Author name cluster

Ruijia Wang

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

6 papers

2 author rows

AAAI Conference 2025 Conference Paper

Blend the Separated: Mixture of Synergistic Experts for Data-Scarcity Drug-Target Interaction Prediction

Xinlong Zhai
Chunchen Wang
Ruijia Wang
Jiazheng Kang
Shujie Li
Boyu Chen
Tengfei Ma
Zikai Zhou

Drug-target interaction prediction (DTI) is essential in various applications including drug discovery and clinical application. There are two perspectives of input data widely used in DTI prediction: Intrinsic data represents how drugs or targets are constructed, and extrinsic data represents how drugs or targets are related to other biological entities. However, any of the two perspectives of input data can be scarce for some drugs or targets, especially for those unpopular or newly discovered. Furthermore, ground-truth labels for specific interaction types can also be scarce. Therefore, we propose the first method to tackle DTI prediction under input data and/or label scarcity. To make our model functional when only one perspective of input data is available, we design two separate experts to process intrinsic and extrinsic data respectively and fuse them adaptively according to different samples. Furthermore, to make the two perspectives complement each other and remedy label scarcity, two experts synergize with each other in a mutually supervised way to exploit the enormous unlabeled data. Extensive experiments on 3 real-world datasets under different extents of input data scarcity and/or label scarcity demonstrate our model outperforms states of the art significantly and steadily, with a maximum improvement of 53.53%. We also test our model without any data scarcity and it still outperforms current methods.

PDF Details DOI

AAAI Conference 2025 Conference Paper

Harnessing Language Model for Cross-Heterogeneity Graph Knowledge Transfer

Jinyu Yang
Ruijia Wang
Cheng Yang
Bo Yan
Qimin Zhou
Yang Juan
Chuan Shi

Heterogeneous graphs (HGs) that contain various node and edge types are ubiquitous in real-world scenarios. Considering the common label sparsity problem in HGs, some researchers propose to pretrain on source HGs to extract general knowledge and then fine-tune on a target HG for knowledge transfer. However, existing methods often assume that source and target HGs share a single heterogeneity, meaning that they have the same types of nodes and edges, which contradicts the real-world scenarios requiring cross-heterogeneity transfer. Although a recent study has made some preliminary attempts in cross-heterogeneity learning, its definition of general knowledge heavily rely on human knowledge, which lacks flexibility and further leads to a suboptimal transfer. To address the problem, we propose a novel Language Model-enhanced Cross-Heterogeneity learning model, namely LMCH. Specifically, we first design a metapath-based corpus construction method to unify HG representations as languages. The corpora of source HGs are then used to fine-tune a pretrained Language Model (LM), enabling the LM to autonomously extract general knowledge across different HGs. Furthermore, to fully utilize the extensive unlabeled nodes in a few-labeled target HG, we propose an iterative training pipeline with the help of an extra Graph Neural Network (GNN) predictor, enhanced by LM-GNN contrastive alignment at the end of each iteration. Extensive experiments on four real-world datasets have demonstrated the superior performance of LMCH over state-of-the-art methods.

PDF Details DOI

NeurIPS Conference 2023 Conference Paper

Injecting Multimodal Information into Rigid Protein Docking via Bi-level Optimization

Ruijia Wang
YiWu Sun
Yujie Luo
Shaochuan Li
Cheng Yang
Xingyi Cheng
Hui Li
Chuan Shi

The structure of protein-protein complexes is critical for understanding binding dynamics, biological mechanisms, and intervention strategies. Rigid protein docking, a fundamental problem in this field, aims to predict the 3D structure of complexes from their unbound states without conformational changes. In this scenario, we have access to two types of valuable information: sequence-modal information, such as coevolutionary data obtained from multiple sequence alignments, and structure-modal information, including the 3D conformations of rigid structures. However, existing docking methods typically utilize single-modal information, resulting in suboptimal predictions. In this paper, we propose xTrimoBiDock (or BiDock for short), a novel rigid docking model that effectively integrates sequence- and structure-modal information through bi-level optimization. Specifically, a cross-modal transformer combines multimodal information to predict an inter-protein distance map. To achieve rigid docking, the roto-translation transformation is optimized to align the docked pose with the predicted distance map. In order to tackle this bi-level optimization problem, we unroll the gradient descent of the inner loop and further derive a better initialization for roto-translation transformation based on spectral estimation. Compared to baselines, BiDock achieves a promising result of a maximum 234% relative improvement in challenging antibody-antigen docking problem.

