Ed's Big Plans

Computing for Science and Awesome

Meeting with Chris Cameron

without comments

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.