EDBT 2026 Demo / reviewers in the wild / expert
Yi Ma 0005
dblp:69/1112-5
· DBLP profile ↗
21ranked-venue papers
4as first author
15since 2021 · last 2026
0000-0001-9375-6605ORCID · conflict
Domains — the database's venue-derived domains; a paper can count in several
Artificial intelligence and machine learning · 17 · 4 first-author · 14 since 2021Graphics, computer vision, multimedia, augmented reality and games · 5 · 3 since 2021Applied, interdisciplinary, general and emerging computing · 4 · 1 since 2021Databases, data management, data science and information retrieval · 3 · 3 since 2021
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2026 | AFE-Master: Enhancing LLM-Driven Autonomous Feature Engineering with Domain-Specific Language Parsing and Guided Local SearchabstractAutonomous Feature Engineering (AFE) is critical for improving predictive performance on tabular data by relieving humans from manual feature crafting. However, traditional AFE lacks the semantic guidance needed to fully exploit domain knowledge. Although large language models (LLMs) can, in principle, emulate experts, existing approaches typically operate in an open code space that directly generates and rewrites entire features; without a compositional structural representation and invariant constraints, edits are coarse and non-local, making it hard to distill interpretable features with high information content and rich hierarchical structure. Hebin Liang, Jianye Hao, Jinyi Liu 0002, Yi Ma 0005, Zilin Cao, Kun Shao, Zhaocheng Du, Fei Ni 0001, Yifu Yuan, Yan Zheng 0002 |
WWW | 4 |
| 2025 | FANS: A Flatness-Aware Network Structure for Generalization in Offline Reinforcement LearningabstractOffline reinforcement learning (RL) aims to learn optimal policies from static datasets while enhancing generalization to out-of-distribution (OOD) data. To mitigate overfitting to suboptimal behaviors in offline datasets, existing methods often relax constraints on policy and data or extract informative patterns through data-driven techniques. However, there has been limited exploration into structurally guiding the optimization process toward flatter regions of the solution space that offer better generalization. Motivated by this observation, we present \textit{FANS}, a generalization-oriented structured network framework that promotes flatter and robust policy learning by guiding the optimization trajectory through modular architectural design. FANS comprises four key components: (1) Residual Blocks, which facilitate compact and expressive representations; (2) Gaussian Activation, which promotes smoother gradients; (3) Layer Normalization, which mitigates overfitting; and (4) Ensemble Modeling, which reduces estimation variance. By integrating FANS into a standard actor-critic framework, we highlight that this remarkably simple architecture achieves superior performance across various tasks compared to many existing advanced methods. Moreover, we validate the effectiveness of FANS in mitigating overestimation and promoting generalization, demonstrating the promising potential of architectural design in advancing offline RL. Yi Ma 0005, Ting Guo 0004, Hongyao Tang, Wei Wei 0018, Jiye Liang |
NeurIPS | 2 |
| 2024 | Uni-RLHF: Universal Platform and Benchmark Suite for Reinforcement Learning with Diverse Human FeedbackabstractReinforcement Learning with Human Feedback (RLHF) has received significant attention for performing tasks without the need for costly manual reward design by aligning human preferences. It is crucial to consider diverse human feedback types and various learning methods in different environments. However, quantifying progress in RLHF with diverse feedback is challenging due to the lack of standardized annotation platforms and widely used unified benchmarks. To bridge this gap, we introduce **Uni-RLHF**, a comprehensive system implementation tailored for RLHF. It aims to provide a complete workflow from *real human feedback*, fostering progress in the development of practical problems. Uni-RLHF contains three packages: 1) a universal multi-feedback annotation platform, 2) large-scale crowdsourced feedback datasets, and 3) modular offline RLHF baseline implementations. Uni-RLHF develops a user-friendly annotation interface tailored to various feedback types, compatible with a wide range of mainstream RL environments. We then establish a systematic pipeline of crowdsourced annotations, resulting in large-scale annotated datasets comprising more than 15 million steps across 30 popular tasks. Through extensive experiments, the results in the collected datasets demonstrate competitive performance compared to those from well-designed manual rewards. We evaluate various design choices and offer insights into their strengths and potential areas of improvement. We wish to build valuable open-source platforms, datasets, and baselines to facilitate the development of more robust and reliable RLHF solutions based on realistic human feedback. The website is available at https://uni-rlhf.github.io/. Yifu Yuan, Jianye Hao, Yi Ma 0005, Zibin Dong, Hebin Liang, Jinyi Liu 0002, Zhixin Feng, Yan Zheng 0002 |
