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Erdös number, update

I just made an update to a post from 2006, because I learned that my Erdös number has went down from 4 to 3. I guess that's pretty much it - it is not likely I'll ever become a 2.

Simia

The Fourth Scream

Janie loved her research. It was at the intersection of so many interesting areas - genetics, linguistics, neuroscience. And the best thing about it - she could work the whole day with these adorable vervet monkeys.

One more time, she showed the video of the flying eagle to Kassandra. The MRI helmet on Kassandra’s little head measured the neuron activation, highlighting the same region on her computer screen as the other times, the same region as with the other monkeys. Kassandra let out the scream that Janie was able to understand herself by now, the scream meaning “Eagle!”, and the other monkeys behind the bars in the far end of the room, in a cage large as half the room, ran to cover in the bushes and small caves, if they were close enough. As they did every time.

That MRI helmet was a masterpiece. She could measure the activation of the neurons in unprecedented high resolution. And not only that, she could even send inferencing waves back, stimulating very fine grained regions in the monkey’s brain. The stimulation wasn’t very fast, but it was a modern miracle.

She slipped a raspberry to Kassandra, and Kassandra quickly snatched it and stuffed it in her mouth. The monkeys came from different populations from all over Southern and Eastern Africa, and yet they all understood the same three screams. Even when the baby monkeys were raised by mute parents, the baby monkeys understood the same three screams. One scream was to warn them from leopards, one scream was to warn them from snakes, and the third scream was to warn them from eagles. The screams were universally understood by everyone across the globe - by every vervet monkey, that is. A language encoded in the DNA of the species.

She called up the aggregated areas from the scream from her last few experiments. In the last five years, she was able to trace back the proteins that were responsible for the growth of these four areas, and thus the DNA encoding these calls. She could prove that these three different screams, the three different words of Vervetian, were all encoded in DNA. That was very different from human language, where every word is learned, arbitrary, and none of the words were encoded in our DNA. Some researchers believed that other parts of our language were encoded in our DNA: deep grammatical patterns, the ability to merge chunks into hierarchies of meaning when parsing sentences, or the categorical difference between hearing the syllable ba and the syllable ga. But she was the first one to provably connect three different concrete genes with three different words that an animal produces and understands.

She told the software to create an overlapping picture of the three different brain areas activated by the three screams. It was a three dimensional picture that she could turn, zoom, and slice freely, in real time. The strands of DNA were highlighted at the bottom of the screen, in the same colors as the three different areas in the brain. One gene, then a break, then the other two genes she had identified. Leopard, snake, eagle.

She started to turn the visualization of the brain areas, as Kassandra started squealing in pain. Her hand was stuck between the cage bars and the plate with raspberries. The little thief was trying to sneak out a raspberry or two! Janie laughed, and helped the monkey get the hand unstuck. Kassandra yanked it back into the cage, looked at Janie accusingly, knowing that the pain was Janie’s fault for not giving her enough raspberries. Janie snickered, took out another raspberry and gave it to the monkey. She snatched it out of Janie’s hand, without stopping the accusing stare, and Janie then put the plate to the other side of the table, in safe distance and out of sight of Kassandra.

She looked back at the screen. When Kassandra cried out, her hand had twitched, and turned the visualization to a weird angle. She just wanted to turn it back to a more common view, when she suddenly stopped.

From this angle, she could see the three different areas, connecting together with the audiovisual cortex at a common point, like the leaves of a clover. But that was just it. It really looked like three leaves of a four-leaf clover. The area where the fourth leaf would be - it looked a lot like the areas where the other three leaves were.

She zoomed into the audiovisual cortex. She marked the neurons that triggered each of the three leaves. And then she looked at the fourth leaf. The connection to the cortex was similar. A bit different, but similar enough. She was able to identify what probably are the trigger-neurons, just like she was able to find them for the other three areas.

She targeted the MRI helmet on the neurons connected to the eagle trigger neurons, and with a click she sent a stimulus. Kassandra looked up, a bit confused. Janie looked at the neurons, how they triggered, unrolled the activation patterns, and saw how the signal was suppressed. She reprogrammed the MRI helmet, refined the neurons to be stimulated, and sent off another stimulus.

