Hien Van Nguyen

Syed Rizvi, Akash Awasthi, Maria J. Peláez et al.

The COVID-19 pandemic has affected countries across the world, demanding drastic public health policies to mitigate the spread of infection, leading to economic crisis as a collateral damage. In this work, we investigated the impact of human mobility (described via international commercial flights) on COVID-19 infection dynamics at the global scale. For this, we developed a graph neural network-based framework referred to as Dynamic Connectivity GraphSAGE (DCSAGE), which operates over spatiotemporal graphs and is well-suited for dynamically changing adjacency information. To obtain insights on the relative impact of different geographical locations, due to their associated air traffic, on the evolution of the pandemic, we conducted local sensitivity analysis on our model through node perturbation experiments. From our analyses, we identified Western Europe, North America, and Middle East as the leading geographical locations fueling the pandemic, attributed to the enormity of air traffic originating or transiting through these regions. We used these observations to identify tangible air traffic reduction strategies that can have a high impact on controlling the pandemic, with minimal interference to human mobility. Our work provides a robust deep learning-based tool to study global pandemics and is of key relevance to policy makers to take informed decisions regarding air traffic restrictions during future outbreaks.

Huy Q. Vo, Pietro A. Cicalese, Surya Seshan et al.

The thrombotic microangiopathies (TMAs) manifest in renal biopsy histology with a broad spectrum of acute and chronic findings. Precise diagnostic criteria for a renal biopsy diagnosis of TMA are missing. As a first step towards a machine learning- and computer vision-based analysis of wholes slide images from renal biopsies, we trained a segmentation model for the decisive diagnostic kidney tissue compartments artery, arteriole, glomerulus on a set of whole slide images from renal biopsies with TMAs and Mimickers (distinct diseases with a similar nephropathological appearance as TMA like severe benign nephrosclerosis, various vasculitides, Bevacizumab-plug glomerulopathy, arteriolar light chain deposition disease). Our segmentation model combines a U-Net-based tissue detection with a Shifted windows-transformer architecture to reach excellent segmentation results for even the most severely altered glomeruli, arterioles and arteries, even on unseen staining domains from a different nephropathology lab. With accurate automatic segmentation of the decisive renal biopsy compartments in human renal vasculopathies, we have laid the foundation for large-scale compartment-specific machine learning and computer vision analysis of renal biopsy repositories with TMAs.

Son T. Ly, Bai Lin, Hung Q. Vo et al.

Reliable large-scale cell detection and segmentation is the fundamental first step to understanding biological processes in the brain. The ability to phenotype cells at scale can accelerate preclinical drug evaluation and system-level brain histology studies. The impressive advances in deep learning offer a practical solution to cell image detection and segmentation. Unfortunately, categorizing cells and delineating their boundaries for training deep networks is an expensive process that requires skilled biologists. This paper presents a novel self-supervised Dual-Loss Adaptive Masked Autoencoder (DAMA) for learning rich features from multiplexed immunofluorescence brain images. DAMA's objective function minimizes the conditional entropy in pixel-level reconstruction and feature-level regression. Unlike existing self-supervised learning methods based on a random image masking strategy, DAMA employs a novel adaptive mask sampling strategy to maximize mutual information and effectively learn brain cell data. To the best of our knowledge, this is the first effort to develop a self-supervised learning method for multiplexed immunofluorescence brain images. Our extensive experiments demonstrate that DAMA features enable superior cell detection, segmentation, and classification performance without requiring many annotations.

