Difference between revisions of "User:RBrennan"

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==== Monday 7/5 ====
 
==== Monday 7/5 ====
 
*Implementing clustering algorithm
 
*Implementing clustering algorithm
−
** Came up with a faster solution for checking counts using a table system
+
** Came up with a faster solution for checking counts using a table system (adjacency matrix)
 
** Had to get more specific for tie breakers
 
** Had to get more specific for tie breakers
 
** Had to get more specific for order of operations
 
** Had to get more specific for order of operations
Line 282: Line 282:
 
* Continued to work on formatting
 
* Continued to work on formatting
 
** Creating, writing, and saving .cxl files
 
** Creating, writing, and saving .cxl files
 +
** Choosing folder UI
 
** Saving file UI
 
** Saving file UI
  
 
==== Thursday 7/8 (morning) ====
 
==== Thursday 7/8 (morning) ====
 +
* Wrote notes  for meeting with Dr. Perouli
 +
* Looked into Markov clustering as an alternate algorithm to my own
  
 
=== Week 6 (7/8 - 7/15) ===
 
=== Week 6 (7/8 - 7/15) ===
 
==== Thursday 7/8 (afternoon) ====
 
==== Thursday 7/8 (afternoon) ====
 +
* Meeting with Dr. Perouli
 +
* Looked more into Markov Clustering
 +
* Looked for alternate ways to find the distance to a cluster for my algorithm
  
 
==== Friday 7/9 ====
 
==== Friday 7/9 ====
 +
* Implemented a rough Markov clustering version of the program
  
 
==== Monday 7/12 ====
 
==== Monday 7/12 ====
 +
* Continued Markov Clustering implementation
  
 
==== Tuesday 7/13 ====
 
==== Tuesday 7/13 ====
 +
* Cleaning up code
 +
** Updating old program to match added features of Markov version
 +
** Updated and added annotations
 +
** Implemented some error checking and small to-do's
  
 
==== Wednesday 7/14 ====
 
==== Wednesday 7/14 ====
 +
* Attended weekly check-in
 +
* Uploaded code to github
 +
* Outlined testing plan
 +
* Added slider to Markov version user inputs
  
 
==== Thursday 7/15 (morning) ====
 
==== Thursday 7/15 (morning) ====
 +
* Prepared for meeting with Dr. Perouli
  
 
=== Week 7 (7/15 - 7/22) ===
 
=== Week 7 (7/15 - 7/22) ===
 
==== Thursday 7/15 (afternoon) ====
 
==== Thursday 7/15 (afternoon) ====
 +
* Meeting with Dr. Perouli
 +
** Went over steps for testing on camp dataset
 +
** Went over code
 +
* Wrote out more detailed testing plan
  
 
==== Friday 7/16 ====
 
==== Friday 7/16 ====
 +
* Started research poster
 +
** Wrote Section for clustering algorithm options
 +
** Wrote section for implementation
 +
** Wrote acknowledgements
  
 
==== Monday 7/19 ====
 
==== Monday 7/19 ====
 +
* Continued working on poster
 +
* Minor code tweaks
 +
* More testing plans
  
 
==== Tuesday 7/20 ====
 
==== Tuesday 7/20 ====
 +
* Picked up dataset from Dr. Perouli
 +
* Digitized student data into Cmap
 +
* Wrote ideas on changes to the program to accommodate maps better
 +
** Split commas into separate concepts
 +
** Ignore spaces, punctuation, new lines
 +
** Check for spelling (Might be too hard to implement right now)
 +
** Rerouting links
 +
** One connection between terms per map
 +
** Ignore plurals
 +
* Wrote ideas for suggestions for students
 +
** Avoid sentences, stick to one or two word terms
 +
** Include cybersecurity (one word)
  
 
==== Wednesday 7/21 ====
 
==== Wednesday 7/21 ====
 +
* Started formatting for paper
 +
* Attended Dr. Brylow's session on graduate school
 +
* Tested functions on real data
 +
** Lots of problems came up
 +
* Fixing problems in code
 +
** Fixed concepts becoming clusters when not supposed to
 +
** Added splitting terms on commas
 +
** Temporarily removed "Extra" clusters while I figure out how to better organize them
 +
* Combined MCL and CCL programs into one for faster editing
 +
** Key functions for the different clustering algorithms have been moved to their own classes
 +
** Other smaller differences are normalized
 +
** User is given the option to choose between methods
  
