Standardized evaluation of algorithms for computer-aided diagnosis of dementia based on structural MRI: the CADDementia challenge

Cortical and subcortical gray matter abnormalities in mild cognitive impairment

Gray matter changes are thought to be closely related to cognitive decline in mild cognitive impairment (MCI) patients. The study aimed to explore cortical and subcortical structural alterations in MCI and their association with cognitive assessment. 24 MCI patients and 22 normal controls (NCs) were included. Voxel-based morphometry (VBM), vertex-based shape analysis and surface-based morphometry (SBM) analysis were applied to explore subcortical nuclei volume, shape and cortical morphology. Correlations between structural changes and cognition were explored using spearman correlation analysis. Support vector machine (SVM) classification evaluated MCI identification accuracy. MCI patients showed significant atrophy in the left thalamus, left hippocampus, left amygdala, right pallidum, right hippocampus, along with inward deformation in the left amygdala. SBM analysis revealed that MCI group exhibited shallower sulci depth in the left hemisphere and increased cortical gyrification index (GI) in the right frontal gyrus. Correlation analysis showed the positive correlation between right hippocampus volume and episodic memory, while negative correlation between the altered GI and memory performance in MCI group. SVM analysis demonstrated superior performance of sulci depth and GI derived from SBM in MCI identification. When combined with cortical and subcortical metrics, SVM achieved a peak accuracy of 89 % in distinguishing MCI from NC. The study reveals significant gray matter structural changes in MCI, suggesting their potential role in underlying functional differences and neural mechanisms behind memory impairment in MCI.

Alzheimer's disease diagnosis in the metaverse

BACKGROUND AND OBJECTIVE

The importance of early diagnosis of Alzheimer's Disease (AD) is by no means negligible because no cure has been recognized for it rather than some therapies only lowering the pace of progression. The research gap reveals information on the lack of an automatic non-invasive approach toward the diagnosis of AD, in particular with the help of Virtual Reality (VR) and Artificial Intelligence. Another perspective highlights that current VR studies fail to incorporate a comprehensive range of cognitive tests and consider design notes for elderlies, leading to unreliable results.

METHODS

This paper tried to design a VR environment suitable for older adults in which three cognitive assessments namely: ADAS-Cog, Montreal Cognitive Assessment (MoCA), and Mini Mental State Exam (MMSE), are implemented. Moreover, a 3DCNN-ML model was trained based on the corresponding cognitive tests and Magnetic Resonance Imaging (MRI) with different modalities using the Alzheimer's Disease Neuroimaging Initiative 2 (ADNI2) dataset and incorporated into the application to predict if the patient suffers from AD.

RESULTS

The model has undergone three experiments with different modalities (Cognitive Scores (CS), MRI images, and CS-MRI). As for the CS-MRI experiment, the trained model achieved 97%, 95%, 95%, 96%, and 94% in terms of precision, recall, F1-score, AUC, and accuracy respectively. The considered design notes were also assessed using a new proposed questionnaire based on existing ones in terms of user experience, user interface, mechanics, in-env assistance, and VR induced symptoms and effects. The designed VR system provided an acceptable level of user experience, with participants reporting an enjoyable and immersive experience. While there were areas for improvement, including graphics and sound quality, as well as comfort issues with prolonged HMD use, the user interface and mechanics of the system were generally well-received.

CONCLUSIONS

The reported results state that our method's comprehensive analysis of 3D brain volumes and incorporation of cognitive scores enabled earlier detection of AD progression, potentially allowing for timely interventions and improved patient outcomes. The proposed integrated system provided us with promising insights for improvements in the diagnosis of AD using technologies.

Where developmental toxicity meets explainable artificial intelligence: state-of-the-art and perspectives

INTRODUCTION

The application of Artificial Intelligence (AI) to predictive toxicology is rapidly increasing, particularly aiming to develop non-testing methods that effectively address ethical concerns and reduce economic costs. In this context, Developmental Toxicity (Dev Tox) stands as a key human health endpoint, especially significant for safeguarding maternal and child well-being.

AREAS COVERED

This review outlines the existing methods employed in Dev Tox predictions and underscores the benefits of utilizing New Approach Methodologies (NAMs), specifically focusing on eXplainable Artificial Intelligence (XAI), which proves highly efficient in constructing reliable and transparent models aligned with recommendations from international regulatory bodies.

EXPERT OPINION

The limited availability of high-quality data and the absence of dependable Dev Tox methodologies render XAI an appealing avenue for systematically developing interpretable and transparent models, which hold immense potential for both scientific evaluations and regulatory decision-making.

Evaluation of a multimodal diagnostic algorithm for prediction of cognitive impairment in elderly patients with dizziness

BACKGROUND

The current diagnostic workup for chronic dizziness in elderly patients often neglects neuropsychological assessment, thus missing a relevant proportion of patients, who perceive dizziness as a subjective chief complaint of a concomitant cognitive impairment. This study aimed to establish risk prediction models for cognitive impairment in chronic dizzy patients based on data sources routinely collected in a dizziness center.

METHODS

One hundred patients (age: 74.7 ± 7.1 years, 41.0% women) with chronic dizziness were prospectively characterized by (1) neuro-otological testing, (2) quantitative gait assessment, (3) graduation of focal brain atrophy and white matter lesion load, and (4) cognitive screening (MoCA). A linear regression model was trained to predict patients' total MoCA score based on 16 clinical features derived from demographics, vestibular testing, gait analysis, and imaging scales. Additionally, we trained a binary logistic regression model on the same data sources to identify those patients with a cognitive impairment (i.e., MoCA < 25).

RESULTS

The linear regression model explained almost half of the variance of patients' total MoCA score (R2 = 0.49; mean absolute error: 1.7). The most important risk-predictors of cognitive impairment were age (β = - 0.75), pathological Romberg's sign (β = - 1.05), normal caloric test results (β = - 0.8), slower timed-up-and-go test (β = - 0.67), frontal (β = - 0.6) and temporal (β = - 0.54) brain atrophy. The binary classification yielded an area under the curve of 0.84 (95% CI 0.70-0.98) in distinguishing between cognitively normal and impaired patients.

CONCLUSIONS

The need for cognitive testing in patients with chronic dizziness can be efficiently approximated by available data sources from routine diagnostic workup in a dizziness center.

The STOIC2021 COVID-19 AI challenge: Applying reusable training methodologies to private data

Challenges drive the state-of-the-art of automated medical image analysis. The quantity of public training data that they provide can limit the performance of their solutions. Public access to the training methodology for these solutions remains absent. This study implements the Type Three (T3) challenge format, which allows for training solutions on private data and guarantees reusable training methodologies. With T3, challenge organizers train a codebase provided by the participants on sequestered training data. T3 was implemented in the STOIC2021 challenge, with the goal of predicting from a computed tomography (CT) scan whether subjects had a severe COVID-19 infection, defined as intubation or death within one month. STOIC2021 consisted of a Qualification phase, where participants developed challenge solutions using 2000 publicly available CT scans, and a Final phase, where participants submitted their training methodologies with which solutions were trained on CT scans of 9724 subjects. The organizers successfully trained six of the eight Final phase submissions. The submitted codebases for training and running inference were released publicly. The winning solution obtained an area under the receiver operating characteristic curve for discerning between severe and non-severe COVID-19 of 0.815. The Final phase solutions of all finalists improved upon their Qualification phase solutions.

Alcohol Use Disorder and Dementia: A Review

PURPOSE

By 2040, 21.6% of Americans will be over age 65, and the population of those older than age 85 is estimated to reach 14.4 million. Although not causative, older age is a risk factor for dementia: every 5 years beyond age 65, the risk doubles; approximately one-third of those older than age 85 are diagnosed with dementia. As current alcohol consumption among older adults is significantly higher compared to previous generations, a pressing question is whether drinking alcohol increases the risk for Alzheimer's disease or other forms of dementia.

SEARCH METHODS

Databases explored included PubMed, Web of Science, and ScienceDirect. To accomplish this narrative review on the effects of alcohol consumption on dementia risk, the literature covered included clinical diagnoses, epidemiology, neuropsychology, postmortem pathology, neuroimaging and other biomarkers, and translational studies. Searches conducted between January 12 and August 1, 2023, included the following terms and combinations: "aging," "alcoholism," "alcohol use disorder (AUD)," "brain," "CNS," "dementia," "Wernicke," "Korsakoff," "Alzheimer," "vascular," "frontotemporal," "Lewy body," "clinical," "diagnosis," "epidemiology," "pathology," "autopsy," "postmortem," "histology," "cognitive," "motor," "neuropsychological," "magnetic resonance," "imaging," "PET," "ligand," "degeneration," "atrophy," "translational," "rodent," "rat," "mouse," "model," "amyloid," "neurofibrillary tangles," "α-synuclein," or "presenilin." When relevant, "species" (i.e., "humans" or "other animals") was selected as an additional filter. Review articles were avoided when possible.