ICLR | 3 |
| 2024 | Unlock the Cognitive Generalization of Deep Reinforcement Learning via Granular Ball RepresentationabstractThe policies learned by humans in simple scenarios can be deployed in complex scenarios with the same task logic through limited feature alignment training, a process referred to as cognitive generalization or systematic generalization. Thus, a plausible conjecture is that unlocking cognitive generalization in DRL could enable effective generalization of policies from simple to complex scenarios through reward-agnostic fine-tuning. This would eliminate the need for designing reward functions in complex scenarios, thus reducing environment-building costs. In this paper, we propose a general framework to enhance the cognitive generalization ability of standard DRL methods. Our framework builds a cognitive latent space in a simple scenario, then segments the latent space to cluster samples with similar environmental influences into same subregion. During the fine-tuning in the complex scenario, the policy uses cognitive latent space to align the new sample with the same subregion sample collected from the simple scenario and approximates the rewards and Q values of the new samples for policy update. Based on this framework, we propose *Granular Ball Reinforcement Leaning* (GBRL), a practical algorithm via Variational Autoencoder (VAE) and Granular Ball Representation. GBRL achieves effective policy generalization on various difficult scenarios with the same task logic. Jiashun Liu, Jianye Hao, Yi Ma 0005, Shuyin Xia |
ICML | 3 |
| 2024 | Rethinking Decision Transformer via Hierarchical Reinforcement LearningabstractDecision Transformer (DT) is an innovative algorithm leveraging recent advances of the transformer architecture in reinforcement learning (RL). However, a notable limitation of DT is its reliance on recalling trajectories from datasets, losing the capability to seamlessly stitch sub-optimal trajectories together. In this work we introduce a general sequence modeling framework for studying sequential decision making through the lens of Hierarchical RL. At the time of making decisions, a high-level policy first proposes an ideal prompt for the current state, a low-level policy subsequently generates an action conditioned on the given prompt. We show DT emerges as a special case of this framework with certain choices of high-level and low-level policies, and discuss the potential failure of these choices. Inspired by these observations, we study how to jointly optimize the high-level and low-level policies to enable the stitching ability, which further leads to the development of new offline RL algorithms. Our empirical results clearly show that the proposed algorithms significantly surpass DT on several control and navigation benchmarks. We hope our contributions can inspire the integration of transformer architectures within the field of RL. Yi Ma 0005, Jianye Hao, Hebin Liang, Chenjun Xiao |
ICML | 1 |
| 2024 | ENOTO: Improving Offline-to-Online Reinforcement Learning with Q-Ensembles
Jianye Hao, Yi Ma 0005, Jinyi Liu 0002, Yan Zheng 0002, Zhaopeng Meng |
IJCAI | 3 |
| 2024 | Iteratively Refined Behavior Regularization for Offline Reinforcement LearningabstractOne of the fundamental challenges for offline reinforcement learning (RL) is ensuring robustness to data distribution. Whether the data originates from a near-optimal policy or not, we anticipate that an algorithm should demonstrate its ability to learn an effective control policy that seamlessly aligns with the inherent distribution of offline data. Unfortunately, behavior regularization, a simple yet effective offline RL algorithm, tends to struggle in this regard. In this paper, we propose a new algorithm that substantially enhances behavior-regularization based on conservative policy iteration. Our key observation is that by iteratively refining the reference policy used for behavior regularization, conservative policy update guarantees gradually improvement, while also implicitly avoiding querying out-of-sample actions to prevent catastrophic learning failures. We prove that in the tabular setting this algorithm is capable of learning the optimal policy covered by the offline dataset, commonly referred to as the in-sample optimal policy. We then explore several implementation details of the algorithm when function approximations are applied. The resulting algorithm is easy to implement, requiring only a few lines of code modification to existing methods. Experimental results on the D4RL benchmark indicate that our method outperforms previous state-of-the-art baselines in most tasks, clearly demonstrate its superiority over behavior regularization. Yi Ma 0005, Jianye Hao, Xiaohan Hu, Yan Zheng 0002, Chenjun Xiao |