 
==== Thursday 7/22 (morning) ====
 
==== Thursday 7/22 (morning) ====
 +
* Added extra cluster back into output map as a list on the side
 +
* Started writing instructions on how to use Cmap for cybersecurity camp
  
 
=== Week 8 (7/22 - 7/29) ===
 
=== Week 8 (7/22 - 7/29) ===
 
==== Thursday 7/22 (afternoon) ====
 
==== Thursday 7/22 (afternoon) ====
 +
* Met with Dr. Perouli
 +
** Went over work from last week
 +
** Discussed changes and additions to the program
 +
** discussed to-dos for final two weeks
 +
* Finished Cmap instructions
 +
* More changes to code to adapt for wider array of problems
  
 
==== Friday 7/23 ====
 
==== Friday 7/23 ====
 +
* Started paper
 +
* Some work on poster
  
 
==== Monday 7/26 ====
 
==== Monday 7/26 ====
 +
* Worked on poster
 +
* Finalizing some elements for code
 +
** Final version for now, just need to annotate
  
 
==== Tuesday 7/27 ====
 
==== Tuesday 7/27 ====
 +
* Worked on paper
 +
* Worked on poster
 +
* Added basic element moving and cluster renaming to program
 +
** Did all the necessary back end additions
 +
** Added a simple UI (Series of drop down menus)
 +
** In the future would want to implement drag-and-drop UI
  
 
==== Wednesday 7/28 ====
 
==== Wednesday 7/28 ====
 +
* Finished first draft of poster
 +
* Polishing code and updating/adding annotations
  
 
==== Thursday 7/29 (morning) ====
 
==== Thursday 7/29 (morning) ====
 +
* Worked on paper
 +
* Prepared for meeting
  
 
=== Week 9 (7/29 - 8/6) ===
 
=== Week 9 (7/29 - 8/6) ===
 
==== Thursday 7/29 (afternoon) ====
 
==== Thursday 7/29 (afternoon) ====
 +
* Met with Dr. Perouli
 +
** Talked about paper
 +
* Worked on paper
  
 
==== Friday 7/30 ====
 
==== Friday 7/30 ====
 +
* Worked on paper
  
 
==== Monday 8/2 ====
 
==== Monday 8/2 ====
 +
* Short REU meeting going over last week schedule
 +
* Worked on paper
 +
** Finished ''Automating Collective Maps'' section
 +
** Finished ''Comparing Clustering Algorithms'' section
 +
** Finished ''Implementation'' section
  
 
==== Tuesday 8/3 ====
 
==== Tuesday 8/3 ====
 +
*Worked on paper
 +
** Finished ''Introduction and Related Work'' section
 +
** Finished ''Conclusion and Future Work'' section
 +
* '''Poster due'''
  
 
==== Wednesday 8/4 ====
 
==== Wednesday 8/4 ====
 +
* Worked on presentation
  
 
==== Thursday 8/5 ====
 
==== Thursday 8/5 ====
 +
* Presentations from 10am-12noon
 +
** '''Presenting last @ 11:45am'''
 +
* Poster presentations from 1:30pm-4pm
 +
** '''Presenting block from 2:30pm-3pm'''
  
 
==== Friday 8/6 ====
 
==== Friday 8/6 ====
 +
* Presentations from 10am-12:15pm
 +
* '''Paper due at end of the day'''

Latest revision as of 14:20, 5 August 2021

Contents

Overview of Schedule

Weekly Schedule
Week Tasks Deliverables
Week 0 (6/1 - 6/3) REU Introduction and Bootcamps

Defining schedule, milestones, and goals

Week 1 (6/3 - 6/10) Researching existing solutions Milestones + Goals (due Fri. 6/4)
Week 2 (6/10 - 6/17) Define research problem