Son Thai Ly, Hien V. Nguyen

Adapting vision transformer foundation models through parameter-efficient fine-tuning (PEFT) methods has become increasingly popular. These methods optimize a limited subset of parameters, enabling efficient adaptation without the need to fine-tune the entire model while still achieving competitive performance. However, traditional PEFT methods may limit the model's capacity to capture complex patterns, especially those associated with high-frequency spectra. This limitation becomes particularly problematic as existing research indicates that high-frequency features are crucial for distinguishing subtle image structures. To address this issue, we introduce FreqFit, a novel Frequency Fine-tuning module between ViT blocks to enhance model adaptability. FreqFit is simple yet surprisingly effective, and can be integrated with all existing PEFT methods to boost their performance. By manipulating features in the frequency domain, our approach allows models to capture subtle patterns more effectively. Extensive experiments on 24 datasets, using both supervised and self-supervised foundational models with various state-of-the-art PEFT methods, reveal that FreqFit consistently improves performance over the original PEFT methods with performance gains ranging from 1% to 16%. For instance, FreqFit-LoRA surpasses the performances of state-of-the-art baselines on CIFAR100 by more than 10% even without applying regularization or strong augmentation. For reproducibility purposes, the source code is available at https://github.com/tsly123/FreqFiT.

Adhrith Vutukuri, Akash Awasthi, David Yang et al.

Chest radiography is widely used in diagnostic imaging. However, perceptual errors -- especially overlooked but visible abnormalities -- remain common and clinically significant. Current workflows and AI systems provide limited support for detecting such errors after interpretation and often lack meaningful human--AI collaboration. We introduce RADAR (Radiologist--AI Diagnostic Assistance and Review), a post-interpretation companion system. RADAR ingests finalized radiologist annotations and CXR images, then performs regional-level analysis to detect and refer potentially missed abnormal regions. The system supports a "second-look" workflow and offers suggested regions of interest (ROIs) rather than fixed labels to accommodate inter-observer variation. We evaluated RADAR on a simulated perceptual-error dataset derived from de-identified CXR cases, using F1 score and Intersection over Union (IoU) as primary metrics. RADAR achieved a recall of 0.78, precision of 0.44, and an F1 score of 0.56 in detecting missed abnormalities in the simulated perceptual-error dataset. Although precision is moderate, this reduces over-reliance on AI by encouraging radiologist oversight in human--AI collaboration. The median IoU was 0.78, with more than 90% of referrals exceeding 0.5 IoU, indicating accurate regional localization. RADAR effectively complements radiologist judgment, providing valuable post-read support for perceptual-error detection in CXR interpretation. Its flexible ROI suggestions and non-intrusive integration position it as a promising tool in real-world radiology workflows. To facilitate reproducibility and further evaluation, we release a fully open-source web implementation alongside a simulated error dataset. All code, data, demonstration videos, and the application are publicly available at https://github.com/avutukuri01/RADAR.

Leila Saadatifard, Aryan Mobiny, Pavel Govyadinov et al.

Maps of brain microarchitecture are important for understanding neurological function and behavior, including alterations caused by chronic conditions such as neurodegenerative disease. Techniques such as knife-edge scanning microscopy (KESM) provide the potential for whole organ imaging at sub-cellular resolution. However, multi-terabyte data sizes make manual annotation impractical and automatic segmentation challenging. Densely packed cells combined with interconnected microvascular networks are a challenge for current segmentation algorithms. The massive size of high-throughput microscopy data necessitates fast and largely unsupervised algorithms. In this paper, we investigate a fully-convolutional, deep, and densely-connected encoder-decoder for pixel-wise semantic segmentation. The excessive memory complexity often encountered with deep and dense networks is mitigated using skip connections, resulting in fewer parameters and enabling a significant performance increase over prior architectures. The proposed network provides superior performance for semantic segmentation problems applied to open-source benchmarks. We finally demonstrate our network for cellular and microvascular segmentation, enabling quantitative metrics for organ-scale neurovascular analysis.

Anh Mai Vu, Tuan L. Vo, Ngoc Lam Quang Bui et al.

