Object-Oriented Genetic Programming for the Automatic Inference of Graph Models for Complex Networks

Complex networks are systems of entities that are interconnected through meaningful relationships. The result of the relations between entities forms a structure that has a statistical complexity that is not formed by random chance. In the study of complex networks, many graph models have been proposed to model the behaviours observed. However, constructing graph models manually is tedious and problematic. Many of the models proposed in the literature have been cited as having inaccuracies with respect to the complex networks they represent. However, recently, an approach that automates the inference of graph models was proposed by Bailey [10] The proposed methodology employs genetic programming (GP) to produce graph models that approximate various properties of an exemplary graph of a targeted complex network. However, there is a great deal already known about complex networks, in general, and often specific knowledge is held about the network being modelled. The knowledge, albeit incomplete, is important in constructing a graph model. However it is difficult to incorporate such knowledge using existing GP techniques. Thus, this thesis proposes a novel GP system which can incorporate incomplete expert knowledge that assists in the evolution of a graph model. Inspired by existing graph models, an abstract graph model was developed to serve as an embryo for inferring graph models of some complex networks. The GP system and abstract model were used to reproduce well-known graph models. The results indicated that the system was able to evolve models that produced networks that had structural similarities to the networks generated by the respective target models.

Disease-Gene Association Using Genetic Programming

As a result of mutation in genes, which is a simple change in our DNA, we will have undesirable phenotypes which are known as genetic diseases or disorders. These small changes, which happen frequently, can have extreme results. Understanding and identifying these changes and associating these mutated genes with genetic diseases can play an important role in our health, by making us able to find better diagnosis and therapeutic strategies for these genetic diseases. As a result of years of experiments, there is a vast amount of data regarding human genome and different genetic diseases that they still need to be processed properly to extract useful information. This work is an effort to analyze some useful datasets and to apply different techniques to associate genes with genetic diseases. Two genetic diseases were studied here: Parkinson’s disease and breast cancer. Using genetic programming, we analyzed the complex network around known disease genes of the aforementioned diseases, and based on that we generated a ranking for genes, based on their relevance to these diseases. In order to generate these rankings, centrality measures of all nodes in the complex network surrounding the known disease genes of the given genetic disease were calculated. Using genetic programming, all the nodes were assigned scores based on the similarity of their centrality measures to those of the known disease genes. Obtained results showed that this method is successful at finding these patterns in centrality measures and the highly ranked genes are worthy as good candidate disease genes for being studied. Using standard benchmark tests, we tested our approach against ENDEAVOUR and CIPHER - two well known disease gene ranking frameworks - and we obtained comparable results.

Water Works Report

A Water Works report (1 page of newsprint which is slightly tattered and taped – this does not affect the text) by Mr. T. C. Keefer regarding proposed works for the supply of water to St. Catharines, Jan. 4, 1876.

GA approach for finding Rough Set decision rules based on bireducts

Feature selection plays an important role in knowledge discovery and data mining nowadays. In traditional rough set theory, feature selection using reduct - the minimal discerning set of attributes - is an important area. Nevertheless, the original definition of a reduct is restrictive, so in one of the previous research it was proposed to take into account not only the horizontal reduction of information by feature selection, but also a vertical reduction considering suitable subsets of the original set of objects. Following the work mentioned above, a new approach to generate bireducts using a multi--objective genetic algorithm was proposed. Although the genetic algorithms were used to calculate reduct in some previous works, we did not find any work where genetic algorithms were adopted to calculate bireducts. Compared to the works done before in this area, the proposed method has less randomness in generating bireducts. The genetic algorithm system estimated a quality of each bireduct by values of two objective functions as evolution progresses, so consequently a set of bireducts with optimized values of these objectives was obtained. Different fitness evaluation methods and genetic operators, such as crossover and mutation, were applied and the prediction accuracies were compared. Five datasets were used to test the proposed method and two datasets were used to perform a comparison study. Statistical analysis using the one-way ANOVA test was performed to determine the significant difference between the results. The experiment showed that the proposed method was able to reduce the number of bireducts necessary in order to receive a good prediction accuracy. Also, the influence of different genetic operators and fitness evaluation strategies on the prediction accuracy was analyzed. It was shown that the prediction accuracies of the proposed method are comparable with the best results in machine learning literature, and some of them outperformed it.

Letter to Louis J. Cahill from the Managing Editor [no indication of who he works for – same signature as is on the Knox, Harvie and Foss letter

Letter (1 typed page) to Louis J. Cahill from the Managing Editor [no indication of who he works for – same signature as is on the Knox, Harvie and Foss letter] saying that he has found various references to Samuel Zimmerman being active in the erection of the first suspension bridge and its Roebling successor, July 20, 1948.

Letter to S.D. Woodruff from William Colburn with the letterhead “Office of Detroit Bridge and Iron Works”

Letter to S.D. Woodruff from William Colburn with the letterhead “Office of Detroit Bridge and Iron Works” regarding stating that he closed up the business with Dewey’s. He states that “we” now have “warranty deeds” from them for exclusive rights for all time for hunting, shooting and trapping, Mar. 20, 1884.

Letter to S.D. Woodruff from J.W. Harper of the Department of Public Works, Toronto

Letter to S.D. Woodruff from J.W. Harper of the Department of Public Works, Toronto. He is sending a copy of an order in Council on the subject of certain charges made by Joshua Manly of Port Colborne against Mr. Woodruff and other persons connected with the Welland Canal, May 12, 1859.

Bill no.71: An act respecting the Public Works of Ontario

Bill no.71: An act respecting the Public Works of Ontario (10 ½ pages, printed). S.D. Woodruff has signed this copy of the bill and has made a note in pension “regulations for management”, 1868.

Receipt from Aetna Works, Sheffield for payment on account

Receipt from Aetna Works, Sheffield for payment on account, Nov. 26, 1873.

Receipt from Chance Brothers and Co. Glass Works near Birmingham, England

Receipt from Chance Brothers and Co. Glass Works near Birmingham, England regarding payment received for glass panes. This is accompanied by an envelope, April 6, 1875.

Receipt from St. Catharines Water Works for water rent

Receipt from St. Catharines Water Works for water rent, Aug. 18, 1887.

Receipt from St. Catharines Water Works for water rent

Receipt from St. Catharines Water Works for water rent, Oct. 1, 1887.

Certificate on the occasion of Samuel DeVeaux Woodruff’s retirement from the Water Works Commission of the City of St. Catharines

Certificate measuring 64 cm. x 48 cm. on the occasion of Samuel DeVeaux Woodruff’s retirement from the Water Works Commission of the City of St. Catharines. Mr. Woodruff served the commission from 1875 to 1899. He also served as chairman of the commission. This is signed by Lucius S. Oille, George C. Carlisle and Connolly B. Hare (members of the committee), Jan. 2, 1900.

Manual básico works : primera parte

UANL

The poetical works

UANL