A Deep Network for Explainable Prediction of Non-Imaging Phenotypes using Anatomical Multi-View Data

Large datasets often contain multiple distinct feature sets, or views, that offer complementary information that can be exploited by multi-view learning methods to improve results. We investigate anatomical multi-view data, where each brain anatomical structure is described with multiple feature sets. In particular, we focus on sets of white matter microstructure and connectivity features from diffusion MRI, as well as sets of gray matter area and thickness features from structural MRI. We investigate machine learning methodology that applies multi-view approaches to improve the prediction of non-imaging phenotypes, including demographics (age), motor (strength), and cognition (picture vocabulary). We present an explainable multi-view network (EMV-Net) that can use different anatomical views to improve prediction performance. In this network, each individual anatomical view is processed by a view-specific feature extractor and the extracted information from each view is fused using a learnable weight. This is followed by a wavelet transform-based module to obtain complementary information across views which is then applied to calibrate the view-specific information. Additionally, the calibrator produces an attention-based calibration score to indicate anatomical structures' importance for interpretation.Comment: 2023 The Medical Image Computing and Computer Assisted Intervention Society worksho

Uncovering convolutional neural network decisions for diagnosing multiple sclerosis on conventional MRI using layer-wise relevance propagation

Machine learning-based imaging diagnostics has recently reached or even superseded the level of clinical experts in several clinical domains. However, classification decisions of a trained machine learning system are typically non-transparent, a major hindrance for clinical integration, error tracking or knowledge discovery. In this study, we present a transparent deep learning framework relying on convolutional neural networks (CNNs) and layer-wise relevance propagation (LRP) for diagnosing multiple sclerosis (MS). MS is commonly diagnosed utilizing a combination of clinical presentation and conventional magnetic resonance imaging (MRI), specifically the occurrence and presentation of white matter lesions in T2-weighted images. We hypothesized that using LRP in a naive predictive model would enable us to uncover relevant image features that a trained CNN uses for decision-making. Since imaging markers in MS are well-established this would enable us to validate the respective CNN model. First, we pre-trained a CNN on MRI data from the Alzheimer's Disease Neuroimaging Initiative (n = 921), afterwards specializing the CNN to discriminate between MS patients and healthy controls (n = 147). Using LRP, we then produced a heatmap for each subject in the holdout set depicting the voxel-wise relevance for a particular classification decision. The resulting CNN model resulted in a balanced accuracy of 87.04% and an area under the curve of 96.08% in a receiver operating characteristic curve. The subsequent LRP visualization revealed that the CNN model focuses indeed on individual lesions, but also incorporates additional information such as lesion location, non-lesional white matter or gray matter areas such as the thalamus, which are established conventional and advanced MRI markers in MS. We conclude that LRP and the proposed framework have the capability to make diagnostic decisions of..

ВАЛИДАЦИЯ ДИАГНОСТИЧЕСКОЙ ТОЧНОСТИ АЛГОРИТМА «ИСКУССТВЕННОГО ИНТЕЛЛЕКТА» ДЛЯ ВЫЯВЛЕНИЯ РАССЕЯННОГО СКЛЕРОЗА В УСЛОВИЯХ ГОРОДСКОЙ ПОЛИКЛИНИКИ

The objective of the study is to evaluate the diagnostic accuracy of an original artificial intelligence (AI) algorithm for detecting MS in the radiology department of primary (outpatient) hospital.Materials and methods. Depersonalized results of brain magnetic resonance imaging (MRI) studies performed in the period from August 22, 2019 to September 26, 2019 in 93 patients (42 men (mean age 47,5±15,9 years) and 51 women (mean age 52,3±16,8 years)) were analyzed. All patients signed a voluntary informed consent form. Brain MRIwere carried out on the VANTAGE Atlas 1,5T MRI scanner (Toshiba, Japan) under a standard protocol.Results. All MRI studies were analyzed by AI-algorithm (index-test). It decisions were compared with a  reference test (groundtruth). The sensitivity of the index-test is 100%, specificity — 75,3%, accuracy —  76,3%, negative predictive value — 100%, area under ROC-curve — 0,861. The algorithm reliably sorts out the studies without signs of MS. The algorithmshows sufficient quality and excellent reproducibility of the results on independent data.Conclusion. The developed AI algorithm ensures effective triage of MRI studies in primary care settings, maintaining an optimal index of suspicion in MS.Цель: оценить диагностическую точность оригинального алгоритма выявления РС в условиях отделения лучевой диагностики медицинской организации, оказывающей первичную (амбулаторно-поликлиническую) медицинскую помощь.Материалы и методы. Проведен анализ деперсонализированных результатов МР-исследований головного мозга, выполненных 93 пациентам в период с 22.08.2019 г. по 26.09.2019 г., из которых 42 мужчины (средний возраст 47,5±15,9 лет) и 51 женщина (средний возраст 52,3±16,8 лет); лица европеоидной расы, жители г. Москвы. Все  пациенты подписали добровольное информированное согласие. Исследования  проводились на томографе VANTAGE Atlas (Toshiba, Япония) с индукцией магнитного поля 1,5 Тл по стандартному протоколу.Результаты. Все МР-исследования проанализированы с применением оригинального  алгоритма «искусственного интеллекта» (ИИ). Решения алгоритма (индекс-теста)  сопоставлены с референс-тестом, значения которого приняты за истинный статус  обследуемых лиц. Чувствительность индекс-теста — 100%, специфичность — 75,3%,  точность — 76,3%, прогностическая ценность отрицательного результата — 100%, площадь под характеристической кривой — 0,861. Результаты свидетельствуют о надежном «отсеивании» алгоритмом результатов исследований без признаков РС.  Показано достаточное качество и отличная воспроизводимость результатов работы  алгоритма на независимых данных.Заключение. Разработанный алгоритм ИИ обеспечивает эффективную сортировку МР-исследований в условиях первичного звена здравоохранения с поддержанием оптимального уровня настороженности относительно РС

