Donald E. Brown

Yash Sharma, Sana Syed, Donald E. Brown

In this work, we propose a mutual information (MI) based unsupervised domain adaptation (UDA) method for the cross-domain nuclei segmentation. Nuclei vary substantially in structure and appearances across different cancer types, leading to a drop in performance of deep learning models when trained on one cancer type and tested on another. This domain shift becomes even more critical as accurate segmentation and quantification of nuclei is an essential histopathology task for the diagnosis/ prognosis of patients and annotating nuclei at the pixel level for new cancer types demands extensive effort by medical experts. To address this problem, we maximize the MI between labeled source cancer type data and unlabeled target cancer type data for transferring nuclei segmentation knowledge across domains. We use the Jensen-Shanon divergence bound, requiring only one negative pair per positive pair for MI maximization. We evaluate our set-up for multiple modeling frameworks and on different datasets comprising of over 20 cancer-type domain shifts and demonstrate competitive performance. All the recently proposed approaches consist of multiple components for improving the domain adaptation, whereas our proposed module is light and can be easily incorporated into other methods (Implementation: https://github.com/YashSharma/MaNi ).

Saurav Sengupta, Johanna Loomba, Suchetha Sharma et al.

Post-acute sequelae of SARS-CoV-2 infection (PASC) or Long COVID is an emerging medical condition that has been observed in several patients with a positive diagnosis for COVID-19. Historical Electronic Health Records (EHR) like diagnosis codes, lab results and clinical notes have been analyzed using deep learning and have been used to predict future clinical events. In this paper, we propose an interpretable deep learning approach to analyze historical diagnosis code data from the National COVID Cohort Collective (N3C) to find the risk factors contributing to developing Long COVID. Using our deep learning approach, we are able to predict if a patient is suffering from Long COVID from a temporally ordered list of diagnosis codes up to 45 days post the first COVID positive test or diagnosis for each patient, with an accuracy of 70.48\%. We are then able to examine the trained model using Gradient-weighted Class Activation Mapping (GradCAM) to give each input diagnoses a score. The highest scored diagnosis were deemed to be the most important for making the correct prediction for a patient. We also propose a way to summarize these top diagnoses for each patient in our cohort and look at their temporal trends to determine which codes contribute towards a positive Long COVID diagnosis.

Nazanin Moradinasab, Yash Sharma, Laura S. Shankman et al.

Two major causes of death in the United States and worldwide are stroke and myocardial infarction. The underlying cause of both is thrombi released from ruptured or eroded unstable atherosclerotic plaques that occlude vessels in the heart (myocardial infarction) or the brain (stroke). Clinical studies show that plaque composition plays a more important role than lesion size in plaque rupture or erosion events. To determine the plaque composition, various cell types in 3D cardiovascular immunofluorescent images of plaque lesions are counted. However, counting these cells manually is expensive, time-consuming, and prone to human error. These challenges of manual counting motivate the need for an automated approach to localize and count the cells in images. The purpose of this study is to develop an automatic approach to accurately detect and count cells in 3D immunofluorescent images with minimal annotation effort. In this study, we used a weakly supervised learning approach to train the HoVer-Net segmentation model using point annotations to detect nuclei in fluorescent images. The advantage of using point annotations is that they require less effort as opposed to pixel-wise annotation. To train the HoVer-Net model using point annotations, we adopted a popularly used cluster labeling approach to transform point annotations into accurate binary masks of cell nuclei. Traditionally, these approaches have generated binary masks from point annotations, leaving a region around the object unlabeled (which is typically ignored during model training). However, these areas may contain important information that helps determine the boundary between cells. Therefore, we used the entropy minimization loss function in these areas to encourage the model to output more confident predictions on the unlabeled areas. Our comparison studies indicate that the HoVer-Net model trained using our weakly ...

Yash Sharma, Nick Coronato, Donald E. Brown

Exercise testing has been available for more than a half-century and is a remarkably versatile tool for diagnostic and prognostic information of patients for a range of diseases, especially cardiovascular and pulmonary. With rapid advancements in technology, wearables, and learning algorithm in the last decade, its scope has evolved. Specifically, Cardiopulmonary exercise testing (CPX) is one of the most commonly used laboratory tests for objective evaluation of exercise capacity and performance levels in patients. CPX provides a non-invasive, integrative assessment of the pulmonary, cardiovascular, and skeletal muscle systems involving the measurement of gas exchanges. However, its assessment is challenging, requiring the individual to process multiple time series data points, leading to simplification to peak values and slopes. But this simplification can discard the valuable trend information present in these time series. In this work, we encode the time series as images using the Gramian Angular Field and Markov Transition Field and use it with a convolutional neural network and attention pooling approach for the classification of heart failure and metabolic syndrome patients. Using GradCAMs, we highlight the discriminative features identified by the model.