Kassandra yanked her head up, looking around, surprised. She looked at her screen, but it showed nothing as well. She walked nervously around inside the little cage, looking worriedly to the ceiling of the lab, confused. Janie again analyzed the activation patterns, and saw how it almost went through. There seemed to be a single last gatekeeper to pass. She reprogrammed the stimulator again. Third time's the charm, they say. She just remembered a former boyfriend, who was going on and on about this proverb. How no one knew how old it was, where it began, and how many different cultures all over the world associate trying something three times with eventual success, or an eventual curse. How some people believed you need to call the devil's name three times to —

Kassandra screamed out the same scream as before, the scream saying “Eagle!”. The MRI helmet had sent the stimulus, and it worked. The other monkeys jumped for cover. Kassandra raised her own arms above her head, peeking through her fingers to find the eagle she had just sensed.

Janie was more than excited! This alone will make a great paper. She could get the monkeys to scream out one of the three words of their language by a simple stimulation of particular neurons! Sure, she expected this to work - why wouldn’t it? But the actual scream, the confirmation, was exhilarating. As expected, the neurons now had a heightened potential, were easier to activate, waiting for more input. They slowly cooled down as Kassandra didn’t see any eagles.

She looked at the neurons connected to the fourth leaf. The gap. Was there a secret, fourth word hidden? One that all the zoologists studying vervet monkeys have missed so far? What would that word be? She reprogrammed the MRI helmet, aiming at the neurons that would trigger the fourth leaf. If her theory was right. With another click she sent a stimulus to the —

Janie was crouching in the corner of the room, breathing heavily, cold sweat was covering her arms, her face, her whole body. Her clothes were clamp. Her arms were slung above her head. She didn’t remember how she got here. The office chair she was just sitting in a moment ago, laid on the floor. The monkeys were quiet. Eerily quiet. She couldn’t see them from where she was, she couldn’t even see Kassandra from here, who was in the cage next to her computer. One of the halogen lamps in the ceiling was flickering. It wasn’t doing that before, was it?

She slowly stood up. Her body was shivering. She felt dizzy. She almost stumbled, just standing up. She slowly lowered her arms, but her arms were shaking. She looked for Kassandra. Kassandra was completely quiet, rolled up in the very corner of her cage, her arms slung around herself, her eyes staring catatonically forward, into nothing.

Janie took a step towards the middle of the room. She could see a bit more of the cage. The monkeys were partly huddled together, shaking in fear. One of them laid in the middle of the cage, his face in a grimace of terror. He was dead. She thought it was Rambo, but she wasn’t sure. She stumbled to the computer, pulled the chair from the floor, slumped into it.

The MRI helmet had recorded the activation pattern. She stepped through it. It did behave partially the same: the neurons triggered the unknown leaf, as expected, and that lead to activate the muscles around the lungs, the throat, the tongue, the mouth - in short, that activated the scream. But, unlike with the eagle scream, the activation potential did not increase, it was now suppressed. Like if it was trying to avoid a second triggering. She checked the pattern: yes, the neuron triggered that suppression itself. That was different. How did this secret scream sound?

Oh no! No, no, no, no, NOO!! She had not recorded the experiment. How stupid!

She was excited. She was scared, too, but she tried to push that away. She needed to record that scream. She needed to record the fourth word, the secret word of vervet monkeys. She switched on all three cameras in the lab, one pointed at the large cage with the monkeys, the other two pointing at Kassandra - and then she changed her mind, and turned one onto herself. What has happened to herself? Why couldn’t she remember hearing the scream? Why was she been crouching on the floor like one of the monkeys?

She checked her computer. The MRI helmet was calibrated as before, pointing at the group of triggering neurons. The suppression was ebbing down, but not as fast as she wanted. She increased the stimulation power. She shouldn’t. She should follow protocol. But this all was crazy. This was a cover story for Nature. With her as first author. She checked the recording devices. All three were on. The streams were feeding back into her computer. She clicked to send the sti—

She felt the floor beneath her. It was dirty and cold. She was laying on the floor, face down. Her ears were ringing. She turned her head, opened her eyes. Her vision was blurred. Over the ringing in her ears she didn’t hear a single sound from the monkeys. She tried to move, and she felt her pants were wet. She tried to stand up, to push herself up.

She couldn’t.

She panicked. Shivered. And when she felt the tears running over her face, she clenched her teeth together. She tried to breath, consciously, to collect herself, to gain control. Again she tried to stand up, and this time her arms and legs moved. Slower than she wanted. Weaker than she hoped. She was shaking. But she moved. She grabbed the chair. Pulled herself up a bit. The computer screen was as before, as if nothing has happened. She looked to Kassandra.

