My research lies at the intersection of machine learning, computer vision, medical image analysis, and computational neuroscience. I work on the automatic analysis of human activities and behaviors from videos and further connect how humans perform actions to the brain by also looking at magnetic resonance images. I explore explainable machine learning algorithms for understanding the underlying factors of neurodegenerative and neuropsychiatric diseases on the brain as well as their ramifications for everyday life.

Academic Appointments

  • Instructor, Psychiatry and Behavioral Sciences

Administrative Appointments

  • Associate Editor, IEEE Journal of Biomedical and Health Informatics (2020 - Present)
  • Associate Editor, Journal of Ambient Intelligence and Smart Environments (2019 - Present)

Honors & Awards

  • Young Investigator Award, Medical Image Computing and Computer Assisted Interventions (MICCAI) (2018)
  • NIH F32 Fellowship Award, NIAAA (2018-2019)

Professional Education

  • Postdoctoral Research Associate, University of North Carolina at Chapel Hill, Machine Learning and Medical Imaging (2017)
  • Research Scholar, Carnegie Mellon University, Computer Vision (2012)

Research & Scholarship

Current Research and Scholarly Interests

My research lies in the intersection of machine learning, computer vision, neuroimaging, and computational neuroscience. Particularly, my research focuses on the investigation of different computational and statistical learning-based methods in processing both natural and biomedical images to extract semantics from the underlying visual content. Machine learning, statistics, signal and image processing, neuroscience, computer vision, and neuroimaging have conventionally evolved independently to tackle problems from different perspectives. Occasionally, these concepts neglected each other, while they can offer complementary viewpoints. In recent years, these fields have begun to intertwine, and it is increasingly becoming clear that we need to make use of multidisciplinary research to better process large-scale visual data. I consider my research interests and direction as located at the intersection of all the aforementioned fields.
Starting my position at the Biomedical Research Imaging Center (BRIC) in the University of North Carolina-Chapel Hill, my main research was focused on expanding my skillset and using my knowledge in machine learning and visual data analysis on the diagnosis of neurodegenerative diseases, and prediction of brain development throughout early years of life, based on neuroimaging data. Although neurodegenerative diseases manifest with diverse pathological features, the cellular level processes resemble similar structures. Therefore, data-driven machine learning methods can lead to great achievements and solve these problems accordingly. I have contributed to the critical studies on these diseases, including Parkinson's Progression Markers Initiative (PPMI) and Alzheimer's Disease Neuroimaging Initiative (ADNI). One of the goals of neuroscience and cognitive sciences is to understand how the brain works. Due to many different factors like technological limitations, this goal remains elusive. Over the past decade, remarkable advances in both hardware and software aspects have established new possibilities for understanding the brain.
Continuing my research at Stanford University, I believe my research advances computational science in identifying biomedical phenotypes that accelerate the detection, understanding, and treatment of medical diseases and specifically neuropsychiatric disorders. Recently, I have started to use my knowledge and expertise in the multidisciplinary fields of machine learning and computational neuroscience to analyses brain images for gaining more insight into the human immunodeficiency virus (HIV) infection and alcoholism, along with their comorbidity. Each of these disorders carries liability for disruption of brain structure integrity. Furthermore, both HIV infection and alcoholism reduce health-related quality of life, and their co-occurrence is highly prevalent. However, few studies examined the potentially heightened burden of disease comorbidity, which often leads to cognitive impairments. I sought to create machine learning techniques to improve the mechanistic understating of their comorbidity effects in the brain.


2019-20 Courses


All Publications

  • Socially and Contextually Aware Human Motion and Pose Forecasting IEEE ROBOTICS AND AUTOMATION LETTERS Adeli, V., Adeli, E., Reid, I., Niebles, J., Rezatofighi, H. 2020; 5 (4): 6033?40
  • Deep Learning Identifies Morphological Determinants of Sex Differences in the Pre-Adolescent Brain. NeuroImage Adeli, E., Zhao, Q., Zahr, N. M., Goldstone, A., Pfefferbaum, A., Sullivan, E. V., Pohl, K. M. 2020: 117293


    The application of data-driven deep learning to identify sex differences in developing brain structures of pre-adolescents has heretofore not been accomplished. Here, the approach identifies sex differences by analyzing the minimally processed MRIs of the first 8,144 participants (age 9 and 10 years) recruited by the Adolescent Brain Cognitive Development (ABCD) study. The identified pattern accounted for confounding factors (i.e., head size, age, puberty development, socioeconomic status) and comprised cerebellar (corpus medullare, lobules III, IV/V, and VI) and subcortical (pallidum, amygdala, hippocampus, parahippocampus, insula, putamen) structures. While these have been individually linked to expressing sex differences, a novel discovery was that their grouping accurately predicted the sex in individual pre-adolescents. Another novelty was relating differences specific to the cerebellum to pubertal development. Finally, we found that reducing the pattern to a single score not only accurately predicted sex but also correlated with cognitive behavior linked to working memory. The predictive power of this score and the constellation of identified brain structures provide evidence for sex differences in pre-adolescent neurodevelopment and may augment understanding of sex-specific vulnerability or resilience to psychiatric disorders and presage sex-linked learning disabilities.

