Tuesday, October 30, 2007

hitting the radio waves

The next laptop you buy might be souped up with some gadgets inspired by top secret satellite systems. Engineers from UC San Diego are shrinking down the "phased array" chips that for years have been used on ships and airplanes to detect incoming ships, planes and missiles.

This is yet another transfer of military technology to the commercial world. Intel is funding a project here at UCSD to develop laptop gadgets capable of blazing fast data transfer over radio waves.

Check out the new press release from UC San Diego here. There is very little written in the popular media about phased array chips, but you can get a start at Wikipedia.

The UCSD student newspaper, The Guardian, ran a story on this research.

"According to Gabriel Rebeiz, the UCSD electrical engineering professor who proposed and oversaw the project, the chip breaks many world records in its intricacy and compact size. 'No one has ever been able to use silicon … to put 16 channels at this frequency range, with excellent amplitude and phase balance between the channels, and with phase control for each channel,' Rebeiz said in an e-mail. 'No one. Not even Raytheon, Boeing or Lockheed. No one. This is a first in every aspect.'

You can read the full UCSD Guardian story here.

Wednesday, October 17, 2007

Metastasis Mystery Unravelling at UC San Diego

The diagrams above are networks of proteins that are involved in the spread of breast cancer.
This image is from a new paper from a UC San Diego bioengineering professor (Trey Ideker) that provides new insights into which patients with breast cancer need chemotherapy and which patients may not need this aggressive therapy.
Technology Review has a great description of this research project, written by journalist Katherine Bourzac.
This is how the Technology Review story starts:
Using Molecular Pathways to Assess Cancer Patients

The first complete map of protein interactions in human cells could lead to
better treatment for breast cancer.

Researchers at the University of California, San Diego, have created a map of all known protein networks in human cells and shown that it can be used to better assess whether a patient's breast cancer will spread. Their work, though in its early stages, could lead to better diagnostic tests that spare patients toxic treatments, such as chemotherapy, if they are unnecessary. The researchers also expect that their approach will be widely applicable to other diseases, including other cancers and diabetes. Read more:

More info:
Read the press release from the UCSD Jacobs School of Engineering.
Read the paper abstract and introduction at Molecular Systems Biology (MBS)
Check out the Ideker lab

Tuesday, October 16, 2007

Context is Next

Looking at the photo above, you see a person on a tennis court, wielding a tennis racket and chasing a...lemon. Right?

Wrong. You don’t think it’s a lemon. You know it's a tennis ball.

A computer might not be so perceptive. A computer with the latest image labeling algorithms would have no problem making the following list of objects for the photo above: person, tennis racket, tennis court, lemon.

The only lemon I can imagine on this tennis court is in the water bottle of the line judge.

Computer scientists at UC San Diego and UCLA are looking to give automated image labeling systems a little more common sense. And that common sense comes in the form of context. And they are squeezing some of that common sense out of a little-known widget from Google Labs called Google Sets.

“We think our paper is the first to bring external semantic context to the problem of object recognition,” said computer science professor Serge Belongie from UC San Diego's Jacobs School of Engineering.

Belongie and his students (including Carolina Galleguillos -- the lead singer for the band Audition Lab) are presenting their "lemon blaster" this week at ICCV 2007 – the 11th IEEE International Conference on Computer Vision in Rio de Janeiro. The computer scientists show that the Google Sets can be used to provide external contextual information to automated object identifiers. The context is added in a post-processing step that comes after the image is split up into parts and labeled by a computer.

A full press release will be available here, on the Jacobs School Web site.

A copy of the paper is available here

Check out the write up on the Wired Science blog

Monday, October 15, 2007

Qualcomm Innovator Challenge

The Voracious Savants: (L-R) David Wong, David Swartz, Andrew Smith, Aaron Swartz
photo credit: Chris Morrow

The biggest challenge for one of the four winners of last weekend's QUALCOMM Innovator Challenge came in a surprising moment: AFTER his team had won first prize and $5,000.

David Wong (far left) had to convince his parents to hand over his social security number so he could fill out the necessary tax-related paperwork to get his check. In the end, after a lot of convincing by the project manager at UCSD, the parents decided it was okay to share the sensitive information.

