solving global unconstrained optimization problems by symmetry-breaking

IEEE Computer Society; International Association for; Computer and Information Science, ACIS

Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.

A Nondeterministic Minimization Algorithm

The problem of minimizing a multivariate function is recurrent in many disciplines as Physics, Mathematics, Engeneering and, of course, Computer Science. In this paper we describe a simple nondeterministic algorithm which is based on the idea of adaptive noise, and that proved to be particularly effective in the minimization of a class of multivariate, continuous valued, smooth functions, associated with some recent extension of regularization theory by Poggio and Girosi (1990). Results obtained by using this method and a more traditional gradient descent technique are also compared.

Site choices in recreational demand: a matter of utility maximization or regret minimization?

This paper compares the Random Regret Minimization and the Random Utility Maximization models for determining recreational choice. The Random Regret approach is based on the idea that, when choosing, individuals aim to minimize their regret – regret being defined as what one experiences when a non-chosen alternative in a choice set performs better than a chosen one in relation to one or more attributes. The Random Regret paradigm, recently developed in transport economics, presents a tractable, regret-based alternative to the dominant choice paradigm based on Random Utility. Using data from a travel cost study exploring factors that influence kayakers’ site-choice decisions in the Republic of Ireland, we estimate both the traditional Random Utility multinomial logit model (RU-MNL) and the Random Regret multinomial logit model (RR-MNL) to gain more insights into site choice decisions. We further explore whether choices are driven by a utility maximization or a regret minimization paradigm by running a binary logit model to examine the likelihood of the two decision choice paradigms using site visits and respondents characteristics as explanatory variables. In addition to being one of the first studies to apply the RR-MNL to an environmental good, this paper also represents the first application of the RR-MNL to compute the Logsum to test and strengthen conclusions on welfare impacts of potential alternative policy scenarios.

Random Regret Minimization: Exploration of a New Choice Model for Environmental and Resource Economics

This paper introduces the discrete choice model-paradigm of Random Regret Minimization (RRM) to the field of environmental and resource economics. The RRM-approach has been very recently developed in the context of travel demand modelling and presents a tractable, regret-based alternative to the dominant choice-modelling paradigm based on Random Utility Maximization-theory (RUM-theory). We highlight how RRM-based models provide closed form, logit-type formulations for choice probabilities that allow for capturing semi-compensatory behaviour and choice set-composition effects while being equally parsimonious as their utilitarian counterparts. Using data from a Stated Choice-experiment aimed at identifying valuations of characteristics of nature parks, we compare RRM-based models and RUM-based models in terms of parameter estimates, goodness of fit, elasticities and consequential policy implications.

Animal group forces resulting from predator avoidance and competition minimization

A new model to explain animal spacing, based on a trade-off between foraging efficiency and predation risk, is derived from biological principles. The model is able to explain not only the general tendency for animal groups to form, but some of the attributes of real groups. These include the independence of mean animal spacing from group population, the observed variation of animal spacing with resource availability and also with the probability of predation, and the decline in group stability with group size. The appearance of "neutral zones" within which animals are not motivated to adjust their relative positions is also explained. The model assumes that animals try to minimize a cost potential combining the loss of intake rate due to foraging interference and the risk from exposure to predators. The cost potential describes a hypothetical field giving rise to apparent attractive and repulsive forces between animals. Biologically based functions are given for the decline in interference cost and increase in the cost of predation risk with increasing animal separation. Predation risk is calculated from the probabilities of predator attack and predator detection as they vary with distance. Using example functions for these probabilities and foraging interference, we calculate the minimum cost potential for regular lattice arrangements of animals before generalizing to finite-sized groups and random arrangements of animals, showing optimal geometries in each case and describing how potentials vary with animal spacing. (C) 1999 Academic Press.</p>

A biofuel strategy for Ireland with an emphasis on production of biomethane and minimization of land-take

