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Quantitative composite decision-theoretic rough set

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Quantitative composite decision-theoretic rough set

International Conference on intelligent System and Knowledge Engineering, ISKE

作者： Linna Wang Ling Liu Xin Yang Pan Zhuo School of Electronic and Information Engineering Sichuan Technology and Business University Chengdu China Key Lab of Cloud Computing and Intelligent Information Processing Sichuan Technology and Business University Chengdu China

In practical decision-making, we prefer to characterize the uncertain problems with the hybrid data, which consists of various types of data, e.g., categorical, numerical, set-valued and interval-valued. The extended rough sets can deal with single types of data based on specific binary relation, including the equivalence relation, neighborhood relation, partial order relation, tolerance relation, etc. However, the fusion of these relations is a significant challenge task in such composite information table. To tackle this issue, this paper proposes the intersection and union composite relation, and further introduces a quantitative composite decision-theoretic rough set model. Moreover, we present a novel matrix-based approach to compute the upper and lower approximations in proposed model. Finally, an numerical example is conducted to illustrate the efficiency of proposed method.

关键词： Rough sets Numerical models Mathematical model Computational modeling Data models Probabilistic logic Business

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning

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arXiv 2018年

作者： Zhang, Haicang Zhang, Qi Ju, Fusong Zhu, Jianwei Sun, Shiwei Gao, Yujuan Xie, Ziwei Deng, Minghua Sun, Shiwei Zheng, Wei-Mou Bu, Dongbo Key Lab of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China Center for Quantitative Biology School of Mathematical Sciences Center for Statistical Sciences Peking University Beijing China Institute of Theoretical Physics Chinese Academy of Sciences Beijing China College of Life Science and Technology Huazhong University of Science and Technology Wuhan China

Accurate prediction of inter-residue contacts of a protein is important to calculating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective to inferring inter-residue contacts. The Markov random field (MRF) technique, although being widely used for contact prediction, suffers from the following dilemma: the actual likelihood function of MRF is accurate but time-consuming to calculate;in contrast, approximations to the actual likelihood, say pseudo-likelihood, are efficient to calculate but inaccurate. Thus, how to achieve both accuracy and efficiency simultaneously remains a challenge. In this study, we present such an approach (called clmDCA) for contact prediction. Unlike plmDCA using pseudo-likelihood, i.e., the product of conditional probability of individual residues, our approach uses composite-likelihood, i.e., the product of conditional probability of all residue pairs. Composite likelihood has been theoretically proved as a better approximation to the actual likelihood function than pseudo-likelihood. Meanwhile, composite likelihood is still efficient to maximize, thus ensuring the efficiency of clmDCA. We present comprehensive experiments on popular benchmark datasets, including PSICOV dataset and CASP-11 dataset, to show that: i) clmDCA alone outperforms the existing MRF-based approaches in prediction accuracy. ii) When equipped with deep learning technique for refinement, the prediction accuracy of clmDCA was further significantly improved, suggesting the suitability of clmDCA for subsequent refinement procedure. We further present successful application of the predicted contacts to accurately build tertiary structures for proteins in the PSICOV dataset. Accessibility: The software clmDCA and a server are publicly accessible through http://***/clmDCA/. Copyright © 2018, The Authors. All rights reserved.

关键词： Proteins

Cross-layer Joint Relay Selection and Power Allocation Scheme for Cooperative Relaying System

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IOP Conference Series: Materials Science and Engineering 2018年第7期322卷

作者： Hui Zhi Mengmeng He Feiyue Wang Ziju Huang Key Lab of Computing Intelligent and Signal Processing (Ministry of Education) Anhui University Hefei China College of Electronics and Information Engineering Anhui University Hefei China

A novel cross-layer joint relay selection and power allocation (CL-JRSPA) scheme over physical layer and data-link layer is proposed for cooperative relaying system in this paper. Our goal is finding the optimal relay selection and power allocation scheme to maximize system achievable rate when satisfying total transmit power constraint in physical layer and statistical delay quality-of-service (QoS) demand in data-link layer. Using the concept of effective capacity (EC), our goal can be formulated into an optimal joint relay selection and power allocation (JRSPA) problem to maximize the EC when satisfying total transmit power limitation. We first solving optimal power allocation (PA) problem with Lagrange multiplier approach, and then solving optimal relay selection (RS) problem. Simulation results demonstrate that CL-JRSPA scheme gets larger EC than other schemes when satisfying delay QoS demand. In addition, the proposed CL-JRSPA scheme achieves the maximal EC when relay located approximately halfway between source and destination, and EC becomes smaller when the QoS exponent becomes larger.

