The papers you publish are the lifeblood of a scientist’s career and as a graduate student will form the basis of my PhD thesis. I’ve been lucky so far to have worked with some very talented people and publish a couple of papers in my first two years. However, recently I stumbled upon a discovery which could get me a paper in, by most metrics, the most prestigious journal in the world, The New England Journal of Medicine. Just typing this sentence blows my mind. Anyway, because I don’t think about much else, I’m going to blog about my experience submitting a paper to NEJM and will share all the ups and downs…. cross your fingers for ups!

Update: April 28, 2010

The goal was to submit the paper today. But right before my advisor and I were about to submit the final draft of the paper, and I realized that I left out a whole set of analyses! Doh, now I have to go back to the database to extract more patient records and analyze another set. Looks like, it won’t be today.

Update: April 29, 2010

Okay, made a whole bunch of new figures today, modified the text where needed and sat down with my advisor again. We made some final edits (some of which we should have caught in the previous 16 iterations of the manuscript), but alas we feel great about the paper. Personally, I think it’s a work of art and couldn’t imagine it getting rejected . Don’t worry, I’m not allowing my hopes to get too high. My advisor let me submit the paper and click on all the “double-check-your-submission” links. In his words “you’re not going to be doing this that often, so you might as well click around.” It was fun and it’s amazing I even get to submit to the NEJM, really.

Paper status is now “Submitted” and we got a confirmation email that it will be forwarded to the editors. Time to order some flowers and wine for our collaborators!

Update: April 30, 2010

I have been neurotically checking the author website at NEJM and today our paper was “Assigned to an Editor”, I have no idea exactly what that means, but it’s movement!

Update: May 2nd, 2010

I went on the website today (yes, and yesterday too), not expecting any updates over the weekend, but much to my surprise the status of the paper has changed. It looks like it made passed the editor and they are now looking for peer reviewers. According to a close friend getting passed the editors is a big deal and a lot of papers don’t make it passed that point. Very exciting! — I just read on the NEJM website about the editorial process and it seems that it has been read by the Editor-in-chief and also another expert editor and has passed both of their filters. Here’s to the reviewers liking it! [crosses-fingers]

Paper status is now “Searching for Reviewers.”

Update: May 10th, 2010

It’s been one week and one day since the last update, and I was starting to think that maybe the next update would come when the reviews came back. That is not the case, however. Looks like they found some reviewers for the paper! Not sure how long they have to review the paper, probably a few weeks at least I imagine. I‘ll check with my PI and add that info in here. Looks like its 2 to 3 weeks.

Paper status is now “Out for Review.”

Update: May 20th, 2010

The reviews of the paper have been returned to the Journal, but a decision has not yet been made. The next step is for the editorial board to discuss the paper and make a decision. I’m not sure how long this process takes, but every other time the status included the word “editor” it only took a few days to get another update. Perhaps I will hear something by weeks end. YIKES! This is getting real.

Paper status is now “With the Editor.”

Update: May 25th, 2010

It’s been a serious roller-coaster ride and I have had quite the experience submitting to the world’s most prestigious journal. The reviews came back a few days ago and we just got a chance to read them today. As far as reviews for The Journal go, they are quite benevolent and really quite positive. They made some great suggestions on how to improve the paper and I have already made most of the changes they suggested (they were quite minor). Unfortunately, for us, the editors were not as favorable on us as the reviewers were and they rejected our paper today. Perhaps the paper is too bold for the New England Journal, perhaps it’s ahead of its time. Perhaps, they just don’t like me or my parentage — I simply can’t be sure. But, what I do know is that this is some of the best work I have ever done and there are many other Journals out there. I will get the good word out about this discovery one way or another.

Paper status is now “Rejected.”

Now let’s say you are given a vector x and y, say:

In this case the y values here represent probabilities and one thing you’ll notice is that we have probs of 1 and 0. Both of which are bad. So we apply a little “laplace smoothing” to them:

Now let’s look at what the data looks like.

Well, it may be sigmoidal, maybe not. For now let’s assume we think it is. Which we do for the most part.

Okay, now let’s solve for a line in our sigmoid function:

Now the left hand side of the equation is a line and the right hand side is some logarithm of the y data. We can plot x versus this right hand side:

Looks pretty interesting and hopefully at this point it also looks kinda linear, which it kinda does.

Now let’s fit it with a line:

Which produces this output:

We can also test the significance of the fit with an ANOVA.

Which produces this output:

And we can plot the resulting fit in linear space:

Now let’s see how our fit looks back in normal space using our formula with our derived a and b values.

Voila! We have fit a sigmoid function to our data.

http://tinyurl.com/2wjoxy

NPR recently did a story that teenagers have been using the above sound as a ring tone to evade the prying eyes ears of adults.

So we started a little investigation of our own, and we need your help! Just click on that sound file, play it, and respond in the comments with your age, gender, and if you can hear it or not.

SCIENCE!

I have to give some serious props to the devs of CUDA because it is very straight forward and makes programming for the GPU rather intuitive.  I have been able to implement the Lloyd’s Algorithm for the K-Means problem in just a few days.  The speed increase is graphically represented in the following graph.

In green is the time in seconds required to compute the kmeans solution using the CPU and in red is the time required for the GPU.  The variance in the times comes from the nature of Lloyd’s algorithm which, depding on the input, can take a variable amount of time.  The GPU times are also varied but it is difficult to see in the figure.

These results are just from running the application on my MBP.  If you have a machine with many graphics processors (or many machines each with their own GPU) then you can parallelize this even more and massively boost your computational power.  In my opinion the GPU architecture is the future of scientific computing as so many of our computational challenges can be addressed using parallelization.

For those that are interested I will be writing up some CUDA tutorials covering Installation/Set Up, A “Hello World” example, and the full K-Means implementation over at MacResearch.org.

(Perhaps definatively, my spellcheck says there both wrong.)