Saturday, March 21, 2020

epidemics and human contact statistics...

way back when, my colleague Eiko Yoneki built the Fluphone project, which has suddenly become rather relevant again after a decade. Some folks in Singapore have nicely done something similar with good privacy properties! NHSx are on it in the UK, as are lots of other people...

we had earlier studied human contacts - here's a paper by Augustin Chaintreau et al based on work in the Haggle project which involved empirical studied of how the time between and duration of encounters between people is distributed.  Some of the data sets are freely available in the excellent Crawdad repository.

When modeling an epidemic (e.g. to figure out whether it will collapse, sustain, or go pandemic), people start with the SIR model (susceptibility, infectiousness and recovery) - this basically leads to classic S curves over time for the number of people infected (or fraction of the population) - the other important number quotes is R0 - the number of people each infected person passes the disease on to. Recovered people usually have some level of immunity, so they are "removed" from the population, and not typically returned to the pool of susceptible people (at least for some time, depending on disease and person).

Some problems with naive models:
the values for S,I,R are population averages. As is R0. In fact, R0 obviously varies over time, as the number of susceptible people an infected person can meet must typically decrease.

In fact susceptibility for a disease also can be influenced by prior incurred immunity. This can vary with age, gender and other factors, inherently, or because of similar prior infections, or because of vaccination.

As can infectiousness (simple example - if you are asymptomatic carrier of a disease spread only by coughing, then if you don't cough, it is hard to spread it.).

The point of the encounter data above is that that also isn't simple. People have varying levels of popularity ("degree") and centrality (they are on the path between more or less friends (of friends (of friends (of friends)))) to the sixth degree and more. One study of this by Watts et al shows how this leads to multi-scale, resurgent outbreaks. Ground truth needs us to test everyone!

Vaccination programs often target the vulnerable groups (seasonal flu), but sometimes target the whole population, but possibly indirectly - e.g. if you vaccinate enough kids against measles, mumps, chickenpox, polio, smallpox, and it lasts til later life, eventually there's almost no-one in the population left to spread the thing anymore. The vaccine can be made from a weakened version of the disease, which then "teaches" the human immune system in a way that lets it respond appropriately to the full-strength one later. Herd immunity normally refers to having enough of the population vaccinated that the SIR model tells you the disease won't get anywhere far before only meeting immune people.

The contact interval/duration models are power law and clustered. This tells us that they are driven by heavy tailed distributions of popularity (aka rich get richer, in trading terms), but also affinity (e.g. kinship, friendship, work relationships, etc).  For social distancing to work, you need to combine breaking all these kinds of links, social, work, entertainment, even (actually, especially family if you have a tight knit generational spread!). but also you need to target high popularity or high centrality people especially - this has been used by people in a wide range of areas such as offering advice on safe sex to sex workers to reduce HIV spreading, and even smoking and obesity (e.g. see Christakis work there).

The point of this blog (which may contain errors-  please send me corrections if you spot any!) is to try to explain that it is relatively complex to deal with real outbreaks. When we have phase changes in epidemics, and power law coefficients, some small changes can really fix things, other changes have to be very significant to make a difference. We need adaptive, and (as seen here on heterogeneous) responses. Above all, we need continuous, and continuously more accurate, measurement of all of the above to do this adaptation precisely.

Saturday, January 25, 2020

An Architecture for Spread Spectrum Computation

This is an unsuccessful proposal to Facebook about an
an intermediate Instruction Set Architecture for Spread Spectrum Computation. We target nano-services constructed 
from lambdas as a backend from an intermediate system, to allow for fine grain, and elastic, fault tolerant 
computations. Was an extension of an earlier idea by Steve Hand.

We believed it fitted in their research call topics on
Scalable, elastic, reliable distributed;
Programming languages&compilers for platform agnostic; and
Resource provisioning for efficient ML.

I guess it was slightly too ambitious:-)

Saturday, January 11, 2020

some memories of Peter Kirstein

Peter Kirstein, who passed away earlier this week (8.1.2020) was my PhD advisor, back in the 1980s. I joined his research group fresh out of the MSc there in 1981, and was working with Rob Cole who ran the collaboration with RSRE (Royal Signal and Radar Establishment, Malvern) who connected via the UCL gateway on to the Internet.

Peter had been at this game for quite a while (records say 1973 was main ARPANET link, with the connection to NDRE in Oslo). Peter had gathered a team of people both for his own research program, and to deliver undergraduate and Masters courses in Computer Science, having recently founded the department (actually it was part of UCL statistics in the Pearson (yes, that Pearson) building, and then separated, as CS grew. But at least til 2000, it remained in the very nice location right at the entrance to the main UCL quad.

Peter's style of management both for the research and for the department was very collegiate, and entailed quite a bit of delegation - to that end, for admin and teaching he'd gotten some very competent people around him who did a great job -- this instilled responsibility in people.