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From social to individuals: A parsimonious path of multi-level models for crowdsourced preference aggregation

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arXiv 2018年

作者： Xu, Qianqian Xiong, Jiechao Cao, Xiaochun Huang, Qingming Yao, Yuan Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing1000190 China Institute of Information Engineering Chinese Academy of Sciences Beijing100093 China Tencent AI Lab Shenzhen518057 BICMR-LMAM-LMEQF-LMP School of Mathematical Sciences Peking University Beijing100871 China University of Chinese Academy of Sciences Institute of Computing Technology of Chinese Academy of Sciences Beijing100190 China Department of Mathematics and by courtesy Computer Science and Engineering Hong Kong University of Science and Technology Hong Kong Hong Kong

In crowdsourced preference aggregation, it is often assumed that all the annotators are subject to a common preference or social utility function which generates their comparison behaviors in experiments. However, in reality annotators are subject to variations due to multi-criteria, abnormal, or a mixture of such behaviors. In this paper, we propose a parsimonious mixed-effects model, which takes into account both the fixed effect that the majority of annotators follows a common linear utility model, and the random effect that some annotators might deviate from the common significantly and exhibit strongly personalized preferences. The key algorithm in this paper establishes a dynamic path from the social utility to individual variations, with different levels of sparsity on personalization. The algorithm is based on the Linearized Bregman Iterations, which leads to easy parallel implementations to meet the need of large-scale data analysis. In this unified framework, three kinds of random utility models are presented, including the basic linear model with L2 loss, Bradley-Terry model, and Thurstone-Mosteller model. The validity of these multi-level models are supported by experiments with both simulated and real-world datasets, which shows that the parsimonious multi-level models exhibit improvements in both interpretability and predictive precision compared with traditional HodgeRank. Copyright © 2018, The Authors. All rights reserved.

关键词： Crowdsourcing

Non-rigid 3D models retrieval based on hierarchical matching

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Computer Aided Drafting,Design and Manufacturing 2017年第1期27卷 39-47页

作者： Liu Yujie Li Wei Song Yang Gong Weiqing Li Zongmin Li Hua Department of Computer & Communication Engineering China University of Petroleum ChinaPetro (Karamay) Data Center Sinopec Exploration & Production Research Institute (PEPRIS) Key Lab of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of Sciences

In 3D models retrieval, feature description and retrieval of non-rigid model face more complex problems due to the isometry transformation of itself. We introduce the hierarchical combination matching into the feature comparison, and build a map between the divided regions of two models, and then achieve accurate feature matching based on patch-by-patch, which successfully introduces the spatial information into feature matching. Verified by experiment, the 3D model retrieval method proposed in this paper based on hierarchical combination matching can make sure more accurate feature matching, so as to enhance the precision of retrieval.

关键词： non-rigid 3D model shape descriptor spatial distribution hierarchical combination matching

PROTEOMIC IDENTIFICATION OF INTACT GLYCOPEPTIDES

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PROTEOMIC IDENTIFICATION OF INTACT GLYCOPEPTIDES

第十七届北京分析测试学术报告会暨展览会(BCEIA2017)——分论坛G

作者： Ming-Qi LIU Wen-Feng ZENG Wei-qian CAO Pan FANG Yang ZHANG Jian-Qiang WU Rui-Xiang SUN Si-Min He Peng-Yuan YANG Institutes of Biomedical Sciences and Department Chemistry Fudan University Key Lab of Intelligent Information Processing of Chinese Academy of Sciences(CAS) Institute of Computing TechnologyCASand University of Chinese Academy of Sciences

We have developed a workflow that robustly identifies intact glycopeptides at a proteome scale using stepped-energy mass-spectrometry.A computational strategy called as p Glyco++has been decoded for this workflow,and ... 详细信息

关键词： PROTEOMIC IDENTIFICATION OF INTACT GLYCOPEPTIDES

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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Reflection invariant and symmetry detection

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arXiv 2017年

作者： Li, Erbo Li, Hua EON Reality Inc IrvineCA92618 United States Key lab of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing100190 China University of Chinese Academy of Sciences Beijing100049 China

Symmetry detection and discrimination are of fundamental meaning in science, technology, and engineering. This paper introduces reflection invariants and defines the directional moments(DMs) to detect symmetry for shape analysis and object recognition. And it demonstrates that detection of reflection symmetry can be done in a simple way by solving a trigonometric system derived from the DMs, and discrimination of reflection symmetry can be achieved by application of the reflection invariants in 2D and 3D. Rotation symmetry can also be determined based on that. Also, if none of reflection invariants is equal to zero, then there is no symmetry. And the experiments in 2D and 3D show that all the reflection lines or planes can be deterministically found using DMs up to order six. This result can be used to simplify the efforts of symmetry detection in research areas,such as protein structure, model retrieval, reverse engineering, and machine vision etc. Copyright © 2017, The Authors. All rights reserved.

关键词： Object recognition

Isomorphism between differential and moment invariants under affine transform

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arXiv 2017年

The invariant is one of central topics in science, technology and engineering. The differential invariant is essential in understanding or describing some important phenomena or procedures in mathematics, physics, chemistry, biology or computer science etc. The derivation of differential invariants is usually difficult or complicated. This paper reports a discovery that under the affine transform, differential invariants have similar structures with moment invariants up to a scalar function of transform parameters. If moment invariants are known, relative differential invariants can be obtained by the substitution of moments by derivatives with the same order. Whereas moment invariants can be calculated by multiple integrals, this method provides a simple way to derive differential invariants without the need to resolve any equation system. Since the definition of moments on different manifolds or in different dimension of spaces is well established, differential invariants on or in them will also be well defined. Considering that moments have a strong background in mathematics and physics, this technique offers a new view angle to the inner structure of invariants. Projective differential invariants can also be found in this way with a screening process. Copyright © 2017, The Authors. All rights reserved.

关键词： Affine transforms