Brainstorm solutions

Week 3 (6/17 - 6/24) Research and review Dr. Perouli’s work

Define solution path and implementation steps

Week 4 (6/24 - 7/1) Start implementation of solution

Put together presentation (Most likely 1 day max)

Mini Presentations (Wed. 6/30)
Week 5 (7/1 - 7/8) Implementation and refinement
Week 6 (7/8 - 7/15) Implementation and refinement
Week 7 (7/15 - 7/22) Test implementation with real data set
Week 8 (7/22 - 7/29) Finish Project

Work on research deliverables

Week 9 (7/29 - 8/6) Finishing Research Deliverables Formal Presentations (Thu.-Fri. 8/6-8/7)

Research Poster (Thu. 8/6) Research Paper (Fri. 8/7)

Devote some time every day to formalizing and logging research:

  • Summaries of what I’m working on for wiki
    • Challenges I’m facing, paths I didn’t take
    • Findings and results
  • Annotated Bibliography
  • Anything else I will forget about when it comes time to work on deliverables

Devote at least half an hour each day to emails, scheduling, and other logistics

2021 Weekly Logs

Week 0 (6/1 - 6/3)

Thursday 5/27

  • Met with Dr. Perouli
    • Introduced the project
    • Discussed first steps
    • Discussed goals for the project

Tuesday 6/1

  • Attended REU introductions and data science bootcamp

Wednesday 6/2

  • Attended data science bootcamp

Thursday 6/3 (morning)

  • Attended Good Research Practices Talk with Dr. Brylow
  • Outlined milestone and goals for research
    • Research ways to characterize sets of multidimensional data
    • Determine the best way to do this for concept maps
    • Create executable code for the direction we’ve determined is the best
    • Create cohesive research deliverables on this topic
  • Outlined broad schedule for first 3 weeks

Week 1 (6/3 - 6/10)

Thursday 6/3 (afternoon)

  • Met with Dr. Perouli
    • Adjusted and finished overview of schedule
    • Talked over what previous research I should be looking into
    • Discussed the overarching problem I'm looking into
  • Created wiki and added schedule

Friday 6/4

Monday 6/7

  • Attended Responsible Conduct of Research session

Tuesday 6/8

  • Researching other visual representations of understanding
  • Researching alternate solutions
    • Scoring concept maps
    • Representing understanding through artwork

Wednesday 6/9

Thursday 6/10 (morning)

  • Completed sessions 2 and 3 of CITI Modules
  • Scheduled plan and wrote questions for meeting with Dr. Perouli

Week 2 (6/10 - 6/17)

Thursday 6/10 (afternoon)

  • Meeting with Dr. Perouli
    • Went over work done in week 1
    • Discussed my research so far and areas to look further into
    • Discussed questions I thought of yesterday
    • Discussed goals for week 2
  • Looked further into concept map scoring

Friday 6/11

  • Researched alternate solutions further and wrote up summaries of relation to project
    • Scoring concept maps
    • Assessing understanding with machine learning
  • Outlined answers for questions posed earlier

Monday 6/14

  • Weekly Python coding practice
  • Researched ML solutions

Tuesday 6/15

  • Organized references in BibTex file
    • Wrote annotations for references

Wednesday 6/16

  • Finished alternate solutions slides
    • Broke it down into Drawbacks, Benefits, and Maturity of the Field
    • Added slide for collective concept maps
  • Started researching concept map tools
    • Listed requirements (wants/needs)

Thursday 6/17 (morning)

  • Write-ups for concept map tools
    • FreeMind
    • MindMup
  • Outlined notes for meeting with Dr. Perouli

Week 3 (6/17 - 6/24)

Thursday 6/17 (afternoon)

  • Met With Dr. Perouli
    • Discussed my work over the last week
    • Discussed Plans for upcoming week
  • Read through Dr. Perouli's work on collective concept maps
  • Read through reviews of the paper
  • Researched concept mapping tools
    • Focused on file formatting of each application

