Hi all, As I’ve discussed before I’m using the python NLTK to predict the Ontology Tags from the Ontology Foundry of microarray annotations. I have a background in machine learning and prediction algorithms but the “natural language” part is new to me. So I’m blindly gathering all of the “features” I can from each sentence [...]
Archive for February, 2009
Featuring the FeatureSet
Posted in Natural Language Processing, tagged NLP on February 26, 2009 | 3 Comments »
Is MiNiML Enough?
Posted in Natural Language Processing, tagged beautifulsoup, GEO, NLP on February 25, 2009 | Leave a Comment »
Hi all, So I started parsing out some of the data from the GEO records for the automated prediction. NCBI has both made my job slightly easier and immeasurably harder at the same time. First the good, in 2006 NCBI adopted the MIAME (Minimal Information About a Microarray Experiment). Shortly afterwards it released MiNiML, an [...]
Unnatural Language Processing
Posted in Natural Language Processing, tagged NLP on February 23, 2009 | 3 Comments »
I discuss my initial reactions to using the Python NLTK to process the natural language definitions of the ontology terms and apply them to the unnatural language of the GSM descriptions.
Games in Tagging
Posted in Future Work on February 19, 2009 | Leave a Comment »
I discuss the possible solutions for my tagging problem. I suggest a crowd-sourcing method similar to Luis Von Ahn’s Games With a Purpose (http://www.gwap.com/gwap/) which could create a long-term solution to continually update relevant tags.
Automatic Bug Assignment?
Posted in Automation, Future Work, Project Management, Quick Thoughts, tagged Automation, fogbugz, unit-testing on February 18, 2009 | 2 Comments »
I discuss the possibility of having my automatic build server send off e-mails to register as bugs in my FogBugz account.
Depending on the Dependencies
Posted in Automation on February 18, 2009 | 1 Comment »
Hi all, In a recent blog post I discussed dealing with dependencies. A post on the Joel on Software blog in gave me the idea of setting up a separate build server to run automatically. Whenever I work on a project and come across a dependency I just beat at it until I can get [...]
Will Going Psycho Help?
Posted in Future Work, tagged pyscho, wxPython on February 17, 2009 | Leave a Comment »
I discuss the possibility of using Pyscho to help speed up parts of my Python code.
Past 100 Commits
Posted in Uncategorized on February 17, 2009 | Leave a Comment »
Hi all, I noticed today that I blew past 100 commits last week. Here’s hoping that the next 100 will go just as quickly -Will
Dependencies you can Depend on
Posted in Development, tagged beautifulsoup, jinja, wxPython on February 17, 2009 | Leave a Comment »
Hi all, Sadly nobody gets to program in a bubble. Everyone has deadlines, legacy code, legacy computers, legacy programmers, etc. We also don’t have unlimited time to “re-invent the wheel” at each opportunity. Assumming you’re doing an open source project (much like this one), you can incorporate other people’s tools into your own code. If [...]
Lifting the Fog Around Time to Completion
Posted in Project Management, tagged fogbugz on February 13, 2009 | 4 Comments »
Hi all, A whirlwind of grant applications have kept me from doinag any programming on my own projects. Although writing a 25 pg R01 grant in 60 straight hours has to be at least a university wide record. During the handful of 5 min breaks I took to allow my brain to re-solidify I [...]
