The progression of complex diseases generally involves a pre-deterioration stage that occurs during the transition from a healthy state to disease deterioration,at which a drastic and qualitative shift occurs.The deve...The progression of complex diseases generally involves a pre-deterioration stage that occurs during the transition from a healthy state to disease deterioration,at which a drastic and qualitative shift occurs.The development of an effective approach is urgently needed to identify such a pre-deterioration stage or critical state just before disease deterioration,which allows the timely implementation of appropriate measures to prevent a catastrophic transition.However,identifying the pre-deterioration stage is a challenging task in clinical medicine,especially when only a single sample is available for most patients,which is responsible for the failure of most statistical methods.In this study,a novel computational method,called single-sample network module biomarkers(sNMB),is presented to predict the pre-deterioration stage or critical point using only a single sample.Specifically,the proposed single-sample index effectively quantifies the disturbance caused by a single sample against a group of given reference samples.Our method successfully detected the early warning signal of the critical transitions when applied to both a numerical simulation and four real datasets,including acute lung injury,stomach adenocarcinoma,esophageal carcinoma,and rectum adenocarcinoma.In addition,it provides signaling biomarkers for further practical application,which helps to discover prognostic indicators and reveal the underlying molecular mechanisms of disease progression.展开更多
In complex networks, network modules play a center role, which carry out a key function. In this paper, we introduce the spatial correIation function to describe the relationships among the network modules. Our focus ...In complex networks, network modules play a center role, which carry out a key function. In this paper, we introduce the spatial correIation function to describe the relationships among the network modules. Our focus is to investigate how the network modules evolve, and what the evolution properties of the modules are. In order to test the proposed method, as the examples, we use our method to analyze and discuss the ER random network and scale-free network. Rigorous analysis of the existing data shows that the introduced correlation function is suitable for describing the evolution properties of network modules. Remarkably, the numerical simulations indicate that the ER random network and scale-free network have different evolution properties.展开更多
With the popularization of microarray experi-ments in biomedical laboratories,how to make context-specific knowledge discovery from expression data becomes a hot topic.While the static“reference networks”for key mod...With the popularization of microarray experi-ments in biomedical laboratories,how to make context-specific knowledge discovery from expression data becomes a hot topic.While the static“reference networks”for key model organisms are nearly at hand,the endeavors to recover context-specific network modules are still at the beginning.Currently,this is achieved through filtering existing edges of the ensemble reference network or constructing gene networks ab initio.In this paper,we briefly review recent progress in the field and point out some research directions awaiting improved work,includ-ing expression-data-guided revision of reference networks.展开更多
Neural networks excel at capturing local spatial patterns through convolutional modules,but they may struggle to identify and effectively utilize the morphological and amplitude periodic nature of physiological signal...Neural networks excel at capturing local spatial patterns through convolutional modules,but they may struggle to identify and effectively utilize the morphological and amplitude periodic nature of physiological signals.In this work,we propose a novel network named filtering module fully convolutional network(FM-FCN),which fuses traditional filtering techniques with neural networks to amplify physiological signals and suppress noise.First,instead of using a fully connected layer,we use an FCN to preserve the time-dimensional correlation information of physiological signals,enabling multiple cycles of signals in the network and providing a basis for signal processing.Second,we introduce the FM as a network module that adapts to eliminate unwanted interference,leveraging the structure of the filter.This approach builds a bridge between deep learning and signal processing methodologies.Finally,we evaluate the performance of FM-FCN using remote photoplethysmography.Experimental results demonstrate that FM-FCN outperforms the second-ranked method in terms of both blood volume pulse(BVP)signal and heart rate(HR)accuracy.It substantially improves the quality of BVP waveform reconstruction,with a decrease of 20.23%in mean absolute error(MAE)and an increase of 79.95%in signal-to-noise ratio(SNR).Regarding HR estimation accuracy,FM-FCN achieves a decrease of 35.85%in MAE,29.65%in error standard deviation,and 32.88%decrease in 95%limits of agreement width,meeting clinical standards for HR accuracy requirements.The results highlight its potential in improving the accuracy and reliability of vital sign measurement through high-quality BVP signal extraction.The codes and datasets are available online at https://github.com/zhaoqi106/FM-FCN.展开更多
The rapid development of network technology and its evolution toward heterogeneous networks has increased the demand to support automatic monitoring and the management of heterogeneous wireless communication networks....The rapid development of network technology and its evolution toward heterogeneous networks has increased the demand to support automatic monitoring and the management of heterogeneous wireless communication networks.This paper presents a multilevel pattern mining architecture to support automatic network management by discovering interesting patterns from telecom network monitoring data.This architecture leverages and combines existing frequent itemset discovery over data streams,association rule deduction,frequent sequential pattern mining,and frequent temporal pattern mining techniques while also making use of distributed processing platforms to achieve high-volume throughput.展开更多
