Mathematical Biosciences and Engineering最新文献_第9页

HRGCNLDA: Forecasting of lncRNA-disease association based on hierarchical refinement graph convolutional neural network. HRGCNLDA：基于分层细化图卷积神经网络的 lncRNA-疾病关联预测。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024212

Li Peng, Yujie Yang, Cheng Yang, Zejun Li, Ngai Cheong

{"title":"HRGCNLDA: Forecasting of lncRNA-disease association based on hierarchical refinement graph convolutional neural network.","authors":"Li Peng, Yujie Yang, Cheng Yang, Zejun Li, Ngai Cheong","doi":"10.3934/mbe.2024212","DOIUrl":"https://doi.org/10.3934/mbe.2024212","url":null,"abstract":"Long non-coding RNA (lncRNA) is considered to be a crucial regulator involved in various human biological processes, including the regulation of tumor immune checkpoint proteins. It has great potential as both a cancer biomolecular biomarker and therapeutic target. Nevertheless, conventional biological experimental techniques are both resource-intensive and laborious, making it essential to develop an accurate and efficient computational method to facilitate the discovery of potential links between lncRNAs and diseases. In this study, we proposed HRGCNLDA, a computational approach utilizing hierarchical refinement of graph convolutional neural networks for forecasting lncRNA-disease potential associations. This approach effectively addresses the over-smoothing problem that arises from stacking multiple layers of graph convolutional neural networks. Specifically, HRGCNLDA enhances the layer representation during message propagation and node updates, thereby amplifying the contribution of hidden layers that resemble the ego layer while reducing discrepancies. The results of the experiments showed that HRGCNLDA achieved the highest AUC-ROC (area under the receiver operating characteristic curve, AUC for short) and AUC-PR (area under the precision versus recall curve, AUPR for short) values compared to other methods. Finally, to further demonstrate the reliability and efficacy of our approach, we performed case studies on the case of three prevalent human diseases, namely, breast cancer, lung cancer and gastric cancer.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The improved stratified transformer for organ segmentation of Arabidopsis. 拟南芥器官分割的改良分层转换器

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024205

Yuhui Zheng, Dongwei Wang, Ning Jin, Xueguan Zhao, Fengmei Li, Fengbo Sun, Gang Dou, Haoran Bai

{"title":"The improved stratified transformer for organ segmentation of Arabidopsis.","authors":"Yuhui Zheng, Dongwei Wang, Ning Jin, Xueguan Zhao, Fengmei Li, Fengbo Sun, Gang Dou, Haoran Bai","doi":"10.3934/mbe.2024205","DOIUrl":"10.3934/mbe.2024205","url":null,"abstract":"Segmenting plant organs is a crucial step in extracting plant phenotypes. Despite the advancements in point-based neural networks, the field of plant point cloud segmentation suffers from a lack of adequate datasets. In this study, we addressed this issue by generating Arabidopsis models using L-system and proposing the surface-weighted sampling method. This approach enables automated point sampling and annotation, resulting in fully annotated point clouds. To create the Arabidopsis dataset, we employed Voxel Centroid Sampling and Random Sampling as point cloud downsampling methods, effectively reducing the number of points. To enhance the efficiency of semantic segmentation in plant point clouds, we introduced the Plant Stratified Transformer. This network is an improved version of the Stratified Transformer, incorporating the Fast Downsample Layer. Our improved network underwent training and testing on our dataset, and we compared its performance with PointNet++, PAConv, and the original Stratified Transformer network. For semantic segmentation, our improved network achieved mean Precision, Recall, F1-score and IoU of 84.20, 83.03, 83.61 and 73.11%, respectively. It outperformed PointNet++ and PAConv and performed similarly to the original network. Regarding efficiency, the training time and inference time were 714.3 and 597.9 ms, respectively, which were reduced by 320.9 and 271.8 ms, respectively, compared to the original network. The improved network significantly accelerated the speed of feeding point clouds into the network while maintaining segmentation performance. We demonstrated the potential of virtual plants and deep learning methods in rapidly extracting plant phenotypes, contributing to the advancement of plant phenotype research.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140319709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ulam type stability for von Bertalanffy growth model with Allee effect. 具有阿利效应的 von Bertalanffy 生长模型的 Ulam 型稳定性。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024206

