One of the critical concerns in wireless sensor networks (WSNs) is the continuous maintenance of sensing coverage. Many particular applications, such as battlefield intrusion detection and object tracking, require a full-coverage at any time, which is typically resolved by adding redundant sensor nodes. With abundant energy, previous studies suggested that the network lifetime can be maximized while maintaining full coverage through organizing sensor nodes into a maximum number of disjoint sets and alternately turning them on. Since the power of sensor nodes is unevenly consumed over time, and early failure of sensor nodes leads to coverage loss, WSNs require dynamic coverage maintenance. Thus, the task of permanently sustaining full coverage is particularly formulated as a hybrid of disjoint set covers and dynamic-coverage-maintenance problems, and both have been proven to be nondeterministic polynomial-complete. In this paper, a hybrid memetic framework for coverage optimization (Hy-MFCO) is presented to cope with the hybrid problem using two major components: 1) a memetic algorithm (MA)-based scheduling strategy and 2) a heuristic recursive algorithm (HRA). First, the MA-based scheduling strategy adopts a dynamic chromosome structure to create disjoint sets, and then the HRA is utilized to compensate the loss of coverage by awaking some of the hibernated nodes in local regions when a disjoint set fails to maintain full coverage. The results obtained from real-world experiments using a WSN test-bed and computer simulations indicate that the proposed Hy-MFCO is able to maximize sensing coverage while achieving energy efficiency at the same time. Moreover, the results also show that the Hy-MFCO significantly outperforms the existing methods with respect to coverage preservation and energy efficiency.

Most alignment algorithms find an initial equivalent residue pair followed by an iterative optimization process to explore better near-optimal alignments in the surrounding solution space of the initial alignment. It plays a decisive role in determining the alignment quality since a poor initial alignment may make the final alignment trapped in an undesirable local optimum even with an iterative optimization. We proposed a vector-based alignment algorithm with a new initial alignment approach accounting for local structure features called MIRAGE-align. The new idea is to enhance the quality of the initial alignment based on encoded local structural alphabets to identify the protein structure pair whose sequence identity falls in or below twilight zone. The statistical analysis of alignment quality based on Match Index (MI) and computation time demonstrated that MIRAGE-align algorithm outperformed four previously published algorithms, i.e., the residue-based algorithm (CE), the vector-based algorithm (SSM), TM-align, and Fr-TM-align. MIRAGE-align yields a better estimate of initial solution to enhance the quality of initial alignment and enable the employment of a non-iterative optimization process to achieve a better alignment.

Wireless real-time surveillance systems are very valuable for monitoring ecology of wildlife, since the in-situ situation could be grasped immediately. Power source is usually constrained in the wild areas. Thus, in this paper, we developed a low power-consumption image transmission system (called energy-efficient visual eyes system) by integrating a MSP430 micro controller, FPGA circuit, a solar powered battery, a digital camera, and a GPRS (General Packet Radio Service) modem. In order to make a monitoring system suitable for circumstances of wild islands, the proposed system is designed with a packet transmitting strategy capable of enhancing pixel validity while effectively decreasing power consumption. Practically, the proposed system is deployed on a wild island in Taiwan near East China Sea, where is a habitat for migrant seabirds. The experimental results show that the system design is feasible to ecological monitoring and able to effectively maintain the completeness of images with energy efficiency.

SUMMARY: Inferring genetic or transcriptional interactions, when done successfully, may provide insights into biological processes or biochemical pathways of interest. Unfortunately, most computational algorithms require a certain level of programming expertise. To provide a simple web interface for users to infer interactions from time course gene expression data, we present WebPARE, which is based on the pattern recognition algorithm (PARE). For expression data, in which each type of interaction (e.g. activator target) and the corresponding paired gene expression pattern are significantly associated, PARE uses a non-linear score to classify gene pairs of interest into a few subclasses of various time lags. In each subclass, PARE learns the parameters in the decision score using known interactions from biological experiments or published literature. Subsequently, the trained algorithm predicts interactions of a similar nature. Previously, PARE was shown to infer two sets of interactions in yeast successfully. Moreover, several predicted genetic interactions coincided with existing pathways; this indicates the potential of PARE in predicting partial pathway components. Given a list of gene pairs or genes of interest and expression data, WebPARE invokes PARE and outputs predicted interactions and their networks in directed graphs.