The characterization of the interacting behaviors of complex biological systems is a pri- mary objective in protein protein network analysis and computational biology. In this paper we present FunMod, an innovative Cy...The characterization of the interacting behaviors of complex biological systems is a pri- mary objective in protein protein network analysis and computational biology. In this paper we present FunMod, an innovative Cytoscape version 2.8 plugin that is able to mine undirected pro- rein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways. This plugin may enable the discovery of new pathways involved in dis- eases. In order to describe the role of each protein within the relevant biological pathways, FunMod computes and scores three topological features of the identified sub-networks. By integrating the results from biological pathway clustering and topological network analysis, FunMod proved to be useful for the data interpretation and the generation of new hypotheses in two case studies.展开更多
Current methods for the detection of differential gene expression focus on finding individual genes that may be responsible for certain diseases or external irritants. However, for common genetic diseases, multiple ge...Current methods for the detection of differential gene expression focus on finding individual genes that may be responsible for certain diseases or external irritants. However, for common genetic diseases, multiple genes and their interactions should be understood and treated together during the exploration of disease causes and possible drug design. The present study focuses on analyzing the dynamic patterns of co-regulated modules during biological progression and determining those having remarkably varying activities, using the yeast cell cycle as a case study. We first constructed dynamic active protein-protein interaction networks by modeling the activity of proteins and assembling the dynamic co-regulation protein network at each time point. The dynamic active modules were detected using a method based on the Bayesian graphical model and then the modules with the most varied dispersion of clustering coefficients, which could be responsible for the dynamic mechanism of the cell cycle, were identified. Comparison of results from our functional module detection with the state-of-art functional module detection methods and validation of the ranking of activities of functional modules using GO annotations demonstrate the efficacy of our method for narrowing the scope of possible essential responding modules that could provide multiple targets for biologists to further experimentally validate.展开更多
Fixed-point attractors with global stability manifest themselves in a number of gene regulatory networks. This property indicates the stability of regulatory networks against small state perturbations and is closely r...Fixed-point attractors with global stability manifest themselves in a number of gene regulatory networks. This property indicates the stability of regulatory networks against small state perturbations and is closely related to other complex dynamics. In this paper, we aim to reveal the core modules in regulatory networks that determine their global attractors and the relationship between these core modules and other motifs. This work has been done via three steps. Firstly, inspired by the signal transmission in the regulation process, we extract the model of chain-like network from regulation networks. We propose a module of "ideal transmission chain(ITC)", which is proved sufficient and necessary(under certain condition) to form a global fixed-point in the context of chain-like network. Secondly, by examining two well-studied regulatory networks(i.e., the cell-cycle regulatory networks of Budding yeast and Fission yeast), we identify the ideal modules in true regulation networks and demonstrate that the modules have a superior contribution to network stability(quantified by the relative size of the biggest attraction basin). Thirdly, in these two regulation networks, we find that the double negative feedback loops, which are the key motifs of forming bistability in regulation, are connected to these core modules with high network stability. These results have shed new light on the connection between the topological feature and the dynamic property of regulatory networks.展开更多
In order to meet the requirements of accurate identification of surface defects on copper strip in industrial production,a detection model of surface defects based on machine vision,CSC-YOLO,is proposed.The model uses...In order to meet the requirements of accurate identification of surface defects on copper strip in industrial production,a detection model of surface defects based on machine vision,CSC-YOLO,is proposed.The model uses YOLOv4-tiny as the benchmark network.First,K-means clustering is introduced into the benchmark network to obtain anchor frames that match the self-built dataset.Second,a cross-region fusion module is introduced in the backbone network to solve the difficult target recognition problem by fusing contextual semantic information.Third,the spatial pyramid pooling-efficient channel attention network(SPP-E)module is introduced in the path aggregation network(PANet)to enhance the extraction of features.Fourth,to prevent the loss of channel information,a lightweight attention mechanism is introduced to improve the performance of the network.Finally,the performance of the model is improved by adding adjustment factors to correct the loss function for the dimensional characteristics of the surface defects.CSC-YOLO was tested on the self-built dataset of surface defects in copper strip,and the experimental results showed that the mAP of the model can reach 93.58%,which is a 3.37% improvement compared with the benchmark network,and FPS,although decreasing compared with the benchmark network,reached 104.CSC-YOLO takes into account the real-time requirements of copper strip production.The comparison experiments with Faster RCNN,SSD300,YOLOv3,YOLOv4,Resnet50-YOLOv4,YOLOv5s,YOLOv7,and other algorithms show that the algorithm obtains a faster computation speed while maintaining a higher detection accuracy.展开更多
基金supported by the National Natural Science Foundation of China(12026608,62172164,12131020,and 12271180)the Natural Science Foundation of Guangdong Province(2021A1515012317).