Interpretability is essential in Whole Slide Image (WSI) analysis for computational pathology, where understanding model predictions helps build trust in AI-assisted diagnostics. While Integrated Gradients (IG) and related attribution methods have shown promise, applying them directly to WSIs introduces challenges due to their high-resolution nature. These methods capture model decision patterns but may overlook class-discriminative signals that are crucial for distinguishing between tumor subtypes. In this work, we introduce Contrastive Integrated Gradients (CIG), a novel attribution method that enhances interpretability by computing contrastive gradients in logit space. First, CIG highlights class-discriminative regions by comparing feature importance relative to a reference class, offering sharper differentiation between tumor and non-tumor areas. Second, CIG satisfies the axioms of integrated attribution, ensuring consistency and theoretical soundness. Third, we propose two attribution quality metrics, MIL-AIC and MIL-SIC, which measure how predictive information and model confidence evolve with access to salient regions, particularly under weak supervision. We validate CIG across three datasets spanning distinct cancer types: CAMELYON16 (breast cancer metastasis in lymph nodes), TCGA-RCC (renal cell carcinoma), and TCGA-Lung (lung cancer). Experimental results demonstrate that CIG yields more informative attributions both quantitatively, using MIL-AIC and MIL-SIC, and qualitatively, through visualizations that align closely with ground truth tumor regions, underscoring its potential for interpretable and trustworthy WSI-based diagnostics

Khang Le, Ha Thach, Anh M. Vu et al.

Weakly supervised semantic segmentation (WSSS) in histopathology relies heavily on classification backbones, yet these models often localize only the most discriminative regions and struggle to capture the full spatial extent of tissue structures. Vision-language models such as CONCH offer rich semantic alignment and morphology-aware representations, while modern segmentation backbones like SegFormer preserve fine-grained spatial cues. However, combining these complementary strengths remains challenging, especially under weak supervision and without dense annotations. We propose a prototype learning framework for WSSS in histopathological images that integrates morphology-aware representations from CONCH, multi-scale structural cues from SegFormer, and text-guided semantic alignment to produce prototypes that are simultaneously semantically discriminative and spatially coherent. To effectively leverage these heterogeneous sources, we introduce text-guided prototype initialization that incorporates pathology descriptions to generate more complete and semantically accurate pseudo-masks. A structural distillation mechanism transfers spatial knowledge from SegFormer to preserve fine-grained morphological patterns and local tissue boundaries during prototype learning. Our approach produces high-quality pseudo masks without pixel-level annotations, improves localization completeness, and enhances semantic consistency across tissue types. Experiments on BCSS-WSSS datasets demonstrate that our prototype learning framework outperforms existing WSSS methods while remaining computationally efficient through frozen foundation model backbones and lightweight trainable adapters.

Anh M. Vu, Khang P. Le, Trang T. K. Vo et al.

Weakly supervised semantic segmentation (WSSS) in histopathology seeks to reduce annotation cost by learning from image-level labels, yet it remains limited by inter-class homogeneity, intra-class heterogeneity, and the region-shrinkage effect of CAM-based supervision. We propose a simple and effective prototype-driven framework that leverages vision-language alignment to improve region discovery under weak supervision. Our method integrates CoOp-style learnable prompt tuning to generate text-based prototypes and combines them with learnable image prototypes, forming a dual-modal prototype bank that captures both semantic and appearance cues. To address oversmoothing in ViT representations, we incorporate a multi-scale pyramid module that enhances spatial precision and improves localization quality. Experiments on the BCSS-WSSS benchmark show that our approach surpasses existing state-of-the-art methods, and detailed analyses demonstrate the benefits of text description diversity, context length, and the complementary behavior of text and image prototypes. These results highlight the effectiveness of jointly leveraging textual semantics and visual prototype learning for WSSS in digital pathology.

Akash Awasthi, Safwan Ahmad, Bryant Le et al.

