O'Really?

July 25, 2006

AAAI’06: Highlights and conclusions

Filed under: semweb — Duncan Hull @ 10:46 pm
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The AAAI conference finished last Thursday, here are some highlights and papers that might be worth reading if you are interested in building and / or using a more “intelligent” (and possibly semantic) web in bioinformatics.

Here are the papers or talks I enjoyed the most and hope you might also find them useful or inspiring.

  1. Unifying Logical and Statistical AI talk given by Pedro Domingos.

    Intelligent agents must be able to handle the complexity and uncertainty of the real world. Logical AI (of which the semantic web is an example) has focused mainly on the former, and statistical AI (e.g. machine learning) on the latter. The two approaches can be united, with significant benefits, some of which are demonstrated by the Alchemy system

  2. Developing an intelligent personal assistant: The CALO (Cognitive Agent at that Learns and Organises) project talk given by Karen Myers.

    CALO is a desktop assistant that learns what you do in the lab / office. Sounds spooky, but involves some interesting technology and fascinating research questions.

  3. Bookmark hierarchies and collaborative recommendation by Ben Markines, Lubomira Stoilova and Filippo Menczer.

    Describes an open-source, academically-oriented social bookmarking site where you can donate your bookmarks to science at givealink

  4. Social network-based Trust in Prioritised Default Logic by Yarden Katz and Jennifer Golbeck.

    Who and how can you trust on the Web?

  5. Google vs Berners-Lee was a memorable debate. According to Jim Hendler, Tim and Peter are reconciling their differences now

Not particularly webby, but…

…entertaining nonetheless.

  1. Stephen Muggletons talk on Computational Biology and Chemical Turing Machines, went down well but unfortunately I was stuck in a parallel track, experiencing “death by ontology”.
  2. Bruce Buchanan gave a talk What Do We Know About Knowledge. A roller-coaster ride through the last 2000+ years of human attempts to understand what knowledge is, how to represent it and why it is powerful
  3. Winning the DARPA Grand Challenge with an AI Robot called Stanley talk given by Sebastian Thrun, amazing presentation on a driving a robotic car through the desert over rough terrain. However, it doesn’t take too much imagination to think of horrific applications of this. Next year they will try to drive it from San Francisco to Los Angeles on a public freeway, and Stanley hasn’t even passed its driving test yet!

Turing’s dream

Appropriately, the conference which was subtitled Celebrating 50 years of AI finished with two talks by Lenhart K. Schubert and Stuart M. Shieber about the Turing test. The first discussed Turing’s dream and the Knowledge Challenge, the second talk asked Does the Turing Test Demonstrate Intelligence or Not? Now I’m back in Manchester, where Turing once worked, I can’t help wondering, what would Alan make of the current state of AI and the semantic web? I think there are several possibilities, he could be thinking:

  • EITHER: Fifty odd years later, they’re not still wasting time working on that Turing test are they?!
  • OR: He is smugly satisifed that he devised a test, that no machine has passed, and perhaps never will, but has provided us with a satisfactory operational definition of “intelligence” ;
  • …AND What the hell is the “Semantic Web”?

We will never know what Alan Turing would make of todays efforts to make a more intelligent web. However, that won’t stop me speculating that he would be impressed by the current uses of computers (intelligent or otherwise) to drive robots through the desert, perform all sort of computations on proteins and to search for information on this massive distributed global knowledge-base we call the “Web”. Not bad for 50 years of work, here’s to the next 50…

References

  1. Alan Turing (1950) Computing Machinery and Intelligence: The Turing TestMind 59(236):433-460
  2. Stephen H. Muggleton (2006) Exceeding human limits: The Chemical Turing MachineNature 440:409-410
  3. Stephen H. Muggleton (2006) Towards Chemical Universal Turing Machines in Proceedings on the 21st National Conference on Artificial Intelligence
  4. Picture credit: Image from Steve Jurvetson
  5. This post was originally published on nodalpoint with comments

July 21, 2006

AAAI: Dude, Where’s My Service?

