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作者： Liu, Shuai Ta, Na Lu, Mengye Liu, Gaocheng Bai, Weiling Li, Wenhui College of Computer Science Inner Mongolia University Hohhot010012 China Inner Mongolia Key Laboratory of Social Computing and Data Processing Hohhot010012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Changchun130012 China College of Computer Science and Technology Jilin University Changchun130012 China

Generated method of transcriptional regulatory networks remains an important research in biology. Many approaches have been proposed to construct transcriptional regulatory networks. However, with the increase of ChIP-seq and RNA-seq data, the speed of constructing transcriptional regulation networks is still a challenge. Moreover, parallel computing lacks application in constructing gene regulatory networks through the analysis of the relationships between transcription factors (TFs) and target genes (TGs). Therefore, in this paper, a parallel generated method of transcriptional regulatory networks was proposed. First, two datasets, Michigan Cancer Foundation – 7 (MCF-7) and Cardiomyocytes (CM) were applied. Then, a parallel method was used to generate transcriptional regulatory network with their transcription factors (TFs) and target genes (TGs). Finally, experimental results showed that 61% regulatory relations in MCF-7 were validated in the Gene Expression Omnibus (GEO), while 29% results needed further experimental verification. Besides, 56% regulatory relations in CM were consistent with GEO, while 33% results were not yet verified. Furthermore, speed of parallel algorithm was faster than traditional serial algorithm in generating transcriptional regulatory networks. © 2018 John Wiley & Sons, Ltd.

关键词： Transcription factors

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Simulation and Field Testing of Multiple Vehicles Collision Avoidance Algorithms

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IEEE/CAA Journal of Automatica Sinica 2020年第4期7卷 1045-1063页

作者： Chaoyue Zu Chao Yang Jian Wang Wenbin Gao Dongpu Cao Fei-Yue Wang the College of Computer Science and Technology Jilin UniversityChangchun 130012China Jiangsu XCMG Construction Machinery Research Institute Ltd. Xuzhou 221004China the College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of EducationJilin UniversityChangchun 130012 Chongqing Xibu Automobile Proving Ground Management Co.Ltd. Chongqing 404100China the State Grid JIBEI Electric Power Company Limited Management Training Center China the Advanced Vehicle Engineering Center Cranfield UniversityCranfield MK430ALUK the State Key Laboratory of Management and Control for Complex Systems Institute of AutomationChinese Academy of SciencesBeijing 100190China

A global planning algorithm for intelligent vehicles is designed based on the A* algorithm, which provides intelligent vehicles with a global path towards their destinations. A distributed real-time multiple vehicle collision avoidance(MVCA)algorithm is proposed by extending the reciprocal n-body collision avoidance method. MVCA enables the intelligent vehicles to choose their destinations and control inputs independently,without needing to negotiate with each other or with the coordinator. Compared to the centralized trajectory-planning algorithm, MVCA reduces computation costs and greatly improves the robustness of the system. Because the destination of each intelligent vehicle can be regarded as private, which can be protected by MVCA, at the same time MVCA can provide a real-time trajectory planning for intelligent vehicles. Therefore,MVCA can better improve the safety of intelligent vehicles. The simulation was conducted in MATLAB, including crossroads scene simulation and circular exchange position simulation. The results show that MVCA behaves safely and reliably. The effects of latency and packet loss on MVCA are also statistically investigated through theoretically formulating broadcasting process based on one-dimensional Markov chain. The results uncover that the tolerant delay should not exceed the half of deciding cycle of trajectory planning, and shortening the sending interval could alleviate the negative effects caused by the packet loss to an extent. The cases of short delay(< 100100 ms) and low packet loss(< 5%) can bring little influence to those trajectory planning algorithms that only depend on V2 V to sense the context, but the unpredictable collision may occur if the delay and packet loss are further worsened. The MVCA was also tested by a real intelligent vehicle, the test results prove the operability of MVCA.

关键词： Collision avoidance intelligent vehicles intervehicle communication simulation testing trajectory planning

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Semantics-Assisted Wasserstein Learning for Topic and Word Embeddings

Semantics-Assisted Wasserstein Learning for Topic and Word E...

