion to Alzheimer's disease using deep survival analysis of MRI images

The prediction of the conversion of healthy individuals and those with mild cognitive impairment to the status of active Alzheimer’s disease is a challenging task. Recently, a survival analysis based upon deep learning was developed to enable predictions regarding the timing of an event in a dataset containing censored data. Here, we investigated whether a deep survival analysis could similarly predict the conversion to Alzheimer’s disease. We selected individuals with mild cognitive impairment and cognitively normal subjects and used the grey matter volumes of brain regions in these subjects as predictive features. We then compared the prediction performances of the traditional standard Cox proportional-hazard model, the DeepHit model and our deep survival model based on a Weibull distribution. Our model achieved a maximum concordance index of 0.835, which was higher than that yielded by the Cox model and comparable to that of the DeepHit model. To our best knowledge, this is the first report to describe the application of a deep survival model to brain magnetic resonance imaging data. Our results demonstrate that this type of analysis could successfully predict the time of an individual’s conversion to Alzheimer’s disease.

Multi-modal neuroimaging feature fusion for diagnosis of Alzheimer's disease

BACKGROUND

Compared with single-modal neuroimages classification of AD, multi-modal classification can achieve better performance by fusing different information. Exploring synergy among various multi-modal neuroimages is contributed to identifying the pathological process of neurological disorders. However, it is still problematic to effectively exploit multi-modal information since the lack of an effective fusion method.

NEW METHOD

In this paper, we propose a deep multi-modal fusion network based on the attention mechanism, which can selectively extract features from MRI and PET branches and suppress irrelevant information. In the attention model, the fusion ratio of each modality is assigned automatically according to the importance of the data. A hierarchical fusion method is adopted to ensure the effectiveness of Multi-modal Fusion.

RESULTS

Evaluating the model on the ADNI dataset, the experimental results show that it outperforms the state-of-the-art methods. In particular, the final classification results of the NC/AD, SMCI/PMCI and Four-Class are 95.21 %, 89.79 %, and 86.15 %, respectively.

COMPARISON WITH EXISTING METHODS

Different from the early fusion and the late fusion, the hierarchical fusion method contributes to learning the synergy between the multi-modal data. Compared with some other prominent algorithms, the attention model enables our network to focus on the regions of interest and effectively fuse the multi-modal data.

CONCLUSION

Benefit from the hierarchical structure with attention model, the proposed network is capable of exploiting low-level and high-level features extracted from the multi-modal data and improving the accuracy of AD diagnosis. Results show its promising performance.

Insights into Systemic Disease through Retinal Imaging-Based Oculomics

Among the most noteworthy developments in ophthalmology over the last decade has been the emergence of quantifiable high-resolution imaging modalities, which are typically non-invasive, rapid and widely available. Such imaging is of unquestionable utility in the assessment of ocular disease however evidence is also mounting for its role in identifying ocular biomarkers of systemic disease, which we term oculomics. In this review, we highlight our current understanding of how retinal morphology evolves in two leading causes of global morbidity and mortality, cardiovascular disease and dementia. Population-based analyses have demonstrated the predictive value of retinal microvascular indices, as measured through fundus photography, in screening for heart attack and stroke. Similarly, the association between the structure of the neurosensory retina and prevalent neurodegenerative disease, in particular Alzheimer's disease, is now well-established. Given the growing size and complexity of emerging multimodal datasets, modern artificial intelligence techniques, such as deep learning, may provide the optimal opportunity to further characterize these associations, enhance our understanding of eye-body relationships and secure novel scalable approaches to the risk stratification of chronic complex disorders of ageing.