    View details for DOI 10.1016/j.neuroimage.2020.117293

    View details for PubMedID 32841716

  • Segmenting the Future IEEE ROBOTICS AND AUTOMATION LETTERS Chiu, H., Adeli, E., Niebles, J. 2020; 5 (3): 4202?9
  • Image-to-Images Translation for Multi-Task Organ Segmentation and Bone Suppression in Chest X-Ray Radiography IEEE TRANSACTIONS ON MEDICAL IMAGING Eslami, M., Tabarestani, S., Albarqouni, S., Adeli, E., Navab, N., Adjouadi, M. 2020; 39 (7): 2553?65


    Chest X-ray radiography is one of the earliest medical imaging technologies and remains one of the most widely-used for diagnosis, screening, and treatment follow up of diseases related to lungs and heart. The literature in this field of research reports many interesting studies dealing with the challenging tasks of bone suppression and organ segmentation but performed separately, limiting any learning that comes with the consolidation of parameters that could optimize both processes. This study, and for the first time, introduces a multitask deep learning model that generates simultaneously the bone-suppressed image and the organ-segmented image, enhancing the accuracy of tasks, minimizing the number of parameters needed by the model and optimizing the processing time, all by exploiting the interplay between the network parameters to benefit the performance of both tasks. The architectural design of this model, which relies on a conditional generative adversarial network, reveals the process on how the wellestablished pix2pix network (image-to-image network) is modified to fit the need for multitasking and extending it to the new image-to-images architecture. The developed source code of this multitask model is shared publicly on Github as the first attempt for providing the two-task pix2pix extension, a supervised/paired/aligned/registered image-to-images translation which would be useful in many multitask applications. Dilated convolutions are also used to improve the results through a more effective receptive field assessment. The comparison with state-of-the-art al-gorithms along with ablation study and a demonstration video1 are provided to evaluate the efficacy and gauge the merits of the proposed approach.

    View details for DOI 10.1109/TMI.2020.2974159

    View details for Web of Science ID 000545410200024

    View details for PubMedID 32078541

  • Skeleton-based structured early activity prediction MULTIMEDIA TOOLS AND APPLICATIONS Arzani, M. M., Fathy, M., Azirani, A. A., Adeli, E. 2020
  • Spatiotemporal Relationship Reasoning for Pedestrian Intent Prediction IEEE ROBOTICS AND AUTOMATION LETTERS Liu, B., Adeli, E., Cao, Z., Lee, K., Shenoi, A., Gaidon, A., Niebles, J. 2020; 5 (2): 3485?92
  • Mammographic mass segmentation using multichannel and multiscale fully convolutional networks INTERNATIONAL JOURNAL OF IMAGING SYSTEMS AND TECHNOLOGY Xu, S., Adeli, E., Cheng, J., Xiang, L., Li, Y., Lee, S., Shen, D. 2020

    View details for DOI 10.1002/ima.22423

    View details for Web of Science ID 000521597700001

  • FCN Based Label Correction for Multi-Atlas Guided Organ Segmentation. Neuroinformatics Zhu, H., Adeli, E., Shi, F., Shen, D. 2020


    Segmentation of medical images using multiple atlases has recently gained immense attention due to their augmented robustness against variabilities across different subjects. These atlas-based methods typically comprise of three steps: atlas selection, image registration, and finally label fusion. Image registration is one of the core steps in this process, accuracy of which directly affects the final labeling performance. However, due to inter-subject anatomical variations, registration errors are inevitable. The aim of this paper is to develop a deep learning-based confidence estimation method to alleviate the potential effects of registration errors. We first propose a fully convolutional network (FCN) with residual connections to learn the relationship between the image patch pair (i.e., patches from the target subject and the atlas) and the related label confidence patch. With the obtained label confidence patch, we can identify the potential errors in the warped atlas labels and correct them. Then, we use two label fusion methods to fuse the corrected atlas labels. The proposed methods are validated on a publicly available dataset for hippocampus segmentation. Experimental results demonstrate that our proposed methods outperform the state-of-the-art segmentation methods.