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IEEE International Conference on Data Mining (ICDM)

作者： Changchun Li Ximing Li Jihong Ouyang Yiming Wang College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education China

ISBN: (数字)9781728183169

ISBN: (纸本)9781728183176

Wasserstein distance, defined as the cost (measured by word embeddings) of optimal transport plan for moving between two histograms, has been proven effective in tasks of natural language processing. In this paper, we extend Nonnegative Matrix Factorization (NMF) to a novel Wasserstein topic model, namely Semantics-Assisted Wasserstein Learning (SAWL), with simultaneous learning of topics and word embeddings. In Sawl, we formulate an NMF-like unified objective that integrates the regularized Wasserstein distance loss with a context factorization of word context information. Therefore, Sawl can refine the word embeddings for capturing corpus-specific semantics, enabling to boost topics and word embeddings each other. We analyze Sawl, and provide its dimensionality-dependent generalization bounds of reconstruction errors. Experimental results indicate that Sawl outperforms the state-of-the-art baseline models.

关键词： Histograms Conferences Semantics Natural language processing Data models Data mining Task analysis

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An unmanned aerial vehicle pose estimation system guided by desired shot 2

An unmanned aerial vehicle pose estimation system guided by ...

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2nd IEEE International Conference on Automation, Electronics and Electrical engineering, AUTEEE 2019

作者： Dou, Xinglei Ding, Qijian Du, Qiao Yang, Min Huo, Yuzhou Wang, Xin College of Software Engineering Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineer Ministry of Education Jilin University Changchun China

ISBN: (纸本)9781728150291

Unmanned aerial vehicles (UAVs) are widely used in aerial photography nowadays for their strong maneuverability, good image quality and high cost performance, while they have limited battery capacity and difficulty in operation. It is difficult to reach the ideal pose and get the desired shot by manual manipulation in a short time. To solve these problems, an UAV pose estimation system guided by desired shot is constructed. Either a sequence of images or a video is taken as input. The user interacts with the system to express the desired shot. The 3D-reconstruction is done by Structure from Motion (SfM). Then the Perspective-n-Point (PnP) problem is solved to estimate the ideal pose of the UAV. The experimental results proves that the system is effective and valid. © 2019 IEEE.

关键词： Aerial photography

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Supervised topic models with weighted words:multi-label document classification

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Frontiers of Information Technology & Electronic engineering 2018年第4期19卷 513-523页

作者： Yue-peng ZOU Ji-hong OUYANG Xi-ming LI College of Computer Science and Technology Jilin University MOE Key Laboratory of Symbolic Computation and Knowledge Engineering Jilin University

Supervised topic modeling algorithms have been successfully applied to multi-label document classification *** models include labeled latent Dirichlet allocation(L-LDA)and ***,these models neglect the class frequency information of words(i.e.,the number of classes where a word has occurred in the training data),which is significant for *** address this,we propose a method,namely the class frequency weight(CF-weight),to weight words by considering the class frequency *** CF-weight is based on the intuition that a word with higher(lower)class frequency will be less(more)*** this study,the CF-weight is used to improve L-LDA and dependency-LDA.A number of experiments have been conducted on real-world multi-label *** results demonstrate that CF-weight based algorithms are competitive with the existing supervised topic models.

关键词： Supervised topic model Multi-label classification Class frequency Labeled latent Dirichlet allocation (L-LDA) Dependency-LDA

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knowledge Compilation Methods Based on the Clausal Relevance and Extension Rule

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Chinese Journal of Electronics 2018年第5期27卷 1037-1042页

作者： NIU Dangdang LIU Lei LYU Shuai College of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering (Jilin University) Ministry of Education

We introduce the concepts of Relevancematrix(RM) and Relevance-set(RS). And we construct the association between RM and the knowledge compilation(KC) methods based on Extension rule(ER). Based on the basic parameters of RS and the relationship between RM and the KC methods based on ER, we design two efficient heuristics, called M2S(maximum sum of elements in RS and sum of literals in RS) and MNE(minimum number of maximum terms not extended by RS). Both of above heuristics intend to find the minimum set of maximum terms which cannot be extended by RS. Furthermore,we apply M2S and MNE on KCER. M2S KCER(KCER with M2S) and MNE KCER(KCER with MNE) are designed and implemented based on M2S and MNE, respectively. Experimentally, for the SAT instances with random lengths of clauses, M2S KCER and MNE KCER can improve the efficiency and quality of KCER sharply, and they are two best KC algorithms of EPCCL(each pair contains complementary literal) theory in all KC algorithms based on KCER.

