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--- ongoing [2010/09/08 16:47] – bil
+++ ongoing [2011/11/21 16:46] (current) – ruppert
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-====== Ongoing projects ======
+====== Previous projects ======
-====== Web-based digital signage system ======
+====== Imputation of missing values in microarray data ======
-**Student**:  Ankit Agrawal
+**Student**:  Michael Larin
-**Supervisor**:  John Amanatides
+**Supervisor**:  S. Datta
 __Description__
-Build a web-based digital signage system for Bethune College. Some of the technologies that you will be expected to learn/use include Javascript, JQuery, HTML, CSS, and ical/CalDAV. We expect to go open source with this software so that others can use it as well. The deliverables will also include an analysis of what it takes to scale this type of signage campus wide, including provisions for campus alerts/emergency announcements and a prototype for such a system.
+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.
-====== Tandem repeat detection using spectral methods ======
+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.
-**Student**:  Mohamad Alsabbagh
+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.
-**Supervisor**:  Suprakash Datta
+Throughout the course, the student is required to maintain a course
+website to report any progress and details about the project.
-__Description__
+====== An Open Source Structural Equation Modeling Graph Drawing Application ======
-DNA sequences of organisms have many repeated substrings. These are called repeats in Biology, and include both exact as well as approximate repeats. Repeats are of two main types – interspersed repeats (which are spread across a genome) and tandem repeats, which occur next to each other. Tandem repeats play important roles in gene regulation and are also used as markers that have several important uses, including human identity testing.
+**Student**:  Doug Scheurich
-Finding tandem repeats is an important problem in Computational Biology. The techniques that have been proposed for it fall into two classes – string matching algorithms and signal processing techniques. In this project, we will explore fast, accurate algorithms for detecting tandem repeats and evaluate the outputs of the algorithms studied by comparing their outputs with those of available packages, including mreps (http://bioinfo.lifl.fr/mreps/), SRF (http://www.imtech.res.in/raghava/srf/) and TRF (http://tandem.bu.edu/trf/trf.html).
+**Supervisor**:  J. Edmonds
-The student will implement the spectral algorithms used in [1] (one based on Fourier Transforms and one on autoregressive models). He will then make changes suggested by the supervisor, and evaluate the effect of the modifications.
-Throughout the course, the student is required to maintain a course Web site to report any progress and details about the project.
-====== Entropy-based concept drift detection ======
-**Student**:  Junjie Guo
-**Supervisor**:  Aijun An
 __Description__
-The student will design and implement an entropy-based concept drift detection method. The method will be an improved version of the entropy-based method described by Vorburger and Bernstein, which is likely to contain flaws. The student will first study the original method, identify problems, implement the method to verify the identified problems, implement a corrected version of the method and evaluate the corrected version on a number of data stream data sets. The student is also expected to improve the corrected version of the entropy-based drift detection method by using the bootstrapping technique to automatically determine the threshold used in the entropy-based method.
+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).
-====== Computer Security Lab Evaluation ======
+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).
-**Student**:  Yongcheol Kim
+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.
-**Supervisor**:  Bil Tzerpos
+====== Exploring the notion of Variability in Business Process Modeling (and its relationship with Goals) ======
-__Description__
+**Student**:  Dean Shaft
-The project will require the student to evaluate a series of computer
+**Supervisor**:  S. Liaskos and Y. Lesperance
-secutiry lab exercises. The exercises will be prepared by the
-supervisor. The student will evaluate the clarity with which the lab
-exercises have been presented, whether the necessary background has been
-sufficiently covered, and whether it is feasible to complete the lab
-exercise in the space of one week.
-A similar evaluation process will take place for the term project. This
-will also be provided by the supervisor.
-====== Assistive Technology Software: Narratives for Information Delivery and Deployment ======
-**Student**:  Sidrah Laldin
-**Supervisor**:  Melanie Baljko
 __Description__
-Assistive technology software refers to a family of software packages and tools that are used by individuals who experience the effects of disability that arise from motor, linguistic, sensory or cognitive disorder or impairment.  Such software is almost always used in conjunction with specialized computer hardware and/or input devices.  For instance, an individual who has quadriplegia might use specialized text entry software in conjunction with a sip’n’puff switch  (a mouth-operated device that emulates two buttons).
+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).
-Assistive technology software falls into several categories: closed- vs open-source; free vs. proprietary software; commercially available (aka “payware”) vs shareware vs freeware. Assistive technology software is most often obtained by clinicians (Speech Language Pathologists, Occupational Therapists, Education Specialists).   If the procurement is being done under the Ontario Ministry of Health and Long-Term Care’s Assistive Devices Program (ADP), then the software is “prescribed” (in the medical sense of the word).
+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.
-A current project underway in the Multimodal Mediated Communcation (MuMeC) Research Lab is the design best practices and the logistical framework for the deployment of assistive technology software that has already been developed.  This is a non-trivial project with not only technical and software aspects, but also commercialization and IP issues.
+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.
-====== Simulation of a 6dof virtual reality tracker ======
+====== Mobile Software Development Platform Comparison: Windows Phone 7 and Android ======
-**Student**:  Kapil Patel
+**Student**:  Ahmad Hasan
-**Supervisor**: Wolfgang Stuerzlinger
+**Supervisor**:  J. Ostroff
 __Description__
-Previous work by the supervisor resulted in a novel and highly accurate Virtual Reality tracking system that matches or exceeds the specifications of all competing systems. However, this system works only in 5 or 6-sided immersive display environment.
+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.
-This project is the first step towards an adaptation of the technology for more general environments. In particular we target normal rooms and immersive displays with less than 5 screens. The technical work involves adapting the simulation software for the previous device to simulate a new design, and iteratively optimizing that design based on the results obtained.
