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I am a research fellow, conducting research into automatic analysis of bird sounds using machine learning.
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Older things: Evolutionary sound · MCLD software · Sponsored haircut · StepMania · Oddmusic · Knots · Tetrastar fractal generator · Cipher cracking · CV · Emancipation fanzine


I'm surprised that Cambridge doesn't have many sushi places. Surely they've always had plenty of Japanese students around, and plenty of posh metropolitan types? Or does it not work like that? Anyway, I have found two proper sushi restaurants in Cambridge (UK) so here's a quick review.

(Actually, as well as these two, in the middle of town there's a Yo Sushi and soon-to-be a Wasabi too. I've nothing against those chain shops but I don't think of them as proper sushi, simply because you can usually only get tuna and salmon stuff, they don't have a proper sushi selection. Good for convenient food but not the full deal.)

  1. U-Sushi near the Grafton Centre is a friendly little place that does a lot of takeaway. The fish could have been fresher, but there's plenty of variety on the menu and I particularly liked their vegetarian california rolls, made with asparagus, avocado, cucumber, shitake mushroom and pickle.

  2. Japas just off Lensfield Road has a bit more of a restauranty vibe, if that's what you're after. They also seem to do plenty of takeaway. The fish is the same quality as U-Sushi and the range is pretty similar too. I wouldn't bother with their deep-fried ice-cream for afters though, it's nowhere near as much fun as it should be.

Anyone got any more tips? Let me know. There must be a secret sushi palace secreted around here somewhere...

food · Permalink / Comment

I want to tell you which is the best DAB radio. I have it here in front of me:

Radio photo

I've seen many DAB radios in my time. My ex worked at the first BBC digital radio station when it launched, so we saw all the early models.

Old analogue radios, like a lot of analogue things, had this great built-in interface quirk. In the old days you couldn't just choose a radio station, you had to turn a dial and that would tune the frequency to the station you wanted. I'm NOT talking nostalgia here, I'm talking usability. This strange quirk meant you could learn the interface really well - the radio stations were always at the same place on the dial, and you very quickly learnt exactly how much to turn to go straight from Radio 4 to Radio 1.

DAB radio designers didn't really have this, they just had a big list of stations. In fact they had it worse than that: if there was any "natural" interface driven by the mechanics of DAB it would be a hierarchical list where first you choose your multiplex, then you choose your station. The early DAB radios forced you to do this. Firstly, navigating a hierarchical list is fecking annoying on any device that doesn't have a massive computer screen. Secondly, the hierarchical list means nothing to anyone. No-one knows intuitively if Smooth FM and the World Service are on the same multiplex or not, and they shouldn't have to know.

DAB radio designers came up with various ways round this. They added presets of course - lots of FM radios have this too. Trouble is, they generally had to add lots of buttons, especially as they needed to support both DAB and FM. Bleh. Clicky interfaces, menus to scroll through. Bleh.

Well now the perfect DAB/FM radio interface has been settled on and it looks like this:

Radio photo

It's from John Lewis (it's called the "Spectrum"), and it's a little portable thing. It does DAB, FM and USB, it runs off battery or mains, it doesn't take more than 4 seconds to turn on (unlike many other digital radios which sit around saying "hello" while secretly they're frantically booting stuff up).

But the one thing I want you to notice is how easy it is to operate it in the dark, with your eyes closed, or with one hand stirring a pot of soup. There is a very small number of buttons/knobs, and when you grab for it without looking you can instantly feel which button you're on. After a day or two you can change the station, change the volume, change DAB/FM, or turn it on/off without looking, and really that's all you need!

The minimalism continues through the interface too: there are no presets, for example. Some might find miss the lack of presets, but it takes away a lot of interface complexity. There's an implicit "two-preset" character anyway, since of course it remembers one DAB station and one FM station, the ones you had on last.

The two dials on the top are not continuous dials, by the way, they're click-wheels. I do miss a little the ability to be as subtle as you like with the volume control, but I don't mind much. On the station dial, for DAB you're wheeling through the alphabetical list, which you can sometimes do with your eyes shut but not always - but at least the stations are always in exactly the same place, it's still a learnable interface. On FM, the dial changes the frequency, as you'd expect, plus the curiously named "Reset" button does auto-scanning for you on FM, and that works fine too.

I actually bought this radio for my ex. After seeing it in action for a while, I went and bought another one, for myself!

design · Permalink / Comment

My Return key is getting a bit flaky, so I've just worked out how to reuse my "AltGr" key as a backup in case of emergency. Noting it down for my own reference.

