Showing posts with label conference. Show all posts
Showing posts with label conference. Show all posts

Friday, October 25, 2013

Bar Camp Boston 2013 talk on automation of science

This is an outline for a talk I gave at Bar Camp Boston 8 on the automation of science. It's a topic I've blogged and spoken about before. The shortened URL for this post is http://goo.gl/rv3Xik.

In 2004, a robot named Adam became the first machine in history to discover new scientific knowledge independently of its human creators. Without human guidance, Adam can create hypotheses to explain observations, design experiments to test those hypotheses, run the experiments using laboratory robotics, interpret the experimental results, and repeat the cycle to generate new knowledge. The principal investigator on the Adam project was Ross King, now at Manchester University, who published a paper on the automation of science (PDF) in 2009. Some of his other publications: 1, 2, 3.

Adam works in a very limited domain, in nearly complete isolation. There is plenty of laboratory automation but (apart from Adam) we don't yet have meaningful computer participation in the theoretical aspect of scientific work. A worldwide scientific collaboration of human and computer theoreticians working with human and computer experimentalists could advance science and medicine and solve human problems faster.

The first step is to formulate a linked language of science that machines can understand. Publish papers in formats like RDF/Turtle or JSON or JSON-LD or YAML. Link scientific literature to existing semantic networks (DBpedia, Freebase, Google Knowledge Graph, LinkedData.org, Schema.org etc). Create schemas for scientific domains and for the scientific method (hypotheses, predictions, experiments, data). Provide tutorials, tools and incentives to encourage researchers to publish machine-tractable papers. Create a distributed graph or database of these papers, in the role of scientific journals, accessible to people and machines everywhere. Maybe use Stackoverflow as a model for peer review.

Begin with very limited scientific domains (high school physics, high school chemistry) to avoid the full complexity and political wrangling of the professional scientific community in the initial stages. As this stuff approaches readiness for professional work, deploy it first in the domain of computer science and other scientific domains where it can hope to avoid overwhelming resistance.

Machine learning algorithms (clustering, classification, regression) can find patterns in data and help to identify useful abstractions. Supervised learning algorithms can provide tools of collaboration between people and computers.

The computational chemistry folks have a cool little program called Babel which translates between a large number of different file formats for representing molecular structures. It does this with a rich internal representation of structures, and pluggable read and write modules for each file format. At some point, something like this for different file formats of scientific literature might become useful, and might help to build consensus among different approaches.


A treasure trove would be available in linked patient data. In the United States this is problematic because of the privacy restrictions associated with HIPAA regulation. In countries like Iceland and Norway which have universal health care, there would be no equivalent of HIPAA, and those would be good places to initiate a Linked Patient Data project.

Monday, September 19, 2011

MakerFaire NYC 2011

I went to MakerFaire at the NY Hall of Science, Queens, NY on September 17th and 18th, and took plenty of photos. Like last year, the location was the site of the 1964 World's Fair. Even though I grew up pretty close to New York, I didn't get to see the World's Fair as a child, so I'm glad to have these opportunities to see what's left of it.
As was true last year, there were lots of 3D printers and CNC milling machines. My impression this year was that a much larger percentage of them were hobbyist efforts rather than high-end commercial projects. I think that's a good thing. There seems to me to be a maturing of the 3D printer hobbyist effort in general, and the gradual emergence of more small businesses like Bre Pettis's Makerbot. The hard technical challenges (the big one being getting the extruder nozzle to work just right) have pretty much been identified now.

As I looked at some of the products, which have been improving in resolution, it occurred to me that an interesting approach would be, instead of going with increasingly fine nozzles, to use a coarse nozzle to place a slightly oversized drop of plastic, let that drop cool and harden, and then bring in a milling tool to shape it. This would mean moving back and forth frequently between the extruder nozzle and the milling tool, so it would need some tinkering and might not end up being an improvement.

There were lots of other tools, things on display, and cool stuff to see. I was really impressed with an elegant (if low-res) volumetric display called Lumarca. Essentially the guy uses a projector to project colors onto lengths of monofilament fishing line in the viewing volume, and by carefully controlling the projected image, he individually controls what colors appear along each length of monofilament.

There were a few interesting vehicles, like motorized skateboards and a Segway clone. Those were fun.

One thing I found interesting was that in addition to the expected Arduino stuff (which has the full weight of O'Reilly Publishing behind it), there were a good number of boards with more advanced microcontrollers, particularly ARM Cortex-M3 controllers. This interests me because with their larger address spaces and fuller feature sets, ARM processors can run Linux OSes or Python interpreters or other big pieces of code  beyond the itty-bitty programs that will fit on an Arduino. Teho Labs had a nice line of Cortex M3 boards. They shared space with Dangerous Prototypes who were showing off their Web Platform board.

I did get pretty tired and sore walking around so much, and needed some Advil. But it was definitely worthwhile. Maybe I'll have some project next year so that I can have a booth of my own.http://www.arm.com/products/processors/cortex-m/cortex-m3.php

Sunday, January 17, 2010

Foresight Institute conference, Jan 16 and 17, 2010

The Foresight conference is just winding down. The talks were live-blogged over at NextBigFuture by Brian Wang who did a good job of concisely capturing the essentials. My own favorite talk was by Hod Lipson, who talked about a number of things, including something I find fascinating, the automation of science, about which I plan to blog more frequently.

I blogged too briefly in the past about the Adam project, but it deserves more. Reported in April 2009 by Ross King at Aberystwyth University. It used lab automation to perform experiments, and data mining to find patterns in the resulting data. Adam developed novel genomics hypotheses about S. cerevisiae yeast and tested them. Adam's conclusions were manually confirmed by human experimenters, and found to be correct. This was the first instance in human history where a machine discovered new scientific knowledge without human oversight.

Here is what I want to see computers doing in the coming years.
  • Look for patterns in data -- data mining
  • Propose falsifiable hypotheses
  • Design experiments to test those hypotheses
  • Perform the experiments and collect data
  • Confirm or deny hypotheses
  • Mine new data for new patterns, repeat the process
In the longer term, I want to see machine theoreticians and experimetalists collaborate with their human counterparts, both working in a scientific literature that is readable and comprehensible for both. This will require the development of a machine-parseable ontology (ideally a widely recognized standard) for sharing elements of the scientific reasoning process: data sets, hypotheses, predictions, deduction, induction, statistical inference, and the design of experiments.

So why do I want all this stuff? For one thing, it's interesting. For another, I am approaching the end of my life and I want to see scientific progress (and particularly medical progress) accelerate considerably in my remaining years. Finally, this looks to me like something where I can make some modestly valuable contribution to humanity with the time and energy I have left.