Phylogenetic inference's algorithms

Phylogenetic inference consist in the search of an evolutionary tree to explain the best way possible genealogical relationships of a set of species. Phylogenetic analysis has a large number of applications in areas such as biology, ecology, paleontology, etc. There are several criterias which has been defined in order to infer phylogenies, among which are the maximum parsimony and maximum likelihood. The first one tries to find the phylogenetic tree that minimizes the number of evolutionary steps needed to describe the evolutionary history among species, while the second tries to find the tree that has the highest probability of produce the observed data according to an evolutionary model. The search of a phylogenetic tree can be formulated as a multi-objective optimization problem, which aims to find trees which satisfy simultaneously (and as much as possible) both criteria of parsimony and likelihood. Due to the fact that these criteria are different there won't be a single optimal solution (a single tree), but a set of compromise solutions. The solutions of this set are called "Pareto Optimal". To find this solutions, evolutionary algorithms are being used with success nowadays.This algorithms are a family of techniques, which aren’t exact, inspired by the process of natural selection. They usually find great quality solutions in order to resolve convoluted optimization problems. The way this algorithms works is based on the handling of a set of trial solutions (trees in the phylogeny case) using operators, some of them exchanges information between solutions, simulating DNA crossing, and others apply aleatory modifications, simulating a mutation. The result of this algorithms is an approximation to the set of the “Pareto Optimal” which can be shown in a graph with in order that the expert in the problem (the biologist when we talk about inference) can choose the solution of the commitment which produces the higher interest. In the case of optimization multi-objective applied to phylogenetic inference, there is open source software tool, called MO-Phylogenetics, which is designed for the purpose of resolving inference problems with classic evolutionary algorithms and last generation algorithms. REFERENCES [1] C.A. Coello Coello, G.B. Lamont, D.A. van Veldhuizen. Evolutionary algorithms for solving multi-objective problems. Spring. Agosto 2007 [2] C. Zambrano-Vega, A.J. Nebro, J.F Aldana-Montes. MO-Phylogenetics: a phylogenetic inference software tool with multi-objective evolutionary metaheuristics. Methods in Ecology and Evolution. En prensa. Febrero 2016.

Two near-optimal layouts for trusslike bridge structures bearing uniform weight between supports

Although the primary objective on designing a structure is to support the external loads, the achievement of an optimal layout that reduces all costs associated with the structure is an aspect of increasing interest. The problem of finding the optimal layout for bridgelike structures subjected to a uniform load is considered. The problem is formulated following a theory on economy of frame structures, using the stress volume as the objective function and including the selection of appropriate values for statically indeterminate reactions. It is solved in a function space of finite dimension instead of using a general variational approach, obtaining near-optimal solutions. The results obtained with this profitable strategy are very close to the best layouts known to date, with differences of less than 2% for the stress volume, but with a simpler layout that can be recognized in some real bridges. This strategy could be a guide to preliminary design of bridges subject to a wide class of costs.

Exact solutions for the agricultural and the two-dimensional packing problems

Objectives and study method: The objective of this study is to develop exact algorithms that can be used as management tools for the agricultural production planning and to obtain exact solutions for two of the most well known twodimensional packing problems: the strip packing problem and the bin packing problem. For the agricultural production planning problem we propose a new hierarchical scheme of three stages to improve the current agricultural practices. The objective of the first stage is to delineate rectangular and homogeneous management zones into the farmer’s plots considering the physical and chemical soil properties. This is an important task because the soil properties directly affect the agricultural production planning. The methodology for this stage is based on a new method called “Positions and Covering” that first generates all the possible positions in which the plot can be delineated. Then, we use a mathematical model of linear programming to obtain the optimal physical and chemical management zone delineation of the plot. In the second stage the objective is to determine the optimal crop pattern that maximizes the farmer’s profit taken into account the previous management zones delineation. In this case, the crop pattern is affected by both management zones delineation, physical and chemical. A mixed integer linear programming is used to solve this stage. The objective of the last stage is to determine in real-time the amount of water to irrigate in each crop. This stage takes as input the solution of the crop planning stage, the atmospheric conditions (temperature, radiation, etc.), the humidity level in plots, and the physical management zones of plots, just to name a few. This procedure is made in real-time during each irrigation period. A linear programming is used to solve this problem. A breakthrough happen when we realize that we could propose some adaptations of the P&C methodology to obtain optimal solutions for the two-dimensional packing problem and the strip packing. We empirically show that our methodologies are efficient on instances based on real data for both problems: agricultural and two-dimensional packing problems. Contributions and conclusions: The exact algorithms showed in this study can be used in the making-decision support for agricultural planning and twodimensional packing problems. For the agricultural planning problem, we show that the implementation of the new hierarchical approach can improve the farmer profit between 5.27% until 8.21% through the optimization of the natural resources. An important characteristic of this problem is that the soil properties (physical and chemical) and the real-time factors (climate, humidity level, evapotranspiration, etc.) are incorporated. With respect to the two-dimensional packing problems, one of the main contributions of this study is the fact that we have demonstrate that many of the best solutions founded in literature by others approaches (heuristics approaches) are the optimal solutions. This is very important because some of these solutions were up to now not guarantee to be the optimal solutions.

