Collaborating Authors


Researchers enhance Alzheimer's disease classification through artificial intelligence


Spotting these clues may allow for lifestyle changes that could possibly delay the disease's destruction of the brain. "Improving the diagnostic accuracy of Alzheimer's disease is an important clinical goal. If we are able to increase the diagnostic accuracy of the models in ways that can leverage existing data such as MRI scans, then that can be hugely beneficial," explained corresponding author Vijaya B. Kolachalama, PhD, assistant professor of medicine at Boston University School of Medicine (BUSM). Using an advanced AI (artificial intelligence) framework based on game theory (known as generative adversarial network or GAN), Kolachalama and his team processed brain images (some low and high quality) to generate a model that was able to classify Alzheimer's disease with improved accuracy. Quality of an MRI scan is dependent on the scanner instrument that is used.

Orthogonal Statistical Inference for Multimodal Data Analysis Machine Learning

Multimodal imaging has transformed neuroscience research. While it presents unprecedented opportunities, it also imposes serious challenges. Particularly, it is difficult to combine the merits of interpretability attributed to a simple association model and flexibility achieved by a highly adaptive nonlinear model. In this article, we propose an orthogonal statistical inferential framework, built upon the Neyman orthogonality and a form of decomposition orthogonality, for multimodal data analysis. We target the setting that naturally arises in almost all multimodal studies, where there is a primary modality of interest, plus additional auxiliary modalities. We successfully establish the root-$N$-consistency and asymptotic normality of the estimated primary parameter, the semi-parametric estimation efficiency, and the asymptotic honesty of the confidence interval of the predicted primary modality effect. Our proposal enjoys, to a good extent, both model interpretability and model flexibility. It is also considerably different from the existing statistical methods for multimodal data integration, as well as the orthogonality-based methods for high-dimensional inferences. We demonstrate the efficacy of our method through both simulations and an application to a multimodal neuroimaging study of Alzheimer's disease.

Enhancing Medical Image Registration via Appearance Adjustment Networks Artificial Intelligence

Deformable image registration is fundamental for many medical image analyses. A key obstacle for accurate image registration is the variations in image appearance. Recently, deep learning-based registration methods (DLRs), using deep neural networks, have computational efficiency that is several orders of magnitude greater than traditional optimization-based registration methods (ORs). A major drawback, however, of DLRs is a disregard for the target-pair-specific optimization that is inherent in ORs and instead they rely on a globally optimized network that is trained with a set of training samples to achieve faster registration. Thus, DLRs inherently have degraded ability to adapt to appearance variations and perform poorly, compared to ORs, when image pairs (fixed/moving images) have large differences in appearance. Hence, we propose an Appearance Adjustment Network (AAN) where we leverage anatomy edges, through an anatomy-constrained loss function, to generate an anatomy-preserving appearance transformation. We designed the AAN so that it can be readily inserted into a wide range of DLRs, to reduce the appearance differences between the fixed and moving images. Our AAN and DLR's network can be trained cooperatively in an unsupervised and end-to-end manner. We evaluated our AAN with two widely used DLRs - Voxelmorph (VM) and FAst IMage registration (FAIM) - on three public 3D brain magnetic resonance (MR) image datasets - IBSR18, Mindboggle101, and LPBA40. The results show that DLRs, using the AAN, improved performance and achieved higher results than state-of-the-art ORs.

Achievements and Challenges in Explaining Deep Learning based Computer-Aided Diagnosis Systems Artificial Intelligence

Remarkable success of modern image-based AI methods and the resulting interest in their applications in critical decision-making processes has led to a surge in efforts to make such intelligent systems transparent and explainable. The need for explainable AI does not stem only from ethical and moral grounds but also from stricter legislation around the world mandating clear and justifiable explanations of any decision taken or assisted by AI. Especially in the medical context where Computer-Aided Diagnosis can have a direct influence on the treatment and well-being of patients, transparency is of utmost importance for safe transition from lab research to real world clinical practice. This paper provides a comprehensive overview of current state-of-the-art in explaining and interpreting Deep Learning based algorithms in applications of medical research and diagnosis of diseases. We discuss early achievements in development of explainable AI for validation of known disease criteria, exploration of new potential biomarkers, as well as methods for the subsequent correction of AI models. Various explanation methods like visual, textual, post-hoc, ante-hoc, local and global have been thoroughly and critically analyzed. Subsequently, we also highlight some of the remaining challenges that stand in the way of practical applications of AI as a clinical decision support tool and provide recommendations for the direction of future research.

Semi-Structured Deep Piecewise Exponential Models Artificial Intelligence

We propose a versatile framework for survival analysis that combines advanced concepts from statistics with deep learning. The presented framework is based on piecewise exponential models and thereby supports various survival tasks, such as competing risks and multi-state modeling, and further allows for estimation of time-varying effects and time-varying features. To also include multiple data sources and higher-order interaction effects into the model, we embed the model class in a neural network and thereby enable the simultaneous estimation of both inherently interpretable structured regression inputs as well as deep neural network components which can potentially process additional unstructured data sources. A proof of concept is provided by using the framework to predict Alzheimer's disease progression based on tabular and 3D point cloud data and applying it to synthetic data.

Detecting Alzheimer's Earlier with the Help of Machine-Learning Algorithm


Functional magnetic resonance imaging (fMRI) is a noninvasive diagnostic technique for brain disorders, such as Alzheimer's disease (AD). It measures minute changes in blood oxygen levels within the brain over time, giving insight into the local activity of neurons; however, fMRI has not been widely used in clinical diagnosis. Their limited use is due to the fact fMRI data are highly susceptible to noise, and the fMRI data structure is very complicated compared to a traditional x-ray or MRI scan. Scientists from Texas Tech University now report they developed a type of deep-learning algorithm known as a convolutional neural network (CNN) that can differentiate among the fMRI signals of healthy people, people with mild cognitive impairment, and people with AD. Their findings, "Spatiotemporal feature extraction and classification of Alzheimer's disease using deep learning 3D-CNN for fMRI data," is published in the Journal of Medical Imaging and led by Harshit Parmar, doctoral student at Texas Tech University.