Revealing cancer subtypes with higher-order correlations applied to imaging and omics data

Figure S9. Screenshot of the interactive Tumor Map visualization, showing HOCUS applied to the TCGA Pancan-12 mutation data. Each point is one tumor sample, which we have color-coded by tissue type. A dotted box highlights the cluster of samples that have both PIK3CA and TP53 mutations, which are usually mutually exclusive. (EPS 751 kb

Uncovering convolutional neural network decisions for diagnosing multiple sclerosis on conventional MRI using layer-wise relevance propagation

Machine learning-based imaging diagnostics has recently reached or even surpassed the level of clinical experts in several clinical domains. However, classification decisions of a trained machine learning system are typically non-transparent, a major hindrance for clinical integration, error tracking or knowledge discovery. In this study, we present a transparent deep learning framework relying on 3D convolutional neural networks (CNNs) and layer-wise relevance propagation (LRP) for diagnosing multiple sclerosis (MS), the most widespread autoimmune neuroinflammatory disease. MS is commonly diagnosed utilizing a combination of clinical presentation and conventional magnetic resonance imaging (MRI), specifically the occurrence and presentation of white matter lesions in T2-weighted images. We hypothesized that using LRP in a naive predictive model would enable us to uncover relevant image features that a trained CNN uses for decision-making. Since imaging markers in MS are well-established this would enable us to validate the respective CNN model. First, we pre-trained a CNN on MRI data from the Alzheimer's Disease Neuroimaging Initiative (n = 921), afterwards specializing the CNN to discriminate between MS patients (n = 76) and healthy controls (n = 71). Using LRP, we then produced a heatmap for each subject in the holdout set depicting the voxel-wise relevance for a particular classification decision. The resulting CNN model resulted in a balanced accuracy of 87.04% and an area under the curve of 96.08% in a receiver operating characteristic curve. The subsequent LRP visualization revealed that the CNN model focuses indeed on individual lesions, but also incorporates additional information such as lesion location, non-lesional white matter or gray matter areas such as the thalamus, which are established conventional and advanced MRI markers in MS. We conclude that LRP and the proposed framework have the capability to make diagnostic decisions of CNN models transparent, which could serve to justify classification decisions for clinical review, verify diagnosis-relevant features and potentially gather new disease knowledge

Alzheimer Disease Detection Techniques and Methods: A Review

Brain pathological changes linked with Alzheimer's disease (AD) can be measured with Neuroimaging. In the past few years, these measures are rapidly integrated into the signatures of Alzheimer disease (AD) with the help of classification frameworks which are offering tools for diagnosis and prognosis. Here is the review study of Alzheimer's disease based on Neuroimaging and cognitive impairment classification. This work is a systematic review for the published work in the field of AD especially the computer-aided diagnosis. The imaging modalities include 1) Magnetic resonance imaging (MRI) 2) Functional MRI (fMRI) 3) Diffusion tensor imaging 4) Positron emission tomography (PET) and 5) amyloid-PET. The study revealed that the classification criterion based on the features shows promising results to diagnose the disease and helps in clinical progression. The most widely used machine learning classifiers for AD diagnosis include Support Vector Machine, Bayesian Classifiers, Linear Discriminant Analysis, and K-Nearest Neighbor along with Deep learning. The study revealed that the deep learning techniques and support vector machine give higher accuracies in the identification of Alzheimer’s disease. The possible challenges along with future directions are also discussed in the paper

Monotonic Gaussian Process for Spatio-Temporal Disease Progression Modeling in Brain Imaging Data

We introduce a probabilistic generative model for disentangling spatio-temporal disease trajectories from series of high-dimensional brain images. The model is based on spatio-temporal matrix factorization, where inference on the sources is constrained by anatomically plausible statistical priors. To model realistic trajectories, the temporal sources are defined as monotonic and time-reparametrized Gaussian Processes. To account for the non-stationarity of brain images, we model the spatial sources as sparse codes convolved at multiple scales. The method was tested on synthetic data favourably comparing with standard blind source separation approaches. The application on large-scale imaging data from a clinical study allows to disentangle differential temporal progression patterns mapping brain regions key to neurodegeneration, while revealing a disease-specific time scale associated to the clinical diagnosis

Monotonic Gaussian Process for Spatio-Temporal Disease Progression Modeling in Brain Imaging Data

International audienceWe introduce a probabilistic generative model for disentangling spatio-temporal disease trajectories from series of high-dimensional brain images. The model is based on spatio-temporal matrix factorization, where inference on the sources is constrained by anatomically plausible statistical priors. To model realistic trajectories, the temporal sources are defined as monotonic and time-reparametrized Gaussian Processes. To account for the non-stationarity of brain images, we model the spatial sources as sparse codes convolved at multiple scales. The method was tested on synthetic data favourably comparing with standard blind source separation approaches. The application on large-scale imaging data from a clinical study allows to disentangle differential temporal progression patterns mapping brain regions key to neurodegeneration, while revealing a disease-specific time scale associated to the clinical diagnosis