Bingbing Li

Huadeng Wang, Hao Xu, Bingbing Li et al.

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.

Huadeng Wang, Zhipeng Liu, Rushi Lan et al.

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.

Hao Wang, Jiatai Lin, Danyi Li et al.

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.

Chu Han, Xipeng Pan, Lixu Yan et al.

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.

Huadeng Wang, Jiejiang Yu, Bingbing Li et al.

Accurate and automated gland segmentation on pathological images can assist pathologists in diagnosing the malignancy of colorectal adenocarcinoma. However, due to various gland shapes, severe deformation of malignant glands, and overlapping adhesions between glands. Gland segmentation has always been very challenging. To address these problems, we propose a DEA model. This model consists of two branches: the backbone encoding and decoding network and the local semantic extraction network. The backbone encoding and decoding network extracts advanced Semantic features, uses the proposed feature decoder to restore feature space information, and then enhances the boundary features of the gland through boundary enhancement attention. The local semantic extraction network uses the pre-trained DeepLabv3+ as a Local semantic-guided encoder to realize the extraction of edge features. Experimental results on two public datasets, GlaS and CRAG, confirm that the performance of our method is better than other gland segmentation methods.

Xuanyu Zhang, Bingbing Li, Qing Yang

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.

Bingchao Zhao, Jiatai Lin, Changhong Liang et al.

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.

Bingbing Li, Hongwu Peng, Rajat Sainju et al.

In this paper, we propose a novel gender bias detection method by utilizing attention map for transformer-based models. We 1) give an intuitive gender bias judgement method by comparing the different relation degree between the genders and the occupation according to the attention scores, 2) design a gender bias detector by modifying the attention module, 3) insert the gender bias detector into different positions of the model to present the internal gender bias flow, and 4) draw the consistent gender bias conclusion by scanning the entire Wikipedia, a BERT pretraining dataset. We observe that 1) the attention matrices, Wq and Wk introduce much more gender bias than other modules (including the embedding layer) and 2) the bias degree changes periodically inside of the model (attention matrix Q, K, V, and the remaining part of the attention layer (including the fully-connected layer, the residual connection, and the layer normalization module) enhance the gender bias while the averaged attentions reduces the bias).

Shaoyi Huang, Dongkuan Xu, Ian E. H. Yen et al.

Conventional wisdom in pruning Transformer-based language models is that pruning reduces the model expressiveness and thus is more likely to underfit rather than overfit. However, under the trending pretrain-and-finetune paradigm, we postulate a counter-traditional hypothesis, that is: pruning increases the risk of overfitting when performed at the fine-tuning phase. In this paper, we aim to address the overfitting problem and improve pruning performance via progressive knowledge distillation with error-bound properties. We show for the first time that reducing the risk of overfitting can help the effectiveness of pruning under the pretrain-and-finetune paradigm. Ablation studies and experiments on the GLUE benchmark show that our method outperforms the leading competitors across different tasks.

Deniz Gurevin, Shanglin Zhou, Lynn Pepin et al.

Network pruning is a widely used technique to reduce computation cost and model size for deep neural networks. However, the typical three-stage pipeline, i.e., training, pruning and retraining (fine-tuning) significantly increases the overall training trails. In this paper, we develop a systematic weight-pruning optimization approach based on Surrogate Lagrangian relaxation (SLR), which is tailored to overcome difficulties caused by the discrete nature of the weight-pruning problem while ensuring fast convergence. We further accelerate the convergence of the SLR by using quadratic penalties. Model parameters obtained by SLR during the training phase are much closer to their optimal values as compared to those obtained by other state-of-the-art methods. We evaluate the proposed method on image classification tasks, i.e., ResNet-18 and ResNet-50 using ImageNet, and ResNet-18, ResNet-50 and VGG-16 using CIFAR-10, as well as object detection tasks, i.e., YOLOv3 and YOLOv3-tiny using COCO 2014 and Ultra-Fast-Lane-Detection using TuSimple lane detection dataset. Experimental results demonstrate that our SLR-based weight-pruning optimization approach achieves higher compression rate than state-of-the-arts under the same accuracy requirement. It also achieves a high model accuracy even at the hard-pruning stage without retraining (reduces the traditional three-stage pruning to two-stage). Given a limited budget of retraining epochs, our approach quickly recovers the model accuracy.

Bingbing Li, Zhenglun Kong, Tianyun Zhang et al.

Pre-trained large-scale language models have increasingly demonstrated high accuracy on many natural language processing (NLP) tasks. However, the limited weight storage and computational speed on hardware platforms have impeded the popularity of pre-trained models, especially in the era of edge computing. In this work, we propose an efficient transformer-based large-scale language representation using hardware-friendly block structure pruning. We incorporate the reweighted group Lasso into block-structured pruning for optimization. Besides the significantly reduced weight storage and computation, the proposed approach achieves high compression rates. Experimental results on different models (BERT, RoBERTa, and DistilBERT) on the General Language Understanding Evaluation (GLUE) benchmark tasks show that we achieve up to 5.0x with zero or minor accuracy degradation on certain task(s). Our proposed method is also orthogonal to existing compact pre-trained language models such as DistilBERT using knowledge distillation, since a further 1.79x average compression rate can be achieved on top of DistilBERT with zero or minor accuracy degradation. It is suitable to deploy the final compressed model on resource-constrained edge devices.

Bingbing Li, Santosh Pandey, Haowen Fang et al.

In natural language processing (NLP), the "Transformer" architecture was proposed as the first transduction model replying entirely on self-attention mechanisms without using sequence-aligned recurrent neural networks (RNNs) or convolution, and it achieved significant improvements for sequence to sequence tasks. The introduced intensive computation and storage of these pre-trained language representations has impeded their popularity into computation and memory-constrained devices. The field-programmable gate array (FPGA) is widely used to accelerate deep learning algorithms for its high parallelism and low latency. However, the trained models are still too large to accommodate to an FPGA fabric. In this paper, we propose an efficient acceleration framework, Ftrans, for transformer-based large scale language representations. Our framework includes enhanced block-circulant matrix (BCM)-based weight representation to enable model compression on large-scale language representations at the algorithm level with few accuracy degradation, and an acceleration design at the architecture level. Experimental results show that our proposed framework significantly reduces the model size of NLP models by up to 16 times. Our FPGA design achieves 27.07x and 81x improvement in performance and energy efficiency compared to CPU, and up to 8.80x improvement in energy efficiency compared to GPU.