When I joined, Peter not only had the main research project in Internet related work outside the US he had great links on into Europe, wth collaborators at CNUCE (CNR in Pisa now), NTA in Oslo, FGAN in Germany and others, and also not just the defense link with RSRE in the UK, but also a big interconnection project with Cambridge, Loughborough, and other universities as well as Logica using Cambridge Rings (10Mbps before ethernet - UTP, not coax:-) with wide area satellite links, both for the US (SATNET - the Atlantic Packet Satellite ) and the UK (I think Stella?).

What this tells you is that Peter thought big - very, very big. And this bought challenges in terms of technology, policy and management. Folks in the US programmes (e.g. at UC Berkeley, and LBL)  found this interesting - for example, the satellite link had a very high latency (.72 seconds) compared with land lines (terrestrial point-to-point cables from telecom companies "the phone" trunks). The link also had unusual errors/losses - i remember seeing really bad performance one day and puzzled, asked a colleague who pointed out the window at a thunderstorm/lightening...but also to get funding for this scale of work was a coordination problem with multiple agencies ("stakeholders" is the trendy term now) from US, Canada, UK, Europe, government, industry, academia. Policies collided - another challenge - how to share a network between different agencies with different funding and collaboration rules? Policy routing (BGP) emerged - folks at MIT were instrumental in extracting the policy rules to see how one might build an inter-domain internet.

Peter was on top of all this, thinking about how to drive forward to the next problem, and showing incredible patience with some of the partners who took years in some case to understand what was needed.

One of the things  helped Peter with was the marvelously vaguely named International Collaboration Board, who actually had a charter for a while, which just said "the purpose of the ICB is to hold meetings".  It was actually the vehicle for the resolution of some of the challenges. We also did a fine line in drawing network maps, sometimes down to specific hardware details of line cards (e..g with BBN folks) and other times just scribbling the now ubiquitous "cloud" image (i.e. abstracting away all the (un)necessary details...).

Sometimes, one had the impression that Peter didn't know what was going on "under the hood, for hours at a time, but then he'd jump in to a discussion with a technical question or a pointed observation, which was bang on the money (in later years, he'd wake up in seminars and do the same thing, much to the surprise of speakers). Another endearing memory is that whenever we were travelling together and there was any hiccup in the transport, he would "jump on the next train or plane heading roughly the right direction". This always worked, somewhat surprisingly.

People left the group (Rob Cole went to HP, Peter Higginson went to Cabletron or was it DEC, Bob Braden went back to ISI, Nigel Martin went and founded the Instruction Set, Ruth Moulton went to Whitechapel Computers, Bruce Wilford went to Cisco...etc etc).

The EU research programmes arrived, and Peter dived in, building the first systems for multimedia real time conferencing - something some folks I recall at the time at BT saying was "impossible" even after we showed them Atanu Ghosh juggling in a conference in Amsterdam, in London, while talking to us. Later on (near end of 1990s, we got a CAVE (3 meter cube immersive VR system) and connected that to other CAVEs in Chicago and North Carolina and did some early work in distributed virtual rehearsal studios with the BBC (pretty much the Star Trek Holodeck) - i remember explaining why distributed music was never going to happen (you can't improvise rallentando with someone more than 100msec away and even at the speed of light, that rules out intercontinental orchestras or even jazz/rock bands. especially jazz.

At Some point, Peter had not only become an actual Post Office, but had also been told by the UK's research funding agency to stop working on the Internet as it was the "wrong kind of network". Given they didn't actually fund his work, this was remarkably obtuse of them.
I also recall a letter from the ISO explaining that OSI was not an acronym. And then there's the great challenge of how to dispose of kit - problem being wither it was loaned or given, it had an import duty (maybe just on depreciation, but could be a shedload of money back in those days). So some of the gear was sent to a US airforce base somewhere in England, allegedly therefore not leaving the UK, and as far as I know, used for target practice.

We worked on all kinds of weird protocols from the UK's University communities own-brew "colour book" protocols (adopted in Australia and I think Japan for a while) on X.25 packet nets, as well as ATM nets and Cambridge's home-brew protocols (including "Universe" datagrams) and the ISO OSI suite itself (with Steve Kille leading a very successful collaboration with Marshall Rose from Northrop - maybe another stealth project like their bomber?). We also messed with various early alternate name and directory services, and with multimedia e-mail. (Do not get me started on the TP4 v. TCP or Bind v. Druid arguments we had).

I also enjoyed the fact that INDRA (after the Indian god, represented as a web whose nodes are jewels that glow when a soul reaches enlightenment) notes and early internet engineering notes contained ample evidence of the input that Peter and his gang had given towards the early evolution of Internet protocols.

There are loads of other people who worked on all this stuff, and i'll add to this note as i can think of stories to link them in. The abiding memory is of a marvellously inclusive and friendly guy, who had some incredibly impactful vision and bought a lot of those people along with him, by sharing the intellectual ownership, completely without ego.