Shan Guleria, Benjamin Schwartz, Yash Sharma et al.

Introduction: Technical burdens and time-intensive review processes limit the practical utility of video capsule endoscopy (VCE). Artificial intelligence (AI) is poised to address these limitations, but the intersection of AI and VCE reveals challenges that must first be overcome. We identified five challenges to address. Challenge #1: VCE data are stochastic and contains significant artifact. Challenge #2: VCE interpretation is cost-intensive. Challenge #3: VCE data are inherently imbalanced. Challenge #4: Existing VCE AIMLT are computationally cumbersome. Challenge #5: Clinicians are hesitant to accept AIMLT that cannot explain their process. Methods: An anatomic landmark detection model was used to test the application of convolutional neural networks (CNNs) to the task of classifying VCE data. We also created a tool that assists in expert annotation of VCE data. We then created more elaborate models using different approaches including a multi-frame approach, a CNN based on graph representation, and a few-shot approach based on meta-learning. Results: When used on full-length VCE footage, CNNs accurately identified anatomic landmarks (99.1%), with gradient weighted-class activation mapping showing the parts of each frame that the CNN used to make its decision. The graph CNN with weakly supervised learning (accuracy 89.9%, sensitivity of 91.1%), the few-shot model (accuracy 90.8%, precision 91.4%, sensitivity 90.9%), and the multi-frame model (accuracy 97.5%, precision 91.5%, sensitivity 94.8%) performed well. Discussion: Each of these five challenges is addressed, in part, by one of our AI-based models. Our goal of producing high performance using lightweight models that aim to improve clinician confidence was achieved.

Nazanin Moradinasab, Rebecca A. Deaton, Laura S. Shankman et al.

Recently, deep learning-based methods achieved promising performance in nuclei detection and classification applications. However, training deep learning-based methods requires a large amount of pixel-wise annotated data, which is time-consuming and labor-intensive, especially in 3D images. An alternative approach is to adapt weak-annotation methods, such as labeling each nucleus with a point, but this method does not extend from 2D histopathology images (for which it was originally developed) to 3D immunofluorescent images. The reason is that 3D images contain multiple channels (z-axis) for nuclei and different markers separately, which makes training using point annotations difficult. To address this challenge, we propose the Label-efficient Contrastive learning-based (LECL) model to detect and classify various types of nuclei in 3D immunofluorescent images. Previous methods use Maximum Intensity Projection (MIP) to convert immunofluorescent images with multiple slices to 2D images, which can cause signals from different z-stacks to falsely appear associated with each other. To overcome this, we devised an Extended Maximum Intensity Projection (EMIP) approach that addresses issues using MIP. Furthermore, we performed a Supervised Contrastive Learning (SCL) approach for weakly supervised settings. We conducted experiments on cardiovascular datasets and found that our proposed framework is effective and efficient in detecting and classifying various types of nuclei in 3D immunofluorescent images.

Saurav Sengupta, Donald E. Brown

Deep learning for histopathology has been successfully used for disease classification, image segmentation and more. However, combining image and text modalities using current state-of-the-art methods has been a challenge due to the high resolution of histopathology images. Automatic report generation for histopathology images is one such challenge. In this work, we show that using an existing pre-trained Vision Transformer in a two-step process of first using it to encode 4096x4096 sized patches of the Whole Slide Image (WSI) and then using it as the encoder and an LSTM decoder for report generation, we can build a fairly performant and portable report generation mechanism that takes into account the whole of the high resolution image, instead of just the patches. We are also able to use representations from an existing powerful pre-trained hierarchical vision transformer and show its usefulness in not just zero shot classification but also for report generation.

Kevin Lin, Donald Brown, Sana Syed et al.

Eosinophilic Esophagitis (EoE) is an allergic condition increasing in prevalence. To diagnose EoE, pathologists must find 15 or more eosinophils within a single high-power field (400X magnification). Determining whether or not a patient has EoE can be an arduous process and any medical imaging approaches used to assist diagnosis must consider both efficiency and precision. We propose an improvement of Adorno et al's approach for quantifying eosinphils using deep image segmentation. Our new approach leverages Monte Carlo Dropout, a common approach in deep learning to reduce overfitting, to provide uncertainty quantification on current deep learning models. The uncertainty can be visualized in an output image to evaluate model performance, provide insight to how deep learning algorithms function, and assist pathologists in identifying eosinophils.

Saurav Sengupta, Scott Kilianski, Suchetha Sharma et al.

