Rethinking Mitosis Detection: Towards Diverse Data and Feature Representation

Mitosis detection is one of the fundamental tasks in computational pathology, which is extremely challenging due to the heterogeneity of mitotic cell. Most of the current studies solve the heterogeneity in the technical aspect by increasing the model complexity. However, lacking consideration of the biological knowledge and the complex model design may lead to the overfitting problem while limited the generalizability of the detection model. In this paper, we systematically study the morphological appearances in different mitotic phases as well as the ambiguous non-mitotic cells and identify that balancing the data and feature diversity can achieve better generalizability. Based on this observation, we propose a novel generalizable framework (MitDet) for mitosis detection. The data diversity is considered by the proposed diversity-guided sample balancing (DGSB). And the feature diversity is preserved by inter- and intra- class feature diversity-preserved module (InCDP). Stain enhancement (SE) module is introduced to enhance the domain-relevant diversity of both data and features simultaneously. Extensive experiments have demonstrated that our proposed model outperforms all the SOTA approaches in several popular mitosis detection datasets in both internal and external test sets using minimal annotation efforts with point annotations only. Comprehensive ablation studies have also proven the effectiveness of the rethinking of data and feature diversity balancing. By analyzing the results quantitatively and qualitatively, we believe that our proposed model not only achieves SOTA performance but also might inspire the future studies in new perspectives. Source code is at https://github.com/Onehour0108/MitDet.

CGCE: A Chinese Generative Chat Evaluation Benchmark for General and Financial Domains

Generative chat models, such as ChatGPT and GPT-4, have revolutionized natural language generation (NLG) by incorporating instructions and human feedback to achieve significant performance improvements. However, the lack of standardized evaluation benchmarks for chat models, particularly for Chinese and domain-specific models, hinders their assessment and progress. To address this gap, we introduce the Chinese Generative Chat Evaluation (CGCE) benchmark, focusing on general and financial domains. The CGCE benchmark encompasses diverse tasks, including 200 questions in the general domain and 150 specific professional questions in the financial domain. Manual scoring evaluates factors such as accuracy, coherence, expression clarity, and completeness. The CGCE benchmark provides researchers with a standardized framework to assess and compare Chinese generative chat models, fostering advancements in NLG research.

A novel dataset and a two-stage mitosis nuclei detection method based on hybrid anchor branch

Mitosis detection is one of the challenging problems in computational pathology, and mitotic count is an important index of cancer grading for pathologists. However, current counts of mitotic nuclei rely on pathologists looking microscopically at the number of mitotic nuclei in hot spots, which is subjective and time-consuming. In this paper, we propose a two-stage cascaded network, named FoCasNet, for mitosis detection. In the first stage, a detection network named M_det is proposed to detect as many mitoses as possible. In the second stage, a classification network M_class is proposed to refine the results of the first stage. In addition, the attention mechanism, normalization method, and hybrid anchor branch classification subnet are introduced to improve the overall detection performance. Our method achieves the current highest F1-score of 0.888 on the public dataset ICPR 2012. We also evaluated our method on the GZMH dataset released by our research team for the first time and reached the highest F1-score of 0.563, which is also better than multiple classic detection networks widely used at present. It confirmed the effectiveness and generalization of our method. The code will be available at: https://github.com/antifen/mitosis-nuclei-detection.

A Novel Dataset and a Deep Learning Method for Mitosis Nuclei Segmentation and Classification

Mitosis nuclei count is one of the important indicators for the pathological diagnosis of breast cancer. The manual annotation needs experienced pathologists, which is very time-consuming and inefficient. With the development of deep learning methods, some models with good performance have emerged, but the generalization ability should be further strengthened. In this paper, we propose a two-stage mitosis segmentation and classification method, named SCMitosis. Firstly, the segmentation performance with a high recall rate is achieved by the proposed depthwise separable convolution residual block and channel-spatial attention gate. Then, a classification network is cascaded to further improve the detection performance of mitosis nuclei. The proposed model is verified on the ICPR 2012 dataset, and the highest F-score value of 0.8687 is obtained compared with the current state-of-the-art algorithms. In addition, the model also achieves good performance on GZMH dataset, which is prepared by our group and will be firstly released with the publication of this paper. The code will be available at: https://github.com/antifen/mitosis-nuclei-segmentation.

Material Prediction for Design Automation Using Graph Representation Learning

Successful material selection is critical in designing and manufacturing products for design automation. Designers leverage their knowledge and experience to create high-quality designs by selecting the most appropriate materials through performance, manufacturability, and sustainability evaluation. Intelligent tools can help designers with varying expertise by providing recommendations learned from prior designs. To enable this, we introduce a graph representation learning framework that supports the material prediction of bodies in assemblies. We formulate the material selection task as a node-level prediction task over the assembly graph representation of CAD models and tackle it using Graph Neural Networks (GNNs). Evaluations over three experimental protocols performed on the Fusion 360 Gallery dataset indicate the feasibility of our approach, achieving a 0.75 top-3 micro-f1 score. The proposed framework can scale to large datasets and incorporate designers' knowledge into the learning process. These capabilities allow the framework to serve as a recommendation system for design automation and a baseline for future work, narrowing the gap between human designers and intelligent design agents.

