I am a research fellow, conducting research into automatic analysis of bird sounds using machine learning.
—> Click here for more about my research.
Based on a conversation we had in the Machine Listening Lab last week, here are some blogs and other things you can read when you're - say - a new PhD student who wants to get started with applying/understanding deep learning. We can recommend plenty of textbooks too, but here it's mainly blogs and other informal introductions. Our recommended reading:
PRACTICAL:
ADVANCED:
I was setting a new laptop up recently. If you're not familiar with Linux you probably don't know how amazing is the ecosystem of software you can have for free, almost instantly. Yes sure the software is free but what's actually impressive is how well it all stitches together through "package managers". I use Ubuntu (based on Debian) and Debian provides this amazing jiu-jitsu wherein you can just type
sudo apt install sonic-visualiser
and hey presto, you get Sonic Visualiser nicely installed and ready to go.
So what that means for me is that when I'm setting up a new computer, I don't need to go running around clicking on a million websites, clicking through download links and licence agreements. I can just copy over the list of all my favourite software packages, and apt will install them for me in just a few steps.
For whatever reason - for my own recollection, at least - here's a list of lots of great packages I tend to install on my desktop/laptop. General useful stuff, plus things that an audio hacker, Python machine-learning developer, and computer science academic might use. I'll add some comments to highlight notable things:
# file sharing, synchronisation
syncthing # for fabulous dropbox-without-dropbox file synchronising
syncthing-gtk
git
transmission-gtk
# graphics/photo editing
cheese
darktable
gimp # great for bitmap (e.g. photo) editing
imagemagick
inkscape # great for vector graphics
openshot # great for video editing
# for a nice desktop environment:
pcmanfm
gnome-tweak-tool
caffeine-indicator # helps to pause screensaver etc when you need to watch a film, give a talk, etc
xcalib # I use this to invert colours sometimes
# academic
jabref
r-base
texlive
texlive-latex-extra
texlive-bibtex-extra
texlive-fonts-extra
texlive-fonts-recommended
texlive-publishers
texlive-science
graphviz
gnuplot
latexdiff # Super-useful for comparing original text against the re-submission text...
poppler-utils # PDF manipulation
psutils
bibtex2html
pandoc
# for python programming fun
jupyter-notebook
virtualenv
python-matplotlib
python-nose
python-numpy
python-pip
python-scipy
python-six
python-skimage
python3-numpy
cython
ipython
ipython3
# for music playback
mopidy
mopidy-local-sqlite
ncmpcpp
pavucontrol
paprefs
brasero
banshee
qjackctl
jack-tools
jackd2
mixxx
mplayer
vlc
# music/audio file manipulation
audacity
youtube-dl
ffmpeg
rubberband-cli
sndfile-tools
sonic-visualiser
sox
id3v2
vorbis-tools
lame
mencoder
# audio programming libraries
libsndfile1
libsndfile1-dev
libfftw3-dev
librubberband-dev
libvorbis-dev
# for blogging / websiting:
pelican
lftp
# office
simple-scan
ttf-ubuntu-font-family
thunderbird-locale-en-gb
orage
xul-ext-lightning # alt calendar software
# misc programming stuff
ansible
ant
build-essential
ccache
cmake
cmake-curses-gui
debhelper
debianutils
default-jdk
default-jre
devscripts
git-buildpackage
vim-gtk
# system utilities
apparmor
apport
anacron
nmap
hfsprogs
printer-driver-hpijs
dconf-editor
chkrootkit
dmidecode
zip
zsh # zsh is so much better than bash
gparted
htop
baobab
wireshark-qt
bzip2
curl
dnsutils
dos2unix
dvd+rw-tools
less
openssh-server
openvpn
screen
unrar
unzip
wget
For a cook, Veganuary was a really interesting challenge. A whole month of being vegan! Here are some things I learnt:
- How to make a chia egg - it's a replacement for egg white made of... crushed seeds. Probably the main party-trick I learnt, since I already knew some of the other vegan voodoo secrets (e.g. aquafaba).
- How to veganise a cake
- Coconut becomes a bit of a fallback for creamy or fatty things: coconut cream, coconut oil, coconut milk... not too healthy to have too much of that!
- THERE@S MILK EXTRACT IN EVERYTHINGGG. This evening I picked up a pack of gnocchi - presumably just made of potato - and looked at the back... milk protein - gah!
- Vegan cheese: avoid Violife. Vegans will tell you "Oh this one tastes OK, this other one is good if you..." - don't listen to them! Violife will put you off vegans AND cheese!
