A gradient descent algorithm for minimizing amino acid coupling reactions when synthesizing cyclic-peptide libraries

Combinatorial chemistry has become an invaluable tool in medicinal chemistry for the identification of new drug leads. For example, libraries of predetermined sequences and head-to-tail cyclized peptides are routinely synthesized in our laboratory using the IRORI approach. Such libraries are used as molecular toolkits that enable the development of pharmacophores that define activity and specificity at receptor targets. These libraries can be quite large and difficult to handle, due to physical and chemical constraints imposed by their size. Therefore, smaller sub-libraries are often targeted for synthesis. The number of coupling reactions required can be greatly reduced if the peptides having common amino acids are grouped into the same sub-library (batching). This paper describes a schedule optimizer to minimize the number of coupling reactions by rotating and aligning sequences while simultaneously batching. The gradient descent method thereby reduces the number of coupling reactions required for synthesizing cyclic peptide libraries. We show that the algorithm results in a 75% reduction in the number of coupling reactions for a typical cyclic peptide library.

Computational methods for the detection of facial palsy

We are developing a telemedicine application which offers automated diagnosis of facial (Bell's) palsy through a Web service. We used a test data set of 43 images of facial palsy patients and 44 normal people to develop the automatic recognition algorithm. Three different image pre-processing methods were used. Machine learning techniques (support vector machine, SVM) were used to examine the difference between the two halves of the face. If there was a sufficient difference, then the SVM recognized facial palsy. Otherwise, if the halves were roughly symmetrical, the SVM classified the image as normal. It was found that the facial palsy images had a greater Hamming Distance than the normal images, indicating greater asymmetry. The median distance in the normal group was 331 (interquartile range 277-435) and the median distance in the facial palsy group was 509 (interquartile range 334-703). This difference was significant (P

Efficient spatial clustering algorithm using binary tree

In this paper we present an efficient k-Means clustering algorithm for two dimensional data. The proposed algorithm re-organizes dataset into a form of nested binary tree*. Data items are compared at each node with only two nearest means with respect to each dimension and assigned to the one that has the closer mean. The main intuition of our research is as follows: We build the nested binary tree. Then we scan the data in raster order by in-order traversal of the tree. Lastly we compare data item at each node to the only two nearest means to assign the value to the intendant cluster. In this way we are able to save the computational cost significantly by reducing the number of comparisons with means and also by the least use to Euclidian distance formula. Our results showed that our method can perform clustering operation much faster than the classical ones. © Springer-Verlag Berlin Heidelberg 2005

A genetic algorithm based method for deregulated electricity market dispatch

In a deregulated electricity market, optimizing dispatch capacity and transmission capacity are among the core concerns of market operators. Many market operators have capitalized on linear programming (LP) based methods to perform market dispatch operation in order to explore the computational efficiency of LP. In this paper, the search capability of genetic algorithms (GAs) is utilized to solve the market dispatch problem. The GA model is able to solve pool based capacity dispatch, while optimizing the interconnector transmission capacity. Case studies and corresponding analyses are performed to demonstrate the efficiency of the GA model.

Genetic algorithm based distance spectrum technique for performance union bound of space-time trellis coded OFDM

This paper derives the performance union bound of space-time trellis codes in orthogonal frequency division multiplexing system (STTC-OFDM) over quasi-static frequency selective fading channels based on the distance spectrum technique. The distance spectrum is the enumeration of the codeword difference measures and their multiplicities by exhausted searching through all the possible error event paths. Exhaustive search approach can be used for low memory order STTC with small frame size. However with moderate memory order STTC and moderate frame size the computational cost of exhaustive search increases exponentially, and may become impractical for high memory order STTCs. This requires advanced computational techniques such as Genetic Algorithms (GAS). In this paper, a GA with sharing function method is used to locate the multiple solutions of the distance spectrum for high memory order STTCs. Simulation evaluates the performance union bound and the complexity comparison of non-GA aided and GA aided distance spectrum techniques. It shows that the union bound give a close performance measure at high signal-to-noise ratio (SNR). It also shows that GA sharing function method based distance spectrum technique requires much less computational time as compared with exhaustive search approach but with satisfactory accuracy.

The moving targets algorithm for difficult temporal credit assignment problems

The 'moving targets' algorithm for training recurrent networks is reviewed and applied to a task which demonstrates the ability of this algorithm to use distant contextual information. Some practical difficulties are discussed, especially with regard to the minimization process. Results on performance and computational requirements of several different 2nd-order minimization algorithms are presented for moving target problems.

The 'moving targets' training algorithm

A simple method for training the dynamical behavior of a neural network is derived. It is applicable to any training problem in discrete-time networks with arbitrary feedback. The algorithm resembles back-propagation in that an error function is minimized using a gradient-based method, but the optimization is carried out in the hidden part of state space either instead of, or in addition to weight space. Computational results are presented for some simple dynamical training problems, one of which requires response to a signal 100 time steps in the past.

