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DeepHBSP:A Deep Learning Framework for Predicting Human Blood-Secretory Proteins Using Transfer Learning

Journal of Computer Science & Technology 2021年第2期36卷 234-247页

作者： Wei Du Yu Sun Hui-Min Bao Liang Chen Ying Li Yan-Chun Liang Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education College of Computer Science and TechnologyJilin UniversityChangchun 130012China Department of Computer Science College of EngineeringShantou UniversityShantou 515063China Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Zhuhai College of Jilin University Zhuhai 519041China

The identification of blood-secretory proteins and the detection of protein biomarkers in the blood have an important clinical application *** methods for predicting blood-secretory proteins are mainly based on traditional machine learning algorithms,and heavily rely on annotated protein *** traditional machine learning algorithms,deep learning algorithms can automatically learn better feature representations from raw data,and are expected to be more promising to predict blood-secretory *** present a novel deep learning model(DeepHBSP)combined with transfer learning by integrating a binary classification network and a ranking network to identify blood-secretory proteins from the amino acid sequence information *** loss function of DeepHBSP in the training step is designed to apply descriptive loss and compactness loss to the binary classification network and the ranking network,*** feature extraction subnetwork of DeepHBSP is composed of a multi-lane capsule ***,transfer learning is used to train a highly accurate generalized model with small samples of blood-secretory *** main contributions of this study are as follows:1)a novel deep learning architecture by integrating a binary classification network and a ranking network is proposed,superior to existing traditional machine learning algorithms and other state-of-the-art deep learning architectures for biological sequence analysis;2)the proposed model for blood-secretory protein prediction uses only amino acid sequences,overcoming the heavy dependence of existing methods on annotated protein features;3)the blood-secretory proteins predicted by our model are statistically significant compared with existing blood-based biomarkers of cancer.

关键词： blood-secretory protein deep learning capsule network transfer learning

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An adaptive fuzzy k-nearest neighbor method based on parallel particle swarm optimization for bankruptcy prediction

An adaptive fuzzy k-nearest neighbor method based on paralle...

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作者： Chen, Hui-Ling Liu, Da-You Yang, Bo Liu, Jie Wang, Gang Wang, Su-Jing Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012 China

ISBN: (纸本)9783642208409

This study proposes an efficient non-parametric classifier for bankruptcy prediction using an adaptive fuzzy k-nearest neighbor (FKNN) method, where the nearest neighbor k and the fuzzy strength parameter m are adaptively specified by the particle swarm optimization (PSO) approach. In addition to performing the parameter optimization for FKNN, PSO is utilized to choose the most discriminative subset of features for prediction as well. Time varying acceleration coefficients (TVAC) and inertia weight (TVIW) are employed to efficiently control the local and global search ability of PSO. Moreover, both the continuous and binary PSO are implemented in parallel on a multi-core platform. The resultant bankruptcy prediction model, named PTVPSO-FKNN, is compared with three classification methods on a real-world case. The obtained results clearly confirm the superiority of the developed model as compared to the other three methods in terms of Classification accuracy, Type I error, Type II error and AUC (area under the receiver operating characteristic (ROC) curve) criterion. It is also observed that the PTVPSO-FKNN is a powerful feature selection tool which has indentified a subset of best discriminative features. Additionally, the proposed model has gained a great deal of efficiency in terms of CPU time owing to the parallel implementation. © 2011 Springer-Verlag.

关键词： Particle swarm optimization (PSO)

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Heterogeneous data mining for planning active surveillance of malaria 15

Heterogeneous data mining for planning active surveillance o...

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ASE BigData and SocialInformatics, ASE BD and SI 2015

作者： Gu, Xiao Chen, Hechang Yang, Bo College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education China

ISBN: (纸本)9781450337359

Malaria is one of the most serious diseases in the world, which is densely distributed in poverty and remote areas. In the prevention and control of malaria, active surveillance is more efficient than passive surveillance to discover the incidences timely and accurately. However, it is always faced with the challenge of how to allocate the limited sources, such as medical staff and medicine, appropriately so as to achieve a maximum infect. In this paper, we propose a novel method to characterize the spatiotemporal patterns of infection risk for active surveillance planning. Specifically, we propose a temporal heterogeneous diffusion network model to discover high risk areas timely, and a mixture optimization method to find high risk areas accurately. The validation on existing real-world data shows that our method outperforms the existing state-of-the-art both in terms of infection risk prediction and planning of active surveillance under different thresholds. © 2015 ACM.