Filed under: biotech — Duncan Hull @ 10:54 pm
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GogloAs the number of bioinformatics services on the web increases, finding a tool or database that performs the task you require can be problematic. At the AAAI poster session on Wednesday, I presented our paper describing a novel solution to this problem. It uses a reasoner to “intelligently” search for web services, by semantically matching service requests with advertisements and has some advantages over comparable solutions…

I won’t go into all the gory details here but our technique extends and complements current approaches for matchmaking services. Some of the key features described in the paper are that it allows you describe to relationship(s) between the input and output of a service. E.g. What is the relationship between the input and output protein sequence of InterProScan? This relationship can help match requests for services with their adverts with higher precision and recall. I don’t mind admitting its been hard work getting this research published because a large part of the AI community use shamelessly toy and fictitious scenarios to motivate their work. Then they build incredibly complicated software stacks that are only understood by the small clique of people that designed them. When you show some of these people real-world bioinformatics services, they don’t seem to care too much, preferring to bury their heads in the sand of make-believe. There, thats got it off my chest!

So it was re-assuring when people came by the poster, listened to my speel and asked lots of questions. Ora Lassila from Nokia (one of the people responsible for hyping the whole idea up in the first place) dropped by to have a look. He was interested in adapting the technique for locating services in a registry, used by mobile devices. (I wonder if anyone out there needs BLAST on their mobile phone?!) It was good to meet Ora, and talk about semantics.

There is nothing quite like standing in front of a poster for three hours and tirelessly explaining it to complete strangers who work in disparate fields. It certainly helps to get your ideas straight. Where would we be without conferences?

References

  1. Danny Leiner (2000) Dude, Where’s My Car?
  2. Massimo Paolucci, Takahiro Kawamura, Terry Payne and Katia Sycara (2002) Semantic Matching of Web Service Capabilities
  3. Duncan Hull, Evgeny Zolin, Andrey Bovykin, Ian Horrocks, Ulrike Sattler and Robert Stevens (2006) Deciding Semantic Matching of Stateless Services in the Proceedings of the Twenty-First National Conference on Artificial Intelligence (AAAI-06)

July 19, 2006

AAAI: Google and the Semantic, Satanic, Romantic Web

Filed under: biotech,google,informatics — Duncan Hull @ 11:07 pm
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Google Blue YellowTim Berners-Lee delivered his one hour keynote at the AAAI’06 conference yesterday on the Semantic Web, after an introduction from Yolanda Gil. Tim gave an impassioned speech covering the last 16 years of the web and discussed the future of sharing data on the web using persistent URI’s and W3C standards like RDF and OWL. At the end of it all, there were some searching questions from Peter Norvig, Director of Research at Google Labs.

Peter opened his questions by saying.

Many people usually ask me, when I stand up and ask questions after keynote speeches at conferences:

“Peter, what do you have against the Semantic Web?”

Here is roughly what Peter said, the semantic web will never work because:

  1. People are stupid: Google has lots of experience of dealing with peoples stoopidity on the web. Many people don’t write well-formed HTML, they don’t run web servers properly and they keep changing what their URIs identify. It sucks, but this is the world, imperfect and messy and we just have to deal with it. These same people can’t be expected to use the Resource Description Framework (RDF) and the Web Ontology Language (OWL), which are much more complicated and considerably less fool-proof. (Perhaps you could call this the dumb-antic web?!)

    Tim replied that a large part of the semantic web can be populated by taking existing relational databases and mapping them into RDF/OWL. The structured data is already there, it just needs web-izing in a mashup-friendly format. (What I like to call the romantic web: people will publish their data freely on the web this way, especially in e-science for example. This will allow sharing and re-use in unexpected ways.)

  2. People are competitive: People working for commercial companies and market leaders can’t be expected to just put their raw data on the web as RDF/OWL, they have little interest in standards. This is how they make a living, beating their competitors and locking their customers into proprietary data formats, so they can keep selling them software / hardware to use their data. (Analagous problems in science, scientists can be reluctant to share and publish data, if someone else will make new discoveries with it and claim all the glory)

    Tim replied that most bookstores thought putting their stock levels and prices on the web was a bad idea as it would give sensitive information away to their competitors. However, they soon realised that this would allow their customers to search, browse and eventually (kerr-ching) buy their books.

  3. People cheat and lie: People lie about what their content is about, again, Google is on the receiving end of this. Cheats try to fool the PageRank algorithm by saying their web pages are about books or movies, when they are really about Viagra or Pornography. The same fate awaits RDF and OWL, cheaters will use ontologies to tell bare-faced lies about their data. (What I like to call the satanic web: people do evil things).

    Tim didn’t have any good answers to this, although later in the day there were some papers touching on the issue of Trust and Policies in the semantic web layer cake.