CycleMorph: Cycle Consistent Unsupervised Deformable Image Registration Machine Learning

Image registration is a fundamental task in medical image analysis. Recently, deep learning based image registration methods have been extensively investigated due to their excellent performance despite the ultra-fast computational time. However, the existing deep learning methods still have limitation in the preservation of original topology during the deformation with registration vector fields. To address this issues, here we present a cycle-consistent deformable image registration. The cycle consistency enhances image registration performance by providing an implicit regularization to preserve topology during the deformation. The proposed method is so flexible that can be applied for both 2D and 3D registration problems for various applications, and can be easily extended to multi-scale implementation to deal with the memory issues in large volume registration. Experimental results on various datasets from medical and non-medical applications demonstrate that the proposed method provides effective and accurate registration on diverse image pairs within a few seconds. Qualitative and quantitative evaluations on deformation fields also verify the effectiveness of the cycle consistency of the proposed method.

Smile-GANs: Semi-supervised clustering via GANs for dissecting brain disease heterogeneity from medical images Machine Learning

Machine learning methods applied to complex biomedical data has enabled the construction of disease signatures of diagnostic/prognostic value. However, less attention has been given to understanding disease heterogeneity. Semi-supervised clustering methods can address this problem by estimating multiple transformations from a (e.g. healthy) control (CN) group to a patient (PT) group, seeking to capture the heterogeneity of underlying pathlogic processes. Herein, we propose a novel method, Smile-GANs (SeMi-supervIsed cLustEring via GANs), for semi-supervised clustering, and apply it to brain MRI scans. Smile-GANs first learns multiple distinct mappings by generating PT from CN, with each mapping characterizing one relatively distinct pathological pattern. Moreover, a clustering model is trained interactively with mapping functions to assign PT into corresponding subtype memberships. Using relaxed assumptions on PT/CN data distribution and imposing mapping non-linearity, Smile-GANs captures heterogeneous differences in distribution between the CN and PT domains. We first validate Smile-GANs using simulated data, subsequently on real data, by demonstrating its potential in characterizing heterogeneity in Alzheimer's Disease (AD) and its prodromal phases. The model was first trained using baseline MRIs from the ADNI2 database and then applied to longitudinal data from ADNI1 and BLSA. Four robust subtypes with distinct neuroanatomical patterns were discovered: 1) normal brain, 2) diffuse atrophy atypical of AD, 3) focal medial temporal lobe atrophy, 4) typical-AD. Further longitudinal analyses discover two distinct progressive pathways from prodromal to full AD: i) subtypes 1 - 2 - 4, and ii) subtypes 1 - 3 - 4. Although demonstrated on an important biomedical problem, Smile-GANs is general and can find application in many biomedical and other domains.

LSSL: Longitudinal Self-Supervised Learning Machine Learning

Longitudinal neuroimaging or biomedical studies often acquire multiple observations from each individual over time, which entails repeated measures with highly interdependent variables. In this paper, we discuss the implication of repeated measures design on unsupervised learning by showing its tight conceptual connection to self-supervised learning and factor disentanglement. Leveraging the ability for `self-comparison' through repeated measures, we explicitly separate the definition of the factor space and the representation space enabling an exact disentanglement of time-related factors from the representations of the images. By formulating deterministic multivariate mapping functions between the two spaces, our model, named Longitudinal Self-Supervised Learning (LSSL), uses a standard autoencoding structure with a cosine loss to estimate the direction linked to the disentangled factor. We apply LSSL to two longitudinal neuroimaging studies to show its unique advantage in extracting the `brain-age' information from the data and in revealing informative characteristics associated with neurodegenerative and neuropsychological disorders. For a downstream task of supervised diagnosis classification, the representations learned by LSSL permit faster convergence and higher (or similar) prediction accuracy compared to several other representation learning techniques.

Deep Learning and Bayesian Deep Learning Based Gender Prediction in Multi-Scale Brain Functional Connectivity Machine Learning

Brain gender differences have been known for a long time and are the possible reason for many psychological, psychiatric and behavioral differences between males and females. Predicting genders from brain functional connectivity (FC) can build the relationship between brain activities and gender, and extracting important gender related FC features from the prediction model offers a way to investigate the brain gender difference. Current predictive models applied to gender prediction demonstrate good accuracies, but usually extract individual functional connections instead of connectivity patterns in the whole connectivity matrix as features. In addition, current models often omit the effect of the input brain FC scale on prediction and cannot give any model uncertainty information. Hence, in this study we propose to predict gender from multiple scales of brain FC with deep learning, which can extract full FC patterns as features. We further develop the understanding of the feature extraction mechanism in deep neural network (DNN) and propose a DNN feature ranking method to extract the highly important features based on their contributions to the prediction. Moreover, we apply Bayesian deep learning to the brain FC gender prediction, which as a probabilistic model can not only make accurate predictions but also generate model uncertainty for each prediction. Experiments were done on the high-quality Human Connectome Project S1200 release dataset comprising the resting state functional MRI data of 1003 healthy adults. First, DNN reaches 83.0%, 87.6%, 92.0%, 93.5% and 94.1% accuracies respectively with the FC input derived from 25, 50, 100, 200, 300 independent component analysis (ICA) components. DNN outperforms the conventional machine learning methods on the 25-ICA-component scale FC, but the linear machine learning method catches up as the number of ICA components increases...