PDF Details

NeurIPS Conference 2022 Conference Paper

Uncovering the Structural Fairness in Graph Contrastive Learning

Ruijia Wang
Xiao Wang
Chuan Shi
Le Song

Recent studies show that graph convolutional network (GCN) often performs worse for low-degree nodes, exhibiting the so-called structural unfairness for graphs with long-tailed degree distributions prevalent in the real world. Graph contrastive learning (GCL), which marries the power of GCN and contrastive learning, has emerged as a promising self-supervised approach for learning node representations. How does GCL behave in terms of structural fairness? Surprisingly, we find that representations obtained by GCL methods are already fairer to degree bias than those learned by GCN. We theoretically show that this fairness stems from intra-community concentration and inter-community scatter properties of GCL, resulting in a much clear community structure to drive low-degree nodes away from the community boundary. Based on our theoretical analysis, we further devise a novel graph augmentation method, called GRAph contrastive learning for DEgree bias (GRADE), which applies different strategies to low- and high-degree nodes. Extensive experiments on various benchmarks and evaluation protocols validate the effectiveness of the proposed method.

PDF Details

AAAI Conference 2020 Conference Paper

Multi-Component Graph Convolutional Collaborative Filtering

Xiao Wang
Ruijia Wang
Chuan Shi
Guojie Song
Qingyong Li

The interactions of users and items in recommender system could be naturally modeled as a user-item bipartite graph. In recent years, we have witnessed an emerging research effort in exploring user-item graph for collaborative ﬁltering methods. Nevertheless, the formation of user-item interactions typically arises from highly complex latent purchasing motivations, such as high cost performance or eye-catching appearance, which are indistinguishably represented by the edges. The existing approaches still remain the differences between various purchasing motivations unexplored, rendering the inability to capture ﬁne-grained user preference. Therefore, in this paper we propose a novel Multi-Component graph convolutional Collaborative Filtering (MCCF) approach to distinguish the latent purchasing motivations underneath the observed explicit user-item interactions. Speciﬁcally, there are two elaborately designed modules, decomposer and combiner, inside MCCF. The former ﬁrst decomposes the edges in user-item graph to identify the latent components that may cause the purchasing relationship; the latter then recombines these latent components automatically to obtain uniﬁed embeddings for prediction. Furthermore, the sparse regularizer and weighted random sample strategy are utilized to alleviate the overﬁtting problem and accelerate the optimization. Empirical results on three real datasets and a synthetic dataset not only show the signiﬁcant performance gains of MCCF, but also well demonstrate the necessity of considering multiple components.

PDF Details

UAI Conference 2019 Conference Paper

A Fast Proximal Point Method for Computing Exact Wasserstein Distance

Yujia Xie
Xiangfeng Wang 0001
Ruijia Wang
Hongyuan Zha

Wasserstein distance plays increasingly important roles in machine learning, stochastic programming and image processing. Major efforts have been under way to address its high computational complexity, some leading to approximate or regularized variations such as Sinkhorn distance. However, as we will demonstrate, regularized variations with large regularization parameter will degradate the performance in several important machine learning applications, and small regularization parameter will fail due to numerical stability issues with existing algorithms. We address this challenge by developing an Inexact Proximal point method for exact Optimal Transport problem (IPOT) with the proximal operator approximately evaluated at each iteration using projections to the probability simplex. The algorithm (a) converges to exact Wasserstein distance with theoretical guarantee and robust regularization parameter selection, (b) alleviates numerical stability issue, (c) has similar computational complexity to Sinkhorn, and (d) avoids the shrinking problem when applies to generative models. Furthermore, a new algorithm is proposed based on IPOT to obtain sharper Wasserstein barycenter.

Details