文摘The progression of complex diseases generally involves a pre-deterioration stage that occurs during the transition from a healthy state to disease deterioration,at which a drastic and qualitative shift occurs.The development of an effective approach is urgently needed to identify such a pre-deterioration stage or critical state just before disease deterioration,which allows the timely implementation of appropriate measures to prevent a catastrophic transition.However,identifying the pre-deterioration stage is a challenging task in clinical medicine,especially when only a single sample is available for most patients,which is responsible for the failure of most statistical methods.In this study,a novel computational method,called single-sample network module biomarkers(sNMB),is presented to predict the pre-deterioration stage or critical point using only a single sample.Specifically,the proposed single-sample index effectively quantifies the disturbance caused by a single sample against a group of given reference samples.Our method successfully detected the early warning signal of the critical transitions when applied to both a numerical simulation and four real datasets,including acute lung injury,stomach adenocarcinoma,esophageal carcinoma,and rectum adenocarcinoma.In addition,it provides signaling biomarkers for further practical application,which helps to discover prognostic indicators and reveal the underlying molecular mechanisms of disease progression.
基金National Natural Science Foundation of China under Grant Nos.60634010 and 60776829New Century Excellent Talents in Universities under Grant No.NCET-06-0074the Key Project of the Ministry of Education of China under Grant No.107007
文摘In complex networks, network modules play a center role, which carry out a key function. In this paper, we introduce the spatial correIation function to describe the relationships among the network modules. Our focus is to investigate how the network modules evolve, and what the evolution properties of the modules are. In order to test the proposed method, as the examples, we use our method to analyze and discuss the ER random network and scale-free network. Rigorous analysis of the existing data shows that the introduced correlation function is suitable for describing the evolution properties of network modules. Remarkably, the numerical simulations indicate that the ER random network and scale-free network have different evolution properties.
基金This work was supported by a grant from Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences(No.2008KIP207)the National Natural Science Foundation of China(Grant No.30770497)the National Key Technologies R&D Program(No.2007AA02Z331).
文摘With the popularization of microarray experi-ments in biomedical laboratories,how to make context-specific knowledge discovery from expression data becomes a hot topic.While the static“reference networks”for key model organisms are nearly at hand,the endeavors to recover context-specific network modules are still at the beginning.Currently,this is achieved through filtering existing edges of the ensemble reference network or constructing gene networks ab initio.In this paper,we briefly review recent progress in the field and point out some research directions awaiting improved work,includ-ing expression-data-guided revision of reference networks.
基金supported by Ministry of Science and Technology of the People’s Republic of China(STI2030-Major Projects 2021ZD0201900)National Natural Science Foundation of China(grant mo.12090052)+2 种基金Natural Science Foundation of Liaoning Province(grant no.2023-MS-288)Fundamental Research Funds for the Central Universities(grant no.20720230017)Basic Public Welfare Research Program of Zhejiang Province(grant no.LGF20F030005).
文摘Neural networks excel at capturing local spatial patterns through convolutional modules,but they may struggle to identify and effectively utilize the morphological and amplitude periodic nature of physiological signals.In this work,we propose a novel network named filtering module fully convolutional network(FM-FCN),which fuses traditional filtering techniques with neural networks to amplify physiological signals and suppress noise.First,instead of using a fully connected layer,we use an FCN to preserve the time-dimensional correlation information of physiological signals,enabling multiple cycles of signals in the network and providing a basis for signal processing.Second,we introduce the FM as a network module that adapts to eliminate unwanted interference,leveraging the structure of the filter.This approach builds a bridge between deep learning and signal processing methodologies.Finally,we evaluate the performance of FM-FCN using remote photoplethysmography.Experimental results demonstrate that FM-FCN outperforms the second-ranked method in terms of both blood volume pulse(BVP)signal and heart rate(HR)accuracy.It substantially improves the quality of BVP waveform reconstruction,with a decrease of 20.23%in mean absolute error(MAE)and an increase of 79.95%in signal-to-noise ratio(SNR).Regarding HR estimation accuracy,FM-FCN achieves a decrease of 35.85%in MAE,29.65%in error standard deviation,and 32.88%decrease in 95%limits of agreement width,meeting clinical standards for HR accuracy requirements.The results highlight its potential in improving the accuracy and reliability of vital sign measurement through high-quality BVP signal extraction.The codes and datasets are available online at https://github.com/zhaoqi106/FM-FCN.
