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Computing RF Tree Distance over Succinct Representations 在简洁表征上计算射频树距离
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-28 DOI: 10.3390/a17010015
Ant'onio Pedro Branco, Cátia Vaz, Alexandre P. Francisco
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks or cancerous cells in tumor progression trees. These tools rely on several inference methods available to produce phylogenetic trees, with resulting trees not being unique. Thus, methods for comparing phylogenies that are capable of revealing where two phylogenetic trees agree or differ are required. An approach is then proposed to compute a similarity or dissimilarity measure between trees, with the Robinson–Foulds distance being one of the most used, and which can be computed in linear time and space. Nevertheless, given the large and increasing volume of phylogenetic data, phylogenetic trees are becoming very large with hundreds of thousands of leaves. In this context, space requirements become an issue both while computing tree distances and while storing trees. We propose then an efficient implementation of the Robinson–Foulds distance over tree succinct representations. Our implementation also generalizes the Robinson–Foulds distances to labelled phylogenetic trees, i.e., trees containing labels on all nodes, instead of only on leaves. Experimental results show that we are able to still achieve linear time while requiring less space. Our implementation in C++ is available as an open-source tool.
有几种工具可用于推断系统发生树,系统发生树描述了生物实体之间的进化关系,如传染病爆发中的病毒和细菌菌株或肿瘤进展树中的癌细胞。这些工具依赖多种推断方法来生成系统发生树,但生成的系统发生树并不是唯一的。因此,需要能够揭示两棵系统发生树相同或不同之处的系统发生比较方法。罗宾逊-富尔德距离(Robinson-Foulds distance)是最常用的方法之一,可以在线性时间和空间内计算。然而,由于系统发育数据量巨大且不断增加,系统发育树变得非常庞大,树叶多达数十万片。在这种情况下,无论是计算系统树距离还是存储系统树,空间需求都成为一个问题。因此,我们提出了一种在树简洁表示上高效实现 Robinson-Foulds 距离的方法。我们的实现方法还将罗宾逊-福尔斯距离推广到带标签的系统发育树,即在所有节点上都包含标签的树,而不是只在叶子上包含标签的树。实验结果表明,我们仍能实现线性时间,同时所需的空间更少。我们的 C++ 实现是一个开源工具。
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引用次数: 0
An Intelligent Control Method for Servo Motor Based on Reinforcement Learning 基于强化学习的伺服电机智能控制方法
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-28 DOI: 10.3390/a17010014
Depeng Gao, Shuai Wang, Yuwei Yang, Haifei Zhang, Hao Chen, Xiangxiang Mei, Shuxi Chen, Jianlin Qiu
Servo motors play an important role in automation equipment and have been used in several manufacturing fields. However, the commonly used control methods need their parameters to be set manually, which is rather difficult, and this means that these methods generally cannot adapt to changes in operation conditions. Therefore, in this study, we propose an intelligent control method for a servo motor based on reinforcement learning and that can train an agent to produce a duty cycle according to the servo error between the current state and the target speed or torque. The proposed method can adjust its control strategy online to reduce the servo error caused by a change in operation conditions. We verify its performance on three different servo motors and control tasks. The experimental results show that the proposed method can achieve smaller servo errors than others in most cases.
伺服电机在自动化设备中发挥着重要作用,并已应用于多个制造领域。然而,常用的控制方法需要手动设置参数,相当困难,这意味着这些方法通常无法适应运行条件的变化。因此,在本研究中,我们提出了一种基于强化学习的伺服电机智能控制方法,该方法可以训练代理根据当前状态与目标速度或扭矩之间的伺服误差来产生占空比。所提出的方法可以在线调整其控制策略,以减少因运行条件变化而导致的伺服误差。我们在三种不同的伺服电机和控制任务上验证了该方法的性能。实验结果表明,所提出的方法在大多数情况下都能获得比其他方法更小的伺服误差。
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引用次数: 0
Machine Learning Model for Multiomics Biomarkers Identification for Menopause Status in Breast Cancer 用于识别乳腺癌绝经状态的多组学生物标记物的机器学习模型
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-28 DOI: 10.3390/a17010013
Firas Alghanim, Ibrahim Al-Hurani, H. Qattous, Abdullah Al-Refai, Osamah Batiha, A. Alkhateeb, Salama Ikki
Identifying menopause-related breast cancer biomarkers is crucial for enhancing diagnosis, prognosis, and personalized treatment at that stage of the patient’s life. In this paper, we present a comprehensive framework for extracting multiomics biomarkers specifically related to breast cancer incidence before and after menopause. Our approach integrates DNA methylation, gene expression, and copy number alteration data using a systematic pipeline encompassing data preprocessing and handling class imbalance, dimensionality reduction, and classification. The framework starts with MutSigCV for data preprocessing and ensuring data quality. The Synthetic Minority Over-sampling Technique (SMOTE) up-sampling technique is applied to address the class imbalance representation. Then, Principal Component Analysis (PCA) transforms the DNA methylation, gene expression, and copy number alteration data into a latent space. The purpose is to discard irrelevant variations and extract relevant information. Finally, a classification model is built based on the transformed multiomics data into a unified representation. The framework contributes to understanding the complex interplay between menopause and breast cancer, thereby revealing more precise diagnostic and therapeutic strategies in the future. The explainable artificial intelligence model Shapley based on the XGBoost regressor showed the power of the selected gene expressions for predicting the menopause status, and the potential biomarkers included RUNX1, PTEN, MAP3K1, and CDH1. The literature confirmed the findings.