- On the other hand, oat milk (Oatly) is ace alternative milk, and can be used for a surprising number of baking recipes with no problem at all. I've cooked Yorkshire puddings, quiches, all kinds of things with it.
You know, I didn't miss real cheese much, but that's probably because a month is not too long really. Didn't even get round to trying all the recipes I wanted to try. Had some lovely vegan junk food (shout out to Vivera shawarma, not to mention McSween's veggie haggis).
And for the record, as well as to show you all how interesting Veganuary can be if you like cooking, here are some of the delicious things we cooked+ate!
OK, "vegan chorizo carbonara" - I think neither the Italians nor the Mexicans will forgive me for this one! But it's a veganuary experiment and I like it.
Thanks to veganuary I'm learning about chia egg, and here it really does work to provide the gloopy egg-like saucing. The chia also gives a little bit of flavour and crunch.
To get the flavour balanced, you add more lemon than you would to a "normal" carbonara - it isn't authentic but it adds some freshness and lightness.
Serves one, takes 15 minutes.
- 1 tbsp chia seeds (white or black, doesn't matter)
- 75g spaghetti
- A small handful (75g) of black bean chorizo, or other vegan chorizo
- Half a lemon, juice and rind
- 50ml oat cream
- A small handful of fresh parsley
- A sprinkle of nutritional yeast
First, prepare the chia egg: grind up the chia seed in a pestle and mortar (or similar), not for too long - it doesn't need to be very fine - then add 3 tbsp of cold water. You can leave this to stand and thicken up as you do the other stuff.
Start the spaghetti cooking: put it in a large pan of boiling salted water. Cook it for maybe 12 mins until it is al dente.
Divide the chorizo into small bites. In a small frying pan, fry the chorizo in olive oil, hot at first but then turn it down to medium.
Chop the parsley roughly.
Mix the lemon juice and rind into the chia egg. You may need to stir the chia egg and poke it to beat out any clumps.
When the pasta has reached the "al dente" stage, drain it in a colander and then return it to the pan you cooked it in. (No need for any more heat at this point.) Add the chia egg and lemon, as well as the oat cream, and mix it through thoroughly. Then add the chorizo and the parsley, and mix them all up.
Serve this up, with nutritional yeast sprinkled on top.
I've been using "black bean chorizo" in my cooking for years. It's based on Hugh Fearnley-Whittingstall's "tupperware chorizo" recipe - it makes a densely-flavoured black bean paste, not as firm as real chorizo but with the same kind of flavour depth.
It keeps in the fridge for a long time (let's say... a month?) and is really handy for a bit of complex strong flavour which, in vegetarian cooking, can otherwise be hard to get!
- 375g black beans (from a tin), drained
- 1 garlic clove, minced or finely chopped
- 1-2 tbsp smoked paprika
- 1/2 tsp salt
- 1 tsp fennel seeds
- 1/4 tsp cayenne pepper
- 25ml red wine
Put the black beans in a bowl and lightly mush/crush them, e.g. with a fork or a masher. They don't need to be fully minced but, at least... not bean-shaped any more!
Add all the other ingredients. Mix it all up thoroughly. It may well seem "too wet" with the red wine but don't worry, it all absorbs and matures.
Put the mix in a tupperware box that you can shut airtight. Shut it, put it in the fridge, and leave it for at least a day before using, ideally 1 to 3 weeks.
Going to try veganuary? We're going for it this year.
Here are some great recipes I made/found recently, all vegan. Maybe they'll help you to enjoy January extra-special:
- Pad thai - do it Vegan Black Metal Chef style! (We used peanut butter instead of peanuts which makes it easier to make the sauce saucy.)
- Chilli sin carne with pulled jackfruit
- Fake fish and chips - battered aubergine. Alex Shaw liked this one so much he messaged from Scotland to say so :)
- Gado gado - an Indonesian dish that's popular in the Netherlands, and with good reason! Fried tofu, fresh salad veg, potatoes, peanut sauce and crispy onions. - of course you'd be leaving the traditional boiled egg out of the recipe, but that's fine. We made our own echt peanut sauce but you can buy it.
- Beetroot nisk soup - a simple warming Kurdish soup
- Vietnamese banana and coconut cake - ah, I have this in a little recipe book here (Vietnamese Fusion by Chat Mingkwan) and I need to type it up. It's basically white bread, sliced bananas and sugar, layered up, soaked in coconut milk (plus a touch of vanilla, brandy, cinnamon for flavouring) and then baked. So, it becomes a kind of bread pudding.