Machine Learning and DWI Brain Communicability Networks for Alzheimer’s Disease Detection

Signal processing and machine learning techniques are changing the clinical practice based on medical imaging from many perspectives. A major topic is related to (i) the development of computer aided diagnosis systems to provide clinicians with novel, non-invasive and low-cost support-tools, and (ii) to the development of new methodologies for the analysis of biomedical data for finding new disease biomarkers. Advancements have been recently achieved in the context of Alzheimer’s disease (AD) diagnosis through the use of diffusion weighted imaging (DWI) data. When combined with tractography algorithms, this imaging modality enables the reconstruction of the physical connections of the brain that can be subsequently investigated through a complex network-based approach. A graph metric particularly suited to describe the disruption of the brain connectivity due to AD is communicability. In this work, we develop a machine learning framework for the classification and feature importance analysis of AD based on communicability at the whole brain level. We fairly compare the performance of three state-of-the-art classification models, namely support vector machines, random forests and artificial neural networks, on the connectivity networks of a balanced cohort of healthy control subjects and AD patients from the ADNI database. Moreover, we clinically validate the information content of the communicability metric by performing a feature importance analysis. Both performance comparison and feature importance analysis provide evidence of the robustness of the method. The results obtained confirm that the whole brain structural communicability alterations due to AD are a valuable biomarker for the characterization and investigation of pathological conditions.

DeepSnap-Deep Learning Approach Predicts Progesterone Receptor Antagonist Activity With High Performance

The progesterone receptor (PR) is important therapeutic target for many malignancies and endocrine disorders due to its role in controlling ovulation and pregnancy via the reproductive cycle. Therefore, the modulation of PR activity using its agonists and antagonists is receiving increasing interest as novel treatment strategy. However, clinical trials using the PR modulators have not yet been found conclusive evidences. Recently, increasing evidence from several fields shows that the classification of chemical compounds, including agonists and antagonists, can be done with recent improvements in deep learning (DL) using deep neural network. Therefore, we recently proposed a novel DL-based quantitative structure-activity relationship (QSAR) strategy using transfer learning to build prediction models for agonists and antagonists. By employing this novel approach, referred as DeepSnap-DL method, which uses images captured from 3-dimension (3D) chemical structure with multiple angles as input data into the DL classification, we constructed prediction models of the PR antagonists in this study. Here, the DeepSnap-DL method showed a high performance prediction of the PR antagonists by optimization of some parameters and image adjustment from 3D-structures. Furthermore, comparison of the prediction models from this approach with conventional machine learnings (MLs) indicated the DeepSnap-DL method outperformed these MLs. Therefore, the models predicted by DeepSnap-DL would be powerful tool for not only QSAR field in predicting physiological and agonist/antagonist activities, toxicity, and molecular bindings; but also for identifying biological or pathological phenomena.

Synthesis of thiazolidin-4-ones and thiazinan-4-ones from 1-(2-aminoethyl)pyrrolidine as acetylcholinesterase inhibitors

The present study describes the synthesis of a novel series of thiazolidin-4-one and thiazinan-4-one using 1-(2-aminoethyl)pyrrolidine as amine precursor. All compounds were synthesised by one-pot three component cyclocondensation reaction from the amine, a substituted benzaldehyde and a mercaptocarboxylic acid. The compounds were obtained in moderate to good yields and were identified and characterised by ¹H, ¹³C, 2 D NMR and GC/MS techniques. The compounds also were screened for their in vitro acetylcholinesterase (AChE) activity in hippocampus and cerebral cortex on Wistar rats. The six most potent compounds have been investigated for their cytotoxicity by cell viability assay of astrocyte primary culture, an important cell of central nervous system. We highlighted two compounds (6a and 6k) that had the lowest IC₅₀ in hippocampus (5.20 and 4.46 µM) and cerebral cortex (7.40 and 6.83 µM). These preliminary and important results could be considered a starting point for the development of new AChE inhibitory agents.

Overview of MR Imaging Volumetric Quantification in Neurocognitive Disorders

This review article provides a general overview on the various methodologies for quantifying brain structure on magnetic resonance images of the human brain. This overview is followed by examples of applications in Alzheimer dementia and mild cognitive impairment. Other examples will include traumatic brain injury and other neurodegenerative dementias. Finally, an overview of general principles for protocol acquisition of magnetic resonance imaging for volumetric quantification will be discussed along with the current choices of FDA cleared algorithms for use in clinical practice.