    View details for DOI 10.1007/s12021-019-09448-5

    View details for PubMedID 31898145

  • Adolescent alcohol use disrupts functional neurodevelopment in sensation seeking girls. Addiction biology Zhao, Q., Sullivan, E. V., M?ller-Oehring, E. M., Honnorat, N., Adeli, E., Podhajsky, S., Baker, F. C., Colrain, I. M., Prouty, D., Tapert, S. F., Brown, S. A., Meloy, M. J., Brumback, T., Nagel, B. J., Morales, A. M., Clark, D. B., Luna, B., De Bellis, M. D., Voyvodic, J. T., Nooner, K. B., Pfefferbaum, A., Pohl, K. M. 2020: e12914


    Exogenous causes, such as alcohol use, and endogenous factors, such as temperament and sex, can modulate developmental trajectories of adolescent neurofunctional maturation. We examined how these factors affect sexual dimorphism in brain functional networks in youth drinking below diagnostic threshold for alcohol use disorder (AUD). Based on the 3-year, annually acquired, longitudinal resting-state functional magnetic resonance imaging (MRI) data of 526 adolescents (12-21 years at baseline) from the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA) cohort, developmental trajectories of 23 intrinsic functional networks (IFNs) were analyzed for (1) sexual dimorphism in 259 participants who were no-to-low drinkers throughout this period; (2) sex-alcohol interactions in two age- and sex-matched NCANDA subgroups (N = 76 each), half no-to-low, and half moderate-to-heavy drinkers; and (3) moderating effects of gender-specific alcohol dose effects and a multifactorial impulsivity measure on IFN connectivity in all NCANDA participants. Results showed that sex differences in no-to-low drinkers diminished with age in the inferior-occipital network, yet girls had weaker within-network connectivity than boys in six other networks. Effects of adolescent alcohol use were more pronounced in girls than boys in three IFNs. In particular, girls showed greater within-network connectivity in two motor networks with more alcohol consumption, and these effects were mediated by sensation-seeking only in girls. Our results implied that drinking might attenuate the naturally diminishing sexual differences by disrupting the maturation of network efficiency more severely in girls. The sex-alcohol-dose effect might explain why women are at higher risk of alcohol-related health and psychosocial consequences than men.

    View details for DOI 10.1111/adb.12914

    View details for PubMedID 32428984

  • Population-guided large margin classifier for high-dimension low-sample-size problems PATTERN RECOGNITION Yin, Q., Adeli, E., Shen, L., Shen, D. 2020; 97
  • Confounder-Aware Visualization of ConvNets. Machine learning in medical imaging. MLMI (Workshop) Zhao, Q., Adeli, E., Pfefferbaum, A., Sullivan, E. V., Pohl, K. M. 2019; 11861: 328?36


    With recent advances in deep learning, neuroimaging studies increasingly rely on convolutional networks (ConvNets) to predict diagnosis based on MR images. To gain a better understanding of how a disease impacts the brain, the studies visualize the salience maps of the ConvNet highlighting voxels within the brain majorly contributing to the prediction. However, these salience maps are generally confounded, i.e., some salient regions are more predictive of confounding variables (such as age) than the diagnosis. To avoid such misinterpretation, we propose in this paper an approach that aims to visualize confounder-free saliency maps that only highlight voxels predictive of the diagnosis. The approach incorporates univariate statistical tests to identify confounding effects within the intermediate features learned by ConvNet. The influence from the subset of confounded features is then removed by a novel partial back-propagation procedure. We use this two-step approach to visualize confounder-free saliency maps extracted from synthetic and two real datasets. These experiments reveal the potential of our visualization in producing unbiased model-interpretation.

    View details for DOI 10.1007/978-3-030-32692-0_38

    View details for PubMedID 32549051

  • Covariance Shrinkage for Dynamic Functional Connectivity. Connectomics in neuroImaging : third International Workshop, CNI 2019, held in conjunction with MICCAI 2019, Shenzhen, China, October 13, 2019, Proceedings. CNI (Workshop) (3rd : 2019 : Shenzhen Shi, China) Honnorat, N., Adeli, E., Zhao, Q., Pfefferbaum, A., Sullivan, E. V., Pohl, K. 2019; 11848: 32?41


    The tracking of dynamic functional connectivity (dFC) states in resting-state fMRI scans aims to reveal how the brain sequentially processes stimuli and thoughts. Despite the recent advances in statistical methods, estimating the high dimensional dFC states from a small number of available time points remains a challenge. This paper shows that the challenge is reduced by linear covariance shrinkage, a statistical method used for the estimation of large covariance matrices from small number of samples. We present a computationally efficient formulation of our approach that scales dFC analysis up to full resolution resting-state fMRI scans. Experiments on synthetic data demonstrate that our approach produces dFC estimates that are closer to the ground-truth than state-of-the-art estimation approaches. When comparing methods on the rs-fMRI scans of 162 subjects, we found that our approach is better at extracting functional networks and capturing differences in rs-fMRI acquisition and diagnosis.