NeurIPS | 1 |
| 2024 | CleanDiffuser: An Easy-to-use Modularized Library for Diffusion Models in Decision MakingabstractLeveraging the powerful generative capability of diffusion models (DMs) to build decision-making agents has achieved extensive success. However, there is still a demand for an easy-to-use and modularized open-source library that offers customized and efficient development for DM-based decision-making algorithms. In this work, we introduce CleanDiffuser, the first DM library specifically designed for decision-making algorithms. By revisiting the roles of DMs in the decision-making domain, we identify a set of essential sub-modules that constitute the core of CleanDiffuser, allowing for the implementation of various DM algorithms with simple and flexible building blocks. To demonstrate the reliability and flexibility of CleanDiffuser, we conduct comprehensive evaluations of various DM algorithms implemented with CleanDiffuser across an extensive range of tasks. The analytical experiments provide a wealth of valuable design choices and insights, reveal opportunities and challenges, and lay a solid groundwork for future research. CleanDiffuser will provide long-term support to the decision-making community, enhancing reproducibility and fostering the development of more robust solutions. Zibin Dong, Yifu Yuan, Jianye Hao, Fei Ni 0001, Yi Ma 0005, Pengyi Li 0001, Yan Zheng 0002 |
NeurIPS | 5 |
| 2024 | Unlock the Intermittent Control Ability of Model Free Reinforcement LearningabstractIntermittent control problems are common in real world. The interactions between the decision maker and the executor can be discontinuous (intermittent) due to various types of interruptions, e.g. unstable communication channel. Due to intermittent interaction, agents are unable to acquire the state sent by the executor and cannot transmit actions to the executor within a period of time step, i.e. bidirectional blockage, which may lead to inefficiencies of reinforcement learning policies and prevent the executors from completing the task. Such problem is not well studied in the RL community. In this paper, we model Intermittent control problem as an Intermittent Control Markov Decision Process, i.e agents are expected to generate action sequences corresponding to the unavailable states and transmit them before disabling interactions to ensure the smooth and effective motion of executors. However, directly generating multiple future actions in the original action space has unnatural motion issue and exploration difficulty. We propose **M**ulti-step **A**ction **R**epre**S**entation (**MARS**), which encodes a sequence of actions from the original action space to a compact and decodable latent space. Then based on the latent action sequence representation, the mainstream RL methods can be easily optimized to learn a smooth and efficient motion policy. Extensive experiments on simulation tasks and real-world robotic grasping tasks show that MARS significantly improves the learning efficiency and final performances compared with existing baselines. Jiashun Liu, Jianye Hao, Xiaotian Hao, Yi Ma 0005, Yan Zheng 0002, Yujing Hu, Tangjie Lv |
NeurIPS | 4 |
| 2023 | SplitNet: A Reinforcement Learning Based Sequence Splitting Method for the MinMax Multiple Travelling Salesman ProblemabstractMinMax Multiple Travelling Salesman Problem (mTSP) is an important class of combinatorial optimization problems with many practical applications, of which the goal is to minimize the longest tour of all vehicles. Due to its high computational complexity, existing methods for solving this problem cannot obtain a solution of satisfactory quality with fast speed, especially when the scale of the problem is large. In this paper, we propose a learning-based method named SplitNet to transform the single TSP solutions into the MinMax mTSP solutions of the same instances. Specifically, we generate single TSP solution sequences and split them into mTSP subsequences using an attention-based model trained by reinforcement learning. We also design a decision region for the splitting policy, which significantly reduces the policy action space on instances of various scales and thus improves the generalization ability of SplitNet. The experimental results show that SplitNet generalizes well and outperforms existing learning-based baselines and Google OR-Tools on widely-used random datasets of different scales and public datasets with fast solving speed. Hebin Liang, Yi Ma 0005, Zilin Cao, Fei Ni 0001, Jianye Hao |