确定与更年期相关的乳腺癌生物标志物对于加强该阶段的诊断、预后和个性化治疗至关重要。在本文中,我们提出了一个提取与绝经前后乳腺癌发病率特别相关的多组学生物标志物的综合框架。我们的方法使用一个系统管道整合了 DNA 甲基化、基因表达和拷贝数改变数据,该管道包括数据预处理、类不平衡处理、降维和分类。该框架从 MutSigCV 开始,进行数据预处理并确保数据质量。应用合成少数群体过度采样技术(SMOTE)向上采样技术来处理类不平衡表示。然后,主成分分析法(PCA)将 DNA 甲基化、基因表达和拷贝数改变数据转化为潜在空间。这样做的目的是摒弃无关变异,提取相关信息。最后,根据转换后的多组学数据建立一个统一表示的分类模型。该框架有助于理解更年期与乳腺癌之间复杂的相互作用,从而揭示未来更精确的诊断和治疗策略。基于 XGBoost 回归器的可解释人工智能模型 Shapley 显示了所选基因表达预测绝经状态的能力,潜在的生物标志物包括 RUNX1、PTEN、MAP3K1 和 CDH1。文献证实了这些发现。
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引用次数: 0
Effect of Data Augmentation on Deep-Learning-Based Segmentation of Long-Axis Cine-MRI 数据增强对基于深度学习的长轴 Cine-MRI 分段的影响
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-25 DOI: 10.3390/a17010010
François Legrand, Richard Macwan, Alain Lalande, Lisa Métairie, Thomas Decourselle
Automated Cardiac Magnetic Resonance segmentation serves as a crucial tool for the evaluation of cardiac function, facilitating faster clinical assessments that prove advantageous for both practitioners and patients alike. Recent studies have predominantly concentrated on delineating structures on short-axis orientation, placing less emphasis on long-axis representations due to the intricate nature of structures in the latter. Taking these consideration into account, we present a robust hierarchy-based augmentation strategy coupled with the compact and fast Efficient-Net (ENet) architecture for the automated segmentation of two-chamber and four-chamber Cine-MRI images. We observed an average Dice improvement of 0.99% on the two-chamber images and of 2.15% on the four-chamber images, and an average Hausdorff distance improvement of 21.3% on the two-chamber images and of 29.6% on the four-chamber images. The practical viability of our approach was validated by computing clinical metrics such as the Left Ventricular Ejection Fraction (LVEF) and left ventricular volume (LVC). We observed acceptable biases, with a +2.81% deviation on the LVEF for the two-chamber images and a +0.11% deviation for the four-chamber images.
