As part of the Welsh Crucible I had an article in the Western Mail today. How computer science can solve problems in biology. We were asked to explain our work in 400-500 words (they chose the title). Much more challenging than I thought it would be, because that's not very many words.
Monday, 3 March 2014
Thursday, 6 February 2014
Final year computer science projects
This term I'm supervising 5 final year student projects. They have one term (just over 3 months) in which to really create something they can be proud of. It's not long, especially when they have to get to grips with new terminology, new equipment, reading and research, specification, design, implementation and experiments, testing, documentation and reflection. They're also asked to keep progress diaries or blogs and use version control to manage their projects.
I've very excited about the projects this year, they're all diverse and fun:
Hopefully, we'll have some good results by May!
I've very excited about the projects this year, they're all diverse and fun:
- Using information theory and machine learning to recognise quality control issues in next gen sequencing lanelets (together with Joshua Randall, Sanger Institute)
- Analysis of the content of NLW's digitised newspapers collection
- Modelling insect choice among plants (together with Lizzy Donkin and John Warren in IBERS)
- A model of the brain of C. elegans that we can play with as a talking point in AI discussions with the public.
- Using image processing and microscope webcams to determine the growth of yeast in microtitre plates.
Hopefully, we'll have some good results by May!
Bioinformatics and computational biology: 500 years of exciting problems?
I gave a talk at Warwick University, Department of Computer Science in January 2014. A look at the intertwining of computer science and biology from the days of Turing through the present and on to the future, including some of my research along the way.
In a 1993 interview, Donald Knuth worried that computer science in the future will be "pretty much working on refinements of well-explored things", whereas "Biology easily has 500 years of exciting problems to work on". I'll describe some of the bioinformatics and computational biology that I've been working on. My talk included a little about where the field has come from, where it's going in the future, and whether it should be considered a branch of computer science at all.
The slides are online at Figshare.
Sunday, 5 January 2014
Storm damage in Aberystwyth in January 2014 and in January 1890
An unusually high tide in Aberystwyth in January 2014 has severely damaged the promenade. We do get some spectacular weather here on the west coast of Wales.
Forceful storms that broke up the promenade also occurred in other years, particularly in 1927 and 1938, and their aftermath was photographed and looks remarkably similar. In January 1890, the Cambrian News reported a storm at Aberystwyth which caused trouble to the train travelling between Aberystwyth and Machynlleth.
"The uptrain from Aberystwyth had to wait in the Junction for over half an hour until the tide had partially subsided. Then the line was cleared of pieces of timber and accumulations of grass and rushes and the train proceeded, though the water was half way up the wheels."
Would the Junction that was referred to here be Dyfi Junction station? The storm in 1890 also caused a hole in the sea wall, in a very similar location to the one that's been opened up this year:
"Unfortunately, the masonry forming the slipway near the Queen's Hotel gave way and subsequently a large hole was washed in the sea wall"
The Queen's Hotel is no longer a hotel, but still exists as a building. It has been used for many purposes since 1890, and has most recently been used as council offices and archives. It's currently up for sale, at a price of approximately £1 million.
The hole in the sea wall caused by this year's weather shows just how powerful the sea is against our buildings and defences.
And in 1890 a steamer in distress was spotted out in the bay, carrying a cargo of pig-iron but having lost its funnel in the storm. The lifeboat was launched, under the command of a Mr Tom Williams, and the crew were rescued and taken to the Belle Vue Hotel for "much-needed refreshments". Our lifeboat was also out rescuing in 2014 and, so far, everyone's safe and sound.
More photos of what happened in 2014 are on Flickr.
Broken railings and paving on Aberystwyth promenade.
Forceful storms that broke up the promenade also occurred in other years, particularly in 1927 and 1938, and their aftermath was photographed and looks remarkably similar. In January 1890, the Cambrian News reported a storm at Aberystwyth which caused trouble to the train travelling between Aberystwyth and Machynlleth.
"The uptrain from Aberystwyth had to wait in the Junction for over half an hour until the tide had partially subsided. Then the line was cleared of pieces of timber and accumulations of grass and rushes and the train proceeded, though the water was half way up the wheels."
Would the Junction that was referred to here be Dyfi Junction station? The storm in 1890 also caused a hole in the sea wall, in a very similar location to the one that's been opened up this year:
"Unfortunately, the masonry forming the slipway near the Queen's Hotel gave way and subsequently a large hole was washed in the sea wall"
The Queen's Hotel is no longer a hotel, but still exists as a building. It has been used for many purposes since 1890, and has most recently been used as council offices and archives. It's currently up for sale, at a price of approximately £1 million.
