DGM-DR: Domain Generalization with Mutual Information Regularized Diabetic Retinopathy Classification

The domain shift between training and testing data presents a significant challenge for training generalizable deep learning models. As a consequence, the performance of models trained with the independent and identically distributed (i.i.d) assumption deteriorates when deployed in the real world. This problem is exacerbated in the medical imaging context due to variations in data acquisition across clinical centers, medical apparatus, and patients. Domain generalization (DG) aims to address this problem by learning a model that generalizes well to any unseen target domain. Many domain generalization techniques were unsuccessful in learning domain-invariant representations due to the large domain shift. Furthermore, multiple tasks in medical imaging are not yet extensively studied in existing literature when it comes to DG point of view. In this paper, we introduce a DG method that re-establishes the model objective function as a maximization of mutual information with a large pretrained model to the medical imaging field. We re-visit the problem of DG in Diabetic Retinopathy (DR) classification to establish a clear benchmark with a correct model selection strategy and to achieve robust domain-invariant representation for an improved generalization. Moreover, we conduct extensive experiments on public datasets to show that our proposed method consistently outperforms the previous state-of-the-art by a margin of 5.25% in average accuracy and a lower standard deviation. Source code available at https://github.com/BioMedIA-MBZUAI/DGM-DR

PECon: Contrastive Pretraining to Enhance Feature Alignment between CT and EHR Data for Improved Pulmonary Embolism Diagnosis

Previous deep learning efforts have focused on improving the performance of Pulmonary Embolism(PE) diagnosis from Computed Tomography (CT) scans using Convolutional Neural Networks (CNN). However, the features from CT scans alone are not always sufficient for the diagnosis of PE. CT scans along with electronic heath records (EHR) can provide a better insight into the patients condition and can lead to more accurate PE diagnosis. In this paper, we propose Pulmonary Embolism Detection using Contrastive Learning (PECon), a supervised contrastive pretraining strategy that employs both the patients CT scans as well as the EHR data, aiming to enhance the alignment of feature representations between the two modalities and leverage information to improve the PE diagnosis. In order to achieve this, we make use of the class labels and pull the sample features of the same class together, while pushing away those of the other class. Results show that the proposed work outperforms the existing techniques and achieves state-of-the-art performance on the RadFusion dataset with an F1-score of 0.913, accuracy of 0.90 and an AUROC of 0.943. Furthermore, we also explore the explainability of our approach in comparison to other methods. Our code is publicly available at https://github.com/BioMedIA-MBZUAI/PECon.

SEDA: Self-Ensembling ViT with Defensive Distillation and Adversarial Training for robust Chest X-rays Classification

Deep Learning methods have recently seen increased adoption in medical imaging applications. However, elevated vulnerabilities have been explored in recent Deep Learning solutions, which can hinder future adoption. Particularly, the vulnerability of Vision Transformer (ViT) to adversarial, privacy, and confidentiality attacks raise serious concerns about their reliability in medical settings. This work aims to enhance the robustness of self-ensembling ViTs for the tuberculosis chest x-ray classification task. We propose Self-Ensembling ViT with defensive Distillation and Adversarial training (SEDA). SEDA utilizes efficient CNN blocks to learn spatial features with various levels of abstraction from feature representations extracted from intermediate ViT blocks, that are largely unaffected by adversarial perturbations. Furthermore, SEDA leverages adversarial training in combination with defensive distillation for improved robustness against adversaries. Training using adversarial examples leads to better model generalizability and improves its ability to handle perturbations. Distillation using soft probabilities introduces uncertainty and variation into the output probabilities, making it more difficult for adversarial and privacy attacks. Extensive experiments performed with the proposed architecture and training paradigm on publicly available Tuberculosis x-ray dataset shows SOTA efficacy of SEDA compared to SEViT in terms of computational efficiency with 70x times lighter framework and enhanced robustness of +9%.

LegoNet: Alternating Model Blocks for Medical Image Segmentation

Since the emergence of convolutional neural networks (CNNs), and later vision transformers (ViTs), the common paradigm for model development has always been using a set of identical block types with varying parameters/hyper-parameters. To leverage the benefits of different architectural designs (e.g. CNNs and ViTs), we propose to alternate structurally different types of blocks to generate a new architecture, mimicking how Lego blocks can be assembled together. Using two CNN-based and one SwinViT-based blocks, we investigate three variations to the so-called LegoNet that applies the new concept of block alternation for the segmentation task in medical imaging. We also study a new clinical problem which has not been investigated before, namely the right internal mammary artery (RIMA) and perivascular space segmentation from computed tomography angiography (CTA) which has demonstrated a prognostic value to major cardiovascular outcomes. We compare the model performance against popular CNN and ViT architectures using two large datasets (e.g. achieving 0.749 dice similarity coefficient (DSC) on the larger dataset). We evaluate the performance of the model on three external testing cohorts as well, where an expert clinician made corrections to the model segmented results (DSC>0.90 for the three cohorts). To assess our proposed model for suitability in clinical use, we perform intra- and inter-observer variability analysis. Finally, we investigate a joint self-supervised learning approach to assess its impact on model performance. The code and the pretrained model weights will be available upon acceptance.