+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.
-====== Electronic voting system ======
-**Student**:  Nauman Rana
-**Supervisor**:  John Amanatides
-__Description__
-Build a stand-alone electronic voting system. It is to be a web-based, open source system that can have on-line elections of several thousand voters. Multiple elections can be going on at the same time. A web front-end for administrators is also required. the test system will run on a Mac OSX server, and be accessed via the web by both administrators and voters.
-====== Cluster visualization using Multi-Core GPUs and CUDA ======
-**Student**:  Roozbeh Takhayorie
-**Supervisor**:  Suprakash Datta
-__Description__
-The development of high-throughput experiments in Biology has made available huge amounts of data, and there is a pressing need for the development of analysis tools for them. In this work we focus on clustering and the visualization of clustered data. While techniques for cluster visualization exist, the computational costs involved result in large running times for large data sets. This project will investigate the use of parallel computing using modern graphics processors (GPU) in speeding up cluster data visualization.
-There are many different high-dimensional datasets and many different clustering algorithms available today. While several analytical cluster evaluation methodologies exist, many experimental scientists like to evaluate cluster quality visually. This is standard practice in many fields of Biology, including Flow Cytometry. We would like to develop a visualization tool that takes two clusters input by the user and displays the clusters from the best possible viewpoint. A good candidate for the best possible viewpoint is one that separates the clusters as much as possible.
-The first responsibility of the student in this project is to learn to write programs in the CUDA architecture [1]. Then he will learn to use a few well-known libraries ported to CUDA, especially BLAS/LAPACK for linear algebra and SVM for machine learning. The student will then work with the supervisor to develop cluster visualization tools using CUDA. The project will use some ideas from the Ggobi package [2], but implement them to exploit the parallelism of GPUs. Since this project is quite ambitious, the emphasis will be on the first part – the development of basic tools using CUDA and the use of well-known libraries.
-The supervisor will provide the datasets and the clustering algorithms that can generate clustered data. The student will use them to demonstrate the output of his visualization tool.
-====== Estimating Registration Error ======
-**Student**: Lalit Walia
-**Supervisor**: Burton Ma
-__Description__
-A fundamental step in computer-assisted surgery is registration where the anatomy of the patient is matched to an image or model of the anatomy. For some types of orthopaedic procedures, registration is performed by digitizing the locations of points on the surface of a bone and matching the point locations to the surface of a model of the bone. Here, a surgeon uses a pointer that is tracked using an optical tracking system to measure registration point locations on a patient. A registration algorithm is used to compute the transformation that best matches the points to a model of the anatomy.
-Virtual navigational information (such as where to drill or cut the bone) can be provided to the surgeon after the registration transformation has been established. Here, a surgeon is using a tracked surgical drill to drill a hole along a pre-operatively defined path. Notice that the surgeon looks at the virtual navigational information instead of the patient when performing this task.
-Computer-assisted surgical navigation depends on having an accurate registration. If the estimated registration is inaccurate then the navigational information will also be inaccurate, which may lead to errors in the surgical procedure. It is of great interest to know the accuracy of the estimated registration.
-Further details on the project can be found [[http://www.cse.yorku.ca/~burton/4080/4080.html|here]].
-====== Programming Multi-Core GPUs with CUDA ======
-**Student**: Huajian Wang
-**Supervisor**: Franck van Breugel
-__Description__
-CUDA stands for "compute unified device architecture."  It is an architecture to program multicore graphical processing units (GPUs for short).  In the past, these GPUs were only used for graphics. However, CUDA allows us to use these GPUs for other types of computation. Since today's GPUs have hundreds of cores, algorithms can be parallelized and, hence, run often much faster.
+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 aim of this project is to get familiar with GPUs and to study how to program them.
+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.
-More details can be found at: [[http://www.cse.yorku.ca/~franck/projects/cuda.html]]
+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.
-(this link is only accessible from machines within the domain yorku.ca.)
-====== Low-Cost Three-Dimensional Face Scanning System ======
+====== CPS/1 Emulator ======
-**Student**: Thomas Young
+**Student**:  Vahid Bahreman
-**Supervisor**:  James Elder
+**Supervisor**:  Z. Stachniak
 __Description__
-Low-cost three-dimensional face-scanning systems have a large range of potential applications in security and retail markets.  Our laboratory at York University has recently developed a prototype face-scanning system that has the potential for very low-cost mass production.  This project involves the development of a second-stage prototype that is one-step closer to commercialization.
+The manufacturers of tablets, pocket PCs, smart-phones, etc.  frequently
+release software simulators (or emulators) of these devices to emulate
+the functionality of actual products for cost-effective development of
+application software   (e.g.  to test how a given device's software,
+screen, keyboard, or trackwheel will  work with an application under
+development). These simulators can also be used as sophisticated tools
+for testing, training and in presentations. The design and
+implementation of such emulators require a broad computer science
+expertise from hardware architecture to operating systems and computer
+graphics.
-The project will involve systems design and development of a specialized real-time 3D face scanner.  A combination of hardware and software design will be required.  The student will work closely with graduate students and postdoctoral fellows at York University, as well as researchers at other institutions involved in the project.  The student will develop skills in both hardware and software design, as well as computer-vision techniques.
+The history of computing is another area that actively supports  the
+development of emulators of historically significant hardware (mostly
+computers   and game consoles).  As a result, there is at least one
+emulator of almost every significant system. This activity contributes,
+in the first place, to the preservation and dissemination of significant
+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.
-For more information on the laboratory: [[http://www.elderlab.yorku.ca]]
+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