Exploring ant-based algorithms for gene expression data analysis

Objective: Recently, much research has been proposed using nature inspired algorithms to perform complex machine learning tasks. Ant colony optimization (ACO) is one such algorithm based on swarm intelligence and is derived from a model inspired by the collective foraging behavior of ants. Taking advantage of the ACO in traits such as self-organization and robustness, this paper investigates ant-based algorithms for gene expression data clustering and associative classification. Methods and material: An ant-based clustering (Ant-C) and an ant-based association rule mining (Ant-ARM) algorithms are proposed for gene expression data analysis. The proposed algorithms make use of the natural behavior of ants such as cooperation and adaptation to allow for a flexible robust search for a good candidate solution. Results: Ant-C has been tested on the three datasets selected from the Stanford Genomic Resource Database and achieved relatively high accuracy compared to other classical clustering methods. Ant-ARM has been tested on the acute lymphoblastic leukemia (ALL)/acute myeloid leukemia (AML) dataset and generated about 30 classification rules with high accuracy. Conclusions: Ant-C can generate optimal number of clusters without incorporating any other algorithms such as K-means or agglomerative hierarchical clustering. For associative classification, while a few of the well-known algorithms such as Apriori, FP-growth and Magnum Opus are unable to mine any association rules from the ALL/AML dataset within a reasonable period of time, Ant-ARM is able to extract associative classification rules.

Incorporating sentiment prior knowledge for weakly supervised sentiment analysis

This article presents two novel approaches for incorporating sentiment prior knowledge into the topic model for weakly supervised sentiment analysis where sentiment labels are considered as topics. One is by modifying the Dirichlet prior for topic-word distribution (LDA-DP), the other is by augmenting the model objective function through adding terms that express preferences on expectations of sentiment labels of the lexicon words using generalized expectation criteria (LDA-GE). We conducted extensive experiments on English movie review data and multi-domain sentiment dataset as well as Chinese product reviews about mobile phones, digital cameras, MP3 players, and monitors. The results show that while both LDA-DP and LDAGE perform comparably to existing weakly supervised sentiment classification algorithms, they are much simpler and computationally efficient, rendering themmore suitable for online and real-time sentiment classification on the Web. We observed that LDA-GE is more effective than LDA-DP, suggesting that it should be preferred when considering employing the topic model for sentiment analysis. Moreover, both models are able to extract highly domain-salient polarity words from text.

Genetic algorithms for discovery of matrix multiplication methods

We present a parallel genetic algorithm for nding matrix multiplication algo-rithms. For 3 x 3 matrices our genetic algorithm successfully discovered algo-rithms requiring 23 multiplications, which are equivalent to the currently best known human-developed algorithms. We also studied the cases with less mul-tiplications and evaluated the suitability of the methods discovered. Although our evolutionary method did not reach the theoretical lower bound it led to an approximate solution for 22 multiplications.

Evaluation of hemifield sector analysis protocol in multifocal visual evoked potential (MFVEP) objective perimetry for the diagnosis and early detection of glaucomatous field defects

Visual field assessment is a core component of glaucoma diagnosis and monitoring, and the Standard Automated Perimetry (SAP) test is considered up until this moment, the gold standard of visual field assessment. Although SAP is a subjective assessment and has many pitfalls, it is being constantly used in the diagnosis of visual field loss in glaucoma. Multifocal visual evoked potential (mfVEP) is a newly introduced method used for visual field assessment objectively. Several analysis protocols have been tested to identify early visual field losses in glaucoma patients using the mfVEP technique, some were successful in detection of field defects, which were comparable to the standard SAP visual field assessment, and others were not very informative and needed more adjustment and research work. In this study, we implemented a novel analysis approach and evaluated its validity and whether it could be used effectively for early detection of visual field defects in glaucoma. OBJECTIVES: The purpose of this study is to examine the effectiveness of a new analysis method in the Multi-Focal Visual Evoked Potential (mfVEP) when it is used for the objective assessment of the visual field in glaucoma patients, compared to the gold standard technique. METHODS: 3 groups were tested in this study; normal controls (38 eyes), glaucoma patients (36 eyes) and glaucoma suspect patients (38 eyes). All subjects had a two standard Humphrey visual field HFA test 24-2 and a single mfVEP test undertaken in one session. Analysis of the mfVEP results was done using the new analysis protocol; the Hemifield Sector Analysis HSA protocol. Analysis of the HFA was done using the standard grading system. RESULTS: Analysis of mfVEP results showed that there was a statistically significant difference between the 3 groups in the mean signal to noise ratio SNR (ANOVA p<0.001 with a 95% CI). The difference between superior and inferior hemispheres in all subjects were all statistically significant in the glaucoma patient group 11/11 sectors (t-test p<0.001), partially significant 5/11 (t-test p<0.01) and no statistical difference between most sectors in normal group (only 1/11 was significant) (t-test p<0.9). sensitivity and specificity of the HAS protocol in detecting glaucoma was 97% and 86% respectively, while for glaucoma suspect were 89% and 79%. DISCUSSION: The results showed that the new analysis protocol was able to confirm already existing field defects detected by standard HFA, was able to differentiate between the 3 study groups with a clear distinction between normal and patients with suspected glaucoma; however the distinction between normal and glaucoma patients was especially clear and significant. CONCLUSION: The new HSA protocol used in the mfVEP testing can be used to detect glaucomatous visual field defects in both glaucoma and glaucoma suspect patient. Using this protocol can provide information about focal visual field differences across the horizontal midline, which can be utilized to differentiate between glaucoma and normal subjects. Sensitivity and specificity of the mfVEP test showed very promising results and correlated with other anatomical changes in glaucoma field loss.