SEARCH RESULTS

The two terms "alcoholism" and "aging" retrieved about 1,350 papers; adding phrases-for example, "postmortem" or "magnetic resonance"-limited the number to fewer than 100 papers. Using the traditional term, "alcoholism" with "dementia" resulted in 876 citations, but using the currently accepted term "alcohol use disorder (AUD)" with "dementia" produced only 87 papers. Similarly, whereas the terms "Alzheimer's" and "alcoholism" yielded 318 results, "Alzheimer's" and "alcohol use disorder (AUD)" returned only 40 citations. As pertinent postmortem pathology papers were published in the 1950s and recent animal models of Alzheimer's disease were created in the early 2000s, articles referenced span the years 1957 to 2024. In total, more than 5,000 articles were considered; about 400 are herein referenced.

DISCUSSION AND CONCLUSIONS

Chronic alcohol misuse accelerates brain aging and contributes to cognitive impairments, including those in the mnemonic domain. The consensus among studies from multiple disciplines, however, is that alcohol misuse can increase the risk for dementia, but not necessarily Alzheimer's disease. Key issues to consider include the reversibility of brain damage following abstinence from chronic alcohol misuse compared to the degenerative and progressive course of Alzheimer's disease, and the characteristic presence of protein inclusions in the brains of people with Alzheimer's disease, which are absent in the brains of those with AUD.

Data-driven modelling of neurodegenerative disease progression: thinking outside the black box

Data-driven disease progression models are an emerging set of computational tools that reconstruct disease timelines for long-term chronic diseases, providing unique insights into disease processes and their underlying mechanisms. Such methods combine a priori human knowledge and assumptions with large-scale data processing and parameter estimation to infer long-term disease trajectories from short-term data. In contrast to 'black box' machine learning tools, data-driven disease progression models typically require fewer data and are inherently interpretable, thereby aiding disease understanding in addition to enabling classification, prediction and stratification. In this Review, we place the current landscape of data-driven disease progression models in a general framework and discuss their enhanced utility for constructing a disease timeline compared with wider machine learning tools that construct static disease profiles. We review the insights they have enabled across multiple neurodegenerative diseases, notably Alzheimer disease, for applications such as determining temporal trajectories of disease biomarkers, testing hypotheses about disease mechanisms and uncovering disease subtypes. We outline key areas for technological development and translation to a broader range of neuroscience and non-neuroscience applications. Finally, we discuss potential pathways and barriers to integrating disease progression models into clinical practice and trial settings.

Breast Multiparametric MRI for Prediction of Neoadjuvant Chemotherapy Response in Breast Cancer: The BMMR2 Challenge

Purpose To describe the design, conduct, and results of the Breast Multiparametric MRI for prediction of neoadjuvant chemotherapy Response (BMMR2) challenge. Materials and Methods The BMMR2 computational challenge opened on May 28, 2021, and closed on December 21, 2021. The goal of the challenge was to identify image-based markers derived from multiparametric breast MRI, including diffusion-weighted imaging (DWI) and dynamic contrast-enhanced (DCE) MRI, along with clinical data for predicting pathologic complete response (pCR) following neoadjuvant treatment. Data included 573 breast MRI studies from 191 women (mean age [±SD], 48.9 years ± 10.56) in the I-SPY 2/American College of Radiology Imaging Network (ACRIN) 6698 trial (ClinicalTrials.gov: NCT01042379). The challenge cohort was split into training (60%) and test (40%) sets, with teams blinded to test set pCR outcomes. Prediction performance was evaluated by area under the receiver operating characteristic curve (AUC) and compared with the benchmark established from the ACRIN 6698 primary analysis. Results Eight teams submitted final predictions. Entries from three teams had point estimators of AUC that were higher than the benchmark performance (AUC, 0.782 [95% CI: 0.670, 0.893], with AUCs of 0.803 [95% CI: 0.702, 0.904], 0.838 [95% CI: 0.748, 0.928], and 0.840 [95% CI: 0.748, 0.932]). A variety of approaches were used, ranging from extraction of individual features to deep learning and artificial intelligence methods, incorporating DCE and DWI alone or in combination. Conclusion The BMMR2 challenge identified several models with high predictive performance, which may further expand the value of multiparametric breast MRI as an early marker of treatment response. Clinical trial registration no. NCT01042379 Keywords: MRI, Breast, Tumor Response Supplemental material is available for this article. © RSNA, 2024.

Explainability of random survival forests in predicting conversion risk from mild cognitive impairment to Alzheimer's disease

Random Survival Forests (RSF) has recently showed better performance than statistical survival methods as Cox proportional hazard (CPH) in predicting conversion risk from mild cognitive impairment (MCI) to Alzheimer's disease (AD). However, RSF application in real-world clinical setting is still limited due to its black-box nature.For this reason, we aimed at providing a comprehensive study of RSF explainability with SHapley Additive exPlanations (SHAP) on biomarkers of stable and progressive patients (sMCI and pMCI) from Alzheimer's Disease Neuroimaging Initiative. We evaluated three global explanations-RSF feature importance, permutation importance and SHAP importance-and we quantitatively compared them with Rank-Biased Overlap (RBO). Moreover, we assessed whether multicollinearity among variables may perturb SHAP outcome. Lastly, we stratified pMCI test patients in high, medium and low risk grade, to investigate individual SHAP explanation of one pMCI patient per risk group.We confirmed that RSF had higher accuracy (0.890) than CPH (0.819), and its stability and robustness was demonstrated by high overlap (RBO > 90%) between feature rankings within first eight features. SHAP local explanations with and without correlated variables had no substantial difference, showing that multicollinearity did not alter the model. FDG, ABETA42 and HCI were the first important features in global explanations, with the highest contribution also in local explanation. FAQ, mPACCdigit, mPACCtrailsB and RAVLT immediate had the highest influence among all clinical and neuropsychological assessments in increasing progression risk, as particularly evident in pMCI patients' individual explanation. In conclusion, our findings suggest that RSF represents a useful tool to support clinicians in estimating conversion-to-AD risk and that SHAP explainer boosts its clinical utility with intelligible and interpretable individual outcomes that highlights key features associated with AD prognosis.

Improving clinical efficiency in screening for cognitive impairment due to Alzheimer's

INTRODUCTION

To reduce demands on expert time and improve clinical efficiency, we developed a framework to evaluate whether inexpensive, accessible data could accurately classify Alzheimer's disease (AD) clinical diagnosis and predict the likelihood of progression.

METHODS

We stratified relevant data into three tiers: obtainable at primary care (low-cost), mostly available at specialty visits (medium-cost), and research-only (high-cost). We trained several machine learning models, including a hierarchical model, an ensemble model, and a clustering model, to distinguish between diagnoses of cognitively unimpaired, mild cognitive impairment, and dementia due to AD.

RESULTS

All models showed viable classification, but the hierarchical and ensemble models outperformed the conventional model. Classifier "error" was predictive of progression rates, and cluster membership identified subgroups with high and low risk of progression within 1.5 to 3 years.

DISCUSSION

Accessible, inexpensive clinical data can be used to guide AD diagnosis and are predictive of current and future disease states.

HIGHLIGHTS

Classification performance using cost-effective features was accurate and robustHierarchical classification outperformed conventional multinomial classificationClassification labels indicated significant changes in conversion risk at follow-upA clustering-classification method identified subgroups at high risk of decline.

An eXplainability Artificial Intelligence approach to brain connectivity in Alzheimer's disease

The advent of eXplainable Artificial Intelligence (XAI) has revolutionized the way human experts, especially from non-computational domains, approach artificial intelligence; this is particularly true for clinical applications where the transparency of the results is often compromised by the algorithmic complexity. Here, we investigate how Alzheimer's disease (AD) affects brain connectivity within a cohort of 432 subjects whose T1 brain Magnetic Resonance Imaging data (MRI) were acquired within the Alzheimer's Disease Neuroimaging Initiative (ADNI). In particular, the cohort included 92 patients with AD, 126 normal controls (NC) and 214 subjects with mild cognitive impairment (MCI). We show how graph theory-based models can accurately distinguish these clinical conditions and how Shapley values, borrowed from game theory, can be adopted to make these models intelligible and easy to interpret. Explainability analyses outline the role played by regions like putamen, middle and superior temporal gyrus; from a class-related perspective, it is possible to outline specific regions, such as hippocampus and amygdala for AD and posterior cingulate and precuneus for MCI. The approach is general and could be adopted to outline how brain connectivity affects specific brain regions.