Manual annotation of spike-wave discharges (SWDs), the electrographic hallmark of absence seizures, is labor-intensive for long-term electroencephalography (EEG) monitoring studies. While machine learning approaches show promise for automated detection, they often struggle with cross-subject generalization due to high inter-individual variability in seizure morphology and signal characteristics. In this study we compare the performance of 15 machine learning classifiers on our own manually annotated dataset of 961 hours of EEG recordings from C3H/HeJ mice, including 22,637 labeled SWDs and find that a 1D U-Net performs the best. We then improve its performance by employing residual connections and data augmentation strategies combining amplitude scaling, Gaussian noise injection, and signal inversion during training to enhance cross-subject generalization. We also compare our method, named AugUNet1D, to a recently published time- and frequency-based algorithmic approach called "Twin Peaks" and show that AugUNet1D performs better on our dataset. AugUNet1D, pretrained on our manually annotated data or untrained, is made public for other users.

Nazanin Moradinasab, Saurav Sengupta, Jiebei Liu et al.

Healthcare relies on multiple types of data, such as medical images, genetic information, and clinical records, to improve diagnosis and treatment. However, missing data is a common challenge due to privacy restrictions, cost, and technical issues, making many existing multi-modal models unreliable. To address this, we propose a new multi-model model called Mixture of Experts, Symmetric Aligning, and Reconstruction (MoSARe), a deep learning framework that handles incomplete multimodal data while maintaining high accuracy. MoSARe integrates expert selection, cross-modal attention, and contrastive learning to improve feature representation and decision-making. Our results show that MoSARe outperforms existing models in situations when the data is complete. Furthermore, it provides reliable predictions even when some data are missing. This makes it especially useful in real-world healthcare settings, including resource-limited environments. Our code is publicly available at https://github.com/NazaninMn/MoSARe.

Saurav Sengupta, Nazanin Moradinasab, Jiebei Liu et al.

Recent research on Vision Language Models (VLMs) suggests that they rely on inherent biases learned during training to respond to questions about visual properties of an image. These biases are exacerbated when VLMs are asked highly specific questions that require focusing on specific areas of the image. For example, a VLM tasked with counting stars on a modified American flag (e.g., with more than 50 stars) will often disregard the visual evidence and fail to answer accurately. We build upon this research and develop a multi-dimensional examination framework to systematically determine which characteristics of the input data, including both the image and the accompanying prompt, lead to such differences in performance. Using open-source VLMs, we further examine how attention values fluctuate with varying input parameters (e.g., image size, number of objects in the image, background color, prompt specificity). This research aims to learn how the behavior of vision language models changes and to explore methods for characterizing such changes. Our results suggest, among other things, that even minor modifications in image characteristics and prompt specificity can lead to large changes in how a VLM formulates its answer and, subsequently, its overall performance.

Yash Sharma, Aman Shrivastava, Lubaina Ehsan et al.

In recent years, the availability of digitized Whole Slide Images (WSIs) has enabled the use of deep learning-based computer vision techniques for automated disease diagnosis. However, WSIs present unique computational and algorithmic challenges. WSIs are gigapixel-sized ($\sim$100K pixels), making them infeasible to be used directly for training deep neural networks. Also, often only slide-level labels are available for training as detailed annotations are tedious and can be time-consuming for experts. Approaches using multiple-instance learning (MIL) frameworks have been shown to overcome these challenges. Current state-of-the-art approaches divide the learning framework into two decoupled parts: a convolutional neural network (CNN) for encoding the patches followed by an independent aggregation approach for slide-level prediction. In this approach, the aggregation step has no bearing on the representations learned by the CNN encoder. We have proposed an end-to-end framework that clusters the patches from a WSI into ${k}$-groups, samples ${k}'$ patches from each group for training, and uses an adaptive attention mechanism for slide level prediction; Cluster-to-Conquer (C2C). We have demonstrated that dividing a WSI into clusters can improve the model training by exposing it to diverse discriminative features extracted from the patches. We regularized the clustering mechanism by introducing a KL-divergence loss between the attention weights of patches in a cluster and the uniform distribution. The framework is optimized end-to-end on slide-level cross-entropy, patch-level cross-entropy, and KL-divergence loss (Implementation: https://github.com/YashSharma/C2C).

Nazanin Moradinasab, Hassan Jafarzadeh, Donald E. Brown

Domain adaptive semantic segmentation is the task of generating precise and dense predictions for an unlabeled target domain using a model trained on a labeled source domain. While significant efforts have been devoted to improving unsupervised domain adaptation for this task, it is crucial to note that many models rely on a strong assumption that the source data is entirely and accurately labeled, while the target data is unlabeled. In real-world scenarios, however, we often encounter partially or noisy labeled data in source and target domains, referred to as Generalized Domain Adaptation (GDA). In such cases, we suggest leveraging weak or unlabeled data from both domains to narrow the gap between them, resulting in effective adaptation. We introduce the Generalized Gaussian-mixture-based (GenGMM) domain adaptation model, which harnesses the underlying data distribution in both domains to refine noisy weak and pseudo labels. The experiments demonstrate the effectiveness of our approach.

