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A Novel Drug-Drug Interaction Prediction Model Based on Line Subgraph Generation Strategy

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A Novel Drug-Drug Interaction Prediction Model Based on Line...

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Tian Bai Chu Li Xinyue Peng Haotian Guan Zefan Zhang Guishen Wang College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun China College of Software Jilin University Changchun China School of Nursing Jilin University Changchun China School of Life Sciences Jilin University Changchun China College of Computer Science and Engineering Changchun University of Technology Changchun China

Drug-Drug Interaction (DDI) prediction task is helpful for better-understanding drugs. In this paper, we propose a novel drug-drug interaction prediction model based on line subgraph generation strategy, named DDI-LSG model. Our DDI-LSG model consists of three main parts which include drug relation graph construction, line subgraph generation strategy, and graph-level classification. To consider more relationships among drugs, we propose a node feature-enhancing method to encode drug features in drug relation graph construction process. To consider drugs and DDI as equivalent factors of our DDI-LSG model, we introduce line graph transformation to integrate DDI with drug feature enhancing vector. Combining Jaccard similarity with cosine similarity, we propose a line subgraph generation strategy to evaluate node relation and extract key structures around target DDI in the line graph. Then, we reformulate the DDI prediction task into a graph-level classification task for the line subgraph of the target DDI. Therefore, in the final part of our DDI-LSG model, we use a graph-level classifier to classify the line subgraphs. Our DDI-LSG model outperforms better experiment results than baselines. Ablation results have validated the node feature enhancing method and line subgraph generation strategy.

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A hybrid discrete PSO-SA algorithm to find optimal elimination orderings for Bayesian networks

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A hybrid discrete PSO-SA algorithm to find optimal eliminati...

International Conference on Industrial and Information Systems, IIS

作者： Xuchu Dong Dantong Ouyang Dianbo Cai Yonggang Zhang Yuxin Ye Department of Computer Science and Technology Jilin University Changchun Jilin China Key Laboratory of Symbol Computation and Knowledge Engineering Ministry of Education Changchun Jilin China Network Monitor Maintenance Centre China Telecom Corporation Limited Changchun Jilin China

In this paper, a hybrid algorithm named DPSOSA is proposed to find near-to-optimal elimination orderings in Bayesian networks. DPSO-SA is a discrete particle swarm optimization method enhanced by simulated annealing. ... 详细信息

关键词： computational modeling Adaptation model

Cooperative coevolutionary genetic algorithms to find optimal elimination orderings for Bayesian networks

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Cooperative coevolutionary genetic algorithms to find optima...

International Conference on Bio-Inspired Computing: Theories and Applications, BICTA

作者： Xuchu Dong HaiHong Yu Dantong Ouyang Dianbo Cai Yuxin Ye Yonggang Zhang Department of Computer Science and Technology Jilin University Changchun Jilin China Key Laboratory of Symbol Computation and Knowledge Engineering Ministry of Education Changchun Jilin China Network Monitor Maintenance Centre China Telecom Corporation Limited Changchun Jilin China

According to the characteristics of the optimal elimination ordering problem in Bayesian networks, a heuristic-based genetic algorithm, a cooperative coevolutionary genetic framework and five grouping schemes are proposed. Based on these works, six cooperative coevolutionary genetic algorithms are constructed. Numerical experiments show that these algorithms are more robust than other existing swarm intelligence methods when solving the elimination ordering problem.

关键词： Genetics Bayesian methods Robustness

A Novel Neural-symbolic System under Statistical Relational Learning

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arXiv 2023年

作者： Yu, Dongran Liu, Xueyan Pan, Shirui Li, Anchen Yang, Bo Key Laboratory of Symbolic Computation and Knowledge Engineer Ministry of Education Jilin University Jilin Changchun130012 China School of Computer Science and Technology Jilin University Jilin Changchun130012 China School of Artificial Intelligence Jilin University Jilin Changchun130012 China School of Information and Communication Technology Griffith University BrisbaneQLD4222 Australia