We'll also be buying some cheez from Black Arts Vegan and making some vegan pizzas etc. Personally, I'd say be careful with vegan cheese, since some of the main brands in the shops might put you off for life...
Next I want to work out how to cook "beet wellington" and how to make vegan mayo. Tips welcome!
I've been struggling with the tension between academia and flying for a long time. The vast majority of my holidays I've done by train and the occasional boat - for example the train from London to southern Germany is a lovely ride, as is London to Edinburgh or Glasgow. But in academia the big issue is conferences and invited seminars - much of the time you don't get to choose where they are, and much of the time there are specific conferences that you "must" be publishing at, or your students "must" be at for their career, or you're invited to give a talk.
What can you do? Well, you can't give up. So here's what I've done, for the past five years at least:
- I've declined various opportunities to fly (e.g. to North America and Australia - I'm Europe based). Sometimes this hurts - there are great meetings that you'd like to be at. In general, though, you usually find there are similar opportunities nearer by. You'll probably meet most of the people in one of those events anyway. In the big picture, it's probably better for academia to be structured as an overlapping patchwork network, rather than having single-point-of-groupthink.
- I've taken the train to many conferences and meetings. From the UK I've taken the train to France, Spain, Germany, Netherlands, and I'm happy to go further. If you haven't done long train journeys for work then maybe you don't realise: with a laptop, many long-distance train journeys are ideal peaceful office days, with a reserved seat and beautiful views scrolling past. (UK folks: ask The Man In Seat 61 for the best train trips.) If your concern is making time for the journey, don't worry! You'll be much more productive than when you fly!
- When invited to fly somewhere, I always discuss lower-carbon ways of doing it. Rome2Rio is a handy site to compare how to get anywhere by different means. If flying is the only way and I'm tempted to accept the invitation, I ask the inviters to pay for carbon offsetting too.
Many university administrations don't want to pay for carbon offsets - why? This needs to change. If they're paying for flights they should be paying for the negative externalities of them. I'm not worried here about whether carbon offsetting is a good excuse or not - I'm concerned about research being more aware of its responsibilities.
- If travelling somewhere (even by train), always try to make the most of the journey by finding other opportunities while out there - e.g. a new research group to say hello to (even if just a cuppa), a company or NGO. It's good to make face-to-face contact because that makes it much easier to do remote collaboration or coordination at other times (with the same people, I mean), reducing the need for extra trips.
(Talking to my German colleagues, I learn that the German finance rules mean you have to travel home as soon as possible after the event, i.e. not roll multiple things into one trip - that's an unfortunate rule, we should change that.)
- And of course I've done plenty of video-conferencing and audio-conferencing. It doesn't replace face-to-face meetings and we should be realistic about that, but it's a tool to use.
There's a cost implication which I haven't mentioned: flights are unfortunately often cheaper than trains and stopovers. This needs to change, of course - and can be a bit tricky when you're invited to speak somewhere and the cost ends up more than the organisers expected. However, I've been managing a funded research project for the past five years and I've noticed that in fact I've spent much less money on travel than I had projected. Why? Well back when I wrote the budget I costed for international flights and so on. But my adapted approach to travel means I take fewer big long-distance trips, but I get more out of them because I combine things into one trip, and I've skipped certain distant meetings in favour of ones closer to home - all of which means the cost is less than it would have been.
By the way, this handy flight CO2 calculator can help to work out the impact of speific trips, including multi-stop trips, so you can calculate if combining flights into a round-trip is sensible.
None of these are absolute rules. We can't carry all the burden solo, and we have to make compromises between different priorities. But if we all make some changes we can adapt academia to current realities. We can do this together - which is why I've signed my name on No Fly Climate Sci, a place for academics collectively to pledge to fly less. As I said, you don't have to be absolute about this, and the No Fly Climate Sci pledge acknowledges that. Join me?
I started collecting examples of "good news" items a couple of years ago - as a personal antidote to some of the bad things going on out there. This year I've ended up collecting almost too many to keep a handle on. Although the year isn't finished, I'm blogging it here so you can read!
Have a look here - what's a good news item that particularly grabs you?