AAAI | 2 |
| 2023 | A Hierarchical Imitation Learning-based Decision Framework for Autonomous DrivingabstractIn this paper, we focus on the decision-making challenge in autonomous driving, a central and intricate problem influencing the safety and practicality of autonomous vehicles. We propose an innovative hierarchical imitation learning framework that effectively alleviates the complexity of learning in autonomous driving decision-making problems by decoupling decision-making tasks into sub-problems. Specifically, the decision-making process is divided into two levels of sub-problems: the upper level directs the vehicle's lane selection and qualitative speed management, while the lower level implements precise control of the driving speed and direction. We harness Transformer-based models for solving each sub-problem, enabling overall hierarchical framework to comprehend and navigate diverse and various road conditions, ultimately resulting in improved decision-making. Through an evaluation in several typical driving scenarios within the SMARTS autonomous driving simulation environment, our proposed hierarchical decision-making framework significantly outperforms end-to-end reinforcement learning algorithms and behavior cloning algorithm, achieving an average pass rate of over 90%. Our framework's effectiveness is substantiated by its commendable achievements at the NeurIPS 2022 Driving SMARTS competition, where it secures dual track championships. Hebin Liang, Zibin Dong, Yi Ma 0005, Xiaotian Hao, Yan Zheng 0002, Jianye Hao |
CIKM | 3 |
| 2023 | Reining Generalization in Offline Reinforcement Learning via Representation DistinctionabstractOffline Reinforcement Learning (RL) aims to address the challenge of distribution shift between the dataset and the learned policy, where the value of out-of-distribution (OOD) data may be erroneously estimated due to overgeneralization. It has been observed that a considerable portion of the benefits derived from the conservative terms designed by existing offline RL approaches originates from their impact on the learned representation. This observation prompts us to scrutinize the learning dynamics of offline RL, formalize the process of generalization, and delve into the prevalent overgeneralization issue in offline RL. We then investigate the potential to rein the generalization from the representation perspective to enhance offline RL. Finally, we present Representation Distinction (RD), an innovative plug-in method for improving offline RL algorithm performance by explicitly differentiating between the representations of in-sample and OOD state-action pairs generated by the learning policy. Considering scenarios in which the learning policy mirrors the behavioral policy and similar samples may be erroneously distinguished, we suggest a dynamic adjustment mechanism for RD based on an OOD data generator to prevent data representation collapse and further enhance policy performance. We demonstrate the efficacy of our approach by applying RD to specially-designed backbone algorithms and widely-used offline RL algorithms. The proposed RD method significantly improves their performance across various continuous control tasks on D4RL datasets, surpassing several state-of-the-art offline RL algorithms. Yi Ma 0005, Hongyao Tang, Dong Li 0016, Zhaopeng Meng |
NeurIPS | 1 |
