MEG are non invasive neuroimaging techniques with excellent temporal and spatial resolution, crucial for studying brain function in dementia and Alzheimer Disease. They identify changes in brain activity at various Alzheimer stages, including preclinical and prodromal phases. MEG may detect pathological changes before clinical symptoms, offering potential biomarkers for intervention. This study evaluates classification techniques using MEG features to distinguish between healthy controls and mild cognitive impairment participants from the BioFIND study. We compare MEG based biomarkers with MRI based anatomical features, both independently and combined. We used 3 Tesla MRI and MEG data from 324 BioFIND participants;158 MCI and 166 HC. Analyses were performed using MATLAB with SPM12 and OSL toolboxes. Machine learning analyses, including 100 Monte Carlo replications of 10 fold cross validation, were conducted on sensor and source spaces. Combining MRI with MEG features achieved the best performance; 0.76 accuracy and AUC of 0.82 for GLMNET using LCMV source based MEG. MEG only analyses using LCMV and eLORETA also performed well, suggesting that combining uncorrected MEG with z-score-corrected MRI features is optimal.

As we incorporate automated decision-making systems into the real world, explainability and accountability questions become increasingly important [1]. In some fields, such as medicine and healthcare, ignoring or failing to address such a challenge can seriously limit the adoption of computer-based systems that rely on machine learning (ML) and computational intelligence methods for data analysis in real-world applications [2-4]. Previous research in eXplainable Artificial Intelligence (XAI) has primarily focused on developing techniques to interpret decisions made by black box ML models. For instance, widely used approaches such as local interpretable model-agnostic explanations (LIME) [5] and shapley additive explanations (SHAP) [6] offer attribution-based explanations to interpret ML models. These methods can assist computer scientists and ML experts in understanding the reasoning behind the predictions made by AI models. However, end-users, including clinicians and patients, may be more interested in understanding the practical implications of the ML model's predictions in relation to themselves, rather than solely focusing on how the models arrived at their predictions. For example, patients' primary concern lies not only in obtaining information about their illness but also in seeking guidance on how to regain their health. Understanding the decision-making process of either the doctor or the ML model is of lesser importance to them. Counterfactual explanations [7, 8] are a form of model-agnostic interpretation technique that identifies the minimal changes needed in input features to yield a different output, aligned with a specific desired outcome.

The analysis and diagnosis of Alzheimer's disease (AD) can be based on genetic variations, e.g., single nucleotide polymorphisms (SNPs) and phenotypic traits, e.g., Magnetic Resonance Imaging (MRI) features. We consider two important and related tasks: i) to select genetic and phenotypical markers for AD diagnosis and ii) to identify associations between genetic and phenotypical data. While previous studies treat these two tasks separately, they are tightly coupled because underlying associations between genetic variations and phenotypical features contain the biological basis for a disease. Here we present a new sparse Bayesian approach for joint association study and disease diagnosis. In this approach, common latent features are extracted from different data sources based on sparse projection matrices and used to predict multiple disease severity levels; in return, the disease status can guide the discovery of relationships between data sources. The sparse projection matrices not only reveal interactions between data sources but also select groups of biomarkers related to the disease. Moreover, to take advantage of the linkage disequilibrium (LD) measuring the non-random association of alleles, we incorporate a graph Laplacian type of prior in the model. To learn the model from data, we develop an efficient variational inference algorithm. Analysis on an imaging genetics dataset for the study of Alzheimer's Disease (AD) indicates that our model identifies biologically meaningful associations between genetic variations and MRI features, and achieves significantly higher accuracy for predicting ordinal AD stages than the competing methods.

In the analysis and diagnosis of many diseases, such as the Alzheimer's disease (AD), two important and related tasks are usually required: i) selecting genetic and phenotypical markers for diagnosis, and ii) identifying associations between genetic and phenotypical features. While previous studies treat these two tasks separately, they are tightly coupled due to the same underlying biological basis. To harness their potential benefits for each other, we propose a new sparse Bayesian approach to jointly carry out the two important and related tasks. In our approach, we extract common latent features from different data sources by sparse projection matrices and then use the latent features to predict disease severity levels; in return, the disease status can guide the learning of sparse projection matrices, which not only reveal interactions between data sources but also select groups of related biomarkers. In order to boost the learning of sparse projection matrices, we further incorporate graph Laplacian priors encoding the valuable linkage disequilibrium (LD) information. To efficiently estimate the model, we develop a variational inference algorithm. Analysis on an imaging genetics dataset for AD study shows that our model discovers biologically meaningful associations between single nucleotide polymorphisms (SNPs) and magnetic resonance imaging (MRI) features, and achieves significantly higher accuracy for predicting ordinal AD stages than competitive methods.

Given genetic variations and various phenotypical traits, such as Magnetic Resonance Imaging (MRI) features, we consider two important and related tasks in biomedical research: i)to select genetic and phenotypical markers for disease diagnosis and ii) to identify associations between genetic and phenotypical data. These two tasks are tightly coupled because underlying associations between genetic variations and phenotypical features contain the biological basis for a disease. While a variety of sparse models have been applied for disease diagnosis and canonical correlation analysis and its extensions have bee widely used in association studies (e.g., eQTL analysis), these two tasks have been treated separately. To unify these two tasks, we present a new sparse Bayesian approach for joint association study and disease diagnosis. In this approach, common latent features are extracted from different data sources based on sparse projection matrices and used to predict multiple disease severity levels based on Gaussian process ordinal regression; in return, the disease status is used to guide the discovery of relationships between the data sources. The sparse projection matrices not only reveal interactions between data sources but also select groups of biomarkers related to the disease. To learn the model from data, we develop an efficient variational expectation maximization algorithm. Simulation results demonstrate that our approach achieves higher accuracy in both predicting ordinal labels and discovering associations between data sources than alternative methods. We apply our approach to an imaging genetics dataset for the study of Alzheimer's Disease (AD). Our method identifies biologically meaningful relationships between genetic variations, MRI features, and AD status, and achieves significantly higher accuracy for predicting ordinal AD stages than the competing methods.