In the realm of chest X-ray (CXR) image analysis, radiologists meticulously examine various regions, documenting their observations in reports. The prevalence of errors in CXR diagnoses, particularly among inexperienced radiologists and hospital residents, underscores the importance of understanding radiologists' intentions and the corresponding regions of interest. This understanding is crucial for correcting mistakes by guiding radiologists to the accurate regions of interest, especially in the diagnosis of chest radiograph abnormalities. In response to this imperative, we propose a novel system designed to identify the primary intentions articulated by radiologists in their reports and the corresponding regions of interest in CXR images. This system seeks to elucidate the visual context underlying radiologists' textual findings, with the potential to rectify errors made by less experienced practitioners and direct them to precise regions of interest. Importantly, the proposed system can be instrumental in providing constructive feedback to inexperienced radiologists or junior residents in the hospital, bridging the gap in face-to-face communication. The system represents a valuable tool for enhancing diagnostic accuracy and fostering continuous learning within the medical community.

Khang Le, Anh Mai Vu, Thi Kim Trang Vo et al.

Weakly supervised semantic segmentation (WSSS) in histopathology reduces pixel-level labeling by learning from image-level labels, but it is hindered by inter-class homogeneity, intra-class heterogeneity, and CAM-induced region shrinkage (global pooling-based class activation maps whose activations highlight only the most distinctive areas and miss nearby class regions). Recent works address these challenges by constructing a clustering prototype bank and then refining masks in a separate stage; however, such two-stage pipelines are costly, sensitive to hyperparameters, and decouple prototype discovery from segmentation learning, limiting their effectiveness and efficiency. We propose a cluster-free, one-stage learnable-prototype framework with diversity regularization to enhance morphological intra-class heterogeneity coverage. Our approach achieves state-of-the-art (SOTA) performance on BCSS-WSSS, outperforming prior methods in mIoU and mDice. Qualitative segmentation maps show sharper boundaries and fewer mislabels, and activation heatmaps further reveal that, compared with clustering-based prototypes, our learnable prototypes cover more diverse and complementary regions within each class, providing consistent qualitative evidence for their effectiveness.

Trong-Thang Pham, Akash Awasthi, Saba Khan et al.

Understanding radiologists' eye movement during Computed Tomography (CT) reading is crucial for developing effective interpretable computer-aided diagnosis systems. However, CT research in this area has been limited by the lack of publicly available eye-tracking datasets and the three-dimensional complexity of CT volumes. To address these challenges, we present the first publicly available eye gaze dataset on CT, called CT-ScanGaze. Then, we introduce CT-Searcher, a novel 3D scanpath predictor designed specifically to process CT volumes and generate radiologist-like 3D fixation sequences, overcoming the limitations of current scanpath predictors that only handle 2D inputs. Since deep learning models benefit from a pretraining step, we develop a pipeline that converts existing 2D gaze datasets into 3D gaze data to pretrain CT-Searcher. Through both qualitative and quantitative evaluations on CT-ScanGaze, we demonstrate the effectiveness of our approach and provide a comprehensive assessment framework for 3D scanpath prediction in medical imaging.

Trong-Thang Pham, Anh Nguyen, Zhigang Deng et al.

Radiologists rely on eye movements to navigate and interpret medical images. A trained radiologist possesses knowledge about the potential diseases that may be present in the images and, when searching, follows a mental checklist to locate them using their gaze. This is a key observation, yet existing models fail to capture the underlying intent behind each fixation. In this paper, we introduce a deep learning-based approach, RadGazeIntent, designed to model this behavior: having an intention to find something and actively searching for it. Our transformer-based architecture processes both the temporal and spatial dimensions of gaze data, transforming fine-grained fixation features into coarse, meaningful representations of diagnostic intent to interpret radiologists' goals. To capture the nuances of radiologists' varied intention-driven behaviors, we process existing medical eye-tracking datasets to create three intention-labeled subsets: RadSeq (Systematic Sequential Search), RadExplore (Uncertainty-driven Exploration), and RadHybrid (Hybrid Pattern). Experimental results demonstrate RadGazeIntent's ability to predict which findings radiologists are examining at specific moments, outperforming baseline methods across all intention-labeled datasets.