A key objective in the field of artificial intelligence is to develop cognitive models that can exhibit human-like intellectual capabilities. One promising approach to achieving this is through neural-symbolic systems, which combine the strengths of deep learning and symbolic reasoning. However, current methodologies in this area face limitations in integration, generalization, and interpretability. To address these challenges, we propose a neural-symbolic framework based on statistical relational learning, referred to as NSF-SRL. This framework effectively integrates deep learning models with symbolic reasoning in a mutually beneficial manner. In NSF-SRL, the results of symbolic reasoning are utilized to refine and correct the predictions made by deep learning models, while deep learning models enhance the efficiency of the symbolic reasoning process. Through extensive experiments, we demonstrate that our approach achieves high performance and exhibits effective generalization in supervised learning, weakly supervised and zero-shot learning tasks. Furthermore, we introduce a quantitative strategy to evaluate the interpretability of the model’s predictions, visualizing the corresponding logic rules that contribute to these predictions and providing insights into the reasoning process. We believe that this approach sets a new standard for neural-symbolic systems and will drive future research in the field of general artificial intelligence. Copyright © 2023, The Authors. All rights reserved.

关键词： Adversarial machine learning

Neural Combinatorial Optimization Algorithms for Solving Vehicle Routing Problems: A Comprehensive Survey with Perspectives

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arXiv 2024年

作者： Wu, Xuan Wang, Di Wen, Lijie Xiao, Yubin Wu, Chunguo Wu, Yuesong Yu, Chaoyu Maskell, Douglas L. Zhou, You The Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education College of Computer Science and Technology Jilin university Changchun130012 China The Joint NTU-UBC Research Centre of Excellence in Active Living for the Elderly Nanyang Technological University 639798 Singapore The School of Software Tsinghua University Beijing100084 China The College of Computing and Data Science Nanyang Technological University 639798 Singapore

Although several surveys on Neural Combinatorial Optimization (NCO) solvers specifically designed to solve Vehicle Routing Problems (VRPs) have been conducted. These existing surveys did not cover the state-of-the-art (SOTA) NCO solvers emerged recently. More importantly, to provide a comprehensive taxonomy of NCO solvers with up-to-date coverage, based on our thorough review of relevant publications and preprints, we divide all NCO solvers into four distinct categories, namely Learning to Construct, Learning to Improve, Learning to Predict-Once, and Learning to Predict-Multiplicity solvers. Subsequently, we present the inadequacies of the SOTA solvers, including poor generalization, incapability to solve large-scale VRPs, inability to address most types of VRP variants simultaneously, and difficulty in comparing these NCO solvers with the conventional Operations Research algorithms. Simultaneously, we propose promising and viable directions to overcome these inadequacies. In addition, we compare the performance of representative NCO solvers from the Reinforcement, Supervised, and Unsupervised Learning paradigms across both small- and large-scale VRPs. Finally, following the proposed taxonomy, we provide an accompanying web page as a live repository for NCO solvers. Through this survey and the live repository, we hope to make the research community of NCO solvers for VRPs more thriving. Copyright © 2024, The Authors. All rights reserved.

关键词： Taxonomies

A novel multi-task learning network for skin lesion classification based on multi-modal clues and label-level fusion

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Computers in Biology and Medicine 2024年 175卷 108549-108549页

作者： Lin, Qifeng Guo, Xiaoxin Feng, Bo Guo, Juntong Ni, Shuang Dong, Hongliang Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Jilin University 2699 Qianjin Street Changchun130012 China College of Computer Science and Technology Jilin University 2699 Qianjin Street Changchun130012 China College of Software Jilin University 2699 Qianjin Street Changchun130012 China

In this paper, we propose a multi-task learning (MTL) network based on the label-level fusion of metadata and hand-crafted features by unsupervised clustering to generate new clustering labels as an optimization goal. We propose a MTL module (MTLM) that incorporates an attention mechanism to enable the model to learn more integrated, variable information. We propose a dynamic strategy to adjust the loss weights of different tasks, and trade off the contributions of multiple branches. Instead of feature-level fusion, we propose label-level fusion and combine the results of our proposed MTLM with the results of the image classification network to achieve better lesion prediction on multiple dermatological datasets. We verify the effectiveness of the proposed model by quantitative and qualitative measures. The MTL network using multi-modal clues and label-level fusion can yield the significant performance improvement for skin lesion classification. © 2024 Elsevier Ltd

关键词： Metadata

Resource Scheduling for UAVs-aided D2D Networks: A Multi-objective Optimization Approach

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arXiv 2023年

作者： Pan, Hongyang Liu, Yanheng Sun, Geng Wang, Pengfei Yuen, Chau College of Computer Science and Technology Jilin University Changchun130012 China Pillar Singapore University of Technology and Design Singapore487372 Singapore Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China School of Computer Science and Technology Dalian University of Technology Dalian116024 China School of Electrical and Electronics Engineering Nanyang Technological University Singapore639798 Singapore

