A Study of Ordered Gene Problems Featuring DNA Error Correction and DNA Fragment Assembly with a Variety of Heuristics, Genetic Algorithm Variations, and Dynamic Representations

Ordered gene problems are a very common classification of optimization problems. Because of their popularity countless algorithms have been developed in an attempt to find high quality solutions to the problems. It is also common to see many different types of problems reduced to ordered gene style problems as there are many popular heuristics and metaheuristics for them due to their popularity. Multiple ordered gene problems are studied, namely, the travelling salesman problem, bin packing problem, and graph colouring problem. In addition, two bioinformatics problems not traditionally seen as ordered gene problems are studied: DNA error correction and DNA fragment assembly. These problems are studied with multiple variations and combinations of heuristics and metaheuristics with two distinct types or representations. The majority of the algorithms are built around the Recentering- Restarting Genetic Algorithm. The algorithm variations were successful on all problems studied, and particularly for the two bioinformatics problems. For DNA Error Correction multiple cases were found with 100% of the codes being corrected. The algorithm variations were also able to beat all other state-of-the-art DNA Fragment Assemblers on 13 out of 16 benchmark problem instances.

Quantifying historical, capital mobility in Canada : an error correction approach.

Rapport de recherche

Implementation and application of basis set superposition error-correction schemes to the theoretical modeling of weak intermolecular interactions

This thesis deals with the so-called Basis Set Superposition Error (BSSE) from both a methodological and a practical point of view. The purpose of the present thesis is twofold: (a) to contribute step ahead in the correct characterization of weakly bound complexes and, (b) to shed light the understanding of the actual implications of the basis set extension effects in the ab intio calculations and contribute to the BSSE debate. The existing BSSE-correction procedures are deeply analyzed, compared, validated and, if necessary, improved. A new interpretation of the counterpoise (CP) method is used in order to define counterpoise-corrected descriptions of the molecular complexes. This novel point of view allows for a study of the BSSE-effects not only in the interaction energy but also on the potential energy surface and, in general, in any property derived from the molecular energy and its derivatives A program has been developed for the calculation of CP-corrected geometry optimizations and vibrational frequencies, also using several counterpoise schemes for the case of molecular clusters. The method has also been implemented in Gaussian98 revA10 package. The Chemical Hamiltonian Approach (CHA) methodology has been also implemented at the RHF and UHF levels of theory for an arbitrary number interacting systems using an algorithm based on block-diagonal matrices. Along with the methodological development, the effects of the BSSE on the properties of molecular complexes have been discussed in detail. The CP and CHA methodologies are used for the determination of BSSE-corrected molecular complexes properties related to the Potential Energy Surfaces and molecular wavefunction, respectively. First, the behaviour of both BSSE-correction schemes are systematically compared at different levels of theory and basis sets for a number of hydrogen-bonded complexes. The Complete Basis Set (CBS) limit of both uncorrected and CP-corrected molecular properties like stabilization energies and intermolecular distances has also been determined, showing the capital importance of the BSSE correction. Several controversial topics of the BSSE correction are addressed as well. The application of the counterpoise method is applied to internal rotational barriers. The importance of the nuclear relaxation term is also pointed out. The viability of the CP method for dealing with charged complexes and the BSSE effects on the double-well PES blue-shifted hydrogen bonds is also studied in detail. In the case of the molecular clusters the effect of high-order BSSE effects introduced with the hierarchical counterpoise scheme is also determined. The effect of the BSSE on the electron density-related properties is also addressed. The first-order electron density obtained with the CHA/F and CHA/DFT methodologies was used to assess, both graphically and numerically, the redistribution of the charge density upon BSSE-correction. Several tools like the Atoms in Molecules topologycal analysis, density difference maps, Quantum Molecular Similarity, and Chemical Energy Component Analysis were used to deeply analyze, for the first time, the BSSE effects on the electron density of several hydrogen bonded complexes of increasing size. The indirect effect of the BSSE on intermolecular perturbation theory results is also pointed out It is shown that for a BSSE-free SAPT study of hydrogen fluoride clusters, the use of a counterpoise-corrected PES is essential in order to determine the proper molecular geometry to perform the SAPT analysis.

The inflation hedging characteristics of US and UK investments: a multi-factor error correction approach

Historic analysis of the inflation hedging properties of stocks produced anomalous results, with equities often appearing to offer a perverse hedge against inflation. This has been attributed to the impact of real and monetary shocks to the economy, which influence both inflation and asset returns. It has been argued that real estate should provide a better hedge: however, empirical results have been mixed. This paper explores the relationship between commercial real estate returns (from both private and public markets) and economic, fiscal and monetary factors and inflation for US and UK markets. Comparative analysis of general equity and small capitalisation stock returns in both markets is carried out. Inflation is subdivided into expected and unexpected components using different estimation techniques. The analyses are undertaken using long-run error correction techniques. In the long-run, once real and monetary variables are included, asset returns are positively linked to anticipated inflation but not to inflation shocks. Adjustment processes are, however, gradual and not within period. Real estate returns, particularly direct market returns, exhibit characteristics that differ from equities.

Intermittently-visual tracking experiments reveal the roles of error-correction and predictive mechanisms in the human visual-motor control system

Prediction mechanism is necessary for human visual motion to compensate a delay of sensory-motor system. In a previous study, “proactive control” was discussed as one example of predictive function of human beings, in which motion of hands preceded the virtual moving target in visual tracking experiments. To study the roles of the positional-error correction mechanism and the prediction mechanism, we carried out an intermittently-visual tracking experiment where a circular orbit is segmented into the target-visible regions and the target-invisible regions. Main results found in this research were following. A rhythmic component appeared in the tracer velocity when the target velocity was relatively high. The period of the rhythm in the brain obtained from environmental stimuli is shortened more than 10%. The shortening of the period of rhythm in the brain accelerates the hand motion as soon as the visual information is cut-off, and causes the precedence of hand motion to the target motion. Although the precedence of the hand in the blind region is reset by the environmental information when the target enters the visible region, the hand motion precedes the target in average when the predictive mechanism dominates the error-corrective mechanism.

