Naive Bayes ant colony optimization for designing high dimensional experiments

In a large number of experimental problems, high dimensionality of the search area and economical constraints can severely limit the number of experimental points that can be tested. Within these constraints, classical optimization techniques perform poorly, in particular, when little a priori knowledge is available. In this work we investigate the possibility of combining approaches from statistical modeling and bio-inspired algorithms to effectively explore a huge search space, sampling only a limited number of experimental points. To this purpose, we introduce a novel approach, combining ant colony optimization (ACO) and naive Bayes classifier (NBC) that is, the naive Bayes ant colony optimization (NACO) procedure. We compare NACO with other similar approaches developing a simulation study. We then derive the NACO procedure with the goal to design artificial enzymes with no sequence homology to the extant one. Our final aim is to mimic the natural fold of 200 amino acids 1AGY serine esterase from Fusarium solani

The cross-entropy method for continuous multi-extremal optimization

In recent years, the cross-entropy method has been successfully applied to a wide range of discrete optimization tasks. In this paper we consider the cross-entropy method in the context of continuous optimization. We demonstrate the effectiveness of the cross-entropy method for solving difficult continuous multi-extremal optimization problems, including those with non-linear constraints

Dispersive flies optimisation and medical imaging

One of the main sources of inspiration for techniques applicable to complex search space and optimisation problems is nature. This paper introduces a new metaheuristic—Dispersive Flies Optimisation (DFO)—whose inspiration is beckoned from the swarming behaviour of flies over food sources in nature. The simplicity of the algorithm facilitates the analysis of its behaviour. A series of experimental trials confirms the promising performance of the optimiser over a set of benchmarks, as well as its competitiveness when compared against three other well-known population based algorithms. The convergence-independent diversity of DFO algorithm makes it a potentially suitable candidate for dynamically changing environment. In addition to diversity, the performance of the newly introduced algorithm is investigated using the three performance measures of accuracy, efficiency and reliability and its outperformance is demonstrated in the paper. Then the proposed swarm intelligence algorithm is used as a tool to identify microcalcifications on the mammographs. This algorithm is adapted for this particular purpose and its performance is investigated by running the agents of the swarm intelligence algorithm on sample mammographs whose status have been determined by the experts. Two modes of the algorithms are introduced in the paper, each providing the clinicians with a different set of outputs, highlighting the areas of interest where more attention should be given by those in charge of the care of the patients

Biomarker discovery and redundancy reduction towards classification using a multi-factorial MALDI-TOF MS T2DM mouse model dataset

Diabetes like many diseases and biological processes is not mono-causal. On the one hand multifactorial studies with complex experimental design are required for its comprehensive analysis. On the other hand, the data from these studies often include a substantial amount of redundancy such as proteins that are typically represented by a multitude of peptides. Coping simultaneously with both complexities (experimental and technological) makes data analysis a challenge for Bioinformatics

Ownership and control in a competitive industry

We study a differentiated product market in which an investor initially owns a controlling stake in one of two competing firms and may acquire a non-controlling or a controlling stake in a competitor, either directly using her own assets, or indirectly via the controlled firm. While industry profits are maximized within a symmetric two product monopoly, the investor attains this only in exceptional cases. Instead, she sometimes acquires a noncontrolling stake. Or she invests asymmetrically rather than pursuing a full takeover if she acquires a controlling one. Generally, she invests indirectly if she only wants to affect the product market outcome, and directly if acquiring shares is profitable per se. --differentiated products,separation of ownership and control,private benefits of control

Disaggregation of SMOS soil moisture over West Africa using the Temperature and Vegetation Dryness Index based on SEVIRI land surface parameters

