Firas Wehbe

A novel information retrieval model for high-throughput molecular medicine modalities

2009-05-27T16:54:00.006-05:00

Finally this paper in Cancer Informatics is indexed by PubMed. This paper describes the early "model formulation" phase of my PhD work. As I approach the end, and obtain more shareable results, I will include more Biomedical Informatics resources on this website.

More information about the paper:

Title: A Novel Information Retrieval Model for High-Throughput Molecular Medicine Modalities
Authors: Firas H. Wehbe, Steven H. Brown, Pierre P. Massion, Cynthia S. Gadd, and Constantin F. Aliferis
Journal: Cancer Informatics
Keywords: clinical bioinformatics, information retrieval, molecular medicine, predictive models
Links: PubMed, PubMed Central, Journal Link, PDF File, Export to bibliography
Licence: Creative Commons Attribution By License

Abstract:

Significant research has been devoted to predicting diagnosis, prognosis, and response to treatment using high-throughput assays. Rapid translation into clinical results hinges upon efficient access to up-to-date and high-quality molecular medicine modalities.We first explain why this goal is inadequately supported by existing databases and portals and then introduce a novel semantic indexing and information retrieval model for clinical bioinformatics. The formalism provides the means for indexing a variety of relevant objects (e.g. papers, algorithms, signatures, datasets) and includes a model of the research processes that creates and validates these objects in order to support their systematic presentation once retrieved.We test the applicability of the model by constructing proof-of-concept encodings and visual presentations of evidence and modalities in molecular profiling and prognosis of: (a) diffuse large B-cell lymphoma (DLBCL) and (b) breast cancer.

344pounds.com

2009-04-10T17:56:00.000-05:00

I am very inspired by Tyler's online pledge to lose 100 pounds. Visit his website and help him meet his goal. I wish I was brave enough to document my training/weight-loss goal.

Magnetic Movie

2009-04-08T16:04:00.000-05:00

Magnetic Movie from Semiconductor on Vimeo.

The secret lives of invisible magnetic fields are revealed as chaotic ever-changing geometries . All action takes place around NASA's Space Sciences Laboratories, UC Berkeley, to recordings of space scientists describing their discoveries . Actual VLF audio recordings control the evolution of the fields as they delve into our inaudible surroundings, revealing recurrent ‘whistlers' produced by fleeting electrons . Are we observing a series of scientific experiments, the universe in flux, or a documentary of a fictional world?

More info here www.semiconductorfilms.com/root/Magnetic_Movie/Magnetic.htm

An Animate Projects commission for Channel 4 in association with Arts Council England.

CakePHP

2009-01-28T20:40:00.002-06:00

If I am to say one thing this month on my blog, I would praise the CakePHP Framework. I love it. The documentation leaves a lot to be desired, but for me the fun of coding in CakePHP is looking at the code and figuring out how well everything is put together and how intuitive the framework is.

Village Cleaners in Hillsboro Village

2008-12-20T19:08:00.004-06:00

I'm going out of town for two weeks tomorrow morning, and I'm running late on my packing. I also haven't blogged in a long while. Then, why am I taking the time out to write this? It's because I can't look at my open luggage bag without remembering the events of this afternoon and I have to get this off my chest. I even went to the gym specifically to "work it out," but my blood still boils when I remember this, so maybe venting about it publicly will help me rid myself of this negativity.

I, a graduate student, have a very small number of long button-down shirts that are good enough to be worn for family events, specifically my girlfriend's family with whom I will be spending the holidays and for whom I need to appear well dressed and having more than one nice shirt. Two-thirds (i.e. two) of said shirts are currently at Village Cleaners. I was stupid enough not to pick them up until today and not to check what time they closed. I realized very late that they close at 4pm on Saturdays instead of 6pm. So I hopped in my car and got there as fast as (safely) possible. I pulled up at 3:59 (according to my iPhone) in front of the shop. The lights were still on, another car was pulling out and another client was loading his clothes into his car. I got out of the car to find that the door was locked. The employee behind the glass made a sign that they were closed. I smiled and made a begging gesture hoping to change her mind, but she SHOOK HER HEAD. I tried, in mime, to explain that I was leaving town tomorrow morning (including emulating plane wings with my hands). She saw that, but shook her head more, TURNED OFF THE LIGHT AND WALKED AWAY. How mean is that?!?!?! I gathered what little dignity I had left, got in my car and called Maggie (I wanted to time-stamp the moment in my next cell-phone bill just to make sure I'm not crazy! Maggie said her Sprint phone got my call at 4:00).

I'm not saying that they wronged me. They don't have to open past their closing time for anyone. I did, after all, show up late. If fault is to be assigned for me not having my shirts (and for me to buy new ones so that I can wear something for the holiday dinners) then I should take the blame for not getting there earlier. I also know that businesses have to enforce business hours, and that employees have to go home to their own families on time and that books and registers need to be closed. I know all that, and again, I'm not saying they faulted me, but REALLY? Did she REALLY have to treat me that way??

