Modeling Disease Progression via Multisource Multitask Learners: A Case Study With Alzheimer's Disease

HiMAL: Multimodal Hierarchical Multi-task Auxiliary Learning framework for predicting Alzheimer's disease progression

Objective

We aimed to develop and validate a novel multimodal framework Hierarchical Multi-task Auxiliary Learning (HiMAL) framework, for predicting cognitive composite functions as auxiliary tasks that estimate the longitudinal risk of transition from Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD).

Materials and Methods

HiMAL utilized multimodal longitudinal visit data including imaging features, cognitive assessment scores, and clinical variables from MCI patients in the Alzheimer's Disease Neuroimaging Initiative dataset, to predict at each visit if an MCI patient will progress to AD within the next 6 months. Performance of HiMAL was compared with state-of-the-art single-task and multitask baselines using area under the receiver operator curve (AUROC) and precision recall curve (AUPRC) metrics. An ablation study was performed to assess the impact of each input modality on model performance. Additionally, longitudinal explanations regarding risk of disease progression were provided to interpret the predicted cognitive decline.

Results

Out of 634 MCI patients (mean [IQR] age: 72.8 [67-78], 60% male), 209 (32%) progressed to AD. HiMAL showed better prediction performance compared to all state-of-the-art longitudinal single-modality singe-task baselines (AUROC = 0.923 [0.915-0.937]; AUPRC = 0.623 [0.605-0.644]; all P < .05). Ablation analysis highlighted that imaging and cognition scores with maximum contribution towards prediction of disease progression.

Discussion

Clinically informative model explanations anticipate cognitive decline 6 months in advance, aiding clinicians in future disease progression assessment. HiMAL relies on routinely collected electronic health records (EHR) variables for proximal (6 months) prediction of AD onset, indicating its translational potential for point-of-care monitoring and managing of high-risk patients.

Neuroimage analysis using artificial intelligence approaches: a systematic review

In the contemporary era, artificial intelligence (AI) has undergone a transformative evolution, exerting a profound influence on neuroimaging data analysis. This development has significantly elevated our comprehension of intricate brain functions. This study investigates the ramifications of employing AI techniques on neuroimaging data, with a specific objective to improve diagnostic capabilities and contribute to the overall progress of the field. A systematic search was conducted in prominent scientific databases, including PubMed, IEEE Xplore, and Scopus, meticulously curating 456 relevant articles on AI-driven neuroimaging analysis spanning from 2013 to 2023. To maintain rigor and credibility, stringent inclusion criteria, quality assessments, and precise data extraction protocols were consistently enforced throughout this review. Following a rigorous selection process, 104 studies were selected for review, focusing on diverse neuroimaging modalities with an emphasis on mental and neurological disorders. Among these, 19.2% addressed mental illness, and 80.7% focused on neurological disorders. It is found that the prevailing clinical tasks are disease classification (58.7%) and lesion segmentation (28.9%), whereas image reconstruction constituted 7.3%, and image regression and prediction tasks represented 9.6%. AI-driven neuroimaging analysis holds tremendous potential, transforming both research and clinical applications. Machine learning and deep learning algorithms outperform traditional methods, reshaping the field significantly.

A feature-aware multimodal framework with auto-fusion for Alzheimer's disease diagnosis

Alzheimer's disease (AD), one of the most common dementias, has about 4.6 million new cases yearly worldwide. Due to the significant amount of suspected AD patients, early screening for the disease has become particularly important. There are diversified types of AD diagnosis data, such as cognitive tests, images, and risk factors, many prior investigations have primarily concentrated on integrating only high-dimensional features and simple fusion concatenation, resulting in less-than-optimal outcomes for AD diagnosis. Therefore, We propose an enhanced multimodal AD diagnostic framework comprising a feature-aware module and an automatic model fusion strategy (AMFS). To preserve the correlation and significance features within a low-dimensional space, the feature-aware module employs a low-dimensional SHapley Additive exPlanation (SHAP) boosting feature selection as the initial step, following this analysis, diverse tiers of low-dimensional features are extracted from patients' biological data. Besides, in the high-dimensional stage, the feature-aware module integrates cross-modal attention mechanisms to capture subtle relationships among different cognitive domains, neuroimaging modalities, and risk factors. Subsequently, we integrate the aforementioned feature-aware module with graph convolutional networks (GCN) to address heterogeneous data in multimodal AD, while also possessing the capability to perceive relationships between different modalities. Lastly, our proposed AMFS autonomously learns optimal parameters for aligning two sub-models. The validation tests using two ADNI datasets show the high accuracies of 95.9% and 91.9% respectively, in AD diagnosis. The methods efficiently select features from multimodal AD data, optimizing model fusion for potential clinical assistance in diagnostics.