A near real-time water surface detection method based on HSV transformation of MODIS multi-Spectral time series data

In the face of global population growth and the uneven distribution of water supply, a better knowledge of the spatial and temporal distribution of surface water resources is critical. Remote sensing provides a synoptic view of ongoing processes, which addresses the intricate nature of water surfaces and allows an assessment of the pressures placed on aquatic ecosystems. However, the main challenge in identifying water surfaces from remotely sensed data is the high variability of spectral signatures, both in space and time. In the last 10 years only a few operational methods have been proposed to map or monitor surface water at continental or global scale, and each of them show limitations. The objective of this study is to develop and demonstrate the adequacy of a generic multi-temporal and multi-spectral image analysis method to detect water surfaces automatically, and to monitor them in near-real-time. The proposed approach, based on a transformation of the RGB color space into HSV, provides dynamic information at the continental scale. The validation of the algorithm showed very few omission errors and no commission errors. It demonstrates the ability of the proposed algorithm to perform as effectively as human interpretation of the images. The validation of the permanent water surface product with an independent dataset derived from high resolution imagery, showed an accuracy of 91.5% and few commission errors. Potential applications of the proposed method have been identified and discussed. The methodology that has been developed 27 is generic: it can be applied to sensors with similar bands with good reliability, and minimal effort. Moreover, this experiment at continental scale showed that the methodology is efficient for a large range of environmental conditions. Additional preliminary tests over other continents indicate that the proposed methodology could also be applied at the global scale without too many difficulties

Servitization capabilities for advanced services:a multi-actor perspective

Servitization is the process by which manufacturers add services to their product offerings and even replace products with services. The capabilities necessary to develop and deliver advanced services as part of servitization are often discussed in the literature from the manufacturer’s perspective, e.g., having a service-focused culture or the ability to sell solutions. Recent research has acknowledged the important role of customers and, to a lesser extent, other actors (e.g., intermediaries) in bringing about successful servitization, particularly for use-oriented and results-oriented advanced services. The objective of this study is to identify the capabilities required to successful develop advanced services as part of servitization by considering the perspective of manufacturers, intermediaries and customers. This study involved interviews with 33 managers in 28 large UK-based companies from these three groups, about servitization capabilities. The findings suggest that there are eight broad capabilities that are important for advanced services; 1) personnel with expertise and deep technical product knowledge, 2) methodologies for improving operational processes, helping to manage risk and reduce costs, 3) the evolution from being a product- focused manufacturer to embracing a services culture, 4) developing trusting relationships with other actors in the network to support the delivery of advanced services, 5) new innovation activities focused on financing contracts (e.g., ‘gain share’) and technology implementation (e.g., Web-based applications), 6) customer intimacy through understanding their business challenges in order to develop suitable solutions, 7) extensive infrastructure (e.g., personnel, service centres) to deliver a local service, and 8) the ability to tailor service offerings to each customer’s requirements and deliver these responsively to changing needs. The capabilities required to develop and deliver advanced services align to a need to enhance the operational performance of supplied products throughout their lifecycles and as such require greater investment than the capabilities for base and intermediate services.