Genetic algorithms based optimized hybrid deep learning model for explainable Alzheimer's prediction based on temporal multimodal cognitive data.. [DOI: 10.21203/rs.3.rs-3250006/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Alzheimer's Disease (AD) is an irreversible neurodegenerative disease. Its early detection is crucial to stop disease progression at an early stage. Most deep learning (DL) literature focused on neuroimage analysis. However, there is no noticed effect of these studies in the real environment. Model's robustness, cost, and interpretability are considered the main reasons for these limitations. The medical intuition of physicians is to evaluate the clinical biomarkers of patients then test their neuroimages. Cognitive scores provide an medically acceptable and cost-effective alternative for the neuroimages to predict AD progression. Each score is calculated from a collection of sub-scores which provide a deeper insight about patient conditions. No study in the literature have explored the role of these multimodal time series sub-scores to predict AD progression. We propose a hybrid CNN-LSTM DL model for predicting AD progression based on the fusion of four longitudinal cognitive sub-scores modalities. Bayesian optimizer has been used to select the best DL architecture. A genetic algorithms based feature selection optimization step has been added to the pipeline to select the best features from extracted deep representations of CNN-LSTM. The SoftMax classifier has been replaced by a robust and optimized random forest classifier. Extensive experiments using the ADNI dataset investigated the role of each optimization step, and the proposed model achieved the best results compared to other DL and classical machine learning models. The resulting model is robust, but it is a black box and it is difficult to understand the logic behind its decisions. Trustworthy AI models must be robust and explainable. We used SHAP and LIME to provide explainability features for the proposed model. The resulting trustworthy model has a great potential to be used to provide decision support in the real environments.

Artificial Intelligence in Neuroradiology: A Review of Current Topics and Competition Challenges

There is an expanding body of literature that describes the application of deep learning and other machine learning and artificial intelligence methods with potential relevance to neuroradiology practice. In this article, we performed a literature review to identify recent developments on the topics of artificial intelligence in neuroradiology, with particular emphasis on large datasets and large-scale algorithm assessments, such as those used in imaging AI competition challenges. Numerous applications relevant to ischemic stroke, intracranial hemorrhage, brain tumors, demyelinating disease, and neurodegenerative/neurocognitive disorders were discussed. The potential applications of these methods to spinal fractures, scoliosis grading, head and neck oncology, and vascular imaging were also reviewed. The AI applications examined perform a variety of tasks, including localization, segmentation, longitudinal monitoring, diagnostic classification, and prognostication. While research on this topic is ongoing, several applications have been cleared for clinical use and have the potential to augment the accuracy or efficiency of neuroradiologists.

Challenges of implementing computer-aided diagnostic models for neuroimages in a clinical setting

Advances in artificial intelligence have cultivated a strong interest in developing and validating the clinical utilities of computer-aided diagnostic models. Machine learning for diagnostic neuroimaging has often been applied to detect psychological and neurological disorders, typically on small-scale datasets or data collected in a research setting. With the collection and collation of an ever-growing number of public datasets that researchers can freely access, much work has been done in adapting machine learning models to classify these neuroimages by diseases such as Alzheimer's, ADHD, autism, bipolar disorder, and so on. These studies often come with the promise of being implemented clinically, but despite intense interest in this topic in the laboratory, limited progress has been made in clinical implementation. In this review, we analyze challenges specific to the clinical implementation of diagnostic AI models for neuroimaging data, looking at the differences between laboratory and clinical settings, the inherent limitations of diagnostic AI, and the different incentives and skill sets between research institutions, technology companies, and hospitals. These complexities need to be recognized in the translation of diagnostic AI for neuroimaging from the laboratory to the clinic.

Machine Learning-Based Routine Laboratory Tests Predict One-Year Cognitive and Functional Decline in a Population Aged 75+ Years

BACKGROUND

Cognitive and functional decline are common problems in older adults, especially in those 75+ years old. Currently, there is no specific plasma biomarker able to predict this decline in healthy old-age people. Machine learning (ML) is a subarea of artificial intelligence (AI), which can be used to predict outcomes Aim: This study aimed to evaluate routine laboratory variables able to predict cognitive and functional impairment, using ML algorithms, in a cohort aged 75+ years, in a one-year follow-up study.

METHOD

One hundred and thirty-two older adults aged 75+ years were selected through a community-health public program or from long-term-care institutions. Their functional and cognitive performances were evaluated at baseline and one year later using a functional activities questionnaire, Mini-Mental State Examination, and the Brief Cognitive Screening Battery. Routine laboratory tests were performed at baseline. ML algorithms-random forest, support vector machine (SVM), and XGBoost-were applied in order to describe the best model able to predict cognitive and functional decline using routine tests as features.

RESULTS

The random forest model showed better accuracy than other algorithms and included triglycerides, glucose, hematocrit, red cell distribution width (RDW), albumin, hemoglobin, globulin, high-density lipoprotein cholesterol (HDL-c), thyroid-stimulating hormone (TSH), creatinine, lymphocyte, erythrocyte, platelet/leucocyte (PLR), and neutrophil/leucocyte (NLR) ratios, and alanine transaminase (ALT), leukocyte, low-density lipoprotein cholesterol (LDL-c), cortisol, gamma-glutamyl transferase (GGT), and eosinophil as features to predict cognitive decline (accuracy = 0.79). For functional decline, the most important features were platelet, PLR and NLR, hemoglobin, globulin, cortisol, RDW, glucose, basophil, B12 vitamin, creatinine, GGT, ALT, aspartate transferase (AST), eosinophil, hematocrit, erythrocyte, triglycerides, HDL-c, and monocyte (accuracy = 0.92).

CONCLUSIONS

Routine laboratory variables could be applied to predict cognitive and functional decline in oldest-old populations using ML algorithms.

Long-Term and Meditation-Specific Modulations of Brain Connectivity Revealed Through Multivariate Pattern Analysis

Neuroimaging studies have provided evidence that extensive meditation practice modifies the functional and structural properties of the human brain, such as large-scale brain region interplay. However, it remains unclear how different meditation styles are involved in the modulation of these large-scale brain networks. Here, using machine learning and fMRI functional connectivity, we investigated how focused attention and open monitoring meditation styles impact large-scale brain networks. Specifically, we trained a classifier to predict the meditation style in two groups of subjects: expert Theravada Buddhist monks and novice meditators. We showed that the classifier was able to discriminate the meditation style only in the expert group. Additionally, by inspecting the trained classifier, we observed that the Anterior Salience and the Default Mode networks were relevant for the classification, in line with their theorized involvement in emotion and self-related regulation in meditation. Interestingly, results also highlighted the role of specific couplings between areas crucial for regulating attention and self-awareness as well as areas related to processing and integrating somatosensory information. Finally, we observed a larger involvement of left inter-hemispheric connections in the classification. In conclusion, our work supports the evidence that extensive meditation practice modulates large-scale brain networks, and that the different meditation styles differentially affect connections that subserve style-specific functions.

Towards better interpretable and generalizable AD detection using collective artificial intelligence

Alzheimer's Disease is the most common cause of dementia. Accurate diagnosis and prognosis of this disease are essential to design an appropriate treatment plan, increasing the life expectancy of the patient. Intense research has been conducted on the use of machine learning to identify Alzheimer's Disease from neuroimaging data, such as structural magnetic resonance imaging. In recent years, advances of deep learning in computer vision suggest a new research direction for this problem. Current deep learning-based approaches in this field, however, have a number of drawbacks, including the interpretability of model decisions, a lack of generalizability information and a lower performance compared to traditional machine learning techniques. In this paper, we design a two-stage framework to overcome these limitations. In the first stage, an ensemble of 125 U-Nets is used to grade the input image, producing a 3D map that reflects the disease severity at voxel-level. This map can help to localize abnormal brain areas caused by the disease. In the second stage, we model a graph per individual using the generated grading map and other information about the subject. We propose to use a graph convolutional neural network classifier for the final classification. As a result, our framework demonstrates comparative performance to the state-of-the-art methods in different datasets for both diagnosis and prognosis. We also demonstrate that the use of a large ensemble of U-Nets offers a better generalization capacity for our framework.