Multitask Learning for Joint Diagnosis of Multiple Mental Disorders in Resting-State fMRI

Facing the increasing worldwide prevalence of mental disorders, the symptom-based diagnostic criteria struggle to address the urgent public health concern due to the global shortfall in well-qualified professionals. Thanks to the recent advances in neuroimaging techniques, functional magnetic resonance imaging (fMRI) has surfaced as a new solution to characterize neuropathological biomarkers for detecting functional connectivity (FC) anomalies in mental disorders. However, the existing computer-aided diagnosis models for fMRI analysis suffer from unstable performance on large datasets. To address this issue, we propose an efficient multitask learning (MTL) framework for joint diagnosis of multiple mental disorders using resting-state fMRI data. A novel multiobjective evolutionary clustering algorithm is presented to group regions of interests (ROIs) into different clusters for FC pattern analysis. On the optimal clustering solution, the multicluster multigate mixture-of-expert model is used for the final classification by capturing the highly consistent feature patterns among related diagnostic tasks. Extensive simulation experiments demonstrate that the performance of the proposed framework is superior to that of the other state-of-the-art methods. Moreover, the potential for practical application of the framework is also validated in terms of limited computational resources, real-time analysis, and insufficient training data. The proposed model can identify the remarkable interpretative biomarkers associated with specific mental disorders for clinical interpretation analysis.

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.

A novel medical image fusion method based on multi-scale shearing rolling weighted guided image filter

Medical image fusion is a crucial technology for biomedical diagnoses. However, current fusion methods struggle to balance algorithm design, visual effects, and computational efficiency. To address these challenges, we introduce a novel medical image fusion method based on the multi-scale shearing rolling weighted guided image filter (MSRWGIF). Inspired by the rolling guided filter, we construct the rolling weighted guided image filter (RWGIF) based on the weighted guided image filter. This filter offers progressive smoothing filtering of the image, generating smooth and detailed images. Then, we construct a novel image decomposition tool, MSRWGIF, by replacing non-subsampled shearlet transform's non-sampling pyramid filter with RWGIF to extract richer detailed information. In the first step of our method, we decompose the original images under MSRWGIF to obtain low-frequency subbands (LFS) and high-frequency subbands (HFS). Since LFS contain a large amount of energy-based information, we propose an improved local energy maximum (ILGM) fusion strategy. Meanwhile, HFS employ a fast and efficient parametric adaptive pulse coupled-neural network (AP-PCNN) model to combine more detailed information. Finally, the inverse MSRWGIF is utilized to generate the final fused image from fused LFS and HFS. To test the proposed method, we select multiple medical image sets for experimental simulation and confirm its advantages by combining seven high-quality representative metrics. The simplicity and efficiency of the method are compared with 11 classical fusion methods, illustrating significant improvements in the subjective and objective performance, especially for color medical image fusion.

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.

Episodic task agnostic contrastive training for multi-task learning

Learning knowledge from different tasks to improve the general learning performance is crucial for designing an efficient algorithm. In this work, we tackle the Multi-task Learning (MTL) problem, where the learner extracts the knowledge from different tasks simultaneously with limited data. Previous works have been designing the MTL models by taking advantage of the transfer learning techniques, requiring the knowledge of the task index, which is not realistic in many practical scenarios. In contrast, we consider the scenario that the task index is not explicitly known, under which the features extracted by the neural networks are task agnostic. To learn the task agnostic invariant features, we implement model agnostic meta-learning by leveraging the episodic training scheme to capture the common features across tasks. Apart from the episodic training scheme, we further implemented a contrastive learning objective to improve the feature compactness for a better prediction boundary in the embedding space. We conduct extensive experiments on several benchmarks compared with several recent strong baselines to demonstrate the effectiveness of the proposed method. The results showed that our method provides a practical solution for real-world scenarios, where the task index is agnostic to the learner and can outperform several strong baselines, achieving state-of-the-art performances.