There's so much good news that it's hard to know how to organise it... I'm writing from a UK perspective so there are plenty of UK things but the big ones are worldwide. I'll try starting with the Big Good News and then grouping other things into categories:
Big Good News
Health
Breast cancer screening improvement - many women can avoid chemo
UK soft drink sugar tax - many firms have cut the sugar in their drinks
Technology
WhatsApp Co-Founder Puts $50M Into Signal To Supercharge Encrypted Messaging - this is great news for digital privacy, and Signal's a lovely app
Linus Torvalds, the inventor and maintainer of the Linux kernel, had an awakening about his rude behviour, wrote a detailed apology, and took time off to work on his behaviour
Microsoft open-sourced its entire patent portfolio (over 60,000 patents), pledging unrestricted use to the Linux world
Opening up MasterMap - Unlocking of Government’s mapping and location data to boost economy by £130m a year
Development
Over the past 20 years, the proportion of people living in extreme poverty has almost halved.
Percent of Indian households with toilets goes from approx 50% (2014) to approx 90% (2017)
'Remarkable' decline in fertility rates worldwide (journal source) - while this is a complex issue, a cause and effect of many things, the reason I include this is that it's great news for women's empowerment, indicative of a "demographic transition" connected with such progress worldwide.
Politics
Spain: Mariano Rajoy and his PP finally ousted by no-confidence vote, after many corruption scandals
The Britain First leaders have been jailed
In Dutch local elections, GroenLinks ("Green Left") goes from 5% up to 8.4% of the vote - they were the biggest party in Amsterdam and in other cities! - while the anti-Islam PVV had a poor showing, collapsing from seven to two seats in The Hague for example
Uber lost its court battles trying to claim its drivers were not actually employees
Malaysia: Mahathir Mohamad says Anwar Ibrahim (who he was previously responsible for deposing) to be given royal pardon
'Gay conversion therapy' to be banned as part of LGBT equality plan
Greece emerges from eurozone bailout programme
Boris Johnson faces court over his well-publicised £350m Brexit claim
The UK government’s independent Migration Advisory Committee concluded that international students are a good thing. Even when considered only in cash terms, "the average non-EEA student makes a net fiscal contribution of more than £5,000 a year"; and that they even benefit domestic students.
The UK's bulk surveillance powers - exposed by the whistleblower Edward Snowden - have been found to be illegal by the European Court of Human Rights.
Environment
All kinds of subsidy-free renewable power schemes announced/commenced, meaning that renewables can be economical in themselves.
New government data confirms support for renewables is at an all time high
Chile creates national parks from donated land. "the area being protected was roughly the size of Switzerland." donated by founder of North Face
UK's total greenhouse gas emissions have fallen from 800 million tonnes in 1990, to less than 500 million
(...though aviation's contribution doubled and no-one's doing anything about it!)
Bikes now most common vehicle type in City of London rush hour, says official traffic count study
Global carbon emissions could be cut 3% by following the UK’s example
UK introduces plans for a bottle deposit scheme (pfand)
Drop in plastic bags littering British seas linked to introduction of 5p charge
Plastic-eating enzyme discovered (and improved) by scientists in Portsmouth which turns plastic back into its components:
Electric Buses Are Hurting the Oil Industry ("with China leading the way" - 17% of China's entire fleet already! Though the UK has the #1 biggest electric bus fleet in Europe.)
"mini-Holland" schemes in outer London boroughs proven successful - including an auxiliary increase in walking
MoD campaign to stop killing of songbirds on Cyprus hailed a success: Poachers killed 800,000 birds on UK base in 2016 but 72% drop was recorded in last year
Organic solar cells (flexible, multi-purpose) reach a new level of efficiency, competitive with silicon and could produce electricity very cheaply
Last year renewable energy made up 30% of UK electricity - a new record!
The number of vegans in the UK has doubled from 2014 to 2016 - and then more than doubled again from 2016 to 2018:
Record-breaking numbers of UK's rarest seabird return to island after near extinction
Groundbreaking 'spinning' wind turbine wins UK Dyson award - interesting design
Aberdeen offshore wind project opposed by Trump is officially opening
Dutch appeals court upholds landmark climate change ruling - the government is legally obliged to actually stick to its climate targets
A survey run by Waitrose (of everyone, not just Waitrose shoppers) finds "1 in 8" people veggie or vegan
Lancashire Fracking protesters walk free after court quashes 'excessive' sentences
Other
UK became the first country to enforce documentation of the gender pay gap in companies
British astrophysicist Jocelyn Bell Burnell, who discovered pulsars, overlooked by the Nobels, finally won a $3m Breakthrough award
Lancaster City Councillors voted unanimously to save Lancaster Music Co-op
...and finally...
Paris hero climbs four-storey building to rescue dangling child – wow watch this video
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