Nazanin Moradinasab, Laura S. Shankman, Rebecca A. Deaton et al.

Domain adaptive semantic segmentation aims to generate accurate and dense predictions for an unlabeled target domain by leveraging a supervised model trained on a labeled source domain. The prevalent self-training approach involves retraining the dense discriminative classifier of $p(class|pixel feature)$ using the pseudo-labels from the target domain. While many methods focus on mitigating the issue of noisy pseudo-labels, they often overlook the underlying data distribution p(pixel feature|class) in both the source and target domains. To address this limitation, we propose the multi-prototype Gaussian-Mixture-based (ProtoGMM) model, which incorporates the GMM into contrastive losses to perform guided contrastive learning. Contrastive losses are commonly executed in the literature using memory banks, which can lead to class biases due to underrepresented classes. Furthermore, memory banks often have fixed capacities, potentially restricting the model's ability to capture diverse representations of the target/source domains. An alternative approach is to use global class prototypes (i.e. averaged features per category). However, the global prototypes are based on the unimodal distribution assumption per class, disregarding within-class variation. To address these challenges, we propose the ProtoGMM model. This novel approach involves estimating the underlying multi-prototype source distribution by utilizing the GMM on the feature space of the source samples. The components of the GMM model act as representative prototypes. To achieve increased intra-class semantic similarity, decreased inter-class similarity, and domain alignment between the source and target domains, we employ multi-prototype contrastive learning between source distribution and target samples. The experiments show the effectiveness of our method on UDA benchmarks.

Debajyoti Datta, Maria Phillips, James P Bywater et al.

High-fidelity, AI-based simulated classroom systems enable teachers to rehearse effective teaching strategies. However, dialogue-oriented open-ended conversations such as teaching a student about scale factors can be difficult to model. This paper builds a text-based interactive conversational agent to help teachers practice mathematical questioning skills based on the well-known Instructional Quality Assessment. We take a human-centered approach to designing our system, relying on advances in deep learning, uncertainty quantification, and natural language processing while acknowledging the limitations of conversational agents for specific pedagogical needs. Using experts' input directly during the simulation, we demonstrate how conversation success rate and high user satisfaction can be achieved.

Debajyoti Datta, Maria Phillips, James P Bywater et al.

A large body of research demonstrates how teachers' questioning strategies can improve student learning outcomes. However, developing new scenarios is challenging because of the lack of training data for a specific scenario and the costs associated with labeling. This paper presents a high-fidelity, AI-based classroom simulator to help teachers rehearse research-based mathematical questioning skills. Using a human-in-the-loop approach, we collected a high-quality training dataset for a mathematical questioning scenario. Using recent advances in uncertainty quantification, we evaluated our conversational agent for usability and analyzed the practicality of incorporating a human-in-the-loop approach for data collection and system evaluation for a mathematical questioning scenario.

Sodiq Adewole, Philip Fernandes, James Jablonski et al.

Temporal activity localization in long videos is an important problem. The cost of obtaining frame level label for long Wireless Capsule Endoscopy (WCE) videos is prohibitive. In this paper, we propose an end-to-end temporal abnormality localization for long WCE videos using only weak video level labels. Physicians use Capsule Endoscopy (CE) as a non-surgical and non-invasive method to examine the entire digestive tract in order to diagnose diseases or abnormalities. While CE has revolutionized traditional endoscopy procedures, a single CE examination could last up to 8 hours generating as much as 100,000 frames. Physicians must review the entire video, frame-by-frame, in order to identify the frames capturing relevant abnormality. This, sometimes could be as few as just a single frame. Given this very high level of redundancy, analyzing long CE videos can be very tedious, time consuming and also error prone. This paper presents a novel multi-step method for an end-to-end localization of target frames capturing abnormalities of interest in the long video using only weak video labels. First we developed an automatic temporal segmentation using change point detection technique to temporally segment the video into uniform, homogeneous and identifiable segments. Then we employed Graph Convolutional Neural Network (GCNN) to learn a representation of each video segment. Using weak video segment labels, we trained our GCNN model to recognize each video segment as abnormal if it contains at least a single abnormal frame. Finally, leveraging the parameters of the trained GCNN model, we replaced the final layer of the network with a temporal pool layer to localize the relevant abnormal frames within each abnormal video segment. Our method achieved an accuracy of 89.9\% on the graph classification task and a specificity of 97.5\% on the abnormal frames localization task.

Mojtaba Heidarysafa, Kamran Kowsari, Masoud Bashiri et al.

