A Study of Archiving Strategies in Multi-Objective PSO for Molecular Docking

Molecular docking is a complex optimization problem aimed at predicting the position of a ligand molecule in the active site of a receptor with the lowest binding energy. This problem can be formulated as a bi-objective optimization problem by minimizing the binding energy and the Root Mean Square Deviation (RMSD) difference in the coordinates of ligands. In this context, the SMPSO multi-objective swarm-intelligence algorithm has shown a remarkable performance. SMPSO is characterized by having an external archive used to store the non-dominated solutions and also as the basis of the leader selection strategy. In this paper, we analyze several SMPSO variants based on different archiving strategies in the scope of a benchmark of molecular docking instances. Our study reveals that the SMPSOhv, which uses an hypervolume contribution based archive, shows the overall best performance.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

A Pareto-metaheuristic for a bi-objective winner determination problem in a combinatorial reverse auction

The bi-objective winner determination problem (2WDP-SC) of a combinatorial procurement auction for transport contracts comes up to a multi-criteria set covering problem. We are given a set B of bundle bids. A bundle bid b in B consists of a bidding carrier c_b, a bid price p_b, and a set tau_b of transport contracts which is a subset of the set T of tendered transport contracts. Additionally, the transport quality q_t,c_b is given which is expected to be realized when a transport contract t is executed by a carrier c_b. The task of the auctioneer is to find a set X of winning bids (X is subset of B), such that each transport contract is part of at least one winning bid, the total procurement costs are minimized, and the total transport quality is maximized. This article presents a metaheuristic approach for the 2WDP-SC which integrates the greedy randomized adaptive search procedure, large neighborhood search, and self-adaptive parameter setting in order to find a competitive set of non-dominated solutions. The procedure outperforms existing heuristics. Computational experiments performed on a set of benchmark instances show that, for small instances, the presented procedure is the sole approach that succeeds to find all Pareto-optimal solutions. For each of the large benchmark instances, according to common multi-criteria quality indicators of the literature, it attains new best-known solution sets.Pareto optimization; multi-criteria winner determination; combinatorial auction; GRASP; LNS

Semantic variation operators for multidimensional genetic programming

Multidimensional genetic programming represents candidate solutions as sets of programs, and thereby provides an interesting framework for exploiting building block identification. Towards this goal, we investigate the use of machine learning as a way to bias which components of programs are promoted, and propose two semantic operators to choose where useful building blocks are placed during crossover. A forward stagewise crossover operator we propose leads to significant improvements on a set of regression problems, and produces state-of-the-art results in a large benchmark study. We discuss this architecture and others in terms of their propensity for allowing heuristic search to utilize information during the evolutionary process. Finally, we look at the collinearity and complexity of the data representations that result from these architectures, with a view towards disentangling factors of variation in application.Comment: 9 pages, 8 figures, GECCO 201

An Assessment to Benchmark the Seismic Performance of a Code-Conforming Reinforced-Concrete Moment-Frame Building

