Wonkyung Jung

Jeongun Ryu, Aaron Valero Puche, JaeWoong Shin et al.

Cell detection is a fundamental task in computational pathology that can be used for extracting high-level medical information from whole-slide images. For accurate cell detection, pathologists often zoom out to understand the tissue-level structures and zoom in to classify cells based on their morphology and the surrounding context. However, there is a lack of efforts to reflect such behaviors by pathologists in the cell detection models, mainly due to the lack of datasets containing both cell and tissue annotations with overlapping regions. To overcome this limitation, we propose and publicly release OCELOT, a dataset purposely dedicated to the study of cell-tissue relationships for cell detection in histopathology. OCELOT provides overlapping cell and tissue annotations on images acquired from multiple organs. Within this setting, we also propose multi-task learning approaches that benefit from learning both cell and tissue tasks simultaneously. When compared against a model trained only for the cell detection task, our proposed approaches improve cell detection performance on 3 datasets: proposed OCELOT, public TIGER, and internal CARP datasets. On the OCELOT test set in particular, we show up to 6.79 improvement in F1-score. We believe the contributions of this paper, including the release of the OCELOT dataset at https://lunit-io.github.io/research/publications/ocelot are a crucial starting point toward the important research direction of incorporating cell-tissue relationships in computation pathology.

Wonkyung Jung, Daejin Jung, and Byeongho Kim et al.

Batch Normalization (BN) has become a core design block of modern Convolutional Neural Networks (CNNs). A typical modern CNN has a large number of BN layers in its lean and deep architecture. BN requires mean and variance calculations over each mini-batch during training. Therefore, the existing memory access reduction techniques, such as fusing multiple CONV layers, are not effective for accelerating BN due to their inability to optimize mini-batch related calculations during training. To address this increasingly important problem, we propose to restructure BN layers by first splitting a BN layer into two sub-layers (fission) and then combining the first sub-layer with its preceding CONV layer and the second sub-layer with the following activation and CONV layers (fusion). The proposed solution can significantly reduce main-memory accesses while training the latest CNN models, and the experiments on a chip multiprocessor show that the proposed BN restructuring can improve the performance of DenseNet-121 by 25.7%.