BACKGROUND: To date, only a limited number of transcriptional regulatory interactions have been uncovered. In a pilot study integrating sequence data with microarray data, a position weight matrix (PWM) performed poorly in inferring transcriptional interactions (TIs), which represent physical interactions between transcription factors (TF) and upstream sequences of target genes. Inferring a TI means that the promoter sequence of a target is inferred to match the consensus sequence motifs of a potential TF, and their interaction type such as AT or RT is also predicted. Thus, a robust PWM (rPWM) was developed to search for consensus sequence motifs. In addition to rPWM, one feature extracted from ChIP-chip data was incorporated to identify potential TIs under specific conditions. An interaction type classifier was assembled to predict activation/repression of potential TIs using microarray data. This approach, combining an adaptive (learning) fuzzy inference system and an interaction type classifier to predict transcriptional regulatory networks, was named AdaFuzzy. RESULTS: AdaFuzzy was applied to predict TIs using real genomics data from Saccharomyces cerevisiae. Following one of the latest advances in predicting TIs, constrained probabilistic sparse matrix factorization (cPSMF), and using 19 transcription factors (TFs), we compared AdaFuzzy to four well-known approaches using over-representation analysis and gene set enrichment analysis. AdaFuzzy outperformed these four algorithms. Furthermore, AdaFuzzy was shown to perform comparably to 'ChIP-experimental method' in inferring TIs identified by two sets of large scale ChIP-chip data, respectively. AdaFuzzy was also able to classify all predicted TIs into one or more of the four promoter architectures. The results coincided with known promoter architectures in yeast and provided insights into transcriptional regulatory mechanisms. CONCLUSION: AdaFuzzy successfully integrates multiple types of data (sequence, ChIP, and microarray) to predict transcriptional regulatory networks. The validated success in the prediction results implies that AdaFuzzy can be applied to uncover TIs in yeast.

A fuzzy logic approach, called FuzzyTRN, to infer transcriptional regulatory networks (TRN) inSaccharomycescerevisiaeis proposed. FuzzyTRN predicts potential regulators and their target genes using sequences analysis on transcription factor binding sites (TFBS) of transcriptional factors (TF) and promoter region of target genes. Those potential regulators and target genes are used to form vertices in the TRN. Furthermore, multiple sets of microarray gene expression data (MGED) are used by FuzzyTRN to predict links in the TRN. FuzzyTRN predicts transcriptional interactions by recognizing expression patterns of genes. In this study, a number of confirmed genetic interactions are utilized to train FuzzyTRN. 112 indirect genetic interactions that were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) experiments, and 259 and 86 direct genetic interactions that were collected by TRANSFAC database and literature surveying, were used as training set in this work. A simulation that encompasses 170 TFs and 40 target genes has been conducted and checked against YEASTRACT database to evaluate the performance of the proposed algorithm.

MOTIVATION: For any time-course microarray data in which the gene interactions and the associated paired patterns are dependent, the proposed pattern recognition (PARE) approach can infer time-lagged genetic interactions, a challenging task due to the small number of time points and large number of genes. PARE utilizes a non-linear score to identify subclasses of gene pairs with different time lags. In each subclass, PARE extracts non-linear characteristics of paired gene-expression curves and learns weights of the decision score applying an optimization algorithm to microarray gene-expression data (MGED) of some known interactions, from biological experiments or published literature. Namely, PARE integrates both MGED and existing knowledge via machine learning, and subsequently predicts the other genetic interactions in the subclass. RESULTS: PARE, a time-lagged correlation approach and the latest advance in graphical Gaussian models were applied to predict 112 (132) pairs of TC/TD (transcriptional regulatory) interactions. Checked against qRT-PCR results (published literature), their true positive rates are 73% (77%), 46% (51%), and 52% (59%), respectively. The false positive rates of predicting TC and TD (AT and RT) interactions in the yeast genome are bounded by 13 and 10% (10 and 14%), respectively. Several predicted TC/TD interactions are shown to coincide with existing pathways involving Sgs1, Srs2 and Mus81. This reinforces the possibility of applying genetic interactions to predict pathways of protein complexes. Moreover, some experimentally testable gene interactions involving DNA repair are predicted. AVAILABILITY: Supplementary data and PARE software are available at http://www.stat.sinica.edu.tw/~gshieh/pare.htm.