I have been a patron of Village Cleaners for more than 7 years! It's a good mom-and-pop business. The employees know me and I've had nothing but good experiences with them, until know. One person who works there, Jerry, doesn't even ask me for my name anymore! He writes down my weird foreign name on the ticket with no spelling errors. How awesome is that? One time I pointed out that the buttons on the cuffs of one of my shirts were melting. The next time I brought that same shirt, and without saying anything, THEY CHANGED THE BUTTONS. Again how awesome is that? That's why I loved that place and kept coming back. That's also why I felt so upset this afternoon. It's like a good friend suddenly turning mean on you. Did you really HAVE TO turn down a desperate-looking client acting like a mime-clown behind the glass on 4pm on a Saturday night in the holiday season?? Really?? I'm not complaining that they did anything wrong per se, but this is a sure way to alienate a loyal client and to squander YEARS of mutual good will. In an age where rich powerful corporations in Detroit and Wall Street are being hung to dry for incompetence and bad products, small businesses need to capitalize on their charms and personal relationships to hold on to consumers not lose them. Now if you'll excuse me, I will be using the money I saved on this trip from cheaper gas to buy me some shirts for the holidays.

My name is Firas Wehbe, their name is Village Cleaners, and they are located at 2010 Acklen Ave Nashville TN 37212 by the post office. I hope every search engine on the internet indexes this post and I approve this rant.

How True, Dr. Asimov

2008-09-16T10:36:00.006-05:00

I am now re-reading Isaac Asimov's The Gods Themselves published in 1972. The events in the book take place in 2100 AD. A maverick scientist is warning a resistant establishment about his discovery of the dangers of Inter-Universe Electron Pumping, a new found supply of abundant free and clean energy that had revolutionized humanity. He wanted it abandoned. This is his exchange with a senator in the International Congress.

"It is a mistake," [the senator] said, "to suppose that the public wants the environment protected or their lives saved and that they will be grateful to any idealist who will fight for such ends. What the public wants is their own individual comfort. We know that well enough from our experience with in the environmental crisis of the twentieth century. Once it was known that cigarettes increased the incidence of lung cancer, the obvious remedy was to stop smoking, but the desired remedy was a cigarette that did not encourage cancer. When it became clear that the internal combustion engine was polluting the atmosphere dangerously, the obvious remedy was to abandon such engines, and the desired remedy was to develop non-polluting engines."

Inter-Universe Electron Pumping is not a danger to humanity as MANBEARPIG is though :).

The World Won't Blow Up and Here's Why

2008-09-10T15:44:00.001-05:00

CERN Rap from Will Barras on Vimeo.

Freedom Fry — "Happy birthday to GNU"

2008-09-03T13:28:00.002-05:00

I was introduced by my brother to Stephen Fry, an English humorist, actor, novelist and filmmaker. He presents a show on the BBC called Q.I. (Quite Interesting). Allan Davies, the "permanently installed guest", is one of the funniest comedians I've ever seen. Fry is featured in a short film that celebrates the 25th anniversary of the GNU operating system and talks about free software. Free as in "free speech", not "free beer". See link for video and more information.

Back from the Lake

2008-09-01T23:05:00.003-05:00

This picture should sum it up. I miss it already.

Photographing the Science Museum

2008-08-28T01:06:00.005-05:00

I took dozens of pictures at the Smithsonian National Museums (Air and Space, and Natural History) this summer when my parents were visiting. I enjoyed it so much that I nearly declared taking photographs in science museums an official hobby. I love taking my time at museums. Having a camera in my hand establishes that and gives me an excuse to linger and wander around. I came across this article about photographing the science museum (via Boing Boing) that gave me a lot of validation. I promise to put more pictures up from previous and (hopefully) future trips. Here's a link to the set.

Music City Star

2008-08-16T11:46:00.002-05:00

Juggling for Jugs

2008-08-12T14:46:00.005-05:00

I will be running in the Komen Race for the Cure with the Juggling for Jugs team. Please join us or support this very good cause by donating here.

Nashville is Second Least Walkable City in America

2008-07-22T08:21:00.005-05:00

Second after Jacksonville. Yay Nashville.

Hat tip, Akarael.

I Have a New Toy

2008-07-01T12:16:00.003-05:00

... and it is awesome.

Foreign Grad Student

2008-06-19T14:34:00.003-05:00

Get Firefox 3

2008-06-17T17:24:00.001-05:00

White People and Bumper Stickers

2008-05-22T09:03:00.003-05:00

Stuff White People Like

When a white person drives an older car (6+ years old) that has a resale value under $2000, they will coat the entire backside of the car in bumper stickers. Because of the abundance of space they are free to include stickers from all areas of white support: music, politics, the environment, insults to right wing politicians, and various movements that tell people to keep a city 'weird'.

But when white people have a nice new car such as a Prius or an Audi station wagon, the fear of losing resale value prevents them from applying more than one sticker. Therefore that one sticker must properly capture the essence of the car and the political views of the driver.