In Linux you can configure anything, including custom keyboard layouts, but it can be tricky to find the advice online that actually matches your system. (Standard Ubuntu has some helper apps that a LXDE desktop doesn't, etc etc.) I think this method will work with any Debian-based system, and I took it from Debian's multimedia-keys guide.

Basically, follow the instructions in that wiki page:

That's enough to enable it for this session. Then you just have to add that last command as one of your autostart programs so it'll be available in future sessions. I did it by running "gnome-session-properties" tool, but also belt-and-braces in my .zshrc because of some other config I have in there.

linux · Permalink / Comment

I hadn't noticed that both Björk and Kim Gordon had split up from their long-term partners. Thing is, last summer I split up from my long-term partner. I think back then I would have gained some solace from the work of fabulous artists who were going through analogous pain - even if the analogies were only superficial. But then, I was deep in it all, too busy with our own difficulties and the horrible pile of practicalities that accompany a long-term breakup, to notice everything around me.

That changed this year, when Kim Gordon published a book, and Björk published an album, both of which foreground their breakups. But the timing has changed - it's not last summer any more, and I'm not in the heat of it, so I don't need to take solace from these things like I did back then. I can feel some empathy, remotely of course. I really wonder what I would have made of it all last summer.

Björk's album Vulnicura is a heartfelt and very raw heartbreak album. It does some amazing things, some really intense sonic moments, which work on these emotional issues universally, and Björk's lyrics are along similar lines but they often dive really deep into uncomfortably intimate detail. A bit like hearing someone listing all the bad things their ex did, and not being sure quite how literally to take it all:

"Family was always our sacred mutual mission/ Which you abandoned."

It's so direct that it makes me want to hear the other side's rejoinder. (I should say, by the way, that that quote is nothing like what was going on in my case.)

It's really quite striking though that it's Björk and Kim Gordon. Björk has for decades expressed a very open and deep emotional literacy in her music, and in recent years it's increasingly been less about torrid excitement and more about family bonds. Kim Gordon and Thurston Moore were the alt-rock equivalent of the ideal family: together for decades, raising kids while pushing Sonic Youth and their other projects ever onward. And if these paragons are not immune, well on the one hand that's really sad, while on the other hand maybe I can take some solace from it after all. Their lives aren't exactly average lives, but then whose is? We're still all tumbling through the same kaleidoscope.

Permalink / Comment

The whole idea of static site generators is interesting, especially for someone who has had to deal with the pain of content management systems for website making. I've been dabbling with a static site generator for our research group website and I think it's a good plan.

What's a static site generator?

Firstly here's a quick historical introduction to get you up to speed on what I'm talking about:

  1. When the web was invented it was largely based on "static" HTML webpages with no interaction, no user-customised content etc.
  2. If you wanted websites to remember user details, or generate content based on the weather, or based on some database, the server-side system had to run software to do the clever stuff. Eventually these evolved into widely-used "content management systems" (CMSes) - such as drupal, wordpress, plone, mediawiki.
  3. However, CMSes can be a major pain in the arse to look after. For example:
    • They're very heavily targeted by spammers these days. You can't just leave the site and forget about it, especially if you actually want to use CMS features such as user-edited content, or comments - you need to moderate the site.
    • You often have to keep updating the CMS software, for security patches, new versions of programming languages, etc.
    • They can be hard to move from one web host to another - they'll often have not-the-right version of PHP or whatever.
  4. More recently, HTML+CSS+JavaScript have developed to the point where they can do a lot of whizzy stuff themselves (such as loading and formatting data from some data source), so there's not quite as much need for the server-side cleverness. This led to the idea of a static site generator - why not do all the clever stuff at the point of authoring the site, rather than at the point of serving the site? The big big benefit there is that the server can be completely dumb, just serving files over the network as if it was 1994 again.
    • That gets rid of many security issues and compatibility issues.
    • It also frees you up a bit: you can use whatever software you like to generate the content, it doesn't have to be software that's designed for responding to HTTP requests.
    • It does prevent you from doing certain things - you can't really have a comments system (as in many blogs) if it's purely client-side, for example. There are workarounds but it's still a limitation.

It's not as if SSGs are poised to wipe out CMSes, not at all. But an SSG can be a really neat alternative for managing a website, if it suits your needs. There are lots of nice static site generators out there.

Static site generators for academic websites

So here in academia, we have loads of old websites everywhere. Some of them are plain HTML, some of them are CMSes set up by PhD students who left years ago, some of them are big whizzy CMSes that the central university admin paid millions for and doesn't quite do everything you want.

