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Yujie Chen

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10 papers

2 author rows

AAAI Conference 2026 Conference Paper

TRACE: Transformation-Aware Graph Refinement for Reaction Condition Prediction

Yujie Chen
Tengfei Ma
Yuansheng Liu
Leyi Wei
Shu Wu
Dongsheng Cao
Yiping Liu
Xiangxiang Zeng

Identifying suitable reaction conditions is critical for chemical synthesis, as they directly affect yield, selectivity, and transformation feasibility. While recent methods have shown promising results, most approaches either encode reactants and products independently or rely on rule-based reaction graphs, both of which constrain the ability of the model to capture condition-relevant structural transformations. In this work, we propose TRACE, a transformation-aware graph refinement framework for reaction condition prediction. TRACE constructs atom-level joint graphs that integrate both reactant and product structures to represent condition-relevant transformations. A structure-aware encoder enriches atom features with local chemical context, followed by a dynamic interaction refinement module that adaptively infers task-specific edges. To further guide the model toward condition-relevant patterns, a mechanism regularized graph encoder incorporates reaction center information, enabling more accurate modeling of transformation mechanisms. Experiments on benchmark datasets show that TRACE achieves state-of-the-art performance across multiple condition types. The integration of transformation-aware refinement leads to improvements in prediction accuracy and generalization, while maintaining robust performance in challenging and realistic synthesis planning scenarios.

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AAAI Conference 2025 Conference Paper

GeCC: Generalized Contrastive Clustering with Domain Shifts Modeling

Yujie Chen
Wenhui Wu
Le Ou-Yang
Ran Wang
Debby D. Wang

Contrastive clustering performs clustering and data representation in a unified model, where instance- and cluster-level constrastive learning are conducted simultaneously. However, commonly-used data augmentation methods make contrastive mechanism effect but may cause representation learning getting stuck in domain-specific information, which further deteriorates clustering performance and limits generalization ability. To this end, we propose a new framework, named Generalized Contrastive Clustering with domain shifts modeling (GeCC), which can integrate diverse domain knowledge to improve the clustering performance. Specifically, we first design a cluster-guided domain shifts modeling module to synthesize a reference view with diverse domain information. Then, we introduce instance representation and cluster assignment contrastive modules with well-designed attention weights to guide the representation learning and clustering. In this way, our method can maximize the extraction of cluster-related information and avoid over-fitting domain-specific features. Experimental results on four benchmark datasets demonstrate that our proposed method consistently outperforms other state-of-the-art methods.

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ECAI Conference 2025 Conference Paper

PuriLight: A Lightweight Shuffle and Purification Framework for Monocular Depth Estimation

Yujie Chen
Li Zhang 0028
Xiaomeng Chu
Tian Zhang

We propose PuriLight, a lightweight and efficient framework for self-supervised monocular depth estimation, to address the dual challenges of computational efficiency and detail preservation. While recent advances in self-supervised depth estimation have reduced reliance on ground truth supervision, existing approaches remain constrained by either bulky architectures compromising practicality or lightweight models sacrificing structural precision. These dual limitations underscore the critical need to develop lightweight yet structurally precise architectures. Our framework addresses these limitations through a three-stage architecture incorporating three novel modules: the Shuffle-Dilation Convolution (SDC) module for local feature extraction, the Rotation-Adaptive Kernel Attention (RAKA) module for hierarchical feature enhancement, and the Deep Frequency Signal Purification (DFSP) module for global feature purification. Through effective collaboration, these modules enable PuriLight to achieve both lightweight and accurate feature extraction and processing. Extensive experiments demonstrate that PuriLight achieves state-of-the-art performance with minimal training parameters while maintaining exceptional computational efficiency. Codes will be available at https: //github. com/ishrouder/PuriLight.

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AAAI Conference 2025 Conference Paper

Region-Based Optimization in Continual Learning for Audio Deepfake Detection

Yujie Chen
Jiangyan Yi
Cunhang Fan
Jianhua Tao
Yong Ren
Siding Zeng
Chu Yuan Zhang
Xinrui Yan

Rapid advancements in speech synthesis and voice conversion bring convenience but also new security risks, creating an urgent need for effective audio deepfake detection. Although current models perform well, their effectiveness diminishes when confronted with the diverse and evolving nature of real-world deepfakes. To address this issue, we propose a continual learning method named Region-Based Optimization (RegO) for audio deepfake detection. Specifically, we use the Fisher information matrix to measure important neuron regions for real and fake audio detection, dividing them into four regions. First, we directly fine-tune the less important regions to quickly adapt to new tasks. Next, we apply gradient optimization in parallel for regions important only to real audio detection, and in orthogonal directions for regions important only to fake audio detection. For regions that are important to both, we use sample proportion-based adaptive gradient optimization. This region-adaptive optimization ensures an appropriate trade-off between memory stability and learning plasticity. Additionally, to address the increase of redundant neurons from old tasks, we further introduce the Ebbinghaus forgetting mechanism to release them, thereby promoting the model’s ability to learn more generalized discriminative features. Experimental results show our method achieves a 21.3 percent improvement in EER over the state-of-the-art continual learning approach RWM for audio deepfake detection. Moreover, the effectiveness of RegO extends beyond the audio deepfake detection domain, showing potential significance in other tasks, such as image recognition.