Increasing energy consumption has exerted great pressure on natural resources; this has led to a move towards sustainable energy resources to improve security of supply and to reduce greenhouse gas emissions. However, the rush to the cure may have been made in haste. Biofuels in particular, have a bad press both in terms of competition with good agricultural land for food, and also in terms of the associated energy balance with the whole life cycle analysis of the biofuel system. The emphasis is now very much on sustainable biofuel production; biofuels from wastes and lignocellulosic material are now seen as good sustainable biofuels that affect significantly better greenhouse gas balances as compared with first generation biofuels. Ireland has a significant resource of organic waste that could be a potential source of energy through anaerobic digestion. Ireland has 8% of the cattle population of the EU with less than 1% of the human population; as a result 91% of agricultural land in Ireland is under grass. Residues such as slurries and slaughter waste together with energy crops such as grass have an excellent potential to produce biogas that may be upgraded to biomethane. This biomethane may be used as a natural gas substitute; bio-compressed natural gas may then be an avenue for a biofuel strategy. It is estimated that a maximum potential of 33% of natural gas may be substituted by 2020 with a practical obtainable level of 7.5% estimated. Together with biodiesel from residues the practical obtainable level of this strategy may effect greater than a 5% substitution by energy of transport. The residues considered in this strategy to produce biofuel (excluding grass) have the potential to save 93,000 ha of agricultural land (23% of Irish arable land) when compared to a rapeseed biodiesel strategy. © 2009 Elsevier Ltd. All rights reserved.

Stated choices and benefit estimates in the context of traffic calming schemes:Utility maximization, regret minimization, or both?

This paper proposes a discrete mixture model which assigns individuals, up to a probability, to either a class of random utility (RU) maximizers or a class of random regret (RR) minimizers, on the basis of their sequence of observed choices. Our proposed model advances the state of the art of RU-RR mixture models by (i) adding and simultaneously estimating a membership model which predicts the probability of belonging to a RU or RR class; (ii) adding a layer of random taste heterogeneity within each behavioural class; and (iii) deriving a welfare measure associated with the RU-RR mixture model and consistent with referendum-voting, which is the adequate mechanism of provision for such local public goods. The context of our empirical application is a stated choice experiment concerning traffic calming schemes. We find that the random parameter RU-RR mixture model not only outperforms its fixed coefficient counterpart in terms of fit-as expected-but also in terms of plausibility of membership determinants of behavioural class. In line with psychological theories of regret, we find that, compared to respondents who are familiar with the choice context (i.e. the traffic calming scheme), unfamiliar respondents are more likely to be regret minimizers than utility maximizers. © 2014 Elsevier Ltd.

Risk minimization in logistic processes with oil products

13.Vidovic M., Miljus M., Vlajic J., (2002), "Risk minimization in logistic processes with oil products", Proceedings of the 6th International Conference on Traffic Science, ICTS 2002, Portorož, Slovenia, pp. 568-577;

Toward Unconstrained Ear Recognition From Two-Dimensional Images

Ear recognition, as a biometric, has several advantages. In particular, ears can be measured remotely and are also relatively static in size and structure for each individual. Unfortunately, at present, good recognition rates require controlled conditions. For commercial use, these systems need to be much more robust. In particular, ears have to be recognized from different angles ( poses), under different lighting conditions, and with different cameras. It must also be possible to distinguish ears from background clutter and identify them when partly occluded by hair, hats, or other objects. The purpose of this paper is to suggest how progress toward such robustness might be achieved through a technique that improves ear registration. The approach focuses on 2-D images, treating the ear as a planar surface that is registered to a gallery using a homography transform calculated from scale-invariant feature-transform feature matches. The feature matches reduce the gallery size and enable a precise ranking using a simple 2-D distance algorithm. Analysis on a range of data sets demonstrates the technique to be robust to background clutter, viewing angles up to +/- 13 degrees, and up to 18% occlusion. In addition, recognition remains accurate with masked ear images as small as 20 x 35 pixels.