Friday 6/18

  • Outlined program steps from individual maps being created to outputting collective map
    • Biggest challenges will be clustering the concepts, stylizing, and creating cluster diagrams (not as necessary)
  • Finished write ups for concept mapping tools
    • Decided on using CMap
  • tested writing sample concept map as propositions and importing to CMap
    • Works, but links are forced to have names and positioning of nodes is messy
    • most likely have to import tan export again as cxl to fix those things (as well as any style changes)
  • Worked on ways to make the map readable
    • Some progress but will likely have to revisit this problem later, will have to research minimum crossing number algorithms

Monday 6/21

  • Created object types for program
    • Concept
    • Connection
    • Cluster
    • ClusterConnection
  • Wrote functions to import a folder of .cxl files and convert them to a list of concept and connection objects

Tuesday 6/22

  • Broke down steps of program into to-do lists
  • Wrote new object classes
    • Map
    • Cluster
    • ClusterConnection
    • Node (superclass for Concept and Cluster)
  • Moved importing code from its own class to Map class
  • Wrote print functions for each list in Map class
  • Minor code improvements

Wednesday 6/23

  • Started to research solutions for clustering problem
  • Attended REU check-in and guest lecture
  • Continued coding
    • Added function for creating ClusterConnections
    • Added functions for tallying Clusters and ClusterConnections
    • Annotated existing code
    • More minor changes and improvements

Thursday 6/24 (morning)

  • Planned meeting with Dr. Perouli
  • Edited research slides

Week 4 (6/24 - 7/1)

Thursday 6/24 (afternoon)

  • Meeting with Dr. Perouli
    • Discussed and asked questions about collective concept map paper
    • Discussed concept mapping software choices
    • Discussed methods for clustering nodes
  • Wrote up more ideas for clustering nodes that came out of meeting
    • Instructor Drag and Drop
    • Instructor Connect Concepts
  • Looked more into pros and cons of yEd and CMap
    • yEd file format still very unusable
    • yEd can organize nodes in a much better way than CMap
    • With inspiration from yEd's circular organization, I think I can create methods to place and organize nodes in the .cxl file

Friday 6/25

  • Worked on ideas for a clustering algorithm based on connections
    • Relies heavily on nodes and connections being featured in multiple maps
    • Probably works best in large groups
    • In smaller groups, it would more likely be very star-shaped

Monday 6/28

  • Attended REU check-in and presentation presentation
  • Conduct of research D2L assignments

Tuesday 6/29

  • More work on clustering solutions
  • Creating presentation for tomorrow
  • Practicing presentation

Wednesday 6/30

  • Attended Presentations
  • More D2L Assignments

Thursday 7/1 (morning)

  • Finished D2L Assignments
  • Made a pro-con list to decide between clustering methods
    • Decided on implementing my algorithm for now
    • Will work on testing and improving the algorithm along the way
    • If it doesn't work out, I will return to the drag-and-drop method

Week 5 (7/1 - 7/8)

Thursday 7/1 (afternoon)

  • Worked on planning out implementation of clustering algorithm

Friday 7/2

  • Off (Moving)

Monday 7/5

  • Implementing clustering algorithm
    • Came up with a faster solution for checking counts using a table system (adjacency matrix)
    • Had to get more specific for tie breakers
    • Had to get more specific for order of operations
    • Probably need to implement some more error checking

Tuesday 7/6

  • Attended presentation by Dr. Zimmer
  • Worked on formatting collective map back into .cxl file
    • Formatting each element into the right syntax
    • Formatting line styling
  • Positioning nodes
    • Pixel width of nodes
    • Circle placement equations
    • Experimenting with distances and margins
  • What's left to do with formatting
    • Creating, writing, and saving .cxl file
    • Connection labels
    • Formatting metadata
      • Title, user info, dates, etc.

