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Learning continuous network emerging dynamics from scarce observations via data-adaptive stochastic processes

Science China(Information Sciences) 2024年第12期67卷 240-255页

作者： Jiaxu CUI Qipeng WANG Bingyi SUN Jiming LIU Bo YANG College of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Public Computer Education and Research Center Jilin University Department of Computer Science Hong Kong Baptist University

Learning network dynamics from the empirical structure and spatio-temporal observation data is crucial to revealing the interaction mechanisms of complex networks in a wide range of domains. However,most existing methods only aim at learning network dynamic behaviors generated by a specific ordinary differential equation instance, resulting in ineffectiveness for new ones, and generally require dense *** observed data, especially from network emerging dynamics, are usually difficult to obtain, which brings trouble to model learning. Therefore, learning accurate network dynamics with sparse, irregularly-sampled,partial, and noisy observations remains a fundamental challenge. We introduce a new concept of the stochastic skeleton and its neural implementation, i.e., neural ODE processes for network dynamics(NDP4ND), a new class of stochastic processes governed by stochastic data-adaptive network dynamics, to overcome the challenge and learn continuous network dynamics from scarce observations. Intensive experiments conducted on various network dynamics in ecological population evolution, phototaxis movement, brain activity, epidemic spreading, and real-world empirical systems, demonstrate that the proposed method has excellent data adaptability and computational efficiency, and can adapt to unseen network emerging dynamics, producing accurate interpolation and extrapolation with reducing the ratio of required observation data to only about 6% and improving the learning speed for new dynamics by three orders of magnitude.

关键词： complex networks network dynamics emerging spatio-temporal dynamics neural processes

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Error Formulas for Lagrange Projectors Determined by Cartesian Sets

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Journal of Systems Science & Complexity 2018年第4期31卷 1090-1102页

作者： LI Zhe ZHANG Shugong DONG Tian GONG Yihe School of Science Changchun University of Science and Technology Changchun 130022 China Key Laboratory of Symbolic Computation and Knowledge Engineering Jilin University Changchun 130012 China School of Mathematics Key Laboratory of Symbolic Computation and Knowledge Engineering (Ministry of Education) Jilin University Changchun 130012 China Northeast Electric Power University Jilin 132012 China School of Mathematics Jilin University Changchun 130012 China

This paper studies error formulas for Lagrange projectors determined by Cartesian sets. Cartesian sets are properly subgrids of tensor product grids. Given interpolated functions with all order continuous partial derivatives, the authors directly construct the good error formulas for Lagrange projectors determined by Cartesian sets. Owing to the special algebraic structure, such a good error formula is useful for error estimate.

关键词： Cartesian sets error formulas ideal interpolation multivariate polynomial interpolation

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Fold-based meta-analysis: a method for identifying differentially expressed genes in microarray data

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Journal of Information and computational Science 2013年第11期10卷 3453-3462页

作者： Tian, Yuan Bai, Tian Liu, Guixia Li, Zhangxiu Wu, Jianan Zhou, Chunguang College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Jilin University Changchun 130012 China College of Computer Science and Technology Changchun University Changchun 130022 China

The increase of microarray experiments brings a fresh challenge to analyze microarray data across datasets. Several methods have been developed and implemented. But the current tools were either complicated software with inefficiency methods or web applications, among which some were limited to specific data format. In this paper, we propose Fold-based Meta-analysis (FM), a method to identify Differentially Expressed Genes (DEGs) in microarray data. It could meta-analyze datasets in either the same or different platforms. We test FMT, respectively, on two published Arabidopsis datasets in one platform and three Mouse datasets in three different platforms, and then analyze the Gene Ontology (GO) terms or metabolic pathways of the most DEGs. Our results show that they are highly agreed on DEGs, and many of them are crucial and functional. In summary, our method is fast and practical. © 2013 Binary Information Press.

