Minimizing the average distance to a closest leaf in a phylogenetic tree

When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized "reference sequences" to a smaller subset that is as close as possible on average to a collection of "query sequences" of interest. Such a representative subset can be useful whenever one wishes to find a set of reference sequences that is appropriate to use for comparative analysis of environmentally-derived sequences, such as for selecting "reference tree" sequences for phylogenetic placement of metagenomic reads. In this paper we formalize these problems in terms of the minimization of the Average Distance to the Closest Leaf (ADCL) and investigate algorithms to perform the relevant minimization. We show that the greedy algorithm is not effective, show that a variant of the Partitioning Among Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Using this exact program we note that the performance of PAM appears to be good for simulated trees, and is faster than the exact algorithm for small trees. On the other hand, the exact program gives solutions for all numbers of leaves less than or equal to the given desired number of leaves, while PAM only gives a solution for the pre-specified number of leaves. Via application to real data, we show that the ADCL criterion chooses chimeric sequences less often than random subsets, while the maximization of phylogenetic diversity chooses them more often than random. These algorithms have been implemented in publicly available software.Comment: Please contact us with any comments or questions

Bartering integer commodities with exogenous prices

The analysis of markets with indivisible goods and fixed exogenous prices has played an important role in economic models, especially in relation to wage rigidity and unemployment. This research report provides a mathematical and computational details associated to the mathematical programming based approaches proposed by Nasini et al. (accepted 2014) to study pure exchange economies where discrete amounts of commodities are exchanged at fixed prices. Barter processes, consisting in sequences of elementary reallocations of couple of commodities among couples of agents, are formalized as local searches converging to equilibrium allocations. A direct application of the analyzed processes in the context of computational economics is provided, along with a Java implementation of the approaches described in this research report.Comment: 30 pages, 5 sections, 10 figures, 3 table

Revisiting minimum profit conditions in uniform price day-ahead electricity auctions

We examine the problem of clearing day-ahead electricity market auctions where each bidder, whether a producer or consumer, can specify a minimum profit or maximum payment condition constraining the acceptance of a set of bid curves spanning multiple time periods in locations connected through a transmission network with linear constraints. Such types of conditions are for example considered in the Spanish and Portuguese day-ahead markets. This helps describing the recovery of start-up costs of a power plant, or analogously for a large consumer, utility reduced by a constant term. A new market model is proposed with a corresponding MILP formulation for uniform locational price day-ahead auctions, handling bids with a minimum profit or maximum payment condition in a uniform and computationally-efficient way. An exact decomposition procedure with sparse strengthened Benders cuts derived from the MILP formulation is also proposed. The MILP formulation and the decomposition procedure are similar to computationally-efficient approaches previously proposed to handle so-called block bids according to European market rules, though the clearing conditions could appear different at first sight. Both solving approaches are also valid to deal with both kinds of bids simultaneously, as block bids with a minimum acceptance ratio, generalizing fully indivisible block bids, are but a special case of the MP bids introduced here. We argue in favour of the MP bids by comparing them to previous models for minimum profit conditions proposed in the academic literature, and to the model for minimum income conditions used by the Spanish power exchange OMIE

Differential Evolution for Multiobjective Portfolio Optimization

Financial portfolio optimization is a challenging problem. First, the problem is multiobjective (i.e.: minimize risk and maximize profit) and the objective functions are often multimodal and non smooth (e.g.: value at risk). Second, managers have often to face real-world constraints, which are typically non-linear. Hence, conventional optimization techniques, such as quadratic programming, cannot be used. Stochastic search heuristic can be an attractive alternative. In this paper, we propose a new multiobjective algorithm for portfolio optimization: DEMPO - Differential Evolution for Multiobjective Portfolio Optimization. The main advantage of this new algorithm is its generality, i.e., the ability to tackle a portfolio optimization task as it is, without simplifications. Our empirical results show the capability of our approach of obtaining highly accurate results in very reasonable runtime, in comparison with quadratic programming and another state-of-art search heuristic, the so-called NSGA II.Portfolio Optimization, Multiobjective, Real-world Constraints, Value at Risk, Expected Shortfall, Differential Evolution

Hybrid behavioural-based multi-objective space trajectory optimization

In this chapter we present a hybridization of a stochastic based search approach for multi-objective optimization with a deterministic domain decomposition of the solution space. Prior to the presentation of the algorithm we introduce a general formulation of the optimization problem that is suitable to describe both single and multi-objective problems. The stochastic approach, based on behaviorism, combinedwith the decomposition of the solutions pace was tested on a set of standard multi-objective optimization problems and on a simple but representative case of space trajectory design