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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

BARGAIN-MATCH: A Game Theoretical Approach for Resource Allocation and Task Offloading in Vehicular Edge Computing Networks

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arXiv 2022年

作者： Sun, Zemin Sun, Geng Liu, Yanheng Wang, Jian Cao, Dongpu The College of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China The School of Vehicle and Mobility Tsinghua University Beijing China

Vehicular edge computing (VEC) is emerging as a promising architecture of vehicular networks (VNs) by deploying the cloud computing resources at the edge of the VNs. However, efficient resource management and task offloading in the VEC network is challenging. In this work, we first present a hierarchical framework that coordinates the heterogeneity among tasks and servers to improve the resource utilization for servers and service satisfaction for vehicles. Moreover, we formulate a joint resource allocation and task offloading problem (JRATOP), aiming to jointly optimize the intra-VEC server resource allocation and inter-VEC server load-balanced offloading by stimulating the horizontal and vertical collaboration among vehicles, VEC servers, and cloud server. Since the formulated JRATOP is NP-hard, we propose a cooperative resource allocation and task offloading algorithm named BARGAIN-MATCH, which consists of a bargaining-based incentive approach for intra-server resource allocation and a matching method-based horizontal-vertical collaboration approach for inter-server task offloading. Besides, BARGAIN-MATCH is proved to be stable, weak Pareto optimal, and polynomial complex. Simulation results demonstrate that the proposed approach achieves superior system utility and efficiency compared to the other methods, especially when the system workload is heavy. Copyright © 2022, The Authors. All rights reserved.

关键词： Game theory

Weakly supervised prototype topic model with discriminative seed words: Modifying the category prior by self-exploring supervised signals

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arXiv 2021年

作者： Wang, Bing Wang, Yue Li, Ximing Ouyang, Jihong College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation Knowledge Engineering of Ministry of Education Jilin University China

Dataless text classification, i.e., a new paradigm of weakly supervised learning, refers to the task of learning with unlabeled documents and a few predefined representative words of categories, known as seed words. The recent generative dataless methods construct document-specific category priors by using seed word occurrences only, however, such category priors often contain very limited and even noisy supervised signals. To remedy this problem, in this paper we propose a novel formulation of category prior. First, for each document, we consider its label membership degree by not only counting seed word occurrences, but also using a novel prototype scheme, which captures pseudo-nearest neighboring categories. Second, for each label, we consider its frequency prior knowledge of the corpus, which is also a discriminative knowledge for classification. By incorporating the proposed category prior into the previous generative dataless method, we suggest a novel generative dataless method, namely Weakly Supervised Prototype Topic Model (Wsptm). The experimental results on real-world datasets demonstrate that Wsptm outperforms the existing baseline methods. © 2021, CC0.

关键词： Text processing

Causal-Inspired Multitask Learning for Video-Based Human Pose Estimation 39

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Causal-Inspired Multitask Learning for Video-Based Human Pos...

39th Annual AAAI Conference on Artificial Intelligence, AAAI 2025

作者： Chen, Haipeng Wu, Sifan Wang, Zhigang Yin, Yifang Jiao, Yingying Lyu, Yingda Liu, Zhenguang 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 Computer Science and Technology Zhejiang Gongshang University China Institute for Infocomm Research (I2R) A*STAR Singapore Public Computer Education and Research Center Jilin University China The State Key Laboratory of Blockchain and Data Security Zhejiang University China Hangzhou High-Tech Zone (Binjiang) Institute of Blockchain and Data Security China

