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A Survey of Sum-Product Networks Structural Learning

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SSRN

SSRN 2022年

作者： Xia, Riting Zhang, Yan Liu, Xueyan Yang, Bo School of Artificial Intelligence Jilin University Jilin Changchun130012 China School of Computer Science and Technology Jilin University Jilin Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineer Jilin University Ministry of Education Jilin Changchun130012 China College of Communication Engineering Jilin University Jilin Changchun130012 China

Sum-product networks (SPNs) in deep probabilistic models have made great progress in computer vision, robotics, neuro-symbolic artificial intelligence, natural language processing, probabilistic programming languages, and other fields. Compared with probabilistic graphical models and deep probabilistic models, SPNs can balance the tractability and expressive efficiency. In addition, SPNs remain more interpretable than deep neural models. The expressiveness and complexity of SPNs depend on its own structure. Thus, how to design an effective SPN structure learning algorithm that can balance expressiveness and complexity has become a hot research topic in recent years. In this paper, we review SPN structure learning comprehensively, including the motivation of SPN structure learning, a systematic review of related theories, the proper categorization of different SPN structure learning algorithms, several evaluation approaches and some helpful online resources. Moreover, we discuss some open issues and research directions for SPN structure learning. To our knowledge, this is the first survey to focus specifically on SPN structure learning, and we hope to provide useful references for researchers in related fields. © 2022, The Authors. All rights reserved.

关键词： Efficiency

AMPCliff: quantitative definition and benchmarking of activity cliffs in antimicrobial peptides

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arXiv 2024年

作者： Li, Kewei Wu, Yuqian Li, Yinheng Guo, Yutong Wang, Yan Liang, Yiyang Fan, Yusi Huang, Lan Zhang, Ruochi Zhou, Fengfeng College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Jilin Changchun130012 China School of Software Jilin University Jilin Changchun130012 China School of Life Sciences Jilin University Jilin Changchun130012 China Department of Computer Science Columbia University 116th and Broadway New York CityNY10027 United States School of Artificial Intelligence Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Jilin Changchun130012 China School of Biology and Engineering Guizhou Medical University Guizhou Guiyang550025 China School of Computer Engineering Changchun University of Engineering Jilin Changchun130103 China Changchun Wenli High School Jilin Changchun130062 China

Since the mechanism of action of drug molecules in the human body is difficult to reproduce in the in vitro environment, it becomes difficult to reveal the causes of the activity cliff phenomenon of drug molecules. We found out the AC of small molecules has been extensively investigated but limited knowledge is accumulated about the AC phenomenon in peptides with canonical amino acids. Understanding the mechanism of AC in canonical amino acids might help understand the one in drug molecules. This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids. A comprehensive analysis of the existing AMP dataset reveals a significant prevalence of AC within AMPs. AMPCliff quantifies the activities of AMPs by the MIC, and defines 0.9 as the minimum threshold for the normalized BLOSUM62 similarity score between a pair of aligned peptides with at least two-fold MIC changes. This study establishes a benchmark dataset of paired AMPs in Staphylococcus aureus from the publicly available AMP dataset GRAMPA, and conducts a rigorous procedure to evaluate various AMP AC prediction models, including nine machine learning, four deep learning algorithms, four masked language models, and four generative language models. Our analysis reveals that these models are capable of detecting AMP AC events and the pre-trained protein language model ESM2 demonstrates superior performance across the evaluations. The predictive performance of AMP activity cliffs remains to be further improved, considering that ESM2 with 33 layers only achieves the Spearman correlation coefficient 0.4669 for the regression task of the MIC values on the benchmark dataset. Source code and additional resources are available at https://***/supp/or https://***/Kewei2023/AMPCliff-generation. © 2024, CC BY-NC-SA.

关键词： Deep learning

Combining Immune with Ant Colony Algorithm for Geometric Constraint Solving

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Combining Immune with Ant Colony Algorithm for Geometric Con...

International Workshop on knowledge Discovery and Data Mining (WKDD)

作者： Hua Yuan Yi Li Wenhui Li Kong Zhao Duo Wang Rongqin Yi Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education College of Computer Science and Technology Jilin University Changchun China School of Computer Science & Engineering Changchun University of Technology China Suzhou Top Institute of Information Technology Suzhou China

Geometric constraint problem can be transformed to an optimization problem which the objective function and constraints are non-convex functions. In this paper an evolutionary algorithm based on ant colony optimization algorithm and the immune system model is proposed to provide solution to the geometric constraints problem. In the new algorithm, affinity calculation process and pheromone trail lying is embedded to maintain diversity and carry out the global search and the local search in many directions rather than one direction around the same individual simultaneously. This new algorithm different with current optimization methods in that it gets the good solution by excluding bad solutions. The experimental results reported here will shed more light into how affects the hybrid algorithm's search power in solving geometric constraint problem.