A Tensorized Multitask Deep Learning Network for Progression Prediction of Alzheimer's Disease

With the advances in machine learning for the diagnosis of Alzheimer's disease (AD), most studies have focused on either identifying the subject's status through classification algorithms or on predicting their cognitive scores through regression methods, neglecting the potential association between these two tasks. Motivated by the need to enhance the prospects for early diagnosis along with the ability to predict future disease states, this study proposes a deep neural network based on modality fusion, kernelization, and tensorization that perform multiclass classification and longitudinal regression simultaneously within a unified multitask framework. This relationship between multiclass classification and longitudinal regression is found to boost the efficacy of the final model in dealing with both tasks. Different multimodality scenarios are investigated, and complementary aspects of the multimodal features are exploited to simultaneously delineate the subject's label and predict related cognitive scores at future timepoints using baseline data. The main intent in this multitask framework is to consolidate the highest accuracy possible in terms of precision, sensitivity, F1 score, and area under the curve (AUC) in the multiclass classification task while maintaining the highest similarity in the MMSE score as measured through the correlation coefficient and the RMSE for all time points under the prediction task, with both tasks, run simultaneously under the same set of hyperparameters. The overall accuracy for multiclass classification of the proposed KTMnet method is 66.85 ± 3.77. The prediction results show an average RMSE of 2.32 ± 0.52 and a correlation of 0.71 ± 5.98 for predicting MMSE throughout the time points. These results are compared to state-of-the-art techniques reported in the literature. A discovery from the multitasking of this consolidated machine learning framework is that a set of hyperparameters that optimize the prediction results may not necessarily be the same as those that would optimize the multiclass classification. In other words, there is a breakpoint beyond which enhancing further the results of one process could lead to the downgrading in accuracy for the other.

Applied machine learning in Alzheimer's disease research: omics, imaging, and clinical data

Alzheimer's disease (AD) remains a devastating neurodegenerative disease with few preventive or curative treatments available. Modern technology developments of high-throughput omics platforms and imaging equipment provide unprecedented opportunities to study the etiology and progression of this disease. Meanwhile, the vast amount of data from various modalities, such as genetics, proteomics, transcriptomics, and imaging, as well as clinical features impose great challenges in data integration and analysis. Machine learning (ML) methods offer novel techniques to address high dimensional data, integrate data from different sources, model the etiological and clinical heterogeneity, and discover new biomarkers. These directions have the potential to help us better manage the disease progression and develop novel treatment strategies. This mini-review paper summarizes different ML methods that have been applied to study AD using single-platform or multi-modal data. We review the current state of ML applications for five key directions of AD research: disease classification, drug repurposing, subtyping, progression prediction, and biomarker discovery. This summary provides insights about the current research status of ML-based AD research and highlights potential directions for future research.

Lesion Segmentation Framework Based on Convolutional Neural Networks with Dual Attention Mechanism

Computational intelligence has been widely used in medical information processing. The deep learning methods, especially, have many successful applications in medical image analysis. In this paper, we proposed an end-to-end medical lesion segmentation framework based on convolutional neural networks with a dual attention mechanism, which integrates both fully and weakly supervised segmentation. The weakly supervised segmentation module achieves accurate lesion segmentation by using bounding-box labels of lesion areas, which solves the problem of the high cost of pixel-level labels with lesions in the medical images. In addition, a dual attention mechanism is introduced to enhance the network’s ability for visual feature learning. The dual attention mechanism (channel and spatial attention) can help the network pay attention to feature extraction from important regions. Compared with the current mainstream method of weakly supervised segmentation using pseudo labels, it can greatly reduce the gaps between ground-truth labels and pseudo labels. The final experimental results show that our proposed framework achieved more competitive performances on oral lesion dataset, and our framework further extended to dermatological lesion segmentation.

A Large-Scale Fully Annotated Low-Cost Cost Microscopy Image Dataset for Deep Learning Framework

This work presents a large-scale three-fold annotated, low-cost microscopy image dataset of potato tubers for plant cell analysis in deep learning (DL) framework which has huge potential in the advancement of plant cell biology research. Indeed, low-cost microscopes coupled with new generation smartphones could open new aspects in DL-based microscopy image analysis, which offers several benefits including portability, easy to use, and maintenance. However, its successful implications demand properly annotated large number of diverse microscopy images, which has not been addressed properly- that confines the advanced image processing based plant cell research. Therefore, in this work, a low-cost microscopy image database of potato tuber cells having total 34,657 number of images, has been generated by Foldscope (costs around 1 USD) coupled with a smartphone. This dataset includes 13,369 unstained and 21,288 stained (safranin-o, toluidine blue-o, and lugol's iodine) images with three-fold annotation based on weight, section areas, and tissue zones of the tubers. The physical image quality (e.g., contrast, focus, geometrical attributes, etc.) and its applicability in the DL framework (CNN-based multi-class and multi-label classification) have been examined and results are compared with the traditional microscope image set. The results show that the dataset is highly compatible for the DL framework.