Saturday, December 07, 2019

Cambridge Comprehensive

Recently, several new members have joined the department, and happened to ask me how everything worked. I had to disappoint them, in that the last person who knew that was Stephen Hawking and he'd sadly died just before they arrive. However, have now been here for 20 years, this time at least, I thought I would have a go at explaining stuff

People are classified as students or UFOs - students are initially manifold, until they expurgated, at which point they can become UFOs. UFOs become UTOs when they are established through ground truths. UTOs can also later become fellows, provided they pass the rigorous exam in Benevolent Dictation. This then qualifies them to say grace and hand out favours such as maundy money, and to hold hands as they walk on the college lawn.

Colleges are basically country houses with nice lawns and  staircases, which only UFOs and UTOs are allowed on. students have to make their way to and from the bars and bedders by way of the outside walls, often climbing up precarious ivy. Over the 8000 years of existence, students have evolved to have primitive wings, but when they become UFOs, they lose the feathers on the wings, and so make do with gowns instead, to cover up their shame.

Departments are a relatively new invention, and are basically knowledge stores, a bit like John Lewis, except that departments are never unknowingly undersold. Other fleeting Institutions such as the Sanger and the Turing have no salience whatsoever.

Colleges are basically country houses with nice lawns and  staircases, as described above - heads of houses dispense classes in benevolent dictation over port and salud.

The University is an act of collective illusion, and (like oxford) only exists in the minds of people who have read law. Tourists arriving at Cambridge station often ask for directions to the University, and as an act of kindness, are usually pointed to the busker outside Great St Mary's church, with the added explanation that this is the Bishop of Ely who is deemed to have progressed beyond all forms of dictation, so that now he is allowed to sing Bach's Aegrotat in the original Welsh.

I hope that this has helped.

Thursday, December 05, 2019


dani had been increasingly frustrated in his relationship, conversations always seemed to end up in arguments, and increasingly frequently, he would lose the argument. his partner seemed to anticipate what he would say, but then (deliberately?) misinterpret it. Even more online than in RL. he decided that it was time to do something about it.

being technically inclined, dani decided to tackle the challenge scientifically.
first of all, he had to understand how the arguments proceeded, so he started to record all the conversations via his smart phone, and then transcribe the speech to text.he then found some open source NLP software that could storify the text, extracting and abstracting the trending topics and the sense and sentiment in the speakers' utterances. then he thought, "why be too clever", why don't i just apply predictive text to the line of argument that I am taking, then invert the sense, and use text-to-speech to replace what I was going to say". indeed, he thought, why not automate both sides of the argument - he'd read about Generative Adversarial Networks in AI, and decided to build his own, dubbed Trouble and Strife (actor and critic).

The technology was a marvellous success, and arguments dissipated, evaporated before they even got going, life was wonderful again, harking back to the early days of their relationship.

then suddenly, out of the blue, he was served divorce papers by his partner's lawyer. and not just separation, but a demand for a massive amount of money that he had no idea he had.
It turned out that mani had known all along about the tech, and had built a massively successful business selling the software, initially to divorce lawyers, and later to barristers and judges, one of whom he ended up getting together with. Oh, and the audio recordings of mani, that dani's software had trained on initially? that was a mashup of snippets of alexa and siri arguing about which of them their owner was speaking to (although curiously, both voice assistants referred to "pet" rather than owner).

still, half of a lot of money is still a lot of money.

Monday, October 28, 2019

the new precariat

I've paraphrased William Gibson in the past - "the future is already here, just it is unfairly distributed".

People (Russell) worry about the way AI may dehumanise us. The less alarmist position (than the AI's will kill us all) might be welcome, but it is still quite a depressing image - the assumption is that that which makes many of us human (trivia, gossip, ephemera) will be automated away from us, and our humdrum existences will become less and less pointful but also that the grand creative goals some of us might set ourselves, will also increasingly fall to the machines. In this world, the human race becomes more and more de-motivated and dispirited. As if this isn't already true - they seem to have missed a  hundred years on work on alienation and the pointlessness of work post-industrial revolution, driven by time-and-motion studies, treating people as pluggable components (the sickness behind the phrase "Human Resources").

The reality will be much more of the same - a mandarin class which already exists will just get stronger-  people that program the AI, can hack the machine in the ML, will be the new hedge fund managers and political manipulators - everyone else will join the new precariat in larger and larger numbers, fed and watered and numbingly entertained just enough to stop them revolting. Maybe that is what they are saying ...Maybe I should read the book:-)

So what's the solution? I've said it before - it is in SF literature (just like all the climate change writing for 50 years) - we need (thanks to Frank Herbert in Dune) a Butlerian Jihad. Not to get rid of machines, but to stop them usurping the charming little nonsense that makes people human. and the challenge of working stuff out in one's head (whether its arithmetic or harmony).

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misery me, there is a floccipaucinihilipilification (*) of chronsynclastic infundibuli in these parts and I must therefore refer you to frank zappa instead, and go home