2 Chapters done and number three on the way…..

What a relief they are done and i’m happy with them Yay!!!
Have all my appendices done and all my experiments and tables/figures sorted so everything is going to plan

All i can say is

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The last few weeks and the 6 weeks to come

Been a few weeks since I lasted posted. Just been too entrenched in the project to put any comments up. Thought it about time! Well I’ve nearly finished the first chapter of my report and I’m now ready to write up of all my experiments which is good. I have my meeting with my project supervisor and assessor tomorrow to show them the work I have completed to date. Pleased with what I have done and I am looking forward to some constructive comments to enable to present my work in the best possible way. Have 6 weeks to go I feel happy at the progress although, the challenge is to ensure that I explain fully on how difficult this has been the challenges i’ve faced and how I overcame them. This has definately been the hardest thing I have done in my life and has stretched my grey matter to the limits!!! Any must go as I have loads to do before tomorrow. The inspiration for today comes from Carly Simon – great song from a great movie “Working Girl”… used to play this alot when i was at work trying to climb up the greasy pole and now its more climbing up the mountain to get this project finished to allow me to move on to fresh new challenges. Enjoy! http://www.youtube.com/watch?v=cv-0mmVnxPA

WEKA Bird!

Well its been a few weeks since I last posted. Haven’t been putting my feet up. oh nooooooooooo! But in fact have been building various arff files to load into WEKA with some of my practice data. I don’t have any verbal autopsy data yet although I do hope to acquire some soon. Currently I am using some anonymised discharge summary data from the US which at least enables me to the the annotations GATE and get me to the position of building an arff file and loading into WEKA. It has been a struggle the last few weeks as I learn GATE and understand its functionality. Despite this I am enjoying the project. Its an excellent opportunity and challenge for me. I hope to be in a position to have completed all my initial experiments by mid next week on the dicharge summaries. Currently I working on predicting Pneumonia, COPD and Coronary Artery Disease diagnosis. My first attempt using the practice data. Will present this to my supervisor. Just need VA data now 🙂

Interim Report – Share the Joy :)

Got some productive and useful feedback from my supervisor on Wednesday on my first draft of my interim report. Today I have found some more research articles, some useful ones on GATE and WEKA. Although in my enthusiasm seems to have put me back a little in the report writing. However, will get the report in on time as I have planned. In need of some fun as its been sorely lacking today and my brain is mashed. Only thing for it The Trammps and “Disco Inferno” – Disco don’t get any better than this! Get down!!!!!! http://www.youtube.com/watch?v=A_sY2rjxq6M

Interim Report Joy!

Had a very productive day on Wednesday of last week – took my supervisor through my mind-map of my project. Its huge! 6 flip chart sheets put together and this just covers the literature review and overview of subject. Will be drafting another for the prototyping which i plan to start after the 18th June. Spent time with a colleague looking at GATE – this hopefully is going to be my text processing tool. Seems quite intuitive but I am going to give it another go on 16 June with some medical text data. Since last week I have spent writing up the first draft chapter … proving to be very challenging considering all the data I have captured. I have circa 50+ articles and ever rising….. Anyway despite the challenge I will have a draft for his perusual by this Weds. Gives me then a day to review before I hand it. Motivation music for tonight… John Parr’s “Man in Motion” an 80’s classic!

Verbal Autopsy Data

Been working all weekend to get information on VA practices, methods and tools. Got significant amounts of information. Whilst doing the searches found a very interesting possibily worrying (maybe not) site www. interVA.net which is already interpreting VA data in children, adults (including one which is female gender specific). To discuss with my supervisor on Wednesday this week, amongst with all the rest of the information I have found. I have put link onto my blog. Have put a selection of all the useful research articles on the blog… Haven’t yet started on discharge summaries or GP notes… must press on tomorrow. Definately bed time now… can’t keep my eyes open anymore.

Elvis has re-entered the Building!! :)

Its a long long time since I been on my page… Had my hands full with my “skool” work and exams but they are now finished hurray! So after a very good bank holiday weekend its now back to work… back to MY PROJECT. Had a good meeting with my tutor on Wednesday -Venn Diagrams will never be the same again! So I am now doing my literature search. Basically its got 3 strands 1. Looking at Medical Text Sources – areas such as verbal autopsies, discharge summaries and GP Notes (System 1 and other Systems) 2. Medical Analysis and Diagnosis Techniques – Current analysis of V.A, Discharge Summaries etc How they are done. In other words look at the manual “efforts” involved. 3. Look into the data mining techniques which underpin the medical text sources – what are they how do they work, are they any good… whats out there already, think about WEKA and Gate. Also have a look at other universities to understand what their research groups are doing.. And then knock up a report (easy said than done!) on these areas… So as you can see will be very busy in next few days. I see from the timetable that the interim report is due on the 18th June so need I to get stuck in. Went to see a colleague who is doing some similar work on Wednesday too… good to see her. So all in all a good week so far… Finding the literature search a challenge, but expected it… so many articles… Been looking at articles since 8.30am this morning…. Rocky IV soundtrack now on for the final push before off to make tea….

NLTK here I come

Just started to work through the tutorials on NLTK…. moby dick, book of genesis and monty python here I come…

Just getting started…..

Well I have set up my first blog…  It will track my journey to hopefully the succesful conclusion of  my Msc project. I have chosen something challenging, but hopefully rewarding and interesting 🙂

My project has 2 main aims – to build a text analytics tool to tag the key aspects of verbal autopsies identifying SNOMED codes which match the natural language terms and then use the SNOMED codes in WEKA to train and test a classfier to predict the diagnosis from the SNOMED codes. 

From this  I know I will be kept busy between now and 2nd September 2010.