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An information entropy-based method to detect microRNA regulatory module

IPSJ Transactions on Bioinformatics 2019年 12卷 1-8页

作者： Yang, Yi Song, Yan cao, buwen Department of Information Technology Hunan Women's University China College of Information and Electronic Engineering Hunan City University China

The detection of miRNA regulatory modules (MRMs) can facilitate the analysis of miRNA combination effects in aberrant transcriptional regulatory networks. Existing methods suffer from stochastic or require a predetermined number of regulatory modules. We here develop a parameter-free computational framework named DeMine to predict MRMs. Briefly, DeMine is an information entropy-based method implemented by three steps. It first transforms miRNA regulatory network into a miRNA-miRNA synergistic network, and then detects miRNA clusters by maximizing the referred cluster entropy density. After that, the co-regulated mRNAs are added into corresponding clusters to form final MRMs. Compared with existing methods Mirsynergy and BCM on synthetic dataset and three real cancer datasets: ovarian cancer (OVCA), breast cancer (BRCA) and thyroid cancer (THCA) datasets, the proposed method can not only exhibit higher accuracy but also extract larger cohesiveness-preserved MRMs. More importantly, DeMine can find more miRNAs as tumor markers for the diagnosis of tumors. © 2019 Information Processing Society of Japan.

关键词： Tumors

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Utilizing VANETs as supplementary communication infrastructure for delay-tolerant bulky data transportation

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AD HOC NETWORKS 2021年 112卷

作者： Qin, Hua Xiao, Xiang Chen, Weihong Li, Ni Zeng, Min cao, buwen Peng, Yang Hunan City Univ Coll Informat & Elect Engn Yiyang Hunan Peoples R China Univ Washington Bothell Div Comp & Software Syst Bothell WA USA

With the advancement of connected vehicles, high-bandwidth wireless technologies such as DSRC and WiFi are envisioned to be pervasively available on vehicles. Such empowered vehicles can form large-scale vehicular ad hoc networks (VANETs), which contain rich bandwidth and storage resources. Despite their critical importance for core safety-related VANET applications, these resources are underutilized in practice due to infrequent occurrence and limited size of safety-related messages. However, for a broad range of delay-tolerant applications, which run on edge networks and demand transmission of bulky data with hours or days of delay allowance, such underutilized bandwidth and storage resources in VANETs can be highly valuable. To efficiently utilize VANET resources for delay-tolerant bulky data transmission without compromising the performance of safety-related VANET applications, we propose a Delay-tolerant Data Transportation (DDT) scheme, which aims to use minimal VANET bandwidth to accomplish long-term data transportation under certain end-to-end delay requirements. Unlike traditional VANET data dissemination schemes which prefer data forwarding, DDT primarily relies on a more bandwidth-conserving data carrying method for data transportation. This unique feature makes our proposed system suitable to serve as a supplementary communication infrastructure for offloading and thus alleviating the data transmission workload on edge networks. Extensive simulations have been conducted using a customized simulator, and the results have demonstrated DDT's reliability and adaptability under various scenarios. Particularly, with moderate traffic density and delay requirements, the VANET bandwidth consumption of DDT is 27.3% lower than that of a naive scheme and 5.3% higher than that of a lower bound obtained from theoretical analysis, while the satisfaction ratio of delay requirements is as high as 0.965.

关键词： Delay-tolerant Data transportation VANETs

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BCS: Bidirectional Cross-Interface Scheduling for Sustainable End-to-End Data Delivery in IoT

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IEEE SYSTEMS JOURNAL 2019年第4期13卷 4146-4157页

作者： Qin, Hua Chen, Weihong cao, buwen He, Jianxin Peng, Yang Hunan City Univ Coll Informat & Elect Engn Yiyang 413000 Hunan Peoples R China Univ Washington Div Comp & Software Syst Bothell WA 98011 USA

In this era of Internet of Things (IoT), a variety of battery-powered devices communicate with each other or some remote gateways via wireless multihop communications. Although Wi-Fi has been shown to be of great benefit to a wide range of IoT applications due to its high data rate, high reliability, and native IP compatibility, it is inherently energy-hungry and potentially suffers from a dilemma: more (less) frequent use of Wi-Fi results in shorter (longer) delay but higher (lower) energy consumption. This dilemma becomes the major obstacle in the use of Wi-Fi in long-term but delay-bounded IoT applications. To address this, we propose a bidirectional cross-interface scheduling (BCS) scheme, which leverages the widely used low-power ZigBee to collaborate with the high data rate and reliable Wi-Fi for sustainable and reliable end-to-end (E2E) data delivery in IoT. The objective is to maximize network lifetime while satisfying certain required E2E delay bound. Extensive simulations and testbed experiments have been conducted. The results show that the network lifetime of BCS is 33.4% and 346.9% longer than those of a state-of-the-art scheme and the IEEE 802.11%'s standard power-saving scheme with the default settings, respectively.

