Particle Swarm Optimisation for Protein Motif Discovery

In this paper, a modified particle swarm optimisation algorithm is proposed for protein sequence motif discovery. Protein sequences are represented as a chain of symbols and a protein sequence motif is a short sequence that exists in most of the protein sequence families. Protein sequence symbols are converted into numbers using a one to one amino acid translation table. The simulation uses EGF protein and C2H2 Zinc Finger protein families obtained from the PROSITE database. Simulation results show that the modified particle swarm optimisation algorithm is effective in obtaining global optimum sequence patterns, achieving 96.9 and 99.5 classification accuracy respectively in EGF and C2H2 Zinc Finger protein families. A better true positive hit result is achieved when compared to the motifs published in PROSITE database.     

Manage Sewer In-Line Storage Control Using Hydraulic Model and Recurrent Neural Network

This paper described manage sewer in-line storage control for the city of Drammen, Norway. The purpose of the control is to use the free space of the pipes to reduce overflow at the wastewater treatment plant (WWTP). This study combined the powerful sides of the hydraulic model and neural networks. A detailed hydraulic model was developed to identify which part of the sewer system have more free space. Subsequently, the effectiveness of the proposed control solution was tested. Simulation results showed that intentionally control sewer with free space could significantly reduce overflow at the WWTP. At last, in order to enhance better decision making and give enough response time for the proposed control solution, Recurrent Neural Network (RNN) was employed to forecast flow. Three RNN architectures, namely Elman, NARX (nonlinear autoregressive network with exogenous inputs) and a novel architecture of neural networks, LSTM (Long Short-Term Memory), were compared. The LSTM exhibits the superior capability for time series prediction.     

Self-organizing hierarchical particle swarm optimizer with time-varying acceleration coefficients

This paper introduces a novel parameter automation strategy for the particle swarm algorithm and two further extensions to improve its performance after a predefined number of generations. Initially, to efficiently control the local search and convergence to the global optimum solution, time-varying acceleration coefficients (TVAC) are introduced in addition to the time-varying inertia weight factor in particle swarm optimization (PSO). From the basis of TVAC, two new strategies are discussed to improve the performance of the PSO. First, the concept of "mutation" is introduced to the particle swarm optimization along with TVAC (MPSO-TVAC), by adding a small perturbation to a randomly selected modulus of the velocity vector of a random particle by predefined probability. Second, we introduce a novel particle swarm concept "self-organizing hierarchical particle swarm optimizer with TVAC (HPSO-TVAC)". Under this method, only the "social" part and the "cognitive" part of the particle swarm strategy are considered to estimate the new velocity of each particle and particles are reinitialized whenever they are stagnated in the search space. In addition, to overcome the difficulties of selecting an appropriate mutation step size for different problems, a time-varying mutation step size was introduced. Further, for most of the benchmarks, mutation probability is found to be insensitive to the performance of MPSO-TVAC method. On the other hand, the effect of reinitialization velocity on the performance of HPSO-TVAC method is also observed. Time-varying reinitialization step size is found to be an efficient parameter optimization strategy for HPSO-TVAC method. The HPSO-TVAC strategy outperformed all the methods considered in this investigation for most of the functions. Furthermore, it has also been observed that both the MPSO and HPSO strategies perform poorly when the acceleration coefficients are fixed at two.