Probabilistic disease progression modeling to characterize diagnostic uncertainty: Application to staging and prediction in Alzheimer's disease

Longitudinal dementia trajectories for Alzheimer's Disease characterization and prediction

BACKGROUND

Alzheimer's Disease (AD) remains one of the most significant neurodegenerative diseases globally, affecting approximately 38.5 million people in 2023. Early identification of individuals at risk of developing AD is essential to managing disease progression and implementing timely interventions. Despite extensive research on predicting individual AD progression and diagnosis conversion, the dynamic and multimodal characterization of AD evolution remains an open challenge.

APPROACH

This study introduces a model leveraging multimodal clinical data to capture and predict both population-level and individual trajectories of dementia over extended timescales. We define a Static Dementia Score (SDS) as a metric representing the current state of dementia, with its temporal evolution modeled using a Bayesian nonlinear mixed-effects approach. This method generates a single continuous curve that delineates the average dementia progression pattern across the population. Additionally, our approach allows for patient-specific SDS progression modeling, enabling the prediction of individual dementia trajectories over a specified time horizon.

RESULTS

The model was trained on a dataset comprising 5,033 observations, including MP-RAGE MRI scans, cognitive assessments, and demographic data from 883 individuals with at least four observations and stable diagnostic trajectories. Population-level curves produced by our model align with established AD progression trends, capturing key stages of disease evolution. Individual-specific deformation parameters were effective in characterizing personalized disease progression, achieving a theoretical diagnosis prediction accuracy of 0.952±0.013 three years in advance and an AD conversion prediction accuracy of 0.916±0.022 within the same period.

CONCLUSION

Our findings underscore the potential of this approach for AD classification and forecasting disease progression. These results emphasize its utility for clinicians and researchers in detecting atypical disease trajectories early in patients with longitudinal follow-up, enhancing decision-making and therapeutic planning.

Disease stage-specific atrophy markers in Alzheimer's disease

INTRODUCTION

Structural MRI often lacks diagnostic, prognostic, and monitoring value in Alzheimer's disease (AD), particularly in early disease stages. To improve its utility, we aimed to identify optimal MRI readouts for different use cases.

METHODS

We included 363 older adults; healthy controls (HC) who were negative or positive for amyloidbeta (Aβ) and Aβ-positive patients with subjective cognitive decline (SCD), mild cognitive impairment, or dementia of the Alzheimer type. MRI and neuropsychological assessments were administered annually for up to three years.

RESULTS

Accelerated atrophy of distinct MTL subregions was evident already during preclinical AD. Symptomatic disease stages most notably differed in their hippocampal and parietal atrophy signatures. Associations of atrophy markers and cognitive inventories varied by intended use and disease stage.

DISCUSSION

With the appropriate readout, MRI can detect abnormal atrophy already during preclinical AD. To optimize performance, MRI readouts should be tailored to the targeted disease stage and intended use.

A 50-year data-driven model of disability and lesion load trajectories in progressive multiple sclerosis

This scientific commentary refers to 'A data-driven model of disability progression in progressive multiple sclerosis', by Garbarino et al. (https://doi.org/10.1093/braincomms/fcae434).

A data-driven model of disability progression in progressive multiple sclerosis

This study applies the Gaussian process progression model, a Bayesian data-driven disease progression model, to analyse the evolution of primary progressive multiple sclerosis. Utilizing data from 1521 primary progressive multiple sclerosis participants collected within the International Progressive Multiple Sclerosis Alliance Project, the analysis includes 18 581 longitudinal time-points (average follow-up time: 28.2 months) of disability assessments including the expanded disability status scale, symbol digit modalities, timed 25-foot-walk, 9-hole-peg test and of MRI metrics such as T1 and T2 lesion volume and normalized brain volume. From these data, Gaussian process progression model infers a data-driven description of the progression common to all individuals, alongside scores measuring the individual progression rates relative to the population, spanning ∼50 years of disease duration. Along this timeline, Gaussian process progression model identifies an initial steep worsening of the expanded disability status scale that stabilizes after ∼30 years of disease duration, suggesting its diminished utility in monitoring disease progression beyond this time. Conversely, it underscores the slower evolution of normalized brain volume across the disease duration. The individual progression rates estimated by Gaussian process progression model can be used to identify three distinct sub-groups within the primary progressive multiple sclerosis population: a normative group (76% of the population) and two 'outlier' sub-groups displaying either accelerated (13% of the population) or decelerated (11%) progression compared to the normative one. Notably, fast progressors exhibit older age at symptom onset (38.5 versus 35.0, P < 0.0001), a higher prevalence of males (61.1% versus 48.5%, P = 0.013) and a higher lesion volumes both in T1 (4.1 versus 0.6, P < 0.0001) and T2 (16.5 versus 7.9, P < 0.0001) compared to slow progressors. Prognostically, fast progressors demonstrate a significantly worse prognosis, with double the risk of experiencing a 3-month confirmed disease progression on expanded disability status scale compared to the normative population according to Cox proportional hazard modelling (HR = 2.09, 95% CI: 1.66-2.62, P < 0.0001) and a shorter median time from the onset of disease symptoms to reaching a confirmed expanded disability status scale 6 (95% CI: 5.83-7.68 years, P < 0.0001). External validation on a test set comprising 227 primary progressive multiple sclerosis participants from the SPI2 trial produced consistent results, with slow progressors exhibiting a reduced risk of experiencing 3-month confirmed disease progression determined through expanded disability status scale (HR = 0.21), while fast progressors facing an increased risk (HR = 1.45). This study contributes to our understanding of disability accrual in primary progressive multiple sclerosis, integrating diverse disability assessments and MRI measurements. Moreover, the identification of distinct sub-groups underscores the heterogeneity in progression rates among patients, offering invaluable insights for patient stratification and monitoring in clinical trials, potentially facilitating more targeted and personalized interventions.

Beyond the usual suspects: multi-factorial computational models in the search for neurodegenerative disease mechanisms

From Alzheimer's disease to amyotrophic lateral sclerosis, the molecular cascades underlying neurodegenerative disorders remain poorly understood. The clinical view of neurodegeneration is confounded by symptomatic heterogeneity and mixed pathology in almost every patient. While the underlying physiological alterations originate, proliferate, and propagate potentially decades before symptomatic onset, the complexity and inaccessibility of the living brain limit direct observation over a patient's lifespan. Consequently, there is a critical need for robust computational methods to support the search for causal mechanisms of neurodegeneration by distinguishing pathogenic processes from consequential alterations, and inter-individual variability from intra-individual progression. Recently, promising advances have been made by data-driven spatiotemporal modeling of the brain, based on in vivo neuroimaging and biospecimen markers. These methods include disease progression models comparing the temporal evolution of various biomarkers, causal models linking interacting biological processes, network propagation models reproducing the spatial spreading of pathology, and biophysical models spanning cellular- to network-scale phenomena. In this review, we discuss various computational approaches for integrating cross-sectional, longitudinal, and multi-modal data, primarily from large observational neuroimaging studies, to understand (i) the temporal ordering of physiological alterations, i(i) their spatial relationships to the brain's molecular and cellular architecture, (iii) mechanistic interactions between biological processes, and (iv) the macroscopic effects of microscopic factors. We consider the extents to which computational models can evaluate mechanistic hypotheses, explore applications such as improving treatment selection, and discuss how model-informed insights can lay the groundwork for a pathobiological redefinition of neurodegenerative disorders.

