projects
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projects [2014/09/03 11:11] – jarek | projects [2015/08/26 21:59] – jarek | ||
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- | ====== Proposed Projects for Fall 2014 ====== | + | ====== Proposed Projects for Fall 2015 ====== |
\\ | \\ | ||
+ | ======Clustering High-Dimensional Data Sets====== | ||
- | ===Dynamic Interface Detection and Control Project=== | + | **Supervisor: |
- | **Supervisor: | + | Clustering is a basic technique for analyzing data sets. Clustering is the process of grouping data points in a way that points within a group are |
+ | more similar to each other than points in other clusters. Many clustering algorithms have been developed over the years. However no single algorithm works well for all data sets. Further, most clustering algorithms have running times of the order of n^2 or n^3, so that they are not feasible for data sets with hundreds of thousands of points. In this project we will design good clustering algorithms for large real data sets. In particular we are interested in | ||
+ | Biological data sets. | ||
+ | |||
+ | Our data sets will include those obtained from Flow Cytometry data. Flow Cytometry is a common technique in many areas of Biology, particularly Immunology. Typical usage involves testing a blood sample for 25 attributes on a per-cell basis, and thus typical data sets are arrays of 500,000 points in a 25 dimensional space. The aim is to identify clusters that correspond to a biologist' | ||
+ | |||
+ | No Biology knowledge is required. The student should be a strong programmer. Knowledge of C/C++ is desirable but not essential. The work involves reading and understanding existing algorithms and working with the supervisor to design and implement improved algorithms and to measure the performance of the proposed algorithm(s). | ||
+ | |||
+ | For more information, | ||
+ | |||
+ | Required Background: General CSE408x prerequisites | ||
+ | |||
+ | |||
+ | \\ | ||
+ | |||
+ | |||
+ | ======Metaheuristic-based Optimization techniques====== | ||
+ | |||
+ | **Supervisor: | ||
+ | |||
+ | Optimization is a crucial step in many computational problems. For computational problems that seem (or are known to be) intractable, | ||
+ | |||
+ | The student should be a strong programmer. A good grasp of algorithms and knowledge of C/C++ are desirable but not essential. The work involves reading and understanding existing algorithms and working with the supervisor to design and implement improved algorithms and to measure the performance of the proposed algorithm(s). | ||
+ | |||
+ | For more information, | ||
+ | |||
+ | Required Background: General CSE408x prerequisites | ||
+ | |||
+ | \\ | ||
+ | |||
+ | ======Data visualization in Skydive====== | ||
+ | |||
+ | **Supervisor: | ||
+ | |||
+ | Skydive is a prototype system designed for database visualization using a concept of the so called | ||
+ | data pyramid. The system is composed of three modules (DB - Database Module, D2I - | ||
+ | Data-to-Image module, and VC - Visualizaton Client). Each is designed to use a different type | ||
+ | of computer memory. The DB module uses disk to store and manage the raw data, and materialized | ||
+ | data pyramids. The D2I module works with a small subset of the aggregated dataset, | ||
+ | and stores data in main memory (RAM). The VC module uses the graphic card’s capabilities to | ||
+ | perform more advanced operations – such as zooming, scaling, panning, and rotation – over the | ||
+ | graphical representation of the data. | ||
+ | Currently the system support three presentation models implemented within the Visualization | ||
+ | Component, namely: | ||
+ | |||
+ | • a 2D heat-map; | ||
+ | |||
+ | • a 2.5 D heat-map by 3D barchart; and | ||
+ | |||
+ | • a 2.5 D terrain (by mesh and UV-mapping). | ||
+ | |||
+ | The goal of the project is to implement two additional ways of data visualization as well as | ||
+ | extend some of existing ones, that is: | ||
+ | |||
+ | 1. Implement and test functions for data pyramid-based visualization of time series. | ||
+ | |||