| 2022 | PAnDR: Fast Adaptation to New Environments from Offline Experiences via Decoupling Policy and Environment RepresentationsabstractDeep Reinforcement Learning (DRL) has been a promising solution to many complex decision-making problems. Nevertheless, the notorious weakness in generalization among environments prevent widespread application of DRL agents in real-world scenarios. Although advances have been made recently, most prior works assume sufficient online interaction on training environments, which can be costly in practical cases. To this end, we focus on an offline-training-online-adaptation setting, in which the agent first learns from offline experiences collected in environments with different dynamics and then performs online policy adaptation in environments with new dynamics. In this paper, we propose Policy Adaptation with Decoupled Representations (PAnDR) for fast policy adaptation. In offline training phase, the environment representation and policy representation are learned through contrastive learning and policy recovery, respectively. The representations are further refined by mutual information optimization to make them more decoupled and complete. With learned representations, a Policy-Dynamics Value Function (PDVF) network is trained to approximate the values for different combinations of policies and environments from offline experiences. In online adaptation phase, with the environment context inferred from few experiences collected in new environments, the policy is optimized by gradient ascent with respect to the PDVF. Our experiments show that PAnDR outperforms existing algorithms in several representative policy adaptation problems. Tong Sang, Hongyao Tang, Yi Ma 0005, Jianye Hao, Yan Zheng 0002, Zhaopeng Meng, Zhen Wang 0004 |
IJCAI | 3 |
| 2021 | A Multi-Graph Attributed Reinforcement Learning based Optimization Algorithm for Large-scale Hybrid Flow Shop Scheduling ProblemabstractHybrid Flow Shop Scheduling Problem (HFSP) is an essential problem in the automated warehouse scheduling, aiming at optimizing the sequence of jobs and the assignment of machines to utilize the makespan or other objectives. Existing algorithms adopt fixed search paradigm based on expert knowledge to seek satisfactory solutions. However, considering the varying data distribution and large scale of the practical HFSP, these methods fail to guarantee the quality of the obtained solution under the real-time requirement, especially facing extremely different data distribution. To address this challenge, we propose a novel Multi-Graph Attributed Reinforcement Learning based Optimization (MGRO) algorithm to better tackle the practical large-scale HFSP and improve the existing algorithm. Owing to incorporating the reinforcement learning-based policy search approach with classic search operators and the powerful multi-graph based representation, MGRO is capable of adjusting the search paradigm according to specific instances and enhancing the search efficiency. Specifically, we formulate the Gantt chart of the instance into the multi-graph-structured data. Then Graph Neural Network (GNN) and attention-based adaptive weighted pooling are employed to represent the state and make MGRO size-agnostic across arbitrary sizes of instances. In addition, a useful reward shaping approach is designed to facilitate model convergence. Extensive numerical experiments on both the publicly available dataset and real industrial dataset from Huawei Supply Chain Business Unit demonstrate the superiority of MGRO over existing baselines. Fei Ni 0001, Jianye Hao, Xialiang Tong, Mingxuan Yuan, Jiahui Duan, Yi Ma 0005, Kun He 0001 |
KDD | 7 |
| 2021 | A Hierarchical Reinforcement Learning Based Optimization Framework for Large-scale Dynamic Pickup and Delivery ProblemsabstractThe Dynamic Pickup and Delivery Problem (DPDP) is an essential problem in the logistics domain, which is NP-hard. The objective is to dynamically schedule vehicles among multiple sites to serve the online generated orders such that the overall transportation cost could be minimized. The critical challenge of DPDP is the orders are not known a priori, i.e., the orders are dynamically generated in real-time. To address this problem, existing methods partition the overall DPDP into fixed-size sub-problems by caching online generated orders and solve each sub-problem, or on this basis to utilize the predicted future orders to optimize each sub-problem further. However, the solution quality and efficiency of these methods are unsatisfactory, especially when the problem scale is very large. In this paper, we propose a novel hierarchical optimization framework to better solve large-scale DPDPs. Specifically, we design an upper-level agent to dynamically partition the DPDP into a series of sub-problems with different scales to optimize vehicles routes towards globally better solutions. Besides, a lower-level agent is designed to efficiently solve each sub-problem by incorporating the strengths of classical operational research-based methods with reinforcement learning-based policies. To verify the effectiveness of the proposed framework, real historical data is collected from the order dispatching system of Huawei Supply Chain Business Unit and used to build a functional simulator. Extensive offline simulation and online testing conducted on the industrial order dispatching system justify the superior performance of our framework over existing baselines. Yi Ma 0005, Xiaotian Hao, Jianye Hao, Xialiang Tong, Mingxuan Yuan, Jie Tang 0001, Zhaopeng Meng |