关键词： Mixtures

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Zero-shot Image Classification with Logic Adapter and Rule Prompt 24

Zero-shot Image Classification with Logic Adapter and Rule P...

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33rd ACM Web Conference, WWW 2024

作者： Yu, Dongran Liu, Xueyan Yang, Bo Key Laboratory of Symbolic Computation and Knowledge Engineer Ministry of Education School of Artificial Intelligence Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineer Ministry of Education School of Computer Science and Technology Jilin University Changchun China

ISBN: (纸本)9798400701719

Zero-shot image classification, which aims to predict unseen classes whose samples have never appeared during the training phase, is crucial in the Web domain because many new web images appear on various websites. Attributes, as annotations for class-level characteristics, are widely used semantic information for this task. However, most current methods often fail to capture discriminative image features between similar images from different classes, leading to unsatisfactory zero-shot image classification results. This is because they solely focus on limited visual-attribute feature alignment. Therefore, we propose a Zero-Shot image Classification with Logic adapter and Rule prompt method called ZSCLR, which utilizes logic adapter and rule prompts to encourage the model to capture discriminative image features and achieve reasoning. Specifically, ZSCLR consists of a visual perception module and a logic adapter. The visual perception module extracts image features from training data. At the same time, the logic adapter utilizes the Markov logic network to encode the extracted image features and rule prompts for refining the discriminative image features. Due to predicates of rule prompts representing symbolic discriminative features, the proposed model can focus more on these discriminative features and achieve more precise image classification. Additionally, the logic adapter enables the model to adapt from recognizing images in seen classes to those in unseen classes through the reasoning of the Markov logic networks. We implement experiments on three standard zero-shot image classification benchmarks, and ZSCLR achieves competitive performance. Furthermore, ZSCLR can provide explanations for its predictions through rule prompts. © 2024 ACM.

关键词： Zero-shot learning

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An approach to accelerate diagnosis by isomorphic determining

An approach to accelerate diagnosis by isomorphic determinin...

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2009 International Conference on Information engineering and Computer Science, ICIECS 2009

作者： Wang, Xiaoyu Ouyang, Dantong Feng, Yuxuan Zhao, Jian College of Computer Science and Technology Jilin University Key Laboratory Symbolic Computation and Knowledge Engineering Ministry of Educaion Changchun China

ISBN: (纸本)9781424449941

When diagnosing dynamic system represented as discrete-event systems, it needs to find what happened to the systems from observations. The behavior of system could be represented by automaton model. The diagnostic task consists in determining the models compatible with the observations, but the global computation which is needed in synchronization costs exponential time. In this paper we propose a new method to simplify the automaton by isomorphic determining. The cost of computation will be significantly cut down by merging the automatons with the same structure, and the time-complexity of the diagnosis process could be reduced by the method. ©2009 IEEE.

关键词： Discrete event simulation

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A novel method to measure graph similarity 12

A novel method to measure graph similarity

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12th IEEE International Conference on E-Business engineering, ICEBE 2015

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

ISBN: (纸本)9781467380027

A novel method to measure the graph similarity is proposed, where the labels, in-degrees, and out-degrees of the vertices in the graph are comprehensively considered in order to conquer the high complexity and information loss in the measurement process. In this proposal, the graph is decomposed into a generalized tree and its similarity can be measured by computing the cost of the node sequence triples in the generalized tree. The proposed method decreases the computational complexity to O(n2) in comparison with the other available graph similarity methods. An example is provided to illustrate that the method is feasible and effective. © 2015 IEEE.