+ | 2. Implement functions for visualization based on cross-product of data pyramids. | ||
+ | |||
+ | 3. Add support for specular and normal maps for 2.5 D terrain presentation model. | ||
+ | |||
+ | Required Background: CSE 3421, Java programming course, (C programming course a plus) | ||
+ | |||
+ | |||
+ | \\ | ||
+ | |||
+ | ======Genome-wide identification of plant micro RNAs====== | ||
+ | |||
+ | |||
+ | **Supervisor: | ||
+ | |||
+ | |||
+ | The Hudak Lab in the Biology Department has an opening for a fourth-year Honours student to assist with a bioinformatics project. We study the pokeweed plant, Phytolacca americana, which displays broad-spectrum virus resistance. To evaluate pokeweed gene expression, we recently sequenced the plant’s mRNA and small RNA transcriptomes under jasmonic acid (JA) treatment. JA is a plant hormone that mediates defence against pathogens and insect herbivores. We are interested in learning how pokeweed gene expression is regulated by miRNAs during biotic stress. | ||
+ | |||
+ | Working with the support of a PhD student, your project will involve: | ||
+ | |||
+ | 1) Prediction of micro RNA (miRNA) targets on the basis of complementary sequence matches | ||
+ | |||
+ | 2) Correlation of miRNA and mRNA expression changes to identify genes that are regulated by miRNAs | ||
+ | |||
+ | 3) Conducting pathway analysis to determine which biological processes are controlled by miRNAs | ||
+ | |||
+ | 4) Construction of a miRNA/ | ||
+ | This work will contribute to a scientific manuscript on miRNA-mediated gene regulation in pokeweed during response to JA. | ||
+ | |||
+ | Requirements: | ||
+ | |||
+ | 1) Pre-requisites as per EECS Calendar | ||
+ | |||
+ | 2) Facility with script-writing/ | ||
+ | |||
+ | 3) Preference for students with knowledge of statistics and familiarity with R programming | ||
+ | |||
+ | 4) Able to begin in September 2015 | ||
+ | |||
+ | Learning outcomes: | ||
+ | |||
+ | 1) Manipulate and analyze quantitative biological data | ||
+ | |||
+ | 2) Develop and test hypotheses by modifying existing software and writing new script | ||
+ | |||
+ | 3) Manage a CentOS computer server to store and facilitate ongoing research | ||
+ | |||
+ | No knowledge of biology is required. | ||
+ | |||
+ | For more information, | ||
+ | Hudak Lab website- http:// | ||
+ | |||
+ | RNA sequencing- http:// | ||
+ | |||
+ | miRNAs- http:// | ||
+ | |||
+ | \\ | ||
+ | |||
+ | ======Dynamic Interface Detection and Control Project====== | ||
+ | |||
+ | **Supervisor: | ||
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Specific goals of the project include: | Specific goals of the project include: | ||
- | | + | |
- | - Evaluate the performance of the system over a range of different (and typical) fluids | + | - Develop a computer vision system that can detect and monitor the interface between two miscible fluids of different density. |
- | - Explore the use of different illuminant/ | + | |
+ | - Evaluate the performance of the system over a range of different (and typical) fluids | ||
+ | |||
+ | - Explore the use of different illuminant/ | ||
The successful candidate(s) will have the experience of working with a diverse group of scientists and engineers toward the design and implementation of an automated liquid extraction device with applications across many industries. Upon successful prototyping, | The successful candidate(s) will have the experience of working with a diverse group of scientists and engineers toward the design and implementation of an automated liquid extraction device with applications across many industries. Upon successful prototyping, | ||
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\\ | \\ | ||
+ | |||
====== DDoS Attack using Google-bots ====== | ====== DDoS Attack using Google-bots ====== | ||
- | **Supervisor**: Ntalija | + | **Supervisor:** Natalija |
**Recommended Background**: | **Recommended Background**: | ||
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\\ | \\ | ||
+ | |||
====== Attentive Sensing for Better Two-Way Communication in Remote Learning Environments ====== | ====== Attentive Sensing for Better Two-Way Communication in Remote Learning Environments ====== | ||
