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1. Prioritizing Amyloid Imaging Biomarkers in Alzheimer’s Disease via Learning to Rank

   https://doi.org/10.1007/978-3-030-33226-6_16  

   Peng, B; Ren, Z; Yao, X; Liu, K; Saykin, AJ; Shen, L (October 2019, MBIA 2019: International Workshop on Multimodal Brain Image Analysis)

   We propose an innovative machine learning paradigm enabling precision medicine for AD biomarker discovery. The paradigm tailors the imaging biomarker discovery process to individual characteristics of a given patient. We implement this paradigm using a newly developed learning-to-rank method 𝙿𝙻𝚃𝚁 . The 𝙿𝙻𝚃𝚁 model seamlessly integrates two objectives for joint optimization: pushing up relevant biomarkers and ranking among relevant biomarkers. The empirical study of 𝙿𝙻𝚃𝚁 conducted on the ADNI data yields promising results to identify and prioritize individual-specific amyloid imaging biomarkers based on the individual’s structural MRI data. The resulting top ranked imaging biomarker has the potential to aid personalized diagnosis and disease subtyping. 

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2. Integrating Static and Dynamic Data for Improved Prediction of Cognitive Declines Using Augmented Genotype-Phenotype Representations

   Seo, Hoon; Brand, Lodewijk; Wang, Hua; Nie, Feiping (January 2021, Proceedings of the AAAI Conference on Artificial Intelligence)

   null (Ed.)

   Alzheimer’s Disease (AD) is a chronic neurodegenerative disease that causes severe problems in patients’ thinking, memory, and behavior. An early diagnosis is crucial to prevent AD progression; to this end, many algorithmic approaches have recently been proposed to predict cognitive decline. However, these predictive models often fail to integrate heterogeneous genetic and neuroimaging biomarkers and struggle to handle missing data. In this work we propose a novel objective function and an associated optimization algorithm to identify cognitive decline related to AD. Our approach is designed to incorporate dynamic neuroimaging data by way of a participant-specific augmentation combined with multimodal data integration aligned via a regression task. Our approach, in order to incorporate additional side-information, utilizes structured regularization techniques popularized in recent AD literature. Armed with the fixed-length vector representation learned from the multimodal dynamic and static modalities, conventional machine learning methods can be used to predict the clinical outcomes associated with AD. Our experimental results show that the proposed augmentation model improves the prediction performance on cognitive assessment scores for a collection of popular machine learning algorithms. The results of our approach are interpreted to validate existing genetic and neuroimaging biomarkers that have been shown to be predictive of cognitive decline. 

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3. Unsupervised Machine Learning to Identify Separable Clinical Alzheimer’s Disease Sub-Populations

   https://doi.org/10.3390/brainsci11080977  

   Prakash, Jayant; Wang, Velda; Quinn, Robert E.; Mitchell, Cassie S. (August 2021, Brain Sciences)

   Heterogeneity among Alzheimer’s disease (AD) patients confounds clinical trial patient selection and therapeutic efficacy evaluation. This work defines separable AD clinical sub-populations using unsupervised machine learning. Clustering (t-SNE followed by k-means) of patient features and association rule mining (ARM) was performed on the ADNIMERGE dataset from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). Patient sociodemographics, brain imaging, biomarkers, cognitive tests, and medication usage were included for analysis. Four AD clinical sub-populations were identified using between-cluster mean fold changes [cognitive performance, brain volume]: cluster-1 represented least severe disease [+17.3, +13.3]; cluster-0 [−4.6, +3.8] and cluster-3 [+10.8, −4.9] represented mid-severity sub-populations; cluster-2 represented most severe disease [−18.4, −8.4]. ARM assessed frequently occurring pharmacologic substances within the 4 sub-populations. No drug class was associated with the least severe AD (cluster-1), likely due to lesser antecedent disease. Anti-hyperlipidemia drugs associated with cluster-0 (mid-severity, higher volume). Interestingly, antioxidants vitamin C and E associated with cluster-3 (mid-severity, higher cognition). Anti-depressants like Zoloft associated with most severe disease (cluster-2). Vitamin D is protective for AD, but ARM identified significant underutilization across all AD sub-populations. Identification and feature characterization of four distinct AD sub-population “clusters” using standard clinical features enhances future clinical trial selection criteria and cross-study comparative analysis. 