    View details for DOI 10.1007/978-3-030-32391-2_4

    View details for PubMedID 32924030

  • Data Augmentation Based on Substituting Regional MRIs Volume Scores. Large-Scale Annotation of Biomedical Data and Expert Label Synthesis and Hardware Aware Learning for Medical Imaging and Computer Assisted Intervention : International Workshops, LABELS 2019, HAL-MICCAI 2019, and CuRIOUS 2019, held in c... Leng, T., Zhao, Q., Yang, C., Lu, Z., Adeli, E., Pohl, K. M. 2019; 11851: 32?41


    Due to difficulties in collecting sufficient training data, recent advances in neural-network-based methods have not been fully explored in the analysis of brain Magnetic Resonance Imaging (MRI). A possible solution to the limited-data issue is to augment the training set with synthetically generated data. In this paper, we propose a data augmentation strategy based on regional feature substitution. We demonstrate the advantages of this strategy with respect to training a simple neural-network-based classifier in predicting when individual youth transition from no-to-low to medium-to-heavy alcohol drinkers solely based on their volumetric MRI measurements. Based on 20-fold cross-validation, we generate more than one million synthetic samples from less than 500 subjects for each training run. The classifier achieves an accuracy of 74.1% in correctly distinguishing non-drinkers from drinkers at baseline and a 43.2% weighted accuracy in predicting the transition over a three year period (5-group classification task). Both accuracy scores are significantly better than training the classifier on the original dataset.

    View details for DOI 10.1007/978-3-030-33642-4_4

    View details for PubMedID 32924031

  • High-Resolution Encoder-Decoder Networks for Low-Contrast Medical Image Segmentation. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society Zhou, S., Nie, D., Adeli, E., Yin, J., Lian, J., Shen, D. 2019


    Automatic image segmentation is an essential step for many medical image analysis applications, include computer-aided radiation therapy, disease diagnosis, and treatment effect evaluation. One of the major challenges for this task is the blurry nature of medical images (e.g., CT, MR and, microscopic images), which can often result in low-contrast and vanishing boundaries. With the recent advances in convolutional neural networks, vast improvements have been made for image segmentation, mainly based on the skip-connection-linked encoder-decoder deep architectures. However, in many applications (with adjacent targets in blurry images), these models often fail to accurately locate complex boundaries and properly segment tiny isolated parts. In this paper, we aim to provide a method for blurry medical image segmentation and argue that skip connections are not enough to help accurately locate indistinct boundaries. Accordingly, we propose a novel high-resolution multi-scale encoder-decoder network (HMEDN), in which multi-scale dense connections are introduced for the encoder-decoder structure to finely exploit comprehensive semantic information. Besides skip connections, extra deeply-supervised high-resolution pathways (comprised of densely connected dilated convolutions) are integrated to collect high-resolution semantic information for accurate boundary localization. These pathways are paired with a difficulty-guided cross-entropy loss function and a contour regression task to enhance the quality of boundary detection. Extensive experiments on a pelvic CT image dataset, a multi-modal brain tumor dataset, and a cell segmentation dataset show the effectiveness of our method for 2D/3D semantic segmentation and 2D instance segmentation, respectively. Our experimental results also show that besides increasing the network complexity, raising the resolution of semantic feature maps can largely affect the overall model performance. For different tasks, finding a balance between these two factors can further improve the performance of the corresponding network.

    View details for DOI 10.1109/TIP.2019.2919937

    View details for PubMedID 31226074

  • Infant Brain Development Prediction With Latent Partial Multi-View Representation Learning IEEE TRANSACTIONS ON MEDICAL IMAGING Zhang, C., Adeli, E., Wu, Z., Li, G., Lin, W., Shen, D. 2019; 38 (4): 909?18


    The early postnatal period witnesses rapid and dynamic brain development. However, the relationship between brain anatomical structure and cognitive ability is still unknown. Currently, there is no explicit model to characterize this relationship in the literature. In this paper, we explore this relationship by investigating the mapping between morphological features of the cerebral cortex and cognitive scores. To this end, we introduce a multi-view multi-task learning approach to intuitively explore complementary information from different time-points and handle the missing data issue in longitudinal studies simultaneously. Accordingly, we establish a novel model, latent partial multi-view representation learning. Our approach regards data from different time-points as different views and constructs a latent representation to capture the complementary information from incomplete time-points. The latent representation explores the complementarity across different time-points and improves the accuracy of prediction. The minimization problem is solved by the alternating direction method of multipliers. Experimental results on both synthetic and real data validate the effectiveness of our proposed algorithm.

    View details for DOI 10.1109/TMI.2018.2874964

    View details for Web of Science ID 000463608000004

    View details for PubMedID 30307859

    View details for PubMedCentralID PMC6450718

  • Novel Machine Learning Identifies Brain Patterns Distinguishing Diagnostic Membership of Human Immunodeficiency Virus, Alcoholism, and Their Comorbidity of Individuals. Biological psychiatry. Cognitive neuroscience and neuroimaging Adeli, E., Zahr, N. M., Pfefferbaum, A., Sullivan, E. V., Pohl, K. M. 2019


    The incidence of alcohol use disorder (AUD) in human immunodeficiency virus (HIV) infection is twice that of the rest of the population. This study documents complex radiologically identified, neuroanatomical effects of AUD+HIV comorbidity by identifying structural brain systems that predicted diagnosis on an individual basis. Applying novel machine learning analysis to 549 participants (199 control subjects, 222 with AUD, 68 with HIV, 60 with AUD+HIV), 298 magnetic resonance imaging brain measurements were automatically reduced to small subsets per group. Significance of each diagnostic pattern was inferred from its accuracy in predicting diagnosis and performance on six cognitive measures. While all three diagnostic patterns predicted the learning and memory score, the AUD+HIV pattern was the largest and had the highest predication accuracy (78.1%). Providing a roadmap for analyzing large, multimodal datasets, the machine learning analysis revealed imaging phenotypes that predicted diagnostic membership of magnetic resonance imaging scans of individuals with AUD, HIV, and their comorbidity.

