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ALMERIA: Boosting Pairwise Molecular Contrasts with Scalable Methods ALMERIA:利用可扩展方法提高成对分子对比度
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-05-14 DOI: 10.15388/24-infor558
Rafael Mena-Yedra, Juana López Redondo, Horacio Pérez-Sánchez, Pilar Martinez Ortigosa
{"title":"ALMERIA: Boosting Pairwise Molecular Contrasts with Scalable Methods","authors":"Rafael Mena-Yedra, Juana López Redondo, Horacio Pérez-Sánchez, Pilar Martinez Ortigosa","doi":"10.15388/24-infor558","DOIUrl":"https://doi.org/10.15388/24-infor558","url":null,"abstract":"This work introduces ALMERIA, a decision-support tool for drug discovery. It estimates compound similarities and predicts activity, considering conformation variability. The methodology spans from data preparation to model selection and optimization. Implemented using scalable software, it handles large data volumes swiftly. Experiments were conducted on a distributed computer cluster using the DUD-E database. Models were evaluated on different data partitions to assess generalization ability with new compounds. The tool demonstrates excellent performance in molecular activity prediction (ROC AUC: 0.99, 0.96, 0.87), indicating good generalization properties of the chosen data representation and modelling. Molecular conformation sensitivity is also evaluated.\u0000PDF  XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"304 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140939399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Deep Learning Model for Multi-Domain MRI Synthesis Using Generative Adversarial Networks 使用生成式对抗网络的多域核磁共振成像合成深度学习模型
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-04-29 DOI: 10.15388/24-infor556
Le Hoang Ngoc Han, Ngo Le Huy Hien, Luu Van Huy, Nguyen Van Hieu
{"title":"A Deep Learning Model for Multi-Domain MRI Synthesis Using Generative Adversarial Networks","authors":"Le Hoang Ngoc Han, Ngo Le Huy Hien, Luu Van Huy, Nguyen Van Hieu","doi":"10.15388/24-infor556","DOIUrl":"https://doi.org/10.15388/24-infor556","url":null,"abstract":"In recent years, Magnetic Resonance Imaging (MRI) has emerged as a prevalent medical imaging technique, offering comprehensive anatomical and functional information. However, the MRI data acquisition process presents several challenges, including time-consuming procedures, prone motion artifacts, and hardware constraints. To address these limitations, this study proposes a novel method that leverages the power of generative adversarial networks (GANs) to generate multi-domain MRI images from a single input MRI image. Within this framework, two primary generator architectures, namely ResUnet and StarGANs generators, were incorporated. Furthermore, the networks were trained on multiple datasets, thereby augmenting the available data, and enabling the generation of images with diverse contrasts obtained from different datasets, given an input image from another dataset. Experimental evaluations conducted on the IXI and BraTS2020 datasets substantiate the efficacy of the proposed method compared to an existing method, as assessed through metrics such as Structural Similarity Index (SSIM), Peak Signal-to-Noise Ratio (PSNR) and Normalized Mean Absolute Error (NMAE). The synthesized images resulting from this method hold substantial potential as invaluable resources for medical professionals engaged in research, education, and clinical applications. Future research gears towards expanding experiments to larger datasets and encompassing the proposed approach to 3D images, enhancing medical diagnostics within practical applications.\u0000PDF  XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"36 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140810285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Temporal Variable-Scale Clustering Method on Feature Identification for Policy Public-Opinion Management 用于政策民意管理的特征识别时变尺度聚类方法
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-04-26 DOI: 10.15388/24-infor554
Ai Wang, Xuedong Gao, Mincong Tang
{"title":"A Temporal Variable-Scale Clustering Method on Feature Identification for Policy Public-Opinion Management","authors":"Ai Wang, Xuedong Gao, Mincong Tang","doi":"10.15388/24-infor554","DOIUrl":"https://doi.org/10.15388/24-infor554","url":null,"abstract":"The development of various digital social network platforms has caused public opinion to play an increasingly important role in the policy making process. However, due to the fact that public opinion hotspots usually change rapidly (such as the phenomenon of public opinion inversion), both the behaviour feature and demand feature of netizens included in the public opinion often vary over time. Therefore, this paper focuses on the feature identification problem