OpenDMAP paper

For the few who might be interested: OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression (PDF).

OpenDMAP advances the performance standards for extracting protein-protein interaction predications from the full texts of biomedical research articles. Furthermore, this level of performance appears to generalize to other information extraction tasks, including extracting information about predicates of more than two arguments. The output of the information extraction system is always constructed from elements of an ontology, ensuring that the knowledge representation is grounded with respect to a carefully constructed model of reality. The results of these efforts can be used to increase the efficiency of manual curation efforts and to provide additional features in systems that integrate multiple sources for information extraction. The open source OpenDMAP code library is freely available at http://bionlp.sourceforge.net/

I worked on an early version of this system.

And so friends …

So, friends, every day do something
that won’t compute. Love the Lord.
Love the world.

expression of the day: 'go off piste'

From ‘In pursuit of the G-d shot‘:

Millions of people probably get great coffee every morning with a standard home machine and ground coffee from a supermarket. I was starting to worry that, with a process that has as many variables as pulling an espresso, once you’re daft enough to go off piste, things get monumentally messy in a way only explicable with chaos theory.

To go off piste is to go off the trail (in cross-country skiing, for example), to do something non-standard. A ‘piste’ is apparently the name of the area in which a fencing match is held. Perhaps ‘fence outside the piste’ would be a new metaphor for ‘think outside the box’.

Cost of the Iraq War and the Economy

More stuff worth reading: Joseph Stiglitz’s testimony before Congress on the cost of the Iraqi War (pdf):

I have, so far, emphasized the direct economic costs as well as the opportunity costs—the diversion of funds that could have been used in so many other and better ways. I would be remiss, however, if I did not note that there are other costs: in the long run, the squandering of America’s leadership role in the international community, the diversion of attention from critical global issues, including issues like global warming and nuclear proliferation in North Korea—that simply won’t go away on their own, and that cannot simply wait to be addressed—may represent the largest and most longstanding legacy of this unfortunate war.

Some have characterized the Iraq War as a “war for oil.” If so, we lost this war, too: oil was $25 per barrel before the war, and over $100 per barrel now. Stiglitz conservatively reckons the war accounts for $5-$10 of the increase (though, confusingly, he actually thinks it is much higher).

And there is a direct connection between the war and the credit crisis (which goes unmentioned, by the way, in the New York Times front page article “Can’t Grasp Credit Crisis? Join the Club“):

It should have come as no surprise that, when America’s great financial institutions, Citibank and Merrill Lynch, needed money quickly, there were no pools of liquid cash available here. High oil prices and high national savings in China and elsewhere have created huge pools of wealth outside the United States, and it was to these that our financial institutions had to turn. It is, and should be, a cause of concern.

Barack Obama on Race and Politics

Obama’s speech is well worth watching.

For we have a choice in this country. We can accept a politics that breeds division, and conflict, and cynicism. We can tackle race only as spectacle – as we did in the OJ trial – or in the wake of tragedy, as we did in the aftermath of Katrina – or as fodder for the nightly news. We can play Reverend Wright’s sermons on every channel, every day and talk about them from now until the election, and make the only question in this campaign whether or not the American people think that I somehow believe or sympathize with his most offensive words. We can pounce on some gaffe by a Hillary supporter as evidence that she’s playing the race card, or we can speculate on whether white men will all flock to John McCain in the general election regardless of his policies.

We can do that.

But if we do, I can tell you that in the next election, we’ll be talking about some other distraction. And then another one. And then another one. And nothing will change.

UAVs at Wired Science

A nice Wired Science video on UAVs (unmanned autonomous vehicles), including some video of the UAV helicopter I worked on at NASA. I miss doing that cool stuff. Of course, I like doing the cool stuff I’m working on now. Autonomous flying search engines! Yes, that’s the ticket!

(via lemondor, who’s always finding cool stuff like this. Thanks, John!)

McCain on torture restrictions, just to be clear

Update: Good comments by Fred Clark at slacktivist.

From the New York Times:

Senator John McCain, the presumptive Republican presidential nominee, has been an outspoken opponent of torture, often referring to his own experience as a prisoner of war in Vietnam. In this case he supported the administration’s position, arguing as Mr. Bush did Saturday that the legislation would have limited the C.I.A.’s ability to gather intelligence.

So, McCain is in favor of allowing the US to practice such cruel and inhuman punishment and torture as:

• controlled drowning (“waterboarding”)
• sexual intimidation and degradation
• leaving prisoners in cold cells naked
• forcing prisoners to stand for days at a time
• mock executions

In other words, the kinds of horrors practiced at Abu Ghraib.

Michigan's primary

Should Michigan redo its Democratic primary for president?

I think it was shameful, scandalous and grossly stupid that our Governor Granholm, Senator Levin, and the state Democratic and Republican committees disenfranchised Michigan voters.

Millions of dollars were spent holding a sham election in which the only Democratic front-runner on the ticket was Senator Clinton. Her presence on the ballot was itself a masterful bit of triangulation, allowing her to garner votes while not spending any money on campaigning in Michigan and publicly committing to honor the Democratic National Committee’s rules.

The only reasonable course is for Michigan to split its delegates evenly between Senators Obama and Clinton. This at least gets Michigan representation at the national convention, is cost-free, and would roughly represent the opinions of Michigan voters (although I don’t know of any polling to support that).

My biggest fear is that Clinton will win the nomination via back-room negotiations using Michigan’s ‘super-delegates’ claiming to represent Michigan; this will be bad for Michigan and bad for the nation. If Granholm deserts the state to join Clinton’s cabinet, I will be very disappointed, and our poor state will suffer even more economic and political hardship.

I still stand by my prediction that Clinton will win the nomination and the election, although this is not an outcome I want. When will a real alternative to the Democrats and Republicans appear?

Powerset in Ruby

I actually needed to use a powerset function (set of all subsets of a set) today in some Ruby testing code I was writing. So I share it with you:

class Array
  def powerset
    if empty?
      [[]]
    else
      ps = self[1..-1].powerset
      ps.map{|i| self[0,1] + i} + ps
    end
  end
end

For example:

>> [1,2,3].powerset
=> [[1, 2, 3], [1, 2], [1, 3], [1], [2, 3], [2], [3], []]