A review on Alzheimer's disease classification from normal controls and mild cognitive impairment using structural MR images

Alzheimer's disease (AD) is an irreversible neurodegenerative brain disorder that degrades the memory and cognitive ability in elderly people. The main reason for memory loss and reduction in cognitive ability is the structural changes in the brain that occur due to neuronal loss. These structural changes are most conspicuous in the hippocampus, cortex, and grey matter and can be assessed by using neuroimaging techniques viz. Positron Emission Tomography (PET), structural Magnetic Resonance Imaging (MRI) and functional MRI (fMRI), etc. Out of these neuroimaging techniques, structural MRI has evolved as the best technique as it indicates the best soft tissue contrast and high spatial resolution which is important for AD detection. Currently, the focus of researchers is on predicting the conversion of Mild Cognitive Impairment (MCI) into AD. MCI represents the transition state between expected cognitive changes with normal aging and Alzheimer's disease. Not every MCI patient progresses into Alzheimer's disease. MCI can develop into stable MCI (sMCI, patients are called non-converters) or into progressive MCI (pMCI, patients are diagnosed as MCI converters). This paper discusses the prognosis of MCI to AD conversion and presents a review of structural MRI-based studies for AD detection. AD detection framework includes feature extraction, feature selection, and classification process. This paper reviews the studies for AD detection based on different feature extraction methods and machine learning algorithms for classification. The performance of various feature extraction methods has been compared and it has been observed that the wavelet transform-based feature extraction method would give promising results for AD classification. The present study indicates that researchers are successful in classifying AD from Normal Controls (N_rmC) but, it still requires a lot of work to be done for MCI/ N_rmC and MCI/AD, which would help in detecting AD at its early stage.

TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity

Herein, a robust and reproducible eXplainable Artificial Intelligence (XAI) approach is presented, which allows prediction of developmental toxicity, a challenging human-health endpoint in toxicology. The application of XAI as an alternative method is of the utmost importance with developmental toxicity being one of the most animal-intensive areas of regulatory toxicology. In this work, the established CAESAR (Computer Assisted Evaluation of industrial chemical Substances According to Regulations) training set made of 234 chemicals for model learning is employed. Two test sets, including as a whole 585 chemicals, were instead used for validation and generalization purposes. The proposed framework favorably compares with the state-of-the-art approaches in terms of accuracy, sensitivity, and specificity, thus resulting in a reliable support system for developmental toxicity ensuring informativeness, uncertainty estimation, generalization, and transparency. Based on the eXtreme Gradient Boosting (XGB) algorithm, our predictive model provides easy interpretative keys based on specific molecular descriptors and structural alerts enabling one to distinguish toxic and nontoxic chemicals. Inspired by the Organisation for Economic Co-operation and Development (OECD) principles for the validation of Quantitative Structure-Activity Relationships (QSARs) for regulatory purposes, the results are summarized in a standard report in portable document format, enclosing also details concerned with a density-based model applicability domain and SHAP (SHapley Additive exPlanations) explainability, the latter particularly useful to better understand the effective roles played by molecular features. Notably, our model has been implemented in TIRESIA (Toxicology Intelligence and Regulatory Evaluations for Scientific and Industry Applications), a free of charge web platform available at http://tiresia.uniba.it.

The KNee OsteoArthritis Prediction (KNOAP2020) challenge: An image analysis challenge to predict incident symptomatic radiographic knee osteoarthritis from MRI and X-ray images

OBJECTIVES

The KNee OsteoArthritis Prediction (KNOAP2020) challenge was organized to objectively compare methods for the prediction of incident symptomatic radiographic knee osteoarthritis within 78 months on a test set with blinded ground truth.

DESIGN

The challenge participants were free to use any available data sources to train their models. A test set of 423 knees from the Prevention of Knee Osteoarthritis in Overweight Females (PROOF) study consisting of magnetic resonance imaging (MRI) and X-ray image data along with clinical risk factors at baseline was made available to all challenge participants. The ground truth outcomes, i.e., which knees developed incident symptomatic radiographic knee osteoarthritis (according to the combined ACR criteria) within 78 months, were not provided to the participants. To assess the performance of the submitted models, we used the area under the receiver operating characteristic curve (ROCAUC) and balanced accuracy (BACC).

RESULTS

Seven teams submitted 23 entries in total. A majority of the algorithms were trained on data from the Osteoarthritis Initiative. The model with the highest ROCAUC (0.64 (95% confidence interval (CI): 0.57-0.70)) used deep learning to extract information from X-ray images combined with clinical variables. The model with the highest BACC (0.59 (95% CI: 0.52-0.65)) ensembled three different models that used automatically extracted X-ray and MRI features along with clinical variables.

CONCLUSION

The KNOAP2020 challenge established a benchmark for predicting incident symptomatic radiographic knee osteoarthritis. Accurate prediction of incident symptomatic radiographic knee osteoarthritis is a complex and still unsolved problem requiring additional investigation.

Investigating Tissue-Specific Abnormalities in Alzheimer's Disease with Multi-Shell Diffusion MRI

BACKGROUND

Most studies using diffusion-weighted MRI (DW-MRI) in Alzheimer's disease (AD) have focused their analyses on white matter (WM) microstructural changes using the diffusion (kurtosis) tensor model. Although recent works have addressed some limitations of the tensor model, such as the representation of crossing fibers and partial volume effects with cerebrospinal fluid (CSF), the focus remains in modeling and analyzing the WM.

OBJECTIVE

In this work, we present a brain analysis approach for DW-MRI that disentangles multiple tissue compartments as well as micro- and macroscopic effects to investigate differences between groups of subjects in the AD continuum and controls.

METHODS

By means of the multi-tissue constrained spherical deconvolution of multi-shell DW-MRI, underlying brain tissue is modeled with a WM fiber orientation distribution function along with the contributions of gray matter (GM) and CSF to the diffusion signal. From this multi-tissue model, a set of measures capturing tissue diffusivity properties and morphology are extracted. Group differences were interrogated following fixel-, voxel-, and tensor-based morphometry approaches while including strong FWE control across multiple comparisons.

RESULTS

Abnormalities related to AD stages were detected in WM tracts including the splenium, cingulum, longitudinal fasciculi, and corticospinal tract. Changes in tissue composition were identified, particularly in the medial temporal lobe and superior longitudinal fasciculus.

CONCLUSION

This analysis framework constitutes a comprehensive approach allowing simultaneous macro and microscopic assessment of WM, GM, and CSF, from a single DW-MRI dataset.

Hierarchical multi-class Alzheimer’s disease diagnostic framework using imaging and clinical features

Due to the clinical continuum of Alzheimer’s disease (AD), the accuracy of early diagnostic remains unsatisfactory and warrants further research. The objectives of this study were: (1) to develop an effective hierarchical multi-class framework for clinical populations, namely, normal cognition (NC), early mild cognitive impairment (EMCI), late mild cognitive impairment (LMCI), and AD, and (2) to explore the geometric properties of cognition-related anatomical structures in the cerebral cortex. A total of 1,670 participants were enrolled in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database, comprising 985 participants (314 NC, 208 EMCI, 258 LMCI, and 205 AD) in the model development set and 685 participants (417 NC, 110 EMCI, 83 LMCI, and 75 AD) after 2017 in the temporal validation set. Four cortical geometric properties for 148 anatomical structures were extracted, namely, cortical thickness (CTh), fractal dimension (FD), gyrification index (GI), and sulcus depth (SD). By integrating these imaging features with Mini-Mental State Examination (MMSE) scores at four-time points after the initial visit, we identified an optimal subset of 40 imaging features using the temporally constrained group sparse learning method. The combination of selected imaging features and clinical variables improved the multi-class performance using the AdaBoost algorithm, with overall accuracy rates of 0.877 in the temporal validation set. Clinical Dementia Rating (CDR) was the primary clinical variable associated with AD-related populations. The most discriminative imaging features included the bilateral CTh of the dorsal part of the posterior cingulate gyrus, parahippocampal gyrus (PHG), parahippocampal part of the medial occipito-temporal gyrus, and angular gyrus, the GI of the left inferior segment of the insula circular sulcus, and the CTh and SD of the left superior temporal sulcus (STS). Our hierarchical multi-class framework underscores the utility of combining cognitive variables with imaging features and the reliability of surface-based morphometry, facilitating more accurate early diagnosis of AD in clinical practice.

Deep transfer learning-based fully automated detection and classification of Alzheimer's disease on brain MRI

OBJECTIVES

To employ different automated convolutional neural network (CNN)-based transfer learning (TL) methods for both binary and multiclass classification of Alzheimer's disease (AD) using brain MRI.

