Yaoru Luo

Jiaxing Huang, Yanfeng Zhou, Yaoru Luo et al.

Accurate segmentation of long and thin tubular structures is required in a wide variety of areas such as biology, medicine, and remote sensing. The complex topology and geometry of such structures often pose significant technical challenges. A fundamental property of such structures is their topological self-similarity, which can be quantified by fractal features such as fractal dimension (FD). In this study, we incorporate fractal features into a deep learning model by extending FD to the pixel-level using a sliding window technique. The resulting fractal feature maps (FFMs) are then incorporated as additional input to the model and additional weight in the loss function to enhance segmentation performance by utilizing the topological self-similarity. Moreover, we extend the U-Net architecture by incorporating an edge decoder and a skeleton decoder to improve boundary accuracy and skeletal continuity of segmentation, respectively. Extensive experiments on five tubular structure datasets validate the effectiveness and robustness of our approach. Furthermore, the integration of FFMs with other popular segmentation models such as HR-Net also yields performance enhancement, suggesting FFM can be incorporated as a plug-in module with different model architectures. Code and data are openly accessible at https://github.com/cbmi-group/FFM-Multi-Decoder-Network.

Yiming Huang, Guole Liu, Yaoru Luo et al.

The scarcity of annotated data, particularly for rare diseases, limits the variability of training data and the range of detectable lesions, presenting a significant challenge for supervised anomaly detection in medical imaging. To solve this problem, we propose a novel unsupervised method for medical image anomaly detection: Attention-Augmented Differentiable top-k Feature Adaptation (ADFA). The method utilizes Wide-ResNet50-2 (WR50) network pre-trained on ImageNet to extract initial feature representations. To reduce the channel dimensionality while preserving relevant channel information, we employ an attention-augmented patch descriptor on the extracted features. We then apply differentiable top-k feature adaptation to train the patch descriptor, mapping the extracted feature representations to a new vector space, enabling effective detection of anomalies. Experiments show that ADFA outperforms state-of-the-art (SOTA) methods on multiple challenging medical image datasets, confirming its effectiveness in medical anomaly detection.

Yaoru Luo, Guole Liu, Yuanhao Guo et al.

Supervised training of deep neural networks (DNNs) by noisy labels has been studied extensively in image classification but much less in image segmentation. Our understanding of the learning behavior of DNNs trained by noisy segmentation labels remains limited. We address this deficiency in both binary segmentation of biological microscopy images and multi-class segmentation of natural images. We classify segmentation labels according to their noise transition matrices (NTMs) and compare performance of DNNs trained by different types of labels. When we randomly sample a small fraction (e.g., 10%) or flip a large fraction (e.g., 90%) of the ground-truth labels to train DNNs, their segmentation performance remains largely unchanged. This indicates that DNNs learn structures hidden in labels rather than pixel-level labels per se in their supervised training for semantic segmentation. We call these hidden structures meta-structures. When labels with different perturbations to the meta-structures are used to train DNNs, their performance in feature extraction and segmentation degrades consistently. In contrast, addition of meta-structure information substantially improves performance of an unsupervised model in binary semantic segmentation. We formulate meta-structures mathematically as spatial density distributions. We show theoretically and experimentally how this formulation explains key observed learning behavior of DNNs.

Tianjie Yang, Yaoru Luo, Wei Ji et al.

Super-resolution microscopy overcomes the diffraction limit of conventional light microscopy in spatial resolution. By providing novel spatial or spatio-temporal information on biological processes at nanometer resolution with molecular specificity, it plays an increasingly important role in life sciences. However, its technical limitations require trade-offs to balance its spatial resolution, temporal resolution, and light exposure of samples. Recently, deep learning has achieved breakthrough performance in many image processing and computer vision tasks. It has also shown great promise in pushing the performance envelope of super-resolution microscopy. In this brief Review, we survey recent advances in using deep learning to enhance performance of super-resolution microscopy. We focus primarily on how deep learning ad-vances reconstruction of super-resolution images. Related key technical challenges are discussed. Despite the challenges, deep learning is set to play an indispensable and transformative role in the development of super-resolution microscopy. We conclude with an outlook on how deep learning could shape the future of this new generation of light microscopy technology.

Yaoru Luo, Guole Liu, Yuanhao Guo et al.

How deep neural networks (DNNs) learn from noisy labels has been studied extensively in image classification but much less in image segmentation. So far, our understanding of the learning behavior of DNNs trained by noisy segmentation labels remains limited. In this study, we address this deficiency in both binary segmentation of biological microscopy images and multi-class segmentation of natural images. We generate extremely noisy labels by randomly sampling a small fraction (e.g., 10%) or flipping a large fraction (e.g., 90%) of the ground truth labels. When trained with these noisy labels, DNNs provide largely the same segmentation performance as trained by the original ground truth. This indicates that DNNs learn structures hidden in labels rather than pixel-level labels per se in their supervised training for semantic segmentation. We refer to these hidden structures in labels as meta-structures. When DNNs are trained by labels with different perturbations to the meta-structure, we find consistent degradation in their segmentation performance. In contrast, incorporation of meta-structure information substantially improves performance of an unsupervised segmentation model developed for binary semantic segmentation. We define meta-structures mathematically as spatial density distributions and show both theoretically and experimentally how this formulation explains key observed learning behavior of DNNs.