    View details for DOI 10.1016/j.bpsc.2019.02.003

    View details for PubMedID 30982583

  • Semi-Supervised Discriminative Classification Robust to Sample-Outliers and Feature-Noises IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE Adeli, E., Thung, K., An, L., Wu, G., Shi, F., Wang, T., Shen, D. 2019; 41 (2): 515?22


    Discriminative methods commonly produce models with relatively good generalization abilities. However, this advantage is challenged in real-world applications (e.g., medical image analysis problems), in which there often exist outlier data points (sample-outliers) and noises in the predictor values (feature-noises). Methods robust to both types of these deviations are somewhat overlooked in the literature. We further argue that denoising can be more effective, if we learn the model using all the available labeled and unlabeled samples, as the intrinsic geometry of the sample manifold can be better constructed using more data points. In this paper, we propose a semi-supervised robust discriminative classification method based on the least-squares formulation of linear discriminant analysis to detect sample-outliers and feature-noises simultaneously, using both labeled training and unlabeled testing data. We conduct several experiments on a synthetic, some benchmark semi-supervised learning, and two brain neurodegenerative disease diagnosis datasets (for Parkinson's and Alzheimer's diseases). Specifically for the application of neurodegenerative diseases diagnosis, incorporating robust machine learning methods can be of great benefit, due to the noisy nature of neuroimaging data. Our results show that our method outperforms the baseline and several state-of-the-art methods, in terms of both accuracy and the area under the ROC curve.

    View details for DOI 10.1109/TPAMI.2018.2794470

    View details for Web of Science ID 000456150600018

    View details for PubMedID 29994560

    View details for PubMedCentralID PMC6050136

  • Multi-task prediction of infant cognitive scores from longitudinal incomplete neuroimaging data NEUROIMAGE Adeli, E., Meng, Y., Li, G., Lin, W., Shen, D. 2019; 185: 783?92


    Early postnatal brain undergoes a stunning period of development. Over the past few years, research on dynamic infant brain development has received increased attention, exhibiting how important the early stages of a child's life are in terms of brain development. To precisely chart the early brain developmental trajectories, longitudinal studies with data acquired over a long-enough period of infants' early life is essential. However, in practice, missing data from different time point(s) during the data gathering procedure is often inevitable. This leads to incomplete set of longitudinal data, which poses a major challenge for such studies. In this paper, prediction of multiple future cognitive scores with incomplete longitudinal imaging data is modeled into a multi-task machine learning framework. To efficiently learn this model, we account for selection of informative features (i.e., neuroimaging morphometric measurements for different time points), while preserving the structural information and the interrelation between these multiple cognitive scores. Several experiments are conducted on a carefully acquired in-house dataset, and the results affirm that we can predict the cognitive scores measured at the age of four years old, using the imaging data of earlier time points, as early as 24 months of age, with a reasonable performance (i.e., root mean square error of 0.18).

    View details for DOI 10.1016/j.neuroimage.2018.04.052

    View details for Web of Science ID 000451628200066

    View details for PubMedID 29709627

    View details for PubMedCentralID PMC6204112

  • Difficulty-Aware Attention Network with Confidence Learning for Medical Image Segmentation Nie, D., Wang, L., Xiang, L., Zhou, S., Adeli, E., Shen, D., AAAI ASSOC ADVANCEMENT ARTIFICIAL INTELLIGENCE. 2019: 1085?92
  • Imitation Learning for Human Pose Prediction Wang, B., Adeli, E., Chiu, H., Huang, D., Niebles, J., IEEE IEEE. 2019: 7123?32
  • Variational AutoEncoder for Regression: Application to Brain Aging Analysis Zhao, Q., Adeli, E., Honnorat, N., Leng, T., Pohl, K. M., Shen, D., Liu, T., Peters, T. M., Staib, L. H., Essert, C., Zhou, S., Yap, P. T., Khan, A. SPRINGER INTERNATIONAL PUBLISHING AG. 2019: 823?31


    While unsupervised variational autoencoders (VAE) have become a powerful tool in neuroimage analysis, their application to supervised learning is under-explored. We aim to close this gap by proposing a unified probabilistic model for learning the latent space of imaging data and performing supervised regression. Based on recent advances in learning disentangled representations, the novel generative process explicitly models the conditional distribution of latent representations with respect to the regression target variable. Performing a variational inference procedure on this model leads to joint regularization between the VAE and a neural-network regressor. In predicting the age of 245 subjects from their structural Magnetic Resonance (MR) images, our model is more accurate than state-of-the-art methods when applied to either region-of-interest (ROI) measurements or raw 3D volume images. More importantly, unlike simple feed-forward neural-networks, disentanglement of age in latent representations allows for intuitive interpretation of the structural developmental patterns of the human brain.

