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Yankai Chen

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9 papers

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AAAI Conference 2026 Conference Paper

ConSurv: Multimodal Continual Learning for Survival Analysis

Dianzhi Yu
Conghao Xiong
Yankai Chen
Wenqian Cui
Xinni Zhang
Yifei Zhang
Hao Chen
Joseph J. Y. Sung

Survival prediction of cancers is crucial for clinical practice, as it informs mortality risks and influences treatment plans. However, a static model trained on a single dataset fails to adapt to the dynamically evolving clinical environment and continuous data streams, limiting its practical utility. While continual learning (CL) offers a solution to learn dynamically from new datasets, existing CL methods primarily focus on unimodal inputs and suffer from severe catastrophic forgetting in survival prediction. In real-world scenarios, multimodal inputs often provide comprehensive and complementary information, such as whole slide images and genomics; and neglecting inter-modal correlations negatively impacts the performance. To address the two challenges of catastrophic forgetting and complex inter-modal interactions between gigapixel whole slide images and genomics, we propose ConSurv, the first multimodal continual learning (MMCL) method for survival analysis. ConSurv incorporates two key components: Multi-staged Mixture of Experts (MS-MoE) and Feature Constrained Replay (FCR). MS-MoE captures both task-shared and task-specific knowledge at different learning stages of the network, including two modality encoders and the modality fusion component, learning inter-modal relationships. FCR further enhances learned knowledge and mitigates forgetting by restricting feature deviation of previous data at different levels, including encoder-level features of two modalities and the fusion-level representations. Additionally, we introduce a new benchmark integrating four datasets, Multimodal Survival Analysis Incremental Learning (MSAIL), for comprehensive evaluation in the CL setting. Extensive experiments demonstrate that ConSurv outperforms competing methods across multiple metrics.

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AAAI Conference 2026 Conference Paper

S²Drug: Bridging Protein Sequence and 3D Structure in Contrastive Representation Learning for Virtual Screening

Bowei He
Bowen Gao
Yankai Chen
Yanyan Lan
Chen Ma
Philip S. Yu
Ya-Qin Zhang
Wei-Ying Ma

Virtual screening (VS) is an essential task in drug discovery, focusing on the identification of small-molecule ligands that bind to specific protein pockets. Existing deep learning methods, from early regression models to recent contrastive learning approaches, primarily rely on structural data while overlooking protein sequences, which are more accessible and can enhance generalizability. However, directly integrating protein sequences poses challenges due to the redundancy and noise in large-scale protein-ligand datasets. To address these limitations, we propose S²Drug, a two-stage framework that explicitly incorporates protein Sequence information and 3D Structure context in protein-ligand contrastive representation learning. In the first stage, we perform protein sequence pretraining on ChemBL using an ESM2-based backbone, combined with a tailored data sampling strategy to reduce redundancy and noise on both protein and ligand sides. In the second stage, we fine-tune on PDBBind by fusing sequence and structure information through a residue-level gating module, while introducing an auxiliary binding site prediction task. This auxiliary task guides the model to accurately localize binding residues within the protein sequence and capture their 3D spatial arrangement, thereby refining protein-ligand matching. Across multiple benchmarks, S²Drug consistently improves virtual screening performance and achieves strong results on binding site prediction, demonstrating the value of bridging sequence and structure in contrastive learning.

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NeurIPS Conference 2025 Conference Paper

AdmTree: Compressing Lengthy Context with Adaptive Semantic Trees

Yangning Li
Shaoshen Chen
Yinghui Li
Yankai Chen
Hai-Tao Zheng
Hui Wang
Wenhao Jiang
Philip S Yu

The quadratic complexity of self-attention limits Large Language Models (LLMs) in processing long contexts, a capability vital for many advanced applications. Context compression aims to mitigate this computational barrier while preserving essential semantic information. However, existing methods often falter: explicit methods can sacrifice local detail, while implicit ones may exhibit positional biases, struggle with information degradation, or fail to capture long-range semantic dependencies. We introduce AdmTree, a novel framework for adaptive, hierarchical context compression designed with a core focus on maintaining high semantic fidelity while keep efficiency. AdmTree dynamically segments input based on information density, employing gist tokens to summarize variable-length segments as leaves in a semantic binary tree. This structure, combined with a lightweight aggregation mechanism and a frozen backbone LLM (minimizing new trainable parameters), enables efficient hierarchical abstraction of the context. By effectively preserving fine-grained details alongside global semantic coherence, mitigating position bias, and adapting dynamically to content, AdmTree comprehensively preserves the semantic information of lengthy context.