Machine learning for modeling the progression of Alzheimer disease dementia using clinical data: a systematic literature review

OBJECTIVE

Alzheimer disease (AD) is the most common cause of dementia, a syndrome characterized by cognitive impairment severe enough to interfere with activities of daily life. We aimed to conduct a systematic literature review (SLR) of studies that applied machine learning (ML) methods to clinical data derived from electronic health records in order to model risk for progression of AD dementia.

MATERIALS AND METHODS

We searched for articles published between January 1, 2010, and May 31, 2020, in PubMed, Scopus, ScienceDirect, IEEE Explore Digital Library, Association for Computing Machinery Digital Library, and arXiv. We used predefined criteria to select relevant articles and summarized them according to key components of ML analysis such as data characteristics, computational algorithms, and research focus.

RESULTS

There has been a considerable rise over the past 5 years in the number of research papers using ML-based analysis for AD dementia modeling. We reviewed 64 relevant articles in our SLR. The results suggest that majority of existing research has focused on predicting progression of AD dementia using publicly available datasets containing both neuroimaging and clinical data (neurobehavioral status exam scores, patient demographics, neuroimaging data, and laboratory test values).

DISCUSSION

Identifying individuals at risk for progression of AD dementia could potentially help to personalize disease management to plan future care. Clinical data consisting of both structured data tables and clinical notes can be effectively used in ML-based approaches to model risk for AD dementia progression. Data sharing and reproducibility of results can enhance the impact, adaptation, and generalizability of this research.

StoCast: Stochastic Disease Forecasting With Progression Uncertainty

Forecasting patients' disease progressions with rich longitudinal clinical data has drawn much attention in recent years due to its impactful application in healthcare and the medical field. Researchers have tackled this problem by leveraging traditional machine learning, statistical techniques and deep learning based models. However, existing methods suffer from either deterministic internal structures or over-simplified stochastic components, failing to deal with complex uncertain scenarios such as progression uncertainty (i.e., multiple possible trajectories) and data uncertainty (i.e., imprecise observations and misdiagnosis). To overcome these major uncertainty issues, we propose a novel deep generative model, Stochastic Disease Forecasting Model (StoCast), along with an associated neural network architecture StoCastNet, that can be trained efficiently via stochastic optimization techniques. Our StoCast model uses internal stochastic components to deal with departures of observed data from patients' true health states, and more importantly, is able to produce a comprehensive estimate of future disease progression trajectories. Based on two public datasets related to Alzheimer's disease and Parkinson's disease, we demonstrate how our StoCast model achieves robust and superior performance than deterministic baseline approaches, and conveys richer information that can potentially assist doctors to make decisions with greater confidence in a complex uncertain scenario.

Task Similarity Estimation Through Adversarial Multitask Neural Network

Multitask learning (MTL) aims at solving the related tasks simultaneously by exploiting shared knowledge to improve performance on individual tasks. Though numerous empirical results supported the notion that such shared knowledge among tasks plays an essential role in MTL, the theoretical understanding of the relationships between tasks and their impact on learning shared knowledge is still an open problem. In this work, we are developing a theoretical perspective of the benefits involved in using information similarity for MTL. To this end, we first propose an upper bound on the generalization error by implementing the Wasserstein distance as the similarity metric. This indicates the practical principles of applying the similarity information to control the generalization errors. Based on those theoretical results, we revisited the adversarial multitask neural network and proposed a new training algorithm to learn the task relation coefficients and neural network parameters automatically. The computer vision benchmarks reveal the abilities of the proposed algorithms to improve the empirical performance. Finally, we test the proposed approach on real medical data sets, showing its advantage for extracting task relations.

