Kyunghyun Paeng

Bio: Kyunghyun Paeng is an academic researcher from KAIST. The author has contributed to research in topics: Medicine & Tumor-infiltrating lymphocytes. The author has an hindex of 7, co-authored 25 publications receiving 305 citations.

A Unified Framework for Tumor Proliferation Score Prediction in Breast Histopathology

Abstract: We present a unified framework to predict tumor proliferation scores from breast histopathology whole slide images. Our system offers a fully automated solution to predicting both a molecular data-based, and a mitosis counting-based tumor proliferation score. The framework integrates three modules, each fine-tuned to maximize the overall performance: An image processing component for handling whole slide images, a deep learning based mitosis detection network, and a proliferation scores prediction module. We have achieved 0.567 quadratic weighted Cohen’s kappa in mitosis counting-based score prediction and 0.652 F1-score in mitosis detection. On Spearman’s correlation coefficient, which evaluates predictive accuracy on the molecular data based score, the system obtained 0.6171. Our approach won first place in all of the three tasks in Tumor Proliferation Assessment Challenge 2016 which is MICCAI grand challenge.

A Robust and Effective Approach Towards Accurate Metastasis Detection and pN-stage Classification in Breast Cancer.

Abstract: Predicting TNM stage is the major determinant of breast cancer prognosis and treatment. The essential part of TNM stage classification is whether the cancer has metastasized to the regional lymph nodes (N-stage). Pathologic N-stage (pN-stage) is commonly performed by pathologists detecting metastasis in histological slides. However, this diagnostic procedure is prone to misinterpretation and would normally require extensive time by pathologists because of the sheer volume of data that needs a thorough review. Automated detection of lymph node metastasis and pN-stage prediction has a great potential to reduce their workload and help the pathologist. Recent advances in convolutional neural networks (CNN) have shown significant improvements in histological slide analysis, but accuracy is not optimized because of the difficulty in the handling of gigapixel images. In this paper, we propose a robust method for metastasis detection and pN-stage classification in breast cancer from multiple gigapixel pathology images in an effective way. pN-stage is predicted by combining patch-level CNN based metastasis detector and slide-level lymph node classifier. The proposed framework achieves a state-of-the-art quadratic weighted kappa score of 0.9203 on the Camelyon17 dataset, outperforming the previous winning method of the Camelyon17 challenge.

PseudoEdgeNet: Nuclei Segmentation only with Point Annotations

Abstract: Nuclei segmentation is one of the important tasks for whole slide image analysis in digital pathology. With the drastic advance of deep learning, recent deep networks have demonstrated successful performance of the nuclei segmentation task. However, a major bottleneck to achieving good performance is the cost for annotation. A large network requires a large number of segmentation masks, and this annotation task is given to pathologists, not the public. In this paper, we propose a weakly supervised nuclei segmentation method, which requires only point annotations for training. This method can scale to large training set as marking a point of a nucleus is much cheaper than the fine segmentation mask. To this end, we introduce a novel auxiliary network, called PseudoEdgeNet, which guides the segmentation network to recognize nuclei edges even without edge annotations. We evaluate our method with two public datasets, and the results demonstrate that the method consistently outperforms other weakly supervised methods.

Artificial Intelligence–Powered Spatial Analysis of Tumor-Infiltrating Lymphocytes as Complementary Biomarker for Immune Checkpoint Inhibition in Non–Small-Cell Lung Cancer

Abstract: PURPOSE Biomarkers on the basis of tumor-infiltrating lymphocytes (TIL) are potentially valuable in predicting the effectiveness of immune checkpoint inhibitors (ICI). However, clinical application remains challenging because of methodologic limitations and laborious process involved in spatial analysis of TIL distribution in whole-slide images (WSI). METHODS We have developed an artificial intelligence (AI)–powered WSI analyzer of TIL in the tumor microenvironment that can define three immune phenotypes (IPs): inflamed, immune-excluded, and immune-desert. These IPs were correlated with tumor response to ICI and survival in two independent cohorts of patients with advanced non–small-cell lung cancer (NSCLC). RESULTS Inflamed IP correlated with enrichment in local immune cytolytic activity, higher response rate, and prolonged progression-free survival compared with patients with immune-excluded or immune-desert phenotypes. At the WSI level, there was significant positive correlation between tumor proportion score (TPS) as determined by the AI model and control TPS analyzed by pathologists (P < .001). Overall, 44.0% of tumors were inflamed, 37.1% were immune-excluded, and 18.9% were immune-desert. Incidence of inflamed IP in patients with programmed death ligand-1 TPS at < 1%, 1%-49%, and ≥ 50% was 31.7%, 42.5%, and 56.8%, respectively. Median progression-free survival and overall survival were, respectively, 4.1 months and 24.8 months with inflamed IP, 2.2 months and 14.0 months with immune-excluded IP, and 2.4 months and 10.6 months with immune-desert IP. CONCLUSION The AI-powered spatial analysis of TIL correlated with tumor response and progression-free survival of ICI in advanced NSCLC. This is potentially a supplementary biomarker to TPS as determined by a pathologist.

Prognostic factors in breast cancer

Abstract: Prognostic factors are clinical and pathological features that give information in estimating the likely clinical outcome of an individual suffering from cancer. The author gives a short review of the most important prognostic factors in breast cancer. 376 breast cancer cases of a ten year interval in a county hospital are summarized. Traditional clinico-pathological parameters i.e. TNM and steroid receptor status are discussed. The more common karyotipic, oncogene and tumor suppressor gene alterations are outlined in the study. Methods for their detection are presented and their value in prognostication is reviewed. Emphasis was laid on steroid receptors, c-erpB-2, p53 and bcl-2 alterations. Genes responsible for heritable forms of increased breast cancer risk are briefly reviewed.

WILDS: A Benchmark of in-the-Wild Distribution Shifts

Abstract: Distribution shifts -- where the training distribution differs from the test distribution -- can substantially degrade the accuracy of machine learning (ML) systems deployed in the wild. Despite their ubiquity, these real-world distribution shifts are under-represented in the datasets widely used in the ML community today. To address this gap, we present WILDS, a curated collection of 8 benchmark datasets that reflect a diverse range of distribution shifts which naturally arise in real-world applications, such as shifts across hospitals for tumor identification; across camera traps for wildlife monitoring; and across time and location in satellite imaging and poverty mapping. On each dataset, we show that standard training results in substantially lower out-of-distribution than in-distribution performance, and that this gap remains even with models trained by existing methods for handling distribution shifts. This underscores the need for new training methods that produce models which are more robust to the types of distribution shifts that arise in practice. To facilitate method development, we provide an open-source package that automates dataset loading, contains default model architectures and hyperparameters, and standardizes evaluations. Code and leaderboards are available at this https URL.

Learning Loss for Active Learning

Abstract: The performance of deep neural networks improves with more annotated data. The problem is that the budget for annotation is limited. One solution to this is active learning, where a model asks human to annotate data that it perceived as uncertain. A variety of recent methods have been proposed to apply active learning to deep networks but most of them are either designed specific for their target tasks or computationally inefficient for large networks. In this paper, we propose a novel active learning method that is simple but task-agnostic, and works efficiently with the deep networks. We attach a small parametric module, named ``loss prediction module,'' to a target network, and learn it to predict target losses of unlabeled inputs. Then, this module can suggest data that the target model is likely to produce a wrong prediction. This method is task-agnostic as networks are learned from a single loss regardless of target tasks. We rigorously validate our method through image classification, object detection, and human pose estimation, with the recent network architectures. The results demonstrate that our method consistently outperforms the previous methods over the tasks.