关键词： Extension rule knowledge compilation Clausal relevance Heuristic strategy

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Warburg Effects in Cancer and Normal Proliferating Cells:Two Tales of the Same Name

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Genomics, Proteomics & Bioinformatics 2019年第3期17卷 273-286页

作者： Huiyan Sun Liang Chen Sha Cao Yanchun Liang Ying Xu The China-Japan Union Hospital Jilin UniversityChangchun 130033China MOE Key Laboratory of Symbolic Computation and Knowledge Engineering College of Computer Science and TechnologyJilin UniversityChangchun 130012China Computational Systems Biology Lab Department of Biochemistry and Molecular Biology and Institute of BioinformaticsUniversity of GeorgiaAthensGA 30602USA Faculty of Health Sciences University of MacaoTaipaMacao SAR 999078China Department of Biostatistics School of MedicineIndiana UniversityIndianapolisIN 46202USA Zhuhai Laboratory of MOE Key Laboratory of Symbolic Computation and Knowledge Engineering Zhuhai College of Jilin UniversityZhuhai 519041China

It has been observed that both cancer tissue cells and normal proliferating cells(NPCs)have the Warburg *** goal here is to demonstrate that they do this for different *** accomplish this,we have analyzed the transcriptomic data of over 7000 cancer and control tissues of 14 cancer types in TCGA and data of five NPC types in *** analyses reveal that NPCs accumulate large quantities of ATPs produced by the respiration process before starting the Warburg effect,to raise the intracellular pH from 6.8 to 7.2 and to prepare for cell division *** cell cycle starts,the cells start to rely on glycolysis for ATP generation followed by ATP hydrolysis and lactic acid release,to maintain the elevated intracellular pH as needed by cell division since together the three processes are pH *** cells go back to the normal respirationbased ATP production once the cell division phase *** comparison,cancer cells have reached their intracellular pH at 7.4 from top down as multiple acid-loading transporters are up-regulated and most acid-extruding ones except for lactic acid exporters are *** cells use continuous glycolysis for ATP production as way to acidify the intracellular space since the lactic acid secretion is decoupled from glycolysis-based ATP generation and is pH balanced by increased expressions of acid-loading ***-expression analyses suggest that lactic acid secretion is regulated by external,non-pH related ***,our data strongly suggest that the two cell types have the Warburg effect for very different reasons.

关键词： Cancer Warburg effect Fenton reaction Cell proliferation pH homeostasis

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GEOM-GCN: GEOMETRIC GRAPH CONVOLUTIONAL NETWORKS 8

GEOM-GCN: GEOMETRIC GRAPH CONVOLUTIONAL NETWORKS

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8th International Conference on Learning Representations, ICLR 2020

作者： Pei, Hongbin Wei, Bingzhe Chang, Kevin Chen-Chuan Lei, Yu Yang, Bo College of Computer Science and Technology Jilin University China Department of Electrical and Computer Engineering University of Illinois Urbana-Champaign United States Department of Computer Science University of Illinois Urbana-Champaign United States Department of Computing Hong Kong Polytechnic University Hong Kong Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education China

Message-passing neural networks (MPNNs) have been successfully applied to representation learning on graphs in a variety of real-world applications. However, two fundamental weaknesses of MPNNs' aggregators limit their ability to represent graph-structured data: losing the structural information of nodes in neighborhoods and lacking the ability to capture long-range dependencies in disassortative graphs. Few studies have noticed the weaknesses from different perspectives. From the observations on classical neural network and network geometry, we propose a novel geometric aggregation scheme for graph neural networks to overcome the two weaknesses. The behind basic idea is the aggregation on a graph can benefit from a continuous space underlying the graph. The proposed aggregation scheme is permutation-invariant and consists of three modules, node embedding, structural neighborhood, and bi-level aggregation. We also present an implementation of the scheme in graph convolutional networks, termed Geom-GCN, to perform transductive learning on graphs. Experimental results show the proposed Geom-GCN achieved state-of-the-art performance on a wide range of open datasets of graphs. © 2020 8th International Conference on Learning Representations, ICLR 2020. All rights reserved.

