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Bao Li

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4 papers

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AIIM Journal 2026 Journal Article

Context-aware heterogeneous graph neural network for multi-level description and invasiveness prediction in renal cell carcinoma

Xiaoming Jiang
Guoying Ji
Ye Yan
Xiongjun Ye
Chao Liang
Bao Li
Wei Wang
Shudong Zhang

The invasiveness prediction in renal cell carcinoma (RCC) is of significant importance for the decision of clinical surgical plans and the patients' prognosis. Currently, besides invasive pathological assessment, it mainly relies on observation through computed tomography (CT) imaging. However, limitations of human vision and qualitative descriptions restrict the accuracy of the diagnosis of renal sinus invasion (RSI). Recently, artificial intelligence approaches have shown promising prospects in cancer diagnosis. Due to the complex imaging characteristics of invasiveness, prediction models that only focus on tumor regions are inadequate, requiring comprehensive evaluation of intratumoral heterogeneity, peritumoral information, and the kidney in which the tumor resides. Therefore, in this study, we propose a context-aware heterogeneous graph neural network for multi-level description and invasiveness prediction in RCC. The superiority of the proposed model lies in its ability to integrate imaging features at multi-level, and to learn disturbance invariant features through a data-driven diffusion perturbation strategy. To evaluate the effectiveness and generalization of our model, we conduct extensive experiments on a multi-center dataset (including CT scan images of 437 patients) to compare our model with a series of state-of-the-art (SOTA) classification models. The experimental results show the superiority of our model for RSI classification ( AUC = 0. 88 ). Additionally, we also perform a comparative study with clinical experts, and the proposed method is significantly better than existing assessment methods and clinical experts ( p < 0. 05 ). In general, our work provides an effective assessment tool for automated diagnosis of RSI in RCC and also offers new insights for constructing more precise tumor prediction models.

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AIIM Journal 2024 Journal Article

Non-invasive fractional flow reserve derived from reduced-order coronary model and machine learning prediction of stenosis flow resistance

Yili Feng
Ruisen Fu
Hao Sun
Xue Wang
Yang Yang
Chuanqi Wen
Yaodong Hao
Yutong Sun

Background and objective Recently, computational fluid dynamics enables the non-invasive calculation of fractional flow reserve (FFR) based on 3D coronary model, but it is time-consuming. Currently, machine learning technique has emerged as an efficient and reliable approach for prediction, which allows saving a lot of analysis time. This study aimed at developing a simplified FFR prediction model for rapid and accurate assessment of functional significance of stenosis. Methods A reduced-order lumped parameter model (LPM) of coronary system and cardiovascular system was constructed for rapidly simulating coronary flow, in which a machine learning model was embedded for accurately predicting stenosis flow resistance at a given flow from anatomical features of stenosis. Importantly, the LPM was personalized in both structures and parameters according to coronary geometries from computed tomography angiography and physiological measurements such as blood pressure and cardiac output for personalized simulations of coronary pressure and flow. Coronary lesions with invasive FFR ≤ 0. 80 were defined as hemodynamically significant. Results A total of 91 patients (93 lesions) who underwent invasive FFR were involved in FFR derived from machine learning (FFRML) calculation. Of the 93 lesions, 27 lesions (29. 0%) showed lesion-specific ischemia. The average time of FFRML simulation was about 10 min. On a per-vessel basis, the FFRML and FFR were significantly correlated (r = 0. 86, p < 0. 001). The diagnostic accuracy, sensitivity, specificity, positive predictive value and negative predictive value were 91. 4%, 92. 6%, 90. 9%, 80. 6% and 96. 8%, respectively. The area under the receiver-operating characteristic curve of FFRML was 0. 984. Conclusion In this selected cohort of patients, the FFRML improves the computational efficiency and ensures the accuracy. The favorable performance of FFRML approach greatly facilitates its potential application in detecting hemodynamically significant coronary stenosis in future routine clinical practice.

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AAAI Conference 2024 Conference Paper

Point Transformer with Federated Learning for Predicting Breast Cancer HER2 Status from Hematoxylin and Eosin-Stained Whole Slide Images

Bao Li
Zhenyu Liu
Lizhi Shao
Bensheng Qiu
Hong Bu
Jie Tian

Directly predicting human epidermal growth factor receptor 2 (HER2) status from widely available hematoxylin and eosin (HE)-stained whole slide images (WSIs) can reduce technical costs and expedite treatment selection. Accurately predicting HER2 requires large collections of multi-site WSIs. Federated learning enables collaborative training of these WSIs without gigabyte-size WSIs transportation and data privacy concerns. However, federated learning encounters challenges in addressing label imbalance in multi-site WSIs from the real world. Moreover, existing WSI classification methods cannot simultaneously exploit local context information and long-range dependencies in the site-end feature representation of federated learning. To address these issues, we present a point transformer with federated learning for multi-site HER2 status prediction from HE-stained WSIs. Our approach incorporates two novel designs. We propose a dynamic label distribution strategy and an auxiliary classifier, which helps to establish a well-initialized model and mitigate label distribution variations across sites. Additionally, we propose a farthest cosine sampling based on cosine distance. It can sample the most distinctive features and capture the long-range dependencies. Extensive experiments and analysis show that our method achieves state-of-the-art performance at four sites with a total of 2687 WSIs. Furthermore, we demonstrate that our model can generalize to two unseen sites with 229 WSIs. Code is available at: https://github.com/boyden/PointTransformerFL

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JBHI Journal 2023 Journal Article

Development of Prognostic Biomarkers by TMB-Guided WSI Analysis: A Two-Step Approach

Xiangyu Liu
Zhenyu Liu
Ye Yan
Kai Wang
Aodi Wang
Xiongjun Ye
Liwei Wang
Wei Wei

The rapid development of computational pathology has brought new opportunities for prognosis prediction using histopathological images. However, the existing deep learning frameworks lack exploration of the relationship between images and other prognostic information, resulting in poor interpretability. Tumor mutation burden (TMB) is a promising biomarker for predicting the survival outcomes of cancer patients, but its measurement is costly. Its heterogeneity may be reflected in histopathological images. Here, we report a two-step framework for prognostic prediction using whole-slide images (WSIs). First, the framework adopts a deep residual network to encode the phenotype of WSIs and classifies patient-level TMB by the deep features after aggregation and dimensionality reduction. Then, the patients' prognosis is stratified by the TMB-related information obtained during the classification model development. Deep learning feature extraction and TMB classification model construction are performed on an in-house dataset of 295 Haematoxylin & Eosin stained WSIs of clear cell renal cell carcinoma (ccRCC). The development and evaluation of prognostic biomarkers are performed on The Cancer Genome Atlas-Kidney ccRCC (TCGA-KIRC) project with 304 WSIs. Our framework achieves good performance for TMB classification with an area under the receiver operating characteristic curve (AUC) of 0. 813 on the validation set. Through survival analysis, our proposed prognostic biomarkers can achieve significant stratification of patients' overall survival (P $< $ 0. 05) and outperform the original TMB signature in risk stratification of patients with advanced disease. The results indicate the feasibility of mining TMB-related information from WSI to achieve stepwise prognosis prediction.

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