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A Combinational Clustering Based Method for cDNA Microarray Image Segmentation

Guifang Shao, Tiejun Li, Wangda Zuo, Shunxiang Wu, Tundong Liu, Shu-Dong Zhang
2015 PLoS ONE  
Microarray technology plays an important role in drawing useful biological conclusions by analyzing thousands of gene expressions simultaneously. Especially, image analysis is a key step in microarray analysis and its accuracy strongly depends on segmentation. The pioneering works of clustering based segmentation have shown that k-means clustering algorithm and moving k-means clustering algorithm are two commonly used methods in microarray image processing. However, they usually face
more » ... ory results because the real microarray image contains noise, artifacts and spots that vary in size, shape and contrast. To improve the segmentation accuracy, in this article we present a combination clustering based segmentation approach that may be more reliable and able to segment spots automatically. First, this new method starts with a very simple but effective contrast enhancement operation to improve the image quality. Then, an automatic gridding based on the maximum between-class variance is applied to separate the spots into independent areas. Next, among each spot region, the moving k-means clustering is first conducted to separate the spot from background and then the k-means clustering algorithms are combined for those spots failing to obtain the entire boundary. Finally, a refinement step is used to replace the false segmentation and the inseparable ones of missing spots. In addition, quantitative comparisons between the improved method and the other four segmentation algorithms-edge detection, thresholding, k-means clustering and moving k-means clustering-are carried out on cDNA microarray images from six different data sets. Experiments on six different data sets, 1) Stanford Microarray Database (SMD), 2) Gene Expression Omnibus (GEO), 3) Baylor College of Medicine (BCM), 4) Swiss Institute of Bioinformatics (SIB), 5) Joe DeRisi's individual tiff files (DeRisi), and 6) University of California, San Francisco (UCSF), indicate that the improved approach is more robust and sensitive to weak spots. More importantly, it can obtain higher segmentation accuracy in the presence of noise, artifacts and weakly expressed spots compared with the other four methods.
doi:10.1371/journal.pone.0133025 pmid:26241767 pmcid:PMC4524615 fatcat:pdnqqrixlnckbdnrusmkoxczxy

DuCaGAN: Unified Dual Capsule Generative Adversarial Network for Unsupervised Image-to-Image Translation

Guifang Shao, Meng Huang, Fengqiang Gao, Tundong Liu, Liduan Li
2020 IEEE Access  
doi:10.1109/access.2020.3007266 fatcat:7dik7bf5e5aodb76swkb5nswgy

WSPT's Competitive Performance for Minimizing the Total Weighted Flow Time: From Single to Parallel Machines

Jiping Tao, Tundong Liu
2013 Mathematical Problems in Engineering  
We consider the classical online scheduling problem over single and parallel machines with the objective of minimizing total weighted flow time. We employ an intuitive and systematic analysis method and show that the weighted shortest processing time (WSPT) is an optimal online algorithm with the competitive ratio ofP+1for the case of single machine, and it is (P+(3/2)−(1/2m))-competitive for the case of parallel machines(m>1), wherePis the ratio of the longest to the shortest processing time.
doi:10.1155/2013/343287 fatcat:4r3am5ez4vdlpb7gn4zq5nwmji

Optimal Design of High-Channel-Count Fiber Bragg Grating Filters With Low Index Modulation Using an Improved Differential Evolution Algorithm

Jing Chen, Hao Jiang, Zengruan Ye, Xiaoli Fu, Jianjie Zhu, Tundong Liu
2013 IEEE Photonics Journal  
An effective optimization method based on a self-adaptive differential evolution (DE) algorithm is proposed to design high-channel-count fiber Bragg grating (FBG) filters. By combining the optimization algorithm with the tailored group delay technology, we have established a mathematical model aiming at minimizing the maximum index modulation of the grating. Equipped with a parameter self-adaptive strategy, the improved DE algorithm shows its powerful global searching ability in finding the
more » ... mal group delay parameter for each channel. Design examples demonstrate that the proposed approach yields better results with a remarkable reduction in the maximum index modulation compared with the previous works. Furthermore, we numerically present a 1037-channel 50-GHz spaced FBG filter enabling to cover the whole bands ðO þ E þ S þ C þ L þ UÞ, which indicates the potential application of this method in the dense wavelength-division multiplexing (DWDM) system.
doi:10.1109/jphot.2013.2292360 fatcat:dri4mbdfajfehlzyz5tc4uheou

Survey on Minimizing Energy Consumption in Mobile Cloud Computing

C. Arun, V. Jaiganesh
2016 International Journal of Computer Applications  
Tundong Liu et. al., proposed an energy-efficient scheduling of tasks [1] , where the mobile device offloads appropriate tasks to the cloud via a Wi-Fi access point.  ...  An offloading decision method is investigated by Liu et al [12] to minimize the energy consumption of mobile device with a reasonable time delay and communication quality.  ... 
doi:10.5120/ijca2016911471 fatcat:ww6tbrz42vc35eonlxlvylfvii

Front Matter [chapter]

International Conference on Mechanical Engineering and Technology (ICMET-London 2011)  
.........................................................................................481 APPLICATION OF A VARIABLE-UNIVERSE AND SELF-ADAPTIVE FUZZY PID CONTROLLER IN DC MOTOR SPEED CONTROL SYSTEM Tundong  ...  Zu-Qiang, Lu Jin-Gui ......................................................................................................................................7 ENVIRONMENT MODELING FOR MOBILE SERVICE ROBOT Liu  ... 
doi:10.1115/1.859896.fm fatcat:ishak2tborbv3jr5nn4rl5gsfi