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Towards Exploring Large Molecular Space:An Efficient Chemical Genetic Algorithm

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Journal of computer Science & technology 2022年第6期37卷 1464-1477页

作者： Jian-Fu Zhu Zhong-Kai Hao Qi Liu Yu Yin Cheng-Qiang Lu Zhen-Ya Huang En-Hong Chen Anhui Province Key laboratory of big data analysis and Application School of Computer Science and TechnologyUniversity of Science and Technology of ChinaHefei 230026China

Generating molecules with desired properties is an important task in chemistry and *** efficient method may have a positive impact on finding drugs to treat diseases like *** mining and artificial intelligence may be good ways to find an efficient ***,both the generative models based on deep learning and the work based on genetic algorithms have made some progress in generating molecules and optimizing the molecule’s ***,existing methods have defects in the experimental evaluation *** methods also need to be improved in efficiency and *** solve these problems,we propose a method named the Chemical Genetic Algorithm for Large Molecular Space(CALM).Specifically,CALM employs a scalable and efficient molecular representation called molecular *** we design corresponding crossover,mutation,and mask operators inspired by domain knowledge and previous *** apply our genetic algorithm to several tasks related to molecular property optimization and constraint molecular *** results of these tasks show that our approach outperforms the other state-of-the-art deep learning and genetic algorithm methods,where the z tests performed on the results of several experiments show that our method is more than 99%likely to be *** the same time,based on the experimental results,we point out the defects in the experimental evaluation standard which affects the fair evaluation of all previous *** these defects helps to objectively evaluate the performance of all work.

关键词： data mining molecular generation genetic algorithm drug discovery artificial intelligence

Study on Information Diffusion analysis in Social Networks and Its Applications

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International Journal of Automation and computing 2018年第4期15卷 377-401页

作者： Biao Chang Tong Xu Qi Liu En-Hong Chen Anhui Province Key laboratory of big data analysis and Application School of Computer ScienceUniversity of Science and Technology of China

Due to the prevalence of social network services, more and more attentions are paid to explore how information diffuses and users affect each other in these networks, which has a wide range of applications, such as viral marketing, reposting prediction and social recommendation. Therefore, in this paper, we review the recent advances on information diffusion analysis in social networks and its applications. Specifically, we first shed light on several popular models to describe the information diffusion process in social networks, which enables three practical applications, i.e., influence evaluation, influence maximization and information source detection. Then, we discuss how to evaluate the authority and influence based on network structures. After that, current solutions to influence maximiza- tion and information source detection are discussed in detail, respectively. Finally, some possible research directions of information diffu- sion analysis are listed for further study.

关键词： Information diffusion influence evaluation influence maximization information source detection social network.

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Snapshot boosting: a fast ensemble framework for deep neural networks

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Science China(Information Sciences) 2020年第1期63卷 77-88页

作者： Wentao ZHANG Jiawei JIANG Yingxia SHAO Bin CUI Center for data Science Peking University national engineering laboratory for big data analysis and Applications Department of computer Science Beijing Key lab of Intelligent Telecommunications Software and Multimedia School of Computer ScienceBeijing University of Posts and Telecommunications Key lab of High Confidence Software Technologies Department of Computer SciencePeking University

Boosting has been proven to be effective in improving the generalization of machine learning models in many fields. It is capable of getting high-diversity base learners and getting an accurate ensemble model by combining a sufficient number of weak learners. However, it is rarely used in deep learning due to the high training budget of the neural network. Another method named snapshot ensemble can significantly reduce the training budget, but it is hard to balance the tradeoff between training costs and diversity. Inspired by the ideas of snapshot ensemble and boosting, we propose a method named snapshot boosting. A series of operations are performed to get many base models with high diversity and accuracy, such as the use of the validation set, the boosting-based training framework, and the effective ensemble strategy. Last, we evaluate our method on the computer vision(CV) and the natural language processing(NLP) tasks, and the results show that snapshot boosting can get a more balanced trade-off between training expenses and ensemble accuracy than other well-known ensemble methods.

