IEEE Transactions on Molecular, Biological, and Multi-Scale Communications最新文献_第7页

2023 Index IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Vol.9 2023 索引 IEEE 分子、生物和多尺度通信论文集第 9 卷

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IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-12-22 DOI: 10.1109/TMBMC.2023.3345590

引用次数: 0

Received Signal and Channel Parameter Estimation in Molecular Communications 分子通信中的接收信号和信道参数估计

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-12-22 DOI: 10.1109/TMBMC.2023.3342731

O. Tansel Baydas;Ozgur B. Akan

{"title":"Received Signal and Channel Parameter Estimation in Molecular Communications","authors":"O. Tansel Baydas;Ozgur B. Akan","doi":"10.1109/TMBMC.2023.3342731","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3342731","url":null,"abstract":"Molecular communication (MC) is a paradigm that employs molecules as information carriers, hence, requiring unconventional transceivers and detection techniques for the Internet of Bio-Nano Things (IoBNT). In this study, we provide a novel MC model that incorporates a spherical transmitter and receiver with partial absorption. This model offers a more realistic representation than receiver architectures in literature, e.g., passive or entirely absorbing configurations. An optimization-based technique utilizing particle swarm optimization (PSO) is employed to accurately estimate the cumulative number of molecules received. This technique yields nearly constant correction parameters and demonstrates a significant improvement of 5 times in terms of root mean square error (RMSE) compared to the literature. The estimated channel model provides an approximate analytical impulse response; hence, it is used for estimating channel parameters such as distance, diffusion coefficient, or a combination of both. The iterative maximum likelihood estimation (MLE) is applied for the parameter estimation, which gives consistent errors compared to the estimated Cramer-Rao Lower Bound (CLRB).","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"92-97"},"PeriodicalIF":2.2,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Advances in Predicting Drug Functions: A Decade-Long Survey in Drug Discovery Research 预测药物功能的进展：药物发现研究十年调查

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-12-21 DOI: 10.1109/TMBMC.2023.3345145

Pranab Das;Dilwar Hussain Mazumder

{"title":"Advances in Predicting Drug Functions: A Decade-Long Survey in Drug Discovery Research","authors":"Pranab Das;Dilwar Hussain Mazumder","doi":"10.1109/TMBMC.2023.3345145","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3345145","url":null,"abstract":"Drug function study is vital in current drug discovery, design, and development. Determining the drug functions of a novel drug is time-consuming, complicated, expensive, and requires many experts and clinical testing phases. The computational-based drug function prediction activity has recently become more attractive due to its capability to reduce drug development design complexity, time, human resources, cost, chemical waste, and the risk of failure. The evolution of the computational model has advanced as an effective tool for predicting and analyzing drug functions, which are derived from Medical Subject Headings (MeSH). However, predicting drug functions still faces several difficulties. Therefore, an exhaustive literature survey was conducted that discusses the application of computational methods to predict drug functions in the past decade. Additionally, this paper discusses the utilization of drug functions as an input feature to predict adverse drug reactions and disease classification. This work also provides an overview of the computational models with their performance, multi-label problem transformation methods, drug properties, and their sources needed for the task of drug function prediction. Finally, unsolved issues, research gaps, and difficulties with the drug function prediction task have been summarized.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"75-91"},"PeriodicalIF":2.2,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Publication Information 电气和电子工程师学会《分子、生物和多尺度通信论文集》（IEEE Transactions on Molecular, Biological, and Multi-Scale Communications）出版信息

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IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-12-18 DOI: 10.1109/TMBMC.2023.3326009

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IEEE Communications Society Information IEEE 通信学会信息

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IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-12-18 DOI: 10.1109/TMBMC.2023.3326011

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What Really is “Molecule” in Molecular Communications? The Quest for Physics of Particle-Based Information Carriers 分子通讯中的 "分子 "究竟是什么？探索基于粒子的信息载体的物理学原理

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-12-04 DOI: 10.1109/TMBMC.2023.3338950