关键词： Immune system Ant colony optimization Nonlinear equations knowledge engineering Computer science educational technology Evolutionary computation Data mining Laboratories Computer science education

Unsupervised key-phrases extraction from scientific papers using domain and linguistic knowledge

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Unsupervised key-phrases extraction from scientific papers u...

International Conference on Digital Information Management (ICDIM)

作者： Mikalai Krapivin Maurizio Marchese Andrei Yadrantsau Yanchun Liang Department of Information Engineering and Computer Science University of Trento Italy Department of Computer Science Belarusian State University Minsk Belarus College of Computer Science and Technology Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Jilin University China

The domain of Digital Libraries presents specific challenges for unsupervised information extraction to support both the automatic classification of documents and the enhancement of userspsila navigation in the digital content. In this paper, we propose a combined use of machine learning techniques (i.e. Support Vector Machines) and Natural Language Processing techniques (i.e. Stanford NLP parser) to tackle the problem of unsupervised key-phrases extraction from scientific papers. The proposed method strongly depends on the robust structural properties of a scientific paper as well as on the lexical knowledge that we are able to mine from its text. For the experimental assessment we have use a subset of ACM papers in the Computer Science domain containing 400 documents. Preliminary evaluation of the approach shows promising result that improves - on the same data-set - on state-of-the-art Bayesian learning system KEA from a minimum 27% to a maximum 77% depending on KEA parameters tuning and specific evaluation set. Our assessment is performed by comparison with key-phrases assigned by human experts in the specific domain and freely available through ACM portal.

关键词： Data mining Software libraries Navigation Machine learning Support vector machines Support vector machine classification Natural language processing Robustness Computer science Bayesian methods

A Novel Distributed Differential Privacy Preserving Based on Random Forest in Data Centers

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Procedia Computer Science 2022年 214卷 1531-1540页

作者： Xi Wang Weibei Fan Jing He Chi-Hung Chi Suzhou Institute of Industrial Technology Suzhou 215006 China Key laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012 P.R. China College of Computer Nanjing University of Posts and Telecommunications Nanjing 210003 China Department of Neuroscience University of Oxford Oxford OX1 3QR England School of Computer Nanyang Technological University Nanyang Avenue 639798 Singapore

Traditional privacy-preserving technologies have been unable to provide adequate protection and are vulnerable to background knowledge. MapReduce is parallel distributed computing model which has the advantages of good scalability and high fault tolerance. In this paper, we design a differential privacy protection based on MapReduce for the security problems faced in the distributed environment. Firstly, we propose a random forest algorithm DPMRRF that satisfies differential privacy under the MapReduce framework. Secondly, we use the MapReduce framework in the Hadoop platform to make the classification results satisfy differential privacy by adding random noise values to the leaf nodes. Finally, through the design of the feature selection scheme combined with the index mechanism, three different privacy budget allocation methods are adopted, namely, equal distribution, equal distribution and equal distribution. Experiments show that the algorithm has better classification accuracy while ensuring data availability. The proposed algorithm effectively improves the classification accuracy and operating efficiency, and greatly reduces the amount of computation.

关键词： MapReduce Differential privacy protection Random forest Privacy budget

Zero-shot user intent detection via capsule neural networks

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arXiv 2018年

作者： Xia, Congying Zhang, Chenwei Yan, Xiaohui Chang, Yi Yu, Philip S. Department of Computer Science University of Illinois at Chicago ChicagoIL60607 United States Huawei Technologies San JoseCA95050 United States College of Artificial Intelligence Jilin University Changchun China College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education China

User intent detection plays a critical role in question-answering and dialog systems. Most previous works treat intent detection as a classification problem where utterances are labeled with predefined intents. However, it is labor-intensive and time-consuming to label users' utterances as intents are diversely expressed and novel intents will continually be involved. Instead, we study the zero-shot intent detection problem, which aims to detect emerging user intents where no labeled utterances are currently available. We propose two capsule-based architectures: IntentCapsNet that extracts semantic features from utterances and aggregates them to discriminate existing intents, and IntentCapsNet-ZSL which gives IntentCapsNet the zero-shot learning ability to discriminate emerging intents via knowledge transfer from existing intents. Experiments on two real-world datasets show that our model not only can better discriminate diversely expressed existing intents, but is also able to discriminate emerging intents when no labeled utterances are available. Copyright © 2018, The Authors. All rights reserved.