关键词： Energy IoT network lifetime Wi-Fi ZigBee

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ECG Data Processing Methods for Intelligent Remote ECG Monitoring System: A Survey

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JOURNAL OF CIRCUITS SYSTEMS AND COMPUTERS 2025年

作者： cao, buwen Xiao, Sainan Li, Renfa Li, Rui Huang, Tian Wang, Jilong Hunan City Univ Informat & Elect Engn Yiyang 413002 Hunan Peoples R China Hunan Univ Coll Comp Sci & Elect Engn Changsha 410082 Hunan Peoples R China Hunan Engn Res Ctr Ecol Environm Intelligent Monit Yiyang 413002 Hunan Peoples R China Hunan City Univ Key Lab City Comp & IoT Yiyang 413002 Hunan Peoples R China Pengcheng Lab Shenzhen 550001 Guangdong Peoples R China

The integration of the Internet of Things (IoT), edge computing and cloud computing has facilitated the development of an advanced intelligent remote ECG monitoring system. This system offers a convenient platform for remote monitoring, consultation services and diagnosis for patients with cardiovascular conditions. However, challenges persist regarding data noise interference and limited diagnostic accuracy. Therefore, mitigating noise interference and improving diagnostic precision remain critical issues to address. In this study, we introduce an intelligent remote ECG monitoring system that consists of three main components: the user terminal (data collection device), the remote ECG monitoring center, and the analysis and diagnosis modules. The data captured by sensors from wearable devices are collected in real time by the user terminal, formatted into a standard structure and then transmitted to the remote electrocardiogram monitoring center. Within the intelligent remote ECG monitoring system, the remote ECG monitoring center performs key tasks, such as preprocessing, feature extraction and classification of ECG data. Subsequently, examining the advancements made within the realm of the intelligent remote ECG monitoring system, a comprehensive overview is presented. This encompasses the refinement process, segmentation of ECG signals and the categorization of arrhythmias. Finally, we propose potential directions for future research in ECG data processing within the context of intelligent remote ECG monitoring systems.

关键词： Intelligent remote ECG monitoring system data processing denoising signal segmentation arrhythmia

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CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

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BMC BIOINFORMATICS 2019年第1期20卷 67-67页

作者： Xiao, Qiu Luo, Jiawei Liang, Cheng Cai, Jie Li, Guanghui cao, buwen Hunan Univ Coll Comp Sci & Elect Engn Changsha 410082 Hunan Peoples R China Hunan Normal Univ Hunan Prov Key Lab Intelligent Comp & Language In Changsha 410081 Hunan Peoples R China Shandong Normal Univ Coll Informat Sci & Engn Jinan 250000 Shandong Peoples R China

BackgroundNon-coding RNAs (ncRNAs) are emerging as key regulators and play critical roles in a wide range of tumorigenesis. Recent studies have suggested that long non-coding RNAs (lncRNAs) could interact with microRNAs (miRNAs) and indirectly regulate miRNA targets through competing interactions. Therefore, uncovering the competing endogenous RNA (ceRNA) regulatory mechanism of lncRNAs, miRNAs and mRNAs in post-transcriptional level will aid in deciphering the underlying pathogenesis of human polygenic diseases and may unveil new diagnostic and therapeutic opportunities. However, the functional roles of vast majority of cancer specific ncRNAs and their combinational regulation patterns are still insufficiently *** we develop an integrative framework called CeModule to discover lncRNA, miRNA and mRNA-associated regulatory modules. We fully utilize the matched expression profiles of lncRNAs, miRNAs and mRNAs and establish a model based on joint orthogonality non-negative matrix factorization for identifying modules. Meanwhile, we impose the experimentally verified miRNA-lncRNA interactions, the validated miRNA-mRNA interactions and the weighted gene-gene network into this framework to improve the module accuracy through the network-based penalties. The sparse regularizations are also used to help this model obtain modular sparse solutions. Finally, an iterative multiplicative updating algorithm is adopted to solve the optimization *** applied CeModule to two cancer datasets including ovarian cancer (OV) and uterine corpus endometrial carcinoma (UCEC) obtained from TCGA. The modular analysis indicated that the identified modules involving lncRNAs, miRNAs and mRNAs are significantly associated and functionally enriched in cancer-related biological processes and pathways, which may provide new insights into the complex regulatory mechanism of human diseases at the system level.

