My current (2012) R&D in computational linguistics – especially for biology text

Now that I’m retired, I spend a lot of time on what is essentially a re-development of the system described in our 1999 paper, 

NLP-NG – A New NLP System for Biomedical Text Analysis accessible at

I have moved beyond the above paper in some ways.  But I’m not throwing out the old, only building on it in a systematic and focused way. Else, I could spend forever on still more variations – that would be my bad.  For those of you in the Java/NLP world, I’ve discover useful capabilities in PostgreSQL, TreeSets, and TreeMaps.

I find that I now have enough time to design code that is tight and well-structured. Much of the code in my earlier work over the years had to be written in haste. Looking back at it, I can see its limitations.

I won’t go into detail, as the system will be under wraps for quite some time, since it’s complicated and I am the only developer.  No release until solid NLP results are produced.

My schedule allows me to spend as much time as necessary on any aspect of the project that I deem important.   For example in late April, 2012, into May and beyond, I am schooling myself in Java Swing.  I’ve used Swing for years, but the time has come to buckle down and become a Swing Master.  I’ll also be looking just as deeply into many  NLP-related areas.

What is Java Swing?  Swing is a set of Java-based tools for constructing GUIs (Graphical User Interfaces).  It’s designed to produce applications (apps), rather than web-based systems (web-apps).  Apps are like Word or a browser that can be run and used without any connection to the Internet.  A web-app  runs in your browser, e.g., Gmail.

A GUI is the “face” aspect of an application, what you see and interact with.

Java runs (essentially) identically on Linux, Mac, and Windows, so Swing does too.

Deepening my approach to my work/research.  In the past, I could get results by choosing the right topics and using my ingenuity to produce good results (to the tune of 60+ papers).  But that has its limits.  It’s time to step up to mastering the hard math, theory, etc. that will raise the level of my systems and their results.

I’ve learned that without this, others can’t understand what I’ve accomplished, no matter how good it is, because they can’t inspect my intuition.

Stay tuned.


About heartandmindandme

Husband and father. Wise and droll wife and three wonderful kids. Scientist all my long life - Physics, Biology, Computer Science, and more. Washington, DC and Leesburg, VA public schools. MIT bachelor's and PhD. Faculty member of U. of Illinois and Northeastern U. for 25 years until recent retirement. Member of Marine Biological Lab, Woods Hole, MA. Like: Classical music plus instrumental folk and old jazz, or just sit and watch the sky, trees, birds, rain, wind, and snow.
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