Masumi Kondo, Masakazu Onitsuka

{"title":"Ulam type stability for von Bertalanffy growth model with Allee effect.","authors":"Masumi Kondo, Masakazu Onitsuka","doi":"10.3934/mbe.2024206","DOIUrl":"https://doi.org/10.3934/mbe.2024206","url":null,"abstract":"In many studies dealing with mathematical models, the subject is examining the fitting between actual data and the solution of the mathematical model by applying statistical processing. However, if there is a solution that fluctuates greatly due to a small perturbation, it is expected that there will be a large difference between the actual phenomenon and the solution of the mathematical model, even in a short time span. In this study, we address this concern by considering Ulam stability, which is a concept that guarantees that a solution to an unperturbed equation exists near the solution to an equation with bounded perturbations. Although it is known that Ulam stability is guaranteed for the standard von Bertalanffy growth model, it remains unsolved for a model containing the Allee effect. This paper investigates the Ulam stability of a von Bertalanffy growth model with the Allee effect. In a sense, we obtain results that correspond to conditions of the Allee effect being very small or very large. In particular, a more preferable Ulam constant than the existing result for the standard von Bertalanffy growth model, is obtained as the Allee effect approaches zero. In other words, this paper even improves the proof of the result in the absence of the Allee effect. By guaranteeing the Ulam stability of the von Bertalanffy growth model with Allee effect, the stability of the model itself is guaranteed, and, even if a small perturbation is added, it becomes clear that even a small perturbation does not have a large effect on the solutions. Several examples and numerical simulations are presented to illustrate the obtained results.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140319714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Analysis of the COVID-19 model with self-protection and isolation measures affected by the environment. 分析 COVID-19 模型中受环境影响的自我保护和隔离措施。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024213

Jiangbo Hao, Lirong Huang, Maoxing Liu, Yangjun Ma

{"title":"Analysis of the COVID-19 model with self-protection and isolation measures affected by the environment.","authors":"Jiangbo Hao, Lirong Huang, Maoxing Liu, Yangjun Ma","doi":"10.3934/mbe.2024213","DOIUrl":"https://doi.org/10.3934/mbe.2024213","url":null,"abstract":"Since the global outbreak of COVID-19, the virus has continuously mutated and can survive in the air for long periods of time. This paper establishes and analyzes a model of COVID-19 with self-protection and quarantine measures affected by viruses in the environment to investigate the influence of viruses in the environment on the spread of the outbreak, as well as to develop a rational prevention and control measure to control the spread of the outbreak. The basic reproduction number was calculated and Lyapunov functions were constructed to discuss the stability of the model equilibrium points. The disease-free equilibrium point was proven to be globally asymptotically stable when $ R_0 < 1 $, and the endemic equilibrium point was globally asymptotically stable when $ R_0 > 1 $. The model was fitted using data from COVID-19 cases in Chongqing between November 1 to November 25, 2022. Based on the numerical analysis, the following conclusion was obtained: clearing the virus in the environment and strengthening the isolation measures for infected people can control the epidemic to a certain extent, but enhancing the self-protection of individuals can be more effective in reducing the risk of being infected and controlling the transmission of the epidemic, which is more conducive to the practical application.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

HIV incidence before and during the COVID-19 pandemic in Japan. 日本 COVID-19 大流行之前和期间的艾滋病毒感染率。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024215

Hiroshi Nishiura, Seiko Fujiwara, Akifumi Imamura, Takuma Shirasaka

{"title":"HIV incidence before and during the COVID-19 pandemic in Japan.","authors":"Hiroshi Nishiura, Seiko Fujiwara, Akifumi Imamura, Takuma Shirasaka","doi":"10.3934/mbe.2024215","DOIUrl":"https://doi.org/10.3934/mbe.2024215","url":null,"abstract":"At the end of 2022, a total of 20,003 diagnoses of human immunodeficiency virus (HIV) infection and 8,983 cases of acquired immunodeficiency syndrome (AIDS) among Japanese nationals, and 3,860 HIV diagnoses and 1,575 AIDS cases among foreign residents, had been notified to the government in Japan. This study updates the estimate of HIV incidence, including during the COVID-19 pandemic. It aimed to reconstruct the incidence of HIV and understand how the disruption caused by COVID-19 affected the epidemiology of HIV. Using a median incubation period of 10.0 years, the number of undiagnosed HIV infections was estimated to be 3,209 (95% confidence interval (CI): 2,642, 3,710) at the end of 2022. This figure has declined steadily over the past 10 years. Assuming that the median incubation period was 10.0 years, the proportion of diagnosed HIV infections, including surviving AIDS cases, was 89.3% (95% CI: 87.8%, 91.0%). When AIDS cases were excluded, the proportion was 86.2% (95% CI: 84.3%, 88.3%). During the COVID-19 pandemic, the estimated annual diagnosis rate was slightly lower than during earlier time intervals, at around 16.5% (95% CI: 14.9%, 18.1%). Japan may already have achieved diagnostic coverage of 90%, given its 9% increment in the diagnosed proportion during the past 5 years. The incidence of HIV infection continued to decrease even during the COVID-19 pandemic from 2020 to 2022, and the annual rate of diagnosis decreased slightly to 16.5%. Monitoring the recovery of diagnosis along with the effective reproduction number is vital in the future.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Adaptive fuzzy fixed time formation control of state constrained nonlinear multi-agent systems against FDI attacks. 针对 FDI 攻击的状态受限非线性多代理系统的自适应模糊定时形成控制。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024207

Jinxin Du, Lei Liu

引用次数: 0

Stability analysis of a SAIR epidemic model on scale-free community networks. 无标度社区网络上 SAIR 流行病模型的稳定性分析。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024204

