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--- ongoing [2011/02/07 20:41] – bil
+++ ongoing [2011/11/21 16:46] (current) – ruppert
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-====== Ongoing projects ======
+====== Previous projects ======
-====== Leadership Election Among Numbered Agents with Constrained Interactions ======
+====== Imputation of missing values in microarray data ======
-**Student**:  Stephen Voland
+**Student**:  Michael Larin
-**Supervisor**:  Patrick Dymond and Michael Jenkin
+**Supervisor**:  S. Datta
 __Description__
-This project is an examination of the efficiency with which numbered distributed agents are able to elect a leader, given certain constraints.  It builds on the paper 'Efficient Leader Election Among Numbered Agents', by R. Chaturvedi, P. Dymond, and M. Jenkin.
+Microarrays are a relatively new technology that have had tremendous
+impact on many areas within biology and bioinformatics.  Microarray
+technology enables researchers to study the behaviour of many genes
+and/or conditions in a single experiment.
-When collections of agents are deployed to solve a problem it can be beneficial to establish a leader among the group. For certain applications it may be desirable to establish this leader in some static manner. For other situations it is desirable to have the group of agents establish the leader themselves. Chatuervedi et al. (2011) developed an algorithm that enables a group of identical agents differentiated only by their unique identification number to elect their own leader. Chaturvedi et al.'s work contained a very simple simulator for a specific algorithm. Ongoing work requires the development of a more sophisticated simulator of this collection of agents, in particular the development of a simulator that allows for systematic evaluation of certain properties of the collection of agents.  It is also desirable to perform a rigorous mathematical analysis of some of the more simpler variants of the existing work.
+Due to technological limitations and experiment design issues,
+microarray data sets typically have several missing values.  It has been
+shown that imputation of these values improves the accuracy of
+different processing tasks, including clustering, that are typically
+done on these data sets.  Therefore, good imputation algorithms are
+required.
-The project will involve the creation of a simulator which will take parameters for the number of agents, their internal initial state such as arrangement in space, and a function to determine the probability of an interaction between two given agents based on their positions.  In the most straightforward case, all paired interactions would be equally likely, and thus the agents would have no associated positions.  Another case would have the agents spread randomly on a bounded plane, where the probability of a pair interacting would be inversely proportional to the distance between them.  A third would have the agents distributed among rooms, and would allow an agent to communicate only with agents in the same or an adjacent room.  The program will simulate a leadership election using the supplied parameters, and report properties of the simulation including how many interactions were necessary to complete the election, if the election was successful, and actual number of interactions taken for election
+In this project, we will explore fast and accurate imputation algorithms
+for microarray data.  The student will first read the papers assigned
+and write a short summary of them.  Then, he will study the performance
+a few algorithms from the literature (many algorithms are already
+implemented but 1 - 2 may need to be implemented).  Finally, he will
+work with the supervisor on the design of better algorithms for the
+problem being studied.  He will use publicly available data sets to
+compare the performance (accuracy and speed) of the new algorithm(s) to
+the GMCImpute algorithm and several other existing ones.
-Theoretical results for such elections will also be determined, and will be compared with the experimental results for mutual validation.
+Throughout the course, the student is required to maintain a course
+website to report any progress and details about the project.
-====== Acoustic cues and self motion ======
+====== An Open Source Structural Equation Modeling Graph Drawing Application ======
-**Student**:  Evangelos Zotos
+**Student**:  Doug Scheurich
-**Supervisor**:  Michael Jenkin
+**Supervisor**:  J. Edmonds
 __Description__
-We are capable of estimating the magnitude of our own self-motion and the relative motion of other objects as we move about in our natural environment. This perception is based on information arising from several sensory modalities including visual, auditory, and physical motion. In general, the perceived distance of self-motion is over-estimated when using visual or physical motion cues solely or even in conjunction, although judgments are more accurate when both cues are available. In other words, the distance we perceive ourselves to have moved is typically greater than the distance we have actually moved. Despite the potential contribution of dynamic auditory localization to the perception of self-motion, few studies have examined the effects on auditory cues on the perception of self-motion and the effect of auditory cues may have on our visual perception and more specifically, our visual motion perception.
+Structural equation modeling (SEM) is a statistical technique that is becoming increasingly popular in the sciences. SEM allows researchers to test the validity of hypothesized models involving complex relationships among multiple variables. These models can include latent variables, which are not measured directly but are constructs inferred by observed variables. Structural equation models can be represented visually by graphs. To generate such graphs currently in R would require over 80 lines of code which has no reusability and has to be re written each time a new graph has to be developed or analyzed (R is a UNIX based command line only program, however it is a very powerful analytic research tool).
