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A parallel ant colonies approach to de novo prediction of protein backbone in CASP8/9

Science China(information Sciences) 2013年第10期56卷 226-238页

作者： LV Qiang WU HongJie WU JinZhen HUANG Xu LUO XiaoHu QIAN PeiDe School of Computer Science and Technology Soochow University Jiangsu Provincial Key Lab for Information Processing Technologies School of Electronic and Information Engineering Suzhou University of Science and Technology

Predicting the three-dimensional structure of proteins from amino acid sequences with only a few remote homologs,or de novo prediction,remains a major challenge in computational *** modeling of the protein backbone represents the initial phase of a protein structure prediction *** a parallel ant colony optimization based on sharing one pheromone matrix,this report proposes a parallel approach to predict the structure of a protein *** parallel approach combines various sources of energy functions and generates protein backbones with the lowest energies jointly determined by the various energy *** free modeling targets in CASP8/9 are used to evaluate the performance of the *** 13 targets in CASP8,two out of the predicted model1s selected by our approach are the best of the published CASP8 results,and seven out of the model1s are ranked in the top *** 29 targets in CASP9,20 out of the best models from our predictions are ranked in the top 10,and 11 out of the model1s are ranked in the top 10.

关键词： protein backbone prediction parallel ant colony optimization

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Improve tree kernel-based event pronoun resolution with competitive information

Improve tree kernel-based event pronoun resolution with comp...

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22nd International Joint Conference on Artificial Intelligence, IJCAI 2011

作者： Kong, Fang Zhou, Guodong JiangSu Provincial Key Lab. for Computer Information Processing Technology School of Computer Science and Technology Soochow University China

ISBN: (纸本)9781577355120

Event anaphora resolution plays a critical role in discourse analysis. This paper proposes a tree kernel- based framework for event pronoun resolution. In particular, a new tree expansion scheme is introduced to automatically determine a proper parse tree structure for event pronoun resolution by considering various kinds of competitive information related with the anaphor and the antecedent candidate. Evaluation on the OntoNotes English corpus shows the appropriateness of the tree kernel-based framework and the effectiveness of competitive information for event pronoun resolution.

关键词： Trees (mathematics)

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A tree kernel-based unified framework for Chinese zero anaphora resolution

A tree kernel-based unified framework for Chinese zero anaph...

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Conference on Empirical Methods in Natural Language processing, EMNLP 2010

作者： Kong, Fang Zhou, Guodong JiangSu Provincial Key Lab. for Computer Information Processing Technology School of Computer Science and Technology Soochow University China

ISBN: (纸本)1932432868

This paper proposes a unified framework for zero anaphora resolution, which can be divided into three sub-tasks: zero anaphor detection, anaphoricity determination and antecedent identification. In particular, all the three sub-tasks are addressed using tree kernel-based methods with appropriate syntactic parse tree structures. Experimental results on a Chinese zero anaphora corpus show that the proposed tree kernel-based methods significantly outperform the feature-based ones. This indicates the critical role of the structural information in zero anaphora resolution and the necessity of tree kernel-based methods in modeling such structural information. To our best knowledge, this is the first systematic work dealing with all the three sub-tasks in Chinese zero anaphora resolution via a unified framework. Moreover, we release a Chinese zero anaphora corpus of 100 documents, which adds a layer of annotation to the manually-parsed sentences in the Chinese Treebank (CTB) 6.0. © 2010 Association for Computational Linguistics.

关键词： Trees (mathematics)

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A Fast Calculation of Metric Scores for Learning Bayesian Network

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International Journal of Automation and computing 2012年第1期9卷 37-44页

作者： Qiang Lv Xiao-Yan Xia Pei-De Qian School of Computer Science and Technology Soochow University Suzhou 215006 PRC Jiangsu Provincial Key Lab for Computer Information Processing Technology Suzhou 215006 PRC

Frequent counting is a very so often required operation in machine learning algorithms. A typical machine learning task, learning the structure of Bayesian network （BN） based on metric scoring, is introduced as an example that heavily relies on frequent counting. A fast calculation method for frequent counting enhanced with two cache layers is then presented for learning BN. The main contribution of our approach is to eliminate comparison operations for frequent counting by introducing a multi-radix number system calculation. Both mathematical analysis and empirical comparison between our method and state-of-the-art solution are conducted. The results show that our method is dominantly superior to state-of-the-art solution in solving the problem of learning BN.

关键词： Frequent counting radix-based calculation ADtree learning Bayesian network metric score

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Prof. Rudolf Emil Kalman OBITUARY

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IEEE CONTROL SYSTEMS MAGAZINE 2017年第1期37卷 151-152页

作者： Antoulas, Athanasios Georgiou, Tryphon T. Khargonekar, Pramod P. Ozguler, A. Bulent Sontag, Eduardo D. Yamamoto, Yutaka JiangSu Provincial Key Lab for Computer Information Processing Technology School of Computer Science and Technology Soochow University Suzhou China

Recounts the career and contributions of Professor Rudolf Emil Kalman.