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\\ | \\ | ||
- | ====== | + | ====== JPF in a Jar ====== |
**Supervisor: | **Supervisor: | ||
Description: | Description: | ||
- | Java PathFinder | + | JPF, which is short for Java PathFinder, is an open source |
- | The Java library Apache log4j allows developers | + | tool that has been developed at NASA's Ames Research Center. |
- | statements are output. | + | The aim of JPF is to find bugs in Java code. |
- | to detect bugs in log4j by means of JPF with very limited succes. | + | using testing |
+ | The facts that JPF is downloaded hundreds of times per month | ||
+ | and that some of the key papers on JPF have been cited more | ||
+ | than a thousand times reflect the popularity | ||
+ | fact it is the most popular model checker for Java. | ||
- | Recently, | + | A study done by Cambridge University |
- | an extension | + | global cost of debugging code has risen to $312 billion annually. |
- | is to apply this extension to log4j. | + | Furthermore, |
+ | programming time with finding and fixing bugs. As a consequence, | ||
+ | advocating the use tools, such as JPF, may have significant impact. | ||
- | [1] David A. Dickey, B. Sinem Dorter, J. Michael German, Benjamin D. Madore, Mark W. Piper, Gabriel L. Zenarosa. " | + | Installing JPF is far from trivial. The tool itself has been |
+ | implemented in Java. | ||
+ | feasible to encapsulate JPF in a Java archive (jar) file. | ||
+ | This would make it significantly simplifying the installation | ||
+ | process of JPF and, therefore, make the tool more easily | ||
+ | accessible to its potential users. | ||
- | **Required Background: | + | The aim of this project is to attempt to put JPF in a jar. |
- | \\ | + | Since JPF relies on a number of configuration files, so-called |
- | ------------ | + | Java properties files, incorporating these properly into the |
- | \\ | + | jar is one of the challenges. |
- | ======Hybrid 2D/3D User Interfaces for 3D Rotation ====== | + | another challenge. |
+ | our modifications to JPF should ideally be limited to only a | ||
+ | few classes, yet another challenge. | ||
- | **Supervisor: | + | In this project you may collaborate with graduate students |
+ | of the DisCoVeri group (discoveri.eecs.yorku.ca) and | ||
+ | computer scientists of NASA. For more information, | ||
+ | free to send email to franck@cse.yorku.ca. | ||
- | **Required Background: | + | **Required Background: |
- | + | ||
- | This project implements and evaluates a new method for 3D Rotation where the user uses both a 2D and 3D user interface to complete the task. The fundamental idea is to use the 3D interface for large-scale manipulation, | + | |
\\ | \\ | ||
------------ | ------------ | ||
\\ | \\ | ||
- | ====== Immersive Virtual Reality Kitchen Planner ====== | ||
- | **Supervisor: | ||
- | **Required Background: | ||
- | This project implements a kitchen planner application for an immersive virtual reality system. The implementation will be based on Unity 4. | ||
- | \\ | ||
- | ------------ | ||
- | \\ | ||
- | ======3D Interaction in Immersive Virtual Reality====== | ||
- | **Supervisor: | ||
- | |||
- | **Required Background: | ||
- | |||
- | This project implements and tests various 3D Navigation and 3D Interaction methods in an immersive virtual reality system. The target is to enable the user to roam freely in a large environment while still being able to interact with the environment. The implementation will be based on Unity 4. | ||
- | \\ | ||
- | ------------ | ||
- | \\ | ||
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\\ | \\ | ||
- | ======Reliably tracking horizontal eye movements====== | ||
- | **Supervisor: | ||
- | |||
- | **Required Background: | ||
- | |||
- | **Description: | ||
- | |||
- | \\ | ||
- | ------------------ | ||
- | \\ | ||
======Model-based Design and Development of Embedded Systems with Code Generation Tools====== | ======Model-based Design and Development of Embedded Systems with Code Generation Tools====== |
projects.txt · Last modified: 2016/01/13 20:05 by stevenc