关键词： Regulatory pattern Module discovery microRNA lncRNA function ceRNA Cancer Machine learning

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DIPS: Dual-Interface Dual-Pipeline Scheduling for Energy-Efficient Multihop Communications in IoT

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IEEE INTERNET OF THINGS JOURNAL 2019年第1期6卷 718-733页

作者： Qin, Hua Chen, Weihong cao, buwen Zeng, Min Li, Jessica Peng, Yang Hunan City Univ Coll Informat & Elect Engn Yiyang 413000 Peoples R China Univ Washington Div Comp & Software Syst Bothell WA 98011 USA

The future Internet of Things (IoT) will enable Internet connectivity for a vast amount of battery-powered devices, which usually need to communicate with each other or to some remote gateways through multihop communications. Although ZigBee has become a widely used communication technology in IoT, Wi-Fi, on the other hand, has its unique advantages such as high throughput and native IP compatibility, despite its potentially higher energy consumption. With the development of IoT, more and more IoT devices are equipped with multiple radio interfaces, such as both Wi-Fi and ZigBee. Inspired by this, we propose a dual-interface dual-pipeline scheduling (DIPS) scheme, which leverages an activation pipeline mainly constructed by low-power ZigBee interfaces to wake up a data pipeline constructed by high-power Wi-Fi interfaces on demand, toward enabling multihop data delivery in IoT. The objective is to minimize network energy consumption while satisfying certain end-to-end delay requirements. Extensive simulations and prototype-based experiments have been conducted. The results show that the energy consumption of DIPS is 96.5% and 92.8% lower than that of the IEEE 802.11's standard power saving scheme and a state-of-the-art pipeline-based scheme in moderate traffic scenarios, respectively.

关键词： Dual radio energy efficiency Internet of Things (IoT) pipeline

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Cognitive routing optimization protocol based on multiple channels in wireless sensor networks

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INTERNATIONAL JOURNAL OF DISTRIBUTED SENSOR NETWORKS 2020年第4期16卷

作者： Deng, Shuguang cao, buwen Xiao, Xiang Qin, Hua Yang, Bing Hunan City Univ Coll Informat & Elect Engn Yiyang 413000 Peoples R China

With the development of modern communication, available spectrum resources are becoming increasingly scarce, which reduce network throughput. Moreover, the mobility of nodes results in the changes of network topological structure. Hence, a considerable amount of control information is consumed, which causes a corresponding increase in network power consumption and exerts a substantial impact on network lifetime. To solve the real-time transmission problem in large-scale wireless mobile sensor networks, opportunistic spectrum access is applied to adjust the transmission power of sensor nodes and the transmission velocity of data. A cognitive routing and optimization protocol based on multiple channels with a cross-layer design is proposed to study joint optimal cognitive routing with maximizing network throughput and network lifetime. Experimental results show that the cognitive routing and optimization protocol based on multiple channels achieves low computational complexity, which maximizes network throughput and network lifetime. This protocol can be also effectively applied to large-scale wireless mobile sensor networks.