of public opinion simultaneously considering the multiple observation time intervals and key time points, in order to support the management of policy-focused online public opinion. According to the variable-scale data analysis theory, the temporal scale space model is established to describe candidate temporal observation scales, which are organized following the time points of relevant policy promulgation (policy time points). After proposing the multi-scale temporal data model, a temporal variable-scale clustering method (T-VSC) is put forward. Compared to the traditional numerical variable-scale clustering method, the proposed T-VSC enables to combine the subjective attention of decision-makers and objective timeliness of public opinion data together during the scale transformation process. The case study collects 48552 raw public opinion data on the double-reduction education policy from Sina Weibo platform during Jan 2023 to Nov 2023. Experimental results indicate that the proposed T-VSC method could divide netizens that participate in the dissemination of policy-focused public opinion into clusters with low behavioural granularity deviation on the satisfied observation time scales, and identify the differentiated demand feature of each netizen cluster at policy time points, which could be applied to build the timely and efficient digital public dialogue mechanism.\u0000PDF  XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"1 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140799774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Three New Design Patterns for Scalable Agent-Based Computing and Simulation 基于代理的可扩展计算和仿真的三种新设计模式
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-04-19 DOI: 10.15388/24-infor555
Mateusz Najdek, Mateusz Paciorek, Wojciech Turek, Aleksander Byrski
{"title":"Three New Design Patterns for Scalable Agent-Based Computing and Simulation","authors":"Mateusz Najdek, Mateusz Paciorek, Wojciech Turek, Aleksander Byrski","doi":"10.15388/24-infor555","DOIUrl":"https://doi.org/10.15388/24-infor555","url":null,"abstract":"Multi-agent approach is very popular for modelling and simulation of complex phenomena, design and programming of decentralised computing systems. Asynchronous beings, which do not share state but communicate using messages are a convenient abstraction for representing various phenomena observed in the real world. When the number of the considered agents grows, the designers and developers of such systems must address the problem of performance. Introducing distribution is often a weapon of choice, which, however, does not guarantee obtaining proper scalability and efficiency. The intensity of communication in a large-scale agent-based system can easily exceed the abilities of a distributed hardware architecture, leading to poor performance. After analysing various distributed agent-based systems, we identified several reasons for limited performance and several architectural solutions, which can help overcoming this problem. The main aim of the presented work is identification and systematization of these architectural solutions in the form of design patterns. As a result, we propose three new design patterns for building scalable distributed agent-based systems. A systematic description of their aims, structure, variants and features is provided, together with examples of applications.\u0000PDF  XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"9 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140630145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A General Framework for Providing Interval Representations of Pareto Optimal Outcomes for Large-Scale Bi- and Tri-Criteria MIP Problems 为大规模双标准和三标准 MIP 问题提供帕累托最优结果区间表示的一般框架
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-04-12 DOI: 10.15388/24-infor549
Grzegorz Filcek, Janusz Miroforidis
{"title":"A General Framework for Providing Interval Representations of Pareto Optimal Outcomes for Large-Scale Bi- and Tri-Criteria MIP Problems","authors":"Grzegorz Filcek, Janusz Miroforidis","doi":"10.15388/24-infor549","DOIUrl":"https://doi.org/10.15388/24-infor549","url":null,"abstract":"The Multi-Objective Mixed-Integer Programming (MOMIP) problem is one of the most challenging. To derive its Pareto optimal solutions one can use the well-known Chebyshev scalarization and Mixed-Integer Programming (MIP) solvers. However, for a large-scale instance of the MOMIP problem, its scalarization may not be solved to optimality, even by state-of-the-art optimization packages, within the time limit imposed on optimization. If a MIP solver cannot derive the optimal solution within the assumed time limit, it provides the optimality gap, which gauges the quality of the approximate solution. However, for the MOMIP case, no information is provided on the lower and upper bounds of the components of the Pareto optimal outcome. For the MOMIP problem with two and three objective functions, an algorithm is proposed to provide the so-called interval representation of the Pareto optimal outcome designated by the weighting vector when there is a time limit on solving the Chebyshev scalarization. Such interval representations can be used to navigate on the Pareto front. The results of several numerical experiments on selected large-scale instances of the multi-objective multidimensional 0–1 knapsack problem illustrate the proposed approach. The limitations and possible enhancements of the proposed method are also discussed.