Positive-unlabeled learning for binary and multi-class cell detection in histopathology images with incomplete annotations

Cell detection in histopathology images is of great interest to clinical practice and research, and convolutional neural networks (CNNs) have achieved remarkable cell detection results. Typically, to train CNN-based cell detection models, every positive instance in the training images needs to be annotated, and instances that are not labeled as positive are considered negative samples. However, manual cell annotation is complicated due to the large number and diversity of cells, and it can be difficult to ensure the annotation of every positive instance. In many cases, only incomplete annotations are available, where some of the positive instances are annotated and the others are not, and the classification loss term for negative samples in typical network training becomes incorrect. In this work, to address this problem of incomplete annotations, we propose to reformulate the training of the detection network as a positive-unlabeled learning problem. Since the instances in unannotated regions can be either positive or negative, they have unknown labels. Using the samples with unknown labels and the positively labeled samples, we first derive an approximation of the classification loss term corresponding to negative samples for binary cell detection, and based on this approximation we further extend the proposed framework to multi-class cell detection. For evaluation, experiments were performed on four publicly available datasets. The experimental results show that our method improves the performance of cell detection in histopathology images given incomplete annotations for network training.Comment: Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) https://melba-journal.org/2022:027. arXiv admin note: text overlap with arXiv:2106.1591

Analyzing temporal dynamics of cell deformation and intracellular movement with video feature aggregation

Abstract Background The research and analysis of cellular physiological properties has been an essential approach to studying some biological and biomedical problems. Temporal dynamics of cells therein are used as a quantifiable indicator of cellular response to extracellular cues and physiological stimuli. Methods This work presents a novel image-based framework to profile and model the cell dynamics in live-cell videos. In the framework, the cell dynamics between frames are represented as frame-level features from cell deformation and intracellular movement. On the one hand, shape context is introduced to enhance the robustness of measuring the deformation of cellular contours. On the other hand, we employ Scale-Invariant Feature Transform (SIFT) flow to simultaneously construct the complementary movement field and appearance change field for the cytoplasmic streaming. Then, time series modeling is performed on these frame-level features. Specifically, temporal feature aggregation is applied to capture the video-wide temporal evolution of cell dynamics. Results Our results demonstrate that the proposed cell dynamic features can effectively capture the cell dynamics in videos. They also prove that the Movement Field and Appearance Change Field Feature (MFAFF) can more precisely model the cytoplasmic streaming. Besides, temporal aggregation of cell dynamic features brings a substantial absolute increase of classification performance. Conclusion Experimental results demonstrate that the proposed framework outperforms competing mainstreaming approaches on the aforementioned datasets. Thus, our method has potential for cell dynamics analysis in videos

Electrical insulator defect detection with incomplete annotations and imbalanced samples

Abstract Insulators are one of the key components in high‐voltage power systems that prevent transmission lines from grounding. Since they are exposed to different kinds of harsh environments and climates, periodic inspection is indispensable for the safety and high quality of power grid. Nowadays, unmanned aerial vehicle (UAV) inspection is more widely used, facilitating incorporation of convolutional neural network‐based detectors in the insulator detection task. However, these methods are generally based on the assumption that the image samples are balanced among different categories and possess completely ideal annotations. The problem of sample imbalance or incomplete annotation is rarely investigated in depth for insulator defect detection. Here, insulator defect detection with imbalanced data and incomplete annotations is focused on. The proposed framework, named Pi‐index, introduces positive unlabelled (PU) learning to solve the problem of incomplete annotation and designs a novel index the class prior, which is a key parameter in PU learning. Moreover, focal loss is integrated in our framework to alleviate the effect of sample imbalance. Experiment results demonstrate that the proposed framework achieves better performance than the baseline methods in situations of sample imbalance and missing annotation