Sol Lee

Kihyun Lee, Jinsub Park, Soyeon Choi et al.

Scanning transmission electron microscopy (STEM) is an indispensable tool for atomic-resolution structural analysis for a wide range of materials. The conventional analysis of STEM images is an extensive hands-on process, which limits efficient handling of high-throughput data. Here we apply a fully convolutional network (FCN) for identification of important structural features of two-dimensional crystals. ResUNet, a type of FCN, is utilized in identifying sulfur vacancies and polymorph types of ${MoS_2}$ from atomic resolution STEM images. Efficient models are achieved based on training with simulated images in the presence of different levels of noise, aberrations, and carbon contamination. The accuracy of the FCN models toward extensive experimental STEM images is comparable to that of careful hands-on analysis. Our work provides a guideline on best practices to train a deep learning model for STEM image analysis and demonstrates FCN's application for efficient processing of a large volume of STEM data.

Sungrae Hong, Jiwon Jeong, Jisu Shin et al.

Multiple Instance Learning (MIL) has emerged as a promising paradigm for Whole Slide Image (WSI) diagnosis, offering effective learning with limited annotations. However, existing MIL frameworks overlook diagnostic priorities and fail to differentiate the severity of misclassifications in multiclass, leaving clinically critical errors unaddressed. We propose a mistake-severity-aware training strategy that organizes diagnostic classes into a hierarchical structure, with each level optimized using a severity-weighted cross-entropy loss that penalizes high-severity misclassifications more strongly. Additionally, hierarchical consistency is enforced through probabilistic alignment, a semantic feature remix applied to the instance bag to robustly train class priority and accommodate clinical cases involving multiple symptoms. An asymmetric Mikel's Wheel-based metric is also introduced to quantify the severity of errors specific to medical fields. Experiments on challenging public and real-world in-house datasets demonstrate that our approach significantly mitigates critical errors in MIL diagnosis compared to existing methods. We present additional experimental results on natural domain data to demonstrate the generalizability of our proposed method beyond medical contexts.

Sungrae Hong, Sol Lee, Jisu Shin et al.

With the increasing demand for histopathological specimen examination and diagnostic reporting, Multiple Instance Learning (MIL) has received heightened research focus as a viable solution for AI-centric diagnostic aid. Recently, to improve its performance and make it work more like a pathologist, several MIL approaches based on the use of multiple-resolution images have been proposed, delivering often higher performance than those that use single-resolution images. Despite impressive recent developments of multiple-resolution MIL, previous approaches only focus on improving performance, thereby lacking research on well-calibrated MIL that clinical experts can rely on for trustworthy diagnostic results. In this study, we propose Uncertainty-Focused Calibrated MIL (UFC-MIL), which more closely mimics the pathologists' examination behaviors while providing calibrated diagnostic predictions, using multiple images with different resolutions. UFC-MIL includes a novel patch-wise loss that learns the latent patterns of instances and expresses their uncertainty for classification. Also, the attention-based architecture with a neighbor patch aggregation module collects features for the classifier. In addition, aggregated predictions are calibrated through patch-level uncertainty without requiring multiple iterative inferences, which is a key practical advantage. Against challenging public datasets, UFC-MIL shows superior performance in model calibration while achieving classification accuracy comparable to that of state-of-the-art methods.

Sungrae Hong, Kyungeun Kim, Juhyeon Kim et al.

Multiple Instance Learning (MIL) is increasingly being used as a support tool within clinical settings for pathological diagnosis decisions, achieving high performance and removing the annotation burden. However, existing approaches for clinical MIL tasks have not adequately addressed the priority issues that exist in relation to pathological symptoms and diagnostic classes, causing MIL models to ignore priority among classes. To overcome this clinical limitation of MIL, we propose a new method that addresses priority issues using two hierarchies: vertical inter-hierarchy and horizontal intra-hierarchy. The proposed method aligns MIL predictions across each hierarchical level and employs an implicit feature re-usability during training to facilitate clinically more serious classes within the same level. Experiments with real-world patient data show that the proposed method effectively reduces misdiagnosis and prioritizes more important symptoms in multiclass scenarios. Further analysis verifies the efficacy of the proposed components and qualitatively confirms the MIL predictions against challenging cases with multiple symptoms.

Sungrae Hong, Sol Lee, Mun Yong Yi

Medical AI diagnosis including histopathology segmentation has derived benefits from the recent development of deep learning technology. However, deep learning itself requires a large amount of training data and the medical image segmentation masking, in particular, requires an extremely high cost due to the shortage of medical specialists. To mitigate this issue, we propose a new data augmentation method built upon the conventional Copy and Paste (CP) augmentation technique, called CP-Dilatation, and apply it to histopathology image segmentation. To the well-known traditional CP technique, the proposed method adds a dilation operation that can preserve the boundary context information of the malignancy, which is important in histopathological image diagnosis, as the boundary between the malignancy and its margin is mostly unclear and a significant context exists in the margin. In our experiments using histopathology benchmark datasets, the proposed method was found superior to the other state-of-the-art baselines chosen for comparison.

Sungrae Hong, Hyeongmin Park, Youngsin Ko et al.

As the frontline data for cancer diagnosis, microscopic pathology images are fundamental for providing patients with rapid and accurate treatment. However, despite their practical value, the deep learning community has largely overlooked their usage. This paper proposes a novel approach to classifying microscopy images as time series data, addressing the unique challenges posed by their manual acquisition and weakly labeled nature. The proposed method fits image sequences of varying lengths to a fixed-length target by leveraging Dynamic Time-series Warping (DTW). Attention-based pooling is employed to predict the class of the case simultaneously. We demonstrate the effectiveness of our approach by comparing performance with various baselines and showcasing the benefits of using various inference strategies in achieving stable and reliable results. Ablation studies further validate the contribution of each component. Our approach contributes to medical image analysis by not only embracing microscopic images but also lifting them to a trustworthy level of performance.