This research explored the relationship between an earlier-year technical course and one later year technical course, for students who graduated between 2010 and 2015 with the degree of bachelor of engineering. The research only focuses on the courses in the program of Electrical Engineering at the University of Victoria. Three approaches based on the two major factors, coefficient and enrolment, were established to select the course grade predictor including Max(Pearson Coefficient), Max(Enrolment), and Max(Pi) which is a combination of the two factors. The prediction algorithm used is linear regression and the prediction results were evaluated by Mean Absolute Error and prediction precision. The results show that the predictions of most course pairs could not be reliably used for the student performance in one course based on another one. However, the fourth-year courses are specialization-related and have relatively small enrolments in general, some of the course pairs with fourth-year CourseYs and having acceptable MAE and prediction precision could be used as early references and advices for the students to select the specialization direction while they are in their first or second academic year. / Graduate

One of the important aims of the continuous software development process is to localize and remove all existing program bugs as fast as possible. Such goal is highly related to software engineering and defectiveness estimation. Many big companies started to store source code in software repositories as the later grew in popularity. These repositories usually include static source code as well as detailed data for defects in software units. This allows analyzing all the data without interrupting programing process. The main problem of large, complex software is impossibility to control everything manually while the price of the error can be very high. This might result in developers missing defects on testing stage and increase of maintenance cost. The general research goal is to find a way of predicting future software defectiveness with high precision. Reducing maintenance and development costs will contribute to reduce the time-to-market and increase software quality. To address the problem of estimating residual defects an approach was found to predict residual defectiveness of a software by the means of machine learning. For a prime machine learning algorithm, a regression decision tree was chosen as a simple and reliable solution. Data for this tree is extracted from static source code repository and divided into two parts: software metrics and defect data. Software metrics are formed from static code and defect data is extracted from reported issues in the repository. In addition to already reported bugs, they are augmented with unreported bugs found on “discussions” section in repository and parsed by a natural language processor. Metrics were filtered to remove ones, that were not related to defect data by applying correlation algorithm. Remaining metrics were weighted to use the most correlated combination as a training set for the decision tree. As a result, built decision tree model allows to forecast defectiveness with 89% chance for the particular product. This experiment was conducted using GitHub repository on a Java project and predicted number of possible bugs in a single file (Java class). The experiment resulted in designed method for predicting possible defectiveness from a static code of a single big (more than 1000 files) software version.

<p>Protein malfunction can cause human diseases, which makes the protein a target in the process of drug discovery. In-depth knowledge of how protein functions can widely contribute to the understanding of the mechanism of these diseases. Protein functions are determined by protein structures and their dynamic properties. Protein dynamics refers to the constant physical movement of atoms in a protein, which may result in the transition between different conformational states of the protein. These conformational transitions are critically important for the proteins to function. Understanding protein dynamics can help to understand and interfere with the conformational states and transitions, and thus with the function of the protein. If we can understand the mechanism of conformational transition of protein, we can design molecules to regulate this process and regulate the protein functions for new drug discovery. Protein Dynamics can be simulated by Molecular Dynamics (MD) Simulations.</p> <p>The MD simulation data generated are spatial-temporal and therefore very high dimensional. To analyze the data, distinguishing various atomic interactions within a protein by interpreting their 3D coordinate values plays a significant role. Since the data is humongous, the essential step is to find ways to interpret the data by generating more efficient algorithms to reduce the dimensionality and developing user-friendly visualization tools to find patterns and trends, which are not usually attainable by traditional methods of data process. The typical allosteric long-range nature of the interactions that lead to large conformational transition, pin-pointing the underlying forces and pathways responsible for the global conformational transition at atomic level is very challenging. To address the problems, Various analytical techniques are performed on the simulation data to better understand the mechanism of protein dynamics at atomic level by developing a new program called Probing Long-distance interactions by Tapping into Paired-Distances (PLITIP), which contains a set of new tools based on analysis of paired distances to remove the interference of the translation and rotation of the protein itself and therefore can capture the absolute changes within the protein.</p> <p>Firstly, we developed a tool called Decomposition of Paired Distances (DPD). This tool generates a distance matrix of all paired residues from our simulation data. This paired distance matrix therefore is not subjected to the interference of the translation or rotation of the protein and can capture the absolute changes within the protein. This matrix is then decomposed by DPD</p> <p>using Principal Component Analysis (PCA) to reduce dimensionality and to capture the largest structural variation. To showcase how DPD works, two protein systems, HIV-1 protease and 14-3-3 σ, that both have tremendous structural changes and conformational transitions as displayed by their MD simulation trajectories. The largest structural variation and conformational transition were captured by the first principal component in both cases. In addition, structural clustering and ranking of representative frames by their PC1 values revealed the long-distance nature of the conformational transition and locked the key candidate regions that might be responsible for the large conformational transitions.</p> <p>Secondly, to facilitate further analysis of identification of the long-distance path, a tool called Pearson Coefficient Spiral (PCP) that generates and visualizes Pearson Coefficient to measure the linear correlation between any two sets of residue pairs is developed. PCP allows users to fix one residue pair and examine the correlation of its change with other residue pairs.</p> <p>Thirdly, a set of visualization tools that generate paired atomic distances for the shortlisted candidate residue and captured significant interactions among them were developed. The first tool is the Residue Interaction Network Graph for Paired Atomic Distances (NG-PAD), which not only generates paired atomic distances for the shortlisted candidate residues, but also display significant interactions by a Network Graph for convenient visualization. Second, the Chord Diagram for Interaction Mapping (CD-IP) was developed to map the interactions to protein secondary structural elements and to further narrow down important interactions. Third, a Distance Plotting for Direct Comparison (DP-DC), which plots any two paired distances at user’s choice, either at residue or atomic level, to facilitate identification of similar or opposite pattern change of distances along the simulation time. All the above tools of PLITIP enabled us to identify critical residues contributing to the large conformational transitions in both HIV-1 protease and 14-3-3σ proteins.</p> <p>Beside the above major project, a side project of developing tools to study protein pseudo-symmetry is also reported. It has been proposed that symmetry provides protein stability, opportunities for allosteric regulation, and even functionality. This tool helps us to answer the questions of why there is a deviation from perfect symmetry in protein and how to quantify it.</p>