METHODS

Herein, we applied three popular pre-trained CNN models (ResNet101, Xception, and InceptionV3) using a fine-tuned approach of TL on 3D T1-weighted brain MRI from a subset of ADNI dataset (n = 305 subjects). To evaluate power of TL, the aforementioned networks were also trained from scratch for performance comparison. Initially, Unet network segmentedthe MRI scans into characteristic components of gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). The proposed networks were trained and tested over the pre-processed and augmented segmented and whole images for both binary (NC/AD + progressive mild cognitive impairment (pMCI)+stable MCI (sMCI)) and 4-class (AD/pMCI/sMCI/NC) classification. Also, two independent test sets from the OASIS (n = 30) and AIBL (n = 60) datasets were used to externally assess the performance of the proposed algorithms.

RESULTS

The proposed TL-based CNN models achieved better performance compared to the training CNN models from scratch. On the ADNI test set, InceptionV3-TL achieved the highest accuracy of 93.75% and AUC of 92.0% for binary classification, as well as the highest accuracy of 93.75% and AUC of 96.0% for multiclass classification of AD on the whole images. On the OASIS test set, InceptionV3-TL outperformed two other models by achieving 93.33% accuracy with 93.0% AUC in binary classification of AD on the whole images. On the AIBL test set, InceptionV3-TL also outperformed two other models in both binary and multiclass classification tasks on the whole MR images and achieved accuracy/AUC of 93.33%/95.0% and 90.0%/93.0%, respectively. The GM segment as input provided the highest performance in both binary and multiclass classification of AD, as compared to the WM and CSF segments.

CONCLUSION

This study demonstrates the potential of applying deep TL approach for automated detection and classification of AD using brain MRI with high accuracy and robustness across internal and external test data, suggesting that these models can possibly be used as a supportive tool to assist clinicians in creating objective opinion and correct diagnosis.

ADVANCES IN KNOWLEDGE

We used CNN-based TL approaches and the augmentation techniques to overcome the insufficient data problem. Our study provides evidence that deep TL algorithms can be used for both binary and multiclass classification of AD with high accuracy.

DAFT: A universal module to interweave tabular data and 3D images in CNNs

Prior work on Alzheimer's Disease (AD) has demonstrated that convolutional neural networks (CNNs) can leverage the high-dimensional image information for diagnosing patients. Beside such data-driven approaches, many established biomarkers exist and are typically represented as tabular data, such as demographics, genetic alterations, or laboratory measurements from cerebrospinal fluid. However, little research has focused on the effective integration of tabular data into existing CNN architectures to improve patient diagnosis. We introduce the Dynamic Affine Feature Map Transform (DAFT), a general-purpose module for CNNs that incites or represses high-level concepts learned from a 3D image by conditioning feature maps of a convolutional layer on both a patient's image and tabular clinical information. This is achieved by using an auxiliary neural network that outputs a scaling factor and offset to dynamically apply an affine transformation to the feature maps of a convolutional layer. In our experiments on AD diagnosis and time-to-dementia prediction, we show that the DAFT is highly effective in combining 3D image and tabular information by achieving a mean balanced accuracy of 0.622 for diagnosis, and mean c-index of 0.748 for time-to-dementia prediction, thus outperforming all baseline methods. Finally, our extensive ablation study and empirical experiments reveal that the performance improvement due to the DAFT is robust with respect to many design choices.

Robust Brain Age Estimation based on sMRI via Nonlinear Age-Adaptive Ensemble Learning

Precise prediction on brain age is urgently needed by many biomedical areas including mental rehabilitation prognosis as well as various medicine or treatment trials. People began to realize that contrasting physical (real) age and predicted brain age can help to highlight brain issues and evaluate if patients' brains are healthy or not. Such age prediction is often challenging for single model-based prediction, while the conditions of brains vary drastically over age. In this work, we present an age-adaptive ensemble model that is based on the combination of four different machine learning algorithms, including a support vector machine (SVR), a convolutional neural network (CNN) model, and the popular GoogLeNet and ResNet deep networks. The ensemble model proposed here is nonlinearly adaptive, where age is taken as a key factor in the nonlinear combination of various single-algorithm-based independent models. In our age-adaptive ensemble method, the weights of each model are learned automatically as nonlinear functions over age instead of fixed values, while brain age estimation is based on such an age-adaptive integration of various single models. The quality of the model is quantified by the mean absolute errors (MAE) and spearman correlation between the predicted age and the actual age, with the least MAE and the highest Spearman correlation representing the highest accuracy in age prediction. By testing on the Predictive Analysis Challenge 2019 (PAC 2019) dataset, our novel ensemble model has achieved a MAE down to 3.19, which is a significantly increased accuracy in this brain age competition. If deployed in the real world, our novel ensemble model having an improved accuracy could potentially help doctors to identify the risk of brain diseases more accurately and quickly, thus helping pharmaceutical companies develop drugs or treatments precisely, and potential offer a new powerful tool for researchers in the field of brain science.

Combined Multi-Atlas and Multi-Layer Perception for Alzheimer's Disease Classification

Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disease. To distinguish the stage of the disease, AD classification technology challenge has been proposed in Pattern Recognition and Computer Vision 2021 (PRCV 2021) which provides the gray volume and average cortical thickness data extracted in multiple atlases from magnetic resonance imaging (MRI). Traditional methods either train with convolutional neural network (CNN) by MRI data to adapt the spatial features of images or train with recurrent neural network (RNN) by temporal features to predict the next stage. However, the morphological features from the challenge have been extracted into discrete values. We present a multi-atlases multi-layer perceptron (MAMLP) approach to deal with the relationship between morphological features and the stage of the disease. The model consists of multiple multi-layer perceptron (MLP) modules, and morphological features extracted from different atlases will be classified by different MLP modules. The final vote of all classification results obtains the predicted disease stage. Firstly, to preserve the diversity of brain features, the most representative atlases are chosen from groups of similar atlases, and one atlas is selected in each group. Secondly, each atlas is fed into one MLP to fetch the score of the classification. Thirdly, to obtain more stable results, scores from different atlases are combined to vote the result of the classification. Based on this approach, we rank 10th among 373 teams in the challenge. The results of the experiment indicate as follows: (1) Group selection of atlas reduces the number of features required without reducing the accuracy of the model; (2) The MLP architecture achieves better performance than CNN and RNN networks in morphological features; and (3) Compared with other networks, the combination of multiple MLP networks has faster convergence of about 40% and makes the classification more stable.

Explainable AI toward understanding the performance of the top three TADPOLE Challenge methods in the forecast of Alzheimer’s disease diagnosis

The Alzheimer′s Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge is the most comprehensive challenge to date with regard to the number of subjects, considered features, and challenge participants. The initial objective of TADPOLE was the identification of the most predictive data, features, and methods for the progression of subjects at risk of developing Alzheimer′s. The challenge was successful in recognizing tree-based ensemble methods such as gradient boosting and random forest as the best methods for the prognosis of the clinical status in Alzheimer’s disease (AD). However, the challenge outcome was limited to which combination of data processing and methods exhibits the best accuracy; hence, it is difficult to determine the contribution of the methods to the accuracy. The quantification of feature importance was globally approached by all the challenge participant methods. In addition, TADPOLE provided general answers that focused on improving performance while ignoring important issues such as interpretability. The purpose of this study is to intensively explore the models of the top three TADPOLE Challenge methods in a common framework for fair comparison. In addition, for these models, the most meaningful features for the prognosis of the clinical status of AD are studied and the contribution of each feature to the accuracy of the methods is quantified. We provide plausible explanations as to why the methods achieve such accuracy, and we investigate whether the methods use information coherent with clinical knowledge. Finally, we approach these issues through the analysis of SHapley Additive exPlanations (SHAP) values, a technique that has recently attracted increasing attention in the field of explainable artificial intelligence (XAI).

Artificial intelligence in brain MRI analysis of Alzheimer's disease over the past 12 years: A systematic review

INTRODUCTION

Multiple structural brain changes in Alzheimer's disease (AD) and mild cognitive impairment (MCI) have been revealed on magnetic resonance imaging (MRI). There is a fast-growing effort in applying artificial intelligence (AI) to analyze these data. Here, we review and evaluate the AI studies in brain MRI analysis with synthesis.

METHODS

A systematic review of the literature, spanning the years from 2009 to 2020, was completed using the PubMed database. AI studies using MRI imaging to investigate normal aging, mild cognitive impairment, and AD-dementia were retrieved for review. Bias assessment was completed using the PROBAST criteria.

RESULTS

97 relevant studies were included in the review. The studies were typically focused on the classification of AD, MCI, and normal aging (71% of the reported studies) and the prediction of MCI conversion to AD (25%). The best performance was achieved by using the deep learning-based convolution neural network algorithms (weighted average accuracy 89%), in contrast to 76-86% using Logistic Regression, Support Vector Machines, and other AI methods.