ISBN: (纸本)157735897X

Video-based human pose estimation has long been a fundamental yet challenging problem in computer vision. Previous studies focus on spatio-temporal modeling through the enhancement of architecture design and optimization strategies. However, they overlook the causal relationships in the joints, leading to models that may be overly tailored and thus estimate poorly to challenging scenes. Therefore, adequate causal reasoning capability, coupled with good interpretability of model, are both indispensable and prerequisite for achieving reliable results. In this paper, we pioneer a causal perspective on pose estimation and introduce a causal-inspired multitask learning framework, consisting of two stages. In the first stage, we try to endow the model with causal spatio-temporal modeling ability by introducing two self-supervision auxiliary tasks. Specifically, these auxiliary tasks enable the network to infer challenging keypoints based on observed keypoint information, thereby imbuing causal reasoning capabilities into the model and making it robust to challenging scenes. In the second stage, we argue that not all feature tokens contribute equally to pose estimation. Prioritizing causal (keypoint-relevant) tokens is crucial to achieve reliable results, which could improve the interpretability of the model. To this end, we propose a Token Causal Importance Selection module to identify the causal tokens and non-causal tokens (e.g., background and objects). Additionally, non-causal tokens could provide potentially beneficial cues but may be redundant. We further introduce a non-causal tokens clustering module to merge the similar non-causal tokens. Extensive experiments show that our method outperforms state-of-the-art methods on three large-scale benchmark datasets. Copyright © 2025, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

关键词： Multi-task learning

Joint Power and 3D Trajectory Optimization for UAV-enabled Wireless Powered Communication Networks with Obstacles

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arXiv 2023年

作者： Pan, Hongyang Liu, Yanheng Sun, Geng Fan, Junsong Liang, Shuang Yuen, Chau The College of Computer Science and Technology Jilin University Changchun130012 China Pillar Singapore University of Technology and Design 487372 Singapore The Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China The School of Information Science and Technology Northeast Normal University Changchun130024 China

Unmanned aerial vehicle (UAV)-enabled wireless powered communication networks (WPCNs) are promising technologies in 5G/6G wireless communications, while there are several challenges about UAV power allocation and scheduling to enhance the energy utilization efficiency, considering the existence of obstacles. In this work, we consider a UAV-enabled WPCN scenario that a UAV needs to cover the ground wireless devices (WDs). During the coverage process, the UAV needs to collect data from the WDs and charge them simultaneously. To this end, we formulate a joint-UAV power and three-dimensional (3D) trajectory optimization problem (JUPTTOP) to simultaneously increase the total number of the covered WDs, increase the time efficiency, and reduce the total flying distance of UAV so as to improve the energy utilization efficiency in the network. Due to the difficulties and complexities, we decompose it into two sub optimization problems, which are the UAV power allocation optimization problem (UPAOP) and UAV 3D trajectory optimization problem (UTTOP), respectively. Then, we propose an improved non-dominated sorting genetic algorithm-II with K-means initialization operator and Variable dimension mechanism (NSGA-II-KV) for solving the UPAOP. For UTTOP, we first introduce a pretreatment method, and then use an improved particle swarm optimization with Normal distribution initialization, Genetic mechanism, Differential mechanism and Pursuit operator (PSO-NGDP) to deal with this sub optimization problem. Simulation results verify the effectiveness of the proposed strategies under different scales and settings of the networks. Copyright © 2023, The Authors. All rights reserved.

关键词： Energy utilization

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 Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education College of Computer Science and Technology Jilin university Changchun130012 China Joint NTU-UBC Research Centre of Excellence in Active Living for the Elderly Nanyang Technological University 639798 Singapore School of Software Tsinghua University Beijing100084 China 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, they did not cover the state-of-the-art (SOTA) NCO solvers emerged recently. More importantly, to establish a comprehensive and up-to-date taxonomy of NCO solvers, we systematically review relevant publications and preprints, categorizing them into four distinct types, 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 discuss on-going efforts, identify open inadequacies, as well as propose promising and viable directions to overcome these inadequacies. Notably, existing efforts focus on only one or two of these inadequacies, with none attempting to address all of them concurrently. In addition, we compare the performance of representative NCO solvers from the Reinforcement, Supervised, and Unsupervised Learning paradigms across VRPs of varying scales. 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 aim to foster further advancements in the NCO community. Copyright © 2024, The Authors. All rights reserved.