NeurIPS | 1 |
| 2020 | Large Scale Deep Reinforcement Learning in War-gamesabstractWar-game is a type of multi-agent real-time strategy game, with challenges of the large-scale decision-making space and the flexible and changeable battlefield situation. In addition to the military field, it has played a role in fields including epidemic prevention and pest control. In recent years, more and more learning algorithms have tried to solve this kind of game. However, the existing methods have not yet given a satisfactory solution for the war-game, especially when preparation time is limited. In this background, we try to solve a traditional war-game based on hexagon grids. We propose a hierarchical multi-agent reinforcement learning framework to rapidly training an AI model for the war-game. The higher-level network in our hierarchical framework is used for task decision, it solves the credit assignment problem between agents through cooperative training. The lower-level network is mainly used for route planning, and it can be reused through parameter sharing for all the agents and all the maps. To deal with various opponents, we improve the robustness of the model through a grouped self-play approach. In experiments, we get encouraging results which show that the hierarchical structure allows agents to learn their strategies effectively. Our final AI model demonstrates that our methods can effectively deal with the challenges in the war-game. Hanchao Wang, Hongyao Tang, Jianye Hao, Xiaotian Hao, Yi Ma 0005 |
BIBM | 6 |
| 2020 | Dynamic Knapsack Optimization Towards Efficient Multi-Channel Sequential AdvertisingabstractIn E-commerce, advertising is essential for merchants to reach their target users. The typical objective is to maximize the advertiser’s cumulative revenue over a period of time under a budget constraint. In real applications, an advertisement (ad) usually needs to be exposed to the same user multiple times until the user finally contributes revenue (e.g., places an order). However, existing advertising systems mainly focus on the immediate revenue with single ad exposures, ignoring the contribution of each exposure to the final conversion, thus usually falls into suboptimal solutions. In this paper, we formulate the sequential advertising strategy optimization as a dynamic knapsack problem. We propose a theoretically guaranteed bilevel optimization framework, which significantly reduces the solution space of the original optimization space while ensuring the solution quality. To improve the exploration efficiency of reinforcement learning, we also devise an effective action space reduction approach. Extensive offline and online experiments show the superior performance of our approaches over state-of-the-art baselines in terms of cumulative revenue. Xiaotian Hao, Zhaoqing Peng, Yi Ma 0005, Junqi Jin, Jianye Hao, Rongquan Bai, Mingzhou Xie, Zhenzhe Zheng 0001, Chuan Yu 0002, Han Li 0005, Jian Xu 0015, Kun Gai |
ICML | 3 |
| 2020 | Learning to Accelerate Heuristic Searching for Large-Scale Maximum Weighted b-Matching Problems in Online AdvertisingabstractBipartite b-matching is fundamental in algorithm design, and has been widely applied into diverse applications, such as economic markets, labor markets, etc. These practical problems usually exhibit two distinct features: large-scale and dynamic, which requires the matching algorithm to be repeatedly executed at regular intervals. However, existing exact and approximate algorithms usually fail in such settings due to either requiring intolerable running time or too much computation resource. To address this issue, based on a key observation that the matching instances vary not too much, we propose NeuSearcher which leverage the knowledge learned from previously instances to solve new problem instances. Specifically, we design a multichannel graph neural network to predict the threshold of the matched edges, by which the search region could be significantly reduced. We further propose a parallel heuristic search algorithm to iteratively improve the solution quality until convergence. Experiments on both open and industrial datasets demonstrate that NeuSearcher can speed up 2 to 3 times while achieving exactly the same matching solution compared with the state-of-the-art approximation approaches. Xiaotian Hao, Junqi Jin, Jianye Hao, Jin Li 0014, Weixun Wang, Yi Ma 0005, Zhenzhe Zheng 0001, Han Li 0005, Jian Xu 0015, Kun Gai |
