Do Sharpness-based Optimizers Improve Generalization in Medical Image Analysis?

Effective clinical deployment of deep learning models in healthcare demands high generalization performance to ensure accurate diagnosis and treatment planning. In recent years, significant research has focused on improving the generalization of deep learning models by regularizing the sharpness of the loss landscape. Among the optimization approaches that explicitly minimize sharpness, Sharpness-Aware Minimization (SAM) has shown potential in enhancing generalization performance on general domain image datasets. This success has led to the development of several advanced sharpness-based algorithms aimed at addressing the limitations of SAM, such as Adaptive SAM, surrogate-Gap SAM, Weighted SAM, and Curvature Regularized SAM. These sharpness-based optimizers have shown improvements in model generalization compared to conventional stochastic gradient descent optimizers and their variants on general domain image datasets, but they have not been thoroughly evaluated on medical images. This work provides a review of recent sharpness-based methods for improving the generalization of deep learning networks and evaluates the methods performance on medical breast ultrasound images. Our findings indicate that the initial SAM method successfully enhances the generalization of various deep learning models. While Adaptive SAM improves generalization of convolutional neural networks, it fails to do so for vision transformers. Other sharpness-based optimizers, however, do not demonstrate consistent results. The results reveal that, contrary to findings in the non-medical domain, SAM is the only recommended sharpness-based optimizer that consistently improves generalization in medical image analysis, and further research is necessary to refine the variants of SAM to enhance generalization performance in this field

Causality Extraction from Nuclear Licensee Event Reports Using a Hybrid Framework

Industry-wide nuclear power plant operating experience is a critical source of raw data for performing parameter estimations in reliability and risk models. Much operating experience information pertains to failure events and is stored as reports containing unstructured data, such as narratives. Event reports are essential for understanding how failures are initiated and propagated, including the numerous causal relations involved. Causal relation extraction using deep learning represents a significant frontier in the field of natural language processing (NLP), and is crucial since it enables the interpretation of intricate narratives and connections contained within vast amounts of written information. This paper proposed a hybrid framework for causality detection and extraction from nuclear licensee event reports. The main contributions include: (1) we compiled an LER corpus with 20,129 text samples for causality analysis, (2) developed an interactive tool for labeling cause effect pairs, (3) built a deep-learning-based approach for causal relation detection, and (4) developed a knowledge based cause-effect extraction approach.

A2DMN: Anatomy-Aware Dilated Multiscale Network for Breast Ultrasound Semantic Segmentation

In recent years, convolutional neural networks for semantic segmentation of breast ultrasound (BUS) images have shown great success; however, two major challenges still exist. 1) Most current approaches inherently lack the ability to utilize tissue anatomy, resulting in misclassified image regions. 2) They struggle to produce accurate boundaries due to the repeated down-sampling operations. To address these issues, we propose a novel breast anatomy-aware network for capturing fine image details and a new smoothness term that encodes breast anatomy. It incorporates context information across multiple spatial scales to generate more accurate semantic boundaries. Extensive experiments are conducted to compare the proposed method and eight state-of-the-art approaches using a BUS dataset with 325 images. The results demonstrate the proposed method significantly improves the segmentation of the muscle, mammary, and tumor classes and produces more accurate fine details of tissue boundaries.

Uncertainty Quantification in Multivariable Regression for Material Property Prediction with Bayesian Neural Networks

With the increased use of data-driven approaches and machine learning-based methods in material science, the importance of reliable uncertainty quantification (UQ) of the predicted variables for informed decision-making cannot be overstated. UQ in material property prediction poses unique challenges, including the multi-scale and multi-physics nature of advanced materials, intricate interactions between numerous factors, limited availability of large curated datasets for model training, etc. Recently, Bayesian Neural Networks (BNNs) have emerged as a promising approach for UQ, offering a probabilistic framework for capturing uncertainties within neural networks. In this work, we introduce an approach for UQ within physics-informed BNNs, which integrates knowledge from governing laws in material modeling to guide the models toward physically consistent predictions. To evaluate the effectiveness of this approach, we present case studies for predicting the creep rupture life of steel alloys. Experimental validation with three datasets of collected measurements from creep tests demonstrates the ability of BNNs to produce accurate point and uncertainty estimates that are competitive or exceed the performance of the conventional method of Gaussian Process Regression. Similarly, we evaluated the suitability of BNNs for UQ in an active learning application and reported competitive performance. The most promising framework for creep life prediction is BNNs based on Markov Chain Monte Carlo approximation of the posterior distribution of network parameters, as it provided more reliable results in comparison to BNNs based on variational inference approximation or related NNs with probabilistic outputs. The codes are available at: https://github.com/avakanski/Creep-uncertainty-quantification.

