Ed's Big Plans

So a more or less solid date has been set for the Masters’ defense– it’ll more likely happen on July 15th.

The final pre-defense revisions for my thesis have already been sent in, and I’ve just signed the request for examination form today.

The primary focus of any slide show I put together for the presentation must be about all of the new work put into the NGN with less emphasis on the background. I’ve also been advised to mention the math while not going into its detail.

I should get going on those slides.

Brief: Met with Stefan today. The conference paper we’re working on has a page limit of eight pages, not six– but I’ve just been told this must include everything including the references and of course figures. With respect to the thesis, the request for examination paperwork has just been completed, and the abstract for the thesis document has been submitted. A few corrections are to be completed on the thesis document. Present work focuses on said corrections, the conference paper and software completion for Chris’ project. There is presently no benefit to working on anything more in parallel.

Brief: Due dates set up — June 22 for all software upgrades and experiments to complete for paper MSc-X1– July 10th is the final due date of the paper to submit. Conference is on November 1 to 4, Washington– note schedule conflict with iGem October 31 to November 2, Boston. No new fields of application to report (would have been nice).

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.

I mentioned in a very hand-wavy fashion that the NGN can also be used in image recognition. I think after the regression stuff is done I should really brain storm with Stefan about what other applications would be quick to implement with good results.

The thesis document is relatively mature. Release-Candidate 2 is going to be the final major revision. A few minor changes remain now for the paper, and after that– it’s off to defend.

What do you know? It turns out Cara was right all along– check out the below diagram of a random-search network– you don’t need to know exactly what a random-search network is, just that there are fat arrows connecting long rectangles.

The problem with this diagram is that the arrow coming out of the Input Layer and going into the Output Layer is placed underneath the Hidden Layer– Cara immediately understood that this was a problem (the visual occlusion makes it confusing), but I didn’t quite “see” it– Stefan added his vote as well, so a clarified diagram (below) will replace this item.

This of course is not the only change needed, but I thought it was a relatively cute and visual one. All diagrams relating to the NGN however need to be retuned so that node layers are now represented by a single node icon (circle or triangle) inside a layer (rectangle) with an integer stating the number of nodes; this is again more abstract than it is now, where each node gets its own icon and no integers are used. The new version of RC-2 along with thesis-style formatting is due out on Friday. I dub it V1.0.

(A part of me still wants to include diagrams describing work from Walsh and Mohr… This may be possible if time permits)

A few requirements go along with the thesis– for one, I need to sign a licensing agreement allowing the University some reign and privelges over the document (that’s fair), but I retain rights to it as well. I think it might make sense to break it up into logical segments and post the contents in my wiki. In particular, diagrams that will be changed will be missed (I find one-bubble-per-node more aesthetically pleasing, but Stefan and I have compromised by putting the integers inside each node bubble icon instead)– so they will likely make it into the wiki version along with the revised diagrams.

This is it… the home stretch…