关键词： knowledge management

Prediction of multiple sequence alignment based on an improved particle swarm optimization

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Journal of Bionanoscience 2013年第1期7卷 92-96页

作者： Gao, Yu-Xi Wang, Yan-Min Pei, Zhi-Li Department of Computer Science Jilin Business and Technology College China Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education College of Computer Science and Technology Jilin University China College of Computer Science and Technology Inner Mongolia University for the Nationalities Tongliao 028000 China

In this paper we use an improved Particle Swarm Optimization algorithm to solve Multiple Sequence Alignment (MSA). MSA is a key problem in bioinformatics. The thesis starts with the theory of Particle swarm optimization algorithm and the design an improved algorithm for Multiple Sequence Alignment. The simulated experiments show that the improved algorithm surpasses existing algorithms in performance. Copyright © 2013 American Scientific Publishers.

关键词： Bioinformatics

When Federated Recommendation Meets Cold-Start Problem: Separating Item Attributes and User Interactions

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arXiv 2023年

作者： Zhang, Chunxu Zhang, Zijian Long, Guodong Yan, Peng Zhou, Tianyi Yang, Bo College of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Changchun China College of Computer Science and Technology Jilin University City University of Hong Kong China Australian Artificial Intelligence Institute FEIT University of Technology Sydney Sydney Australia Computer Science and UMIACS University of Maryland Maryland United States

Federated recommendation systems usually trains a global model on the server without direct access to users’ private data on their own devices. However, this separation of the recommendation model and users’ private data poses a challenge in providing quality service, particularly when it comes to new items, namely cold-start recommendations in federated settings. This paper introduces a novel method called Item-aligned Federated Aggregation (IFedRec) to address this challenge. It is the first research work in federated recommendation to specifically study the cold-start scenario. The proposed method learns two sets of item representations by leveraging item attributes and interaction records simultaneously. Additionally, an item representation alignment mechanism is designed to align two item representations and learn the meta attribute network at the server within a federated learning framework. Experiments on four benchmark datasets demonstrate IFedRec’s superior performance for cold-start scenarios. Furthermore, we also verify IFedRec owns good robustness when the system faces limited client participation and noise injection, which brings promising practical application potential in privacy-protection enhanced federated recommendation systems. The implementation code is available1 Copyright © 2023, The Authors. All rights reserved.

关键词： Recommender systems

PepLand: A large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids

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arXiv 2023年

作者： Zhang, Ruochi Wu, Haoran Xiu, Yuting Li, Kewei Chen, Ningning Wang, Yu Wang, Yan Gao, Xin Zhou, Fengfeng Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Jilin Changchun130012 China School of Artificial Intelligence Jilin University Changchun130012 China Syneron Technology Guangzhou510700 China College of Computer Science and Technology Jilin University Jilin Changchun130012 China Thuwal23955 Saudi Arabia Thuwal23955 Saudi Arabia

In recent years, the scientific community has become increasingly interested on peptides with non-canonical amino acids due to their superior stability and resistance to proteolytic degradation. These peptides present promising modifications to biological, pharmacological, and physiochemical attributes in both endogenous and engineered peptides. Notwithstanding their considerable advantages, the scientific community exhibits a conspicuous absence of an effective pre-trained model adept at distilling feature representations from such complex peptide sequences. We herein propose PepLand, a novel pre-training architecture for representation and property analysis of peptides spanning both canonical and non-canonical amino acids. In essence, PepLand leverages a comprehensive multi-view heterogeneous graph neural network tailored to unveil the subtle structural representations of peptides. Empirical validations underscore PepLand's effectiveness across an array of peptide property predictions, encompassing protein-protein interactions, permeability, solubility, and synthesizability. The rigorous evaluation confirms PepLand's unparalleled capability in capturing salient synthetic peptide features, thereby laying a robust foundation for transformative advances in peptide-centric research domains. We have made all the source code utilized in this study publicly accessible via GitHub at https://***/zhangruochi/pepland. © 2023, CC BY-NC-ND.

关键词： Peptides