DISCUSSION

The synthesized evidence is paramount to developing sophisticated AI approaches to reliably capture and quantify multiple subtle MRI changes in the whole brain that exemplify the complexity and heterogeneity of AD and brain aging.

Adaptive Multimodal Neuroimage Integration for Major Depression Disorder Detection

Major depressive disorder (MDD) is one of the most common mental health disorders that can affect sleep, mood, appetite, and behavior of people. Multimodal neuroimaging data, such as functional and structural magnetic resonance imaging (MRI) scans, have been widely used in computer-aided detection of MDD. However, previous studies usually treat these two modalities separately, without considering their potentially complementary information. Even though a few studies propose integrating these two modalities, they usually suffer from significant inter-modality data heterogeneity. In this paper, we propose an adaptive multimodal neuroimage integration (AMNI) framework for automated MDD detection based on functional and structural MRIs. The AMNI framework consists of four major components: (1) a graph convolutional network to learn feature representations of functional connectivity networks derived from functional MRIs, (2) a convolutional neural network to learn features of T1-weighted structural MRIs, (3) a feature adaptation module to alleviate inter-modality difference, and (4) a feature fusion module to integrate feature representations extracted from two modalities for classification. To the best of our knowledge, this is among the first attempts to adaptively integrate functional and structural MRIs for neuroimaging-based MDD analysis by explicitly alleviating inter-modality heterogeneity. Extensive evaluations are performed on 533 subjects with resting-state functional MRI and T1-weighted MRI, with results suggesting the efficacy of the proposed method.

Ten years of image analysis and machine learning competitions in dementia

Machine learning methods exploiting multi-parametric biomarkers, especially based on neuroimaging, have huge potential to improve early diagnosis of dementia and to predict which individuals are at-risk of developing dementia. To benchmark algorithms in the field of machine learning and neuroimaging in dementia and assess their potential for use in clinical practice and clinical trials, seven grand challenges have been organized in the last decade: MIRIAD (2012), Alzheimer's Disease Big Data DREAM (2014), CADDementia (2014), Machine Learning Challenge (2014), MCI Neuroimaging (2017), TADPOLE (2017), and the Predictive Analytics Competition (2019). Based on two challenge evaluation frameworks, we analyzed how these grand challenges are complementing each other regarding research questions, datasets, validation approaches, results and impact. The seven grand challenges addressed questions related to screening, clinical status estimation, prediction and monitoring in (pre-clinical) dementia. There was little overlap in clinical questions, tasks and performance metrics. Whereas this aids providing insight on a broad range of questions, it also limits the validation of results across challenges. The validation process itself was mostly comparable between challenges, using similar methods for ensuring objective comparison, uncertainty estimation and statistical testing. In general, winning algorithms performed rigorous data pre-processing and combined a wide range of input features. Despite high state-of-the-art performances, most of the methods evaluated by the challenges are not clinically used. To increase impact, future challenges could pay more attention to statistical analysis of which factors (i.e., features, models) relate to higher performance, to clinical questions beyond Alzheimer's disease, and to using testing data beyond the Alzheimer's Disease Neuroimaging Initiative. Grand challenges would be an ideal venue for assessing the generalizability of algorithm performance to unseen data of other cohorts. Key for increasing impact in this way are larger testing data sizes, which could be reached by sharing algorithms rather than data to exploit data that cannot be shared. Given the potential and lessons learned in the past ten years, we are excited by the prospects of grand challenges in machine learning and neuroimaging for the next ten years and beyond.

Domain Adaptation for Medical Image Analysis: A Survey

Machine learning techniques used in computer-aided medical image analysis usually suffer from the domain shift problem caused by different distributions between source/reference data and target data. As a promising solution, domain adaptation has attracted considerable attention in recent years. The aim of this paper is to survey the recent advances of domain adaptation methods in medical image analysis. We first present the motivation of introducing domain adaptation techniques to tackle domain heterogeneity issues for medical image analysis. Then we provide a review of recent domain adaptation models in various medical image analysis tasks. We categorize the existing methods into shallow and deep models, and each of them is further divided into supervised, semi-supervised and unsupervised methods. We also provide a brief summary of the benchmark medical image datasets that support current domain adaptation research. This survey will enable researchers to gain a better understanding of the current status, challenges and future directions of this energetic research field.

The accuracy of T1-weighted voxel-wise and region-wise metrics for brain age estimation

INTRODUCTION

The brain age score has recently been introduced for robust monitoring of brain morphological alterations throughout the lifespan, prediction of mortality risk, and early detection of neurological disorders.

METHODS

We assessed the brain age prediction accuracy of the widely used T1-weighted voxel-wise and region-wise metrics (i.e., T1-weighted magnetic resonance imaging [MRI]-wise metrics)) separately and their integration. We assessed 788 healthy individuals (age, 18-94 years) in a training set to build a brain age estimation framework based on different T1-weighted MRI-wise metrics (15 different metrics in total) and then validated each T1-weighted MRI-wise metric in an independent test set comprising 88 healthy individuals. We also assessed the accuracy of each T1-weighted MRI-wise metric in a clinical set of 70 patients with mild cognitive impairment and another of 30 patients with Alzheimer's disease.

RESULTS

Integration of gray matter voxel-wise maps and all region-wise metrics achieved the highest brain age prediction accuracy (mean absolute error, 4.63 years). These metrics on their own achieved lower accuracy (mean absolute error, 4.97 years and 5.75 years, respectively).

DISCUSSION

For tracing brain atrophy levels in neurological disorders at the clinical level, integration of voxel-wise and region-wise metrics may contribute to a more sensitive brain age framework than when these metrics are used on their own.

A comparative study of machine learning methods for predicting the evolution of brain connectivity from a baseline timepoint

BACKGROUND

Predicting the evolution of the brain network, also called connectome, by foreseeing changes in the connectivity weights linking pairs of anatomical regions makes it possible to spot connectivity-related neurological disorders in earlier stages and detect the development of potential connectomic anomalies. Remarkably, such a challenging prediction problem remains least explored in the predictive connectomics literature. It is a known fact that machine learning (ML) methods have proven their predictive abilities in a wide variety of computer vision problems. However, ML techniques specifically tailored for the prediction of brain connectivity evolution trajectory from a single timepoint are almost absent.

NEW METHOD

To fill this gap, we organized a Kaggle competition where 20 competing teams designed advanced machine learning pipelines for predicting the brain connectivity evolution from a single timepoint. The teams developed their ML pipelines with combination of data pre-processing, dimensionality reduction and learning methods. Each ML framework inputs a baseline brain connectivity matrix observed at baseline timepoint t₀ and outputs the brain connectivity map at a follow-up timepoint t₁. The longitudinal OASIS-2 dataset was used for model training and evaluation. Both random data split and 5-fold cross-validation strategies were used for ranking and evaluating the generalizability and scalability of each competing ML pipeline.

RESULTS

Utilizing an inclusive approach, we ranked the methods based on two complementary evaluation metrics (mean absolute error (MAE) and Pearson Correlation Coefficient (PCC)) and their performances using different training and testing data perturbation strategies (single random split and cross-validation). The final rank was calculated using the rank product for each competing team across all evaluation measures and validation strategies. Furthermore, we added statistical significance values to each proposed pipeline.

CONCLUSION

In support of open science, the developed 20 ML pipelines along with the connectomic dataset are made available on GitHub (https://github.com/basiralab/Kaggle-BrainNetPrediction-Toolbox). The outcomes of this competition are anticipated to lead the further development of predictive models that can foresee the evolution of the brain connectivity over time, as well as other types of networks (e.g., genetic networks).

MRI-based Alzheimer's disease prediction via distilling the knowledge in multi-modal data

Mild cognitive impairment (MCI) conversion prediction, i.e., identifying MCI patients of high risks converting to Alzheimer's disease (AD), is essential for preventing or slowing the progression of AD. Although previous studies have shown that the fusion of multi-modal data can effectively improve the prediction accuracy, their applications are largely restricted by the limited availability or high cost of multi-modal data. Building an effective prediction model using only magnetic resonance imaging (MRI) remains a challenging research topic. In this work, we propose a multi-modal multi-instance distillation scheme, which aims to distill the knowledge learned from multi-modal data to an MRI-based network for MCI conversion prediction. In contrast to existing distillation algorithms, the proposed multi-instance probabilities demonstrate a superior capability of representing the complicated atrophy distributions, and can guide the MRI-based network to better explore the input MRI. To our best knowledge, this is the first study that attempts to improve an MRI-based prediction model by leveraging extra supervision distilled from multi-modal information. Experiments demonstrate the advantage of our framework, suggesting its potentials in the data-limited clinical settings.

