Zhichao Feng

Liangrui Pan, Yutao Dou, Zhichao Feng et al.

Histopathological images are the gold standard for diagnosing liver cancer. However, the accuracy of fully digital diagnosis in computational pathology needs to be improved. In this paper, in order to solve the problem of multi-label and low classification accuracy of histopathology images, we propose a locally deep convolutional Swim framework (LDCSF) to classify multi-label histopathology images. In order to be able to provide local field of view diagnostic results, we propose the LDCSF model, which consists of a Swin transformer module, a local depth convolution (LDC) module, a feature reconstruction (FR) module, and a ResNet module. The Swin transformer module reduces the amount of computation generated by the attention mechanism by limiting the attention to each window. The LDC then reconstructs the attention map and performs convolution operations in multiple channels, passing the resulting feature map to the next layer. The FR module uses the corresponding weight coefficient vectors obtained from the channels to dot product with the original feature map vector matrix to generate representative feature maps. Finally, the residual network undertakes the final classification task. As a result, the classification accuracy of LDCSF for interstitial area, necrosis, non-tumor and tumor reached 0.9460, 0.9960, 0.9808, 0.9847, respectively. Finally, we use the results of multi-label pathological image classification to calculate the tumor-to-stromal ratio, which lays the foundation for the analysis of the microenvironment of liver cancer histopathological images. Second, we released a multilabel histopathology image of liver cancer, our code and data are available at https://github.com/panliangrui/LSF.

Bin Yin, Junjie Xie, Yu Qin et al.

The analysis and mining of user heterogeneous behavior are of paramount importance in recommendation systems. However, the conventional approach of incorporating various types of heterogeneous behavior into recommendation models leads to feature sparsity and knowledge fragmentation issues. To address this challenge, we propose a novel approach for personalized recommendation via Large Language Model (LLM), by extracting and fusing heterogeneous knowledge from user heterogeneous behavior information. In addition, by combining heterogeneous knowledge and recommendation tasks, instruction tuning is performed on LLM for personalized recommendations. The experimental results demonstrate that our method can effectively integrate user heterogeneous behavior and significantly improve recommendation performance.

Liangrui Pan, Zhichao Feng, Shaoliang Peng

Computational pathology is part of precision oncology medicine. The integration of high-throughput data including genomics, transcriptomics, proteomics, metabolomics, pathomics, and radiomics into clinical practice improves cancer treatment plans, treatment cycles, and cure rates, and helps doctors open up innovative approaches to patient prognosis. In the past decade, rapid advances in artificial intelligence, chip design and manufacturing, and mobile computing have facilitated research in computational pathology and have the potential to provide better-integrated solutions for whole-slide images, multi-omics data, and clinical informatics. However, tumor computational pathology now brings some challenges to the application of tumour screening, diagnosis and prognosis in terms of data integration, hardware processing, network sharing bandwidth and machine learning technology. This review investigates image preprocessing methods in computational pathology from a pathological and technical perspective, machine learning-based methods, and applications of computational pathology in breast, colon, prostate, lung, and various tumour disease scenarios. Finally, the challenges and prospects of machine learning in computational pathology applications are discussed.

Liangrui Pan, Lian Wang, Zhichao Feng et al.

Histopathology image segmentation is the gold standard for diagnosing cancer, and can indicate cancer prognosis. However, histopathology image segmentation requires high-quality masks, so many studies now use imagelevel labels to achieve pixel-level segmentation to reduce the need for fine-grained annotation. To solve this problem, we propose an attention-based cross-view feature consistency end-to-end pseudo-mask generation framework named CVFC based on the attention mechanism. Specifically, CVFC is a three-branch joint framework composed of two Resnet38 and one Resnet50, and the independent branch multi-scale integrated feature map to generate a class activation map (CAM); in each branch, through down-sampling and The expansion method adjusts the size of the CAM; the middle branch projects the feature matrix to the query and key feature spaces, and generates a feature space perception matrix through the connection layer and inner product to adjust and refine the CAM of each branch; finally, through the feature consistency loss and feature cross loss to optimize the parameters of CVFC in co-training mode. After a large number of experiments, An IoU of 0.7122 and a fwIoU of 0.7018 are obtained on the WSSS4LUAD dataset, which outperforms HistoSegNet, SEAM, C-CAM, WSSS-Tissue, and OEEM, respectively.

Liangrui Pan, Lian Wang, Zhichao Feng et al.

Colorectal cancer (CRC) is among the top three malignant tumor types in terms of morbidity and mortality. Histopathological images are the gold standard for diagnosing colon cancer. Cellular nuclei instance segmentation and classification, and nuclear component regression tasks can aid in the analysis of the tumor microenvironment in colon tissue. Traditional methods are still unable to handle both types of tasks end-to-end at the same time, and have poor prediction accuracy and high application costs. This paper proposes a new UNet model for handling nuclei based on the UNet framework, called MGTUNet, which uses Mish, Group normalization and transposed convolution layer to improve the segmentation model, and a ranger optimizer to adjust the SmoothL1Loss values. Secondly, it uses different channels to segment and classify different types of nucleus, ultimately completing the nuclei instance segmentation and classification task, and the nuclei component regression task simultaneously. Finally, we did extensive comparison experiments using eight segmentation models. By comparing the three evaluation metrics and the parameter sizes of the models, MGTUNet obtained 0.6254 on PQ, 0.6359 on mPQ, and 0.8695 on R2. Thus, the experiments demonstrated that MGTUNet is now a state-of-the-art method for quantifying histopathological images of colon cancer.

Liangrui Pan, Dazheng Liu, Zhichao Feng et al.

Due to the high heterogeneity and clinical characteristics of cancer, there are significant differences in multi-omic data and clinical characteristics among different cancer subtypes. Therefore, accurate classification of cancer subtypes can help doctors choose the most appropriate treatment options, improve treatment outcomes, and provide more accurate patient survival predictions. In this study, we propose a supervised multi-head attention mechanism model (SMA) to classify cancer subtypes successfully. The attention mechanism and feature sharing module of the SMA model can successfully learn the global and local feature information of multi-omics data. Second, it enriches the parameters of the model by deeply fusing multi-head attention encoders from Siamese through the fusion module. Validated by extensive experiments, the SMA model achieves the highest accuracy, F1 macroscopic, F1 weighted, and accurate classification of cancer subtypes in simulated, single-cell, and cancer multiomics datasets compared to AE, CNN, and GNN-based models. Therefore, we contribute to future research on multiomics data using our attention-based approach.

Wayne Xin Zhao, Shanlei Mu, Yupeng Hou et al.

In recent years, there are a large number of recommendation algorithms proposed in the literature, from traditional collaborative filtering to deep learning algorithms. However, the concerns about how to standardize open source implementation of recommendation algorithms continually increase in the research community. In the light of this challenge, we propose a unified, comprehensive and efficient recommender system library called RecBole, which provides a unified framework to develop and reproduce recommendation algorithms for research purpose. In this library, we implement 73 recommendation models on 28 benchmark datasets, covering the categories of general recommendation, sequential recommendation, context-aware recommendation and knowledge-based recommendation. We implement the RecBole library based on PyTorch, which is one of the most popular deep learning frameworks. Our library is featured in many aspects, including general and extensible data structures, comprehensive benchmark models and datasets, efficient GPU-accelerated execution, and extensive and standard evaluation protocols. We provide a series of auxiliary functions, tools, and scripts to facilitate the use of this library, such as automatic parameter tuning and break-point resume. Such a framework is useful to standardize the implementation and evaluation of recommender systems. The project and documents are released at https://recbole.io/.