Multi-class subcellular location prediction for bacterial proteins

Two algorithms, based onBayesian Networks (BNs), for bacterial subcellular location prediction, are explored in this paper: one predicts all locations for Gram+ bacteria and the other all locations for Gram- bacteria. Methods were evaluated using different numbers of residues (from the N-terminal 10 residues to the whole sequence) and residue representation (amino acid-composition, percentage amino acid-composition or normalised amino acid-composition). The accuracy of the best resulting BN was compared to PSORTB. The accuracy of this multi-location BN was roughly comparable to PSORTB; the difference in predictions is low, often less than 2%. The BN method thus represents both an important new avenue of methodological development for subcellular location prediction and a potentially value new tool of true utilitarian value for candidate subunit vaccine selection.

A diversity dilemma in evolutionary markets

Markets are useful mechanisms for performing resource al- location in fully decentralised computational and other systems, since they can possess a range of desirable properties, such as efficiency, decentralisation, robustness and scalability. In this paper we investigate the behaviour of co-evolving evolutionary market agents as adaptive offer generators for sellers in a multi-attribute posted-offer market. We demonstrate that the evolutionary approach enables sellers to automatically position themselves in market niches, created by heterogeneous buyers. We find that a trade-off exists for the evolutionary sellers between maintaining high population diversity to facilitate movement between niches and low diversity to exploit the current niche and maximise cumulative payoff. We characterise the trade-off from the perspective of the system as a whole, and subsequently from that of an individual seller. Our results highlight a decision on risk aversion for resource providers, but crucially we show that rational self-interested sellers would not adopt the behaviour likely to lead to the ideal result from the system point of view.

Multi-level genetic algorithm for the resource-constrained re-entrant scheduling problem in the flow shop

The re-entrant flow shop scheduling problem (RFSP) is regarded as a NP-hard problem and attracted the attention of both researchers and industry. Current approach attempts to minimize the makespan of RFSP without considering the interdependency between the resource constraints and the re-entrant probability. This paper proposed Multi-level genetic algorithm (GA) by including the co-related re-entrant possibility and production mode in multi-level chromosome encoding. Repair operator is incorporated in the Multi-level genetic algorithm so as to revise the infeasible solution by resolving the resource conflict. With the objective of minimizing the makespan, Multi-level genetic algorithm (GA) is proposed and ANOVA is used to fine tune the parameter setting of GA. The experiment shows that the proposed approach is more effective to find the near-optimal schedule than the simulated annealing algorithm for both small-size problem and large-size problem. © 2013 Published by Elsevier Ltd.

Large scale multi-view stereopsis evaluation

The seminal multiple view stereo benchmark evaluations from Middlebury and by Strecha et al. have played a major role in propelling the development of multi-view stereopsis methodology. Although seminal, these benchmark datasets are limited in scope with few reference scenes. Here, we try to take these works a step further by proposing a new multi-view stereo dataset, which is an order of magnitude larger in number of scenes and with a significant increase in diversity. Specifically, we propose a dataset containing 80 scenes of large variability. Each scene consists of 49 or 64 accurate camera positions and reference structured light scans, all acquired by a 6-axis industrial robot. To apply this dataset we propose an extension of the evaluation protocol from the Middlebury evaluation, reflecting the more complex geometry of some of our scenes. The proposed dataset is used to evaluate the state of the art multiview stereo algorithms of Tola et al., Campbell et al. and Furukawa et al. Hereby we demonstrate the usability of the dataset as well as gain insight into the workings and challenges of multi-view stereopsis. Through these experiments we empirically validate some of the central hypotheses of multi-view stereopsis, as well as determining and reaffirming some of the central challenges.

More than money:developing an integrative multi-factorial measure of entrepreneurial success

This article conceptualises and operationalizes ‘subjective entrepreneurial success’ in a manner which reflects the criteria employed by entrepreneurs, rather than those imposed by researchers. Using two studies, a first qualitative enquiry investigated success definitions using interviews with 185 German entrepreneurs; five factors emerged from their reports: firm performance, workplace relationships, personal fulfilment, community impact, and personal financial rewards. The second study developed a questionnaire, the Subjective Entrepreneurial Success–Importance Scale (SES-IS), to measure these five factors using a sample of 184 entrepreneurs. We provide evidence for the validity of the SES-IS, including establishing systematic relationships of SES-IS with objective indicators of firm success, annual income and entrepreneur satisfaction with life and financial situation. We also provide evidence for the cross-cultural invariance of SES-IS using a sample of Polish entrepreneurs. The quintessence of our studies being that subjective entrepreneurial success is a multi-factorial construct, i.e. entrepreneurs value various indicators of success with money as only one possible option.