A neuro-fuzzy inference system that recognizes the expression patterns of genes in microarray gene expression (MGE) data, called GeneCFE-ANFIS, is proposed to infer gene interactions. In this study, three primary features are utilized to extract genes' expression patterns and used as inputs to neuro-fuzzy inference system. The proposed algorithm learns expression patterns from the known genetic interactions, such as the interactions confirmed by qRT-PCR experiments or collected through text-mining technique by surveying previously published literatures, and then predicts other gene interactions according to the learned patterns. The proposed neuro-fuzzy inference system was applied to a public yeast MGE data set. Two simulations were conducted and checked against 112 pairs of qRT-PCR confirmed gene interactions and 77 TFs pairs collected from literature respectively to evaluate the performance of the proposed algorithm.

A novel method for evolutionary optimization, called integrated radiation optimization (IRO), is proposed for solving nonlinear multidimensional optimization problems. Many modern optimization techniques explore the search space by sharing information they have found. In this study, the con cept of gravitational radiation in Einstein’s theory of general relativity is utilized as a fundamental theory for searching optimal solution in the search space. The idea of developing the algorithm and its detailed procedures are introduced. This work applied the proposed IRO to find the minimum value of a static polynomial function, and some applications that are known to be difficult. The preliminary experimental results show that the performance of the proposed IRO is promising, and IRO shows great performance in solving other NP-hard search and optimization problems.

In this paper, an optimum approach to design PID controllers has been proposed. PID control schema based on classical control theory has been widely used in industrial control processes. Since most of the control systems have nonlinear properties, it is difficult to determine optimal parameters for a given PID controllers. This study utilizes the particle swarm optimization algorithm as solution method to search for PID parameters that capable of minimizing the integral absolute control error. At the same time, the transient response is guaranteed by minimizing the maximum overshoot, settling time, rising time of step response. Moreover, we also utilize ε-constraint method to improve the performance of the controllers. Finally, experimental results demonstrate that better control performance and robustness can be achieved in comparison with known methods.

In this paper, a novel robust unsupervised video object tracking algorithm is proposed. The proposed algorithm combines several techniques: mathematical morphology, region growing, region merging, and trajectory estimation, for tracking several predetermined video objects, simultaneously. A modified mathematical morphological edge detector was employed to sketch the contour of the video frame; and an edge-based object segmentation algorithm was applied to the contour for partitioning the predetermined objects; moreover, according to the motion of the objects, the proposed algorithm can estimate and partition the objects in following video frames, automatically. The proposed algorithm is also robustness against mobile cameras. The experimental results show that the proposed algorithm can precisely partition and track multiple video objects

A new concept for the optimization of nonlinear functions is proposed. For most of the proposed evolutionary optimization algorithms, such as particle swarm optimization and ant colony optimization, they search the solution space by sharing known knowledge. The proposed algorithm is based on the Einstein's general theory of relativity, which we utilize the concept of gravitational field to search for the global optimal solution for a given problem. In this paper, detail procedure of the proposed algorithm is introduced. The proposed algorithm has been tested on an application that is known difficult with promising and exciting results.

In this paper, a novel approach for edge-based image segmentation is proposed. Image segmentation and object extraction play an important role in supporting content-based image coding, indexing, and retrieval. However, it's always a tough task to partition an object in a graph-based image. We proposed an image segmentation algorithm by integrating mathematical morphological edge detector with region growing technique. The images are first enhanced by morphological closing operations, and then detect the edge of the image by morphological dilation residue edge detector. Moreover, we deploy growing seeds into the edge image that obtained by the edge detection procedure. By cross comparing the growing result and the detected edges, the partition lines of the image are generated. In this paper, we presented the theoretical backgrounds and procedure illustrations of the proposed algorithm. Furthermore, the proposed algorithm is implemented in C++ language and evaluate on several images with promising results.