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NeurIPS Conference 2025 Conference Paper

Embracing Trustworthy Brain-Agent Collaboration as Paradigm Extension for Intelligent Assistive Technologies

Yankai Chen
Xinni Zhang
Yifei Zhang
Yangning Li
Henry Zou
Chunyu Miao
Weizhi Zhang
Steve (Xue) Liu

Brain-Computer Interfaces (BCIs) offer a direct communication pathway between the human brain and external devices, holding significant promise for individuals with severe neurological impairments. However, their widespread adoption is hindered by critical limitations, such as low information transfer rates and extensive user-specific calibration. To overcome these challenges, recent research has explored the integration of Large Language Models (LLMs), extending the focus from simple command decoding to understanding complex cognitive states. Despite these advancements, deploying agentic AI faces technical hurdles and ethical concerns. Due to the lack of comprehensive discussion on this emerging direction, this position paper argues that the field is poised for a paradigm extension from BCI to Brain-Agent Collaboration (BAC). We emphasize reframing agents as active and collaborative partners for intelligent assistance rather than passive brain signal data processors, demanding a focus on ethical data handling, model reliability, and a robust human-agent collaboration framework to ensure these systems are safe, trustworthy, and effective.

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AAAI Conference 2024 Conference Paper

Deep Structural Knowledge Exploitation and Synergy for Estimating Node Importance Value on Heterogeneous Information Networks

Yankai Chen
Yixiang Fang
Qiongyan Wang
Xin Cao
Irwin King

The classic problem of node importance estimation has been conventionally studied with homogeneous network topology analysis. To deal with practical network heterogeneity, a few recent methods employ graph neural models to automatically learn diverse sources of information. However, the major concern revolves around that their fully adaptive learning process may lead to insufficient information exploration, thereby formulating the problem as the isolated node value prediction with underperformance and less interpretability. In this work, we propose a novel learning framework namely SKES. Different from previous automatic learning designs, SKES exploits heterogeneous structural knowledge to enrich the informativeness of node representations. Then based on a sufficiently uninformative reference, SKES estimates the importance value for any input node, by quantifying its informativeness disparity against the reference. This establishes an interpretable node importance computation paradigm. Furthermore, SKES dives deep into the understanding that "nodes with similar characteristics are prone to have similar importance values" whilst guaranteeing that such informativeness disparity between any different nodes is orderly reflected by the embedding distance of their associated latent features. Extensive experiments on three widely-evaluated benchmarks demonstrate the performance superiority of SKES over several recent competing methods.

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AAAI Conference 2024 Conference Paper

HiHPQ: Hierarchical Hyperbolic Product Quantization for Unsupervised Image Retrieval

Zexuan Qiu
Jiahong Liu
Yankai Chen
Irwin King

Existing unsupervised deep product quantization methods primarily aim for the increased similarity between different views of the identical image, whereas the delicate multi-level semantic similarities preserved between images are overlooked. Moreover, these methods predominantly focus on the Euclidean space for computational convenience, compromising their ability to map the multi-level semantic relationships between images effectively. To mitigate these shortcomings, we propose a novel unsupervised product quantization method dubbed Hierarchical Hyperbolic Product Quantization (HiHPQ), which learns quantized representations by incorporating hierarchical semantic similarity within hyperbolic geometry. Specifically, we propose a hyperbolic product quantizer, where the hyperbolic codebook attention mechanism and the quantized contrastive learning on the hyperbolic product manifold are introduced to expedite quantization. Furthermore, we propose a hierarchical semantics learning module, designed to enhance the distinction between similar and non-matching images for a query by utilizing the extracted hierarchical semantics as an additional training supervision. Experiments on benchmark image datasets show that our proposed method outperforms state-of-the-art baselines.