Multi-objective optimization of material model parameters of an adhesive layer by using SPEA2

The usage of multi material structures in industry, especially in the automotive industry are increasing. To overcome the difficulties in joining these structures, adhesives have several benefits over traditional joining methods. Therefore, accurate simulations of the entire process of fracture including the adhesive layer is crucial. In this paper, material parameters of a previously developed meso mechanical finite element (FE) model of a thin adhesive layer are optimized using the Strength Pareto Evolutionary Algorithm (SPEA2). Objective functions are defined as the error between experimental data and simulation data. The experimental data is provided by previously performed experiments where an adhesive layer was loaded in monotonically increasing peel and shear. Two objective functions are dependent on 9 model parameters (decision variables) in total and are evaluated by running two FEsimulations, one is loading the adhesive layer in peel and the other in shear. The original study converted the two objective functions into one function that resulted in one optimal solution. In this study, however, a Pareto frontis obtained by employing the SPEA2 algorithm. Thus, more insight into the material model, objective functions, optimal solutions and decision space is acquired using the Pareto front. We compare the results and show good agreement with the experimental data.

Knowledge discovery for adaptive negotiation agents in e-marketplaces

Intelligent software agents are promising in improving the effectiveness of e-marketplaces for e-commerce. Although a large amount of research has been conducted to develop negotiation protocols and mechanisms for e-marketplaces, existing negotiation mechanisms are weak in dealing with complex and dynamic negotiation spaces often found in e-commerce. This paper illustrates a novel knowledge discovery method and a probabilistic negotiation decision making mechanism to improve the performance of negotiation agents. Our preliminary experiments show that the probabilistic negotiation agents empowered by knowledge discovery mechanisms are more effective and efficient than the Pareto optimal negotiation agents in simulated e-marketplaces.

Robot path planning in dynamic environments using a simulated annealing based approach

Mobile robots are widely used in many industrial fields. Research on path planning for mobile robots is one of the most important aspects in mobile robots research. Path planning for a mobile robot is to find a collision-free route, through the robot’s environment with obstacles, from a specified start location to a desired goal destination while satisfying certain optimization criteria. Most of the existing path planning methods, such as the visibility graph, the cell decomposition, and the potential field are designed with the focus on static environments, in which there are only stationary obstacles. However, in practical systems such as Marine Science Research, Robots in Mining Industry, and RoboCup games, robots usually face dynamic environments, in which both moving and stationary obstacles exist. Because of the complexity of the dynamic environments, research on path planning in the environments with dynamic obstacles is limited. Limited numbers of papers have been published in this area in comparison with hundreds of reports on path planning in stationary environments in the open literature. Recently, a genetic algorithm based approach has been introduced to plan the optimal path for a mobile robot in a dynamic environment with moving obstacles. However, with the increase of the number of the obstacles in the environment, and the changes of the moving speed and direction of the robot and obstacles, the size of the problem to be solved increases sharply. Consequently, the performance of the genetic algorithm based approach deteriorates significantly. This motivates the research of this work. This research develops and implements a simulated annealing algorithm based approach to find the optimal path for a mobile robot in a dynamic environment with moving obstacles. The simulated annealing algorithm is an optimization algorithm similar to the genetic algorithm in principle. However, our investigation and simulations have indicated that the simulated annealing algorithm based approach is simpler and easier to implement. Its performance is also shown to be superior to that of the genetic algorithm based approach in both online and offline processing times as well as in obtaining the optimal solution for path planning of the robot in the dynamic environment. The first step of many path planning methods is to search an initial feasible path for the robot. A commonly used method for searching the initial path is to randomly pick up some vertices of the obstacles in the search space. This is time consuming in both static and dynamic path planning, and has an important impact on the efficiency of the dynamic path planning. This research proposes a heuristic method to search the feasible initial path efficiently. Then, the heuristic method is incorporated into the proposed simulated annealing algorithm based approach for dynamic robot path planning. Simulation experiments have shown that with the incorporation of the heuristic method, the developed simulated annealing algorithm based approach requires much shorter processing time to get the optimal solutions in the dynamic path planning problem. Furthermore, the quality of the solution, as characterized by the length of the planned path, is also improved with the incorporated heuristic method in the simulated annealing based approach for both online and offline path planning.