-The purpose of this project is twofold: i) develop software that will permit conducting of psychophysical experiments that examine audio + visual motion perception, and ii) conduct an experiment that will investigate the interaction of audio + visual cues on our perception of self-motion.  The software will be developed using the Unity Game Development Tool and will be developed to allow for maximum robustness.  More specifically, it will allow for various experimental parameters (rate of acceleration, size of the environment/hallway where the motion takes place, amongst others) to be easily modified thus allowing to investigate their effect on self-motion perception.
+Collected data is used to estimate the parameters of the equations and assessing the fit of the model. There are several SEM software options available to researchers, however all have serious limitations (Windows only, Unix only, expensive licensing fees, text based or command line only, no GUI, etc).
-====== Implementation and Analysis of a Non-blocking Chromatic Search Tree ======
+We propose developing an application which will allow the user to load observed variables from a data file to create graphs, or allow using an intuitive graphical interface, and convert the graphs into a text based model specification file (ie generate the code required so the graph can be used in other programs such as R).  This text file can then be used as input for the sem() function in R.  The application will be implemented in Java, which can then be used with any OS.  Later versions may include the ability to call R functions directly from within the application and provide options for more advanced structural equation modeling techniques.
-**Student**:  Trevor Brown
+====== Exploring the notion of Variability in Business Process Modeling (and its relationship with Goals) ======
-**Supervisor**:  Eric Ruppert
+**Student**:  Dean Shaft
+**Supervisor**:  S. Liaskos and Y. Lesperance
 __Description__
-This project seeks to take the theoretical description of the
+Business Process Modeling (BPM) notations are an increasingly popular subject of investigation in the analysis and design of Information Systems. Such notations allow analysts to represent different ways by which actors of a domain can collaboratively perform tasks in order to meet certain business goals. The diagrammatic result allows understanding of the involved activities at various levels of abstraction each being useful for different stakeholders, such as business versus technical ones. It also provides a basis for further formalization and analysis of the modeled business process or its translation into implementation models such as service composition programs. Several BPM languages have been introduced, most prominent being the Business Process Modeling Notation (BPMN).
-non-blocking chromatic search tree that was developed in a
-previous CSE4080 project and produce a Java implementation, then perform
-experiments to test it and compare it with other leading concurrent dictionary structures.
-Additionally, many potential performance improvements and structural or
+Variability occurs in business processes, in that the same business process may need to either be reused in a different context (e.g. a different organization) or adapt to changing requirements or environmental constraints. Thus, each variation of the business process is applicable to a different situation affects specified customization criteria in a different way. Such criteria may include high-level qualities or non-functional goals e.g. such as key performance indicators (KPIs) or operational constraints that prescribe patterns which the business process must follow. To some extend BPMs offer constructs for modeling such variability. However, both the problems of modeling customization criteria and that of using them to derive business process variations that best satisfy them have not enjoyed significant attention in the literature.
-algorithmic variations on the aforementioned theoretical description
-were identified during the last project.
-This project would attempt to explore many of these variations to
-further refine the theoretical description, and produce a competitive
-dictionary algorithm.
-In particular, this project would
-provide a dictionary implementation with better
-worst-case performance guarantees than previous
-non-blocking dictionary implementations.
-Finally, the project would attempt to establish formal proofs that the
+In this project we shall investigate ways of modeling and reasoning about business process variability. We will pick a BPM, possibly BPMN, and explore different ways by which variability can be expressed. Then we will look at criteria that define variant selection and how such can be represented as well. Through possible formalizations in specification frameworks that are used in AI such as Situation Calculus or planning definition languages, the problem of automatically selecting variants of interest in order to meet certain customization criteria shall be studied. In the end we are hoping to develop a concrete framework for representing and reasoning about business process variability in light of high-level goal-based customization criteria.
-structure provides guarantees regarding balance and worst-case performance.
-If time permits, further work will be done towards establishing the
-correctness of the algorithm.
-====== UCOSP: Development for Encyclopedia of Life ======
+====== Mobile Software Development Platform Comparison: Windows Phone 7 and Android ======
-**Student**:  Feng Sun
+**Student**:  Ahmad Hasan
-**Supervisor**:  Vassilios Tzerpos
+**Supervisor**:  J. Ostroff
 __Description__
-The Encyclopedia of Life (EOL) is a free, online collaborative
+Over the past decade the development and use of smartphone technologies has become increasingly sophisticated. The computational power of modern smartphones is growing to match the power of conventional desktop computers. More people and organizations are becoming increasingly dependent on their mobile devices being able to perform sophisticated computations. As the leaders in the technology industry move towards providing advanced products and development platforms, the environment of traditional software development is changing rapidly. Mobile applications that provide a variety of services involving cloud computing, GPS, games, and automation.