Towards cascading genetic risk in Alzheimer's disease

Alzheimer's disease typically progresses in stages, which have been defined by the presence of disease-specific biomarkers: amyloid (A), tau (T) and neurodegeneration (N). This progression of biomarkers has been condensed into the ATN framework, in which each of the biomarkers can be either positive (+) or negative (-). Over the past decades, genome-wide association studies have implicated ∼90 different loci involved with the development of late-onset Alzheimer's disease. Here, we investigate whether genetic risk for Alzheimer's disease contributes equally to the progression in different disease stages or whether it exhibits a stage-dependent effect. Amyloid (A) and tau (T) status was defined using a combination of available PET and CSF biomarkers in the Alzheimer's Disease Neuroimaging Initiative cohort. In 312 participants with biomarker-confirmed A-T- status, we used Cox proportional hazards models to estimate the contribution of APOE and polygenic risk scores (beyond APOE) to convert to A+T- status (65 conversions). Furthermore, we repeated the analysis in 290 participants with A+T- status and investigated the genetic contribution to conversion to A+T+ (45 conversions). Both survival analyses were adjusted for age, sex and years of education. For progression from A-T- to A+T-, APOE-e4 burden showed a significant effect [hazard ratio (HR) = 2.88; 95% confidence interval (CI): 1.70-4.89; P < 0.001], whereas polygenic risk did not (HR = 1.09; 95% CI: 0.84-1.42; P = 0.53). Conversely, for the transition from A+T- to A+T+, the contribution of APOE-e4 burden was reduced (HR = 1.62; 95% CI: 1.05-2.51; P = 0.031), whereas the polygenic risk showed an increased contribution (HR = 1.73; 95% CI: 1.27-2.36; P < 0.001). The marginal APOE effect was driven by e4 homozygotes (HR = 2.58; 95% CI: 1.05-6.35; P = 0.039) as opposed to e4 heterozygotes (HR = 1.74; 95% CI: 0.87-3.49; P = 0.12). The genetic risk for late-onset Alzheimer's disease unfolds in a disease stage-dependent fashion. A better understanding of the interplay between disease stage and genetic risk can lead to a more mechanistic understanding of the transition between ATN stages and a better understanding of the molecular processes leading to Alzheimer's disease, in addition to opening therapeutic windows for targeted interventions.

Disease progression modeling with temporal realignment: An emerging approach to deepen knowledge on chronic diseases

The recent development of the first disease-modifying drug for Alzheimer's disease represents a major advancement in dementia treatment. Behind this breakthrough is a quarter century of research efforts to understand the disease not by a particular symptom at a given moment, but by long-term sequential changes in multiple biomarkers. Disease progression modeling with temporal realignment (DPM-TR) is an emerging computational approach proposed with this biomarker-based disease concept. By integrating short-term clinical observations of multiple disease biomarkers in a data-driven manner, DPM-TR provides a way to understand the progression of chronic diseases over decades and predict individual disease stages more accurately. DPM-TR has been developed primarily in the area of neurodegenerative diseases but has recently been extended to non-neurodegenerative diseases, including chronic obstructive pulmonary, autoimmune, and ophthalmologic diseases. This review focuses on opportunities for DPM-TR in clinical practice and drug development and discusses its current status and challenges.

MAPPING ALZHEIMER'S DISEASE PSEUDO-PROGRESSION WITH MULTIMODAL BIOMARKER TRAJECTORY EMBEDDINGS

Alzheimer's Disease (AD) is a neurodegenerative disorder characterized by progressive cognitive degeneration and motor impairment, affecting millions worldwide. Mapping the progression of AD is crucial for early detection of loss of brain function, timely intervention, and development of effective treatments. However, accurate measurements of disease progression are still challenging at present. This study presents a novel approach to understanding the heterogeneous pathways of AD through longitudinal biomarker data from medical imaging and other modalities. We propose an analytical pipeline adopting two popular machine learning methods from the single-cell transcriptomics domain, PHATE and Slingshot, to project multimodal biomarker trajectories to a low-dimensional space. These embeddings serve as our pseudotime estimates. We applied this pipeline to the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset to align longitudinal data across individuals at various disease stages. Our approach mirrors the technique used to cluster single-cell data into cell types based on developmental timelines. Our pseudotime estimates revealed distinct patterns of disease evolution and biomarker changes over time, providing a deeper understanding of the temporal dynamics of AD. The results show the potential of the approach in the clinical domain of neurodegenerative diseases, enabling more precise disease modeling and early diagnosis.

Data-driven Stochastic Model for Quantifying the Interplay Between Amyloid-beta and Calcium Levels in Alzheimer's Disease

The abnormal aggregation of extracellular amyloid-β ( A β ) in senile plaques resulting in calcium C a + 2 dyshomeostasis is one of the primary symptoms of Alzheimer's disease (AD). Significant research efforts have been devoted in the past to better understand the underlying molecular mechanisms driving A β deposition and C a + 2 dysregulation. Importantly, synaptic impairments, neuronal loss, and cognitive failure in AD patients are all related to the buildup of intraneuronal A β accumulation. Moreover, increasing evidence show a feed-forward loop between A β and C a + 2 levels, i.e. A β disrupts neuronal C a + 2 levels, which in turn affects the formation of A β . To better understand this interaction, we report a novel stochastic model where we analyze the positive feedback loop between A β and C a + 2 using ADNI data. A good therapeutic treatment plan for AD requires precise predictions. Stochastic models offer an appropriate framework for modelling AD since AD studies are observational in nature and involve regular patient visits. The etiology of AD may be described as a multi-state disease process using the approximate Bayesian computation method. So, utilizing ADNI data from 2-year visits for AD patients, we employ this method to investigate the interplay between A β and C a + 2 levels at various disease development phases. Incorporating the ADNI data in our physics-based Bayesian model, we discovered that a sufficiently large disruption in either A β metabolism or intracellular C a + 2 homeostasis causes the relative growth rate in both C a + 2 and A β , which corresponds to the development of AD. The imbalance of C a + 2 ions causes A β disorders by directly or indirectly affecting a variety of cellular and subcellular processes, and the altered homeostasis may worsen the abnormalities of C a + 2 ion transportation and deposition. This suggests that altering the C a + 2 balance or the balance between A β and C a + 2 by chelating them may be able to reduce disorders associated with AD and open up new research possibilities for AD therapy.

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.

Machine learning in neurological disorders: A multivariate LSTM and AdaBoost approach to Alzheimer's disease time series analysis

Introduction

Alzheimer's disease (AD) is a progressive brain disorder that impairs cognitive functions, behavior, and memory. Early detection is crucial as it can slow down the progression of AD. However, early diagnosis and monitoring of AD's advancement pose significant challenges due to the necessity for complex cognitive assessments and medical tests.

Methods

This study introduces a data acquisition technique and a preprocessing pipeline, combined with multivariate long short-term memory (M-LSTM) and AdaBoost models. These models utilize biomarkers from cognitive assessments and neuroimaging scans to detect the progression of AD in patients, using The AD Prediction of Longitudinal Evolution challenge cohort from the Alzheimer's Disease Neuroimaging Initiative database.

Results

The methodology proposed in this study significantly improved performance metrics. The testing accuracy reached 80% with the AdaBoost model, while the M-LSTM model achieved an accuracy of 82%. This represents a 20% increase in accuracy compared to a recent similar study.

Discussion

The findings indicate that the multivariate model, specifically the M-LSTM, is more effective in identifying the progression of AD compared to the AdaBoost model and methodologies used in recent research.

Estimating Dementia Onset: AT(N) Profiles and Predictive Modeling in Mild Cognitive Impairment Patients

BACKGROUND

Mild Cognitive Impairment (MCI) usually precedes the symptomatic phase of dementia and constitutes a window of opportunities for preventive therapies.

OBJECTIVES

The objective of this study was to predict the time an MCI patient has left to reach dementia and obtain the most likely natural history in the progression of MCI towards dementia.