\u0000PDF  XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"49 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140567342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advancing Research Reproducibility in Machine Learning through Blockchain Technology 通过区块链技术提高机器学习研究的可重复性
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-04-11 DOI: 10.15388/24-infor553
Ernestas Filatovas, Linas Stripinis, Francisco Orts, Remigijus Paulavičius
{"title":"Advancing Research Reproducibility in Machine Learning through Blockchain Technology","authors":"Ernestas Filatovas, Linas Stripinis, Francisco Orts, Remigijus Paulavičius","doi":"10.15388/24-infor553","DOIUrl":"https://doi.org/10.15388/24-infor553","url":null,"abstract":"Like other disciplines, machine learning is currently facing a reproducibility crisis that hinders the advancement of scientific research. Researchers face difficulties reproducing key results due to the lack of critical details, including the disconnection between publications and associated models, data, parameter settings, and experimental results. To promote transparency and trust in research, solutions that improve the accessibility of models and data, facilitate experiment tracking, and allow audit of experimental results are needed. Blockchain technology, characterized by its decentralization, data immutability, cryptographic hash functions, consensus algorithms, robust security measures, access control mechanisms, and innovative smart contracts, offers a compelling pathway for the development of such solutions. To address the reproducibility challenges in machine learning, we present a novel concept of a blockchain-based platform that operates on a peer-to-peer network. This network comprises organizations and researchers actively engaged in machine learning research, seamlessly integrating various machine learning research and development frameworks. To validate the viability of our proposed concept, we implemented a blockchain network using the Hyperledger Fabric infrastructure and conducted experimental simulations in several scenarios to thoroughly evaluate its effectiveness. By fostering transparency and facilitating collaboration, our proposed platform has the potential to significantly improve reproducible research in machine learning and can be adapted to other domains within artificial intelligence.\u0000PDF  XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"52 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140567462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Minimal Surfaces and the Plateau Problem: Numerical Methods and Applications 最小曲面与高原问题:数值方法与应用
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-04-09 DOI: 10.15388/24-infor552
Mifodijus Sapagovas, Vytautas Būda, Saulius Maskeliūnas, Olga Štikonienė, Artūras Štikonas
{"title":"Minimal Surfaces and the Plateau Problem: Numerical Methods and Applications","authors":"Mifodijus Sapagovas, Vytautas Būda, Saulius Maskeliūnas, Olga Štikonienė, Artūras Štikonas","doi":"10.15388/24-infor552","DOIUrl":"https://doi.org/10.15388/24-infor552","url":null,"abstract":"This article offers a comprehensive overview of the results obtained through numerical methods in solving the minimal surface equation, along with exploring the applications of minimal surfaces in science, technology, and architecture. The content is enriched with practical examples highlighting the diverse applications of minimal surfaces.\u0000PDF  XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"30 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140567479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimized Multi-Modular Services: Empowering Earth Observation Data Processing 优化的多模块服务:增强地球观测数据处理能力
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-04-04 DOI: 10.15388/24-infor551
Arthur Lalayan, Hrachya Astsatryan, Suren Poghosyan, Gregory Giuliani