    View details for DOI 10.1007/978-3-030-32245-8_91

    View details for Web of Science ID 000548438900091

    View details for PubMedID 32705091

    View details for PubMedCentralID PMC7377006

  • Logistic Regression Confined by Cardinality-Constrained Sample and Feature Selection. IEEE transactions on pattern analysis and machine intelligence Adeli, E., Li, X., Kwon, D., Zhang, Y., Pohl, K. 2019


    Many vision-based applications rely on logistic regression for embedding classification within a probabilistic context, such as recognition in images and videos or identifying disease-specific image phenotypes from neuroimages. Logistic regression, however, often performs poorly when trained on data that is noisy, has irrelevant features, or when the samples are distributed across the classes in an imbalanced setting; a common occurrence in visual recognition tasks. To deal with those issues, researchers generally rely on ad-hoc regularization techniques or model a subset of these issues. We instead propose a mathematically sound logistic regression model that selects a subset of (relevant) features and (informative and balanced) set of samples during the training process. The model does so by applying cardinality constraints (via l0 -'norm' sparsity) on the features and samples. l0 defines sparsity in mathematical settings but in practice has mostly been approximated (e.g., via l1 or its variations) for computational simplicity. We prove that a local minimum to the non-convex optimization problems induced by cardinality constraints can be computed by combining block coordinate descent with penalty decomposition. On synthetic, image recognition, and neuroimaging datasets, we furthermore show that the accuracy of the method is higher than alternative methods and classifiers commonly used in the literature.

    View details for DOI 10.1109/TPAMI.2019.2901688

    View details for PubMedID 30835210

  • Variational Autoencoder with Truncated Mixture of Gaussians for Functional Connectivity Analysis. Information processing in medical imaging : proceedings of the ... conference Zhao, Q., Honnorat, N., Adeli, E., Pohl, K. M. 2019; 11492: 867?79


    Resting-state functional connectivity states are often identified as clusters of dynamic connectivity patterns. However, existing clustering approaches do not distinguish major states from rarely occurring minor states and hence are sensitive to noise. To address this issue, we propose to model major states using a non-linear generative process guided by a Gaussian-mixture distribution in a low-dimensional latent space, while separately modeling the connectivity patterns of minor states by a non-informative uniform distribution. We embed this truncated Gaussian-Mixture model in a Variational Autoencoder framework to obtain a general joint clustering and outlier detection approach, tGM-VAE. When applied to synthetic data with known ground-truth, tGM-VAE is more accurate in clustering connectivity patterns than existing approaches. On the rs-fMRI of 593 healthy adolescents, tGM-VAE identifies meaningful major connectivity states. The dwell time of these states significantly correlates with age.

    View details for DOI 10.1007/978-3-030-20351-1_68

    View details for PubMedID 32699491

    View details for PubMedCentralID PMC7375028

  • Variational Autoencoder with Truncated Mixture of Gaussians for Functional Connectivity Analysis Zhao, Q., Honnorat, N., Adeli, E., Pfefferbaum, A., Sullivan, E. V., Pohl, K. M., Chung, A. C., Gee, J. C., Yushkevich, P. A., Bao, S. SPRINGER INTERNATIONAL PUBLISHING AG. 2019: 867?79
  • Action-Agnostic Human Pose Forecasting Chiu, H., Adeli, E., Wang, B., Huang, D., Niebles, J., IEEE IEEE. 2019: 1423?32
  • UNSUPERVISED FEATURE RANKING AND SELECTION BASED ON AUTOENCODERS Sharifipour, S., Fayyazi, H., Sabokrou, M., Adeli, E., IEEE IEEE. 2019: 3172?76
  • AVID: Adversarial Visual Irregularity Detection Sabokrou, M., Pourreza, M., Fayyaz, M., Entezari, R., Fathy, M., Gall, J., Adeli, E., Jawahar, C. V., Li, H., Mori, G., Schindler, K. SPRINGER INTERNATIONAL PUBLISHING AG. 2019: 488?505
  • Chained regularization for identifying brain patterns specific to HIV infection NEUROIMAGE Adeli, E., Kwon, D., Zhao, Q., Pfefferbaum, A., Zahr, N. M., Sullivan, E. V., Pohl, K. M. 2018; 183: 425?37
  • Chained regularization for identifying brain patterns specific to HIV infection. NeuroImage Adeli, E., Kwon, D., Zhao, Q., Pfefferbaum, A., Zahr, N. M., Sullivan, E. V., Pohl, K. M. 2018