The growth of the data science field requires better tools to understand such a fast-paced growing domain. Moreover, individuals from different backgrounds became interested in following a career as data scientists. Therefore, providing a quantitative guide for individuals and organizations to understand the skills required in the job market would be crucial. This paper introduces a framework to analyze the job market for data science-related jobs within the US while providing an interface to access insights in this market. The proposed framework includes three sub-modules allowing continuous data collection, information extraction, and a web-based dashboard visualization to investigate the spatial and temporal distribution of data science-related jobs and skills. The result of this work shows important skills for the main branches of data science jobs and attempts to provide a skill-based definition of these data science branches. The current version of this application is deployed on the web and allows individuals and institutes to investigate skills required for data science positions through the industry lens.

Yash Sharma, Lubaina Ehsan, Sana Syed et al.

Advancement in digital pathology and artificial intelligence has enabled deep learning-based computer vision techniques for automated disease diagnosis and prognosis. However, WSIs present unique computational and algorithmic challenges. WSIs are gigapixel-sized, making them infeasible to be used directly for training deep neural networks. Hence, for modeling, a two-stage approach is adopted: Patch representations are extracted first, followed by the aggregation for WSI prediction. These approaches require detailed pixel-level annotations for training the patch encoder. However, obtaining these annotations is time-consuming and tedious for medical experts. Transfer learning is used to address this gap and deep learning architectures pre-trained on ImageNet are used for generating patch-level representation. Even though ImageNet differs significantly from histopathology data, pre-trained networks have been shown to perform impressively on histopathology data. Also, progress in self-supervised and multi-task learning coupled with the release of multiple histopathology data has led to the release of histopathology-specific networks. In this work, we compare the performance of features extracted from networks trained on ImageNet and histopathology data. We use an attention pooling network over these extracted features for slide-level aggregation. We investigate if features learned using more complex networks lead to gain in performance. We use a simple top-k sampling approach for fine-tuning framework and study the representation similarity between frozen and fine-tuned networks using Centered Kernel Alignment. Further, to examine if intermediate block representation is better suited for feature extraction and ImageNet architectures are unnecessarily large for histopathology, we truncate the blocks of ResNet18 and DenseNet121 and examine the performance.

William Adorno, Alexis Catalano, Lubaina Ehsan et al.

Eosinophilic Esophagitis (EoE) is an inflammatory esophageal disease which is increasing in prevalence. The diagnostic gold-standard involves manual review of a patient's biopsy tissue sample by a clinical pathologist for the presence of 15 or greater eosinophils within a single high-power field (400x magnification). Diagnosing EoE can be a cumbersome process with added difficulty for assessing the severity and progression of disease. We propose an automated approach for quantifying eosinophils using deep image segmentation. A U-Net model and post-processing system are applied to generate eosinophil-based statistics that can diagnose EoE as well as describe disease severity and progression. These statistics are captured in biopsies at the initial EoE diagnosis and are then compared with patient metadata: clinical and treatment phenotypes. The goal is to find linkages that could potentially guide treatment plans for new patients at their initial disease diagnosis. A deep image classification model is further applied to discover features other than eosinophils that can be used to diagnose EoE. This is the first study to utilize a deep learning computer vision approach for EoE diagnosis and to provide an automated process for tracking disease severity and progression.

Sodiq Adewole, Philip Fernandez, Michelle Yeghyayan et al.

Effective and rapid detection of lesions in the Gastrointestinal tract is critical to gastroenterologist's response to some life-threatening diseases. Wireless Capsule Endoscopy (WCE) has revolutionized traditional endoscopy procedure by allowing gastroenterologists visualize the entire GI tract non-invasively. Once the tiny capsule is swallowed, it sequentially capture images of the GI tract at about 2 to 6 frames per second (fps). A single video can last up to 8 hours producing between 30,000 to 100,000 images. Automating the detection of frames containing specific lesion in WCE video would relieve gastroenterologists the arduous task of reviewing the entire video before making diagnosis. While the WCE produces large volume of images, only about 5\% of the frames contain lesions that aid the diagnosis process. Convolutional Neural Network (CNN) based models have been very successful in various image classification tasks. However, they suffer excessive parameters, are sample inefficient and rely on very large amount of training data. Deploying a CNN classifier for lesion detection task will require time-to-time fine-tuning to generalize to any unforeseen category. In this paper, we propose a metric-based learning framework followed by a few-shot lesion recognition in WCE data. Metric-based learning is a meta-learning framework designed to establish similarity or dissimilarity between concepts while few-shot learning (FSL) aims to identify new concepts from only a small number of examples. We train a feature extractor to learn a representation for different small bowel lesions using metric-based learning. At the testing stage, the category of an unseen sample is predicted from only a few support examples, thereby allowing the model to generalize to a new category that has never been seen before. We demonstrated the efficacy of this method on real patient capsule endoscopy data.