A multilayer multimodal detection and prediction model based on explainable artificial intelligence for Alzheimer's disease

Alzheimer's disease (AD) is the most common type of dementia. Its diagnosis and progression detection have been intensively studied. Nevertheless, research studies often have little effect on clinical practice mainly due to the following reasons: (1) Most studies depend mainly on a single modality, especially neuroimaging; (2) diagnosis and progression detection are usually studied separately as two independent problems; and (3) current studies concentrate mainly on optimizing the performance of complex machine learning models, while disregarding their explainability. As a result, physicians struggle to interpret these models, and feel it is hard to trust them. In this paper, we carefully develop an accurate and interpretable AD diagnosis and progression detection model. This model provides physicians with accurate decisions along with a set of explanations for every decision. Specifically, the model integrates 11 modalities of 1048 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) real-world dataset: 294 cognitively normal, 254 stable mild cognitive impairment (MCI), 232 progressive MCI, and 268 AD. It is actually a two-layer model with random forest (RF) as classifier algorithm. In the first layer, the model carries out a multi-class classification for the early diagnosis of AD patients. In the second layer, the model applies binary classification to detect possible MCI-to-AD progression within three years from a baseline diagnosis. The performance of the model is optimized with key markers selected from a large set of biological and clinical measures. Regarding explainability, we provide, for each layer, global and instance-based explanations of the RF classifier by using the SHapley Additive exPlanations (SHAP) feature attribution framework. In addition, we implement 22 explainers based on decision trees and fuzzy rule-based systems to provide complementary justifications for every RF decision in each layer. Furthermore, these explanations are represented in natural language form to help physicians understand the predictions. The designed model achieves a cross-validation accuracy of 93.95% and an F1-score of 93.94% in the first layer, while it achieves a cross-validation accuracy of 87.08% and an F1-Score of 87.09% in the second layer. The resulting system is not only accurate, but also trustworthy, accountable, and medically applicable, thanks to the provided explanations which are broadly consistent with each other and with the AD medical literature. The proposed system can help to enhance the clinical understanding of AD diagnosis and progression processes by providing detailed insights into the effect of different modalities on the disease risk.

Guitar Chord Sensing and Recognition Using Multi-Task Learning and Physical Data Augmentation with Robotics

In recent years, many researchers have shown increasing interest in music information retrieval (MIR) applications, with automatic chord recognition being one of the popular tasks. Many studies have achieved/demonstrated considerable improvement using deep learning based models in automatic chord recognition problems. However, most of the existing models have focused on simple chord recognition, which classifies the root note with the major, minor, and seventh chords. Furthermore, in learning-based recognition, it is critical to collect high-quality and large amounts of training data to achieve the desired performance. In this paper, we present a multi-task learning (MTL) model for a guitar chord recognition task, where the model is trained using a relatively large-vocabulary guitar chord dataset. To solve data scarcity issues, a physical data augmentation method that directly records the chord dataset from a robotic performer is employed. Deep learning based MTL is proposed to improve the performance of automatic chord recognition with the proposed physical data augmentation dataset. The proposed MTL model is compared with four baseline models and its corresponding single-task learning model using two types of datasets, including a human dataset and a human combined with the augmented dataset. The proposed methods outperform the baseline models, and the results show that most scores of the proposed multi-task learning model are better than those of the corresponding single-task learning model. The experimental results demonstrate that physical data augmentation is an effective method for increasing the dataset size for guitar chord recognition tasks.

Predicting Alzheimer's disease progression using deep recurrent neural networks

Early identification of individuals at risk of developing Alzheimer’s disease (AD) dementia is important for developing disease-modifying therapies. In this study, given multimodal AD markers and clinical diagnosis of an individual from one or more timepoints, we seek to predict the clinical diagnosis, cognition and ventricular volume of the individual for every month (indefinitely) into the future. We proposed and applied a minimal recurrent neural network (minimalRNN) model to data from The Alzheimer’s Disease Prediction Of Longitudinal Evolution (TADPOLE) challenge, comprising longitudinal data of 1677 participants (Marinescu et al., 2018) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). We compared the performance of the minimalRNN model and four baseline algorithms up to 6 years into the future. Most previous work on predicting AD progression ignore the issue of missing data, which is a prevalent issue in longitudinal data. Here, we explored three different strategies to handle missing data. Two of the strategies treated the missing data as a “preprocessing” issue, by imputing the missing data using the previous timepoint (“forward filling”) or linear interpolation (“linear filling). The third strategy utilized the minimalRNN model itself to fill in the missing data both during training and testing (“model filling”). Our analyses suggest that the minimalRNN with “model filling” compared favorably with baseline algorithms, including support vector machine/regression, linear state space (LSS) model, and long short-term memory (LSTM) model. Importantly, although the training procedure utilized longitudinal data, we found that the trained minimalRNN model exhibited similar performance, when using only 1 input timepoint or 4 input timepoints, suggesting that our approach might work well with just cross-sectional data. An earlier version of our approach was ranked 5th (out of 53 entries) in the TADPOLE challenge in 2019. The current approach is ranked 2nd out of 63 entries as of June 3rd, 2020.