Kassandra was dead. Her eyes were bloodshot. Her face was a mask of pure terror, staring at nothing in the middle of the room. Janie tried to look at the cage with the other monkeys, but she couldn’t focus her gaze. She tried to yank herself into the chair.

The chair rolled away, and she crashed to the floor.

She had went too far. She had made a mistake. She should have had followed protocol. She was too ambitious, her curiosity and her impatience took the best of her. She had to focus. She had to fix things. But first she needed to call for help. She crawled to the chair. She pulled herself up, tried to sit in the chair, and she did it. She was sitting. Success.

Slowly, she rolled back to the computer. Her office didn’t have a phone. She double-clicked on the security app on her desktop. She had no idea how it worked, she never had to call security before. She hoped it would just work. A screen opened, asking her for some input. She couldn’t read it. She tried to focus. She didn’t know what to do. After a few moments the app changed, and it said in big letters: HELP IS ON THE WAY. STAY CALM. She closed her eyes. Breathed. Good.

After a few moments she felt better. She opened her eyes. HELP IS ON THE WAY. STAY CALM. She read it, once, twice. She nodded, her gaze jumping over the rest of the screen.

The recording was still on.

She moved the mouse cursor to the recording app. She wanted to see what has happened. There was nothing to do anyway, until security came. She clicked on the play button.

The recording filled three windows, one for each of the cameras. One pointed at the large cage with the vervet monkeys, two at Kassandra. Then, one of the cameras pointing at Kassandra was moved, pointing at Janie, just moments ago - it was moments, was it? - sitting at the desk. She saw herself getting ready to send the second stimulus to Kassandra, to make her call the secret scream a second time.

And then, from the recording, Kassandra called for a third time.

The end

Fiction

History of knowledge graphs

An overview on the history of ideas leading to knowledge graphs, with plenty of references. Useful for anyone who wants to understand the background of the field, and probably the best current such overview.

knowledge graph

On the competence of conspiracists

“Look, I’ll be honest, if living in the US for the last five years has taught me anything is that any government assemblage large enough to try to control a big chunk of the human population would in no way be consistently competent enough to actually cover it up. Like, we would have found out in three months and it wouldn’t even have been because of some investigative reporter, it would have been because one of the lizards forgot to put on their human suit on day and accidentally went out to shop for a pint of milk and like, got caught in a tik-tok video.” -- Os Keyes, WikidataCon, Keynote "Questioning Wikidata"

Quote

Power in California

It is wonderful to live in the Bay Area, where the future is being invented.

Sure, we might not have a reliable power supply, but hey, we have an app that connects people with dogs who don't want to pick up their poop with people who are desperate enough to do this shit.

Another example how the capitalism that we currently live failed massively: last year, PG&E was found responsible for killing people and destroying a whole city. Now they really want to play it safe, and switch off the power for millions of people. And they say this will go on for a decade. So in 2029 when we're supposed to have AIs, self-driving cars, and self-tieing Nikes, there will be cities in California that will get their power shut off for days when there is a hot wind for an afternoon.

Why? Because the money that should have gone into, that was already earmarked for, making the power infrastructure more resilient and safe went into bonus payments for executives (that sounds so cliché!). They tried to externalize the cost of an aging power infrastructure - the cost being literally the life and homes of people. And when told not to, they put millions of people in the dark.

This is so awfully on the nose that there is no need for metaphors.

San Francisco offered to buy the local power grid, to put it into public hands. But PG&E refused that offer of several billion dollars.

So if you live in an area that has a well working power infrastructure, appreciate it.

rant
California

Academic Lineage

Sorry for showing off, but it is just too cool not to: here is a visualization of my academic lineage according to Wikidata.

Query: w.wiki/AE8

Wikidata
Academia
PhD

Bring me to your leader!

"Bring me to your leader!", the explorer demanded.

"What's a leader?", the natives asked.

"The guy who tells everyone what to do.", he explained with some consternation.

"Oh yeah, we have one like that, but why would you want to talk to him? He's unbearable."

fiction

AKTS 2019

September 24 was the AKTS workshop - Advanced Knowledge Technologies for Science in a FAIR world - co-located with the eScience and Gateways conferences in San Diego. As usual with my trip reports, I won't write about every single talk, but offer only my own personal selection and view. This is not an official report on the workshop.

