Ed's Big Plans

Options options. One of the problems I’m encountering now is that I’ve hit the edge of knowledge that both me and Stefan are capable of accomodating. When it comes to cheminformatics, having me probe the edges of this space has me realizing I’d probably need some help. If performance is good enough in the next experiments, then I think we would both benefit from snagging in a third person involved with chemistry to help author the paper. Basically, we’ve got experience writing for the machine learning and computer science crowd, but I think a potential paper is most viable in the chemistry and biomedical crowd– Just look at the number of ACS publications with the phrase “QSAR” in the tagline. Someone that’s written chemistry papers in the past and can figure out what looks best in that culture would improve the odds of an accepted paper… This of course opens the door to gearing a more general publication for the comp sci crowd once a different problem area has been formalized.

Just a thought.

Chris is a student working on a summer project towards starting a Master’s degree soon. We’ve been meeting semi-regularly so that we can discuss his project ideas and so that I can offer assistance with whatever cheminformatics / bioinformatics software, datasets and any other technologies that have come up in his work.

Today’s meeting was kind of interesting– it involved revisiting the idea that the NGN can be integrated in a larger expert decision system, and also that the NGN can itself operate as a molecular kernel whose output can be then fed into some other decision machine. Dr. Kremer had a few ideas, but I didn’t quite grasp what was being conveyed– it can however be narrowed down to three specific designs.

• The NGN output can be used as features in a larger molecular descriptor vector space.
• A different NGN tuned toward a specific kind of problem is selected from a panel of NGNs trained at different problems; this selection is done by an expert (decision tree, or some other state machine).
• The NGN can output an x-dimension array; for instance, a 3D grid of outputs is output so that on the three axes are labeled ‘species’, ‘LD50 class’ (lethal dose for 50% of the population), and ‘target organ or tissue’

As a side note, we decided it might be good to look at the traditional QSAR task with traditional descriptors and the good ol’ feed forward neural network. I’ll prepare the general neural network software for Chris that I used in Experimental Design; the first version I sent in had too much stuff in it, I’ll basically strip it down to “just operational” so he can actually understand the thing.