Ruijiang Li

JBHI Journal 2024 Journal Article

Single-Cell Heterogeneity-Aware Transformer-Guided Multiple Instance Learning for Cancer Aneuploidy Prediction From Whole Slide Histopathology Images

• Feiyang Yu
• Xi Wang
• Rasoul Sali
• Ruijiang Li

Aneuploidy is a hallmark of aggressive malignancies associated with therapeutic resistance and poor survival. Measuring aneuploidy requires expensive specialized techniques that are not clinically applicable. Deep learning analysis of routine histopathology slides has revealed associations with genetic mutations. However, existing studies focus on image tiles, and there is no prior work that predicts aneuploidy using single-cell analysis. Here, we present a single-cell heterogeneity-aware and transformer-guided deep learning framework to predict aneuploidy from whole slide histopathology images. First, we perform nuclei segmentation and classification to obtain individual cancer cells, which are clustered into multiple subtypes. The cell subtype distributions are computed to measure cancer cell heterogeneity. Additionally, morphological features of different cell subtypes are extracted. Further, we leverage a multiple instance learning module with Transformer, which encourages the network to focus on the most informative cancer cells. Lastly, a hybrid network is built to unify cell heterogeneity, morphology, and deep features for aneuploidy prediction. We train and validate our method on two public datasets from TCGA: lung adenocarcinoma (LUAD) and head and neck squamous cell carcinoma (HNSC), with 339 and 245 patients. Our model achieves promising performance with AUC of 0. 818 (95% CI: 0. 718–0. 919) and 0. 827 (95% CI: 0. 704–0. 949) on the LUAD and HNSC test sets, respectively. Through extensive ablation and comparison studies, we demonstrate the effectiveness of each component of the model and superior performance over alternative networks. In conclusion, we present a novel deep learning approach to predict aneuploidy from histopathology images, which could inform personalized cancer treatment.

ICML Conference 2012 Conference Paper

Groupwise Constrained Reconstruction for Subspace Clustering

• Ruijiang Li
• Bin Li 0015
• Cheng Jin 0001
• Xiangyang Xue 0001

IJCAI Conference 2011 Conference Paper

Cross-Domain Collaborative Filtering over Time

• Bin Li
• Xingquan Zhu
• Ruijiang Li
• Chengqi Zhang
• Xiangyang Xue
• Xindong Wu

Collaborative filtering (CF) techniques recommend items to users based on their historical ratings. In real-world scenarios, user interests may drift over time since they are affected by moods, contexts, and pop culture trends. This leads to the fact that a user's historical ratings comprise many aspects of user interests spanning a long time period. However, at a certain time slice, one user's interest may only focus on one or a couple of aspects. Thus, CF techniques based on the entire historical ratings may recommend inappropriate items. In this paper, we consider modeling user-interest drift over time based on the assumption that each user has multiple counterparts over temporal domains and successive counterparts are closely related. We adopt the cross-domain CF framework to share the static group-level rating matrix across temporal domains, and let user-interest distribution over item groups drift slightly between successive temporal domains. The derived method is based on a Bayesian latent factor model which can be inferred using Gibbs sampling. Our experimental results show that our method can achieve state-of-the-art recommendation performance as well as explicitly track and visualize user-interest drift over time.

AAAI Conference 2011 Conference Paper

Tracking User-Preference Varying Speed in Collaborative Filtering

• Ruijiang Li
• Bin Li
• Cheng Jin
• Xiangyang Xue
• Xingquan Zhu

In real-world recommender systems, some users are easily influenced by new products and whereas others are unwilling to change their minds. So the preference varying speeds for users are different. Based on this observation, we propose a dynamic nonlinear matrix factorization model for collaborative filtering, aimed to improve the rating prediction performance as well as track the preference varying speeds for different users. We assume that user-preference changes smoothly over time, and the preference varying speeds for users are different. These two assumptions are incorporated into the proposed model as prior knowledge on user feature vectors, which can be learned efficiently by MAP estimation. The experimental results show that our method not only achieves state-of-the-art performance in the rating prediction task, but also provides an effective way to track userpreference varying speed.