If you're setting up a new research group website, questions that come to mind are:

So using a static site generator (SSG) might be a really handy idea. So that's what I've done. I used a static site generator called Poole which is written in Python and it appealed to me because of how minimal it is.


It has one HTML template which you can make yourself, and then it takes content written in markdown syntax and puts the two together to produce your HTML website. It lets you embed bits of python code in the markdown too, if there's any whizzy stuff needed during page generation. And that's it, it doesn't do anything else. Fab!

But there's more: how do people in our research group edit the site? Do they need to understand this crazy little coding system? No! I plugged Poole together with github for editing the markdown pages. The markdown files are in a github project. As with any github project, anyone can propose a change to one of the textfiles. If they're not pre-authorised then it becomes a "Pull Request" which someone like me checks before approving. Then, I have a little script that regularly checks the github project and regenerates the site if the content has changed.

(This is edging a little bit more towards the CMS side of things, with the server actually having to do stuff. But the neat thing is firstly that this auto-update is optional - this paradigm would work even if the server couldn't regularly poll github, for example - and secondly, because Poole is minimal the server requirements are minimal. It just needs Python plus the python-markdown module.)

We did need a couple of whizzy things for the research site: a publications list, and a listing of research group members. We wanted these to come from data such as a spreadsheet so it could be used in multiple pages and easily updated. This is achieved via the embedded bits of python code I mentioned: we have publications stored in bibtex files, and people stored in a CSV file, and the python loads the data and transforms it into HTML.

It's really neat that the SSG means we have all our content stored in a really portable format: a single git repository containing some of the most widely-handled file formats: markdown, bibtex and CSV.

So where is this website? Here:

IT · Permalink / Comment

Non-negative matrix factorisation (NMF) is a technique we use for various purposes in audio analysis, to decompose a sound spectrogram.

I've been dabbling with the Stan programming environment here and there. It's an elegant design for specifying and solving arbitrary probabilistic models.

(One thing I want to point out is that it's really for solving for continuous-valued parameters only - this means you can't explicitly do things like clustering etc (unless your approach makes sense with fuzzy cluster assignments). So it's not a panacea. In my experience it's not always obvious which problems it's going to be most useful for.)

So let's try putting NMF and Stan together.

First off, NMF is not always a probabilistic approach - at its core, NMF simply assumes you have a matrix V, which happens to be the product of two "narrower" matrices W and H, and all these matrices have non-negative values. And since Stan is a probilistic environment we need to choose a generative model for that matrix. Here are two alternatives I tried:

  1. We can assume that our data was generated by an independent random complex Gaussian for each "bin" in the spectrogram, each one scaled by some weight value specified by a "pixel" of WH. If we're working with the power spectrogram, this set of assumptions matches the model of Itakura-Saito NMF, as described in Fevotte et al 2009. (See also Turner and Sahani 2014, section 4A.)
  2. We can assume that our spectrogram data itself, if we normalise it, actually just represents one big multinomial probability distribution. Imagine that a "quantum" of energy is going to appear at some randomly-selected bin on your spectrogram (a random location in time AND frequency). There's a multinomial distribution which represents the probabilities, and we assume that our spectrogram represents it. This is a bit weird but if you assume we got our spectrogram by sampling lots of independent quanta and piling them up in a histogram, it would converge to that multinomial in the limit. This is the model used in PLCA.

So here is the Stan source code for my implementations of these models, plus a simple toy dataset as an example. They both converge pretty quickly and give decent results.

I designed these implementations with audio transcription in mind. When we're transcribing music or everyday sound, we often have some pre-specified categories that we want to identify. So rather than leaving the templates W completely free to choose, in these implementations I specify pre-defined spectral templates "Winit".

(Specifying these also breaks a permutation symmetry in the model, which probably helps the model to converge since it shouldn't keep flipping around through different permutations of the solution. Another thing I do is fix the templates W to sum up to 1 each [i.e. I force them to be simplexes] because otherwise there's a scaling indeterminacy: you could double W and halve H and have the same solution.)

I use a concentration parameter "Wconc" to tell the model how closely to stick to the Winit values, i.e. how tight to make the prior around them. I also use an exponential prior on the activations H, to encourage sparsity.