Post-Hoc Explainability of BI-RADS Descriptors in a Multi-task Framework for Breast Cancer Detection and Segmentation

Despite recent medical advancements, breast cancer remains one of the most prevalent and deadly diseases among women. Although machine learning-based Computer-Aided Diagnosis (CAD) systems have shown potential to assist radiologists in analyzing medical images, the opaque nature of the best-performing CAD systems has raised concerns about their trustworthiness and interpretability. This paper proposes MT-BI-RADS, a novel explainable deep learning approach for tumor detection in Breast Ultrasound (BUS) images. The approach offers three levels of explanations to enable radiologists to comprehend the decision-making process in predicting tumor malignancy. Firstly, the proposed model outputs the BI-RADS categories used for BUS image analysis by radiologists. Secondly, the model employs multi-task learning to concurrently segment regions in images that correspond to tumors. Thirdly, the proposed approach outputs quantified contributions of each BI-RADS descriptor toward predicting the benign or malignant class using post-hoc explanations with Shapley Values.

Breast Ultrasound Tumor Classification Using a Hybrid Multitask CNN-Transformer Network

Capturing global contextual information plays a critical role in breast ultrasound (BUS) image classification. Although convolutional neural networks (CNNs) have demonstrated reliable performance in tumor classification, they have inherent limitations for modeling global and long-range dependencies due to the localized nature of convolution operations. Vision Transformers have an improved capability of capturing global contextual information but may distort the local image patterns due to the tokenization operations. In this study, we proposed a hybrid multitask deep neural network called Hybrid-MT-ESTAN, designed to perform BUS tumor classification and segmentation using a hybrid architecture composed of CNNs and Swin Transformer components. The proposed approach was compared to nine BUS classification methods and evaluated using seven quantitative metrics on a dataset of 3,320 BUS images. The results indicate that Hybrid-MT-ESTAN achieved the highest accuracy, sensitivity, and F1 score of 82.7%, 86.4%, and 86.0%, respectively.

Multi-Level Global Context Cross Consistency Model for Semi-Supervised Ultrasound Image Segmentation with Diffusion Model

Medical image segmentation is a critical step in computer-aided diagnosis, and convolutional neural networks are popular segmentation networks nowadays. However, the inherent local operation characteristics make it difficult to focus on the global contextual information of lesions with different positions, shapes, and sizes. Semi-supervised learning can be used to learn from both labeled and unlabeled samples, alleviating the burden of manual labeling. However, obtaining a large number of unlabeled images in medical scenarios remains challenging. To address these issues, we propose a Multi-level Global Context Cross-consistency (MGCC) framework that uses images generated by a Latent Diffusion Model (LDM) as unlabeled images for semi-supervised learning. The framework involves of two stages. In the first stage, a LDM is used to generate synthetic medical images, which reduces the workload of data annotation and addresses privacy concerns associated with collecting medical data. In the second stage, varying levels of global context noise perturbation are added to the input of the auxiliary decoder, and output consistency is maintained between decoders to improve the representation ability. Experiments conducted on open-source breast ultrasound and private thyroid ultrasound datasets demonstrate the effectiveness of our framework in bridging the probability distribution and the semantic representation of the medical image. Our approach enables the effective transfer of probability distribution knowledge to the segmentation network, resulting in improved segmentation accuracy. The code is available at https://github.com/FengheTan9/Multi-Level-Global-Context-Cross-Consistency.