关键词： Multiple channels cognitive routing optimization protocol network throughput network lifetime

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A Novel Approach to Identify the miRNA-mRNA Causal Regulatory Modules in Cancer

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018年第1期15卷 309-315页

作者： Luo, Jiawei Huang, Wei cao, buwen Hunan Univ Coll Comp Sci & Elect Engn Changsha 410082 Hunan Peoples R China

MicroRNAs (miRNAs) play an essential role in many biological processes by regulating the target genes, especially in the initiation and development of cancers. Therefore, the identification of the miRNA-mRNA regulatory modules is important for understanding the regulatory mechanisms. Most computational methods only used statistical correlations in predicting miRNA-mRNA modules, and neglected the fact there are causal relationships between miRNAs and their target genes. In this paper, we propose a novel approach called CALM (the causal regulatory modules) to identify the miRNA-mRNA regulatory modules through integrating the causal interactions and statistical correlations between the miRNAs and their target genes. Our algorithm largely consists of three steps: it first forms the causal regulatory relationships of miRNAs and genes from gene expression profiles and detects the miRNA clusters according to the GO function information of their target genes, then expands each miRNA cluster by greedy adding (discarding) the target genes to maximize the modularity score. To show the performance of our method, we apply CALM on four datasets including EMT, breast, ovarian, and thyroid cancer and validate our results. The experiment results show that our method can not only out perform the compared method, but also achieve ideal overall performance in terms of the functional enrichment.

关键词： Synergistic regulations causality regulatory modules modularity miRNA-mRNA regulatory modules

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Identification of overlapping protein complexes by fuzzy K-medoids clustering algorithm in yeast protein-protein interaction networks

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JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2018年第1期34卷 93-103页

作者： cao, buwen Deng, Shuguang Luo, Jiawei Ding, Pingjian Wang, Shulin Hunan City Univ Sch Informat Sci & Engn Yiyang 413000 Peoples R China Hunan City Univ Coll Commun & Elect Engn Yiyang Peoples R China Hunan Univ Coll Comp Sci & Elect Engn Changsha Hunan Peoples R China

The identification of overlapping protein complexes in proteinprotein interaction (PPI) networks may elucidate cellular functional organizations and their underlying cellular mechanisms. Recently, many protein complex mining algorithms have been developed for PPI networks. However, the majority of available algorithms primarily depend on mining dense subgraphs as protein complexes, thereby failing to consider the inherent biological meanings between protein pairs. Thus, methods for identifying protein complexes using the biological significance hidden in edges need to be investigated. In this paper, we propose IK-medoids, an improved method that detects overlapping protein complexes from weighted PPI networks based on the rough fuzzy relationships between protein pairs. The presented algorithm is primarily based on the fuzzy relationship that obtains the non-overlapping protein substructure, and then K-medoids is executed from the proteins in the PPI network. Next, the similarity between one protein and each candidate complex is calculated to determine whether the protein belongs to one or multiple complexes with the ration of each similarity to maximum similarity. In the end, overlapped protein complexes are merged to form the final protein complexes. We apply the method to three PPI networks and validate the results using two reference protein complexes retrieved from public databases. Experimental results show that our method outperforms classical algorithms, such as ClusterONE, CMC, MCL, OSLOM, and RFC, and achieves ideal overall performance in terms of F-measure, sensitivity, and accuracy.

关键词： PPI protein complex overlapping K-medoids Fuzzy relation

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A cross-interface design for energy-efficient and delay-bounded multi-hop communications in IoT

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AD HOC NETWORKS 2018年 70卷 103-120页

作者： Qin, Hua Chen, Weihong cao, buwen Zeng, Min Peng, Yang Hunan City Univ Coll Informat & Elect Engn Yiyang Hunan Peoples R China Univ Washington Div Comp & Software Syst Bothell WA USA

The future Internet of Things (loT) will enable Internet connectivity for a vast amount of battery-powered devices, which usually need to wirelessly communicate with each other or to some remote gateways through multi-hop communications. Although ZigBee has become a widely used communication technology in loT, Wi-Fi, on the other hand, has its unique advantages such as high throughput and native IP compatibility, despite its potentially higher energy consumption. With the development of IoT, more and more loT devices are equipped with multiple radio interfaces, such as both Wi-Fi and ZigBee. Inspired by this, we propose a cross-interface power saving management (CPSM) scheme, which leverages the existing low-power ZigBee interfaces to wake up the high-power Wi-Fi interfaces on demand towards enabling multi-hop communications in loT. The objective is to minimize the network energy consumption while satisfying certain end-to-end delay requirements. The results of extensive simulations and prototype-based experiments have demonstrated that the energy consumption of our proposed CPSM is 79.2% and 68.9% lower than those of the IEEE 802.11's standard power saving scheme and a state-of-the-art scheme in moderate traffic scenarios, respectively. (C) 2017 Elsevier B.V. All rights reserved.

关键词： IoT Energy Multi-hop communications

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