Patients' and physicians' experiences of atrial fibrillation consultations and anticoagulation decision-making:a multi-perspective IPA design

OBJECTIVE: To explore patients' and physicians' experiences of atrial fibrillation consultations and oral anticoagulation decision-making. DESIGN: Multi-perspective interpretative phenomenological analyses. METHODS: Participants included small homogeneous subgroups: AF patients who accepted (n=4), refused (n=4), or discontinued (n=3) warfarin, and four physician subgroups (n=4 each group): consultant cardiologists, consultant general physicians, general practitioners and cardiology registrars. Semi-structured interviews were conducted. Transcripts were analysed using multi-perspective IPA analyses to attend to individuals within subgroups and making comparisons within and between groups. RESULTS: Three themes represented patients' experiences: Positioning within the physician-patient dyad, Health-life balance, and Drug myths and fear of stroke. Physicians' accounts generated three themes: Mechanised metaphors and probabilities, Navigating toward the 'right' decision, and Negotiating systemic factors. CONCLUSIONS: This multi-perspective IPA design facilitated an understanding of the diagnostic consultation and treatment decision-making which foregrounded patients' and physicians' experiences. We drew on Habermas' theory of communicative action to recommend broadening the content within consultations and shifting the focus to patients' life contexts. Interventions including specialist multidisciplinary teams, flexible management in primary care, and multifaceted interventions for information provision may enable the creation of an environment that supports genuine patient involvement and participatory decision-making.

Amplification schemes and multi-channel DBP for unrepeatered transmission

The performance of unrepeatered transmission of a seven Nyquist-spaced 10 GBd PDM-16QAM superchannel using full signal band coherent detection and multi-channel digital back propagation (MC-DBP) to mitigate nonlinear effects is analysed. For the first time in unrepeatered transmission, the performance of two amplification systems is investigated and directly compared in terms of achievable information rates (AIRs): 1) erbium-doped fibre amplifier (EDFA) and 2) second-order bidirectional Raman pumped amplification. The experiment is performed over different span lengths, demonstrating that, for an AIR of 6.8 bit/s/Hz, the Raman system enables an increase of 93 km (36 %) in span length. Further, at these distances, MC-DBP gives an improvement in AIR of 1 bit/s/Hz (to 7.8 bit/s/Hz) for both amplification schemes. The theoretical AIR gains for Raman and MC-DBP are shown to be preserved when considering low-density parity-check codes. Additionally, MC-DBP algorithms for both amplification schemes are compared in terms of performance and computational complexity. It is shown that to achieve the maximum MC-DBP gain, the Raman system requires approximately four times the computational complexity due to the distributed impact of fibre nonlinearity.

Analyzing evacuation decisions using multi-attribute utility theory (MAUT)

Emergency managers are faced with critical evacuation decisions. These decisions must balance conflicting objectives as well as high levels of uncertainty. Multi-Attribute Utility Theory (MAUT) provides a framework through which objective trade-offs can be analyzed to make optimal evacuation decisions. This paper is the result of data gathered during the European Commission Project, Evacuation Responsiveness by Government Organizations (ERGO) and outlines a preliminary decision model for the evacuation decision. The illustrative model identifies levels of risk at which point evacuation actions should be taken by emergency managers in a storm surge scenario with forecasts at 12 and 9 hour intervals. The results illustrate how differences in forecast precision affect the optimal evacuation decision. Additional uses for this decision model are also discussed along with improvements to the model through future ERGO data-gathering.

Matching theory based travel plan aware charging algorithms in V2G smart grid networks

The frequency, time and places of charging have large impact on the Quality of Experience (QoE) of EV drivers. It is critical to design effective EV charging scheduling system to improve the QoE of EV drivers. In order to improve EV charging QoE and utilization of CSs, we develop an innovative travel plan aware charging scheduling scheme for moving EVs to be charged at Charging Stations (CS). In the design of the proposed charging scheduling scheme for moving EVs, the travel routes of EVs and the utility of CSs are taken into consideration. The assignment of EVs to CSs is modeled as a two-sided many-to-one matching game with the objective of maximizing the system utility which reflects the satisfactory degrees of EVs and the profits of CSs. A Stable Matching Algorithm (SMA) is proposed to seek stable matching between charging EVs and CSs. Furthermore, an improved Learning based On-LiNe scheduling Algorithm (LONA) is proposed to be executed by each CS in a distributed manner. The performance gain of the average system utility by the SMA is up to 38.2% comparing to the Random Charging Scheduling (RCS) algorithm, and 4.67% comparing to Only utility of Electric Vehicle Concerned (OEVC) scheme. The effectiveness of the proposed SMA and LONA is also demonstrated by simulations in terms of the satisfactory ratio of charging EVs and the the convergence speed of iteration.