关键词： Obituaries Kalman, Rudolf Emil

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A parallel ACO approach based on one pheromone matrix

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Ant Colony Optimization and Swarm Intelligence - 5th International Workshop, ANTS 2006, Proceedings

作者： Qiang, Lv Xiaoyan, Xia Peide, Qian School of Computer Science and Technology Soochow Univeristy China Jiangsu Provincial Key Lab. of Computer Information Processing Technology Suzhou China

ISBN: (纸本)3540384820

This paper presents and implements an approach to parallel ACO algorithms. The principal idea is to make multiple ant colonies share and utilize only one pheromone matrix. We call it SHOP (SHaring One Pheromone matrix) approach. We apply this idea to the two currently best instances of ACO sequential algorithms (MMAS and ACS), and try to hybridize these two different ACO instances. We mainly describe how to design parallel ACS and MMAS based on SHOP. We present our computing results of applying our approach to solving 10 symmetric traveling salesman problems, and give comparisons with the relevant sequential versions under the fair computing environment. The experimental results indicate that SHOP-ACO algorithms perform overall better than the sequential ACO algorithms in both the computation time and solution quality. © Springer-Verlag Berlin Heidelberg 2006.

关键词： Global optimization

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Global learning of noun phrase anaphoricity in coreference resolution via lab.l propagation

Global learning of noun phrase anaphoricity in coreference r...

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2009 Conference on Empirical Methods in Natural Language processing, EMNLP 2009, Held in Conjunction with ACL-IJCNLP 2009

作者： Zhou, Guo Dong Kong, Fang JiangSu Provincial Key Lab. for Computer Information Processing Technology School of Computer Science and Technology Soochow University Suzhou 215006 China

Knowledge of noun phrase anaphoricity might be profitably exploited in coreference resolution to bypass the resolution of non-anaphoric noun phrases. However, it is surprising to notice that recent attempts to incorporate automatically acquired anaphoricity information into coreference resolution have been somewhat disappointing. This paper employs a global learning method in determining the anaphoricity of noun phrases via a lab.l propagation algorithm to improve learning-based coreference resolution. In particular, two kinds of kernels, i.e. the feature-based RBF kernel and the convolution tree kernel, are employed to compute the anaphoricity similarity between two noun phrases. Experiments on the ACE 2003 corpus demonstrate the effectiveness of our method in anaphoricity determination of noun phrases and its application in learning-based coreference resolution. © 2009 ACL and AFNLP.

关键词： Natural language processing systems

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Topic-driven multi-document summarization

Topic-driven multi-document summarization

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International Conference on Asian Language processing

作者： Wang, Hongling Zhou, Guodong Jiangsu Provincial Key Lab. for Computer Information Processing Technology School of Computer Science and Technology Soochow University Suzhou 215006 China

ISBN: (纸本)9780769542881

This paper presents a topic-driven framework for generating a generic summary from multi-documents. Our approach is based on the intuition that, from the statistical point of view, the summary's probability distribution over the topics should be consistent with the multi-documents'probability distribution over the inherent topics. Here, the topics are defined as weighted "bag-of-words" and derived by Latent Dirichlet Allocation from a collection of documents, either the given multi-documents or a related large-scale corpus. In this sense, we could represent various kinds of text units, such as word, sentence, summary, document and multi-documents, using a single vector space model via their corresponding probability distributions over the derived topics. Therefore, we are able to extract a sentence or summary by calculating the similarity between a sentence/summary and the given multi-documents via their topic probability distributions. In particular, we propose two methods in similarity measurement: the static method and the dynamic method. While the former is employed to detect the salience of information in a static way, the later further controls redundancy in a dynamic way. In addition, we integrate various popular features to improve the performance. Evaluation on the TAC 2008 update summarization task shows encouraging results. © 2010 IEEE.

关键词： Probability distributions

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Employing the centering theory in pronoun resolution from the semantic perspective

Employing the centering theory in pronoun resolution from th...

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2009 Conference on Empirical Methods in Natural Language processing, EMNLP 2009, Held in Conjunction with ACL-IJCNLP 2009

作者： Kong, Fang Zhou, Guo Dong Zhu, Qiaoming JiangSu Provincial Key Lab. for Computer Information Processing Technology School of Computer Science and Technology Soochow University Suzhou 215006 China

In this paper, we employ the centering theory in pronoun resolution from the semantic perspective. First, diverse semantic role features with regard to different predicates in a sentence are explored. Moreover, given a pronominal anaphor, its relative ranking among all the pronouns in a sentence, according to relevant semantic role information and its surface position, is incorporated. In particular, the use of both the semantic role features and the relative pronominal ranking feature in pronoun resolution is guided by extending the centering theory from the grammatical level to the semantic level in tracking the local discourse focus. Finally, detailed pronominal subcategory features are incorporated to enhance the discriminative power of both the semantic role features and the relative pronominal ranking feature. Experimental results on the ACE 2003 corpus show that the centering-motivated features contribute much to pronoun resolution. © 2009 ACL and AFNLP.

关键词： Semantics

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Towards termination criteria of ant colony optimization

Towards termination criteria of ant colony optimization

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3rd International Conference on Natural Computation, ICNC 2007

作者： Lv, Qiang Xia, Oyan School of Computer Science and Technology Suzhou University Suzhou Jiangsu 215006 China Provincial Key Lab. for Computer Information Processing Technology Suzhou Jiangsu 215006 China

ISBN: (纸本)0769528759

Ant colony optimization (ACO for short) has been proved a successful meta-heuristic by a huge of empirical studies. This paper discusses the termination criteria of ACO and therefore provides research ideas to other meta-heuristics. A general discussion about four types of termination criteria has been firstly discussed in this article. Then some measures of convergence based on pheromone have been introduced. And a new termination criterion based on Bayesian approach is presented. Finally a new convergence proof for a class of ACO algorithms is presented. © 2007 IEEE.

关键词： Heuristic methods

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