Report from IJCAI09 conference - ONS and AI

On July 12, 2009 I presented a talk at the IJCAI'09 Workshop on Abductive & Inductive Knowledge Development in Pasadena, CA. While I was waiting to speak my computer permanently failed to reboot so I was not able to record my talk. Luckily I did have a copy on a flash drive and the slides are available on SlideShare.

The workshop had a mix of theoretical and practical talks about using automated reasoning. Lorenzo Magnani gave an interesting view of "manipulative abduction", where the thinker creates a hypothesis from interacting physically with the world without a preconceived plan. That generated some more discussion during the panel session and the question of whether a machine is capable of such activity was explored but not resolved. It sounded to me a lot like play.

Other talks that I particularly enjoyed included Deborah Chasman's presentation of using abductive logic programming in bioinformatics to understand how the Brome Mozaic Virus infects and replicates. Bassel Habib demonstrated the reconstruction of Claude Bernard's curare experiments on frogs from his original lab notebooks. He noted that Bernard did not usually explicitly state his hypotheses in his notebook - perhaps he was operating on manipulative abduction...

The most interesting talk for me was certainly Oliver Ray's presentation. He described his work on writing the logic behind Ross King's robot scientist. Basically the code creates hypotheses, checks them against the data obtained from the robot's experiments then reports those that seem to be valid. In this application the robot was trying to work out the metabolic pathways of yeast and some of the strongest hypotheses were strange. For example, indole was correlating with yeast growth in an expected way. It turned out that tryptophan was a contaminant in the indole supply. This was really a great example of how machine intelligence can amplify the ability of humans to reason. I'm hoping that Oliver can collaborate with us to apply similar tools to our solubility and synthesis projects.

ONS talk at AI conference in July 2009

I've been invited to talk at the IJCAI'09 Workshop on Abductive & Inductive Knowledge Development in Pasadena on July 12, 2009. This will be a great opportunity to focus what might become possible on the machine side of Open Notebook Science.

Although Ross King (of Robot Scientist fame) won't be there in person, his collaborator Oliver Ray will be giving a talk on their project. That should be quite interesting.

My abstract:

The Role of Openness in Scientific Automation: a case for Open Notebook Science

The use of Open Notebook Science to collect and make publicly available non-aqueous solubility measurements and the synthesis of anti-malarial agents will be described. ONS involves the real time sharing of all experiments and associated raw data by a community of collaborators who are geographically distributed and may have never communicated using channels other than these shared projects. Monthly cash prizes are awarded to participating students by means of the ONS Challenge Submeta Awards for solubility measurements. The laboratory notebook pages are recorded on a public wiki and the solubility measurements, including relevant calculations, are stored in public Google Spreadsheets. A combination of ChemSpider, the GoogleDoc visualization API and web services is used to enable flexible searching and display of desired subsets of the data.

The use of such a distributed and open platform with virtually zero read/write costs for the communication of science creates new opportunities for rapid collaboration. By using a redundant information dissemination system, channels that are more human friendly can be integrated with those that are more geared to machine readability. For example a publicly editable Google Spreadsheet tied to the operation of a robotic liquid handling system opens up the possibility of integrating crowdsourced intelligence with human workflows. In another example, web services called from within a publicly editable Google Spreadsheet to perform calculations on NMR spectra can be integrated readily with manually executed steps to accelerate progress and minimize the possibility of errors.

The advantages and disadvantages of ONS and related bottom-up Open Science strategies will be discussed. The key concerns revolve around intellectual property, trust, reference-ability, publication in traditional academic vehicles and other implications for collaborations.