关键词： ensemble learning deep learning boosting neural network snapshot ensemble

Unsupervised feature selection based on Markov blanket and particle swarm optimization

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Journal of Systems engineering and Electronics 2017年第1期28卷 151-161页

作者： Yintong Wang Jiandong Wang Hao Liao Haiyan Chen College of computer Science and technology Nanjing University of Aeronautics and Astronautics Key laboratory of Trusted Cloud Computing and big data analysis Nanjing Xiaozhuang University College of computer Science and Software engineering Shenzhen University

Feature selection plays an important role in data mining and recognition, especially in the large scale text, image and biological data. Specifically, the class label information is unavailable to guide the selection of minimal feature subset in unsupervised feature selection, which is challenging and interesting. An unsupervised feature selection based on Markov blanket and particle swarm optimization is proposed named as UFSMB-PSO. The proposed method seeks to find the high-quality feature subset through multi-particles' cooperation of particle swarm optimization without using any learning algorithms. Moreover, the features' relevance will be computed based on an information metric of relevance gain, which provides an information theoretical foundation for finding the minimization of the redundancy between features. Our results on several benchmark datasets demonstrate that UFSMB-PSO can achieve significant improvement over state of the art unsupervised methods. © 1990-2011 Beijing Institute of Aerospace Information.

关键词： Character recognition data mining Feature extraction Information theory

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A survey on dynamic graph processing on GPUs: concepts, terminologies and systems

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Frontiers of computer Science 2024年第4期18卷 1-23页

作者： Hongru GAO Xiaofei LIAO Zhiyuan SHAO Kexin LI Jiajie CHEN Hai JIN national engineering Research Center for big data technology and System/Services Computing technology and System lab/Cluster and Grid Computing lab School of Computer Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China Zhejiang lab Hangzhou 311121China

Graphs that are used to model real-world entities with vertices and relationships among entities with edges,have proven to be a powerful tool for describing real-world problems in *** most real-world scenarios,entities and their relationships are subject to constant *** that record such changes are called dynamic *** recent years,the widespread application scenarios of dynamic graphs have stimulated extensive research on dynamic graph processing systems that continuously ingest graph updates and produce up-to-date graph analytics *** the scale of dynamic graphs becomes larger,higher performance requirements are demanded to dynamic graph processing *** the massive parallel processing power and high memory bandwidth,GPUs become mainstream vehicles to accelerate dynamic graph processing ***-based dynamic graph processing systems mainly address two challenges:maintaining the graph data when updates occur(i.e.,graph updating)and producing analytics results in time(i.e.,graph computing).In this paper,we survey GPU-based dynamic graph processing systems and review their methods on addressing both graph updating and graph *** comprehensively discuss existing dynamic graph processing systems on GPUs,we first introduce the terminologies of dynamic graph processing and then develop a taxonomy to describe the methods employed for graph updating and graph *** addition,we discuss the challenges and future research directions of dynamic graph processing on GPUs.

关键词： dynamic graphs graph processing graph algorithms GPUs

The Existence of a Class of Balanced Multi-output Rotation Symmetric Boolean Functions

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Chinese Journal of Electronics 2018年第5期27卷 995-1001页

作者： DU Jiao FU Shaojing QU Longjiang LI Chao PANG Shanqi College of Mathematics and Information Science Henan Normal University Henan engineering laboratory for big data Statistical analysis and Optimal Control Henan Normal University College of computer Science National University of Defense Technology College of Liberal Arts and Science National University of Defense Technology

A new characterization of balanced rotation symmetric（n, m）-functions is presented. Based on the characterization, the nonexistence of balanced rotation symmetric（p;, m）-functions is determined, where p is an odd prime and m ≥ 2. And there exist balanced rotation symmetric（2;, m）-functions for 2 ≤ m ≤ 2;-r. With the help of these results, we also prove that there exist rotation symmetric resilient（2;, m）-functions for 2 ≤ m ≤ 2;-r-1.