自动心脏磁共振分割是评估心脏功能的重要工具,有助于更快地进行临床评估,对医生和患者都很有利。近期的研究主要集中在短轴方向上的结构划分,而对长轴方向上的结构划分重视不够,因为长轴方向上的结构错综复杂。考虑到这些因素,我们提出了一种基于层次结构的稳健增强策略,并结合紧凑快速的 Efficient-Net (ENet) 架构,用于两腔和四腔 Cine-MRI 图像的自动分割。我们观察到两腔图像的 Dice 平均改善率为 0.99%,四腔图像的 Dice 平均改善率为 2.15%,两腔图像的 Hausdorff 距离平均改善率为 21.3%,四腔图像的 Hausdorff 距离平均改善率为 29.6%。通过计算左室射血分数(LVEF)和左室容积(LVC)等临床指标,验证了我们方法的实际可行性。我们观察到了可接受的偏差,两腔图像的 LVEF 偏差为 +2.81%,四腔图像的 LVEF 偏差为 +0.11%。
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引用次数: 0
A Self-Adaptive Meta-Heuristic Algorithm Based on Success Rate and Differential Evolution for Improving the Performance of Ridesharing Systems with a Discount Guarantee 基于成功率和差分进化的自适应元算法,用于提高有折扣保证的共享乘车系统的性能
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-25 DOI: 10.3390/a17010009
Fu-Shiung Hsieh
One of the most significant financial benefits of a shared mobility mode such as ridesharing is cost savings. For this reason, a lot of studies focus on the maximization of cost savings in shared mobility systems. Cost savings provide an incentive for riders to adopt ridesharing. However, if cost savings are not properly allocated to riders or the financial benefit of cost savings is not sufficient to attract riders to use a ridesharing mode, riders will not accept a ridesharing mode even if the overall cost savings is significant. In a recent study, the concept of discount-guaranteed ridesharing has been proposed to provide an incentive for riders to accept ridesharing services through ensuring a minimal discount for drivers and passengers. In this study, an algorithm is proposed to improve the performance of the discount-guaranteed ridesharing systems. Our approach combines a success rate-based self-adaptation scheme with an evolutionary computation approach. We propose a new self-adaptive metaheuristic algorithm based on success rate and differential evolution for the Discount-Guaranteed Ridesharing Problem (DGRP). We illustrate effectiveness of the proposed algorithm by comparing the results obtained using our proposed algorithm with other competitive algorithms developed for this problem. Preliminary results indicate that the proposed algorithm outperforms other competitive algorithms in terms of performance and convergence rate. The results of this study are consistent with the empirical experience that two people working together are more likely to come to a correct decision than they would if working alone.
共享出行等共享交通模式最重要的经济效益之一就是节约成本。因此,很多研究都关注如何在共享交通系统中最大限度地节约成本。成本节约为乘客采用共享出行提供了动力。然而,如果节约的成本没有适当地分配给乘客,或者节约成本带来的经济利益不足以吸引乘客使用共乘模式,那么即使整体成本节约效果显著,乘客也不会接受共乘模式。最近的一项研究提出了 "折扣保证共乘 "的概念,通过确保司机和乘客获得最低折扣,激励乘客接受共乘服务。本研究提出了一种算法来提高折扣保证共享乘车系统的性能。我们的方法结合了基于成功率的自适应方案和进化计算方法。我们针对折扣保证共乘问题(DGRP)提出了一种基于成功率和差分进化的新的自适应元启发式算法。我们将所提算法的结果与针对该问题开发的其他竞争性算法进行比较,以说明所提算法的有效性。初步结果表明,所提出的算法在性能和收敛速度方面都优于其他竞争性算法。这项研究的结果与经验是一致的,即两个人一起工作比单独工作更有可能做出正确的决定。
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引用次数: 0
Heuristic Greedy-Gradient Route Search Method for Finding an Optimal Traffic Distribution in Telecommunication Networks 在电信网络中寻找最佳流量分布的启发式贪婪梯度路由搜索法
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-23 DOI: 10.3390/a17010007
Konstantin Gaipov, Daniil Tausnev, Sergey Khodenkov, N. Shepeta, Dmitry Malyshev, Aleksey Popov, L. Kazakovtsev
Rapid growth in the volume of transmitted information has lead to the emergence of new wireless networking technologies with variable heterogeneous topologies. With limited radio frequency resources, optimal routing problems arise, both at the network design stage and during its operation. We propose an algorithm based on a minimum loss intensity (greedy-gradient algorithm) to search for optimal routes of information transmission in telecommunication networks. The relevance of the developed algorithm is determined by its practical use in data-transmitting modeling systems. The proposed algorithm satisfies several requirements, such as the speed of the calculations performed, the fulfillment of the conditions for its convergence, and its independence on the selected loss probability function, as well as on the network topology. The idea of the algorithm is a step-by-step recalculation of metrics based on derivatives of the loss intensity function with simultaneous redistribution of information flows along the routes determined by the Floyd algorithm. The comparative efficiency of the proposed algorithm is demonstrated by computational experiments on various network topologies (up to 100 nodes) with various traffic intensities.