Hanlin Xiao;Kamela Dokaj;Ozgur B. Akan

{"title":"What Really is “Molecule” in Molecular Communications? The Quest for Physics of Particle-Based Information Carriers","authors":"Hanlin Xiao;Kamela Dokaj;Ozgur B. Akan","doi":"10.1109/TMBMC.2023.3338950","DOIUrl":"10.1109/TMBMC.2023.3338950","url":null,"abstract":"Molecular communication, as implied by its name, uses molecules as information carriers for communication between objects. It has an advantage over traditional electromagnetic-wave-based communication in that molecule-based systems could be biocompatible, operable in challenging environments, and energetically undemanding. Consequently, they are envisioned to have a broad range of applications, such as in the Internet of Bio-Nano Things, targeted drug delivery, and agricultural monitoring. Despite the rapid development of the field, with an increasing number of theoretical models and experimental testbeds established by researchers, a fundamental aspect of the field has often been sidelined, namely, the nature of the molecule in molecular communication. The potential information molecules could exhibit a wide range of properties, making them require drastically different treatments when being modeled and experimented upon. Therefore, in this paper, we delve into the intricacies of commonly used information molecules, examining their fundamental physical characteristics, associated communication systems, and potential applications in a more realistic manner, focusing on the influence of their own properties. Through this comprehensive survey, we aim to offer a novel yet essential perspective on molecular communication, thereby bridging the current gap between theoretical research and real-world applications.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"43-74"},"PeriodicalIF":2.2,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139234475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Diffusion-Based Anti-Interference Joint Modulation in MIMO Molecular Communication 多输入多输出分子通信中基于扩散的抗干扰联合调制

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-29 DOI: 10.1109/TMBMC.2023.3336259

Guodong Yue;Guoying Lin;Qiang Liu;Kun Yang

{"title":"Diffusion-Based Anti-Interference Joint Modulation in MIMO Molecular Communication","authors":"Guodong Yue;Guoying Lin;Qiang Liu;Kun Yang","doi":"10.1109/TMBMC.2023.3336259","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3336259","url":null,"abstract":"Molecular communication (MC) is a significant technology in the field of nano-biology, which uses molecules as message carriers to transmit information. Diffusion channel model is the most common channel model base on Brownian motion in molecular communication since molecules can diffuse to the destination without the need of extra energy supply. However, the random Brownian motion brings high delay and uncertainty to the communication process and thus modulation methods are required to improve the communication performance. The molecular communication system in the SISO (Single Input Single Output) scenario will be seriously affected by ISI (Inter Symbol Interference). In MIMO (Multi-Input Multi-Output) scenario, since there are multiple transmitters and receivers, in addition to ISI, there will be ILI (Inter Link Interference) as well. At present, most modulations are based on the concentration, type, time and space of molecules and only focus on SISO scenario. In this study, inspired by the MoSK (Molecule Shift Keying) modulation method, we proposed a new joint modulation method for MIMO communication in order to minimize the effect of ISI and ILI. Numerical results show that compared with the current modulation scheme, the proposed scheme allows the MIMO system achieve better BER (Bit error rate) performance and transmission rate.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"112-121"},"PeriodicalIF":2.2,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Intercellular Chemical Communication Through EV Exchange: Evaluation of the EV Fusion Process Parameters at the Receiving Cell 通过 EV 交换进行细胞间化学交流：评估接收细胞的电动汽车融合过程参数

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-28 DOI: 10.1109/TMBMC.2023.3336322