Deep Learning Approach for Early Detection of Alzheimer's Disease

Alzheimer's disease (AD) is a chronic, irreversible brain disorder, no effective cure for it till now. However, available medicines can delay its progress. Therefore, the early detection of AD plays a crucial role in preventing and controlling its progression. The main objective is to design an end-to-end framework for early detection of Alzheimer's disease and medical image classification for various AD stages. A deep learning approach, specifically convolutional neural networks (CNN), is used in this work. Four stages of the AD spectrum are multi-classified. Furthermore, separate binary medical image classifications are implemented between each two-pair class of AD stages. Two methods are used to classify the medical images and detect AD. The first method uses simple CNN architectures that deal with 2D and 3D structural brain scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset based on 2D and 3D convolution. The second method applies the transfer learning principle to take advantage of the pre-trained models for medical image classifications, such as the VGG19 model. Due to the COVID-19 pandemic, it is difficult for people to go to hospitals periodically to avoid gatherings and infections. As a result, Alzheimer's checking web application is proposed using the final qualified proposed architectures. It helps doctors and patients to check AD remotely. It also determines the AD stage of the patient based on the AD spectrum and advises the patient according to its AD stage. Nine performance metrics are used in the evaluation and the comparison between the two methods. The experimental results prove that the CNN architectures for the first method have the following characteristics: suitable simple structures that reduce computational complexity, memory requirements, overfitting, and provide manageable time. Besides, they achieve very promising accuracies, 93.61% and 95.17% for 2D and 3D multi-class AD stage classifications. The VGG19 pre-trained model is fine-tuned and achieved an accuracy of 97% for multi-class AD stage classifications.

Technical and clinical validation of commercial automated volumetric MRI tools for dementia diagnosis-a systematic review

Developments in neuroradiological MRI analysis offer promise in enhancing objectivity and consistency in dementia diagnosis through the use of quantitative volumetric reporting tools (QReports). Translation into clinical settings should follow a structured framework of development, including technical and clinical validation steps. However, published technical and clinical validation of the available commercial/proprietary tools is not always easy to find and pathways for successful integration into the clinical workflow are varied. The quantitative neuroradiology initiative (QNI) framework highlights six necessary steps for the development, validation and integration of quantitative tools in the clinic. In this paper, we reviewed the published evidence regarding regulatory-approved QReports for use in the memory clinic and to what extent this evidence fulfils the steps of the QNI framework. We summarize unbiased technical details of available products in order to increase the transparency of evidence and present the range of reporting tools on the market. Our intention is to assist neuroradiologists in making informed decisions regarding the adoption of these methods in the clinic. For the 17 products identified, 11 companies have published some form of technical validation on their methods, but only 4 have published clinical validation of their QReports in a dementia population. Upon systematically reviewing the published evidence for regulatory-approved QReports in dementia, we concluded that there is a significant evidence gap in the literature regarding clinical validation, workflow integration and in-use evaluation of these tools in dementia MRI diagnosis.

An Optimized Decision Tree with Genetic Algorithm Rule-Based Approach to Reveal the Brain's Changes During Alzheimer's Disease Dementia

BACKGROUND

It is desirable to achieve acceptable accuracy for computer aided diagnosis system (CADS) to disclose the dementia-related consequences on the brain. Therefore, assessing and measuring these impacts is fundamental in the diagnosis of dementia.

OBJECTIVE

This study introduces a new CADS for deep learning of magnetic resonance image (MRI) data to identify changes in the brain during Alzheimer's disease (AD) dementia.

METHODS

The proposed algorithm employed a decision tree with genetic algorithm rule-based optimization to classify input data which were extracted from MRI. This pipeline is applied to the healthy and AD subjects of the Open Access Series of Imaging Studies (OASIS).

RESULTS

Final evaluation of the CADS and its comparison with other systems supported the potential of the proposed model as a novel tool for investigating the progression of AD and its great ability as an innovative computerized help to facilitate the decision-making procedure for the diagnosis of AD.

CONCLUSION

The one-second time response, together with the identified high accurate performance, suggests that this system could be useful in future cognitive and computational neuroscience studies.

A parallel attention-augmented bilinear network for early magnetic resonance imaging-based diagnosis of Alzheimer's disease

Structural magnetic resonance imaging (sMRI) can capture the spatial patterns of brain atrophy in Alzheimer's disease (AD) and incipient dementia. Recently, many sMRI‐based deep learning methods have been developed for AD diagnosis. Some of these methods utilize neural networks to extract high‐level representations on the basis of handcrafted features, while others attempt to learn useful features from brain regions proposed by a separate module. However, these methods require considerable manual engineering. Their stepwise training procedures would introduce cascading errors. Here, we propose the parallel attention‐augmented bilinear network, a novel deep learning framework for AD diagnosis. Based on a 3D convolutional neural network, the framework directly learns both global and local features from sMRI scans without any prior knowledge. The framework is lightweight and suitable for end‐to‐end training. We evaluate the framework on two public datasets (ADNI‐1 and ADNI‐2) containing 1,340 subjects. On both the AD classification and mild cognitive impairment conversion prediction tasks, our framework achieves competitive results. Furthermore, we generate heat maps that highlight discriminative areas for visual interpretation. Experiments demonstrate the effectiveness of the proposed framework when medical priors are unavailable or the computing resources are limited. The proposed framework is general for 3D medical image analysis with both efficiency and interpretability.

Data analysis with Shapley values for automatic subject selection in Alzheimer's disease data sets using interpretable machine learning

BACKGROUND

For the recruitment and monitoring of subjects for therapy studies, it is important to predict whether mild cognitive impaired (MCI) subjects will prospectively develop Alzheimer's disease (AD). Machine learning (ML) is suitable to improve early AD prediction. The etiology of AD is heterogeneous, which leads to high variability in disease patterns. Further variability originates from multicentric study designs, varying acquisition protocols, and errors in the preprocessing of magnetic resonance imaging (MRI) scans. The high variability makes the differentiation between signal and noise difficult and may lead to overfitting. This article examines whether an automatic and fair data valuation method based on Shapley values can identify the most informative subjects to improve ML classification.

METHODS

An ML workflow was developed and trained for a subset of the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. The validation was executed for an independent ADNI test set and for the Australian Imaging, Biomarker and Lifestyle Flagship Study of Ageing (AIBL) cohort. The workflow included volumetric MRI feature extraction, feature selection, sample selection using Data Shapley, random forest (RF), and eXtreme Gradient Boosting (XGBoost) for model training as well as Kernel SHapley Additive exPlanations (SHAP) values for model interpretation.

RESULTS

The RF models, which excluded 134 of the 467 training subjects based on their RF Data Shapley values, outperformed the base models that reached a mean accuracy of 62.64% by 5.76% (3.61 percentage points) for the independent ADNI test set. The XGBoost base models reached a mean accuracy of 60.00% for the AIBL data set. The exclusion of those 133 subjects with the smallest RF Data Shapley values could improve the classification accuracy by 2.98% (1.79 percentage points). The cutoff values were calculated using an independent validation set.

CONCLUSION

The Data Shapley method was able to improve the mean accuracies for the test sets. The most informative subjects were associated with the number of ApolipoproteinE ε4 (ApoE ε4) alleles, cognitive test results, and volumetric MRI measurements.

MRI Deep Learning-Based Solution for Alzheimer's Disease Prediction

BACKGROUND

Alzheimer's is a degenerative dementing disorder that starts with a mild memory impairment and progresses to a total loss of mental and physical faculties. The sooner the diagnosis is made, the better for the patient, as preventive actions and treatment can be started. Although tests such as the Mini-Mental State Tests Examination are usually used for early identification, diagnosis relies on magnetic resonance imaging (MRI) brain analysis.

METHODS

Public initiatives such as the OASIS (Open Access Series of Imaging Studies) collection provide neuroimaging datasets openly available for research purposes. In this work, a new method based on deep learning and image processing techniques for MRI-based Alzheimer's diagnosis is proposed and compared with previous literature works.

RESULTS

Our method achieves a balance accuracy (BAC) up to 0.93 for image-based automated diagnosis of the disease, and a BAC of 0.88 for the establishment of the disease stage (healthy tissue, very mild and severe stage).

CONCLUSIONS

Results obtained surpassed the state-of-the-art proposals using the OASIS collection. This demonstrates that deep learning-based strategies are an effective tool for building a robust solution for Alzheimer's-assisted diagnosis based on MRI data.