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NeurIPS Conference 2025 Conference Paper

Self-supervised Blending Structural Context of Visual Molecules for Robust Drug Interaction Prediction

Tengfei Ma
Kun Chen
Yongsheng Zang
Yujie Chen
Xuanbai Ren
Bosheng Song
Hongxin Xiang
Yiping Liu

Identifying drug-drug interactions (DDIs) is critical for ensuring drug safety and advancing drug development, a topic that has garnered significant research interest. While existing methods have made considerable progress, approaches relying solely on known DDIs face a key challenge when applied to drugs with limited data: insufficient exploration of the space of unlabeled pairwise drugs. To address these issues, we innovatively introduce S$^2$VM, a Self-supervised Visual pretraining framework for pair-wise Molecules, to fully fuse structural representations and explore the space of drug pairs for DDI prediction. S$^2$VM incorporates the explicit structure and correlations of visual molecules, such as the positional relationships and connectivity between functional substructures. Specifically, we blend the visual fragments of drug pairs into a unified input for joint encoding and then recover molecule-specific visual information for each drug individually. This approach integrates fine-grained structural representations from unlabeled drug pair data. By using visual fragments as anchors, S$^2$VM effectively captures the spatial information of local molecular components within visual molecules, resulting in more comprehensive embeddings of drug pairs. Experimental results show that S$^2$VM achieves state-of-the-art performance on widely used benchmarks, with Macro-F1 score improvements of 4. 21% and 3. 31%, respectively. Further extensive results and theoretical analysis demonstrate the effectiveness of S$^2$VM for both few-shot and novel drugs.

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AAAI Conference 2025 Conference Paper

S²DN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion

Tengfei Ma
Yujie Chen
Liang Wang
Xuan Lin
Bosheng Song
Xiangxiang Zeng

Inductive Knowledge Graph Completion (KGC) aims to infer missing facts between newly emerged entities within knowledge graphs (KGs), posing a significant challenge. While recent studies have shown promising results in inferring such entities through knowledge subgraph reasoning, they suffer from (i) the semantic inconsistencies of similar relations, and (ii) noisy interactions inherent in KGs due to the presence of unconvincing knowledge for emerging entities. To address these challenges, we propose a Semantic Structure-aware Denoising Network (S2DN) for inductive KGC. Our goal is to learn adaptable general semantics and reliable structures to distill consistent semantic knowledge while preserving reliable interactions within KGs. Specifically, we introduce a semantic smoothing module over the enclosing subgraphs to retain the universal semantic knowledge of relations. We incorporate a structure refining module to filter out unreliable interactions and offer additional knowledge, retaining robust structure surrounding target links. Extensive experiments conducted on three benchmark KGs demonstrate that S2DN surpasses the performance of state-of-the-art models. These results demonstrate the effectiveness of S2DN in preserving semantic consistency and enhancing the robustness of filtering out unreliable interactions in contaminated KGs.

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TMLR Journal 2024 Journal Article

Enhancing Low-Precision Sampling via Stochastic Gradient Hamiltonian Monte Carlo

Ziyi Wang
Yujie Chen
Qifan Song
Ruqi Zhang

Low-precision training has emerged as a promising low-cost technique to enhance the training efficiency of deep neural networks without sacrificing much accuracy. Its Bayesian counterpart can further provide uncertainty quantification and improved generalization accuracy. This paper investigates low-precision sampling via Stochastic Gradient Hamiltonian Monte Carlo (SGHMC) with low-precision and full-precision gradient accumulators for both strongly log-concave and non-log-concave distributions. Theoretically, our results show that to achieve $\epsilon$-error in the 2-Wasserstein distance for non-log-concave distributions, low-precision SGHMC achieves quadratic improvement ($\tilde{\mathcal{O}}\left({\epsilon^{-2}{\mu^*}^{-2}\log^2\left({\epsilon^{-1}}\right)}\right)$) compared to the state-of-the-art low-precision sampler, Stochastic Gradient Langevin Dynamics (SGLD) ($\tilde{\mathcal{O}}\left({{\epsilon}^{-4}{\lambda^{*}}^{-1}\log^5\left({\epsilon^{-1}}\right)}\right)$). Moreover, we prove that low-precision SGHMC is more robust to the quantization error compared to low-precision SGLD due to the robustness of the momentum-based update w.r.t. gradient noise. Empirically, we conduct experiments on synthetic data, and MNIST, CIFAR-10 \& CIFAR-100 datasets, which validate our theoretical findings. Our study highlights the potential of low-precision SGHMC as an efficient and accurate sampling method for large-scale and resource-limited machine learning.