关键词： Combinatorial optimization

A Multi-Agent Deep Reinforcement Learning Method for Fully Noisy Observations

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SSRN

SSRN 2023年

作者： Wang, Kaiyu Zhang, Menglin Qu, Bohao Wang, Xianchang College of Computer Science and Technology Jilin University Jilin Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin Changchun130012 China School of Artificial Intelligence Jilin University Jilin Changchun130012 China Chengdu Kestrel Artificial Intelligence Institute Chengdu611730 China

Multi-agent reinforcement learning (MARL) algorithms have achieved great breakthroughs in many aspects. The MARL algorithms can learn effective policies in ideal simulation environments. But different from the ideal simulation environments, noise is unavoidable in the real world. MARL algorithms need to learn effective policies in unavoidable fully noisy environments. In this paper, we consider a challenging multi-agent reinforcement learning problem: All agents cannot observe any noiseless observations from environments during the whole training process and MARL algorithms cannot learn effective policies in these fully noisy observation environments. To solve this problem, we propose a method called Robust Policy Learning under Fully Noisy Observation viA DeNoising REpresentation NeTwork (PLANET), which enables MARL algorithms learning effective policies in fully noisy observation environments. The PLANET method learns the effective policy through two steps. (1) Extracting the noise characteristics and motion laws information from fully noisy observation histories. (2) Making MARL algorithms extract information from the noise characteristics and motion laws information and learn effective policies. The results of a series of exhaustive experiments show that our method can eliminate the effects of noise and learn effective policies in fully noisy observation environments. © 2023, The Authors. All rights reserved.

关键词： Learning algorithms

Categorizing npm Packages by Analyzing the Text Information in Software Repositories

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Categorizing npm Packages by Analyzing the Text Information ...

Asia-Pacific Conference on Software engineering

作者： Yu Wang Huaxiao Liu Shanquan Gao Shujia Li College of computer science and technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Changchun China

ISBN: (纸本)9781665437851

To prevent JavaScript developers from reinventing wheels, npm ecosystem provides numerous third-party libraries for developers to realize relevant functionalities. Npm displays the tags provided by the creators for these packages to help developers find suitable ones. However, not all creators have the habit of tagging their packages, and thus npm cannot provide tag information of a lot of packages for developers to help them understand the package functionalities effectively. Considering that many tags are unrelated to the functionality of packages, we propose a method to find out the tags that are important to distinguish the functionality categories of packages and assign them to untagged packages for assisting developers in the process of retrieving the packages. Firstly, we analyze the attribute of existing tags in npm to establish category tags (functionality categories). Then, we further mine the readme of tagged packages to generate keywords for each category tag. Finally, our method identifies category tags for untagged packages by measuring the similarity between their readme and the keywords of category tags. The evaluation demonstrates that our approach has a good performance in assigning category tags to untagged packages.

关键词： Correlation Codes Ecosystems Wheels Tagging Software Libraries

A Unified Collaborative Representation Learning for Neural-Network based Recommender Systems

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arXiv 2022年

作者： Xu, Yuanbo Wang, En Yang, Yongjian Chang, Yi The Department of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering The Ministry of Education Jilin University Changchun130012 China The School of Artificial Intelligence Jilin University Jilin Changchun130012 China

With the boosting of neural networks, recommendation methods become significantly improved by their powerful ability of prediction and inference. Existing neural-network based recommender systems (NN-RSs) usually first employ matrix embedding (ME) as a pre-process to learn users’ and items’ representations (latent vectors), then input these representations to a specific modified neural network framework to make accurate Top-k recommendations. Obviously, the performance of ME has a significant effect on RS models. However, most NN-RSs focus on accuracy by building representations from the direct user-item interactions (e.g., user-item rating matrix), while ignoring the underlying relatedness between users and items (e.g., users who rate the same ratings for the same items should be embedded into similar representations), which is an ideological disadvantage. On the other hand, ME models directly employ inner products as a default loss function metric that cannot project users and items into a proper latent space, which is a methodological disadvantage. In this paper, we propose a supervised collaborative representation learning model - Magnetic Metric Learning (MML) - to map users and items into a unified latent vector space, enhancing the representation learning for NN-RSs. Firstly, MML utilizes dual triplets to model not only the observed relationships between users and items, but also the underlying relationships between users as well as items to overcome the ideological disadvantage. Specifically, a modified metric-based dual loss function is proposed in MML to gather similar entities and disperse the dissimilar ones. With MML, we can easily compare all the relationships (user to user, item to item, user to item) according to the weighted metric, which overcomes the methodological disadvantage. We conduct extensive experiments on four real-world datasets with large item space. The results demonstrate that MML can learn a proper unified latent space for representa

关键词： Recommender systems