Transition from an anti-phase error-correction-mode to a synchronization mode in the mutual hand tracking

Proactive motion in hand tracking and in finger bending, in which the body motion occurs prior to the reference signal, was reported by the preceding researchers when the target signals were shown to the subjects at relatively high speed or high frequencies. These phenomena indicate that the human sensory-motor system tends to choose an anticipatory mode rather than a reactive mode, when the target motion is relatively fast. The present research was undertaken to study what kind of mode appears in the sensory-motor system when two persons were asked to track the hand position of the partner with each other at various mean tracking frequency. The experimental results showed a transition from a mutual error-correction mode to a synchronization mode occurred in the same region of the tracking frequency with that of the transition from a reactive error-correction mode to a proactive anticipatory mode in the mechanical target tracking experiments. Present research indicated that synchronization of body motion occurred only when both of the pair subjects operated in a proactive anticipatory mode. We also presented mathematical models to explain the behavior of the error-correction mode and the synchronization mode.

A method for improving the code rate and error correction capability of a cyclic code

Currently, there has been an increasing demand for operational and trustworthy digital data transmission and storage systems. This demand has been augmented by the appearance of large-scale, high-speed data networks for the exchange, processing and storage of digital information in the different spheres. In this paper, we explore a way to achieve this goal. For given positive integers n,r, we establish that corresponding to a binary cyclic code C0[n,n-r], there is a binary cyclic code C[(n+1)3k-1,(n+1)3k-1-3kr], where k is a nonnegative integer, which plays a role in enhancing code rate and error correction capability. In the given scheme, the new code C is in fact responsible to carry data transmitted by C0. Consequently, a codeword of the code C0 can be encoded by the generator matrix of C and therefore this arrangement for transferring data offers a safe and swift mode. © 2013 SBMAC - Sociedade Brasileira de Matemática Aplicada e Computacional.

Convergence Property of the Measurement Gross Error Correction in Power System State Estimation, Using Geometrical Background

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Polar Codes for error correction: Analysis and Decoding Algorithms

I Polar Codes sono la prima classe di codici a correzione d’errore di cui è stato dimostrato il raggiungimento della capacità per ogni canale simmetrico, discreto e senza memoria, grazie ad un nuovo metodo introdotto recentemente, chiamato ”Channel Polarization”. In questa tesi verranno descritti in dettaglio i principali algoritmi di codifica e decodifica. In particolare verranno confrontate le prestazioni dei simulatori sviluppati per il ”Successive Cancellation Decoder” e per il ”Successive Cancellation List Decoder” rispetto ai risultati riportati in letteratura. Al fine di migliorare la distanza minima e di conseguenza le prestazioni, utilizzeremo uno schema concatenato con il polar code come codice interno ed un CRC come codice esterno. Proporremo inoltre una nuova tecnica per analizzare la channel polarization nel caso di trasmissione su canale AWGN che risulta il modello statistico più appropriato per le comunicazioni satellitari e nelle applicazioni deep space. In aggiunta, investigheremo l’importanza di una accurata approssimazione delle funzioni di polarizzazione.

Static and Dynamic Error Correction of a Computer-Aided Mechanical Navigation Linkage for Arthroscopic Hip Surgery

While beneficially decreasing the necessary incision size, arthroscopic hip surgery increases the surgical complexity due to loss of joint visibility. To ease such difficulty, a computer-aided mechanical navigation system was developed to present the location of the surgical tool relative to the patient¿s hip joint. A preliminary study reduced the position error of the tracking linkage with limited static testing trials. In this study, a correction method, including a rotational correction factor and a length correction function, was developed through more in-depth static testing. The developed correction method was then applied to additional static and dynamic testing trials to evaluate its effectiveness. For static testing, the position error decreased from an average of 0.384 inches to 0.153 inches, with an error reduction of 60.5%. Three parameters utilized to quantify error reduction of dynamic testing did not show consistent results. The vertex coordinates achieved 29.4% of error reduction, yet with large variation in the upper vertex. The triangular area error was reduced by 5.37%, however inconsistent among all five dynamic trials. Error of vertex angles increased, indicating a shape torsion using the developed correction method. While the established correction method effectively and consistently reduced position error in static testing, it did not present consistent results in dynamic trials. More dynamic paramters should be explored to quantify error reduction of dynamic testing, and more in-depth dynamic testing methodology should be conducted to further improve the accuracy of the computer-aided nagivation system.

Development of a transmission error model and an error control model /

"Georgia Institute of Technology."

Quantum-error correction on linear-nearest-neighbor qubit arrays

A quantum circuit implementing 5-qubit quantum-error correction on a linear-nearest-neighbor architecture is described. The canonical decomposition is used to construct fast and simple gates that incorporate the necessary swap operations allowing the circuit to achieve the same depth as the current least depth circuit. Simulations of the circuit's performance when subjected to discrete and continuous errors are presented. The relationship between the error rate of a physical qubit and that of a logical qubit is investigated with emphasis on determining the concatenated error correction threshold.

Continuous quantum error correction by cooling

We describe an implementation of quantum error correction that operates continuously in time and requires no active interventions such as measurements or gates. The mechanism for carrying away the entropy introduced by errors is a cooling procedure. We evaluate the effectiveness of the scheme by simulation, and remark on its connections to some recently proposed error prevention procedures.