Translating state-of-the-art brain magnetic resonance imaging (MRI) techniques into clinical practice: multimodal MRI differentiates dementia subtypes in a traditional clinical setting

BACKGROUND

This study sought to validate the clinical utility of multimodal magnetic resonance imaging (MRI) techniques in the assessment of neurodegenerative disorders. We intended to demonstrate that advanced neuroimaging techniques commonly used in research can effectively be employed in clinical practice to accurately differentiate heathy aging and dementia subtypes.

METHODS

Twenty patients with dementia of the Alzheimer's type (DAT) and 18 patients with Parkinson's disease dementia (PDD) were identified using gold-standard techniques. Twenty-three healthy, age and sex matched control participants were also recruited. All participants underwent multimodal MRI including T1 structural, diffusion tensor imaging (DTI), arterial spin labeling (ASL), and magnetic resonance spectroscopy (MRS). MRI modalities were evaluated by trained neuroimaging readers and were separately assessed using cross-validated, iterative discriminant function analyses with subsequent feature reduction techniques. In this way, each modality was evaluated for its ability to differentiate patients with dementia from healthy controls as well as to differentiate dementia subtypes.

RESULTS

Following individual and group feature reduction, each of the multimodal MRI metrics except MRS successfully differentiated healthy aging from dementia and also demonstrated distinct dementia subtypes. Using the following ten metrics, excellent separation (95.5% accuracy, 92.3% sensitivity; 100.0% specificity) was achieved between healthy aging and neurodegenerative conditions: volume of the left frontal pole, left occipital pole, right posterior superior temporal gyrus, left posterior cingulate gyrus, right planum temporale; perfusion of the left hippocampus and left occipital lobe; fractional anisotropy (FA) of the forceps major and bilateral anterior thalamic radiation. Using volume of the left frontal pole, right posterior superior temporal gyrus, left posterior cingulate gyrus, perfusion of the left hippocampus and left occipital lobe; FA of the forceps major and bilateral anterior thalamic radiation, neurodegenerative subtypes were accurately differentiated as well (87.8% accuracy, 95.2% sensitivity; 85.0% specificity).

CONCLUSIONS

Regional volumetrics, DTI metrics, and ASL successfully differentiated dementia patients from controls with sufficient sensitivity to differentiate dementia subtypes. Similarly, feature reduction results suggest that advanced analyses can meaningfully identify brain regions with the most positive predictive value and discriminant validity. Together, these advanced neuroimaging techniques can contribute significantly to diagnosis and treatment planning for individual patients.

Neuroplasticity within and between Functional Brain Networks in Mental Training Based on Long-Term Meditation

(1) The effects of intensive mental training based on meditation on the functional and structural organization of the human brain have been addressed by several neuroscientific studies. However, how large-scale connectivity patterns are affected by long-term practice of the main forms of meditation, Focused Attention (FA) and Open Monitoring (OM), as well as by aging, has not yet been elucidated. (2) Using functional Magnetic Resonance Imaging (fMRI) and multivariate pattern analysis, we investigated the impact of meditation expertise and age on functional connectivity patterns in large-scale brain networks during different meditation styles in long-term meditators. (3) The results show that fMRI connectivity patterns in multiple key brain networks can differentially predict the meditation expertise and age of long-term meditators. Expertise-predictive patterns are differently affected by FA and OM, while age-predictive patterns are not influenced by the meditation form. The FA meditation connectivity pattern modulated by expertise included nodes and connections implicated in focusing, sustaining and monitoring attention, while OM patterns included nodes associated with cognitive control and emotion regulation. (4) The study highlights a long-term effect of meditation practice on multivariate patterns of functional brain connectivity and suggests that meditation expertise is associated with specific neuroplastic changes in connectivity patterns within and between multiple brain networks.

A Novel Method for Differential Prognosis of Brain Degenerative Diseases Using Radiomics-Based Textural Analysis and Ensemble Learning Classifiers

We propose a novel approach to develop a computer-aided decision support system for radiologists to help them classify brain degeneration process as physiological or pathological, aiding in early prognosis of brain degenerative diseases. Our approach applies computational and mathematical formulations to extract quantitative information from biomedical images. Our study explores the longitudinal OASIS-3 dataset, which consists of 4096 brain MRI scans collected over a period of 15 years. We perform feature extraction using Pyradiomics python package that quantizes brain MRI images using different texture analysis methods. Studies indicate that Radiomics has rarely been used for analysis of brain cognition; hence, our study is also a novel effort to determine the efficiency of Radiomics features extracted from structural MRI scans for classification of brain degenerative diseases and to create awareness about Radiomics. For classification tasks, we explore various ensemble learning classification algorithms such as random forests, bagging-based ensemble classifiers, and gradient-boosted ensemble classifiers such as XGBoost and AdaBoost. Such ensemble learning classifiers have not been used for biomedical image classification. We also propose a novel texture analysis matrix, Decreasing Gray-Level Matrix or DGLM. The features extracted from this filter helped to further improve the accuracy of our decision support system. The proposed system based on XGBoost ensemble learning classifiers achieves an accuracy of 97.38%, with sensitivity 99.82% and specificity 97.01%.

WavBERT: Exploiting Semantic and Non-semantic Speech using Wav2vec and BERT for Dementia Detection

In this paper, we exploit semantic and non-semantic information from patient's speech data using Wav2vec and Bidirectional Encoder Representations from Transformers (BERT) for dementia detection. We first propose a basic WavBERT model by extracting semantic information from speech data using Wav2vec, and analyzing the semantic information using BERT for dementia detection. While the basic model discards the non-semantic information, we propose extended WavBERT models that convert the output of Wav2vec to the input to BERT for preserving the non-semantic information in dementia detection. Specifically, we determine the locations and lengths of inter-word pauses using the number of blank tokens from Wav2vec where the threshold for setting the pauses is automatically generated via BERT. We further design a pre-trained embedding conversion network that converts the output embedding of Wav2vec to the input embedding of BERT, enabling the fine-tuning of WavBERT with non-semantic information. Our evaluation results using the ADReSSo dataset showed that the WavBERT models achieved the highest accuracy of 83.1% in the classification task, the lowest Root-Mean-Square Error (RMSE) score of 4.44 in the regression task, and a mean F1 of 70.91% in the progression task. We confirmed the effectiveness of WavBERT models exploiting both semantic and non-semantic speech.

Cross-cohort generalizability of deep and conventional machine learning for MRI-based diagnosis and prediction of Alzheimer's disease

This work validates the generalizability of MRI-based classification of Alzheimer’s disease (AD) patients and controls (CN) to an external data set and to the task of prediction of conversion to AD in individuals with mild cognitive impairment (MCI).

We used a conventional support vector machine (SVM) and a deep convolutional neural network (CNN) approach based on structural MRI scans that underwent either minimal pre-processing or more extensive pre-processing into modulated gray matter (GM) maps. Classifiers were optimized and evaluated using cross-validation in the Alzheimer’s Disease Neuroimaging Initiative (ADNI; 334 AD, 520 CN). Trained classifiers were subsequently applied to predict conversion to AD in ADNI MCI patients (231 converters, 628 non-converters) and in the independent Health-RI Parelsnoer Neurodegenerative Diseases Biobank data set. From this multi-center study representing a tertiary memory clinic population, we included 199 AD patients, 139 participants with subjective cognitive decline, 48 MCI patients converting to dementia, and 91 MCI patients who did not convert to dementia.

AD-CN classification based on modulated GM maps resulted in a similar area-under-the-curve (AUC) for SVM (0.940; 95%CI: 0.924–0.955) and CNN (0.933; 95%CI: 0.918–0.948). Application to conversion prediction in MCI yielded significantly higher performance for SVM (AUC = 0.756; 95%CI: 0.720-0.788) than for CNN (AUC = 0.742; 95%CI: 0.709-0.776) (p<0.01 for McNemar’s test). In external validation, performance was slightly decreased. For AD-CN, it again gave similar AUCs for SVM (0.896; 95%CI: 0.855–0.932) and CNN (0.876; 95%CI: 0.836–0.913). For prediction in MCI, performances decreased for both SVM (AUC = 0.665; 95%CI: 0.576-0.760) and CNN (AUC = 0.702; 95%CI: 0.624-0.786). Both with SVM and CNN, classification based on modulated GM maps significantly outperformed classification based on minimally processed images (p=0.01).

Deep and conventional classifiers performed equally well for AD classification and their performance decreased only slightly when applied to the external cohort. We expect that this work on external validation contributes towards translation of machine learning to clinical practice.