A Length Adaptive Algorithm-Hardware Co-design of Transformer on FPGA Through Sparse Attention and Dynamic Pipelining

Transformers are considered one of the most important deep learning models since 2018, in part because it establishes state-of-the-art (SOTA) records and could potentially replace existing Deep Neural Networks (DNNs). Despite the remarkable triumphs, the prolonged turnaround time of Transformer models is a widely recognized roadblock. The variety of sequence lengths imposes additional computing overhead where inputs need to be zero-padded to the maximum sentence length in the batch to accommodate the parallel computing platforms. This paper targets the field-programmable gate array (FPGA) and proposes a coherent sequence length adaptive algorithm-hardware co-design for Transformer acceleration. Particularly, we develop a hardware-friendly sparse attention operator and a length-aware hardware resource scheduling algorithm. The proposed sparse attention operator brings the complexity of attention-based models down to linear complexity and alleviates the off-chip memory traffic. The proposed length-aware resource hardware scheduling algorithm dynamically allocates the hardware resources to fill up the pipeline slots and eliminates bubbles for NLP tasks. Experiments show that our design has very small accuracy loss and has 80.2 $\times$ and 2.6 $\times$ speedup compared to CPU and GPU implementation, and 4 $\times$ higher energy efficiency than state-of-the-art GPU accelerator optimized via CUBLAS GEMM.

WSSS4LUAD: Grand Challenge on Weakly-supervised Tissue Semantic Segmentation for Lung Adenocarcinoma

Lung cancer is the leading cause of cancer death worldwide, and adenocarcinoma (LUAD) is the most common subtype. Exploiting the potential value of the histopathology images can promote precision medicine in oncology. Tissue segmentation is the basic upstream task of histopathology image analysis. Existing deep learning models have achieved superior segmentation performance but require sufficient pixel-level annotations, which is time-consuming and expensive. To enrich the label resources of LUAD and to alleviate the annotation efforts, we organize this challenge WSSS4LUAD to call for the outstanding weakly-supervised semantic segmentation (WSSS) techniques for histopathology images of LUAD. Participants have to design the algorithm to segment tumor epithelial, tumor-associated stroma and normal tissue with only patch-level labels. This challenge includes 10,091 patch-level annotations (the training set) and over 130 million labeled pixels (the validation and test sets), from 87 WSIs (67 from GDPH, 20 from TCGA). All the labels were generated by a pathologist-in-the-loop pipeline with the help of AI models and checked by the label review board. Among 532 registrations, 28 teams submitted the results in the test phase with over 1,000 submissions. Finally, the first place team achieved mIoU of 0.8413 (tumor: 0.8389, stroma: 0.7931, normal: 0.8919). According to the technical reports of the top-tier teams, CAM is still the most popular approach in WSSS. Cutmix data augmentation has been widely adopted to generate more reliable samples. With the success of this challenge, we believe that WSSS approaches with patch-level annotations can be a complement to the traditional pixel annotations while reducing the annotation efforts. The entire dataset has been released to encourage more researches on computational pathology in LUAD and more novel WSSS techniques.

PoseTriplet: Co-evolving 3D Human Pose Estimation, Imitation, and Hallucination under Self-supervision

Existing self-supervised 3D human pose estimation schemes have largely relied on weak supervisions like consistency loss to guide the learning, which, inevitably, leads to inferior results in real-world scenarios with unseen poses. In this paper, we propose a novel self-supervised approach that allows us to explicitly generate 2D-3D pose pairs for augmenting supervision, through a self-enhancing dual-loop learning framework. This is made possible via introducing a reinforcement-learning-based imitator, which is learned jointly with a pose estimator alongside a pose hallucinator; the three components form two loops during the training process, complementing and strengthening one another. Specifically, the pose estimator transforms an input 2D pose sequence to a low-fidelity 3D output, which is then enhanced by the imitator that enforces physical constraints. The refined 3D poses are subsequently fed to the hallucinator for producing even more diverse data, which are, in turn, strengthened by the imitator and further utilized to train the pose estimator. Such a co-evolution scheme, in practice, enables training a pose estimator on self-generated motion data without relying on any given 3D data. Extensive experiments across various benchmarks demonstrate that our approach yields encouraging results significantly outperforming the state of the art and, in some cases, even on par with results of fully-supervised methods. Notably, it achieves 89.1% 3D PCK on MPI-INF-3DHP under self-supervised cross-dataset evaluation setup, improving upon the previous best self-supervised methods by 8.6%. Code can be found at: https://github.com/Garfield-kh/PoseTriplet

RestainNet: a self-supervised digital re-stainer for stain normalization

Color inconsistency is an inevitable challenge in computational pathology, which generally happens because of stain intensity variations or sections scanned by different scanners. It harms the pathological image analysis methods, especially the learning-based models. A series of approaches have been proposed for stain normalization. However, most of them are lack flexibility in practice. In this paper, we formulated stain normalization as a digital re-staining process and proposed a self-supervised learning model, which is called RestainNet. Our network is regarded as a digital restainer which learns how to re-stain an unstained (grayscale) image. Two digital stains, Hematoxylin (H) and Eosin (E) were extracted from the original image by Beer-Lambert's Law. We proposed a staining loss to maintain the correctness of stain intensity during the restaining process. Thanks to the self-supervised nature, paired training samples are no longer necessary, which demonstrates great flexibility in practical usage. Our RestainNet outperforms existing approaches and achieves state-of-the-art performance with regard to color correctness and structure preservation. We further conducted experiments on the segmentation and classification tasks and the proposed RestainNet achieved outstanding performance compared with SOTA methods. The self-supervised design allows the network to learn any staining style with no extra effort.