This report describes a state-of-the-art performance-based earthquake engineering methodology that is used to assess the seismic performance of a four-story reinforced concrete (RC) office building that is generally representative of low-rise office buildings constructed in highly seismic regions of California. This “benchmark” building is considered to be located at a site in the Los Angeles basin, and it was designed with a ductile RC special moment-resisting frame as its seismic lateral system that was designed according to modern building codes and standards. The building’s performance is quantified in terms of structural behavior up to collapse, structural and nonstructural damage and associated repair costs, and the risk of fatalities and their associated economic costs. To account for different building configurations that may be designed in practice to meet requirements of building size and use, eight structural design alternatives are used in the performance assessments. Our performance assessments account for important sources of uncertainty in the ground motion hazard, the structural response, structural and nonstructural damage, repair costs, and life-safety risk. The ground motion hazard characterization employs a site-specific probabilistic seismic hazard analysis and the evaluation of controlling seismic sources (through disaggregation) at seven ground motion levels (encompassing return periods ranging from 7 to 2475 years). Innovative procedures for ground motion selection and scaling are used to develop acceleration time history suites corresponding to each of the seven ground motion levels. Structural modeling utilizes both “fiber” models and “plastic hinge” models. Structural modeling uncertainties are investigated through comparison of these two modeling approaches, and through variations in structural component modeling parameters (stiffness, deformation capacity, degradation, etc.). Structural and nonstructural damage (fragility) models are based on a combination of test data, observations from post-earthquake reconnaissance, and expert opinion. Structural damage and repair costs are modeled for the RC beams, columns, and slabcolumn connections. Damage and associated repair costs are considered for some nonstructural building components, including wallboard partitions, interior paint, exterior glazing, ceilings, sprinkler systems, and elevators. The risk of casualties and the associated economic costs are evaluated based on the risk of structural collapse, combined with recent models on earthquake fatalities in collapsed buildings and accepted economic modeling guidelines for the value of human life in loss and cost-benefit studies. The principal results of this work pertain to the building collapse risk, damage and repair cost, and life-safety risk. These are discussed successively as follows. When accounting for uncertainties in structural modeling and record-to-record variability (i.e., conditional on a specified ground shaking intensity), the structural collapse probabilities of the various designs range from 2% to 7% for earthquake ground motions that have a 2% probability of exceedance in 50 years (2475 years return period). When integrated with the ground motion hazard for the southern California site, the collapse probabilities result in mean annual frequencies of collapse in the range of [0.4 to 1.4]x10 -4 for the various benchmark building designs. In the development of these results, we made the following observations that are expected to be broadly applicable: (1) The ground motions selected for performance simulations must consider spectral shape (e.g., through use of the epsilon parameter) and should appropriately account for correlations between motions in both horizontal directions; (2) Lower-bound component models, which are commonly used in performance-based assessment procedures such as FEMA 356, can significantly bias collapse analysis results; it is more appropriate to use median component behavior, including all aspects of the component model (strength, stiffness, deformation capacity, cyclic deterioration, etc.); (3) Structural modeling uncertainties related to component deformation capacity and post-peak degrading stiffness can impact the variability of calculated collapse probabilities and mean annual rates to a similar degree as record-to-record variability of ground motions. Therefore, including the effects of such structural modeling uncertainties significantly increases the mean annual collapse rates. We found this increase to be roughly four to eight times relative to rates evaluated for the median structural model; (4) Nonlinear response analyses revealed at least six distinct collapse mechanisms, the most common of which was a story mechanism in the third story (differing from the multi-story mechanism predicted by nonlinear static pushover analysis); (5) Soil-foundation-structure interaction effects did not significantly affect the structural response, which was expected given the relatively flexible superstructure and stiff soils. The potential for financial loss is considerable. Overall, the calculated expected annual losses (EAL) are in the range of $52,000 to$97,000 for the various code-conforming benchmark building designs, or roughly 1% of the replacement cost of the building ($8.8M). These losses are dominated by the expected repair costs of the wallboard partitions (including interior paint) and by the structural members. Loss estimates are sensitive to details of the structural models, especially the initial stiffness of the structural elements. Losses are also found to be sensitive to structural modeling choices, such as ignoring the tensile strength of the concrete (40 EAL) or the contribution of the gravity frames to overall building stiffness and strength (15 change in EAL). Although there are a number of factors identified in the literature as likely to affect the risk of human injury during seismic events, the casualty modeling in this study focuses on those factors (building collapse, building occupancy, and spatial location of building occupants) that directly inform the building design process. The expected annual number of fatalities is calculated for the benchmark building, assuming that an earthquake can occur at any time of any day with equal probability and using fatality probabilities conditioned on structural collapse and based on empirical data. The expected annual number of fatalities for the code-conforming buildings ranges between 0.05*10 -2 and 0.21*10 -2 , and is equal to 2.30*10 -2 for a non-code conforming design. The expected loss of life during a seismic event is perhaps the decision variable that owners and policy makers will be most interested in mitigating. The fatality estimation carried out for the benchmark building provides a methodology for comparing this important value for various building designs, and enables informed decision making during the design process. The expected annual loss associated with fatalities caused by building earthquake damage is estimated by converting the expected annual number of fatalities into economic terms. Assuming the value of a human life is$3.5M, the fatality rate translates to an EAL due to fatalities of $3,500 to$5,600 for the code-conforming designs, and $79,800 for the non-code conforming design. Compared to the EAL due to repair costs of the code-conforming designs, which are on the order of$66,000, the monetary value associated with life loss is small, suggesting that the governing factor in this respect will be the maximum permissible life-safety risk deemed by the public (or its representative government) to be appropriate for buildings. Although the focus of this report is on one specific building, it can be used as a reference for other types of structures. This report is organized in such a way that the individual core chapters (4, 5, and 6) can be read independently. Chapter 1 provides background on the performance-based earthquake engineering (PBEE) approach. Chapter 2 presents the implementation of the PBEE methodology of the PEER framework, as applied to the benchmark building. Chapter 3 sets the stage for the choices of location and basic structural design. The subsequent core chapters focus on the hazard analysis (Chapter 4), the structural analysis (Chapter 5), and the damage and loss analyses (Chapter 6). Although the report is self-contained, readers interested in additional details can find them in the appendices

Mutations that Separate the Functions of the Proofreading Subunit of the Escherichia coli Replicase

The dnaQ gene of Escherichia coli encodes the Ɛ subunit of DNA polymerase III, which provides the 3\u27 - 5\u27 exonuclease proofreading activity of the replicative polymerase. Prior studies have shown that loss of Ɛ leads to high mutation frequency, partially constitutive SOS, and poor growth. In addition, a previous study from our laboratory identified dnaQ knockout mutants in a screen for mutants specifically defective in the SOS response after quinolone (nalidixic acid) treatment. To explain these results, we propose a model whereby, in addition to proofreading, Ɛ plays a distinct role in replisome disassembly and/or processing of stalled replication forks. To explore this model, we generated a pentapeptide insertion mutant library of the dnaQgene, along with site-directed mutants, and screened for separation of function mutants. We report the identification of separation of function mutants from this screen, showing that proofreading function can be uncoupled from SOS phenotypes (partially constitutive SOS and the nalidixic acid SOS defect). Surprisingly, the two SOS phenotypes also appear to be separable from each other. These findings support the hypothesis that Ɛ has additional roles aside from proofreading. Identification of these mutants, especially those with normal proofreading but SOS phenotype(s), also facilitates the study of the role of e in SOS processes without the confounding results of high mutator activity associated with dnaQ knockout mutants