CFR-ICL: Cascade-Forward Refinement with Iterative Click Loss for Interactive Image Segmentation

The click-based interactive segmentation aims to extract the object of interest from an image with the guidance of user clicks. Recent work has achieved great overall performance by employing the segmentation from the previous output. However, in most state-of-the-art approaches, 1) the inference stage involves inflexible heuristic rules and a separate refinement model; and 2) the training cannot balance the number of user clicks and model performance. To address the challenges, we propose a click-based and mask-guided interactive image segmentation framework containing three novel components: Cascade-Forward Refinement (CFR), Iterative Click Loss (ICL), and SUEM image augmentation. The proposed ICL allows model training to improve segmentation and reduce user interactions simultaneously. The CFR offers a unified inference framework to generate segmentation results in a coarse-to-fine manner. The proposed SUEM augmentation is a comprehensive way to create large and diverse training sets for interactive image segmentation. Extensive experiments demonstrate the state-of-the-art performance of the proposed approach on five public datasets. Remarkably, our model achieves an average of 2.9 and 7.5 clicks of NoC@95 on the Berkeley and DAVIS sets, respectively, improving by 33.2% and 15.5% over the previous state-of-the-art results. The code and trained model are available at https://github.com/TitorX/CFR-ICL-Interactive-Segmentation.

An Efficient Instance Segmentation Approach for Extracting Fission Gas Bubbles on U-10Zr Annular Fuel

U-10Zr-based nuclear fuel is pursued as a primary candidate for next-generation sodium-cooled fast reactors. However, more advanced characterization and analysis are needed to form a fundamental understating of the fuel performance, and make U-10Zr fuel qualify for commercial use. The movement of lanthanides across the fuel section from the hot fuel center to the cool cladding surface is one of the key factors to affect fuel performance. In the advanced annular U-10Zr fuel, the lanthanides present as fission gas bubbles. Due to a lack of annotated data, existing literature utilized a multiple-threshold method to separate the bubbles and calculate bubble statistics on an annular fuel. However, the multiple-threshold method cannot achieve robust performance on images with different qualities and contrasts, and cannot distinguish different bubbles. This paper proposes a hybrid framework for efficient bubble segmentation. We develop a bubble annotation tool and generate the first fission gas bubble dataset with more than 3000 bubbles from 24 images. A multi-task deep learning network integrating U-Net and ResNet is designed to accomplish instance-level bubble segmentation. Combining the segmentation results and image processing step achieves the best recall ratio of more than 90% with very limited annotated data. Our model shows outstanding improvement by comparing the previously proposed thresholding method. The proposed method has promising to generate a more accurate quantitative analysis of fission gas bubbles on U-10Zr annular fuels. The results will contribute to identifying the bubbles with lanthanides and finally build the relationship between the thermal gradation and lanthanides movements of U-10Zr annular fuels. Mover, the deep learning model is applicable to other similar material micro-structure segmentation tasks.

Enhanced Sharp-GAN For Histopathology Image Synthesis

Histopathology image synthesis aims to address the data shortage issue in training deep learning approaches for accurate cancer detection. However, existing methods struggle to produce realistic images that have accurate nuclei boundaries and less artifacts, which limits the application in downstream tasks. To address the challenges, we propose a novel approach that enhances the quality of synthetic images by using nuclei topology and contour regularization. The proposed approach uses the skeleton map of nuclei to integrate nuclei topology and separate touching nuclei. In the loss function, we propose two new contour regularization terms that enhance the contrast between contour and non-contour pixels and increase the similarity between contour pixels. We evaluate the proposed approach on the two datasets using image quality metrics and a downstream task (nuclei segmentation). The proposed approach outperforms Sharp-GAN in all four image quality metrics on two datasets. By integrating 6k synthetic images from the proposed approach into training, a nuclei segmentation model achieves the state-of-the-art segmentation performance on TNBC dataset and its detection quality (DQ), segmentation quality (SQ), panoptic quality (PQ), and aggregated Jaccard index (AJI) is 0.855, 0.863, 0.691, and 0.683, respectively.