The hole in the sea wall caused by this year's weather shows just how powerful the sea is against our buildings and defences.
And in 1890 a steamer in distress was spotted out in the bay, carrying a cargo of pig-iron but having lost its funnel in the storm. The lifeboat was launched, under the command of a Mr Tom Williams, and the crew were rescued and taken to the Belle Vue Hotel for "much-needed refreshments". Our lifeboat was also out rescuing in 2014 and, so far, everyone's safe and sound.
Waves wash over the promenade in front of Alexandra Hall and flood the ground floor.
Tuesday, 15 October 2013
My Ada Lovelace post: Donna Robinson
My post for this Ada Lovelace Day is about a woman in computing who inspired me, a friend of mine called Donna Robinson. I first met Donna when living in Guildford, when I was 23. We shared a house (with two other people). She took me shopping for a toolbox (metal, not plastic) and tools (hammers, pliers, mole grips, hacksaw, screwdrivers, and lots more, everything I'd need to be self-sufficient). I didn't have much money. "Trust me", she said, "it's worth investing in good tools". I still have those tools and the toolbox and they're still in use, more than 15 years later.
Donna writes open source code. She made the Oxford College Student Database. She made Valkyrie for Valgrind. She made a library of Scottish Country Dances for the SCDS. She's continually making open source stuff for people, but most of it isn't visible on the web (and neither is she). She financed her open source work by doing up run-down houses in the day, and hacking her code all evening. She chooses not to have an ordinary 9-5 stable job, and it takes a lot of time and effort to do that.
What has most inspired me about Donna is not her coding (though she does that), or her handiness at any manual jobs (though she does that), or her dedication to whatever she chooses to do (see for example how she helped her cat get better after an accident) but her attitude: she knows that with enough time and research she can do whatever she wants to achieve, and she never seemed to have that worry that she wouldn't be taken seriously because she's not male.
Donna writes open source code. She made the Oxford College Student Database. She made Valkyrie for Valgrind. She made a library of Scottish Country Dances for the SCDS. She's continually making open source stuff for people, but most of it isn't visible on the web (and neither is she). She financed her open source work by doing up run-down houses in the day, and hacking her code all evening. She chooses not to have an ordinary 9-5 stable job, and it takes a lot of time and effort to do that.
What has most inspired me about Donna is not her coding (though she does that), or her handiness at any manual jobs (though she does that), or her dedication to whatever she chooses to do (see for example how she helped her cat get better after an accident) but her attitude: she knows that with enough time and research she can do whatever she wants to achieve, and she never seemed to have that worry that she wouldn't be taken seriously because she's not male.
Thursday, 26 September 2013
ECML PKDD 2013
Machine learning, data mining and statistical data analysis is clearly a popular area now, judging by the number of attendees of this year's European conference, ECMLPKDD 2013.
It's been a long time since I last attended (2001 for multi-label classification by a modification to C4.5). I think the field has grown and matured a lot. There are far fewer papers now showing the results of a new algorithm on 10 different UCI datasets. There is far more presence from people in industry. And industry is varied: search engines, internet shopping and finance. Yahoo, Amazon, Zalando, Deloitte and many others sponsored the conference and sent people to speak or attend. There was an "industry track", and that room was full.
Themes that I picked up on were: regression (still popular!), lots of tensors and matrices, numerical analysis methods for large data sets, network mining, sequence mining, and generally using ML/DM to influence people (buying, voting, doing good, giving your system feedback).
The organisers this year have really done a good job: working wifi, lots of food and coffee, sessions running on time, plenty of mingling time, and choosing a venue in a beautiful city, with accommodation in a wide range of hotels within easy walking distance booked as an easy part of the registration process. It is appreciated!
Diversity is something that the ECMLPKDD community have started to work on improving. It has the usual male/female imbalance of a technical conference. Perhaps slightly more women than I expected, or maybe I'm just getting used to this. I'd hazard a guess at about 20% or a bit less. But next year's organising committee are more gender-balanced, and there will also be a Diversity Chair to keep an eye on the issue.
Openness of code and data is something else the community are working on improving. This year for the first time they had an award for "Open Science", and encouraged paper submissions to include a link to code/data. In order to award this, the organisers had to download, compile, run and test lots of submitted code. I don't know which of the organisers did this onerous task, but I'm very pleased they did.