Weakly Supervised Deep Learning for Brain Disease Prognosis Using MRI and Incomplete Clinical Scores

As a hot topic in brain disease prognosis, predicting clinical measures of subjects based on brain magnetic resonance imaging (MRI) data helps to assess the stage of pathology and predict future development of the disease. Due to incomplete clinical labels/scores, previous learning-based studies often simply discard subjects without ground-truth scores. This would result in limited training data for learning reliable and robust models. Also, existing methods focus only on using hand-crafted features (e.g., image intensity or tissue volume) of MRI data, and these features may not be well coordinated with prediction models. In this paper, we propose a weakly supervised densely connected neural network (wiseDNN) for brain disease prognosis using baseline MRI data and incomplete clinical scores. Specifically, we first extract multiscale image patches (located by anatomical landmarks) from MRI to capture local-to-global structural information of images, and then develop a weakly supervised densely connected network for task-oriented extraction of imaging features and joint prediction of multiple clinical measures. A weighted loss function is further employed to make full use of all available subjects (even those without ground-truth scores at certain time-points) for network training. The experimental results on 1469 subjects from both ADNI-1 and ADNI-2 datasets demonstrate that our proposed method can efficiently predict future clinical measures of subjects.

A distributed multitask multimodal approach for the prediction of Alzheimer's disease in a longitudinal study

Predicting the progression of Alzheimer's Disease (AD) has been held back for decades due to the lack of sufficient longitudinal data required for the development of novel machine learning algorithms. This study proposes a novel machine learning algorithm for predicting the progression of Alzheimer's disease using a distributed multimodal, multitask learning method. More specifically, each individual task is defined as a regression model, which predicts cognitive scores at a single time point. Since the prediction tasks for multiple intervals are related to each other in chronological order, multitask regression models have been developed to track the relationship between subsequent tasks. Furthermore, since subjects have various combinations of recording modalities together with other genetic, neuropsychological and demographic risk factors, special attention is given to the fact that each modality may experience a specific sparsity pattern. The model is hence generalized by exploiting multiple individual multitask regression coefficient matrices for each modality. The outcome for each independent modality-specific learner is then integrated with complementary information, known as risk factor parameters, revealing the most prevalent trends of the multimodal data. This new feature space is then used as input to the gradient boosting kernel in search for a more accurate prediction. This proposed model not only captures the complex relationships between the different feature representations, but it also ignores any unrelated information which might skew the regression coefficients. Comparative assessments are made between the performance of the proposed method with several other well-established methods using different multimodal platforms. The results indicate that by capturing the interrelatedness between the different modalities and extracting only relevant information in the data, even in an incomplete longitudinal dataset, will yield minimized prediction errors.

Joint and Long Short-Term Memory Regression of Clinical Scores for Alzheimer's Disease Using Longitudinal Data

Alzheimer's disease (AD), the most common type of the dementia, is a progressive neurodegenerative disease that mainly affects elderly. It causes a high financial burden for patients and their families. For effective treatment of AD, it is important to identify the AD progression of clinical disease over time. As the cognitive scores can effectively indicate the disease status, the prediction of the scores using the longitudinal magnetic resonance imaging (MRI) data is highly desirable. In this paper, we propose a joint learning and clinical scores prediction method for AD diagnosis via longitudinal MRI data. Specifically, we devise a novel feature selection method that consists of a temporally constrained group LASSO model and the correntropy. The baseline MRI data is used to jointly select the most discriminative features. Then, we use the stacked long short-term memory (SLSTM) to effectively capture useful information in the input sequence to predict the clinical scores of future time points. Extensive experiments on the Alzheimer's disease Neuroimaging Initiative (ADNI) database are conducted to demonstrate the effectiveness of the proposed model. Our model can accurately describe the relationship between MRI data and scores, and thus it can be effective in predicting longitudinal scores.