Debajyoti Datta, Maria Phillips, Jennifer Chiu et al.

Machine learning techniques applied to the Natural Language Processing (NLP) component of conversational agent development show promising results for improved accuracy and quality of feedback that a conversational agent can provide. The effort required to develop an educational scenario specific conversational agent is time consuming as it requires domain experts to label and annotate noisy data sources such as classroom videos. Previous approaches to modeling annotations have relied on labeling thousands of examples and calculating inter-annotator agreement and majority votes in order to model the necessary scenarios. This method, while proven successful, ignores individual annotator strengths in labeling a data point and under-utilizes examples that do not have a majority vote for labeling. We propose using a multi-task weak supervision method combined with active learning to address these concerns. This approach requires less labeling than traditional methods and shows significant improvements in precision, efficiency, and time-requirements than the majority vote method (Ratner 2019). We demonstrate the validity of this method on the Google Jigsaw data set and then propose a scenario to apply this method using the Instructional Quality Assessment(IQA) to define the categories for labeling. We propose using probabilistic modeling of annotator labeling to generate active learning examples to further label the data. Active learning is able to iteratively improve the training performance and accuracy of the original classification model. This approach combines state-of-the art labeling techniques of weak supervision and active learning to optimize results in the educational domain and could be further used to lessen the data requirements for expanded scenarios within the education domain through transfer learning.

Rasoul Sali, Sodiq Adewole, Lubaina Ehsan et al.

Deep convolutional neural networks(CNNs) have been successful for a wide range of computer vision tasks, including image classification. A specific area of the application lies in digital pathology for pattern recognition in the tissue-based diagnosis of gastrointestinal(GI) diseases. This domain can utilize CNNs to translate histopathological images into precise diagnostics. This is challenging since these complex biopsies are heterogeneous and require multiple levels of assessment. This is mainly due to structural similarities in different parts of the GI tract and shared features among different gut diseases. Addressing this problem with a flat model that assumes all classes (parts of the gut and their diseases) are equally difficult to distinguish leads to an inadequate assessment of each class. Since the hierarchical model restricts classification error to each sub-class, it leads to a more informative model than a flat model. In this paper, we propose to apply the hierarchical classification of biopsy images from different parts of the GI tract and the receptive diseases within each. We embedded a class hierarchy into the plain VGGNet to take advantage of its layers' hierarchical structure. The proposed model was evaluated using an independent set of image patches from 373 whole slide images. The results indicate that the hierarchical model can achieve better results than the flat model for multi-category diagnosis of GI disorders using histopathological images.

Sodiq Adewole, Erfaneh Gharavi, Benjamin Shpringer et al.

Existing simulations designed for cultural and interpersonal skill training rely on pre-defined responses with a menu option selection interface. Using a multiple-choice interface and restricting trainees' responses may limit the trainees' ability to apply the lessons in real life situations. This systems also uses a simplistic evaluation model, where trainees' selected options are marked as either correct or incorrect. This model may not capture sufficient information that could drive an adaptive feedback mechanism to improve trainees' cultural awareness. This paper describes the design of a dialogue-based simulation for cultural awareness training. The simulation, built around a disaster management scenario involving a joint coalition between the US and the Chinese armies. Trainees were able to engage in realistic dialogue with the Chinese agent. Their responses, at different points, get evaluated by different multi-label classification models. Based on training on our dataset, the models score the trainees' responses for cultural awareness in the Chinese culture. Trainees also get feedback that informs the cultural appropriateness of their responses. The result of this work showed the following; i) A feature-based evaluation model improves the design, modeling and computation of dialogue-based training simulation systems; ii) Output from current automatic speech recognition (ASR) systems gave comparable end results compared with the output from manual transcription; iii) A multi-label classification model trained as a cultural expert gave results which were comparable with scores assigned by human annotators.

Mojtaba Heidarysafa, Kamran Kowsari, Tolu Odukoya et al.

Online propaganda is central to the recruitment strategies of extremist groups and in recent years these efforts have increasingly extended to women. To investigate ISIS' approach to targeting women in their online propaganda and uncover implications for counterterrorism, we rely on text mining and natural language processing (NLP). Specifically, we extract articles published in Dabiq and Rumiyah (ISIS's online English language publications) to identify prominent topics. To identify similarities or differences between these texts and those produced by non-violent religious groups, we extend the analysis to articles from a Catholic forum dedicated to women. We also perform an emotional analysis of both of these resources to better understand the emotional components of propaganda. We rely on Depechemood (a lexical-base emotion analysis method) to detect emotions most likely to be evoked in readers of these materials. The findings indicate that the emotional appeal of ISIS and Catholic materials are similar

Rasoul Sali, Lubaina Ehsan, Kamran Kowsari et al.

