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Modelling vocal interactions

Last year I took part in the Dagstuhl seminar on Vocal Interactivity in-and-between Humans, Animals and Robots (VIHAR). Many fascinating discussions with phoneticians, roboticists, and animal behaviourists (ethologists).

One surprisingly difficult topic was to come up with a basic data model for describing multi-party interactions. It was so easy to pick a hole in any given model: for example, if we describe actors taking "turns" which have start-times and end-times, then are we really saying that the actor is not actively interacting when it's not their turn? Do conversation participants really flip discretely between an "on" mode and an "off" mode, or does that model ride roughshod over the phenomena we want to understand?

I was reminded of this modelling question when I read this very interesting new journal article by a Japanese research group: "HARKBird: Exploring Acoustic Interactions in Bird Communities Using a Microphone Array". They have developed this really neat setup with a portable microphone array attached to a laptop which does direction-estimation and decodes which birds are heard from which direction. In the paper they use this to help annotate the time-regions in which birds are active, a bit like on/off model I mentioned above. Here's a quick sketch:

boxes diagram

From this type of data, Suzuki et al calculate a measure called the transfer entropy which quantifies the extent to which one individual's vocalisation patterns contain information that predicts the patterns of another. It gives them a hypothesis test for whether one particular individual affects another, in a network: who is listening to whom?

That's a very similar question to the question we were asking in our journal article last year, "Detailed temporal structure of communication networks in groups of songbirds". I talked about our model at the Dagstuhl event. Here I'll merely emphasise that our model doesn't use regions of time, but point-like events:

boxes diagram

So our model works well for short calls, but is not appropriate for data that can't be well-described via single moments in time (e.g. extended sounds that aren't easily subdivided). The advantage of our model is that it's a generative probabilistic model: we're directly estimating the characteristics of a detailed temporal model of the communication. The transfer-entropy method, by contrast, doesn't model how the birds influence each other, just detects whether the influence has happened.

I'd love to get the best of both worlds. a generative and general model for extended sound events influencing one another. It's a tall order because for point-like events, we have point process theory; for extended events I don't think the theory is quite so well-developed. Markov models work OK but don't deal very neatly with multiple parallel streams. The search continues.

Friday 24th February 2017 | science | Permalink / Comment

Paper: Applications of machine learning in animal behaviour studies

A colleague pointed out this new review paper in the journal "Animal Behaviour": Applications of machine learning in animal behaviour studies.

It's a useful introduction to machine learning for animal behaviour people. In particular, the distinction between machine learning (ML) and classical statistical modelling is nicely described (sometimes tricky to convey that without insulting one or other paradigm).

The use of illustrative case studies is good. Most introductions to machine learning base themselves around standard examples predicting "unstructured" outcomes such as house prices (i.e. predict a number) or image categories (i.e. predict a discrete label). Two of the three case studies (all of which are by the authors themselves) similarly are about predicting categorical labels, but couched in useful biological context. It was good to see the case study relating to social networks and jackdaws. Not only because it relates to my own recent work with colleagues (specifically: this on communication networks in songbirds and this on monitoring the daily activities of jackdaws - although in our case we're using audio as the data source), but also because it shows an example of using machine learning to help elucidate structured information about animal behaviour rather than just labels.

The paper is sometimes mathematically imprecise: it's incorrect that Gaussian mixture models "lack a global optimum solution", for example (it's just that the global optimum can be hard to find). But the biggest omission, given that the paper was written so recently, is any real mention of deep learning. Deep learning has been showing its strengths for years now, and is not yet widely used in animal behaviour but certainly will be in years to come; researchers reading a review of "machine learning" should really come away with at least a sense of what deep learning is, and how it sits alongside other methods such as random forests. I encourage animal behaviour researchers to look at the very readable overview by LeCun et al in Nature.

Tuesday 31st January 2017 | science | Permalink / Comment

Spy in the Wild

Last year, when I took part in the Dagstuhl workshop on Vocal Interactivity in-and-between Humans, Animals and Robots, we had a brainstorming session, fantasising about how advanced robots might help us with animal behaviour research. "Spy" animals, if you will. Imagine a robot bird or a robot chimp, living as part of an ecosystem, but giving us the ability to modify its behaviour and study what happens. If you could send a spy to live among a group of animals, sharing food, communicating, collaborating, imagine how much you could learn about those animals!

So it particularly makes me smile to see the BBC nature doc Spy in the Wild, in which they've... gone there and done it already.

--- Well, not quite. It's a great documentary, some really astounding footage that makes you think again about what animals' inner lives are like. They use animatronic "spy" animals with film cameras in, which let them get up very close, to film from the middle of an animal's social group. These aren't autonomous robots though, they're remotely operated, and they're not capable of the full range of an animal's behaviours. They're pretty capable though: in order both to blend in and to interact, the spies can do things such as adopt submissive body language - crouching, ear movements, mouth movements, etc. And...

...some of them vocalise too. Yes there's some vocal interaction between animals and (human-piloted) robots. The vocal interaction is at a pretty simple level, it seems some of the robots have one or two pre-recorded calls built in and triggered by the operator, but it's interesting to see some occasional vocal back-and-forth between the animals and their electrical counterparts.