METHODS

This study was conducted on 633 MCI patients and 145 subjects with dementia through 4726 visits over 15 years from Alzheimer Disease Neuroimaging Initiative (ADNI) cohort. A combination of data from AT(N) profiles at baseline and longitudinal predictive modeling was applied. A data-driven approach was proposed for categorical diagnosis prediction and timeline estimation of cognitive decline progression, which combined supervised and unsupervised learning techniques.

RESULTS

A reduced vector of only neuropsychological measures was selected for training the models. At baseline, this approach had high performance in detecting subjects at high risk of converting from MCI to dementia in the coming years. Furthermore, a Disease Progression Model (DPM) was built and also verified using three metrics. As a result of the DPM focused on the studied population, it was inferred that amyloid pathology (A+) appears about 7 years before dementia, and tau pathology (T+) and neurodegeneration (N+) occur almost simultaneously, between 3 and 4 years before dementia. In addition, MCI-A+ subjects were shown to progress more rapidly to dementia compared to MCI-A- subjects.

CONCLUSION

Based on proposed natural histories and cross-sectional and longitudinal analysis of AD markers, the results indicated that only a single cerebrospinal fluid sample is necessary during the prodromal phase of AD. Prediction from MCI into dementia and its timeline can be achieved exclusively through neuropsychological measures.

Artificial intelligence for dementia research methods optimization

Artificial intelligence (AI) and machine learning (ML) approaches are increasingly being used in dementia research. However, several methodological challenges exist that may limit the insights we can obtain from high-dimensional data and our ability to translate these findings into improved patient outcomes. To improve reproducibility and replicability, researchers should make their well-documented code and modeling pipelines openly available. Data should also be shared where appropriate. To enhance the acceptability of models and AI-enabled systems to users, researchers should prioritize interpretable methods that provide insights into how decisions are generated. Models should be developed using multiple, diverse datasets to improve robustness, generalizability, and reduce potentially harmful bias. To improve clarity and reproducibility, researchers should adhere to reporting guidelines that are co-produced with multiple stakeholders. If these methodological challenges are overcome, AI and ML hold enormous promise for changing the landscape of dementia research and care. HIGHLIGHTS: Machine learning (ML) can improve diagnosis, prevention, and management of dementia. Inadequate reporting of ML procedures affects reproduction/replication of results. ML models built on unrepresentative datasets do not generalize to new datasets. Obligatory metrics for certain model structures and use cases have not been defined. Interpretability and trust in ML predictions are barriers to clinical translation.

Disease progression model anchored around clinical diagnosis in longitudinal cohorts: example of Alzheimer's disease and related dementia

BACKGROUND

Alzheimer's disease and related dementia (ADRD) are characterized by multiple and progressive anatomo-clinical changes including accumulation of abnormal proteins in the brain, brain atrophy and severe cognitive impairment. Understanding the sequence and timing of these changes is of primary importance to gain insight into the disease natural history and ultimately allow earlier diagnosis. Yet, modeling changes over disease course from cohort data is challenging as the usual timescales (time since inclusion, chronological age) are inappropriate and time-to-clinical diagnosis is available on small subsamples of participants with short follow-up durations prior to diagnosis. One solution to circumvent this challenge is to define the disease time as a latent variable.

METHODS

We developed a multivariate mixed model approach that realigns individual trajectories into the latent disease time to describe disease progression. In contrast with the existing literature, our methodology exploits the clinical diagnosis information as a partially observed and approximate reference to guide the estimation of the latent disease time. The model estimation was carried out in the Bayesian Framework using Stan. We applied the methodology to the MEMENTO study, a French multicentric clinic-based cohort of 2186 participants with 5-year intensive follow-up. Repeated measures of 12 ADRD markers stemmed from cerebrospinal fluid (CSF), brain imaging and cognitive tests were analyzed.

RESULTS

The estimated latent disease time spanned over twenty years before the clinical diagnosis. Considering the profile of a woman aged 70 with a high level of education and APOE4 carrier (the main genetic risk factor for ADRD), CSF markers of tau proteins accumulation preceded markers of brain atrophy by 5 years and cognitive decline by 10 years. However we observed that individual characteristics could substantially modify the sequence and timing of these changes, in particular for CSF level of A[Formula: see text].

CONCLUSION

By leveraging the available clinical diagnosis timing information, our disease progression model does not only realign trajectories into the most homogeneous way. It accounts for the inherent residual inter-individual variability in dementia progression to describe the long-term anatomo-clinical degradations according to the years preceding clinical diagnosis, and to provide clinically meaningful information on the sequence of events.

TRIAL REGISTRATION

clinicaltrials.gov, NCT01926249. Registered on 16 August 2013.

Disease progression modelling of Alzheimer's disease using probabilistic principal components analysis

The recent biological redefinition of Alzheimer's Disease (AD) has spurred the development of statistical models that relate changes in biomarkers with neurodegeneration and worsening condition linked to AD. The ability to measure such changes may facilitate earlier diagnoses for affected individuals and help in monitoring the evolution of their condition. Amongst such statistical tools, disease progression models (DPMs) are quantitative, data-driven methods that specifically attempt to describe the temporal dynamics of biomarkers relevant to AD. Due to the heterogeneous nature of this disease, with patients of similar age experiencing different AD-related changes, a challenge facing longitudinal mixed-effects-based DPMs is the estimation of patient-realigning time-shifts. These time-shifts are indispensable for meaningful biomarker modelling, but may impact fitting time or vary with missing data in jointly estimated models. In this work, we estimate an individual's progression through Alzheimer's disease by combining multiple biomarkers into a single value using a probabilistic formulation of principal components analysis. Our results show that this variable, which summarises AD through observable biomarkers, is remarkably similar to jointly estimated time-shifts when we compute our scores for the baseline visit, on cross-sectional data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Reproducing the expected properties of clinical datasets, we confirm that estimated scores are robust to missing data or unavailable biomarkers. In addition to cross-sectional insights, we can model the latent variable as an individual progression score by repeating estimations at follow-up examinations and refining long-term estimates as more data is gathered, which would be ideal in a clinical setting. Finally, we verify that our score can be used as a pseudo-temporal scale instead of age to ignore some patient heterogeneity in cohort data and highlight the general trend in expected biomarker evolution in affected individuals.

The temporal event-based model: Learning event timelines in progressive diseases

Timelines of events, such as symptom appearance or a change in biomarker value, provide powerful signatures that characterise progressive diseases. Understanding and predicting the timing of events is important for clinical trials targeting individuals early in the disease course when putative treatments are likely to have the strongest effect. However, previous models of disease progression cannot estimate the time between events and provide only an ordering in which they change. Here, we introduce the temporal event-based model (TEBM), a new probabilistic model for inferring timelines of biomarker events from sparse and irregularly sampled datasets. We demonstrate the power of the TEBM in two neurodegenerative conditions: Alzheimer's disease (AD) and Huntington's disease (HD). In both diseases, the TEBM not only recapitulates current understanding of event orderings but also provides unique new ranges of timescales between consecutive events. We reproduce and validate these findings using external datasets in both diseases. We also demonstrate that the TEBM improves over current models; provides unique stratification capabilities; and enriches simulated clinical trials to achieve a power of 80 % with less than half the cohort size compared with random selection. The application of the TEBM naturally extends to a wide range of progressive conditions.