A grouping model for distributed pipeline assets maintenance decision

Distributed pipeline assets systems are crucial to society. The deterioration of these assets and the optimal allocation of limited budget for their maintenance correspond to crucial challenges for water utility managers. Decision makers should be assisted with optimal solutions to select the best maintenance plan concerning available resources and management strategies. Much research effort has been dedicated to the development of optimal strategies for maintenance of water pipes. Most of the maintenance strategies are intended for scheduling individual water pipe. Consideration of optimal group scheduling replacement jobs for groups of pipes or other linear assets has so far not received much attention in literature. It is a common practice that replacement planners select two or three pipes manually with ambiguous criteria to group into one replacement job. This is obviously not the best solution for job grouping and may not be cost effective, especially when total cost can be up to multiple million dollars. In this paper, an optimal group scheduling scheme with three decision criteria for distributed pipeline assets maintenance decision is proposed. A Maintenance Grouping Optimization (MGO) model with multiple criteria is developed. An immediate challenge of such modeling is to deal with scalability of vast combinatorial solution space. To address this issue, a modified genetic algorithm is developed together with a Judgment Matrix. This Judgment Matrix is corresponding to various combinations of pipe replacement schedules. An industrial case study based on a section of a real water distribution network was conducted to test the new model. The results of the case study show that new schedule generated a significant cost reduction compared with the schedule without grouping pipes.

Active transonic aerofoil design optimization using robust multiobjective evolutionary algorithms

The use of adaptive wing/aerofoil designs is being considered, as they are promising techniques in aeronautic/ aerospace since they can reduce aircraft emissions and improve aerodynamic performance of manned or unmanned aircraft. This paper investigates the robust design and optimization for one type of adaptive techniques: active flow control bump at transonic flow conditions on a natural laminar flow aerofoil. The concept of using shock control bump is to control supersonic flow on the suction/pressure side of natural laminar flow aerofoil that leads to delaying shock occurrence (weakening its strength) or boundary layer separation. Such an active flow control technique reduces total drag at transonic speeds due to reduction of wave drag. The location of boundary-layer transition can influence the position and structure of the supersonic shock on the suction/pressure side of aerofoil. The boundarylayer transition position is considered as an uncertainty design parameter in aerodynamic design due to the many factors, such as surface contamination or surface erosion. This paper studies the shock-control-bump shape design optimization using robust evolutionary algorithms with uncertainty in boundary-layer transition locations. The optimization method is based on a canonical evolution strategy and incorporates the concepts of hierarchical topology, parallel computing, and asynchronous evaluation. The use of adaptive wing/aerofoil designs is being considered, as they are promising techniques in aeronautic/ aerospace since they can reduce aircraft emissions and improve aerodynamic performance of manned or unmanned aircraft. This paper investigates the robust design and optimization for one type of adaptive techniques: active flow control bump at transonic flow conditions on a natural laminar flow aerofoil. The concept of using shock control bump is to control supersonic flow on the suction/pressure side of natural laminar flow aerofoil that leads to delaying shock occurrence (weakening its strength) or boundary-layer separation. Such an active flow control technique reduces total drag at transonic speeds due to reduction of wave drag. The location of boundary-layer transition can influence the position and structure of the supersonic shock on the suction/pressure side of aerofoil. The boundarylayer transition position is considered as an uncertainty design parameter in aerodynamic design due to the many factors, such as surface contamination or surface erosion. This paper studies the shock-control-bump shape design optimization using robust evolutionary algorithms with uncertainty in boundary-layer transition locations. The optimization method is based on a canonical evolution strategy and incorporates the concepts of hierarchical topology, parallel computing, and asynchronous evaluation. Two test cases are conducted: the first test assumes the boundary-layer transition position is at 45% of chord from the leading edge, and the second test considers robust design optimization for the shock control bump at the variability of boundary-layer transition positions. The numerical result shows that the optimization method coupled to uncertainty design techniques produces Pareto optimal shock-control-bump shapes, which have low sensitivity and high aerodynamic performance while having significant total drag reduction.