Akash Awasthi, Ngan Le, Zhigang Deng et al.

Human-AI collaboration to identify and correct perceptual errors in chest radiographs has not been previously explored. This study aimed to develop a collaborative AI system, CoRaX, which integrates eye gaze data and radiology reports to enhance diagnostic accuracy in chest radiology by pinpointing perceptual errors and refining the decision-making process. Using public datasets REFLACX and EGD-CXR, the study retrospectively developed CoRaX, employing a large multimodal model to analyze image embeddings, eye gaze data, and radiology reports. The system's effectiveness was evaluated based on its referral-making process, the quality of referrals, and performance in collaborative diagnostic settings. CoRaX was tested on a simulated error dataset of 271 samples with 28% (93 of 332) missed abnormalities. The system corrected 21% (71 of 332) of these errors, leaving 7% (22 of 312) unresolved. The Referral-Usefulness score, indicating the accuracy of predicted regions for all true referrals, was 0.63 (95% CI 0.59, 0.68). The Total-Usefulness score, reflecting the diagnostic accuracy of CoRaX's interactions with radiologists, showed that 84% (237 of 280) of these interactions had a score above 0.40. In conclusion, CoRaX efficiently collaborates with radiologists to address perceptual errors across various abnormalities, with potential applications in the education and training of novice radiologists.

Akash Awasthi, Ngan Le, Zhigang Deng et al.

Predicting human gaze behavior within computer vision is integral for developing interactive systems that can anticipate user attention, address fundamental questions in cognitive science, and hold implications for fields like human-computer interaction (HCI) and augmented/virtual reality (AR/VR) systems. Despite methodologies introduced for modeling human eye gaze behavior, applying these models to medical imaging for scanpath prediction remains unexplored. Our proposed system aims to predict eye gaze sequences from radiology reports and CXR images, potentially streamlining data collection and enhancing AI systems using larger datasets. However, predicting human scanpaths on medical images presents unique challenges due to the diverse nature of abnormal regions. Our model predicts fixation coordinates and durations critical for medical scanpath prediction, outperforming existing models in the computer vision community. Utilizing a two-stage training process and large publicly available datasets, our approach generates static heatmaps and eye gaze videos aligned with radiology reports, facilitating comprehensive analysis. We validate our approach by comparing its performance with state-of-the-art methods and assessing its generalizability among different radiologists, introducing novel strategies to model radiologists' search patterns during CXR image diagnosis. Based on the radiologist's evaluation, MedGaze can generate human-like gaze sequences with a high focus on relevant regions over the CXR images. It sometimes also outperforms humans in terms of redundancy and randomness in the scanpaths.

Akash Awasthi, Son Ly, Jaer Nizam et al.

The definition of anomaly detection is the identification of an unexpected event. Real-time detection of extreme events such as wildfires, cyclones, or floods using satellite data has become crucial for disaster management. Although several earth-observing satellites provide information about disasters, satellites in the geostationary orbit provide data at intervals as frequent as every minute, effectively creating a video from space. There are many techniques that have been proposed to identify anomalies in surveillance videos; however, the available datasets do not have dynamic behavior, so we discuss an anomaly framework that can work on very high-frequency datasets to find very fast-moving anomalies. In this work, we present a diffusion model which does not need any motion component to capture the fast-moving anomalies and outperforms the other baseline methods.