I had the honor of kicking off the day. I made the proposal of using Wikidata for describing datasets so that dataset catalogs can add these descriptions to their indexes. The standard way to do so is to use Schema.org annotations describing the datasets, but our idea here was to provide a fallback solution in case Schema.org cannot be applied for one reason or the other. Since the following talks would also be talking about Wikidata I used the talk to introduce Wikidata in a bit more depth. In parallel, I kicked the same conversation off on Wikidata as well. The idea was well received, but one good question was raised by Andrew Su: why not add Schema.org annotations to Wikidata instead?

After that, Daniel Garijo of USC's ISI presented WDPlus, Wikidata Plus, which presented a prototype for how to extend Wikidata with more data (particularly tabular data) from external data sources, such as censuses and statistical publications. The idea is to surround Wikidata with a layer of so-called satellites, which materialize statistical and other external data into Wikidata's schema. They implemented a mapping languages, T2WDML, that allows to grab CSV numbers and turn them into triples that are compatible with Wikidata's schema, and thus can be queried together. There seems to be huge potential in this idea, particularly if one can connect the idea of federated SPARQL querying with on-the-fly mappings, extending Wikidata to a virtual knowledge base that would be easily several times its current size.

Andrew Su from Scripps Research talked about using Wikidata as a knowledge graph in a FAIR world. He presented their brilliant Gene Wiki project, about adding knowledge about genes and proteins to Wikidata. He presented the idea of using Wikidata as a generalized back-end for customized frontend-applications - which is perfect. Wikidata's frontend is solid and functional, but in many domains there is a large potential to improve the UX for users in specific domains (and we are seeing some if flowering more around Lexemes, with Lucas Werkmeister's work on lexical forms). Su and his lab developed ChlamBase which allows the Chlamydia research community to look at the data they are interested in, and to easily add missing data. Another huge advantage of using Wikidata? Your data is going to live beyond the life of the grant. A great overview of the relevant data in Wikidata can be seen in this rich and huge and complex diagram.

The talks switched more to FAIR principles, first by Jeffrey Grethe of UCSD and then Mark Musen of Stanford. Mark was pointing out how quickly FAIR turned from a new idea to a meme that was pervasive everywhere, and the funding agencies now starting to require it. But data often has issues. One example: BioSample is the best metadata NIH has to offer. But 73% of the Boolean metadata values are not 'true' or 'false' but have values like "nonsmoker" or "recently quitted". 26% of the integers were not parseable. 68% of the entries from a controlled vocabulary were not. Having UX that helped with entering this data would be improving the quality considerably, such as CEDAR.

Carole Goble then talked about moving towards using Schema.org for FAIRer Life Sciences resources and defining a Schema.org profile that make datasets easier to use. The challenges in the field have been mostly social - there was a lot of confidence that we know how to solve the technical issues, but the social ones provide to be challenging. Carol named four of those explicitly:

  1. ontology-itis
  2. building consensus (it's harder than you think)
  3. the Schema.org Catch-22 (Schema.org won't take it if there is no usage, but people won't use it until it is in Schema.org)
  4. dedicated resources (people think you can do the social stuff in your spare time, but you can't)

Natasha Noy gave the keynote, talking about Google Dataset Search. The lessons learned from building it:

  1. Build an ecosystem first, be technically light-weight (a great lesson which was also true for Wikipedia and Wikidata)
  2. Use open, non-proprietary, standard solutions, don't ask people to build it just for Google (so in this case, use Schema.org for describing datasets)
  3. bootstrapping requires influencers (i.e. important players in the field, that need explicit outreach) and incentives (to increase numbers)
  4. semantics and the KG are critical ingredients (for quality assurance, to get the data in quickly, etc.)

At the same time, Natasha also reiterated one of Mark's points: no matter how simple the system is, people will get it wrong. The number of ways a date field can be written wrong is astounding. And often it is easier to make the ingester more accepting than try to get people to correct their metadata.

Chris Gorgolewski followed with a session on increasing findability for datasets, basically a session on SEO for dataset search: add generic descriptions, because people who need to find your dataset probably don't know your dataset and the exact terms (or they would already use it). Ensure people coming to your landing site have a pleasant experience. And the description is markup, so you can even use images.