There are obviously some limitations. The spies generally can't move fast or dramatically. The spy birds can't fly. But - maybe soon?

In the mean time, watch the programme, it has loads of great moments caught on film.

Friday 20th January 2017 | media | Permalink / Comment

Making eye contact with strangers

If you're looking for a New Year's resolution how about this one: make more eye contact with strangers.

I was reading this powerful little list of Twenty Lessons from the 20th Century by some Professor of History. One idea that struck me is a very simple one:

11: Make eye contact and small talk. This is not just polite. It is a way to stay in touch with your surroundings, break down unnecessary social barriers, and come to understand whom you should and should not trust.

In a large city like the one I live in, eye contact and small talk are rare. They're even rarer thanks to smartphones, of course - although, twenty years ago, Londoners were still avoiding each other, but using newspapers, novels and Gameboys instead. Anyway I do think smartphones create a mode of interaction which reduces incidental eye contact etc.

So I decided to take the advice. Over the past month or so I took those little opportunities - at the bus stop, at the pedestrian crossing, at the supermarket. A bit of eye contact, a few words about the traffic or whatever. I was surprised how many opportunities for effortless (and not awkward!) tiny bits of smalltalk there were and how worthwhile it was to take them. After the year we've had, this is a little tweak you can try, and who knows, it might help.

Saturday 31st December 2016 | politics | Permalink / Comment

The best vegetarian recipes of 2016

I've been cooking vegetarian in 2016. It's about climate change: meat-eating is a big part of our carbon footprint, and it's something we can change. So here I'm sharing some of the best veggie recipes I found this year. Most of them are not too complex, the point is everyday meals not dinner parties.

Note: you don't have to go full-vegan - phew. You can do meat-free Mondays, you can try Veganuary, you can give up beef, or whatever, it all makes a difference. It's true that vegans have the smallest carbon footprint but it's pretty unlikely we're all going to go that far, and a more vegetarian diet makes a big improvement. (Here's an article with some data about that...)

So here we go, the best vegetarian recipes of 2016 - as judged by a meat-eater! ;)

Spring

Untitled

Summer

  • Asparagus, pea, feta and mint salad - great combination.
  • Pea, mozzarella & lemon tart (from Take One Veg) - wasn't quite as "speedy" as the recipe's name suggested (40 min when I did it...). But maybe it gets quicker once you get handier with the puff pastry. It was really nice, fresh-tasting.
  • Untitled Sweet onion and puy lentil stew - I was so impressed with this, one of those simple meals that if you do it well is really satisfying. The texture+flavour contrast from the onions on top is the key.
  • Grilled orange, carrot & halloumi (from "River Cottage Fruit") - ace, just an ace combination of three flavours, lightly dressed. Easy to make and the ingredients are not exotic. Really handy.

Autumn

  • Untitled Jackfruit "pulled pork". This is extremely handy - it fills a gap that a lot of veggy stuff doesn't, i.e. it's a big barbecue nom with a meaningful texture. Really all you need is to keep a tin of green jackfruit in your store-cupboard, it doesn't need anything else exotic. It's easy to cook (just a pan on a gentle heat for half an hour, really). (However, one tin of jackfruit feeds about me-and-a-quarter. If only we were perfectly size-matched...)
  • Big aubergine and lemon tagine - OH YEAH is really all I've got to say about this.
  • Roast pumpkin and aubergine spaghetti

Winter

  • Butternut squash toad-in-the-hole
  • Untitled Slow-roasted tomato lasagne (from Take One Veg) - great flavour, and easy to make - though the tomatoes take a while to slow-roast, so do note that it's slow even though really easy. Also note that you need loads of tomatoes, you'll be surprised. I was low on creme fraiche so I used half creme fraiche half greek yogurt, that worked fine and makes it a bit lighter.

These are all ones that were new discoveries. Of course there's plenty of standard stuff too. Anyway - pick a recipe, give it a go.

Thursday 22nd December 2016 | food | Permalink / Comment

Twelvetrees ramp is open! First pics

The Twelvetrees Ramp is open! It's the "missing link" in the walk down the River Lea from the Olympic Park all the way down to Cody Dock. Previously, to complete the walk you had to come off the river at Three Mills and go on an ugly detour round the Tesco's and the Blackwall Tunnel Approach. This ramp links up two bits so you can go more-or-less continuously down the river paths.

It was supposed to be open in September but... well... you know. And finally today it's open! Here are my exciting first pictures of it, looking robust against the wintry fog:

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A fun bit of ironwork on top there. In the evening, the old streetlamp on the bridge lights up, and the new ironwork and the old streetlamp work well together.

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It would have been nice if it had been open for all those autumnnal walks in the evening sun and the lengthening shadows. Instead, now you can walk all the way down to Cody Dock, except you won't find much going on down there in winter time. But hey ho, it's ready for 2017!

Oh and by the way here's Twelvetrees Ramp on the map

Saturday 17th December 2016 | london | 1 Comment
Butternut squash toad-in-the-hole (Sunday 6th November 2016)
Vegetarian food in Paris (Sunday 30th October 2016)
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