Adaptive wing/aerofoil design optimisation using MOEA coupled to uncertainty design method

The use of adaptive wing/aerofoil designs is being considered as promising techniques in aeronautic/aerospace since they can reduce aircraft emissions, improve aerodynamic performance of manned or unmanned aircraft. The paper investigates the robust design and optimisation for one type of adaptive techniques; Active Flow Control (AFC) bump at transonic flow conditions on a Natural Laminar Flow (NLF) aerofoil designed to increase aerodynamic efficiency (especially high lift to drag ratio). The concept of using Shock Control Bump (SCB) is to control supersonic flow on the suction/pressure side of NLF aerofoil: RAE 5243 that leads to delaying shock occurrence or weakening its strength. Such AFC technique reduces total drag at transonic speeds due to reduction of wave drag. The location of Boundary Layer Transition (BLT) can influence the position the supersonic shock occurrence. The BLT position is an uncertainty in aerodynamic design due to the many factors, such as surface contamination or surface erosion. The paper studies the SCB shape design optimisation using robust Evolutionary Algorithms (EAs) with uncertainty in BLT positions. The optimisation method is based on a canonical evolution strategy and incorporates the concepts of hierarchical topology, parallel computing and asynchronous evaluation. Two test cases are conducted; the first test assumes the BLT is at 45% of chord from the leading edge and the second test considers robust design optimisation for SCB at the variability of BLT positions and lift coefficient. Numerical result shows that the optimisation method coupled to uncertainty design techniques produces Pareto optimal SCB shapes which have low sensitivity and high aerodynamic performance while having significant total drag reduction.

The RatSLAM project : robot spatial navigation

Rats are superior to the most advanced robots when it comes to creating and exploiting spatial representations. A wild rat can have a foraging range of hundreds of meters, possibly kilometers, and yet the rodent can unerringly return to its home after each foraging mission, and return to profitable foraging locations at a later date (Davis, et al., 1948). The rat runs through undergrowth and pipes with few distal landmarks, along paths where the visual, textural, and olfactory appearance constantly change (Hardy and Taylor, 1980; Recht, 1988). Despite these challenges the rat builds, maintains, and exploits internal representations of large areas of the real world throughout its two to three year lifetime. While algorithms exist that allow robots to build maps, the questions of how to maintain those maps and how to handle change in appearance over time remain open. The robotic approach to map building has been dominated by algorithms that optimise the geometry of the map based on measurements of distances to features. In a robotic approach, measurements of distance to features are taken with range-measuring devices such as laser range finders or ultrasound sensors, and in some cases estimates of depth from visual information. The features are incorporated into the map based on previous readings of other features in view and estimates of self-motion. The algorithms explicitly model the uncertainty in measurements of range and the measurement of self-motion, and use probability theory to find optimal solutions for the geometric configuration of the map features (Dissanayake, et al., 2001; Thrun and Leonard, 2008). Some of the results from the application of these algorithms have been impressive, ranging from three-dimensional maps of large urban strucutures (Thrun and Montemerlo, 2006) to natural environments (Montemerlo, et al., 2003).