Celiac Disease (CD) is a chronic autoimmune disease that affects the small intestine in genetically predisposed children and adults. Gluten exposure triggers an inflammatory cascade which leads to compromised intestinal barrier function. If this enteropathy is unrecognized, this can lead to anemia, decreased bone density, and, in longstanding cases, intestinal cancer. The prevalence of the disorder is 1% in the United States. An intestinal (duodenal) biopsy is considered the "gold standard" for diagnosis. The mild CD might go unnoticed due to non-specific clinical symptoms or mild histologic features. In our current work, we trained a model based on deep residual networks to diagnose CD severity using a histological scoring system called the modified Marsh score. The proposed model was evaluated using an independent set of 120 whole slide images from 15 CD patients and achieved an AUC greater than 0.96 in all classes. These results demonstrate the diagnostic power of the proposed model for CD severity classification using histological images.

Aman Shrivastava, Will Adorno, Yash Sharma et al.

Hematoxylin and Eosin (H&E) stained Whole Slide Images (WSIs) are utilized for biopsy visualization-based diagnostic and prognostic assessment of diseases. Variation in the H&E staining process across different lab sites can lead to significant variations in biopsy image appearance. These variations introduce an undesirable bias when the slides are examined by pathologists or used for training deep learning models. To reduce this bias, slides need to be translated to a common domain of stain appearance before analysis. We propose a Self-Attentive Adversarial Stain Normalization (SAASN) approach for the normalization of multiple stain appearances to a common domain. This unsupervised generative adversarial approach includes self-attention mechanism for synthesizing images with finer detail while preserving the structural consistency of the biopsy features during translation. SAASN demonstrates consistent and superior performance compared to other popular stain normalization techniques on H&E stained duodenal biopsy image data.

Aman Shrivastava, Karan Kant, Saurav Sengupta et al.

Physicians use biopsies to distinguish between different but histologically similar enteropathies. The range of syndromes and pathologies that could cause different gastrointestinal conditions makes this a difficult problem. Recently, deep learning has been used successfully in helping diagnose cancerous tissues in histopathological images. These successes motivated the research presented in this paper, which describes a deep learning approach that distinguishes between Celiac Disease (CD) and Environmental Enteropathy (EE) and normal tissue from digitized duodenal biopsies. Experimental results show accuracies of over 90% for this approach. We also look into interpreting the neural network model using Gradient-weighted Class Activation Mappings and filter activations on input images to understand the visual explanations for the decisions made by the model.

Kamran Kowsari, Rasoul Sali, Marium N. Khan et al.

Celiac Disease (CD) and Environmental Enteropathy (EE) are common causes of malnutrition and adversely impact normal childhood development. CD is an autoimmune disorder that is prevalent worldwide and is caused by an increased sensitivity to gluten. Gluten exposure destructs the small intestinal epithelial barrier, resulting in nutrient mal-absorption and childhood under-nutrition. EE also results in barrier dysfunction but is thought to be caused by an increased vulnerability to infections. EE has been implicated as the predominant cause of under-nutrition, oral vaccine failure, and impaired cognitive development in low-and-middle-income countries. Both conditions require a tissue biopsy for diagnosis, and a major challenge of interpreting clinical biopsy images to differentiate between these gastrointestinal diseases is striking histopathologic overlap between them. In the current study, we propose a convolutional neural network (CNN) to classify duodenal biopsy images from subjects with CD, EE, and healthy controls. We evaluated the performance of our proposed model using a large cohort containing 1000 biopsy images. Our evaluations show that the proposed model achieves an area under ROC of 0.99, 1.00, and 0.97 for CD, EE, and healthy controls, respectively. These results demonstrate the discriminative power of the proposed model in duodenal biopsies classification.

Mojtaba Heidarysafa, James Reed, Kamran Kowsari et al.

Tracking users' activities on the World Wide Web (WWW) allows researchers to analyze each user's internet behavior as time passes and for the amount of time spent on a particular domain. This analysis can be used in research design, as researchers may access to their participant's behaviors while browsing the web. Web search behavior has been a subject of interest because of its real-world applications in marketing, digital advertisement, and identifying potential threats online. In this paper, we present an image-processing based method to extract domains which are visited by a participant over multiple browsers during a lab session. This method could provide another way to collect users' activities during an online session given that the session recorder collected the data. The method can also be used to collect the textual content of web-pages that an individual visits for later analysis

Brian An, Inki Kim, Erfan Pakdamanian et al.