Prompt-based Tuning of Transformer Models for Multi-Center Medical Image Segmentation

Medical image segmentation is a vital healthcare endeavor requiring precise and efficient models for appropriate diagnosis and treatment. Vision transformer-based segmentation models have shown great performance in accomplishing this task. However, to build a powerful backbone, the self-attention block of ViT requires large-scale pre-training data. The present method of modifying pre-trained models entails updating all or some of the backbone parameters. This paper proposes a novel fine-tuning strategy for adapting a pretrained transformer-based segmentation model on data from a new medical center. This method introduces a small number of learnable parameters, termed prompts, into the input space (less than 1\% of model parameters) while keeping the rest of the model parameters frozen. Extensive studies employing data from new unseen medical centers show that prompts-based fine-tuning of medical segmentation models provides excellent performance on the new center data with a negligible drop on the old centers. Additionally, our strategy delivers great accuracy with minimum re-training on new center data, significantly decreasing the computational and time costs of fine-tuning pre-trained models.

Surgical tool classification and localization: results and methods from the MICCAI 2022 SurgToolLoc challenge

The ability to automatically detect and track surgical instruments in endoscopic videos can enable transformational interventions. Assessing surgical performance and efficiency, identifying skilled tool use and choreography, and planning operational and logistical aspects of OR resources are just a few of the applications that could benefit. Unfortunately, obtaining the annotations needed to train machine learning models to identify and localize surgical tools is a difficult task. Annotating bounding boxes frame-by-frame is tedious and time-consuming, yet large amounts of data with a wide variety of surgical tools and surgeries must be captured for robust training. Moreover, ongoing annotator training is needed to stay up to date with surgical instrument innovation. In robotic-assisted surgery, however, potentially informative data like timestamps of instrument installation and removal can be programmatically harvested. The ability to rely on tool installation data alone would significantly reduce the workload to train robust tool-tracking models. With this motivation in mind we invited the surgical data science community to participate in the challenge, SurgToolLoc 2022. The goal was to leverage tool presence data as weak labels for machine learning models trained to detect tools and localize them in video frames with bounding boxes. We present the results of this challenge along with many of the team's efforts. We conclude by discussing these results in the broader context of machine learning and surgical data science. The training data used for this challenge consisting of 24,695 video clips with tool presence labels is also being released publicly and can be accessed at https://console.cloud.google.com/storage/browser/isi-surgtoolloc-2022.

Improving Performance of Private Federated Models in Medical Image Analysis

Federated learning (FL) is a distributed machine learning (ML) approach that allows data to be trained without being centralized. This approach is particularly beneficial for medical applications because it addresses some key challenges associated with medical data, such as privacy, security, and data ownership. On top of that, FL can improve the quality of ML models used in medical applications. Medical data is often diverse and can vary significantly depending on the patient population, making it challenging to develop ML models that are accurate and generalizable. FL allows medical data to be used from multiple sources, which can help to improve the quality and generalizability of ML models. Differential privacy (DP) is a go-to algorithmic tool to make this process secure and private. In this work, we show that the model performance can be further improved by employing local steps, a popular approach to improving the communication efficiency of FL, and tuning the number of communication rounds. Concretely, given the privacy budget, we show an optimal number of local steps and communications rounds. We provide theoretical motivations further corroborated with experimental evaluations on real-world medical imaging tasks.

MGMT promoter methylation status prediction using MRI scans? An extensive experimental evaluation of deep learning models

The number of studies on deep learning for medical diagnosis is expanding, and these systems are often claimed to outperform clinicians. However, only a few systems have shown medical efficacy. From this perspective, we examine a wide range of deep learning algorithms for the assessment of glioblastoma - a common brain tumor in older adults that is lethal. Surgery, chemotherapy, and radiation are the standard treatments for glioblastoma patients. The methylation status of the MGMT promoter, a specific genetic sequence found in the tumor, affects chemotherapy's effectiveness. MGMT promoter methylation improves chemotherapy response and survival in several cancers. MGMT promoter methylation is determined by a tumor tissue biopsy, which is then genetically tested. This lengthy and invasive procedure increases the risk of infection and other complications. Thus, researchers have used deep learning models to examine the tumor from brain MRI scans to determine the MGMT promoter's methylation state. We employ deep learning models and one of the largest public MRI datasets of 585 participants to predict the methylation status of the MGMT promoter in glioblastoma tumors using MRI scans. We test these models using Grad-CAM, occlusion sensitivity, feature visualizations, and training loss landscapes. Our results show no correlation between these two, indicating that external cohort data should be used to verify these models' performance to assure the accuracy and reliability of deep learning systems in cancer diagnosis.

CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

Weakly Unsupervised Domain Adaptation for Vestibular Schwannoma Segmentation

Vestibular schwannoma (VS) is a non-cancerous tumor located next to the ear that can cause hearing loss. Most brain MRI images acquired from patients are contrast-enhanced T1 (ceT1), with a growing interest in high-resolution T2 images (hrT2) to replace ceT1, which involves the use of a contrast agent. As hrT2 images are currently scarce, it is less likely to train robust machine learning models to segment VS or other brain structures. In this work, we propose a weakly supervised machine learning approach that learns from only ceT1 scans and adapts to segment two structures from hrT2 scans: the VS and the cochlea from the crossMoDA dataset. Our model 1) generates fake hrT2 scans from ceT1 images and segmentation masks, 2) is trained using the fake hrT2 scans, 3) predicts the augmented real hrT2 scans, and 4) is retrained again using both the fake and real hrT2. The final result of this model has been computed on an unseen testing dataset provided by the 2022 crossMoDA challenge organizers. The mean dice score and average symmetric surface distance (ASSD) are 0.78 and 0.46, respectively. The predicted segmentation masks achieved a dice score of 0.83 and an ASSD of 0.56 on the VS, and a dice score of 0.74 and an ASSD of 0.35 on the cochleas.