The first prize winners called themselves the Voracious Savants. They envisioned a portable device that lets you watch TV while you do your homework won first prize and $5,000 last night at the QUALCOMM Innovator Challenge. With BookPal you can also take digital notes, page through hundreds of pounds of text books and cruise the Internet. Turn BookPal on its side and you can start typing as if it were a laptop.

The Voracious Savants (majors: mechanical engineering (2), electrical engineering and undeclared) – was one of 17 teams that presented their designs for how you could use QUALCOMM’s new, ultra powerful Snapdragon platform. Three of the four winners were high school friends from Carlsbad.

The event was organized by the Jacobs School’s Corporate Affiliates Program and QUALCOMM.

Second prize and $3,000 went to another all-freshman team: Athena. The four bioengineering majors envisioned a portable electronic device with a screen that rolls up and fits in your pocket when you’re not using it. You unroll it when you want to watch Internet videos or do anything else you can do with today’s PDAs.

Athena had a
sweet video in their presentation. I think you need to be a member of facebook to see it...below...here they about to roll-out (literally) their organic light emitting diode screen.

Team Athena rolls out its design concept. photo credit: Chris Morrow

Third prize and $2,000 went to the five seniors (four engineering majors and one Cog Sci major) who make up team Greek Fire. They designed “MediBoard.” This digital clipboard is supposed to help doctors and other health care professionals work together better – both within the same hospital and across the world. MediBoard will also help doctors share their medical expertise and provide better support to doctors working in areas with little or no medical infrastructure.

Monday, October 8, 2007

Which came first, the chicken genome or the egg genome?

Looks kinda like a chicken, right?

I thought so too. This is genomic duplication data from figure 2 from a Nature Genetics paper published online today.

The title of the press release is: "Which came first, the chicken genome or the egg genome?"

But the paper is really about a different "which came first" question facing scientists? and one that -- if answered fully -- will help to explain exactly how we modern humans came to be. And it will give us a whole lot of new insights on genomic disease as well. The human genome is full of duplicated chunks of DNA that have played important roles in evolution, and which are involved in disease. The new research provides tons of new data on which of the copies of thousands of DNA segmental duplications in the human genome are the originals and which are the copies.

“Identifying the original duplications is a prerequisite to understanding what makes the human genome unstable,” said Pavel Pevzner a UCSD computer science professor who modified an algorithmic genome assembly technique in order to deconstruct the mosaics of repeated stretches of DNA and identify the original sequences. “Maybe there is something special about the originals, some clue or insight into what causes this colonization of the human genome,” said Pevzner.

You can read the press release here. If you're a journalist and would like a PDF of the paper, send me an email at dbkane AT ucsd DOT edu

Below if the full figure 2 from the paper: This colorful image (figure 2 in the paper) illustrates the process of ancestral-state determination for one 750-kb duplication block on human chromosome 2p11. In this example, 15 of 16 ancestral loci were accurately predicted by the computational method.

Do you see the chicken? What shapes do you see?

Login for a greater good

When you want to post a comment to a blog or send an email from a relatively new email account, you have to type in a series of distorted letters and numbers (a CAPTCHA) to prove you're a person and not a computer looking to add comment spam to a blog.

What if – instead of wasting your time and energy on typing ‘SGO9DXG’ you could label an image that will help someone who is visually impaired go shopping?

That’s exactly what computer scientists from UC San Diego led by computer science professor Serge Belongie are working on. They are presenting this work at a computer vision conference in October in Rio (
ICCV 2007).
The image describes one of the many useful tasks that could be done by people who are proving that they are live humans and not computers trying to put spam comments on a blog. These kinds of labeling tasks are time consuming but important for Belongie's Grozi project -- which is an effort to create a grocery shopping assistant for the visually impaired (2006 press release).

You can download the PDF of the paper here.

Here is the press release.

Parlez-vour francais? Read the story in on the French tech site: L'Atelier

This work is related the work from Luis von Ahn that has been described by the BBC, TechCrunch and others.