The recent growth of sophisticated digital gaming technologies has spawned an \$8.1B industry around using these games for pedagogical purposes. Though Digital Game-Based Learning Systems have been adopted by industries ranging from military to medical applications, these systems continue to rely on traditional measures of explicit interactions to gauge player performance which can be subject to guessing and other factors unrelated to actual performance. This study presents a novel implicit eye-tracking based metric for digital game-based learning environments. The proposed metric introduces a weighted eye-tracking measure of traditional in-game scoring to consider the mental schema of a player's decision making. In order to validate the efficacy of this metric, we conducted an experiment with 25 participants playing a game designed to evaluate Chinese cultural competency and communication. This experiment showed strong correlation between the novel eye-tracking performance metric and traditional measures of in-game performance.

Mojtaba Heidarysafa, Kamran Kowsari, Laura E. Barnes et al.

Automatic understanding of domain specific texts in order to extract useful relationships for later use is a non-trivial task. One such relationship would be between railroad accidents' causes and their correspondent descriptions in reports. From 2001 to 2016 rail accidents in the U.S. cost more than $4.6B. Railroads involved in accidents are required to submit an accident report to the Federal Railroad Administration (FRA). These reports contain a variety of fixed field entries including primary cause of the accidents (a coded variable with 389 values) as well as a narrative field which is a short text description of the accident. Although these narratives provide more information than a fixed field entry, the terminologies used in these reports are not easy to understand by a non-expert reader. Therefore, providing an assisting method to fill in the primary cause from such domain specific texts(narratives) would help to label the accidents with more accuracy. Another important question for transportation safety is whether the reported accident cause is consistent with narrative description. To address these questions, we applied deep learning methods together with powerful word embeddings such as Word2Vec and GloVe to classify accident cause values for the primary cause field using the text in the narratives. The results show that such approaches can both accurately classify accident causes based on report narratives and find important inconsistencies in accident reporting.

Mojtaba Heidarysafa, Kamran Kowsari, Donald E. Brown et al.

The exponential growth in the number of complex datasets every year requires more enhancement in machine learning methods to provide robust and accurate data classification. Lately, deep learning approaches have achieved surpassing results in comparison to previous machine learning algorithms. However, finding the suitable structure for these models has been a challenge for researchers. This paper introduces Random Multimodel Deep Learning (RMDL): a new ensemble, deep learning approach for classification. RMDL solves the problem of finding the best deep learning structure and architecture while simultaneously improving robustness and accuracy through ensembles of deep learning architectures. In short, RMDL trains multiple randomly generated models of Deep Neural Network (DNN), Convolutional Neural Network (CNN) and Recurrent Neural Network (RNN) in parallel and combines their results to produce better result of any of those models individually. In this paper, we describe RMDL model and compare the results for image and text classification as well as face recognition. We used MNIST and CIFAR-10 datasets as ground truth datasets for image classification and WOS, Reuters, IMDB, and 20newsgroup datasets for text classification. Lastly, we used ORL dataset to compare the model performance on face recognition task.

Kamran Kowsari, Donald E. Brown, Mojtaba Heidarysafa et al.

The continually increasing number of documents produced each year necessitates ever improving information processing methods for searching, retrieving, and organizing text. Central to these information processing methods is document classification, which has become an important application for supervised learning. Recently the performance of these traditional classifiers has degraded as the number of documents has increased. This is because along with this growth in the number of documents has come an increase in the number of categories. This paper approaches this problem differently from current document classification methods that view the problem as multi-class classification. Instead we perform hierarchical classification using an approach we call Hierarchical Deep Learning for Text classification (HDLTex). HDLTex employs stacks of deep learning architectures to provide specialized understanding at each level of the document hierarchy.

Wei Xie, Yang Wang, Steven M. Boker et al.

Safeguarding privacy in machine learning is highly desirable, especially in collaborative studies across many organizations. Privacy-preserving distributed machine learning (based on cryptography) is popular to solve the problem. However, existing cryptographic protocols still incur excess computational overhead. Here, we make a novel observation that this is partially due to naive adoption of mainstream numerical optimization (e.g., Newton method) and failing to tailor for secure computing. This work presents a contrasting perspective: customizing numerical optimization specifically for secure settings. We propose a seemingly less-favorable optimization method that can in fact significantly accelerate privacy-preserving logistic regression. Leveraging this new method, we propose two new secure protocols for conducting logistic regression in a privacy-preserving and distributed manner. Extensive theoretical and empirical evaluations prove the competitive performance of our two secure proposals while without compromising accuracy or privacy: with speedup up to 2.3x and 8.1x, respectively, over state-of-the-art; and even faster as data scales up. Such drastic speedup is on top of and in addition to performance improvements from existing (and future) state-of-the-art cryptography. Our work provides a new way towards efficient and practical privacy-preserving logistic regression for large-scale studies which are common for modern science.