The overarching objective of this study was to produce a disaggregated SMOS Soil Moisture (SM) product using land surface parameters from a geostationary satellite in a region covering a diverse range of ecosystem types. SEVIRI data at 15 minute temporal resolution were used to derive the Temperature and Vegetation Dryness Index (TVDI) that served as SM proxy within the disaggregation process. West Africa (3 N, 26 W; 28 N, 26 E) was selected as a case study as it presents both an important North-South climate gradient and a diverse range of ecosystem types. The main challenge was to set up a methodology applicable over a large area that overcomes the constraints of SMOS (low spatial resolution) and TVDI (requires similar atmospheric forcing and triangular shape formed when plotting morning rise temperature versus fraction of vegetation cover) in order to produce a 0.05 degree resolution disaggregated SMOS SM product at sub-continental scale. Consistent cloud cover appeared as one of the main constraints for deriving TVDI, especially during the rainy season and in the southern parts of the region and a large adjustment window (105x105 SEVIRI pixels) was therefore deemed necessary. Both the original and the disaggregated SMOS SM products described well the seasonal dynamics observed at six locations of in situ observations. However, there was an overestimation in both products for sites in the humid southern regions; most likely caused by the presence of forest. Both TVDI and the associated disaggregated SM product was found to be highly sensitive to algorithm input parameters; especially of conditions of high fraction of vegetation cover. Additionally, seasonal dynamics in TVDI did not follow the seasonal patters of SM. Still, its spatial heterogeneity was found to be a good proxy for disaggregating SMOS SM data; main river networks and spatial patterns of SM extremes (i.e. droughts and floods) not seen in the original SMOS SM product were revealed in the disaggregated SM product for a test case of July-September 2012. The disaggregation methodology thereby successfully increased the spatial resolution of SMOS SM, with potential application for local drought/flood monitoring of importance for the livelihood of the population of West Africa

A Study of Time-Dependent CP-Violating Asymmetries and Flavor Oscillations in Neutral B Decays at the Upsilon(4S)

We present a measurement of time-dependent CP-violating asymmetries in neutral B meson decays collected with the BABAR detector at the PEP-II asymmetric-energy B Factory at the Stanford Linear Accelerator Center. The data sample consists of 29.7 ${\rm fb}^{-1}$ recorded at the $\Upsilon(4S)$ resonance and 3.9 ${\rm fb}^{-1}$ off-resonance. One of the neutral B mesons, which are produced in pairs at the $\Upsilon(4S)$, is fully reconstructed in the CP decay modes $J/\psi K^0_S$, $\psi(2S) K^0_S$, $\chi_{c1} K^0_S$, $J/\psi K^{*0}$ ($K^{*0}\to K^0_S\pi^0$) and $J/\psi K^0_L$, or in flavor-eigenstate modes involving $D^{(*)}\pi/\rho/a_1$ and $J/\psi K^{*0}$ ($K^{*0}\to K^+\pi^-$). The flavor of the other neutral B meson is tagged at the time of its decay, mainly with the charge of identified leptons and kaons. The proper time elapsed between the decays is determined by measuring the distance between the decay vertices. A maximum-likelihood fit to this flavor eigenstate sample finds $\Delta m_d = 0.516\pm 0.016 {\rm (stat)} \pm 0.010 {\rm (syst)} {\rm ps}^{-1}$. The value of the asymmetry amplitude $\sin2\beta$ is determined from a simultaneous maximum-likelihood fit to the time-difference distribution of the flavor-eigenstate sample and about 642 tagged $B^0$ decays in the CP-eigenstate modes. We find $\sin2\beta=0.59\pm 0.14 {\rm (stat)} \pm 0.05 {\rm (syst)}$, demonstrating that CP violation exists in the neutral B meson system. (abridged)Comment: 58 pages, 35 figures, submitted to Physical Review

Inclusive Search for Anomalous Production of High-pT Like-Sign Lepton Pairs in Proton-Antiproton Collisions at sqrt{s}=1.8 TeV

We report on a search for anomalous production of events with at least two charged, isolated, like-sign leptons with pT > 11 GeV/c using a 107 pb^-1 sample of 1.8 TeV ppbar collisions collected by the CDF detector. We define a signal region containing low background from Standard Model processes. To avoid bias, we fix the final cuts before examining the event yield in the signal region using control regions to test the Monte Carlo predictions. We observe no events in the signal region, consistent with an expectation of 0.63^(+0.84)_(-0.07) events. We present 95% confidence level limits on new physics processes in both a signature-based context as well as within a representative minimal supergravity (tanbeta = 3) model.Comment: 15 pages, 4 figures. Minor textual changes, cosmetic improvements to figures and updated and expanded reference