关键词： Message passing

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Grid Partition and Agglomeration for Bidirectional Hierarchical Clustering 2nd

Grid Partition and Agglomeration for Bidirectional Hierarchi...

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2nd EAI International Conference on Security and Privacy in New Computing Environments, SPNCE 2019

作者： Wu, Lei Chen, Hechang Yu, Xiangchun Chao, Sun Yu, Zhezhou Dou, RuiTing College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Changchun China

ISBN: (纸本)9783030213725

Clustering is an important data processing tool, which can be used to reveal the distribution structure of unfamiliar domain data, or as preprocess methods to magnify data object to accelerate subsequent processing or simplify models. However, the distribution of many real-world data in feature space is very complex or uneven. Besides, the similarity/distance is not easy to be properly defined in feature space with different dimensional quantity. Therefore, many existing clustering algorithms are not stable in real datasets, and better performance of different datasets relies on artificial special design, such as scale normalization. In this paper, we propose a bidirectional hierarchical clustering (BHC) algorithm with two phases. In the first phase (Top-down), based on the probability density function of data in different dimensions, the feature space is divided into over-segmented grids to adapt to the complex distribution of data. In the second phase (Bottom-up), based on statistical information, a robust distance instead of geometrical distance is defined to agglomerate the grids into a dendrogram. Compared with the individual data points, grids created in the first phase can carry more statistical information, and the magnified processing objects can accelerate the clustering process. The second phase enhances the algorithm’s ability by the ability of recognize arbitrary shape data clusters. The effectiveness of BHC is compared with 20 popular or recent clustering algorithms on 8 artificial datasets and 6 real-world datasets. And the results show that our algorithm can achieve good results on most datasets. In particular, BHC surpasses all the comparison algorithms involved in the experiment on all real-world datasets. In addition, in order to test the efficiency of the algorithm, we design an experiment which can test the influence of dimension and data size on the operation time. © 2019, ICST Institute for Computer Sciences, Social Informatics and Telecommuni

关键词： Clustering algorithms

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Reducing Fault-tolerant Overhead for Distributed Stream Processing with Approximate Backup

Reducing Fault-tolerant Overhead for Distributed Stream Proc...

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International Conference on Computer Communications and Networks (ICCCN)

作者： Yuan Zhuang Xiaohui Wei Hongliang Li Mingkai Hou Yundi Wang College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education Changchun China

ISBN: (数字)9781728166070

ISBN: (纸本)9781728166087

The stream processing model continuously processes online data in an on-pass fashion that can be more vulnerable to failures than other offline-data processing schemes. Checkpoint-based fault-tolerant methods have been widely used to enhance the reliability of stream processing systems. To ensure exact data recoveries upon failures, full-backup mechanisms are used to store a complete copy of data, which introduces substantial runtime overhead and increases output latency. In the meantime, a wide range of online processing applications prefer quick-and-dirty results with a slight degradation inaccuracy to delayed exact results. This paper introduces a novel approximate fault-tolerant problem (OAFP) with the objective of reducing the failure-free fault-tolerant overhead and ensuring user-defiled output accuracy requirement upon failure at the same time. We present an approximate fault-tolerant scheme based on sampling backup mechanism and study the trade-off between fault-tolerant overhead and output accuracy in stream processing systems. We proposed two algorithms to compute backup plans for both single-node failure and correlated failure scenarios. Extensive experiments with different types of stream topologies are conducted on our simulator to verify the correctness and effectiveness of our approach. We prove our solution guarantees the output accuracy requirement with minimum FT latency for directed acyclic graph (DAG) stream topologies with single-node failures.

关键词： Task analysis Fault tolerance Fault tolerant systems Topology Checkpointing computational modeling Data models

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