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4. The Eye as the Window to the Heart: Optical Coherence Tomography Angiography Biomarkers as Indicators of Cardiovascular Disease

   https://doi.org/10.3390/jcm13030829  

   Kellner, Rebecca L; Harris, Alon; Ciulla, Lauren; Guidoboni, Giovanna; Verticchio_Vercellin, Alice; Oddone, Francesco; Carnevale, Carmela; Zaid, Mohamed; Antman, Gal; Kuvin, Jeffrey T; et al (February 2024, Journal of Clinical Medicine)

   Alterations in microvasculature represent some of the earliest pathological processes across a wide variety of human diseases. In many organs, however, inaccessibility and difficulty in directly imaging tissues prevent the assessment of microvascular changes, thereby significantly limiting their translation into improved patient care. The eye provides a unique solution by allowing for the non-invasive and direct visualization and quantification of many aspects of the human microvasculature, including biomarkers for structure, function, hemodynamics, and metabolism. Optical coherence tomography angiography (OCTA) studies have specifically identified reduced capillary densities at the level of the retina in several eye diseases including glaucoma. This narrative review examines the published data related to OCTA-assessed microvasculature biomarkers and major systemic cardiovascular disease. While loss of capillaries is being established in various ocular disease, pilot data suggest that changes in the retinal microvasculature, especially within the macula, may also reflect small vessel damage occurring in other organs resulting from cardiovascular disease. Current evidence suggests retinal microvascular biomarkers as potential indicators of major systemic cardiovascular diseases, including systemic arterial hypertension, atherosclerotic disease, and congestive heart failure. 

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5. Machine learning based multi-modal prediction of future decline toward Alzheimer’s disease: An empirical study

   https://doi.org/10.1371/journal.pone.0277322  

   Karaman, Batuhan K.; Mormino, Elizabeth C.; Sabuncu, Mert R. (November 2022, PLOS ONE)

   Thung, Kim Han (Ed.)

   Alzheimer’s disease (AD) is a neurodegenerative condition that progresses over decades. Early detection of individuals at high risk of future progression toward AD is likely to be of critical significance for the successful treatment and/or prevention of this devastating disease. In this paper, we present an empirical study to characterize how predictable an individual subjects’ future AD trajectory is, several years in advance, based on rich multi-modal data, and using modern deep learning methods. Crucially, the machine learning strategy we propose can handle different future time horizons and can be trained with heterogeneous data that exhibit missingness and non-uniform follow-up visit times. Our experiments demonstrate that our strategy yields predictions that are more accurate than a model trained on a single time horizon (e.g. 3 years), which is common practice in prior literature. We also provide a comparison between linear and nonlinear models, verifying the well-established insight that the latter can offer a boost in performance. Our results also confirm that predicting future decline for cognitively normal (CN) individuals is more challenging than for individuals with mild cognitive impairment (MCI). Intriguingly, however, we discover that prediction accuracy decreases with increasing time horizon for CN subjects, but the trend is in the opposite direction for MCI subjects. Additionally, we quantify the contribution of different data types in prediction, which yields novel insights into the utility of different biomarkers. We find that molecular biomarkers are not as helpful for CN individuals as they are for MCI individuals, whereas magnetic resonance imaging biomarkers (hippocampus volume, specifically) offer a significant boost in prediction accuracy for CN individuals. Finally, we show how our model’s prediction reveals the evolution of individual-level progression risk over a five-year time horizon. Our code is available at https://github.com/batuhankmkaraman/mlbasedad . 

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