Impact of sex and APOE-ε4 genotype on patterns of regional brain atrophy in Alzheimer's disease and healthy aging

Alzheimer's Disease (AD) is a heterogeneous disease that disproportionately affects women and people with the APOE-ε4 susceptibility gene. We aim to describe the not-well-understood influence of both risk factors on the dynamics of brain atrophy in AD and healthy aging. Regional cortical thinning and brain atrophy were modeled over time using non-linear mixed-effect models and the FreeSurfer software with t1-MRI scans from the Alzheimer's Disease Neuroimaging Initiative (N = 1,502 subjects, 6,728 images in total). Covariance analysis was used to disentangle the effect of sex and APOE genotype on the regional onset age and pace of atrophy, while correcting for educational level. A map of the regions mostly affected by neurodegeneration is provided. Results were confirmed on gray matter density data from the SPM software. Women experience faster atrophic rates in the temporal, frontal, parietal lobes and limbic system and earlier onset in the amygdalas, but slightly later onset in the postcentral and cingulate gyri as well as all regions of the basal ganglia and thalamus. APOE-ε4 genotypes leads to earlier and faster atrophy in the temporal, frontal, parietal lobes, and limbic system in AD patients, but not in healthy patients. Higher education was found to slightly delay atrophy in healthy patients, but not for AD patients. A cohort of amyloid positive patients with MCI showed a similar impact of sex as in the healthy cohort, while APOE-ε4 showed similar associations as in the AD cohort. Female sex is as strong a risk factor for AD as APOE-ε4 genotype regarding neurodegeneration. Women experience a sharper atrophy in the later stages of the disease, although not a significantly earlier onset. These findings may have important implications for the development of targeted intervention.

Transferability of Alzheimer's disease progression subtypes to an independent population cohort

In the past, methods to subtype or biotype patients using brain imaging data have been developed. However, it is unclear whether and how these trained machine learning models can be successfully applied to population cohorts to study the genetic and lifestyle factors underpinning these subtypes. This work, using the Subtype and Stage Inference (SuStaIn) algorithm, examines the generalisability of data-driven Alzheimer's disease (AD) progression models. We first compared SuStaIn models trained separately on Alzheimer's disease neuroimaging initiative (ADNI) data and an AD-at-risk population constructed from the UK Biobank dataset. We further applied data harmonization techniques to remove cohort effects. Next, we built SuStaIn models on the harmonized datasets, which were then used to subtype and stage subjects in the other harmonized dataset. The first key finding is that three consistent atrophy subtypes were found in both datasets, which match the previously identified subtype progression patterns in AD: 'typical', 'cortical' and 'subcortical'. Next, the subtype agreement was further supported by high consistency in individuals' subtypes and stage assignment based on the different models: more than 92% of the subjects, with reliable subtype assignment in both ADNI and UK Biobank dataset, were assigned to an identical subtype under the model built on the different datasets. The successful transferability of AD atrophy progression subtypes across cohorts capturing different phases of disease development enabled further investigations of associations between AD atrophy subtypes and risk factors. Our study showed that (1) the average age is highest in the typical subtype and lowest in the subcortical subtype; (2) the typical subtype is associated with statistically more-AD-like cerebrospinal fluid biomarkers values in comparison to the other two subtypes; and (3) in comparison to the subcortical subtype, the cortical subtype subjects are more likely to associate with prescription of cholesterol and high blood pressure medications. In summary, we presented cross-cohort consistent recovery of AD atrophy subtypes, showing how the same subtypes arise even in cohorts capturing substantially different disease phases. Our study opened opportunities for future detailed investigations of atrophy subtypes with a broad range of early risk factors, which will potentially lead to a better understanding of the disease aetiology and the role of lifestyle and behaviour on AD.

MC-RVAE: Multi-channel recurrent variational autoencoder for multimodal Alzheimer's disease progression modelling

The progression of neurodegenerative diseases, such as Alzheimer's Disease, is the result of complex mechanisms interacting across multiple spatial and temporal scales. Understanding and predicting the longitudinal course of the disease requires harnessing the variability across different data modalities and time, which is extremely challenging. In this paper, we propose a model based on recurrent variational autoencoders that is able to capture cross-channel interactions between different modalities and model temporal information. These are achieved thanks to its multi-channel architecture and its shared latent variational space, parametrized with a recurrent neural network. We evaluate our model on both synthetic and real longitudinal datasets, the latter including imaging and non-imaging data, with N=897 subjects. Results show that our multi-channel recurrent variational autoencoder outperforms a set of baselines (KNN, random forest, and group factor analysis) for the task of reconstructing missing modalities, reducing the mean absolute error by 5% (w.r.t. the best baseline) for both subcortical volumes and cortical thickness. Our model is robust to missing features within each modality and is able to generate realistic synthetic imaging biomarkers trajectories from cognitive scores.

A multidimensional ODE-based model of Alzheimer's disease progression

Data-driven Alzheimer's disease (AD) progression models are useful for clinical prediction, disease mechanism understanding, and clinical trial design. Most dynamic models were inspired by the amyloid cascade hypothesis and described AD progression as a linear chain of pathological events. However, the heterogeneity observed in healthy and sporadic AD populations challenged the amyloid hypothesis, and there is a need for more flexible dynamical models that accompany this conceptual shift. We present a statistical model of the temporal evolution of biomarkers and cognitive tests that allows diverse biomarker paths throughout the disease. The model consists of two elements: a multivariate dynamic model of the joint evolution of biomarkers and cognitive tests; and a clinical prediction model. The dynamic model uses a system of ordinary differential equations to jointly model the rate of change of an individual's biomarkers and cognitive tests. The clinical prediction model is an ordinal logistic model of the diagnostic label. Prognosis and time-to-onset predictions are obtained by computing the clinical label probabilities throughout the forecasted biomarker trajectories. The proposed dynamical model is interpretable, free of one-dimensional progression hypotheses or disease staging paradigms, and can account for the heterogeneous dynamics observed in sporadic AD. We developed the model using longitudinal data from the Alzheimer's Disease Neuroimaging Initiative. We illustrate the patterns of biomarker rates of change and the model performance to predict the time to conversion from MCI to dementia.

Forecasting individual progression trajectories in Alzheimer's disease

The anticipation of progression of Alzheimer's disease (AD) is crucial for evaluations of secondary prevention measures thought to modify the disease trajectory. However, it is difficult to forecast the natural progression of AD, notably because several functions decline at different ages and different rates in different patients. We evaluate here AD Course Map, a statistical model predicting the progression of neuropsychological assessments and imaging biomarkers for a patient from current medical and radiological data at early disease stages. We tested the method on more than 96,000 cases, with a pool of more than 4,600 patients from four continents. We measured the accuracy of the method for selecting participants displaying a progression of clinical endpoints during a hypothetical trial. We show that enriching the population with the predicted progressors decreases the required sample size by 38% to 50%, depending on trial duration, outcome, and targeted disease stage, from asymptomatic individuals at risk of AD to subjects with early and mild AD. We show that the method introduces no biases regarding sex or geographic locations and is robust to missing data. It performs best at the earliest stages of disease and is therefore highly suitable for use in prevention trials.

Italian, European, and international neuroinformatics efforts: An overview

Neuroinformatics is a research field that focusses on software tools capable of identifying, analysing, modelling, organising and sharing multiscale neuroscience data. Neuroinformatics has exploded in the last two decades with the emergence of the Big Data phenomenon, characterised by the so-called 3Vs (volume, velocity and variety), which provided neuroscientists with an improved ability to acquire and process data faster and more cheaply thanks to technical improvements in clinical, genomic and radiological technologies. This situation has led to a 'data deluge', as neuroscientists can routinely collect more study data in a few days than they could in a year just a decade ago. To address this phenomenon, several neuroimaging-focussed neuroinformatics platforms have emerged, funded by national or transnational agencies, with the following goals: (i) development of tools for archiving and organising analytical data (XNAT, REDCap and LabKey); (ii) development of data-driven models evolving from reductionist approaches to multidimensional models (RIN, IVN, HBD, EuroPOND, E-DADS and GAAIN BRAIN); and (iii) development of e-infrastructures to provide sufficient computational power and storage resources (neuGRID, HBP-EBRAINS, LONI and CONP). Although the scenario is still fragmented, there are technological and economical attempts at both national and international levels to introduce high standards for open and Findable, Accessible, Interoperable and Reusable (FAIR) neuroscience worldwide.

