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arXiv 2018年

作者： Zhang, Xi Sheryl Chen, Dandi Zhu, Yongjun Che, Chao Su, Chang Zhao, Sendong Min, Xu Wang, Fei Department of Healthcare Policy and Research Weill Cornell Medicine Cornell University Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University School of Electronic and Information Engineering Xian Jiaotong University China Research Center for Social Computing and Information Retrieval Harbin Institute of Technology China Department of Computer Science and Engineering Tsinghua University China

This paper presents details of our winning solutions to the task IV of NIPS 2017 Competition Track entitled Classifying Clinically Actionable Genetic Mutations. The machine learning task aims to classify genetic mutations based on text evidence from clinical literature with promising performance. We develop a novel multi-view machine learning framework with ensemble classification models to solve the problem. During the Challenge, feature combinations derived from three views including document view, entity text view, and entity name view, which complements each other, are comprehensively explored. As the final solution, we submitted an ensemble of nine basic gradient boosting models which shows the best performance in the evaluation. The approach scores 0.5506 and 0.6694 in terms of logarithmic loss on a fixed split in stage-1 testing phase and 5-fold cross validation respectively, which also makes us ranked as a top-1 team1 out of more than 1300 solutions in NIPS 2017 Competition Track IV. Copyright © 2018, The Authors. All rights reserved.

关键词： Machine learning

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Palmprint recognition using phase congruency and region-based orientation code

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Journal of Computational and Theoretical Nanoscience 2016年第4期13卷 2461-2466页

作者： Zhang, Jianxin Liu, Ligang Key Lab of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian116622 China

In this paper, a novel palmprint recognition method by a combination of phase congruency model and region-based orientation code approach is proposed. Palmprint phase congruency feature images are firstly achieved by the multi-scale and multi-orientation 2D Log-Gabor wavelet filters. Then, a region orientation code approach, which is based on the orientation competition result of the sub-region images, is put forward to give more compact representation of palmprint phase congruency feature images. The proposed palmprint recognition method can provide more robust discriminant feature. The experiment results on the public PolyU palmprint database show the good recognition performance of proposed method. © Copyright 2016 American Scientific Publishers All rights reserved.

关键词： Palmprint recognition

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Solving probability reasoning based on DNA strand displacement and probability modules

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Computational biology and chemistry 2017年 71卷 274-279页

作者： Qiang Zhang Xiaobiao Wang Xiaojun Wang Changjun Zhou Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian 116622 China School of Computer Science and Technology Dalian University of Technology Dalian 116024 China. Electronic address: zhangq@***. Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian 116622 China.

In computation biology, DNA strand displacement technology is used to simulate the computation process and has shown strong computing ability. Most researchers use it to solve logic problems, but it is only rarely used in probabilistic reasoning. To process probabilistic reasoning, a conditional probability derivation model and total probability model based on DNA strand displacement were established in this paper. The models were assessed through the game "read your mind." It has been shown to enable the application of probabilistic reasoning in genetic diagnosis.

关键词： Conditional probability DNA strand displacement Probability reasoning Total probability

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Stability Analysis and Hopf Bifurcation Research for DNA Strand Displacement with Time Delay

Stability Analysis and Hopf Bifurcation Research for DNA Str...

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Symposia and Workshops on Ubiquitous, Autonomic and Trusted computing, UIC-ATC

作者： Yanhong Liu Hui Lv Changjun Zhou Zhixiang Yin Xianwen Fang Zhonglong Zheng Qiang Zhang Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian China School of Mathematics and Big Data Anhui University of Science and Technology Huaian China College of Mathematics Zhejiang Normal University Jinhua China Department of Computer Science and Technology Dalian University of Technology Dalian China

ISBN: (纸本)9781538693810;9781538693803

In this paper, a nonlinear system with time delay mode for DNA strand displacement based on toehold exchange firstly is proposed. The boundedness of all the state variables of the DNA strand displacement system is proved. After that, local stability analysis is performed around the positive equilibrium point to obtain a necessary and sufficient condition for local stability, which depend on the coefficients of the characteristic equation corresponding to linearization of the system. In addition, the existence of the Hopf bifurcation is analyzed, which shows that the time delay parameter will guarantee that the system is stable within a certain range. However, Hopf bifurcation and chaos occur when the time delay parameter increases continuously and even exceeds the critical value. At last, numerical simulations have verified the correctness and validity of the DNA strand displacement studies.

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An improved stochastic fractal search algorithm for 3D protein structure prediction

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Journal of molecular modeling 2018年第6期24卷 125页

作者： Changjun Zhou Chuan Sun Bin Wang Xiaojun Wang Key Laboratory of Advanced Design and Intelligent Computing (Dalian University) Ministry of Education Dalian 116622 China. zhou-chang231@***. Key Laboratory of Advanced Design and Intelligent Computing (Dalian University) Ministry of Education Dalian 116622 China.

Protein structure prediction (PSP) is a significant area for biological information research, disease treatment, and drug development and so on. In this paper, three-dimensional structures of proteins are predicted based on the known amino acid sequences, and the structure prediction problem is transformed into a typical NP problem by an AB off-lattice model. This work applies a novel improved Stochastic Fractal Search algorithm (ISFS) to solve the problem. The Stochastic Fractal Search algorithm (SFS) is an effective evolutionary algorithm that performs well in exploring the search space but falls into local minimums sometimes. In order to avoid the weakness, Lvy flight and internal feedback information are introduced in ISFS. In the experimental process, simulations are conducted by ISFS algorithm on Fibonacci sequences and real peptide sequences. Experimental results prove that the ISFS performs more efficiently and robust in terms of finding the global minimum and avoiding getting stuck in local minimums.