-encyclopedia intended to document all of the 1.8 million living species
-known to science. It is compiled from existing databases and from
+The goal of this project is to explore and compare the software development platforms for popular mobile phone operating systems for the development of applications and games.
-contributions by experts and non-experts throughout the world.
+Business applications and games have distinctive features in the context of mobile platforms. For regular applications, platform capabilities relating to cloud computing, GPS and everyday consumer applications have a unique development cycle that differ from regular desktop applications. Mobile applications are usually lightweight and efficient tools for everyday administrative tasks. Under Windows Phone 7 such apps are usually built under the Microsoft Silverlight framework, and the the application must adhere to guidelines and best practices laid out in the Windows Phone 7 documentation. The Android platform provides no such single framework for developing these types of applications but all of the tools and functionalities are available to provide the same services, again this app will also follow the guidelines and best practices described in the official Android documentation.
+The games developed in each platform are intended to serve as explorations into the graphics capabilities of both systems. Graphics environments and frameworks are another area in mobile devices that are becoming increasingly important. Rich graphics and animation capabilities are important for providing immersive user experiences and games are excellent environments to develop and test interactive graphics capabilities on mobile devices. The Windows Phone 7 game development framework uses and extension of Microsoft’s well established XNA framework. This provides libraries to develop and debug game and graphics engines and easily integrate multimedia content into mobile games. Android game applications depend on a to be determined open source game engine.
+This project aims to compare the mobile platforms with respect to development languages, the use of object oriented software development principles and the utility of the tools. The applications and documentation developed through the course of this project should also provide a good source of information for computer science and engineering students who might want to develop software on mobile platforms. Using standard libraries and working with established frameworks and as well as open source frameworks to develop reliable, extendible and reusable code for mobile platforms would be an excellent experience for students to learn about new emerging technologies and the software engineering concepts that apply to them.
+====== CPS/1 Emulator ======
+**Student**:  Vahid Bahreman
+**Supervisor**:  Z. Stachniak
+__Description__
-The ultimate criteria of success for a web application is the user
+The manufacturers of tablets, pocket PCs, smart-phones, etc.  frequently
-experience. EOL is no exception. This project involves creating a
+release software simulators (or emulators) of these devices to emulate
-framework for describing how visitors are supposed to interact with
+the functionality of actual products for cost-effective development of
-Encyclopedia of Life. It automatically checks that a new version the EOL
+application software   (e.g.  to test how a given device's software,
-code is functioning as expected. It is very beneficial for open source
+screen, keyboard, or trackwheel will  work with an application under
-projects to be released often, and automated tests decrease the cost of
+development). These simulators can also be used as sophisticated tools
-releases dramatically and ensure the integrity of the data, code, and
+for testing, training and in presentations. The design and
-visual representation. The tests are run either in production or a
+implementation of such emulators require a broad computer science
-duplicate of the production environment. The acceptance testing
+expertise from hardware architecture to operating systems and computer
-framework can be extended to check any website, not only EOL, by
+graphics.
-changing the configuration and defining new test suites. It also enables
-testing a web application with different browsers and operating systems.
-Acceptance testing is an import skill for aspiring developers. By
+The history of computing is another area that actively supports  the
-participating in this project you will learn the inner mechanics of
+development of emulators of historically significant hardware (mostly
-operating a browser automatically using scripts, emulating a real
+computers   and game consoles).  As a result, there is at least one
-person's actions. This project will provide experience using Selenium (a
+emulator of almost every significant system. This activity contributes,
-leading open source acceptance testing tool), XML, XPATH, CSS selectors,
+in the first place, to the preservation and dissemination of significant
-and Behavior Driven Development.
+hardware and software technologies. The project's objective is to design
+and implement an emulator of the CPS/1 computer -- one of the   earliest
+commercially available microprocessor-powered computers. York University
+Computer Museum is in the possession of CPS-1's design blueprints and
+other technical documentation. The completed project would be a
+significant contribution to the preservation of unique Canadian computer
+technologies.
-More information: [[http://www.eol.org]]
+Background information: The CPS/1 computer was designed and built   by a
+Canadian company Microsystems International Ltd. between 1972 and 73.
+The computer   was built around the first Canadian microprocessor--the
+MF7114--one of world's  earliest microprocessors.  Although none of the
+CPS/1 computers have survived, technical information about the CPS/1 has
+been preserved. This makes the design and  implementation  of an
+emulator possible. More information on
+http://www.cse.yorku.ca/museum/collections/MIL/MIL.htm