A Seeded Genetic Algorithm for RNA Secondary Structural Prediction with Pseudoknots

This work explores a new approach in using genetic algorithm to predict RNA secondary structures with pseudoknots. Since only a small portion of most RNA structures is comprised of pseudoknots, the majority of structural elements from an optimal pseudoknot-free structure are likely to be part of the true structure. Thus seeding the genetic algorithm with optimal pseudoknot-free structures will more likely lead it to the true structure than a randomly generated population. The genetic algorithm uses the known energy models with an additional augmentation to allow complex pseudoknots. The nearest-neighbor energy model is used in conjunction with Turner’s thermodynamic parameters for pseudoknot-free structures, and the H-type pseudoknot energy estimation for simple pseudoknots. Testing with known pseudoknot sequences from PseudoBase shows that it out performs some of the current popular algorithms

Two-Timescale Learning Using Idiotypic Behaviour Mediation For A Navigating Mobile Robot

A combined Short-Term Learning (STL) and Long-Term Learning (LTL) approach to solving mobile-robot navigation problems is presented and tested in both the real and virtual domains. The LTL phase consists of rapid simulations that use a Genetic Algorithm to derive diverse sets of behaviours, encoded as variable sets of attributes, and the STL phase is an idiotypic Artificial Immune System. Results from the LTL phase show that sets of behaviours develop very rapidly, and significantly greater diversity is obtained when multiple autonomous populations are used, rather than a single one. The architecture is assessed under various scenarios, including removal of the LTL phase and switching off the idiotypic mechanism in the STL phase. The comparisons provide substantial evidence that the best option is the inclusion of both the LTL phase and the idiotypic system. In addition, this paper shows that structurally different environments can be used for the two phases without compromising transferability.Comment: 40 pages, 12 tables, Journal of Applied Soft Computin

Adapting kk-means algorithms for outliers

This paper shows how to adapt several simple and classical sampling-based algorithms for the $k$-means problem to the setting with outliers. Recently, Bhaskara et al. (NeurIPS 2019) showed how to adapt the classical $k$-means++ algorithm to the setting with outliers. However, their algorithm needs to output $O(\log (k) \cdot z)$ outliers, where $z$ is the number of true outliers, to match the $O(\log k)$-approximation guarantee of $k$-means++. In this paper, we build on their ideas and show how to adapt several sequential and distributed $k$-means algorithms to the setting with outliers, but with substantially stronger theoretical guarantees: our algorithms output $(1+\varepsilon)z$ outliers while achieving an $O(1 / \varepsilon)$-approximation to the objective function. In the sequential world, we achieve this by adapting a recent algorithm of Lattanzi and Sohler (ICML 2019). In the distributed setting, we adapt a simple algorithm of Guha et al. (IEEE Trans. Know. and Data Engineering 2003) and the popular $k$-means$\|$ of Bahmani et al. (PVLDB 2012). A theoretical application of our techniques is an algorithm with running time $\tilde{O}(nk^2/z)$ that achieves an $O(1)$-approximation to the objective function while outputting $O(z)$ outliers, assuming $k \ll z \ll n$. This is complemented with a matching lower bound of $\Omega(nk^2/z)$ for this problem in the oracle model

Optimized battery sizing for merchant solar PV capacity firming in different electricity markets

Comunicació presentada a IECON 2019 - 45th Annual Conference of the IEEE Industrial Electronics Society (Lisbon, Portugal 14-17 Oct. 2019)This work analyses the minimum energy capacity requirements to be demanded to battery energy storage systems used in megawatt-range merchant solar PV plants to grant capacity firming. The operation of such a plant is simulated (with a 2-minute time step, at three different locations of the Iberian Peninsula, and for different battery sizes) after solving a quadratic programming optimization problem. The control algorithm takes into account the irradiance forecast and the intraday electricity market configuration, which presents certain peculiarities in the Iberian region with regard to other European markets. The analysis has been performed in an annual basis and current irradiance measured values have been used

Cost-Sensitive Classification: Empirical Evaluation of a Hybrid Genetic Decision Tree Induction Algorithm

This paper introduces ICET, a new algorithm for cost-sensitive classification. ICET uses a genetic algorithm to evolve a population of biases for a decision tree induction algorithm. The fitness function of the genetic algorithm is the average cost of classification when using the decision tree, including both the costs of tests (features, measurements) and the costs of classification errors. ICET is compared here with three other algorithms for cost-sensitive classification - EG2, CS-ID3, and IDX - and also with C4.5, which classifies without regard to cost. The five algorithms are evaluated empirically on five real-world medical datasets. Three sets of experiments are performed. The first set examines the baseline performance of the five algorithms on the five datasets and establishes that ICET performs significantly better than its competitors. The second set tests the robustness of ICET under a variety of conditions and shows that ICET maintains its advantage. The third set looks at ICET's search in bias space and discovers a way to improve the search.Comment: See http://www.jair.org/ for any accompanying file

Comparison of Methods of Pump Scheduling in Water Supply Systems

In the domestic water supply industry, the reduction of pumping costs is a continuing objective. With the efficient scheduling of pumping operations, it is considered that 10% of the annual expenditure on energy and related costs may be saved. A typical cost function will include all of the expenditure caused by the pumping process and also consider the electrical cost of pumping taking into account the various electrical tariffs, as well as peak demand and pump switching costs. Using only fixed speed pumps, it is possible to use an efficient dynamic programming based method, provided that the storage reservoir levels are known. Other techniques that are showing fruitful results in optimisation are genetic programming and simulated annealing. This paper compares these methods and discusses which is more appropriate in this type of pump scheduling problem