Samira Zare, Hien Van Nguyen

Set-input deep networks have recently drawn much interest in computer vision and machine learning. This is in part due to the increasing number of important tasks such as meta-learning, clustering, and anomaly detection that are defined on set inputs. These networks must take an arbitrary number of input samples and produce the output invariant to the input set permutation. Several algorithms have been recently developed to address this urgent need. Our paper analyzes these algorithms using both synthetic and real-world datasets, and shows that they are not effective in dealing with common data variations such as image translation or viewpoint change. To address this limitation, we propose a permutation-invariant cascaded attentional set operator (PICASO). The gist of PICASO is a cascade of multihead attention blocks with dynamic templates. The proposed operator is a stand-alone module that can be adapted and extended to serve different machine learning tasks. We demonstrate the utilities of PICASO in four diverse scenarios: (i) clustering, (ii) image classification under novel viewpoints, (iii) image anomaly detection, and (iv) state prediction. PICASO increases the SmallNORB image classification accuracy with novel viewpoints by about 10% points. For set anomaly detection on CelebA dataset, our model improves the areas under ROC and PR curves dataset by about 22% and 10%, respectively. For the state prediction on CLEVR dataset, it improves the AP by about 40%.

Pengyu Yuan, Wenyi Hu, Xuqing Wu et al.

We proposed a robust segmentation and picking workflow to solve the first arrival picking problem for seismic signal processing. Unlike traditional classification algorithm, image segmentation method can utilize the location information by outputting a prediction map which has the same size of the input image. A parameter-free nearest point picking algorithm is proposed to further improve the accuracy of the first arrival picking. The algorithm is test on synthetic clean data, synthetic noisy data, synthetic picking-disconnected data and field data. It performs well on all of them and the picking deviation reaches as low as 4.8ms per receiver. The first arrival picking problem is formulated as the contour detection problem. Similar to \cite{wu2019semi}, we use U-net to perform the segmentation as it is proven to be state-of-the-art in many image segmentation tasks. Particularly, a Lovasz loss instead of the traditional cross-entropy loss is used to train the network for a better segmentation performance. Lovasz loss is a surrogate loss for Jaccard index or the so-called intersection-over-union (IoU) score, which is often one of the most used metrics for segmentation tasks. In the picking part, we use a novel nearest point picking (NPP) method to take the advantage of the coherence of the first arrival picking among adjacent receivers. Our model is tested and validated on both synthetic and field data with harmonic noises. The main contributions of this paper are as follows: 1. Used Lovasz loss to directly optimize the IoU for segmentation task. Improvement over the cross-entropy loss with regard to the segmentation accuracy is verified by the test result. 2. Proposed a nearest point picking post processing method to overcome any defects left by the segmentation output. 3. Conducted noise analysis and verified the model with both noisy synthetic and field datasets.

S. Kevin Zhou, Hoang Ngan Le, Khoa Luu et al.

Deep reinforcement learning (DRL) augments the reinforcement learning framework, which learns a sequence of actions that maximizes the expected reward, with the representative power of deep neural networks. Recent works have demonstrated the great potential of DRL in medicine and healthcare. This paper presents a literature review of DRL in medical imaging. We start with a comprehensive tutorial of DRL, including the latest model-free and model-based algorithms. We then cover existing DRL applications for medical imaging, which are roughly divided into three main categories: (I) parametric medical image analysis tasks including landmark detection, object/lesion detection, registration, and view plane localization; (ii) solving optimization tasks including hyperparameter tuning, selecting augmentation strategies, and neural architecture search; and (iii) miscellaneous applications including surgical gesture segmentation, personalized mobile health intervention, and computational model personalization. The paper concludes with discussions of future perspectives.

Maoqiang Wu, Xinyue Zhang, Jiahao Ding et al.

Deep learning has attracted broad interest in healthcare and medical communities. However, there has been little research into the privacy issues created by deep networks trained for medical applications. Recently developed inference attack algorithms indicate that images and text records can be reconstructed by malicious parties that have the ability to query deep networks. This gives rise to the concern that medical images and electronic health records containing sensitive patient information are vulnerable to these attacks. This paper aims to attract interest from researchers in the medical deep learning community to this important problem. We evaluate two prominent inference attack models, namely, attribute inference attack and model inversion attack. We show that they can reconstruct real-world medical images and clinical reports with high fidelity. We then investigate how to protect patients' privacy using defense mechanisms, such as label perturbation and model perturbation. We provide a comparison of attack results between the original and the medical deep learning models with defenses. The experimental evaluations show that our proposed defense approaches can effectively reduce the potential privacy leakage of medical deep learning from the inference attacks.