关键词： Forestry

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Simulating the Folding Pathway of RNA Secondary Structure Using the Modified Ant Colony Algorithm

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Journal of Bionic engineering 2010年第4期7卷 382-389页

作者： Jun Yu~(1,2),Changhai Zhang~(1,2),Yuanning Liu~(1,2),Xin Li~(1,2) 1.College of Computer Science and Technology,Jilin University,Changchun 130012,P.R.China 2.key laboratory of symbolic computation and knowledge engineering (Ministry of Education,China) Jilin University,Changchun 130012,P.R.China [a] College of Computer Science Technology Jilin University Changchun 130012 P. R. China [b] Key Laboratory of Symbolic Computation Knowledge Engineering (Ministry of Education China) Jilin University Changchun 130012 P. R. China

A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithmis *** a given RNA sequence,the set of all possible stems is obtained and the energy of each stem iscalculated and stored at the initial ***,a more realistic formula is used to compute the energy ofmulti-branch loop in the following *** a folding pathway is simulated,including such processes as constructionof the heuristic information,the rule of initializing the pheromone,the mechanism of choosing the initial andnext stem and the strategy of updating the pheromone between two different *** by testing RNA sequences withknown secondary structures from the public databases,we analyze the experimental data to select appropriate values *** measure indexes show that our procedure is more consistent with phylogenetically proven structures thansoftware RNAstructure sometimes and more effective than the standard Genetic Algorithm.

关键词： RNA secondary structure folding pathway ant colony algorithm

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A pseudo label based dataless naive bayes algorithm for text classification with seed words 27

A pseudo label based dataless naive bayes algorithm for text...

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27th International Conference on computational Linguistics, COLING 2018

作者： Li, Ximing Yang, Bo College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education China

ISBN: (纸本)9781948087506

Traditional supervised text classifiers require a large number of manually labeled documents, which are often expensive to obtain. Recently, dataless text classification has attracted more attention, since it only requires very few seed words of categories that are much cheaper. In this paper, we develop a pseudo-label based dataless Naive Bayes (PL-DNB) classifier with seed words. We initialize pseudo-labels for each document using seed word occurrences, and employ the expectation maximization algorithm to train PL-DNB in a semi-supervised manner. The pseudo-labels are iteratively updated using a mixture of seed word occurrences and estimations of label posteriors. To avoid noisy pseudo-labels, we also consider the information of nearest neighboring documents in the pseudo-label update step, i.e., preserving local neighborhood structure of documents. We empirically show that PL-DNB outperforms traditional dataless text classification algorithms with seed words. Especially, PL-DNB performs well on the imbalanced dataset. © 2018 COLING 2018 - 27th International Conference on computational Linguistics, Proceedings. All rights reserved.

关键词： Iterative methods

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A conditioned secure access control model based on multi-weighted roles in workflow system

A conditioned secure access control model based on multi-wei...

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5th International Conference on Control and Automation, ICCA'05

作者： Zhang, Jian Sun, Jigui Li, Niya Hu, Chengquan College of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University China

ISBN: (纸本)0780391381

The traditional RBAC model already cannot express the complicated secure access control constraint of the workflow. Based on the traditional RBAC model, a new conditioned RBAC model named as CMWRBSAC is proposed on the basis of multi-weighted roles. A conditioned RBAC strategy is discussed on the basis of dynamic role assignment. A new concept of workflow access authorization is defined on the basis of roles with multi-weights, including the hierarchy weight, the degree weight and the sequence weight. Furthermore, in order to solve the problems of the sequence constraint of cooperative activating task by multi-roles and multi-users, a sort algorithm based on token and a sort algorithm based on weighted roles synthesis are presented respectively. Finally, an example is given to show the work processes of these algorithms. This model can express complicated workflow secure access control constraint. © 2005 IEEE.

关键词： Security systems

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A globally optimal approach for surveillance video cropping

A globally optimal approach for surveillance video cropping

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作者： Liu, Jin Shi, Xiaohu Zhang, Yu College of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education 130012 Changchun China

In this paper, a novel approach for surveillance video cropping is presented. The basic idea is to obtain a trajectory that a small sub-window can take through the video, selecting the most important regions of the video for display on a smaller monitor. In this framework, the video content is firstly modeled by whether image frames change at each pixel. Then a shortest path algorithm is used to find the globally optimal trajectory for a cropping window. After that a second shortest path formulation is employed to find good cuts from one trajectory to another, improving the coverage of interesting events in the video content. Finally, additional techniques are demonstrated to improve the quality and efficiency of the algorithm, and results are shown on surveillance videos from PETS 2006.

关键词： Trajectories

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