    Human Immunodeficiency Virus (HIV) infection continues to have major adverse public health and clinical consequences despite the effectiveness of combination Antiretroviral Therapy (cART) in reducing HIV viral load and improving immune function. As successfully treated individuals with HIV infection age, their cognition declines faster than reported for normal aging. This phenomenon underlines the importance of improving long-term care, which requires better understanding of the impact of HIV on the brain. In this paper, automated identification of patients and brain regions affected by HIV infection are modeled as a classification problem, whose solution is determined in two steps within our proposed Chained-Regularization framework. The first step focuses on selecting the HIV pattern (i.e., the most informative constellation of brain region measurements for distinguishing HIV infected subjects from healthy controls) by constraining the search for the optimal parameter setting of the classifier via group sparsity (?2,1-norm). The second step improves classification accuracy by constraining the parameterization with respect to the selected measurements and the Euclidean regularization (?2-norm). When applied to the cortical and subcortical structural Magnetic Resonance Images (MRI) measurements of 65 controls and 65 HIV infected individuals, this approach is more accurate in distinguishing the two cohorts than more common models. Finally, the brain regions of the identified HIV pattern concur with the HIV literature that uses traditional group analysis models.

    View details for PubMedID 30138676

  • Exploring diagnosis and imaging biomarkers of Parkinson's disease via iterative canonical correlation analysis based feature selection COMPUTERIZED MEDICAL IMAGING AND GRAPHICS Liu, L., Wang, Q., Adeli, E., Zhang, L., Zhang, H., Shen, D. 2018; 67: 21?29


    Parkinson's disease (PD) is a neurodegenerative disorder that progressively hampers the brain functions and leads to various movement and non-motor symptoms. However, it is difficult to attain early-stage PD diagnosis based on the subjective judgment of physicians in clinical routines. Therefore, automatic and accurate diagnosis of PD is highly demanded, so that the corresponding treatment can be implemented more appropriately. In this paper, we focus on finding the most discriminative features from different brain regions in PD through T1-weighted MR images, which can help the subsequent PD diagnosis. Specifically, we proposed a novel iterative canonical correlation analysis (ICCA) feature selection method, aiming at exploiting MR images in a more comprehensive manner and fusing features of different types into a common space. To state succinctly, we first extract the feature vectors from the gray matter and the white matter tissues separately, represented as insights of two different anatomical feature spaces for the subject's brain. The ICCA feature selection method aims at iteratively finding the optimal feature subset from two sets of features that have inherent high correlation with each other. In experiments we have conducted thorough investigations on the optimal feature set extracted by our ICCA method. We also demonstrate that using the proposed feature selection method, the PD diagnosis performance is further improved, and also outperforms many state-of-the-art methods.

    View details for DOI 10.1016/j.compmedimag.2018.04.002

    View details for Web of Science ID 000447358800003

    View details for PubMedID 29702348

  • End-To-End Alzheimer's Disease Diagnosis and Biomarker Identification. Machine learning in medical imaging. MLMI (Workshop) Esmaeilzadeh, S., Belivanis, D. I., Pohl, K. M., Adeli, E. 2018; 11046: 337?45


    As shown in computer vision, the power of deep learning lies in automatically learning relevant and powerful features for any perdition task, which is made possible through end-to-end architectures. However, deep learning approaches applied for classifying medical images do not adhere to this architecture as they rely on several pre- and post-processing steps. This shortcoming can be explained by the relatively small number of available labeled subjects, the high dimensionality of neuroimaging data, and difficulties in interpreting the results of deep learning methods. In this paper, we propose a simple 3D Convolutional Neural Networks and exploit its model parameters to tailor the end-to-end architecture for the diagnosis of Alzheimer's disease (AD). Our model can diagnose AD with an accuracy of 94.1% on the popular ADNI dataset using only MRI data, which outperforms the previous state-of-the-art. Based on the learned model, we identify the disease biomarkers, the results of which were in accordance with the literature. We further transfer the learned model to diagnose mild cognitive impairment (MCI), the prodromal stage of AD, which yield better results compared to other methods.

    View details for DOI 10.1007/978-3-030-00919-9_39

    View details for PubMedID 32832936

    View details for PubMedCentralID PMC7440044

  • Multi-label Transduction for Identifying Disease Comorbidity Patterns Adeli, E., Kwon, D., Pohl, K. M., Frangi, A. F., Schnabel, J. A., Davatzikos, C., AlberolaLopez, C., Fichtinger, G. SPRINGER INTERNATIONAL PUBLISHING AG. 2018: 575?83
  • End-To-End Alzheimer's Disease Diagnosis and Biomarker Identification Esmaeilzadeh, S., Belivanis, D., Pohl, K. M., Adeli, E., Shi, Y., Suk, H. I., Liu, M. SPRINGER INTERNATIONAL PUBLISHING AG. 2018: 337?45
  • INFANT BRAIN DEVELOPMENT PREDICTION WITH LATENT PARTIAL MULTI-VIEW REPRESENTATION LEARNING. Proceedings. IEEE International Symposium on Biomedical Imaging Zhang, C., Adeli, E., Wu, Z., Li, G., Lin, W., Shen, D. 2018; 2018: 1048?51