Pengyu Yuan, Aryan Mobiny, Jahandar Jahanipour et al.

Deep Neural Networks (or DNNs) must constantly cope with distribution changes in the input data when the task of interest or the data collection protocol changes. Retraining a network from scratch to combat this issue poses a significant cost. Meta-learning aims to deliver an adaptive model that is sensitive to these underlying distribution changes, but requires many tasks during the meta-training process. In this paper, we propose a tAsk-auGmented actIve meta-LEarning (AGILE) method to efficiently adapt DNNs to new tasks by using a small number of training examples. AGILE combines a meta-learning algorithm with a novel task augmentation technique which we use to generate an initial adaptive model. It then uses Bayesian dropout uncertainty estimates to actively select the most difficult samples when updating the model to a new task. This allows AGILE to learn with fewer tasks and a few informative samples, achieving high performance with a limited dataset. We perform our experiments using the brain cell classification task and compare the results to a plain meta-learning model trained from scratch. We show that the proposed task-augmented meta-learning framework can learn to classify new cell types after a single gradient step with a limited number of training samples. We show that active learning with Bayesian uncertainty can further improve the performance when the number of training samples is extremely small. Using only 1% of the training data and a single update step, we achieved 90% accuracy on the new cell type classification task, a 50% points improvement over a state-of-the-art meta-learning algorithm.

Pietro Antonio Cicalese, Aryan Mobiny, Pengyu Yuan et al.

The classification of Antibody Mediated Rejection (AMR) in kidney transplant remains challenging even for experienced nephropathologists; this is partly because histological tissue stain analysis is often characterized by low inter-observer agreement and poor reproducibility. One of the implicated causes for inter-observer disagreement is the variability of tissue stain quality between (and within) pathology labs, coupled with the gradual fading of archival sections. Variations in stain colors and intensities can make tissue evaluation difficult for pathologists, ultimately affecting their ability to describe relevant morphological features. Being able to accurately predict the AMR status based on kidney histology images is crucial for improving patient treatment and care. We propose a novel pipeline to build robust deep neural networks for AMR classification based on StyPath, a histological data augmentation technique that leverages a light weight style-transfer algorithm as a means to reduce sample-specific bias. Each image was generated in 1.84 +- 0.03 seconds using a single GTX TITAN V gpu and pytorch, making it faster than other popular histological data augmentation techniques. We evaluated our model using a Monte Carlo (MC) estimate of Bayesian performance and generate an epistemic measure of uncertainty to compare both the baseline and StyPath augmented models. We also generated Grad-CAM representations of the results which were assessed by an experienced nephropathologist; we used this qualitative analysis to elucidate on the assumptions being made by each model. Our results imply that our style-transfer augmentation technique improves histological classification performance (reducing error from 14.8% to 11.5%) and generalization ability.

Aryan Mobiny, Pengyu Yuan, Pietro Antonio Cicalese et al.

Capsule Networks (CapsNets) have demonstrated to be a promising alternative to Convolutional Neural Networks (CNNs). However, they often fall short of state-of-the-art accuracies on large-scale high-dimensional datasets. We propose a Detail-Oriented Capsule Network (DECAPS) that combines the strength of CapsNets with several novel techniques to boost its classification accuracies. First, DECAPS uses an Inverted Dynamic Routing (IDR) mechanism to group lower-level capsules into heads before sending them to higher-level capsules. This strategy enables capsules to selectively attend to small but informative details within the data which may be lost during pooling operations in CNNs. Second, DECAPS employs a Peekaboo training procedure, which encourages the network to focus on fine-grained information through a second-level attention scheme. Finally, the distillation process improves the robustness of DECAPS by averaging over the original and attended image region predictions. We provide extensive experiments on the CheXpert and RSNA Pneumonia datasets to validate the effectiveness of DECAPS. Our networks achieve state-of-the-art accuracies not only in classification (increasing the average area under ROC curves from 87.24% to 92.82% on the CheXpert dataset) but also in the weakly-supervised localization of diseased areas (increasing average precision from 41.7% to 80% for the RSNA Pneumonia detection dataset).