A Novel Coupling Model of Physiological Degradation and Emotional State for Prediction of Alzheimer's Disease Progression

The prediction of Alzheimer's disease (AD) progression plays a very important role in the early intervention of patients and the improvement of life quality. Cognitive scales are commonly used to assess the patient's status. However, due to the complicated pathogenesis of AD and the individual differences in AD, the prediction of AD progression is challenging. This paper proposes a novel coupling model (P-E model) that takes into account the processes of physiological degradation and emotional state transition of AD patients. We conduct experiments on synthetic data to validate the effectiveness of the proposed P-E model. Next, we conduct experiments on 134 subjects with more than 10 follow-ups from the Alzheimer's Disease Neuroimaging Initiative. The prediction performance of the P-E model is significantly better than other state-of-the-art methods, which achieves the mean squared error of 7.137 ± 0.035. The experimental results show that the P-E model can well characterize the non-monotonic properties of AD cognitive data and can also have a good predictive ability for time series data with individual differences.

Categorical predictive and disease progression modeling in the early stage of Alzheimer's disease

BACKGROUND

A preclinical stage of Alzheimer's disease (AD) precedes the symptomatic phases of mild cognitive impairment (MCI) and dementia, which constitutes a window of opportunities for preventive therapies or delaying dementia onset.

NEW METHOD

We propose to use categorical predictive models based on survival analysis with longitudinal data which are capable of determining subsets of markers to classify cognitively unimpaired (CU) subjects who progress into MCI/dementia or not. Subsequently, the proposed combination of markers was used to construct disease progression models (DPMs), which reveal long-term pathological trajectories from short-term clinical data. The proposed methodology was applied to a population recruited by the ADNI.

RESULTS

A very small subset of standard MRI-based data, CSF markers and cognitive measures was used to predict CU-to-MCI/dementia progression. The longitudinal data of these selected markers were used to construct DPMs using the algorithms of growth models by alternating conditional expectation (GRACE) and the latent time joint mixed effects model (LTJMM). The results show that the natural history of the proposed cognitive decline classifies the subjects well according to the clinical groups and shows a moderate correlation between the conversion times and their estimates by the algorithms.

COMPARISON WITH EXISTING METHODS

Unlike the training of the DPM algorithms without preselection of the markers, here, it is proposed to construct and evaluate the DPMs using the subsets of markers defined by the categorical predictive models.

CONCLUSIONS

The estimates of the natural history of the proposed cognitive decline from GRACE were more robust than those using LTJMM. The transition from normal to cognitive decline is mostly associated with an increase in temporal atrophy, worsening of clinical scores and pTAU/Aβ. Furthermore, pTAU/Aβ, Everyday Cognition score and the normalized volume of the entorhinal cortex show alterations of more than 20% fifteen years before the onset of cognitive decline.

Comparison and aggregation of event sequences across ten cohorts to describe the consensus biomarker evolution in Alzheimer's disease

BACKGROUND

Previous models of Alzheimer's disease (AD) progression were primarily hypothetical or based on data originating from single cohort studies. However, cohort datasets are subject to specific inclusion and exclusion criteria that influence the signals observed in their collected data. Furthermore, each study measures only a subset of AD-relevant variables. To gain a comprehensive understanding of AD progression, the heterogeneity and robustness of estimated progression patterns must be understood, and complementary information contained in cohort datasets be leveraged.

METHODS

We compared ten event-based models that we fit to ten independent AD cohort datasets. Additionally, we designed and applied a novel rank aggregation algorithm that combines partially overlapping, individual event sequences into a meta-sequence containing the complementary information from each cohort.

RESULTS

We observed overall consistency across the ten event-based model sequences (average pairwise Kendall's tau correlation coefficient of 0.69 ± 0.28), despite variance in the positioning of mainly imaging variables. The changes described in the aggregated meta-sequence are broadly consistent with the current understanding of AD progression, starting with cerebrospinal fluid amyloid beta, followed by tauopathy, memory impairment, FDG-PET, and ultimately brain deterioration and impairment of visual memory.

CONCLUSION

Overall, the event-based models demonstrated similar and robust disease cascades across independent AD cohorts. Aggregation of data-driven results can combine complementary strengths and information of patient-level datasets. Accordingly, the derived meta-sequence draws a more complete picture of AD pathology compared to models relying on single cohorts.

Degenerative adversarial neuroimage nets for brain scan simulations: Application in ageing and dementia

Accurate and realistic simulation of high-dimensional medical images has become an important research area relevant to many AI-enabled healthcare applications. However, current state-of-the-art approaches lack the ability to produce satisfactory high-resolution and accurate subject-specific images. In this work, we present a deep learning framework, namely 4D-Degenerative Adversarial NeuroImage Net (4D-DANI-Net), to generate high-resolution, longitudinal MRI scans that mimic subject-specific neurodegeneration in ageing and dementia. 4D-DANI-Net is a modular framework based on adversarial training and a set of novel spatiotemporal, biologically-informed constraints. To ensure efficient training and overcome memory limitations affecting such high-dimensional problems, we rely on three key technological advances: i) a new 3D training consistency mechanism called Profile Weight Functions (PWFs), ii) a 3D super-resolution module and iii) a transfer learning strategy to fine-tune the system for a given individual. To evaluate our approach, we trained the framework on 9852 T1-weighted MRI scans from 876 participants in the Alzheimer's Disease Neuroimaging Initiative dataset and held out a separate test set of 1283 MRI scans from 170 participants for quantitative and qualitative assessment of the personalised time series of synthetic images. We performed three evaluations: i) image quality assessment; ii) quantifying the accuracy of regional brain volumes over and above benchmark models; and iii) quantifying visual perception of the synthetic images by medical experts. Overall, both quantitative and qualitative results show that 4D-DANI-Net produces realistic, low-artefact, personalised time series of synthetic T1 MRI that outperforms benchmark models.

pySuStaIn: a Python implementation of the Subtype and Stage Inference algorithm

Progressive disorders are highly heterogeneous. Symptom-based clinical classification of these disorders may not reflect the underlying pathobiology. Data-driven subtyping and staging of patients has the potential to disentangle the complex spatiotemporal patterns of disease progression. Tools that enable this are in high demand from clinical and treatment-development communities. Here we describe the pySuStaIn software package, a Python-based implementation of the Subtype and Stage Inference (SuStaIn) algorithm. SuStaIn unravels the complexity of heterogeneous diseases by inferring multiple disease progression patterns (subtypes) and individual severity (stages) from cross-sectional data. The primary aims of pySuStaIn are to enable widespread application and translation of SuStaIn via an accessible Python package that supports simple extension and generalization to novel modelling situations within a single, consistent architecture.