Hierarchical robust design optimisation of shock control bump devices for airfoil drag reduction

The paper investigates a detailed Active Shock Control Bump Design Optimisation on a Natural Laminar Flow (NLF) aerofoil; RAE 5243 to reduce cruise drag at transonic flow conditions using Evolutionary Algorithms (EAs) coupled to a robust design approach. For the uncertainty design parameters, the positions of boundary layer transition (xtr) and the coefficient of lift (Cl) are considered (250 stochastic samples in total). In this paper, two robust design methods are considered; the first approach uses a standard robust design method, which evaluates one design model at 250 stochastic conditions for uncertainty. The second approach is the combination of a standard robust design method and the concept of hierarchical (multi-population) sampling (250, 50, 15) for uncertainty. Numerical results show that the evolutionary optimization method coupled to uncertainty design techniques produces useful and reliable Pareto optimal SCB shapes which have low sensitivity and high aerodynamic performance while having significant total drag reduction. In addition,it also shows the benefit of using hierarchical robust method for detailed uncertainty design optimization.

A new approach to automatically producing schedules for cane railways

The scheduling of locomotive movements on cane railways has proven to be a very complex task. Various optimisation methods have been used over the years to try and produce an optimised schedule that eliminates or minimises bin supply delays to harvesters and the factory, while minimising the number of locomotives, locomotive shifts and cane bins, and also the cane age. This paper reports on a new attempt to develop an automatic scheduler using a mathematical model solved using mixed integer programming and constraint programming approaches and blocking parallel job shop scheduling fundamentals. The model solution has been explored using conventional constraint programming search techniques and found to produce a reasonable schedule for small-scale problems with up to nine harvesters. While more effort is required to complete the development of the full model with metaheuristic search techniques, the work completed to date gives confidence that the metaheuristic techniques will provide near optimal solutions in reasonable time.

Genetic algorithms to schedule container transfers at multimodal terminals

Optimising the container transfer schedule at the multimodal terminals is known to be NP-hard, which implies that the best solution becomes computationally infeasible as problem sizes increase. Genetic Algorithm (GA) techniques are used to reduce container handling/transfer times and ships' time at the port by speeding up handling operations. The GA is chosen due to the relatively good results that have been reported even with the simplest GA implementations to obtain near-optimal solutions in reasonable time. Also discussed, is the application of the model to assess the consequences of increased scheduled throughput time as well as different strategies such as the alternative plant layouts, storage policies and number of yard machines. A real data set used for the solution and subsequent sensitivity analysis is applied to the alternative plant layouts, storage policies and number of yard machines.

A human-simulated immune evolutionary computation approach

Premature convergence to local optimal solutions is one of the main difficulties when using evolutionary algorithms in real-world optimization problems. To prevent premature convergence and degeneration phenomenon, this paper proposes a new optimization computation approach, human-simulated immune evolutionary algorithm (HSIEA). Considering that the premature convergence problem is due to the lack of diversity in the population, the HSIEA employs the clonal selection principle of artificial immune system theory to preserve the diversity of solutions for the search process. Mathematical descriptions and procedures of the HSIEA are given, and four new evolutionary operators are formulated which are clone, variation, recombination, and selection. Two benchmark optimization functions are investigated to demonstrate the effectiveness of the proposed HSIEA.

Second international workshop on theory and applications of process visualization

The representation of business process models has been a continuing research topic for many years now. However, many process model representations have not developed beyond minimally interactive 2D icon-based representations of directed graphs and networks, with little or no annotation for information overlays. In addition, very few of these representations have undergone a thorough analysis or design process with reference to psychological theories on data and process visualization. This dearth of visualization research, we believe, has led to problems with BPM uptake in some organizations, as the representations can be difficult for stakeholders to understand, and thus remains an open research question for the BPM community. In addition, business analysts and process modeling experts themselves need visual representations that are able to assist with key BPM life cycle tasks in the process of generating optimal solutions. With the rise of desktop computers and commodity mobile devices capable of supporting rich interactive 3D environments, we believe that much of the research performed in computer human interaction, virtual reality, games and interactive entertainment have much potential in areas of BPM; to engage, provide insight, and to promote collaboration amongst analysts and stakeholders alike. We believe this is a timely topic, with research emerging in a number of places around the globe, relevant to this workshop. This is the second TAProViz workshop being run at BPM. The intention this year is to consolidate on the results of last year's successful workshop by further developing this important topic, identifying the key research topics of interest to the BPM visualization community.