Tiancheng Lin

Zijiang Yang, Zhongwei Qiu, Tiancheng Lin et al.

It is clinically crucial and potentially very beneficial to be able to analyze and model directly the spatial distributions of cells in histopathology whole slide images (WSI). However, most existing WSI datasets lack cell-level annotations, owing to the extremely high cost over giga-pixel images. Thus, it remains an open question whether deep learning models can directly and effectively analyze WSIs from the semantic aspect of cell distributions. In this work, we construct a large-scale WSI dataset with more than 5 billion cell-level annotations, termed WSI-Cell5B, and a novel hierarchical Cell Cloud Transformer (CCFormer) to tackle these challenges. WSI-Cell5B is based on 6,998 WSIs of 11 cancers from The Cancer Genome Atlas Program, and all WSIs are annotated per cell by coordinates and types. To the best of our knowledge, WSI-Cell5B is the first WSI-level large-scale dataset integrating cell-level annotations. On the other hand, CCFormer formulates the collection of cells in each WSI as a cell cloud and models cell spatial distribution. Specifically, Neighboring Information Embedding (NIE) is proposed to characterize the distribution of cells within the neighborhood of each cell, and a novel Hierarchical Spatial Perception (HSP) module is proposed to learn the spatial relationship among cells in a bottom-up manner. The clinical analysis indicates that WSI-Cell5B can be used to design clinical evaluation metrics based on counting cells that effectively assess the survival risk of patients. Extensive experiments on survival prediction and cancer staging show that learning from cell spatial distribution alone can already achieve state-of-the-art (SOTA) performance, i.e., CCFormer strongly outperforms other competing methods.

Zhimiao Yu, Tiancheng Lin, Yi Xu

Recent few-shot segmentation (FSS) methods introduce an extra pre-training stage before meta-training to obtain a stronger backbone, which has become a standard step in few-shot learning. Despite the effectiveness, current pre-training scheme suffers from the merged background problem: only base classes are labelled as foregrounds, making it hard to distinguish between novel classes and actual background. In this paper, we propose a new pre-training scheme for FSS via decoupling the novel classes from background, called Background Clustering Pre-Training (BCPT). Specifically, we adopt online clustering to the pixel embeddings of merged background to explore the underlying semantic structures, bridging the gap between pre-training and adaptation to novel classes. Given the clustering results, we further propose the background mining loss and leverage base classes to guide the clustering process, improving the quality and stability of clustering results. Experiments on PASCAL-5i and COCO-20i show that BCPT yields advanced performance. Code will be available.

Jiancheng Yang, Jiajun Chen, Kaiming Kuang et al.

Predicting clinical outcome is remarkably important but challenging. Research efforts have been paid on seeking significant biomarkers associated with the therapy response or/and patient survival. However, these biomarkers are generally costly and invasive, and possibly dissatifactory for novel therapy. On the other hand, multi-modal, heterogeneous, unaligned temporal data is continuously generated in clinical practice. This paper aims at a unified deep learning approach to predict patient prognosis and therapy response, with easily accessible data, e.g., radiographics, laboratory and clinical information. Prior arts focus on modeling single data modality, or ignore the temporal changes. Importantly, the clinical time series is asynchronous in practice, i.e., recorded with irregular intervals. In this study, we formalize the prognosis modeling as a multi-modal asynchronous time series classification task, and propose a MIA-Prognosis framework with Measurement, Intervention and Assessment (MIA) information to predict therapy response, where a Simple Temporal Attention (SimTA) module is developed to process the asynchronous time series. Experiments on synthetic dataset validate the superiory of SimTA over standard RNN-based approaches. Furthermore, we experiment the proposed method on an in-house, retrospective dataset of real-world non-small cell lung cancer patients under anti-PD-1 immunotherapy. The proposed method achieves promising performance on predicting the immunotherapy response. Notably, our predictive model could further stratify low-risk and high-risk patients in terms of long-term survival.

Tiancheng Lin, Yuanfan Guo, Canqian Yang et al.

Early diagnosis of signet ring cell carcinoma dramatically improves the survival rate of patients. Due to lack of public dataset and expert-level annotations, automatic detection on signet ring cell (SRC) has not been thoroughly investigated. In MICCAI DigestPath2019 challenge, apart from foreground (SRC region)-background (normal tissue area) class imbalance, SRCs are partially annotated due to costly medical image annotation, which introduces extra label noise. To address the issues simultaneously, we propose Decoupled Gradient Harmonizing Mechanism (DGHM) and embed it into classification loss, denoted as DGHM-C loss. Specifically, besides positive (SRCs) and negative (normal tissues) examples, we further decouple noisy examples from clean examples and harmonize the corresponding gradient distributions in classification respectively. Without whistles and bells, we achieved the 2nd place in the challenge. Ablation studies and controlled label missing rate experiments demonstrate that DGHM-C loss can bring substantial improvement in partially annotated object detection.