DeepAtrophy: Teaching a neural network to detect progressive changes in longitudinal MRI of the hippocampal region in Alzheimer's disease

Measures of change in hippocampal volume derived from longitudinal MRI are a well-studied biomarker of disease progression in Alzheimer's disease (AD) and are used in clinical trials to track therapeutic efficacy of disease-modifying treatments. However, longitudinal MRI change measures based on deformable registration can be confounded by MRI artifacts, resulting in over-estimation or underestimation of hippocampal atrophy. For example, the deformation-based-morphometry method ALOHA (Das et al., 2012) finds an increase in hippocampal volume in a substantial proportion of longitudinal scan pairs from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study, unexpected, given that the hippocampal gray matter is lost with age and disease progression. We propose an alternative approach to quantify disease progression in the hippocampal region: to train a deep learning network (called DeepAtrophy) to infer temporal information from longitudinal scan pairs. The underlying assumption is that by learning to derive time-related information from scan pairs, the network implicitly learns to detect progressive changes that are related to aging and disease progression. Our network is trained using two categorical loss functions: one that measures the network's ability to correctly order two scans from the same subject, input in arbitrary order; and another that measures the ability to correctly infer the ratio of inter-scan intervals between two pairs of same-subject input scans. When applied to longitudinal MRI scan pairs from subjects unseen during training, DeepAtrophy achieves greater accuracy in scan temporal ordering and interscan interval inference tasks than ALOHA (88.5% vs. 75.5% and 81.1% vs. 75.0%, respectively). A scalar measure of time-related change in a subject level derived from DeepAtrophy is then examined as a biomarker of disease progression in the context of AD clinical trials. We find that this measure performs on par with ALOHA in discriminating groups of individuals at different stages of the AD continuum. Overall, our results suggest that using deep learning to infer temporal information from longitudinal MRI of the hippocampal region has good potential as a biomarker of disease progression, and hints that combining this approach with conventional deformation-based morphometry algorithms may lead to improved biomarkers in the future.

Revealing the Timeline of Structural MRI Changes in Premanifest to Manifest Huntington Disease

BACKGROUND AND OBJECTIVES

Longitudinal measurements of brain atrophy using structural MRI (sMRI) can provide powerful markers for tracking disease progression in neurodegenerative diseases. In this study, we use a disease progression model to learn individual-level disease times and hence reveal a new timeline of sMRI changes in Huntington disease (HD).

METHODS

We use data from the 2 largest cohort imaging studies in HD-284 participants from TRACK-HD (100 control, 104 premanifest, and 80 manifest) and 159 participants from PREDICT-HD (36 control and 128 premanifest)-to train and test the model. We longitudinally register T1-weighted sMRI scans from 3 consecutive time points to reduce intraindividual variability and calculate regional brain volumes using an automated segmentation tool with rigorous manual quality control.

RESULTS

Our model reveals, for the first time, the relative magnitude and timescale of subcortical and cortical atrophy changes in HD. We find that the largest (∼20% average change in magnitude) and earliest (∼2 years before average abnormality) changes occur in the subcortex (pallidum, putamen, and caudate), followed by a cascade of changes across other subcortical and cortical regions over a period of ∼11 years. We also show that sMRI, when combined with our disease progression model, provides improved prediction of onset over the current best method (root mean square error = 4.5 years and maximum error = 7.9 years vs root mean square error = 6.6 years and maximum error = 18.2 years).

DISCUSSION

Our findings support the use of disease progression modeling to reveal new information from sMRI, which can potentially inform imaging marker selection for clinical trials.

Disease Modelling of Cognitive Outcomes and Biomarkers in the European Prevention of Alzheimer's Dementia Longitudinal Cohort

A key challenge for the secondary prevention of Alzheimer’s dementia is the need to identify individuals early on in the disease process through sensitive cognitive tests and biomarkers. The European Prevention of Alzheimer’s Dementia (EPAD) consortium recruited participants into a longitudinal cohort study with the aim of building a readiness cohort for a proof-of-concept clinical trial and also to generate a rich longitudinal data-set for disease modelling. Data have been collected on a wide range of measurements including cognitive outcomes, neuroimaging, cerebrospinal fluid biomarkers, genetics and other clinical and environmental risk factors, and are available for 1,828 eligible participants at baseline, 1,567 at 6 months, 1,188 at one-year follow-up, 383 at 2 years, and 89 participants at three-year follow-up visit. We novelly apply state-of-the-art longitudinal modelling and risk stratification approaches to these data in order to characterise disease progression and biological heterogeneity within the cohort. Specifically, we use longitudinal class-specific mixed effects models to characterise the different clinical disease trajectories and a semi-supervised Bayesian clustering approach to explore whether participants can be stratified into homogeneous subgroups that have different patterns of cognitive functioning evolution, while also having subgroup-specific profiles in terms of baseline biomarkers and longitudinal rate of change in biomarkers.

DPVis: Visual Analytics With Hidden Markov Models for Disease Progression Pathways

Clinical researchers use disease progression models to understand patient status and characterize progression patterns from longitudinal health records. One approach for disease progression modeling is to describe patient status using a small number of states that represent distinctive distributions over a set of observed measures. Hidden Markov models (HMMs) and its variants are a class of models that both discover these states and make inferences of health states for patients. Despite the advantages of using the algorithms for discovering interesting patterns, it still remains challenging for medical experts to interpret model outputs, understand complex modeling parameters, and clinically make sense of the patterns. To tackle these problems, we conducted a design study with clinical scientists, statisticians, and visualization experts, with the goal to investigate disease progression pathways of chronic diseases, namely type 1 diabetes (T1D), Huntington's disease, Parkinson's disease, and chronic obstructive pulmonary disease (COPD). As a result, we introduce DPVis which seamlessly integrates model parameters and outcomes of HMMs into interpretable and interactive visualizations. In this article, we demonstrate that DPVis is successful in evaluating disease progression models, visually summarizing disease states, interactively exploring disease progression patterns, and building, analyzing, and comparing clinically relevant patient subgroups.

Deep recurrent model for individualized prediction of Alzheimer's disease progression

Alzheimer's disease (AD) is known as one of the major causes of dementia and is characterized by slow progression over several years, with no treatments or available medicines. In this regard, there have been efforts to identify the risk of developing AD in its earliest time. While many of the previous works considered cross-sectional analysis, more recent studies have focused on the diagnosis and prognosis of AD with longitudinal or time series data in a way of disease progression modeling. Under the same problem settings, in this work, we propose a novel computational framework that can predict the phenotypic measurements of MRI biomarkers and trajectories of clinical status along with cognitive scores at multiple future time points. However, in handling time series data, it generally faces many unexpected missing observations. In regard to such an unfavorable situation, we define a secondary problem of estimating those missing values and tackle it in a systematic way by taking account of temporal and multivariate relations inherent in time series data. Concretely, we propose a deep recurrent network that jointly tackles the four problems of (i) missing value imputation, (ii) phenotypic measurements forecasting, (iii) trajectory estimation of a cognitive score, and (iv) clinical status prediction of a subject based on his/her longitudinal imaging biomarkers. Notably, the learnable parameters of all the modules in our predictive models are trained in an end-to-end manner by taking the morphological features and cognitive scores as input, with our circumspectly defined loss function. In our experiments over The Alzheimers Disease Prediction Of Longitudinal Evolution (TADPOLE) challenge cohort, we measured performance for various metrics and compared our method to competing methods in the literature. Exhaustive analyses and ablation studies were also conducted to better confirm the effectiveness of our method.

Simulating the outcome of amyloid treatments in Alzheimer's disease from imaging and clinical data

In this study, we investigate SimulAD, a novel quantitative instrument for the development of intervention strategies for disease-modifying drugs in Alzheimer's disease. SimulAD is based on the modeling of the spatio-temporal dynamics governing the joint evolution of imaging and clinical biomarkers along the history of the disease, and allows the simulation of the effect of intervention time and drug dosage on the biomarkers' progression. When applied to multi-modal imaging and clinical data from the Alzheimer's Disease Neuroimaging Initiative the method enables to generate hypothetical scenarios of amyloid lowering interventions. The results quantify the crucial role of intervention time, and provide a theoretical justification for testing amyloid modifying drugs in the pre-clinical stage. Our experimental simulations are compatible with the outcomes observed in past clinical trials, and suggest that anti-amyloid treatments should be administered at least 7 years earlier than what is currently being done in order to obtain statistically powered improvement of clinical endpoints.