传输信息量的快速增长导致了具有可变异构拓扑结构的新型无线网络技术的出现。由于射频资源有限,在网络设计阶段和运行过程中都会出现优化路由问题。我们提出了一种基于最小损耗强度的算法(贪婪梯度算法),用于搜索电信网络中的最佳信息传输路径。所开发算法的相关性取决于其在数据传输建模系统中的实际应用。所提出的算法满足多项要求,如计算速度快、满足收敛条件、与所选损失概率函数和网络拓扑无关。该算法的思路是根据损失强度函数的导数逐步重新计算指标,同时沿 Floyd 算法确定的路由重新分配信息流。通过对各种网络拓扑结构(最多 100 个节点)和各种流量强度的计算实验,证明了所提算法的比较效率。
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引用次数: 0
Predicting Decompensation Risk in Intensive Care Unit Patients Using Machine Learning 利用机器学习预测重症监护室患者的脱功能风险
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-22 DOI: 10.3390/a17010006
Nosa Aikodon, S. Ortega-Martorell, I. Olier
Patients in Intensive Care Units (ICU) face the threat of decompensation, a rapid decline in health associated with a high risk of death. This study focuses on creating and evaluating machine learning (ML) models to predict decompensation risk in ICU patients. It proposes a novel approach using patient vitals and clinical data within a specified timeframe to forecast decompensation risk sequences. The study implemented and assessed long short-term memory (LSTM) and hybrid convolutional neural network (CNN)-LSTM architectures, along with traditional ML algorithms as baselines. Additionally, it introduced a novel decompensation score based on the predicted risk, validated through principal component analysis (PCA) and k-means analysis for risk stratification. The results showed that, with PPV = 0.80, NPV = 0.96 and AUC-ROC = 0.90, CNN-LSTM had the best performance when predicting decompensation risk sequences. The decompensation score’s effectiveness was also confirmed (PPV = 0.83 and NPV = 0.96). SHAP plots were generated for the overall model and two risk strata, illustrating variations in feature importance and their associations with the predicted risk. Notably, this study represents the first attempt to predict a sequence of decompensation risks rather than single events, a critical advancement given the challenge of early decompensation detection. Predicting a sequence facilitates early detection of increased decompensation risk and pace, potentially leading to saving more lives.
重症监护病房(ICU)的病人面临着失代偿的威胁,这是一种与高死亡风险相关的健康状况急剧下降的现象。本研究的重点是创建和评估机器学习(ML)模型,以预测重症监护室患者的失代偿风险。它提出了一种新颖的方法,利用特定时间范围内的患者生命体征和临床数据来预测失代偿风险序列。研究实施并评估了长短期记忆(LSTM)和混合卷积神经网络(CNN)-LSTM 架构,以及作为基线的传统 ML 算法。此外,它还引入了基于预测风险的新型分解评分,并通过主成分分析 (PCA) 和 k-means 分析对风险分层进行了验证。结果显示,CNN-LSTM 在预测失代偿风险序列时表现最佳,PPV = 0.80,NPV = 0.96,AUC-ROC = 0.90。失代偿评分的有效性也得到了证实(PPV = 0.83,NPV = 0.96)。为整体模型和两个风险分层生成了 SHAP 图,说明了特征重要性的变化及其与预测风险的关联。值得注意的是,这项研究首次尝试预测一系列失代偿风险,而不是单一事件,这是一项重要的进步,因为早期失代偿检测是一项挑战。预测一连串事件有助于及早发现失代偿风险的增加和速度的加快,从而挽救更多的生命。
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引用次数: 0
Special Issue “Algorithms in Data Classification” 数据分类算法 "特刊
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-22 DOI: 10.3390/a17010005
Ioannis G. Tsoulos
Data classification is a well-known procedure, with many applications to real-world problems [...]
数据分类是一种众所周知的程序,在现实世界的许多问题中都有应用 [...]