{"title":"Optimized Multi-Modular Services: Empowering Earth Observation Data Processing","authors":"Arthur Lalayan, Hrachya Astsatryan, Suren Poghosyan, Gregory Giuliani","doi":"10.15388/24-infor551","DOIUrl":"https://doi.org/10.15388/24-infor551","url":null,"abstract":"The significance of earth observation data spans diverse fields and domains, driving the need for efficient management. Nevertheless, the exponential increase in data volume brings new challenges that complicate processing and storing data. This article proposes an optimized multi-modular service for earth observation data management in response to these challenges. The suggested approach focuses on choosing the optimal configurations for the storage and processing layers to improve the performance and cost-effectiveness of managing data. By employing the recommended optimized strategies, earth observation data can be managed more effectively, resulting in fast data processing and reduced costs.\u0000PDF  XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"87 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140567362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Proportional Fuzzy Set Extensions and Imprecise Proportions 比例模糊集扩展和不精确比例
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-03-29 DOI: 10.15388/24-infor550
Cengiz Kahraman
{"title":"Proportional Fuzzy Set Extensions and Imprecise Proportions","authors":"Cengiz Kahraman","doi":"10.15388/24-infor550","DOIUrl":"https://doi.org/10.15388/24-infor550","url":null,"abstract":"The extensions of ordinary fuzzy sets are problematic because they require decimal numbers for membership, non-membership and indecision degrees of an element from the experts, which cannot be easily determined. This will be more difficult when three or more digits’ membership degrees have to be assigned. Instead, proportional relations between the degrees of parameters of a fuzzy set extension will make it easier to determine the membership, non-membership, and indecision degrees. The objective of this paper is to present a simple but effective technique for determining these degrees with several decimal digits and to enable the expert to assign more stable values when asked at different time points. Some proportion-based models for the fuzzy sets extensions, intuitionistic fuzzy sets, Pythagorean fuzzy sets, picture fuzzy sets, and spherical fuzzy sets are proposed, including their arithmetic operations and aggregation operators. Proportional fuzzy sets require only the proportional relations between the parameters of the extensions of fuzzy sets. Their contribution is that these models will ease the use of fuzzy set extensions with the data better representing expert judgments. The imprecise definition of proportions is also incorporated into the given models. The application and comparative analyses result in that proportional fuzzy sets are easily applied to any problem and produce valid outcomes. Furthermore, proportional fuzzy sets clearly showed the role of the degree of indecision in the ranking of alternatives in binomial and trinomial fuzzy sets. In the considered car selection problem, it has been observed that there are minor changes in the ordering of intuitionistic and spherical fuzzy sets.\u0000PDF  XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"1 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140323438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Review and Computational Study on Practicality of Derivative-Free DIRECT-Type Methods 无衍生 DIRECT 类型方法实用性回顾与计算研究
IF 2.9 4区 计算机科学
Informatica Pub Date : 2024-03-26 DOI: 10.15388/24-infor548
Linas Stripinis, Remigijus Paulavičius
{"title":"Review and Computational Study on Practicality of Derivative-Free DIRECT-Type Methods","authors":"Linas Stripinis, Remigijus Paulavičius","doi":"10.15388/24-infor548","DOIUrl":"https://doi.org/10.15388/24-infor548","url":null,"abstract":"Derivative-free <tt>DIRECT</tt>-type global optimization algorithms are increasingly favoured for their simplicity and effectiveness in addressing real-world optimization challenges. This review examines their practical applications through a systematic analysis of scientific journals and computational studies. In particular, significant challenges in reproducibility have been identified with practical problems. To address this, we conducted an experimental study using practical problems from reputable CEC libraries, comparing <tt>DIRECT</tt>-type techniques against their state-of-the-art counterparts. Therefore, this study sheds light on current gaps, opportunities, and future prospects for advanced research in this domain, laying the foundation for replicating and expanding the research findings presented herein.\u0000PDF&nbsp;&nbsp;XML","PeriodicalId":56292,"journal":{"name":"Informatica","volume":"32 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140298439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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