Dynamics of Cortical Degeneration Over a Decade in Huntington's Disease

BACKGROUND

Characterizing changing brain structure in neurodegeneration is fundamental to understanding long-term effects of pathology and ultimately providing therapeutic targets. It is well established that Huntington's disease (HD) gene carriers undergo progressive brain changes during the course of disease, yet the long-term trajectory of cortical atrophy is not well defined. Given that genetic therapies currently tested in HD are primarily expected to target the cortex, understanding atrophy across this region is essential.

METHODS

Capitalizing on a unique longitudinal dataset with a minimum of 3 and maximum of 7 brain scans from 49 HD gene carriers and 49 age-matched control subjects, we implemented a novel dynamical systems approach to infer patterns of regional neurodegeneration over 10 years. We use Bayesian hierarchical modeling to map participant- and group-level trajectories of atrophy spatially and temporally, additionally relating atrophy to the genetic marker of HD (CAG-repeat length) and motor and cognitive symptoms.

RESULTS

We show, for the first time, that neurodegenerative changes exhibit complex temporal dynamics with substantial regional variation around the point of clinical diagnosis. Although widespread group differences were seen across the cortex, the occipital and parietal regions undergo the greatest rate of cortical atrophy. We have established links between atrophy and genetic markers of HD while demonstrating that specific cortical changes predict decline in motor and cognitive performance.

CONCLUSIONS

HD gene carriers display regional variability in the spatial pattern of cortical atrophy, which relates to genetic factors and motor and cognitive symptoms. Our findings indicate a complex pattern of neuronal loss, which enables greater characterization of HD progression.

Investigating hypotheses of neurodegeneration by learning dynamical systems of protein propagation in the brain

We introduce a theoretical framework for estimating, comparing and interpreting mechanistic hypotheses on long term protein propagation across brain networks in neurodegenerative disorders (ND). The model is expressed within a Bayesian non-parametric regression setting, where mechanisms of protein dynamics are inferred by means of gradient matching on dynamical systems (DS). The Bayesian formalism, combined with stochastic variational inference, naturally allows for model comparison via assessment of model evidence, while providing uncertainty quantification of causal relationship underlying protein progressions. When applied to in-vivo AV45-PET brain imaging data measuring topographic amyloid deposition in Alzheimer's disease (AD), our model identified the mechanisms of accumulation, clearance and propagation as the best suited DS for bio-mechanical description of amyloid dynamics in AD, enabling realistic and accurate personalized simulation of amyloidosis.

Robust Bayesian Analysis of Early-Stage Parkinson's Disease Progression Using DaTscan Images

This paper proposes a mixture of linear dynamical systems model for quantifying the heterogeneous progress of Parkinson's disease from DaTscan Images. The model is fitted to longitudinal DaTscans from the Parkinson's Progression Marker Initiative. Fitting is accomplished using robust Bayesian inference with collapsed Gibbs sampling. Bayesian inference reveals three image-based progression subtypes which differ in progression speeds as well as progression trajectories. The model reveals characteristic spatial progression patterns in the brain, each pattern associated with a time constant. These patterns can serve as disease progression markers. The subtypes also have different progression rates of clinical symptoms measured by MDS-UPDRS Part III scores.

Robust parametric modeling of Alzheimer's disease progression

Quantitative characterization of disease progression using longitudinal data can provide long-term predictions for the pathological stages of individuals. This work studies the robust modeling of Alzheimer's disease progression using parametric methods. The proposed method linearly maps the individual's age to a disease progression score (DPS) and jointly fits constrained generalized logistic functions to the longitudinal dynamics of biomarkers as functions of the DPS using M-estimation. Robustness of the estimates is quantified using bootstrapping via Monte Carlo resampling, and the estimated inflection points of the fitted functions are used to temporally order the modeled biomarkers in the disease course. Kernel density estimation is applied to the obtained DPSs for clinical status classification using a Bayesian classifier. Different M-estimators and logistic functions, including a novel type proposed in this study, called modified Stannard, are evaluated on the data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) for robust modeling of volumetric magnetic resonance imaging (MRI) and positron emission tomography (PET) biomarkers, cerebrospinal fluid (CSF) measurements, as well as cognitive tests. The results show that the modified Stannard function fitted using the logistic loss achieves the best modeling performance with an average normalized mean absolute error (NMAE) of 0.991 across all biomarkers and bootstraps. Applied to the ADNI test set, this model achieves a multiclass area under the ROC curve (AUC) of 0.934 in clinical status classification. The obtained results for the proposed model outperform almost all state-of-the-art results in predicting biomarker values and classifying clinical status. Finally, the experiments show that the proposed model, trained using abundant ADNI data, generalizes well to data from the National Alzheimer's Coordinating Center (NACC) with an average NMAE of 1.182 and a multiclass AUC of 0.929.

Analyzing the effect of APOE on Alzheimer's disease progression using an event-based model for stratified populations

Alzheimer's disease (AD) is the most common form of dementia and is phenotypically heterogeneous. APOE is a triallelic gene which correlates with phenotypic heterogeneity in AD. In this work, we determined the effect of APOE alleles on the disease progression timeline of AD using a discriminative event-based model (DEBM). Since DEBM is a data-driven model, stratification into smaller disease subgroups would lead to more inaccurate models as compared to fitting the model on the entire dataset. Hence our secondary aim is to propose and evaluate novel approaches in which we split the different steps of DEBM into group-aspecific and group-specific parts, where the entire dataset is used to train the group-aspecific parts and only the data from a specific group is used to train the group-specific parts of the DEBM. We performed simulation experiments to benchmark the accuracy of the proposed approaches and to select the optimal approach. Subsequently, the chosen approach was applied to the baseline data of 417 cognitively normal, 235 mild cognitively impaired who convert to AD within 3 years, and 342 AD patients from the Alzheimers Disease Neuroimaging Initiative (ADNI) dataset to gain new insights into the effect of APOE carriership on the disease progression timeline of AD. In the ε4 carrier group, the model predicted with high confidence that CSF Amyloidβ₄₂ and the cognitive score of Alzheimer's Disease Assessment Scale (ADAS) are early biomarkers. Hippocampus was the earliest volumetric biomarker to become abnormal, closely followed by the CSF Phosphorylated Tau₁₈₁ (PTAU) biomarker. In the homozygous ε3 carrier group, the model predicted a similar ordering among CSF biomarkers. However, the volume of the fusiform gyrus was identified as one of the earliest volumetric biomarker. While the findings in the ε4 carrier and the homozygous ε3 carrier groups fit the current understanding of progression of AD, the finding in the ε2 carrier group did not. The model predicted, with relatively low confidence, CSF Neurogranin as one of the earliest biomarkers along with cognitive score of Mini-Mental State Examination (MMSE). Amyloid β₄₂ was found to become abnormal after PTAU. The presented models could aid understanding of the disease, and in selecting homogeneous group of presymptomatic subjects at-risk of developing symptoms for clinical trials.

Deep learning for brain disorders: from data processing to disease treatment

In order to reach precision medicine and improve patients' quality of life, machine learning is increasingly used in medicine. Brain disorders are often complex and heterogeneous, and several modalities such as demographic, clinical, imaging, genetics and environmental data have been studied to improve their understanding. Deep learning, a subpart of machine learning, provides complex algorithms that can learn from such various data. It has become state of the art in numerous fields, including computer vision and natural language processing, and is also growingly applied in medicine. In this article, we review the use of deep learning for brain disorders. More specifically, we identify the main applications, the concerned disorders and the types of architectures and data used. Finally, we provide guidelines to bridge the gap between research studies and clinical routine.

Digital biomarker-based individualized prognosis for people at risk of dementia

Background

Research investigating treatments and interventions for cognitive decline fail due to difficulties in accurately recognizing behavioral signatures in the presymptomatic stages of the disease. For this validation study, we took our previously constructed digital biomarker‐based prognostic models and focused on generalizability and robustness of the models.

