I'm a biomedical and electrical engineer with interests in information theory, complexity, evolution, genetics, signal processing, IndieWeb, theoretical mathematics, and big history.
I'm also a talent manager-producer-publisher in the entertainment industry with expertise in representation, distribution, finance, production, content delivery, and new media.
One of the most important use cases of ontologies is the calculation of similarity scores between a query and items annotated with classes of an ontology. The hierarchical structure of an ontology does not necessarily reflect all relevant aspects of the domain it is modelling, and this can reduce the performance of ontology-based search algorithms. For instance, the classes of phenotype ontologies may be arranged according to anatomical criteria, but individual phenotypic features may affect anatomic entities in opposite ways. Thus, "opposite" classes may be located in close proximity in an ontology; for example enlarged liver and small liver are grouped under abnormal liver size. Using standard similarity measures, these would be scored as being similar, despite in fact being opposites. In this paper, we use information about opposite ontology classes to extend two large phenotype ontologies, the human and the mammalian phenotype ontology. We also show that this information can be used to improve rankings based on similarity measures that incorporate this information. In particular, cosine similarity based measures show large improvements. We hypothesize this is due to the natural embedding of opposite phenotypes in vector space. We support the idea that the expressivity of semantic web technologies should be explored more extensively in biomedical ontologies and that similarity measures should be extended to incorporate more than the pure graph structure defined by the subclass or part-of relationships of the underlying ontologies.
In a project which I started just before IndieWebCamp LA in November, I’ve moved a big step closer to perfecting my “Read” posts!
Thanks in large part to WordPress, PressForward, friends and help on the IndieWeb site too numerous to count, and a little bit of elbow grease, I can now receive and read RSS feeds in my own website UI (farewell Feedly), bookmark posts I want to read later (so long Pocket, Instagram, Delicious and Pinboard), mark them as read when done, archive them on my site (and hopefully on the Internet Archive as well) for future reference, highlight and annotate them (I still love you hypothes.is, but…), and even syndicate (POSSE) them automatically (with emoji) to silos like Facebook, Twitter (with Twitter Cards), Tumblr, Flipboard, LinkedIn, Pinterest, StumbleUpon, Reddit, and Delicious among others.
Syndicated copies in the silos when clicked will ping my site for a second and then automatically redirect to the canonical URL for the original content to give the credit to the originating author/site. And best of all, I can still receive comments, likes, and other responses from the siloed copies via webmention to stay in the loop on the conversations they generate without leaving my site.
Here’s an example of a syndicated post to Twitter:
I made this video when I worked in south of France a few years ago.
I now work at "The Artisan Bakery" in London, where the croissant we make are even better, but I'm really a bread baker and our bread is the best.
Jeremy Cherfas is right, I think the majority of the secret is the tools. I am quite jealous of that massive dough roller, but I don’t think that a typical little home pasta machine would be quite as easy to use as Jeremy might hope.
My other favorite was the magic croissant cutter. I’ll have to look for one of those the next time I’m at a restaurant supply house. I imagine they’re pretty rare. It reminded me a little bit of the old school hand push lawn mowers.
The quick camera pan down at 5:34 with the CCR musical overlay was a lovely touch, but is a painful reminder of the fact that this type of mass manufacture is overkill for the home chef who may want as many as a dozen at a time (remember, pastries start their inevitable death the minute they’re done cooking). Though I do have to say watching this makes me want to open up a bakery, but which days is that not a thought I have?
The nice part about having this much dough was seeing some of the myriad of creative things one could do other than just croissants. Now, off to find a nice oranais.
Rebroadcast — Monday 02/20/2017
Donald Trump talks about his recent "comeback" after flirting with bankruptcy, his support of Mike Tyson after his imprisonment for rape, his divorce from Ivana Trump, and the rumors that he would run for president.
It’s amazing watching this interview from over 23 years ago. Charlie Rose takes it possibly too easy on Trump because of his entertainer status. There’s a lot of hemming and hawing on Trump’s side and he still shows these same verbal tics as he dodges questions in a somewhat charming manner. There’s no adherence to facts, yet everything is “just great”, “the best”, “this”, “that”, and so on.
It’s amazing to see some of the things Rose brings up then are still issues now. Questions about his manner and vanity still linger all these years later. The difference is that he at least acknowledged them to some extent back then.
Wednesday on the NewsHour, hundreds flee amid flooding in Northern California. Also: A major change on school bathrooms and transgender youth, newspaper editors explain readers' views on the political climate, Syrian refugees who would prefer not to move to the U.S., hope for alien life in a newly discovered solar system and an industrial towns puts its faith in revitalized manufacturing.
Based on the interview of the Mayor of San Jose Mayor Sam Liccardo it sounds like Norther California is handling the heavy rains better than I would have expected.
The segment with newspaper editors around the country was alright, but seemed oddly stilted. Several of the interviewees obviously didn’t have a lot of on-camera experience. It wasn’t obvious that some of their thoughts were so much that of their constituencies as they were of themselves based on their answers.
Professor Arrow, one of the most brilliant minds in his field during the 20th century, became the youngest economist ever to earn a Nobel at the age of 51.
Mark Zuckerberg’s manifesto outlines his vision for a centralised global colony ruled by the Silicon Valley oligarchy. I say we must do the exact opposite and create a world with individual sovereignty and a healthy commons.
The verbiage here is a bit inflammatory and very radical sounding, but the overarching thesis is fairly sound. The people who are slowly, but surely building the IndieWeb give me a lot of hope that the unintended (by the people anyway) consequences that are unfolding can be relatively quickly remedied.
Marginalia
We are sharded beings; the sum total of our various aspects as contained within our biological beings as well as the myriad of technologies that we use to extend our biological abilities.
To some extent, this thesis could extend Cesar Hidalgo’s concept of the personbyte as in putting part of one’s self out onto the internet, one can, in some sense, contain more information than previously required.
Richard Dawkin’s concept of meme extends the idea a bit further in that an individual’s thoughts can infect others and spread with a variable contagion rate dependent on various variables.
I would suspect that though this does extend the idea of personbyte, there is still some limit to how large the size of a particular person’s sphere could expand.
While technological implants are certainly feasible, possible, and demonstrable, the main way in which we extend ourselves with technology today is not through implants but explants.
in a tiny number of hands.
or in a number of tiny hands, as the case can sometimes be.
The reason we find ourselves in this mess with ubiquitous surveillance, filter bubbles, and fake news (propaganda) is precisely due to the utter and complete destruction of the public sphere by an oligopoly of private infrastructure that poses as public space.
This is a whole new tragedy of the commons: people don’t know where the commons actually are anymore.
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