My implementation of the PLCA assumptions isn't quite traditional, because I think in PLCA the spectrogram is assumed to be a sample from a multinomial (which implies it's quantised). I felt it would be a bit nicer to assume the spectrogram is itself a multinomial, sampled from a Dirichlet. There's little difference in practice.

science · Permalink / Comment

I'm quite naive about Islam, so it's hard to get a clear idea of "normal" Islam underneath the headlines about the tiny proportion of violent extremists. Part of the Charlie Hebdo thing was the question about whether it's OK to depict the prophet. So just for reference I found this quote from Tariq Ali in the LRB helpful:

"On the question of images there has always been a debate within Islam. The Quran itself contains warnings against the worship of idols and graven images, but this is taken straight from the Abrahamic tradition and the Old Testament. It’s a stricture on forms of worship. After all, images of the prophet were embossed on early Muslim coins to replace Byzantine and Persian potentates. A number of paintings by Muslim artists in the late medieval period depict the prophet with loving care. The Shia tradition has always ignored the supposed ban on images and portraits of Shia imams have never been forbidden. All the different schools of Sunni jurisprudence don’t agree on the question. It has only become a big issue since Saudi money pushed Wahhabi clerics onto the world stage to fight communism during the Cold War (with the total backing of Washington). Wahhabi literalism misinterprets the Quran and its hostility to images led the Saudi government to destroy the graves in Mecca of the prophet, his companions and his wives. There were no protests except by architects and historians who denounced the vandalism. One can only imagine the response in the world of Islam had the destruction of the graves been carried out, deliberately or accidentally, by a Western power."

Permalink / Comment

Just finished reading Thomas Piketty's now-famous book Capital in the Twenty-First Century. It's a big book, takes a while, but it's thoroughly worth it. It's admirably data-driven, yet clear and readable.

One thing it gives you is a lot of tips about whether the future will be the same as the past. Will inflation, growth, inequality be similar in the next 50 years as in the past 50 years? There are some perennial factors, and some things that are actually blips (caused e.g. by the World Wars) when considered on a timescale of centuries - and many of these are not quite as I had expected. Plenty of interesting titbits about, for example, how the amount of wealth we inherit is or isn't changing as our average lifespan gets longer, and how much "gift-giving" has grown in recent years as an "alternative" to inheritance.

And the readability is enhanced with details from history and literature, such as the way authors such as Jane Austen reflect the financial certainties of their time in their prose.

(It's worth mentioning that the Financial Times briefly smudged the book's reputation by alleging some of the data was wrong. (See here for example.) However, as The Economist noted, "the analysis does not seem to support many of the allegations made by the FT, or the conclusion that the book's argument is wrong." The FT later awarded Piketty's book their business book of the year, perhaps sensing which way the wind was blowing.)

I agree with the LRB's review of the book that "nothing about the book is more impressive than the range and richness of its statistical information. [The book] both insists on the importance of data and, at least where modern societies are concerned, highlights the uncertainties involved in its collection." (Note: the LRB also takes issue with some of Piketty's interpretations - interesting review.)

The LRB review also points out that Piketty's proposed mechanism for fixing some of the problems of modern markets and global captialism - namely, a global progressive tax on capital - may be a nice theory to consider but it's so unrealistic as to be unhelpful. Piketty claims (p515) that even though it's utopian, it's worth considering, maybe even working towards. But to me it seems obviously to neglect so many extremely powerful problems. Of course the richest people have the most political power, and will fight to prevent such taxes being adopted (or if they are adopted, to build a new tax haven state on an oil-rig somewhere). Maybe this is just a practical problem, to be solved by politics. But the tax would require all forms of wealth, owned by every person on and off the planet, to be enumerated. If not, the rich and their financial engineers would transfer their assets into un-enumerated assets. This reminds me of the "information asymmetry" critique of neo-classical economics: many market theories assume that all market participants have perfect information, and this unrealistic assumption is required to prove those markets' effectiveness. Similarly, the effectiveness of the global capital tax in balancing out inequality rests really quite heavily on the idea of some tax agencies somewhere having essentially perfect knowledge. Unfortunately (and as Piketty notes) modern financial engineering means that many taxes, even progressive taxes, become a bit regressive when everyone is subject to them except for the super-rich.

Piketty also says (p519) that the main benefit of the wealth tax (charged at low annual rates, nothing too scary) is "more in the nature of a compulsory reporting law than a true tax" - in a sense, he's less interested in taxing wealth than encouraging transparency in wealth ownership. This again is a bit utopian, since of course people will be motivated to avoid some things being reported, but not so problematic, since the benefits of transparency don't require 100% transparency. And it chimes well with Piketty's insistence that it's not financial rules that can fix the world, but publicly-available information and democratic debate combined with the rule of law. Piketty points out (p570) that most businesses don't publish enough financial details for us to work out how the wealth is divided between profits and wages. If they were required to, that would empower workers. As well as economists ;)

economics · Permalink / Comment

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