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AAAI Conference 2024 Conference Paper

Progressive Distillation Based on Masked Generation Feature Method for Knowledge Graph Completion

Cunhang Fan
Yujie Chen
Jun Xue
Yonghui Kong
Jianhua Tao
Zhao Lv

In recent years, knowledge graph completion (KGC) models based on pre-trained language model (PLM) have shown promising results. However, the large number of parameters and high computational cost of PLM models pose challenges for their application in downstream tasks. This paper proposes a progressive distillation method based on masked generation features for KGC task, aiming to significantly reduce the complexity of pre-trained models. Specifically, we perform pre-distillation on PLM to obtain high-quality teacher models, and compress the PLM network to obtain multi-grade student models. However, traditional feature distillation suffers from the limitation of having a single representation of information in teacher models. To solve this problem, we propose masked generation of teacher-student features, which contain richer representation information. Furthermore, there is a significant gap in representation ability between teacher and student. Therefore, we design a progressive distillation method to distill student models at each grade level, enabling efficient knowledge transfer from teachers to students. The experimental results demonstrate that the model in the pre-distillation stage surpasses the existing state-of-the-art methods. Furthermore, in the progressive distillation stage, the model significantly reduces the model parameters while maintaining a certain level of performance. Specifically, the model parameters of the lower-grade student model are reduced by 56.7\% compared to the baseline.

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NeurIPS Conference 2023 Conference Paper

OFCOURSE: A Multi-Agent Reinforcement Learning Environment for Order Fulfillment

Yiheng Zhu
Yang Zhan
Xuankun Huang
Yuwei Chen
Yujie Chen
Jiangwen Wei
Wei Feng
Yinzhi Zhou

The dramatic growth of global e-commerce has led to a surge in demand for efficient and cost-effective order fulfillment which can increase customers' service levels and sellers' competitiveness. However, managing order fulfillment is challenging due to a series of interdependent online sequential decision-making problems. To clear this hurdle, rather than solving the problems separately as attempted in some recent researches, this paper proposes a method based on multi-agent reinforcement learning to integratively solve the series of interconnected problems, encompassing order handling, packing and pickup, storage, order consolidation, and last-mile delivery. In particular, we model the integrated problem as a Markov game, wherein a team of agents learns a joint policy via interacting with a simulated environment. Since no simulated environment supporting the complete order fulfillment problem exists, we devise Order Fulfillment COoperative mUlti-agent Reinforcement learning Scalable Environment (OFCOURSE) in the OpenAI Gym style, which allows reproduction and re-utilization to build customized applications. By constructing the fulfillment system in OFCOURSE, we optimize a joint policy that solves the integrated problem, facilitating sequential order-wise operations across all fulfillment units and minimizing the total cost of fulfilling all orders within the promised time. With OFCOURSE, we also demonstrate that the joint policy learned by multi-agent reinforcement learning outperforms the combination of locally optimal policies. The source code of OFCOURSE is available at: https: //github. com/GitYiheng/ofcourse.

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AAMAS Conference 2019 Conference Paper

Can Sophisticated Dispatching Strategy Acquired by Reinforcement Learning? : A Case Study in Dynamic Courier Dispatching System

Yujie Chen
Yu Qian
Yichen Yao
Zili Wu
Rongqi Li
Yinzhi Zhou
Haoyuan Hu
Yinghui Xu

In this paper, we study a courier dispatching problem (CDP) raised from an online pickup-service platform of Alibaba. The CDP aims to assign a set of couriers to serve pickup requests with stochastic spatial and temporal arrival rate among urban regions. The objective is to maximize the revenue of served requests given a limited number of couriers over a period of time. Many online algorithms such as dynamic matching and vehicle routing strategy from existing literature could be applied to tackle this problem. However, these methods rely on appropriately predefined optimization objectives at each decision point, which is hard in dynamic situations. This paper formulates the CDP as a Markov decision process (MDP) and proposes a data-driven approach to derive the optimal dispatching rule-set under different scenarios. Our method stacks multi-layer images of the spatial-and-temporal map and apply multi-agent reinforcement learning (MARL) techniques to evolve dispatching models. This method solves the learning inefficiency caused by traditional centralized MDP modeling. Through comprehensive experiments on both artificial dataset and real-world dataset, we show: 1) By utilizing historical data and considering long-term revenue gains, MARL achieves better performance than myopic online algorithms; 2) MARL is able to construct the mapping between complex scenarios to sophisticated decisions such as the dispatching rule. 3) MARL has the scalability to adopt in large-scale real-world scenarios. Proc. of the 18th International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2019), N. Agmon, M. E. Taylor, E. Elkind, M. Veloso (eds.), May 13–17, 2019, Montreal, Canada. © 2019 International Foundation for Autonomous Agents and Multiagent Systems (www. ifaamas. org). All rights reserved.

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