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.

Eigenfunction-Based Multitask Learning in a Reproducing Kernel Hilbert Space

Multitask learning aims to improve the performance on related tasks by exploring the interdependence among them. Existing multitask learning methods explore the relatedness among tasks on the basis of the input features and the model parameters. In this paper, we focus on nonparametric multitask learning and propose to measure task relatedness from a novel perspective in a reproducing kernel Hilbert space (RKHS). Past works have shown that the objective function for a given task can be approximated using the top eigenvalues and corresponding eigenfunctions of a predefined integral operator on an RKHS. In our method, we formulate our objective for multitask learning as a linear combination of two sets of eigenfunctions, common eigenfunctions shared by different tasks and unique eigenfunctions in individual tasks, such that the eigenfunctions for one task can provide additional information on another and help to improve its performance. We present both theoretical and empirical validations of our proposed approach. The theoretical analysis demonstrates that our learning algorithm is uniformly argument stable and that the convergence rate of the generalization upper bound can be improved by learning multiple tasks. Experiments on several benchmark multitask learning data sets show that our method yields promising results.

Joint Classification and Regression via Deep Multi-Task Multi-Channel Learning for Alzheimer's Disease Diagnosis

In the field of computer-aided Alzheimer's disease (AD) diagnosis, jointly identifying brain diseases and predicting clinical scores using magnetic resonance imaging (MRI) have attracted increasing attention since these two tasks are highly correlated. Most of existing joint learning approaches require hand-crafted feature representations for MR images. Since hand-crafted features of MRI and classification/regression models may not coordinate well with each other, conventional methods may lead to sub-optimal learning performance. Also, demographic information (e.g., age, gender, and education) of subjects may also be related to brain status, and thus can help improve the diagnostic performance. However, conventional joint learning methods seldom incorporate such demographic information into the learning models. To this end, we propose a deep multi-task multi-channel learning (DM 2L) framework for simultaneous brain disease classification and clinical score regression, using MRI data and demographic information of subjects. Specifically, we first identify the discriminative anatomical landmarks from MR images in a data-driven manner, and then extract multiple image patches around these detected landmarks. We then propose a deep multi-task multi-channel convolutional neural network for joint classification and regression. Our DM 2L framework can not only automatically learn discriminative features for MR images, but also explicitly incorporate the demographic information of subjects into the learning process. We evaluate the proposed method on four large multi-center cohorts with 1984 subjects, and the experimental results demonstrate that DM 2L is superior to several state-of-the-art joint learning methods in both the tasks of disease classification and clinical score regression.

Multi-task exclusive relationship learning for alzheimer's disease progression prediction with longitudinal data

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive impairment of memory and other cognitive functions. Currently, many multi-task learning approaches have been proposed to predict the disease progression at the early stage using longitudinal data, with each task corresponding to a particular time point. However, the underlying association among different time points in disease progression is still under-explored in previous studies. To this end, we propose a multi-task exclusive relationship learning model to automatically capture the intrinsic relationship among tasks at different time points for estimating clinical measures based on longitudinal imaging data. The proposed method can select the most discriminative features for different tasks and also model the intrinsic relatedness among different time points, by utilizing an exclusive lasso regularization and a relationship induced regularization. Specifically, the exclusive lasso regularization enables partial group structure feature selection among the longitudinal data, while the relationship induced regularization efficiently introduces the relationship information from data to guide knowledge transfer. We further develop an efficient optimization algorithm to solve the proposed objective function. Extensive experiments on both synthetic and real datasets demonstrate the effectiveness of our proposed method. In comparison with several state-of-the-art methods, our proposed method can achieve promising performance for cognitive status prediction and also can help discover disease-related biomarkers.

Neuroimaging Retrieval via Adaptive Ensemble Manifold Learning for Brain Disease Diagnosis

Alzheimer's disease (AD) is a neurodegenerative and non-curable disease, with serious cognitive impairment, such as dementia. Clinically, it is critical to study the disease with multi-source data in order to capture a global picture of it. In this respect, an adaptive ensemble manifold learning (AEML) algorithm is proposed to retrieve multi-source neuroimaging data. Specifically, an objective function based on manifold learning is formulated to impose geometrical constraints by similarity learning. The complementary characteristics of various sources of brain disease data for disorder discovery are investigated by tuning weights from ensemble learning. In addition, a generalized norm is explicitly explored for adaptive sparseness degree control. The proposed AEML algorithm is evaluated by the public AD neuroimaging initiative database. Results obtained from the extensive experiments demonstrate that our algorithm outperforms the traditional methods.