Aryan Mobiny, Pietro Antonio Cicalese, Samira Zare et al.

Radiographic images offer an alternative method for the rapid screening and monitoring of Coronavirus Disease 2019 (COVID-19) patients. This approach is limited by the shortage of radiology experts who can provide a timely interpretation of these images. Motivated by this challenge, our paper proposes a novel learning architecture, called Detail-Oriented Capsule Networks (DECAPS), for the automatic diagnosis of COVID-19 from Computed Tomography (CT) scans. Our network combines the strength of Capsule Networks with several architecture improvements meant to boost classification accuracies. First, DECAPS uses an Inverted Dynamic Routing mechanism which increases model stability by preventing the passage of information from non-descriptive regions. Second, DECAPS employs a Peekaboo training procedure which uses a two-stage patch crop and drop strategy to encourage the network to generate activation maps for every target concept. The network then uses the activation maps to focus on regions of interest and combines both coarse and fine-grained representations of the data. Finally, we use a data augmentation method based on conditional generative adversarial networks to deal with the issue of data scarcity. Our model achieves 84.3% precision, 91.5% recall, and 96.1% area under the ROC curve, significantly outperforming state-of-the-art methods. We compare the performance of the DECAPS model with three experienced, well-trained thoracic radiologists and show that the architecture significantly outperforms them. While further studies on larger datasets are required to confirm this finding, our results imply that architectures like DECAPS can be used to assist radiologists in the CT scan mediated diagnosis of COVID-19.

Aryan Mobiny, Hien V. Nguyen, Supratik Moulik et al.

Deep neural networks (DNNs) have achieved state-of-the-art performances in many important domains, including medical diagnosis, security, and autonomous driving. In these domains where safety is highly critical, an erroneous decision can result in serious consequences. While a perfect prediction accuracy is not always achievable, recent work on Bayesian deep networks shows that it is possible to know when DNNs are more likely to make mistakes. Knowing what DNNs do not know is desirable to increase the safety of deep learning technology in sensitive applications. Bayesian neural networks attempt to address this challenge. However, traditional approaches are computationally intractable and do not scale well to large, complex neural network architectures. In this paper, we develop a theoretical framework to approximate Bayesian inference for DNNs by imposing a Bernoulli distribution on the model weights. This method, called MC-DropConnect, gives us a tool to represent the model uncertainty with little change in the overall model structure or computational cost. We extensively validate the proposed algorithm on multiple network architectures and datasets for classification and semantic segmentation tasks. We also propose new metrics to quantify the uncertainty estimates. This enables an objective comparison between MC-DropConnect and prior approaches. Our empirical results demonstrate that the proposed framework yields significant improvement in both prediction accuracy and uncertainty estimation quality compared to the state of the art.

Aryan Mobiny, Supratik Moulik, Hien Van Nguyen

In this paper, we investigate the effectiveness of deep learning techniques for lung nodule classification in computed tomography scans. Using less than 10,000 training examples, our deep networks perform two times better than a standard radiology software. Visualization of the networks' neurons reveals semantically meaningful features that are consistent with the clinical knowledge and radiologists' perception. Our paper also proposes a novel framework for rapidly adapting deep networks to the radiologists' feedback, or change in the data due to the shift in sensor's resolution or patient population. The classification accuracy of our approach remains above 80% while popular deep networks' accuracy is around chance. Finally, we provide in-depth analysis of our framework by asking a radiologist to examine important networks' features and perform blind re-labeling of networks' mistakes.