I feel lame... my choice of the one bumper sticker is WPLN... and it's hanging on an SUV...

Rambo Sambo is Nashville's Starbuck

2008-05-18T11:02:00.008-05:00

That's a combined Roller Derby - Battlestar Galactica reference for ya. Yesterday, we blew away Atlanta 150-65. Rambo Sambo (ramb0 samb0) is my favorite athlete in Nashville. Fullstop. I love how she towers behind the other jammer when - rarely - she's behind and intimidates them. She did that with those tiny devils from Alabama. She also has great spirit and showmanship. I happened to be ringside in the second jam of the third period when she "pulled off" umm... a stunt. I was *gay voice* ecstaaaaatic! After the show my girlfriend, because she is the awesomest girlfriend in the world, asked her for a picture with me. This picture will hit the web soon

ps: I'm deliberately not blogging here about the shituation in Lebanon. I am not in the mood for negativity and comment wars.

pps: Here's the picture

I'm Going to See HER Today

2008-05-05T10:31:00.002-05:00

Third world democracy. Represent.

Dog Mauled by Stray Dogs

2008-03-26T10:10:00.004-05:00

Oh man. Meerah and I were walking this morning when we ran into a woman who witnessed two stray dogs (one of which is probably a pit bull) attack a medium size one. The poor dog was still there wrapped in a blanket. It was bleeding and was not able to move. When I was talking to her, animal control came and took the dog away. She will follow up on its situation, but I think that they will have to put it down. It is a brown-yellow medium size dog with a red collar and no tag. The exact location of where we found it is on the map below. I should have taken a picture to hopefully help the owners find it and rescue it. The two stray dogs had wandered off, and another animal control unit was looking for them. Very sad.

View Larger Map

This is Where I Work

2008-03-25T14:35:00.002-05:00

Sorry for not blogging.

This is Eskind Biomedical Library

It's Snows in the South Too Y'all

2008-03-08T17:25:00.002-06:00

Leaving Town for the Weekend

2008-02-22T14:08:00.003-06:00

Short personal note: I'll be out of town, and possibly out of cell phone range for this weekend, on a small get-away trip. Check out Jude's eclipse photos taken from Edwin Warner Park area. Cheers.

Don't Miss the Lunar Eclipse Tomorrow

2008-02-19T17:06:00.002-06:00

This hemisphere will see a complete eclipse tomorrow, Wednesday February 20, the last one before December 2010. The partial eclipse will begin at 7:50pm. The total eclipse will start at 9:01pm and end at 9:51pm (CST). I want to be outside to watch it, might go to Lover's Circle or even Edwin Warner as one of my friends wants to take pictures with her fancy SLR. The Adventure Science Center will be open with telescopes. Hope you enjoy it.

Progress to Reach Bell's Bend

2008-02-15T12:00:00.005-06:00

Please sir, don't turn Bell's Bend into concrete. [Where Meerah and I have been spending Sundays recently with human and canine friends]. The developers proudly proclaim that:

Their vision includes an amphitheater, a hotel, stores, condos and offices clustered around a central area designed to attract corporate headquarters.

... BUT they need a little help from the governement...

Access to the area also may prove to be a problem. May's proposal is contingent on the construction of a new bridge across the Cumberland and a new interchange with Interstate 40, projects that would need government approval and funding.

... more details (emphasis mine)...

The developers' $4 billion concept, called May Town Center, would create a dense commercial and residential district near the southern end of the Bells Bend area.
It calls for building up to 5,000 townhouses and condos and at least 5 million square feet of office space mixed in with street-level stores. A hotel would stand at the center of the development, and four building sites for corporate headquarters would be created on its western end.
Construction would cover 453 acres, leaving 981 acres as a conservation area. That area would be connected to the 808-acre Bells Bend Park, which lies to the west. Equestrian, bicycle and footpaths also would connect May Town Center to areas to the north.
The design is meant to preserve as much of Bells Bend as possible while giving Nashville a new site to attract big corporate development in the same way that Cool Springs has drawn companies to Williamson County, said Giarratana, whom May hired to advise him on the project.

Yes, just like Cool Springs! I can't wait to have a place with a unique character that doesn't look like anything else in the United States. I'm a techie, a scientist, and an avid believer in the boundless opportunities of human ingenuity, but somehow this doesn't strike me as progress. Sorry. I do also have a strong libertarian streak. That's why I can't really understand how building and maintaining expensive roads and bridges to nowhere [to seed economic growth and tax base expansion, i know i know] isn't a form of government community engineering. I really can't see how subsidizing such endeavors helps existing and neighboring communities. I'm not saying it's necessarily harmful or wrong. I'm just pointing that increasing land value, expanding the tax base, and creating jobs aren't sufficient indicators of the future wellbeing of the existing population there, also known as the current constituency.

My argument is stupid, of course, if we assume that the goal of local governments is to swap the existing constituencies that elected them with others that are more willing to produce and to consume.