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引用次数: 0
Comparing Direct Deliveries and Automated Parcel Locker Systems with Respect to Overall CO2 Emissions for the Last Mile 比较直接递送和自动包裹柜系统在最后一英里的总体二氧化碳排放量
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-21 DOI: 10.3390/a17010004
K. Gutenschwager, Markus Rabe, Jorge Chicaiza-Vaca
Fast growing e-commerce has a significant impact both on CEP providers and public entities. While service providers have the first priority on factors such as costs and reliable service, both are increasingly focused on environmental effects, in the interest of company image and the inhabitants’ health and comfort. Significant additional factors are traffic density, pollution, and noise. While in the past direct delivery with distribution trucks from regional depots to the customers might have been justified, this is no longer valid when taking the big and growing numbers into account. Several options are followed in the literature, especially variants that introduce an additional break in the distribution chain, like local mini-hubs, mobile distribution points, or Automated Parcel Lockers (APLs). The first two options imply a “very last mile” stage, e.g., by small electrical vehicles or cargo bikes, and APLs rely on the customers to operate the very last step. The usage of this schema will significantly depend on the density of the APLs and, thus, on the density of the population within quite small regions. The relationships between the different elements of these technologies and the potential customers are studied with respect to their impact on the above-mentioned factors. A variety of scenarios is investigated, covering different options for customer behaviors. As an additional important point, reported studies with APLs only consider the section up to the APLs and the implied CO2 emission. This, however, fully neglects the potentially very relevant pollution created by the customers when fetching their parcels from the APL. Therefore, in this paper this impact is systematically estimated via a simulation-based sensitivity analysis. It can be shown that taking this very last transport step into account in the calculation significantly changes the picture, especially within areas in outer city districts.
快速发展的电子商务对社区环保服务提供商和公共实体都产生了重大影响。虽然服务提供商首先考虑的是成本和可靠服务等因素,但为了公司形象和居民的健康与舒适,两者都越来越重视环境影响。交通密度、污染和噪音是重要的附加因素。过去,用配送卡车从地区仓库直接运送到客户手中可能是合理的,但考虑到数量庞大且不断增加,这种做法已不再有效。文献中提到了几种方案,特别是在配送链中引入额外中断的变体,如本地迷你枢纽、移动配送点或自动包裹柜(APL)。前两种方案意味着 "最后一英里 "阶段,例如通过小型电动车或货运自行车,而自动包裹柜则依靠客户来操作最后一个步骤。这种模式的使用在很大程度上取决于 APL 的密度,因此也取决于相当小区域内的人口密度。我们研究了这些技术的不同要素与潜在客户之间的关系,以及它们对上述因素的影响。对各种方案进行了研究,涵盖了客户行为的不同选择。还有一点很重要,已报道的有关 APL 的研究只考虑到了 APL 和隐含的二氧化碳排放量。然而,这完全忽略了顾客从 APL 取包裹时可能造成的相关污染。因此,本文通过模拟敏感性分析系统地估算了这种影响。结果表明,在计算中将最后一个运输步骤考虑在内会大大改变情况,尤其是在城市外围地区。
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引用次数: 0
A Survey on Swarm Robotics for Area Coverage Problem 针对区域覆盖问题的蜂群机器人技术概览
IF 2.3 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2023-12-20 DOI: 10.3390/a17010003
Dena Kadhim Muhsen, Ahmed T. Sadiq, Firas Abdulrazzaq Raheem
The area coverage problem solution is one of the vital research areas which can benefit from swarm robotics. The greatest challenge to the swarm robotics system is to complete the task of covering an area effectively. Many domains where area coverage is essential include exploration, surveillance, mapping, foraging, and several other applications. This paper introduces a survey of swarm robotics in area coverage research papers from 2015 to 2022 regarding the algorithms and methods used, hardware, and applications in this domain. Different types of algorithms and hardware were dealt with and analysed; according to the analysis, the characteristics and advantages of each of them were identified, and we determined their suitability for different applications in covering the area for many goals. This study demonstrates that naturally inspired algorithms have the most significant role in swarm robotics for area coverage compared to other techniques. In addition, modern hardware has more capabilities suitable for supporting swarm robotics to cover an area, even if the environment is complex and contains static or dynamic obstacles.
区域覆盖问题的解决方案是可以从蜂群机器人技术中受益的重要研究领域之一。蜂群机器人系统面临的最大挑战是完成有效覆盖区域的任务。许多领域都需要区域覆盖,包括勘探、监控、测绘、觅食和其他一些应用。本文介绍了 2015 年至 2022 年蜂群机器人在区域覆盖方面的研究论文调查,涉及该领域使用的算法和方法、硬件和应用。本文对不同类型的算法和硬件进行了处理和分析;根据分析结果,确定了每种算法和硬件的特点和优势,并确定了它们在不同应用中对多种目标区域覆盖的适用性。这项研究表明,与其他技术相比,自然启发算法在蜂群机器人技术的区域覆盖中发挥着最重要的作用。此外,即使环境复杂,包含静态或动态障碍物,现代硬件也有更多适合支持蜂群机器人覆盖区域的功能。
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引用次数: 0
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Algorithms
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