基金funded by the Enterprise Ireland Innovation Partnership Programme with Ericsson under grant agreement IP/2011/0135[6]supported by the National Natural Science Foundation of China(No.61373131,61303039,61232016,61501247)+1 种基金the PAPDCICAEET funds
文摘The rapid development of network technology and its evolution toward heterogeneous networks has increased the demand to support automatic monitoring and the management of heterogeneous wireless communication networks.This paper presents a multilevel pattern mining architecture to support automatic network management by discovering interesting patterns from telecom network monitoring data.This architecture leverages and combines existing frequent itemset discovery over data streams,association rule deduction,frequent sequential pattern mining,and frequent temporal pattern mining techniques while also making use of distributed processing platforms to achieve high-volume throughput.
文摘The characterization of the interacting behaviors of complex biological systems is a pri- mary objective in protein protein network analysis and computational biology. In this paper we present FunMod, an innovative Cytoscape version 2.8 plugin that is able to mine undirected pro- rein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways. This plugin may enable the discovery of new pathways involved in dis- eases. In order to describe the role of each protein within the relevant biological pathways, FunMod computes and scores three topological features of the identified sub-networks. By integrating the results from biological pathway clustering and topological network analysis, FunMod proved to be useful for the data interpretation and the generation of new hypotheses in two case studies.
基金supported by the National Natural Science Foundation of China (No.30970780)Ph.D.Programs Foundation of Ministry of Education of China (No.20091103110005)
文摘Current methods for the detection of differential gene expression focus on finding individual genes that may be responsible for certain diseases or external irritants. However, for common genetic diseases, multiple genes and their interactions should be understood and treated together during the exploration of disease causes and possible drug design. The present study focuses on analyzing the dynamic patterns of co-regulated modules during biological progression and determining those having remarkably varying activities, using the yeast cell cycle as a case study. We first constructed dynamic active protein-protein interaction networks by modeling the activity of proteins and assembling the dynamic co-regulation protein network at each time point. The dynamic active modules were detected using a method based on the Bayesian graphical model and then the modules with the most varied dispersion of clustering coefficients, which could be responsible for the dynamic mechanism of the cell cycle, were identified. Comparison of results from our functional module detection with the state-of-art functional module detection methods and validation of the ranking of activities of functional modules using GO annotations demonstrate the efficacy of our method for narrowing the scope of possible essential responding modules that could provide multiple targets for biologists to further experimentally validate.
基金supported by the National Natural Science Foundation of China(Grant No.11331011)Support from the Center for Statistical Science of Peking University was also gratefully acknowledged
文摘Fixed-point attractors with global stability manifest themselves in a number of gene regulatory networks. This property indicates the stability of regulatory networks against small state perturbations and is closely related to other complex dynamics. In this paper, we aim to reveal the core modules in regulatory networks that determine their global attractors and the relationship between these core modules and other motifs. This work has been done via three steps. Firstly, inspired by the signal transmission in the regulation process, we extract the model of chain-like network from regulation networks. We propose a module of "ideal transmission chain(ITC)", which is proved sufficient and necessary(under certain condition) to form a global fixed-point in the context of chain-like network. Secondly, by examining two well-studied regulatory networks(i.e., the cell-cycle regulatory networks of Budding yeast and Fission yeast), we identify the ideal modules in true regulation networks and demonstrate that the modules have a superior contribution to network stability(quantified by the relative size of the biggest attraction basin). Thirdly, in these two regulation networks, we find that the double negative feedback loops, which are the key motifs of forming bistability in regulation, are connected to these core modules with high network stability. These results have shed new light on the connection between the topological feature and the dynamic property of regulatory networks.
基金the Key Project of Basic Research of Yunnan Province(No.202101AS070016)。
文摘In order to meet the requirements of accurate identification of surface defects on copper strip in industrial production,a detection model of surface defects based on machine vision,CSC-YOLO,is proposed.The model uses YOLOv4-tiny as the benchmark network.First,K-means clustering is introduced into the benchmark network to obtain anchor frames that match the self-built dataset.Second,a cross-region fusion module is introduced in the backbone network to solve the difficult target recognition problem by fusing contextual semantic information.Third,the spatial pyramid pooling-efficient channel attention network(SPP-E)module is introduced in the path aggregation network(PANet)to enhance the extraction of features.Fourth,to prevent the loss of channel information,a lightweight attention mechanism is introduced to improve the performance of the network.Finally,the performance of the model is improved by adding adjustment factors to correct the loss function for the dimensional characteristics of the surface defects.CSC-YOLO was tested on the self-built dataset of surface defects in copper strip,and the experimental results showed that the mAP of the model can reach 93.58%,which is a 3.37% improvement compared with the benchmark network,and FPS,although decreasing compared with the benchmark network,reached 104.CSC-YOLO takes into account the real-time requirements of copper strip production.The comparison experiments with Faster RCNN,SSD300,YOLOv3,YOLOv4,Resnet50-YOLOv4,YOLOv5s,YOLOv7,and other algorithms show that the algorithm obtains a faster computation speed while maintaining a higher detection accuracy.