Wednesday 7/7

  • Attended Dr. Brylow's talk on creating posters
  • Continued to work on formatting
    • Creating, writing, and saving .cxl files
    • Choosing folder UI
    • Saving file UI

Thursday 7/8 (morning)

  • Wrote notes for meeting with Dr. Perouli
  • Looked into Markov clustering as an alternate algorithm to my own

Week 6 (7/8 - 7/15)

Thursday 7/8 (afternoon)

  • Meeting with Dr. Perouli
  • Looked more into Markov Clustering
  • Looked for alternate ways to find the distance to a cluster for my algorithm

Friday 7/9

  • Implemented a rough Markov clustering version of the program

Monday 7/12

  • Continued Markov Clustering implementation

Tuesday 7/13

  • Cleaning up code
    • Updating old program to match added features of Markov version
    • Updated and added annotations
    • Implemented some error checking and small to-do's

Wednesday 7/14

  • Attended weekly check-in
  • Uploaded code to github
  • Outlined testing plan
  • Added slider to Markov version user inputs

Thursday 7/15 (morning)

  • Prepared for meeting with Dr. Perouli

Week 7 (7/15 - 7/22)

Thursday 7/15 (afternoon)

  • Meeting with Dr. Perouli
    • Went over steps for testing on camp dataset
    • Went over code
  • Wrote out more detailed testing plan

Friday 7/16

  • Started research poster
    • Wrote Section for clustering algorithm options
    • Wrote section for implementation
    • Wrote acknowledgements

Monday 7/19

  • Continued working on poster
  • Minor code tweaks
  • More testing plans

Tuesday 7/20

  • Picked up dataset from Dr. Perouli
  • Digitized student data into Cmap
  • Wrote ideas on changes to the program to accommodate maps better
    • Split commas into separate concepts
    • Ignore spaces, punctuation, new lines
    • Check for spelling (Might be too hard to implement right now)
    • Rerouting links
    • One connection between terms per map
    • Ignore plurals
  • Wrote ideas for suggestions for students
    • Avoid sentences, stick to one or two word terms
    • Include cybersecurity (one word)

Wednesday 7/21

  • Started formatting for paper
  • Attended Dr. Brylow's session on graduate school
  • Tested functions on real data
    • Lots of problems came up
  • Fixing problems in code
    • Fixed concepts becoming clusters when not supposed to
    • Added splitting terms on commas
    • Temporarily removed "Extra" clusters while I figure out how to better organize them
  • Combined MCL and CCL programs into one for faster editing
    • Key functions for the different clustering algorithms have been moved to their own classes
    • Other smaller differences are normalized
    • User is given the option to choose between methods

Thursday 7/22 (morning)

  • Added extra cluster back into output map as a list on the side
  • Started writing instructions on how to use Cmap for cybersecurity camp

Week 8 (7/22 - 7/29)

Thursday 7/22 (afternoon)

  • Met with Dr. Perouli
    • Went over work from last week
    • Discussed changes and additions to the program
    • discussed to-dos for final two weeks
  • Finished Cmap instructions
  • More changes to code to adapt for wider array of problems

Friday 7/23

  • Started paper
  • Some work on poster

Monday 7/26

  • Worked on poster
  • Finalizing some elements for code
    • Final version for now, just need to annotate

Tuesday 7/27

  • Worked on paper
  • Worked on poster
  • Added basic element moving and cluster renaming to program
    • Did all the necessary back end additions
    • Added a simple UI (Series of drop down menus)
    • In the future would want to implement drag-and-drop UI

Wednesday 7/28

  • Finished first draft of poster
  • Polishing code and updating/adding annotations

Thursday 7/29 (morning)

  • Worked on paper
  • Prepared for meeting

Week 9 (7/29 - 8/6)

Thursday 7/29 (afternoon)

  • Met with Dr. Perouli
    • Talked about paper
  • Worked on paper

Friday 7/30

  • Worked on paper

Monday 8/2

  • Short REU meeting going over last week schedule
  • Worked on paper
    • Finished Automating Collective Maps section
    • Finished Comparing Clustering Algorithms section
    • Finished Implementation section

Tuesday 8/3

  • Worked on paper
    • Finished Introduction and Related Work section
    • Finished Conclusion and Future Work section
  • Poster due

Wednesday 8/4

  • Worked on presentation

Thursday 8/5

  • Presentations from 10am-12noon
    • Presenting last @ 11:45am
  • Poster presentations from 1:30pm-4pm
    • Presenting block from 2:30pm-3pm

Friday 8/6

  • Presentations from 10am-12:15pm
  • Paper due at end of the day
Retrieved from "https://reu.cs.mu.edu/index.php?title=User:RBrennan&oldid=4662"