These lively debates are raging on un-abated, in the corridors, lecture theatres and bars. AAAI is now in full swing and its great to be here!

May 24, 2006

Dub Dub Dub 2006

Filed under: web,web of science — Duncan Hull @ 5:41 pm
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WWW2006
The 15th International World Wide Web conference is currently underway in Edinburgh, Bonny Scotland. As usual, this popular conference has some good papers, only 11%* of submissions are accepted. One particular paper caught my eye: One Document to Bind Them: Combining XML, Web Services, and the Semantic Web. This paper has probably been selected because it will wind people up (sorry I mean “spark a debate”) so its an entertaining and sometimes enlightening read.

In this paper, Harry Halpin and Henry Thompson make some observations about the state of the web in 2006:

But, according to the authors, it doesn’t have to be this way…

  1. Many (but not all) web services are functions that are available on the web,
  2. The semantic web gives us an elaborate type system, using ontologies, which can extend what we already have with XML Schema
  3. The combination of the first two, gives us Semantic Web Services which are typed functions. This allows us to invoke web services not just by their URI (e.g. http://xml.nig.ac.jp/xddbj/Blast for a Blast service), but by the type of information they have. E.g. you have an output of type BLAST_report or perhaps InterProScan_report, what services will take this as input? What operations can be performed on this data? This sounds a lot like BioMOBY, with bells on.

What Harry and Henry propose is tying all this together using a single XML vocabulary, called Semantic fXML, to put “a unified abstraction of data, types and functions” so that the web can compute. This is all a bit pie-in-the-sky vision of the future stuff, but what might it mean for your average bioinformatican? It would be seriously useful if we could make the current molecular biology web services easier to use, but agreeing on and using an ontology for annotating the types of the inputs and outputs of all the services is non-trivial task. Bioinformaticians already have a (somewhat limited) universal type system for describing all data in bioinformatics, its called string. Persuading them to use something more powerful is not easy unless the benefits are immediately obvious.

At the moment, it is difficult to tell if sfXML will ever have any impact on bioinformatics but who cares? Despite this, the paper is enjoyable reminder of what is interesting about services on the Web. They transform the web from a place where we can merely search and browse for data (sequences, genes, proteins, metabolic pathways, systems etc), into “one vast de-centralised computer” a bit like the one described in can computers explain biology? This, in my humble opinion, is what makes the web and bioinformatics an exciting place to work in 2006.

* Footnote: Of nearly 700 papers submitted: only 81 research papers were accepted (11%). This is a 25% increase on the number of submissions last year to www2005 in Chiba, Japan.

References

  1. Harry Halpin and Henry S. Thompson (2006) One Document to Bind Them: Combining XML, Web Services, and the Semantic Web in Proceedings of the 15th international conference on World Wide Web, Edinburgh Scotland DOI:10.1145/1135777.1135877
  2. This post originally published on nodalpoint with comments

May 5, 2006

Bioinformatics at the BBC: Demonstrating the power of metadata

Filed under: informatics — Duncan Hull @ 10:02 pm
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The BBC programme catalogue has recently gone online, and provides a demonstration of the applications that can be built using web technology such as Ruby on Rails, RDF, FOAF, web feeds, tag clouds and sparklines. This impressive online catalogue has:IMGP4697

Unfortunately this catalogue currently includes no data, only metadata at the moment, so there are no audio or video streams yet, as this is an experimental prototype. As mentioned earlier the catalogue is based on RDF which will no doubt please Semantic Webhead Tim Berners-Lee and allows the database to be queried with SPARQL. One of the brains behind this is Matt Biddulph.

I wonder if a similar application could be built using the UniProt protein sequence and annotation data in RDF or the data currently being produced by the W3C BioRDF subgroup? Compared to biological databases the BBC catalogue is relatively small, although there are no figures on the size of the catalogue, which has been extensively hand-curated by experts over the years. The ratio of metadata to data is probably different too, where a typical biological database might have lots of data (e.g. raw protein sequence data) but poor quality and a low quantity of metadata (interactions, structures, functions etc).

However, this catalogue is an interesting prototype, which is addictively fun to play with and might spark a few imaginations in the bioinformatics community.

[update: seeAlso Alf Eaton’s visual TouchGraph of BBC TV/Radio Collaborators which allows you to browse this data more graphically. Unfortunately, this fantastic BBC Database is not always online. This post was originally posted on nodalpoint with comments].

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