This past week, we participated in our school's Undergraduate Symposium. Simmons holds this event annually, allowing students to showcase the work they've done throughout the year. Many students present their work at panels, but for our project it made more sense to participate in the two hour poster session. It was really interesting to see what other students have been working on and I think our work was well received! We talked to a lot of professors and students, many of whom were in the health sciences. We had one of the few computer science posters, and many people we talked to were interested in the intersection of those fields.
I think there are still questions to be answered about our corpus, like how clearly medication affects future symptoms. But overall, I'm happy with the work we did and the final poster we created. It was a great experience and I'm excited to be attending and sharing our work at the Tapia conference next fall!
This week Katie, Stephanie and I worked on our poster for the Undergraduate Research Symposium here at Simmons. We worked on finalizing data and planned out what information and graphics to include on the poster. Of course, we also spent a while picking out the best color scheme to use. I participated in the poster session last year, but this is my first time really working on a research-focused poster, so I'm excited!
Over the past few weeks, I've been working on a number of things. I had to alter some of the CSVs I created, because my original files were counting symptoms as mentions of a condition. Analyzing symptoms would be interesting as well, but at this stage we are only looking at direct mentions of medical conditions. To simplify things I created a program that will populate any CSV based on the tag you input.
We recently submitted a proposal for the undergraduate research symposium here at Simmons. Since we're nearing the end of the semester, we've also begun writing a final paper on our project.
I've been working on primarily the same project throughout this time. Trying to find the total number of discrepancies in smoking status was pretty tricky, but I was able to find this number after doing some research and much perseverence (yay!). I also took some time to learn how to use knitr, a package in R that allows me to create html documents so I can easily share my code and results and reduce risk of error. As a group we also submitted a proposal to the undergraduate research conference at our university.
This week I will finish the functions in R that I began to code this week to check for patients with smoking discrepancies, I will also begin to write a function to check for total numbers of discrepancies. Lastly I will write a report for the discrepancies for diabetes status.
Last week I began to brainstorm on ways to attack the problem of smoking status. This week I will be meeting with an outside professor to get some advice on how to go about doing this. I will also be rerunning the analysis on the diabetes discrepancies and creating a report on the findings.
During week 15, I worked on extracting diabetes mentions from each medical record and writing them to a CSV file. I formatted the file based on what will work best for Stephanie when she goes on to analyze the CSV in R. It took me a while to work out all the bugs, but I had an accurate CSV by the end of the week. Just skimming the file I could see that a surprising number of records never mention the fact that the patient has diabetes.
Now that I've developed the script to go through each record, extract diabetes mentions, and write them to a CSV, doing the same with other tags will be much easier. I also created a CSV file detailing the patient's smoking status. Though this file was relatively simple for me to create, it will be harder to analyze since someone's smoking status can change over time.
Currently, I'm working on going through this same process to create CSV files for family history and other tags.
This week I will begin to work on the problem of finding discrepancies of smoking statuses. In our weekly meeting we discussed some of the challenges that will come with this - primarily that smoking status can change in a much more complicated way than diabetes status. In the case of diabetes the patient must have had diabetes, so if they did not we knew there was a discrepancy. Smoking status, on the other hand, can switch back and forth many times However, if a patient is listed as a smoker in the first visit, and then as never having smoked in any later visits then there is a discrepancy. This is definitely going to be an interesting project.
These weeks were spent writing code in R in order to look for discrepancies pertaining to the diabetes status of the patients in our corpus. I met a few bumps in the road but was able to collaborate with an R expert and found a solution. I also learned of the perils of using loops and R!
This week, we worked on completing our poster proposal. I did a lot of background reading for this, mostly from the Journal of Biomedical Informatics. They recently released a special volume full of articles pertaining to the i2b2 Shared Task, which is where our corpus of records came from. Seeing how other teams approached the task was interesting, as well as seeing if they addressed missing and inaccurate data.