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AAAI Conference 2024 Conference Paper

Influential Exemplar Replay for Incremental Learning in Recommender Systems

Xinni Zhang
Yankai Chen
Chenhao Ma
Yixiang Fang
Irwin King

Personalized recommender systems have found widespread applications for effective information filtering. Conventional models engage in knowledge mining within the static setting to reconstruct singular historical data. Nonetheless, the dynamics of real-world environments are in a constant state of flux, rendering acquired model knowledge inadequate for accommodating emergent trends and thus leading to notable recommendation performance decline. Given the typically prohibitive cost of exhaustive model retraining, it has emerged to study incremental learning for recommender systems with ever-growing data. In this paper, we propose an effective model-agnostic framework, namely INFluential Exemplar Replay (INFER). INFER facilitates recommender models in retaining the earlier assimilated knowledge, e.g., users' enduring preferences, while concurrently accommodating evolving trends manifested in users' new interaction behaviors. We commence with a vanilla implementation that centers on identifying the most representative data samples for effective consolidation of early knowledge. Subsequently, we propose an advanced solution, namely INFERONCE, to optimize the computational overhead associated with the vanilla implementation. Extensive experiments on four prototypical backbone models, two classic recommendation tasks, and four widely used benchmarks consistently demonstrate the effectiveness of our method as well as its compatibility for extending to several incremental recommender models.

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NeurIPS Conference 2023 Conference Paper

Mitigating the Popularity Bias of Graph Collaborative Filtering: A Dimensional Collapse Perspective

Yifei Zhang
Hao Zhu
Yankai Chen
Zixing Song
Piotr Koniusz
Irwin King

Graph-based Collaborative Filtering (GCF) is widely used in personalized recommendation systems. However, GCF suffers from a fundamental problem where features tend to occupy the embedding space inefficiently (by spanning only a low-dimensional subspace). Such an effect is characterized in GCF by the embedding space being dominated by a few of popular items with the user embeddings highly concentrated around them. This enhances the so-called Matthew effect of the popularity bias where popular items are highly recommend whereas remaining items are ignored. In this paper, we analyze the above effect in GCF and reveal that the simplified graph convolution operation (typically used in GCF) shrinks the singular space of the feature matrix. As typical approaches (i. e. , optimizing the uniformity term) fail to prevent the embedding space degradation, we propose a decorrelation-enhanced GCF objective that promotes feature diversity by leveraging the so-called principle of redundancy reduction in embeddings. However, unlike conventional methods that use the Euclidean geometry to relax hard constraints for decorrelation, we exploit non-Euclidean geometry. Such a choice helps maintain the range space of the matrix and obtain small condition number, which prevents the embedding space degradation. Our method outperforms contrastive-based GCF models on several benchmark datasets and improves the performance for unpopular items.

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IJCAI Conference 2020 Conference Paper

Efficient Community Search over Large Directed Graph: An Augmented Index-based Approach

Yankai Chen
Jie Zhang
Yixiang Fang
Xin Cao
Irwin King

Given a graph G and a query vertex q, the topic of community search (CS), aiming to retrieve a dense subgraph of G containing q, has gained much attention. Most existing works focus on undirected graphs which overlooks the rich information carried by the edge directions. Recently, the problem of community search over directed graphs (or CSD problem) has been studied [Fang et al. , 2019b]; it finds a connected subgraph containing q, where the in-degree and out-degree of each vertex within the subgraph are at least k and l, respectively. However, existing solutions are inefficient, especially on large graphs. To tackle this issue, in this paper we propose a novel index called D-Forest, which allows a CSD query to be completed within the optimal time cost. We further propose efficient index construction methods. Extensive experiments on six real large graphs show that our index-based query algorithm is up to two orders of magnitude faster than existing solutions.

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