关键词： Cryptography Rotation symmetric Orbit matrix Correlation immune Resilient functions

ARCHER:a ReRAM-based accelerator for compressed recommendation systems

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Frontiers of computer Science 2024年第5期18卷 147-160页

作者： Xinyang SHEN Xiaofei LIAO Long ZHENG Yu HUANG Dan CHEN Hai JIN national engineering Research Center for big data technology and System Services Computing Technology and System LabClusters and Grid Computing LabSchool of Computer Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China

Modern recommendation systems are widely used in modern data *** random and sparse embedding lookup operations are the main performance bottleneck for processing recommendation systems on traditional platforms as they induce abundant data movements between computing units and ***-based processing-in-memory(PIM)can resolve this problem by processing embedding vectors where they are ***,the embedding table can easily exceed the capacity limit of a monolithic ReRAM-based PIM chip,which induces off-chip accesses that may offset the PIM ***,we deploy the decomposed model on-chip and leverage the high computing efficiency of ReRAM to compensate for the decompression performance *** this paper,we propose ARCHER,a ReRAM-based PIM architecture that implements fully yon-chip recommendations under resource ***,we make a full analysis of the computation pattern and access pattern on the decomposed *** on the computation pattern,we unify the operations of each layer of the decomposed model in multiply-and-accumulate *** on the access observation,we propose a hierarchical mapping schema and a specialized hardware design to maximize resource *** the unified computation and mapping strategy,we can coordinatethe inter-processing elements *** evaluation shows that ARCHER outperforms the state-of-the-art GPU-based DLRM system,the state-of-the-art near-memory processing recommendation system RecNMP,and the ReRAM-based recommendation accelerator REREC by 15.79×,2.21×,and 1.21× in terms of performance and 56.06×,6.45×,and 1.71× in terms of energy savings,respectively.

关键词： recommendation system ReRAM processing-in-memory embedding layer

Variational reconstruction using subdivision surfaces with continuous sharpness control

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Computational Visual Media 2017年第3期3卷 217-228页

作者： Xiaoqun Wu Jianmin Zheng Yiyu Cai Haisheng Li Beijing Key lab of big data technology for Food Safety School of Computer and Information EngineeringBeijing Technology and Business University College of engineering Nanyang Technological University

We present a variational method for subdivision surface reconstruction from a noisy dense mesh. A new set of subdivision rules with continuous sharpness control is introduced into Loop subdivision for better modeling subdivision surface features such as semi-sharp creases, creases, and corners. The key idea is to assign a sharpness value to each edge of the control mesh to continuously control the surface *** on the new subdivision rules, a variational model with L_1 norm is formulated to find the control mesh and the corresponding sharpness values of the subdivision surface that best fits the input mesh. An iterative solver based on the augmented Lagrangian method and particle swarm optimization is used to solve the resulting non-linear, non-differentiable optimization problem. Our experimental results show that our method can handle meshes well with sharp/semi-sharp features and noise.

关键词： variational model subdivision surface sharpness surface reconstruction L1 norm

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A hybrid memory architecture supporting fine-grained data migration

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Frontiers of computer Science 2024年第2期18卷 31-41页

作者： Ye CHI Jianhui YUE Xiaofei LIAO Haikun LIU Hai JIN national engineering Research Center for big data technology and System Services Computing Technology and System LabCluster and Grid Computing LabSchool of Computer Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China Department of computer Science Michigan Technological UniversityMichigan 49931USA

Hybrid memory systems composed of dynamic random access memory(DRAM)and Non-volatile memory(NVM)often exploit page migration technologies to fully take the advantages of different memory *** previous proposals usually migrate data at a granularity of 4 KB pages,and thus waste memory bandwidth and DRAM *** this paper,we propose Mocha,a non-hierarchical architecture that organizes DRAM and NVM in a flat address space physically,but manages them in a cache/memory *** the commercial NVM device-Intel Optane DC Persistent Memory Modules(DCPMM)actually access the physical media at a granularity of 256 bytes(an Optane block),we manage the DRAM cache at the 256-byte size to adapt to this feature of *** design not only enables fine-grained data migration and management for the DRAM cache,but also avoids write amplification for Intel Optane *** also create an Indirect Address Cache(IAC)in Hybrid Memory Controller(HMC)and propose a reverse address mapping table in the DRAM to speed up address translation and cache ***,we exploit a utility-based caching mechanism to filter cold blocks in the NVM,and further improve the efficiency of the DRAM *** implement Mocha in an architectural *** results show that Mocha can improve application performance by 8.2%on average(up to 24.6%),reduce 6.9%energy consumption and 25.9%data migration traffic on average,compared with a typical hybrid memory architecture-HSCC.

关键词： non-volatile memory hybrid memory system data migration fine-grained caching