Unmanned aerial vehicles (UAVs)-aided device-to-device (D2D) networks have attracted great interests with the development of 5G/6G communications, while there are several challenges about resource scheduling in UAVs-aided D2D networks. In this work, we formulate a UAVs-aided D2D network resource scheduling optimization problem (NetResSOP) to comprehensively consider the number of deployed UAVs, UAV positions, UAV transmission powers, UAV flight velocities, communication channels, and UAV-device pair assignment so as to maximize the D2D network capacity, minimize the number of deployed UAVs, and minimize the average energy consumption over all UAVs simultaneously. The formulated NetResSOP is a mixed-integer programming problem (MIPP) and an NP-hard problem, which means that it is difficult to be solved in polynomial time. Moreover, there are trade-offs between the optimization objectives, and hence it is also difficult to find an optimal solution that can simultaneously make all objectives be optimal. Thus, we propose a non-dominated sorting genetic algorithm-III with a Flexible solution dimension mechanism, a Discrete part generation mechanism, and a UAV number adjustment mechanism (NSGA-III-FDU) for solving the problem comprehensively. Simulation results demonstrate the effectiveness and the stability of the proposed NSGA-III-FDU under different scales and settings of the D2D networks. Copyright © 2023, The Authors. All rights reserved.

关键词： Energy utilization

Event Prediction Model Combining Ordinary Differential Equation and Hypernetworks

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SSRN

SSRN 2023年

作者： Zhang, Junhe Ma, Fuyuan Wang, Xin Yang, Bo Wang, Ying College of Computer Science and Technology Jilin University Jilin Changchun130012 China College of Artificial Intelligence Jilin University Jilin Changchun130012 China Key Laboratory of Symbol Computation and Knowledge Engineering Jilin University Ministry of Education Jilin Changchun130012 China

Modeling the temporal evolution patterns of network events is crucial for enhancing user experience and creating commercial value. Existing methods combine graph neural networks and time-series models to capture spatial and temporal features, but they assume non-interaction among nodes when the network structure is stable, implying that node states do not undergo updates. Moreover, utilizing a single model to fit all events in these methods may lead to an excessive emphasis on global evolutionary patterns, potentially neglecting the individual heterogeneity among events. In this paper, we propose an event prediction model combining Ordinary Differential Equations and Hypernetworks, named ODEH. Firstly, to model the continuous evolution process of network structures under stability, we utilize ordinary differential equations based on graph neural networks to capture the continuous information dissemination among nodes and the interaction between node representation channels. Then, we use a message passing mechanism to model the direct impact of network topology changes on network entities. Finally, a hypernetwork is used to capture the individual characteristics of events and fine-tune the prediction model. Experimental results on multiple datasets demonstrate ODEH's superiority over baseline methods, highlighting its effectiveness in event prediction. © 2023, The Authors. All rights reserved.

关键词： Graph neural networks

An Empirical Study on Information Extraction using Large Language Models

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arXiv 2023年

作者： Han, Ridong Yang, Chaohao Peng, Tao Tiwari, Prayag Wan, Xiang Liu, Lu Wang, Benyou College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China College of Software Jilin University China Shenzhen Research Institute of Big Data The Chinese University of Hong Kong Shenzhen China School of Data Science The Chinese University of Hong Kong Shenzhen China School of Information Technology Halmstad University Sweden

Human-like large language models (LLMs), especially the most powerful and popular ones in OpenAI’s GPT family, have proven to be very helpful for many natural language processing (NLP) related tasks. Therefore, various attempts have been made to apply LLMs to information extraction (IE), which is a fundamental NLP task that involves extracting information from unstructured plain text. To demonstrate the latest representative progress in LLMs’ information extraction ability, we assess the information extraction ability of GPT-4 (the latest version of GPT at the time of writing this paper) from four perspectives: Performance, Evaluation Criteria, Robustness, and Error Types. Our results suggest a visible performance gap between GPT-4 and state-of-the-art (SOTA) IE methods. To alleviate this problem, considering the LLMs’ human-like characteristics, we propose and analyze the effects of a series of simple prompt-based methods, which can be generalized to other LLMs and NLP tasks. Rich experiments show our methods’ effectiveness and some of their remaining issues in improving GPT-4’s information extraction ability. Copyright © 2023, The Authors. All rights reserved.

关键词： Information retrieval