Heuristic-Based Ant Colony Optimization Algorithm For Protein Functional Module Detection In Protein Interaction Network

Ant colony optimization (ACO) is a metaheuristic algorithm that has been successfully applied to several types of optimization problems such as scheduling, routing, and more recently for solving protein functional module detection (PFMD) problem in protein-protein interaction (PPI) networks. For a small PPI data size, ACO has been successfully applied to but it is not suitable for large and noisy PPI data, which has caused to premature convergence and stagnation in the searching process. To cope with the aforementioned limitations, we propose two new enhancements of ACO to solve PFMD problem

PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks

Background How can we obtain fast and high-quality clusters in genome scale bio-networks? Graph clustering is a powerful tool applied on bio-networks to solve various biological problems such as protein complexes detection, disease module detection, and gene function prediction. Especially, MCL (Markov Clustering) has been spotlighted due to its superior performance on bio-networks. MCL, however, is skewed towards finding a large number of very small clusters (size 1-3) and fails to detect many larger clusters (size 10+). To resolve this fragmentation problem, MLR-MCL (Multi-level Regularized MCL) has been developed. MLR-MCL still suffers from the fragmentation and, in cases, unrealistically large clusters are generated. Results In this paper, we propose PS-MCL (Parallel Shotgun Coarsened MCL), a parallel graph clustering method outperforming MLR-MCL in terms of running time and cluster quality. PS-MCL adopts an efficient coarsening scheme, called SC (Shotgun Coarsening), to improve graph coarsening in MLR-MCL. SC allows merging multiple nodes at a time, which leads to improvement in quality, time and space usage. Also, PS-MCL parallelizes main operations used in MLR-MCL which includes matrix multiplication. Conclusions Experiments show that PS-MCL dramatically alleviates the fragmentation problem, and outperforms MLR-MCL in quality and running time. We also show that the running time of PS-MCL is effectively reduced with parallelization.Publication of this article has been funded by National Research Foundation of Korea grant funded by the Korea government (NRF-2018R1A5A1060031, NRF-2018R1A1A3A0407953) and by Korea Institute of Science and Technology Information (K-18-L03-C02)

Information extraction and transmission techniques for spaceborne synthetic aperture radar images

Information extraction and transmission techniques for synthetic aperture radar (SAR) imagery were investigated. Four interrelated problems were addressed. An optimal tonal SAR image classification algorithm was developed and evaluated. A data compression technique was developed for SAR imagery which is simple and provides a 5:1 compression with acceptable image quality. An optimal textural edge detector was developed. Several SAR image enhancement algorithms have been proposed. The effectiveness of each algorithm was compared quantitatively