关键词： Genes

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A Simplified Rational Representation for Positive-Dimensional Polynomial Systems and SHEPWM Equations Solving

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Journal of Systems Science & Complexity 2017年第6期30卷 1470-1482页

作者： SHANG Baoxin ZHANG Shugong TAN Chang XIA Peng School of Mathematics Key Laboratory of Symbolic Computation and Knowledge Engineering (Ministry of Education) Jilin University College of Science Northeast Electric Power University College of Science Northeast Forestry University School of Mathematics Liaoning University

The paper is concerned with the improvement of the rational representation theory for solving positive-dimensional polynomial systems. The authors simplify the expression of rational representation set proposed by Tan and Zhang(2010), obtain the simplified rational representation with less rational representation sets, and hence reduce the complexity for representing the variety of a positive-dimensional ideal. As an application, the authors compute a "nearly" parametric solution for the SHEPWM problem with a fixed number of switching angles.

关键词： Positive-dimensional polynomial system solving rational univariate representation SHEPWM simplified rational representation

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SEOE:an option graph based semantically embedding method for prenatal depression detection

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Frontiers of Computer Science 2024年第6期18卷 245-258页

作者： Xiaosong HAN Mengchen CAO Dong XU Xiaoyue FENG Yanchun LIANG Xiaoduo LANG Renchu GUAN College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of EducationJilin UniversityChangchun 130012China Department of Electrical Engineering and Computer Science and Christopher S.Bond Life Sciences Center University of MissouriColumbiaMO 65211USA Department of Computer Science and Technology Zhuhai Laboratory of Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of EducationZhuhai College of Science and TechnologyZhuhai 519041China Jilin Provincial Institute of Population Science and Technology Changchun 130000China

Prenatal depression,which can affect pregnant women’s physical and psychological health and cause postpartum depression,is increasing ***,it is essential to detect prenatal depression early and conduct an attribution *** studies have used questionnaires to screen for prenatal depression,but the existing methods lack *** diagnose the early signs of prenatal depression and identify the key factors that may lead to prenatal depression from questionnaires,we present the semantically enhanced option embedding(SEOE)model to represent questionnaire *** can quantitatively determine the relationship and patterns between options and *** first quantifies options and resorts them,gathering options with little difference,since Word2Vec is highly dependent on *** resort task is transformed into an optimization problem involving the traveling salesman ***,all questionnaire samples are used to train the options’vector using ***,an LSTM and GRU fused model incorporating the cycle learning rate is constructed to detect whether a pregnant woman is suffering from *** verify the model,we compare it with other deep learning and traditional machine learning *** experiment results show that our proposed model can accurately identify pregnant women with depression and reach an F1 score of *** most relevant factors of depression found by SEOE are also verified in the *** addition,our model is of low computational complexity and strong generalization,which can be widely applied to other questionnaire analyses of psychiatric disorders.

关键词： questionnaire analyses text classification graph representation learning traveling salesman problem prenatal depression

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Combining GCN and Bi-LSTM for Protein Secondary Structure Prediction

Combining GCN and Bi-LSTM for Protein Secondary Structure Pr...

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2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

作者： Jin, Hailong Du, Wei Gu, Jiawei Zhang, Tianhao Shi, Xiaohu College of Computer Science and Technology of Jilin University Changchun China Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Changchun China

ISBN: (纸本)9781665401265

Protein secondary structure prediction is still a challenging task in bioinformatics, especially for 8-state (Q8) classification. To address this problem, we have proposed a deep learning based model by integrating graph convolutional network(GCN) and bidirectional long short-term memory (Bi-LSTM) network in this paper. In the model, GCN is utilized to synthesize the information of amino acids and their interactions, while Bi-LSTM has strong ability to capture the long-range dependencies of amino acids. For sequence representation, a new protein embedding derived by ProtTrans is used instead of the traditional amino acid one-hot encoding, together with evolutionary features of PSSM and HHM profiles. Amino acid contact potential derived from SPOTContact-Helical is used to construct amino acid graph. To verify the effectiveness of our proposed model, it is applied to several benchmark datasets, and obtained 78.05%, 76.81% 72.84%, 74.46% and 76.04% Q8 accuracy on CASP10, CASP11, CASP12, CB513 and TS115 datasets, respectively. Compared with 8 state-of-the-art competitions, our model obtained the best performance in most of datasets. © 2021 IEEE.