I particularly enjoyed a trio of paper presentations by Daniel Garijo, Maria Stoica, Basel Shbita and Binh Vu. Daniel spoke about OntoSoft, an ontology to describe software workflows in sufficient detail to allow executing them, and also to create input and output definitions, describe the execution environment, etc. Close to those in- and output definition we find Maria's work on an ontology of variables. Maria presented a lot of work to identify the meaning of variables, based on linguistic, semantic, and ontological reasoning. Basel and Binh talked about understanding data catalogs deepers, being able to go deeper into the tables and understand the actual content in them. If one would connect the results of these three papers, one could potentially see how data from published tables and datasets could become alive and answer questions almost out of the box: extracting knowledge from tables, understanding their roles with regards to the input variables, and how to execute the scientific workflows.

Sure, science fiction, and the question is how well would each of the methods work, and how well would they work in concert, but hey, it's a workshop. It's meant for crazy ideas.

Ibrahim Burak Ozyurt presented an approach towards question answering in the bio-domain using Deep Learning, including Glove and BERT and all the other state of the art work. And it's all on Github! Go try it out.

The day closed with a panel with Mark Musen, Natasha Noy, and me, moderated by Yolanda Gil, discussing what we learned today. It quickly centered on the question how to ensure that people publishing datasets get appropriate credit. For most researchers, and particularly for universities, paper publications and impact factors are the main metric to evaluate researchers. So how do we ensure that people creating datasets (and I might add, tools, workflows, and social consensus) receive the fair share of credit?

Thanks to Yolanda Gil and Andrew Su for organizing the workshop! It was an exhausting, but lovely experience, and it is great to see the interest in this field.

trip report

Illuminati and Wikibase

When I was a teenager I was far too much fascinated by the Illuminati. Much less about the actual historical order, and more about the memetic complex, the trilogy by Shea and Wilson, the card game by Steve Jackson, the secret society and esoteric knowledge, the Templar Story, Holy Blood of Jesus, the rule of 5, the secret of 23, all the literature and offsprings, etc etc...

Eventually I went to actual order meetings of the Rosicrucians, and learned about some of their "secret" teachings, and also read Eco's Foucault's Pendulum. That, and access to the Web and eventually Wikipedia, helped to "cure" me from this stuff: Wikipedia allowed me to put a lot of the bits and pieces into context, and the (fascinating) stories that people like Shea & Wilson or von Däniken or Baigent, Leigh & Lincoln tell, start falling apart. Eco's novel, by deconstructing the idea, helps to overcome it.

He probably doesn't remember it anymore, but it was Thomas Römer who, many years ago, told me that the trick of these authors is to tell ten implausible, but verifiable facts, and tie them together with one highly plausible, but made-up fact. The appeal of their stories is that all of it seems to check out (because back then it was hard to fact check stuff, so you would use your time to check the most implausible stuff).

I still understand the allure of these stories, and love to indulge in them from time to time. But it was the Web, and it was learning about knowledge representation, that clarified the view on the underlying facts, and when I tried to apply the methods I was learning to it, it fell apart quickly.

So it is rather fascinating to see that one of the largest and earliest applications of Wikibase, the software we developed for Wikidata, turned out to be actual bona fide historians (not the conspiracy theorists) using it to work on the Illuminati, to catalog the letters they sent to each other, to visualize the flow of information through the order, etc. Thanks to Olaf Simons for heading this project, and for this write up of their current state.

It's amusing to see things go round and round and realize that, indeed, everything is connected.

Wikibase
Illuminati

Wikidatan in residence at Google

Over the last few years, more and more research teams all around the world have started to use Wikidata. Wikidata is becoming a fundamental resource. That is also true for research at Google. One advantage of using Wikidata as a research resource is that it is available to everyone. Results can be reproduced and validated externally. Yay!

I had used my 20% time to support such teams. The requests became more frequent, and now I am moving to a new role in Google Research, akin to a Wikimedian in Residence: my role is to promote understanding of the Wikimedia projects within Google, work with Googlers to share more resources with the Wikimedia communities, and to facilitate the improvement of Wikimedia content by the Wikimedia communities, all with a strong focus on Wikidata.

One deeply satisfying thing for me is that the goals of my new role and the goals of the communities are so well aligned: it is really about improving the coverage and quality of the content, and about pushing the projects closer towards letting everyone share in the sum of all knowledge.

Expect to see more from me again - there are already a number of fun ideas in the pipeline, and I am looking forward to see them get out of the gates! I am looking forward to hearing your ideas and suggestions, and to continue contributing to the Wikimedia goals.

Wikidata
Google

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