Method

We validated prognostic models characterizing subjects using digital biomarkers in a longitudinal, multi‐site, 40‐month prospective study collecting data in memory clinics, general practitioner offices, and home environments.

Results

Our models were able to accurately discriminate between healthy subjects and individuals at risk to progress to dementia within 3 years. The model was also able to differentiate between people with or without amyloid neuropathology and classify fast and slow cognitive decliners with a very good diagnostic performance.

Conclusion

Digital biomarker prognostic models can be a useful tool to assist large‐scale population screening for the early detection of cognitive impairment and patient monitoring over time.

NODDI in clinical research

Diffusion MRI (dMRI) has proven to be a useful imaging approach for both clinical diagnosis and research investigating the microstructures of nervous tissues, and it has helped us to better understand the neurophysiological mechanisms of many diseases. Though diffusion tensor imaging (DTI) has long been the default tool to analyze dMRI data in clinical research, acquisition with stronger diffusion weightings beyond the DTI regimen is now possible with modern clinical scanners, potentially enabling even more detailed characterization of tissue microstructures. To take advantage of such data, neurite orientation dispersion and density imaging (NODDI) has been proposed as a way to relate the dMRI signal to tissue features via biophysically inspired modeling. The number of reports demonstrating the potential clinical utility of NODDI is rapidly increasing. At the same time, the pitfalls and limitations of NODDI, and general challenges in microstructure modeling, are becoming increasingly recognized by clinicians. dMRI microstructure modeling is a rapidly evolving field with great promise, where people from different scientific backgrounds, such as physics, medicine, biology, neuroscience, and statistics, are collaborating to build novel tools that contribute to improving human healthcare. Here, we review the applications of NODDI in clinical research and discuss future perspectives for investigations toward the implementation of dMRI microstructure imaging in clinical practice.

Analysis of MRI Data in Diagnostic Neuroradiology

Magnetic resonance imaging (MRI) is a noninvasive imaging tool for neuroradiological diagnosis. Numerous concepts of automated MRI analysis and the use of machine learning have been proposed to assist diagnosis and prognosis. While these academic innovations have proven effective in principle within controlled environments, their application to clinical practice has faced unmet requirements, such as the ability to perform reliably across a heterogeneous population, to work robustly in the presence of comorbidities, and to be invariant to scanner hardware and image quality. The lack of realistic confidence bounds and the inability to handle missing data have also reduced the application of most of these methods outside of academic studies. Mastering the complex challenges in the diagnostic process may help researchers discover novel biological constructs in multimodal data and improve stratification for clinical trials, paving the way for precision medicine. This review presents the state of the art of computerized brain MRI analysis for diagnostic purposes. We critically evaluate the current clinical usefulness of the methods and highlight challenges and future perspectives of the field.

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

BACKGROUND AND OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Voxel-based assessments of treatment effects on longitudinal brain changes in the Multidomain Alzheimer Preventive Trial cohort

The Multidomain Alzheimer Preventive Trial was designed to assess the effect of omega-3 supplementation and multidomain intervention on cognitive decline of subjects with subjective memory complaint. In terms of cognitive testing, no significant effect was found. In this paper, we evaluate the effect of the interventions on the brain morphological changes. Subjects with magnetic resonance imaging acquisitions at baseline and at 36 months were included (N = 376). Morphological changes were characterized by volume measurements and nonlinear deformation. The multidomain intervention was associated with a significant effect on the 3-year brain morphological changes in the deformation-based approach. Differences were mainly located in the left periventricular area next to the temporoparietal junction. These changes were associated with better cognitive performance and mood/behavior stabilization. No effect of the omega-3 supplementation was observed. This result suggests a possible effect on cognition, not yet observable after 3 years. We argue that neuroimaging could help define whether early intervention strategies are effective to delay cognitive decline and dementia.

Evolution of white matter damage in amyotrophic lateral sclerosis

OBJECTIVE

To characterize disease evolution in amyotrophic lateral sclerosis using an event-based model designed to extract temporal information from cross-sectional data. Conventional methods for understanding mechanisms of rapidly progressive neurodegenerative disorders are limited by the subjectivity inherent in the selection of a limited range of measurements, and the need to acquire longitudinal data.

METHODS

The event-based model characterizes a disease as a series of events, each comprising a significant change in subject state. The model was applied to data from 154 patients and 128 healthy controls selected from five independent diffusion MRI datasets acquired in four different imaging laboratories between 1999 and 2016. The biomarkers modeled were mean fractional anisotropy values of white matter tracts implicated in amyotrophic lateral sclerosis. The cerebral portion of the corticospinal tract was divided into three segments.

RESULTS

Application of the model to the pooled datasets revealed that the corticospinal tracts were involved before other white matter tracts. Distal corticospinal tract segments were involved earlier than more proximal (i.e., cephalad) segments. In addition, the model revealed early ordering of fractional anisotropy change in the corpus callosum and subsequently in long association fibers.

INTERPRETATION

These findings represent data-driven evidence for early involvement of the corticospinal tracts and body of the corpus callosum in keeping with conventional approaches to image analysis, while providing new evidence to inform directional degeneration of the corticospinal tracts. This data-driven model provides new insight into the dynamics of neuronal damage in amyotrophic lateral sclerosis.

[Machine learning in radiology : Terminology from individual timepoint to trajectory]

METHODICAL ISSUE

Machine learning (ML) algorithms have an increasingly relevant role in radiology tackling tasks such as the automatic detection and segmentation of diagnosis-relevant markers, the quantification of progression and response, and their prediction in individual patients.

STANDARD RADIOLOGICAL METHODS

ML algorithms are relevant for all image acquisition techniques from computed tomography (CT) and magnetic resonance imaging (MRI) to ultrasound. However, different modalities result in different challenges with respect to standardization and variability.

METHODICAL INNOVATIONS

ML algorithms are increasingly able to analyze longitudinal data for the training of prediction models. This is relevant since it enables the use of comprehensive information for predicting individual progression and response, and the associated support of treatment decisions by ML models.

PERFORMANCE

The quality of detection and segmentation algorithms of lesions has reached an acceptable level in several areas. The accuracy of prediction models is still increasing, but is dependent on the availability of representative training data.

ACHIEVEMENTS

The development of ML algorithms in radiology is progressing although many solutions are still at a validation stage. It is accompanied by a parallel and increasingly interlinked development of basic methods and techniques which will gradually be put into practice in radiology.

PRACTICAL CONSIDERATIONS

Two factors will impact the relevance of ML in radiological practice: the thorough validation of algorithms and solutions, and the creation of representative diverse data for the training and validation in a realistic context.

Differences in topological progression profile among neurodegenerative diseases from imaging data

The spatial distribution of atrophy in neurodegenerative diseases suggests that brain connectivity mediates disease propagation. Different descriptors of the connectivity graph potentially relate to different underlying mechanisms of propagation. Previous approaches for evaluating the influence of connectivity on neurodegeneration consider each descriptor in isolation and match predictions against late-stage atrophy patterns. We introduce the notion of a topological profile - a characteristic combination of topological descriptors that best describes the propagation of pathology in a particular disease. By drawing on recent advances in disease progression modeling, we estimate topological profiles from the full course of pathology accumulation, at both cohort and individual levels. Experimental results comparing topological profiles for Alzheimer's disease, multiple sclerosis and normal ageing show that topological profiles explain the observed data better than single descriptors. Within each condition, most individual profiles cluster around the cohort-level profile, and individuals whose profiles align more closely with other cohort-level profiles show features of that cohort. The cohort-level profiles suggest new insights into the biological mechanisms underlying pathology propagation in each disease.