Xing Zhang, Zhitao Li, Lixin Gao

引用次数: 0

Cross-subject EEG-based emotion recognition through dynamic optimization of random forest with sparrow search algorithm. 利用麻雀搜索算法对随机森林进行动态优化，从而实现基于脑电图的跨主体情感识别。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024210

Xiaodan Zhang, Shuyi Wang, Kemeng Xu, Rui Zhao, Yichong She

{"title":"Cross-subject EEG-based emotion recognition through dynamic optimization of random forest with sparrow search algorithm.","authors":"Xiaodan Zhang, Shuyi Wang, Kemeng Xu, Rui Zhao, Yichong She","doi":"10.3934/mbe.2024210","DOIUrl":"10.3934/mbe.2024210","url":null,"abstract":"The objective of EEG-based emotion recognition is to classify emotions by decoding signals, with potential applications in the fields of artificial intelligence and bioinformatics. Cross-subject emotion recognition is more difficult than intra-subject emotion recognition. The poor adaptability of classification model parameters is a significant factor of low accuracy in cross-subject emotion recognition. We propose a model of a dynamically optimized Random Forest based on the Sparrow Search Algorithm (SSA-RF). The decision trees number (DTN) and the leave minimum number (LMN) of the RF are dynamically optimized by the SSA. 12 features are used to construct feature combinations for selecting the optimal feature combination. DEAP and SEED datasets are employed for testing the performance of SSA-RF. The experimental results show that the accuracy of binary classification is 76.81% on DEAP, and the accuracy of triple classification is 75.96% on SEED based on SSA-RF, which are both higher than that of traditional RF. This study provides new insights for the development of cross-subject emotion recognition, and has significant theoretical value.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140319687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A network model of social contacts with small-world and scale-free features, tunable connectivity, and geographic restrictions. 具有小世界和无尺度特征、可调连通性和地理限制的社会接触网络模型。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024211

A Newton Licciardi Jr, L H A Monteiro

{"title":"A network model of social contacts with small-world and scale-free features, tunable connectivity, and geographic restrictions.","authors":"A Newton Licciardi Jr, L H A Monteiro","doi":"10.3934/mbe.2024211","DOIUrl":"https://doi.org/10.3934/mbe.2024211","url":null,"abstract":"Small-world networks and scale-free networks are well-known theoretical models within the realm of complex graphs. These models exhibit \"low\" average shortest-path length; however, key distinctions are observed in their degree distributions and average clustering coefficients: in small-world networks, the degree distribution is bell-shaped and the clustering is \"high\"; in scale-free networks, the degree distribution follows a power law and the clustering is \"low\". Here, a model for generating scale-free graphs with \"high\" clustering is numerically explored, since these features are concurrently identified in networks representing social interactions. In this model, the values of average degree and exponent of the power-law degree distribution are both adjustable, and spatial limitations in the creation of links are taken into account. Several topological metrics are calculated and compared for computer-generated graphs. Unexpectedly, the numerical experiments show that, by varying the model parameters, a transition from a power-law to a bell-shaped degree distribution can occur. Also, in these graphs, the degree distribution is most accurately characterized by a pure power-law for values of the exponent typically found in real-world networks.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Secure multimedia communication: advanced asymmetric key authentication with grayscale visual cryptography. 安全多媒体通信：利用灰度可视加密技术进行高级非对称密钥验证。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-02-29 DOI: 10.3934/mbe.2024209

Tao Liu, Shubhangi Vairagar, Sushadevi Adagale, T Karthick, Catherine Esther Karunya, John Blesswin A, Selva Mary G

{"title":"Secure multimedia communication: advanced asymmetric key authentication with grayscale visual cryptography.","authors":"Tao Liu, Shubhangi Vairagar, Sushadevi Adagale, T Karthick, Catherine Esther Karunya, John Blesswin A, Selva Mary G","doi":"10.3934/mbe.2024209","DOIUrl":"https://doi.org/10.3934/mbe.2024209","url":null,"abstract":"The secure authentication of user data is crucial in various sectors, including digital banking, medical applications and e-governance, especially for images. Secure communication protects against data tampering and forgery, thereby bolstering the foundation for informed decision-making, whether managing traffic, enhancing public safety, or monitoring environmental conditions. Conventional visual cryptographic protocols offer solutions, particularly for color images, though they grapple with challenges such as high computational demands and reliance on multiple cover images. Additionally, they often require third-party authorization to verify the image integrity. On the other hand, visual cryptography offers a streamlined approach. It divides images into shares, where each pixel represented uniquely, thus allowing visual decryption without complex computations. The optimized multi-tiered authentication protocol (OMTAP), which is integrated with the visual sharing scheme (VSS), takes secure image sharing to the next level. It reduces share count, prioritizes image fidelity and transmission security, and introduces the self-verification of decrypted image integrity through asymmetric key matrix generators, thus eliminating external validation. Rigorous testing has confirmed OMTAP's robustness and broad applicability, thereby ensuring that decrypted images maintain their quality with a peak signal-to-noise ratio (PSNR) of 40 dB and full integrity at the receiver's end.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140319662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0