Deep Learning in Microscopy Image Analysis: A Survey

Computerized microscopy image analysis plays an important role in computer aided diagnosis and prognosis. Machine learning techniques have powered many aspects of medical investigation and clinical practice. Recently, deep learning is emerging as a leading machine learning tool in computer vision and has attracted considerable attention in biomedical image analysis. In this paper, we provide a snapshot of this fast-growing field, specifically for microscopy image analysis. We briefly introduce the popular deep neural networks and summarize current deep learning achievements in various tasks, such as detection, segmentation, and classification in microscopy image analysis. In particular, we explain the architectures and the principles of convolutional neural networks, fully convolutional networks, recurrent neural networks, stacked autoencoders, and deep belief networks, and interpret their formulations or modelings for specific tasks on various microscopy images. In addition, we discuss the open challenges and the potential trends of future research in microscopy image analysis using deep learning.

Multi-task fused sparse learning for mild cognitive impairment identification

BACKGROUND

Brain functional connectivity network (BFCN) has been widely applied to identify biomarkers for the brain function understanding and brain diseases analysis.

OBJECTIVE

Building a biologically meaningful brain network is a crucial work in these applications. For this task, sparse learning has been widely applied for the network construction. If multiple time-point data is added to the brain imaging application, the disease progression pattern in the longitudinal analysis can be better revealed.

METHODS

A novel longitudinal analysis for MCI classification is devised based on resting-state functional magnetic resonating imaging (rs-fMRI). Specifically, this paper proposes a novel multi-task learning method to integrate fused penalty by regularization. In addition, a novel objective function is developed for fused sparse learning via smoothness constraint.

RESULTS

The proposed method achieves the best classification performance with an accuracy of 95.74% for baseline and 93.64% for year 1 data.

CONCLUSIONS

The experimental results show that our proposed method achieves quite promising classification performance.

Predicting Alzheimer's Disease Cognitive Assessment via Robust Low-Rank Structured Sparse Model

Alzheimer's disease (AD) is a neurodegenerative disorder with slow onset, which could result in the deterioration of the duration of persistent neurological dysfunction. How to identify the informative longitudinal phenotypic neuroimaging markers and predict cognitive measures are crucial to recognize AD at early stage. Many existing models related imaging measures to cognitive status using regression models, but they did not take full consideration of the interaction between cognitive scores. In this paper, we propose a robust low-rank structured sparse regression method (RLSR) to address this issue. The proposed model simultaneously selects effective features and learns the underlying structure between cognitive scores by utilizing novel mixed structured sparsity inducing norms and low-rank approximation. In addition, an efficient algorithm is derived to solve the proposed non-smooth objective function with proved convergence. Empirical studies on cognitive data of the ADNI cohort demonstrate the superior performance of the proposed method.

Relational-Regularized Discriminative Sparse Learning for Alzheimer's Disease Diagnosis

Accurate identification and understanding informative feature is important for early Alzheimer's disease (AD) prognosis and diagnosis. In this paper, we propose a novel discriminative sparse learning method with relational regularization to jointly predict the clinical score and classify AD disease stages using multimodal features. Specifically, we apply a discriminative learning technique to expand the class-specific difference and include geometric information for effective feature selection. In addition, two kind of relational information are incorporated to explore the intrinsic relationships among features and training subjects in terms of similarity learning. We map the original feature into the target space to identify the informative and predictive features by sparse learning technique. A unique loss function is designed to include both discriminative learning and relational regularization methods. Experimental results based on a total of 805 subjects [including 226 AD patients, 393 mild cognitive impairment (MCI) subjects, and 186 normal controls (NCs)] from AD neuroimaging initiative database show that the proposed method can obtain a classification accuracy of 94.68% for AD versus NC, 80.32% for MCI versus NC, and 74.58% for progressive MCI versus stable MCI, respectively. In addition, we achieve remarkable performance for the clinical scores prediction and classification label identification, which has efficacy for AD disease diagnosis and prognosis. The algorithm comparison demonstrates the effectiveness of the introduced learning techniques and superiority over the state-of-the-arts methods.