The 'moving targets' training algorithm

A simple method for training the dynamical behavior of a neural network is derived. It is applicable to any training problem in discrete-time networks with arbitrary feedback. The method resembles back-propagation in that it is a least-squares, gradient-based optimization method, but the optimization is carried out in the hidden part of state space instead of weight space. A straightforward adaptation of this method to feedforward networks offers an alternative to training by conventional back-propagation. Computational results are presented for simple dynamical training problems, with varied success. The failures appear to arise when the method converges to a chaotic attractor. A patch-up for this problem is proposed. The patch-up involves a technique for implementing inequality constraints which may be of interest in its own right.

A hybrid genetic algorithm for the multi-depot vehicle routing problem

The distribution of finished products from depots to customers is a practical and challenging problem in logistics management. Better routing and scheduling decisions can result in higher level of customer satisfaction because more customers can be served in a shorter time. The distribution problem is generally formulated as the vehicle routing problem (VRP). Nevertheless, there is a rigid assumption that there is only one depot. In cases, for instance, where a logistics company has more than one depot, the VRP is not suitable. To resolve this limitation, this paper focuses on the VRP with multiple depots, or multi-depot VRP (MDVRP). The MDVRP is NP-hard, which means that an efficient algorithm for solving the problem to optimality is unavailable. To deal with the problem efficiently, two hybrid genetic algorithms (HGAs) are developed in this paper. The major difference between the HGAs is that the initial solutions are generated randomly in HGA1. The Clarke and Wright saving method and the nearest neighbor heuristic are incorporated into HGA2 for the initialization procedure. A computational study is carried out to compare the algorithms with different problem sizes. It is proved that the performance of HGA2 is superior to that of HGA1 in terms of the total delivery time.

Application of the manakov-PMD equation to a computational investigation of low-PMD fibres

The phenomenon of low-PMD fibres is examined through numerical simulations. Instead of the coarse-step method we are using an algorithm developed through the Manakov-PMD equation. With the integration of the Manakov-PMD equation we have access to the fibre spin which relates to the orientation of the birefringence. The simulation results produced correspond to the behaviour of a low-PMD spun fibre. Furthermore we provide an analytical approximation compared to the numerical data. © 2005 Optical Society of America.

Relaxation procedures for an iterative MFS algorithm for the stable reconstruction of elastic fields from Cauchy data in two-dimensional isotropic linear elasticity

We investigate two numerical procedures for the Cauchy problem in linear elasticity, involving the relaxation of either the given boundary displacements (Dirichlet data) or the prescribed boundary tractions (Neumann data) on the over-specified boundary, in the alternating iterative algorithm of Kozlov et al. (1991). The two mixed direct (well-posed) problems associated with each iteration are solved using the method of fundamental solutions (MFS), in conjunction with the Tikhonov regularization method, while the optimal value of the regularization parameter is chosen via the generalized cross-validation (GCV) criterion. An efficient regularizing stopping criterion which ceases the iterative procedure at the point where the accumulation of noise becomes dominant and the errors in predicting the exact solutions increase, is also presented. The MFS-based iterative algorithms with relaxation are tested for Cauchy problems for isotropic linear elastic materials in various geometries to confirm the numerical convergence, stability, accuracy and computational efficiency of the proposed method.

A relaxation method of an alternating iterative algorithm for the Cauchy problem in linear isotropic elasticity

We propose two algorithms involving the relaxation of either the given Dirichlet data (boundary displacements) or the prescribed Neumann data (boundary tractions) on the over-specified boundary in the case of the alternating iterative algorithm of Kozlov et al. [16] applied to Cauchy problems in linear elasticity. A convergence proof of these relaxation methods is given, along with a stopping criterion. The numerical results obtained using these procedures, in conjunction with the boundary element method (BEM), show the numerical stability, convergence, consistency and computational efficiency of the proposed method.

Replication-based inference algorithms for hard computational problems

Inference algorithms based on evolving interactions between replicated solutions are introduced and analyzed on a prototypical NP-hard problem: the capacity of the binary Ising perceptron. The efficiency of the algorithm is examined numerically against that of the parallel tempering algorithm, showing improved performance in terms of the results obtained, computing requirements and simplicity of implementation. © 2013 American Physical Society.

A multiple pheromone ant clustering algorithm

Ant colony optimisation algorithms model the way ants use pheromones for marking paths to important locations in their environment. Pheromone traces are picked up, followed, and reinforced by other ants but also evaporate over time. Optimal paths attract more pheromone and less useful paths fade away. The main innovation of the proposed Multiple Pheromone Ant Clustering Algorithm (MPACA) is to mark objects using many pheromones, one for each value of each attribute describing the objects in multidimensional space. Every object has one or more ants assigned to each attribute value and the ants then try to find other objects with matching values, depositing pheromone traces that link them. Encounters between ants are used to determine when ants should combine their features to look for conjunctions and whether they should belong to the same colony. This paper explains the algorithm and explores its potential effectiveness for cluster analysis. © 2014 Springer International Publishing Switzerland.

Genetic Algorithm Approach for Solving the Task Assignment Problem

This research was partially supported by the Serbian Ministry of Science and Ecology under project 144007. The authors are grateful to Ivana Ljubić for help in testing and to Vladimir Filipović for useful suggestions and comments.