If I had to point out one thing that could still be improved, my number 1 would be that the proceedings are owned by Springer, and are not open. For reasons known only to Springer, I can't make an account with them or reactive an existing account. Maybe Springer will reply to my email eventually. But if the proceedings were open access (papers deposited at arXiv for example) then this would really benefit the ML/DM community and others, and more widely promote the work of everyone who presented.
Next year, 2014, the conference moves to Nancy, France, a city with Art Nouveau architecture, and with many fine wines. www.ecmlpkdd2014.org
It's been a long time since I last attended (2001 for multi-label classification by a modification to C4.5). I think the field has grown and matured a lot. There are far fewer papers now showing the results of a new algorithm on 10 different UCI datasets. There is far more presence from people in industry. And industry is varied: search engines, internet shopping and finance. Yahoo, Amazon, Zalando, Deloitte and many others sponsored the conference and sent people to speak or attend. There was an "industry track", and that room was full.
Themes that I picked up on were: regression (still popular!), lots of tensors and matrices, numerical analysis methods for large data sets, network mining, sequence mining, and generally using ML/DM to influence people (buying, voting, doing good, giving your system feedback).
The organisers this year have really done a good job: working wifi, lots of food and coffee, sessions running on time, plenty of mingling time, and choosing a venue in a beautiful city, with accommodation in a wide range of hotels within easy walking distance booked as an easy part of the registration process. It is appreciated!
Diversity is something that the ECMLPKDD community have started to work on improving. It has the usual male/female imbalance of a technical conference. Perhaps slightly more women than I expected, or maybe I'm just getting used to this. I'd hazard a guess at about 20% or a bit less. But next year's organising committee are more gender-balanced, and there will also be a Diversity Chair to keep an eye on the issue.
Openness of code and data is something else the community are working on improving. This year for the first time they had an award for "Open Science", and encouraged paper submissions to include a link to code/data. In order to award this, the organisers had to download, compile, run and test lots of submitted code. I don't know which of the organisers did this onerous task, but I'm very pleased they did.
If I had to point out one thing that could still be improved, my number 1 would be that the proceedings are owned by Springer, and are not open. For reasons known only to Springer, I can't make an account with them or reactive an existing account. Maybe Springer will reply to my email eventually. But if the proceedings were open access (papers deposited at arXiv for example) then this would really benefit the ML/DM community and others, and more widely promote the work of everyone who presented.
Next year, 2014, the conference moves to Nancy, France, a city with Art Nouveau architecture, and with many fine wines. www.ecmlpkdd2014.org
Friday, 23 August 2013
Venn diagrams
I'd always thought that drawing Venn diagrams were quite trivial, until I needed to create some recently. They are trivial, if we only have 2 equal-sized sets. If we have 3 sets, and we want the circle sizes to represent the number of data items in each set, then the layout algorithm is more complex. Luckily there's a great package for Python called matplotlib-venn which does exactly what I wanted.
However, if I have 4 sets, then it gets more complicated (and isn't yet handled by matplotlib-venn). A Venn diagram must show all possible intersections. Venn used overlapping ellipses to show how this could be achieved.
This is where Venn diagrams differ from Euler diagrams. Euler diagrams don't show empty intersections, so they can look much simpler than Venn diagrams, and can contain fully-nested circles. There are Venn diagrams that can represent all the overlaps of 5 and 6 sets, but we'd end up with some extremely complex diagrams that don't really aid the visualisation of our data.
Update (9 Oct 2013): Here's a Javascript/D3.js interactive version with more thoughts on why it's a difficult problem.
Update (20th March 2014): Here are a couple of completely over the top diagrams: a pine tree and a banana. Venn or Euler?
However, if I have 4 sets, then it gets more complicated (and isn't yet handled by matplotlib-venn). A Venn diagram must show all possible intersections. Venn used overlapping ellipses to show how this could be achieved.
 |
| Diagram by RupertMillard from Wikimedia Commons |
This is where Venn diagrams differ from Euler diagrams. Euler diagrams don't show empty intersections, so they can look much simpler than Venn diagrams, and can contain fully-nested circles. There are Venn diagrams that can represent all the overlaps of 5 and 6 sets, but we'd end up with some extremely complex diagrams that don't really aid the visualisation of our data.
Update (9 Oct 2013): Here's a Javascript/D3.js interactive version with more thoughts on why it's a difficult problem.
Update (20th March 2014): Here are a couple of completely over the top diagrams: a pine tree and a banana. Venn or Euler?
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