关键词： AB off-lattice model Internal feedback information Lvy flight Protein structure prediction Stochastic fractal search algorithm

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Sliding mode control of decaying-dimerizing system

Sliding mode control of decaying-dimerizing system

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Chinese Control Conference (CCC)

作者： Hui Lv Changjun Zhou Qiang Zhang Ministry of Education Key Laboratory of Advanced Design and Intelligent Computing (Dalian university) Dalian P.R.China

ISBN: (纸本)9781538629185

This paper is concerned with the sliding mode control of decaying-dimerizing system with three molecular species and four reaction channels. An integral sliding surface is designed, and the resulting dynamics is a nonlinear biochemical reaction system. By introducing some specified matrices, a sufficient condition is proposed in terms of strict linear matrix inequality (LMI), which guarantees the stability of the sliding mode dynamics. A sliding mode control law is also synthesized for reaching motion. Finally, simulation results illustrate the effectiveness of our methods.

关键词： Sliding mode control Stochastic processes Linear matrix inequalities Stability analysis Trajectory Biological system modeling

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On robust stabilization of uncertain singular Markovian jump systems with time-delay

On robust stabilization of uncertain singular Markovian jump...

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Chinese Control Conference (CCC)

作者： Hui Lv Changjun Zhou Qiang Zhang Key Laboratory of Advanced Design and Intelligent Computing (Dalian university) Ministry of Education Dalian P. R. China

ISBN: (纸本)9781538629185

This paper is concerned with the robust normalization and stochastic stabilizing problem for singular Markovian jump systems with norm-bounded parameter uncertainties and time delay. A novel proportional-derivative controller with memory is designed. Sufficient conditions are derived to ensure that the closed-loop system is not only robust normal, but also stochastically stable. In addition, the explicit expression of the desired control gains is also given by solving strict linear matrix inequalities. Finally, simulation results illustrate the effectiveness of our methods.

关键词： Robustness Symmetric matrices Delay effects Uncertainty Linear matrix inequalities Markov processes Control systems

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Reversible Data Hiding Based on DNA computing

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Computational Intelligence and Neuroscience 2017年第20170101期2017卷 7276084-7276084页

作者： Wang, Bin Xie, Yingjie Zhou, Shihua Zhou, Changjun Zheng, Xuedong Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian116622 China Applied Technology College Dalian Ocean University Dalian116300 China

Biocomputing, especially DNA, computing has got great development. It is widely used in information security. In this paper, a novel algorithm of reversible data hiding based on DNA computing is proposed. Inspired by the algorithm of histogram modification, which is a classical algorithm for reversible data hiding, we combine it with DNA computing to realize this algorithm based on biological technology. Compared with previous results, our experimental results have significantly improved the ER (Embedding Rate). Furthermore, some PSNR (peak signal-to-noise ratios) of test images are also improved. Experimental results show that it is suitable for protecting the copyright of cover image in DNA-based information security. © 2017 Bin Wang et al.

关键词： Signal to noise ratio

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Four digits BCD adder with DNA strand displacement

Four digits BCD adder with DNA strand displacement

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International Conference on Systems and Informatics (ICSAI)

作者： Lanlan Shi Changjun Zhou Qiang Zhang Key Laboratory of Advanced Design and Intelligent Computing Dalian University Dalian China School of Computer Science and Technology Dalian University of Technology Dalian China

As a way of biological computing technology, DNA strand displacement has become more and more popular in recent years. With the principle of the DNA strand displacement, a four digits BCD adder is presented in this paper, in which single-stranded DNA express input signals and output signals, and double-stranded DNA represent gates. The progress of DNA strand displacement reaction can be easily achieved and operated. The proposed adder can autonomously correct its computing results, when the computing results overflows. Then, the reaction progress is simulated in the Visual DSD software. The experiment results of the four digits BCD adder show that the design of the four digits BCD adder is feasible and successful. The proposed BCD adder provides a new pattern to the development of DNA strand displacement computing.

关键词： DNA Adders Logic gates Visualization Logic circuits Software Integrated circuit modeling

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DNA self-assembly model to solve compound logic operators problem 11th

DNA self-assembly model to solve compound logic operators pr...

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11th International Conference on Bio-inspired computing – Theories and Applications, BIC-TA 2016

作者： Zhou, Shihua Wang, Bin Zheng, Xuedong Zhou, Changjun Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian116622 China

ISBN: (纸本)9789811036101

Self-assembly is the process that the component form an ordered form or structure. Because of the biochemical characteristics of DNA molecules, they become a research emphasis in the field of selfassembly. DNA-based self-assembly technology has been widely used in the fields of nanometer machining, molecular circuit, polymer materials, and so on. DNA self-assembly is an effective mechanism that nanometer structure is built bottom-up. In order to overcome the problem that any kind of self-assembled model can only solve the single algorithm, in this paper, a new DNA self-assembly algorithmic model is designed to solve compound logic operators problem. Five types of DNA tiles are designed according to the characteristic of compound operation problem, namely Initial Tile, Process Tile, Operation Tile, End Tile and Boundary Tile. At last, the process of self-assembly are demonstrated by an instance. © Springer Nature Singapore Pte Ltd. 2016.

关键词： Self assembly

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