IJCAI | 6 |
| 2020 | KoGuN: Accelerating Deep Reinforcement Learning via Integrating Human Suboptimal KnowledgeabstractReinforcement learning agents usually learn from scratch, which requires a large number of interactions with the environment. This is quite different from the learning process of human. When faced with a new task, human naturally have the common sense and use the prior knowledge to derive an initial policy and guide the learning process afterwards. Although the prior knowledge may be not fully applicable to the new task, the learning process is significantly sped up since the initial policy ensures a quick-start of learning and intermediate guidance allows to avoid unnecessary exploration. Taking this inspiration, we propose knowledge guided policy network (KoGuN), a novel framework that combines human prior suboptimal knowledge with reinforcement learning. Our framework consists of a fuzzy rule controller to represent human knowledge and a refine module to finetune suboptimal prior knowledge. The proposed framework is end-to-end and can be combined with existing policy-based reinforcement learning algorithm. We conduct experiments on several control tasks. The empirical results show that our approach, which combines suboptimal human knowledge and RL, achieves significant improvement on learning efficiency of flat RL algorithms, even with very low-performance human prior knowledge. Jianye Hao, Weixun Wang, Hongyao Tang, Yi Ma 0005, Yihai Duan, Yan Zheng 0002 |
IJCAI | 5 |
| 2020 | Combining sequence and network information to enhance protein-protein interaction predictionabstractBACKGROUND: Protein-protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. Most proteins perform their functions by interacting with other proteins, so predicting PPIs accurately is crucial for understanding cell physiology. RESULTS: Recently, graph convolutional networks (GCNs) have been proposed to capture the graph structure information and generate representations for nodes in the graph. In our paper, we use GCNs to learn the position information of proteins in the PPIs networks graph, which can reflect the properties of proteins to some extent. Combining amino acid sequence information and position information makes a stronger representation for protein, which improves the accuracy of PPIs prediction. CONCLUSION: In previous research methods, most of them only used protein amino acid sequence as input information to make predictions, without considering the structural information of PPIs networks graph. We first time combine amino acid sequence information and position information to make representations for proteins. The experimental results indicate that our method has strong competitiveness compared with several sequence-based methods. Leilei Liu, Xianglei Zhu, Yi Ma 0005, Haiyin Piao, Yaodong Yang 0002, Xiaotian Hao, Jiajie Peng |
BMC Bioinform. | 3 |
| 2019 | Integrating Sequence and Network Information to Enhance Protein-Protein Interaction Prediction Using Graph Convolutional NetworksabstractIdentification of protein-protein interactions (PPIs) is an important problem in biology, since PPIs are related to many essential cellular processes. The development of large-scale high-throughput experiments has produced a large number of PPIs data, however, these data are often noisy and their coverage is still limited. To overcome the shortcomings of experimental methods, many computational methods have been proposed for the prediction of PPIs. Among these methods, most of them solely take the amino acid sequence of protein as input information to make predictions. As PPIs data form the PPIs networks graph, the position information of proteins in the graph can reflect the properties of proteins to some extent, which is an important complement to protein sequence information. But previous works did not consider the graph structure information to improve the prediction performance. In this work, we first time apply graph convolutional networks (GCNs) to capture the protein's position information in the graph and combine amino acid sequence information and position information to make representations in the prediction task. Our experimental results show that our work outperforms the state-of-the-art sequence-based methods on several benchmark datasets and our work computationally is more efficient compared with previous works. Leilei Liu, Yi Ma 0005, Xianglei Zhu, Yaodong Yang 0002, Xiaotian Hao, Jiajie Peng |
BIBM | 2 |