Alfio Lombardo;Giacomo Morabito;Carla Panarello;Fabrizio Pappalardo

{"title":"Intercellular Chemical Communication Through EV Exchange: Evaluation of the EV Fusion Process Parameters at the Receiving Cell","authors":"Alfio Lombardo;Giacomo Morabito;Carla Panarello;Fabrizio Pappalardo","doi":"10.1109/TMBMC.2023.3336322","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3336322","url":null,"abstract":"Cells communicate with each other exploiting a variety of chemical signals. Among them, Extracellular Vesicles (EVs) have attracted large interest by the scientific community. In fact, thanks to the advances in bio-nano-technology and the possibility of engineering EVs, they are envisioned as a perfect means for distributing biological information among receiving cells. However, deciphering the molecular mechanisms that regulate the delivery of EV cargo is, today, a necessary, yet challenging, step toward the exploitation of EV signaling to support innovative and efficient therapeutic protocols, alternative to current drug delivery technologies. In particular, very little information is currently available on the processes of EV fusion, which is the EV internalization process occurring when the EV membrane dissolves into the plasma membrane of the target cell, and the EV content is released into the cytosol. In order to understand the dynamics of this process, this paper introduces an analytical model of the evolution of the fusion process. Moreover, since the measurement of the biological parameters driving the fusion process is far to be achieved, in this paper we use the model as a tool to infer likely values of such parameters from parameters that are measurable with current technology.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"21-31"},"PeriodicalIF":2.2,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10330635","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Metagenomic Binning Problem: Clustering Markov Sequences 元基因组分选问题：马尔可夫序列聚类

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-28 DOI: 10.1109/TMBMC.2023.3336254

Grant Greenberg;Ilan Shomorony

{"title":"The Metagenomic Binning Problem: Clustering Markov Sequences","authors":"Grant Greenberg;Ilan Shomorony","doi":"10.1109/TMBMC.2023.3336254","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3336254","url":null,"abstract":"The goal of metagenomics is to study the composition of microbial communities, typically using high-throughput shotgun sequencing. In the metagenomic binning problem, we observe random substrings (called contigs) from a mixture of genomes and aim to cluster them according to their genome of origin. Based on the empirical observation that genomes of different bacterial species can be distinguished based on their tetranucleotide frequencies, we model this task as the problem of clustering \u0000<inline-formula> <tex-math>${N}$ </tex-math></inline-formula>\u0000 sequences generated by \u0000<inline-formula> <tex-math>${M}$ </tex-math></inline-formula>\u0000 distinct Markov processes, where \u0000<inline-formula> <tex-math>$M ll N$ </tex-math></inline-formula>\u0000. Utilizing the large-deviation principle for Markov processes, we establish the information-theoretic limit for perfect binning. Specifically, we show that the length of the contigs must scale with the inverse of the Chernoff divergence rate between the two most similar species. Furthermore, our result implies that contigs should be binned using the KL divergence rate as a measure of distance, as opposed to the Euclidean distance often used in practice.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"10 1","pages":"32-42"},"PeriodicalIF":2.2,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140161172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deep Joint Source-Channel Coding for DNA Image Storage: A Novel Approach With Enhanced Error Resilience and Biological Constraint Optimization 用于 DNA 图像存储的深度源-信道联合编码：增强抗错能力和生物约束优化的新方法

IF 2.2

IEEE Transactions on Molecular, Biological, and Multi-Scale Communications Pub Date : 2023-11-09 DOI: 10.1109/TMBMC.2023.3331579

Wenfeng Wu;Luping Xiang;Qiang Liu;Kun Yang

{"title":"Deep Joint Source-Channel Coding for DNA Image Storage: A Novel Approach With Enhanced Error Resilience and Biological Constraint Optimization","authors":"Wenfeng Wu;Luping Xiang;Qiang Liu;Kun Yang","doi":"10.1109/TMBMC.2023.3331579","DOIUrl":"10.1109/TMBMC.2023.3331579","url":null,"abstract":"In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme for DNA image storage, designated as DJSCC-DNA. This paradigm distinguishes itself from conventional DNA storage techniques through three key modifications: 1) it employs advanced deep learning methodologies, employing convolutional neural networks for DNA encoding and decoding processes; 2) it seamlessly integrates DNA polymerase chain reaction (PCR) amplification into the network architecture, thereby augmenting data recovery precision; and 3) it restructures the loss function by targeting biological constraints for optimization. The performance of the proposed model is demonstrated via numerical results from specific channel testing, suggesting that it surpasses conventional deep learning methodologies in terms of peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM). Additionally, the model effectively ensures positive constraints on both homopolymer run-length and GC content.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"461-471"},"PeriodicalIF":2.2,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135562109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0