    The early postnatal period witnesses rapid and dynamic brain development. Understanding the cognitive development patterns can help identify various disorders at early ages of life and is essential for the health and well-being of children. This inspires us to investigate the relation between cognitive ability and the cerebral cortex by exploiting brain images in a longitudinal study. Specifically, we aim to predict the infant brain development status based on the morphological features of the cerebral cortex. For this goal, we introduce a multi-view multi-task learning approach to dexterously explore complementary information from different time points and handle the missing data simultaneously. Specifically, we establish a novel model termed as Latent Partial Multi-view Representation Learning. The approach regards data of different time points as different views, and constructs a latent representation to capture the complementary underlying information from different and even incomplete time points. It uncovers the latent representation that can be jointly used to learn the prediction model. This formulation elegantly explores the complementarity, effectively reduces the redundancy of different views, and improves the accuracy of prediction. The minimization problem is solved by the Alternating Direction Method of Multipliers (ADMM). Experimental results on real data validate the proposed method.

    View details for PubMedID 30464798

    View details for PubMedCentralID PMC6242279

  • Landmark-based deep multi-instance learning for brain disease diagnosis MEDICAL IMAGE ANALYSIS Liu, M., Zhang, J., Adeli, E., Shen, D. 2018; 43: 157?68


    In conventional Magnetic Resonance (MR) image based methods, two stages are often involved to capture brain structural information for disease diagnosis, i.e., 1) manually partitioning each MR image into a number of regions-of-interest (ROIs), and 2) extracting pre-defined features from each ROI for diagnosis with a certain classifier. However, these pre-defined features often limit the performance of the diagnosis, due to challenges in 1) defining the ROIs and 2) extracting effective disease-related features. In this paper, we propose a landmark-based deep multi-instance learning (LDMIL) framework for brain disease diagnosis. Specifically, we first adopt a data-driven learning approach to discover disease-related anatomical landmarks in the brain MR images, along with their nearby image patches. Then, our LDMIL framework learns an end-to-end MR image classifier for capturing both the local structural information conveyed by image patches located by landmarks and the global structural information derived from all detected landmarks. We have evaluated our proposed framework on 1526 subjects from three public datasets (i.e., ADNI-1, ADNI-2, and MIRIAD), and the experimental results show that our framework can achieve superior performance over state-of-the-art approaches.

    View details for DOI 10.1016/

    View details for Web of Science ID 000418627400012

    View details for PubMedID 29107865

    View details for PubMedCentralID PMC6203325

  • Multi-Layer Multi-View Classification for Alzheimer's Disease Diagnosis Zhang, C., Adeli, E., Zhou, T., Chen, X., Shen, D., AAAI ASSOC ADVANCEMENT ARTIFICIAL INTELLIGENCE. 2018: 4406?13


    In this paper, we propose a novel multi-view learning method for Alzheimer's Disease (AD) diagnosis, using neuroimaging and genetics data. Generally, there are several major challenges associated with traditional classification methods on multi-source imaging and genetics data. First, the correlation between the extracted imaging features and class labels is generally complex, which often makes the traditional linear models ineffective. Second, medical data may be collected from different sources (i.e., multiple modalities of neuroimaging data, clinical scores or genetics measurements), therefore, how to effectively exploit the complementarity among multiple views is of great importance. In this paper, we propose a Multi-Layer Multi-View Classification (ML-MVC) approach, which regards the multi-view input as the first layer, and constructs a latent representation to explore the complex correlation between the features and class labels. This captures the high-order complementarity among different views, as we exploit the underlying information with a low-rank tensor regularization. Intrinsically, our formulation elegantly explores the nonlinear correlation together with complementarity among different views, and thus improves the accuracy of classification. Finally, the minimization problem is solved by the Alternating Direction Method of Multipliers (ADMM). Experimental results on Alzheimers Disease Neuroimaging Initiative (ADNI) data sets validate the effectiveness of our proposed method.

    View details for Web of Science ID 000485488904061

    View details for PubMedID 30416868

    View details for PubMedCentralID PMC6223635

  • Fine-Grained Segmentation Using Hierarchical Dilated Neural Networks Zhou, S., Nie, D., Adeli, E., Gao, Y., Wang, L., Yin, J., Shen, D., Frangi, A. F., Schnabel, J. A., Davatzikos, C., AlberolaLopez, C., Fichtinger, G. SPRINGER INTERNATIONAL PUBLISHING AG. 2018: 488?96
  • Predictive Modeling of Longitudinal Data for Alzheimer's Disease Diagnosis Using RNNs Aghili, M., Tabarestani, S., Adjouadi, M., Adeli, E., Rekik, Unal, G., Adeli, E., Park, S. H. SPRINGER INTERNATIONAL PUBLISHING AG. 2018: 112?19
  • Structured Prediction with Short/Long-Range Dependencies for Human Activity Recognition from Depth Skeleton Data Arzani, M. M., Fathy, M., Aghajan, H., Azirani, A. A., Raahemifar, K., Adeli, E., Bicchi, A., Okamura, A. IEEE. 2017: 560?67

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