关键词： Amino acids

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Applying model-transformation techniques to ontology evolution

Applying model-transformation techniques to ontology evoluti...

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2nd International Conference on Grid Service engineering and Management, GSEM 2005 - Co-located with the 6th International Conference on Net.ObjectDays 2005, NODe 2005

作者： Jin, Longfei Liu, Lei Guo, Degui Key Laboratory of Symbolic Computation Knowledge Engineering of Ministry of Education of China Jilin University Changchun China

ISBN: (纸本)3885793989

Ontology evolution in the Model Driven Semantic Web can be looked as a process of model transformations. A model-transformation based conceptual framework for ontology evolution is presented in the paper. Applications of model transformations in every phase of ontology evolution process are described. The framework combines technologies of ontology evolution, Ontology Definition Metamodel and model transformations, and it can be looked as a method for ontology evolution in the Model Driven Semantic Web.

关键词： Ontology

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Computing minimal diagnosis with binary decision diagrams algorithm

Computing minimal diagnosis with binary decision diagrams al...

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6th International Conference on Fuzzy Systems and knowledge Discovery, FSKD 2009

作者： Wang, Kun Li, Zhan-Shan Ai, Yang Zhang, Yong-Gang Key Laboratory of Symbolic Computation Knowledge Engineering for Ministry of Education Jilin University Jilin Changchun China

ISBN: (纸本)9780769537351

In this paper we propose an algorithm of computing minimal diagnosis based on BDD (Binary Decision Diagram). First we give the concept of disjunction equations, and map the collection of conflict sets into disjunction equations, then we compile the system into a BDD, further we compute the minimal hitting sets by solving the BDD and minimizing hitting sets. The reliability and completeness of the algorithm are proved. Variable ordering and construct controlling of BDD are used to further reduce the size of final BDD and the number of non-minimal hitting sets to be generated. The efficiency of computing minimal hitting sets is highly improved. Experimental results show that the algorithm isn't restricted by the structure of system and conflict sets, compared with three algorithms in the references, it can generate all the minimal hitting sets, and it works well in random circumstances. © 2009 IEEE.

关键词： Binary decision diagrams

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Design for network camera based on DSP

Design for network camera based on DSP

引用

2006 International Conference on Hybrid Information Technology, ICHIT 2006

作者： Zhezhou, Yu Yuchen, Xie Congying, Lv Chunguang, Zhou Faner, Meng Lei, Liu Key Laboratory of Symbolic Computation and Knowledge Engineering Jilin University Ministry of Education Changchun 130012 China

ISBN: (纸本)0769526748

The hardware design of the DSP-based network camera is described in this paper which includes the implementation of CCD camera, DSP, Flash, SDRAM, CPLD, and Ethernet. The program of JPEG2000has been tested on the designed board and the result turns out to be good. It'll be implemented as a network camera with real-time video compression and transmission which can be connected to the Ethernet. © 2006 IEEE.

关键词： Cameras

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Extracting initial and reliable negative documents to enhance classification performance 1

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PAKDD 2006 International Workshop on knowledge Discovery in Life Science Literature, KDLL 2006

作者： Wang, Hui Zuo, Wanli Key Laboratory of Symbolic Computation and Knowledge Engineering Jilin University Ministry of Education Changchun 130012 China

ISBN: (数字)9783540328100

ISBN: (纸本)3540328092

Most existing text classification work assumes that training data are completely labeled. In real life, some information retrieval problems can only be described as learning a binary classifier from a set of incompletely labeled examples, where a small set of labeled positive examples and a very large set of unlabeled ones are provided. In this case, all of the traditional text classification methods can't work properly. In this paper, we propose a method called Weighted Voting Classifier, which is an improved 1-DNF algorithm. Experimental results on the Reuters-21578 set show that our algorithm Weighting Voting Classifier outperforms PEBL and one-class SVM in terms of F measure. Weighting Voting Classifier can achieve high F score when comparing with PEBL and one-class SVM. Furthermore, the reduction of iterations is 2.26 when comparing the method of PEBL with ours. © Springer-Verlag Berlin Heidelberg 2006.

关键词： Information retrieval

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