Saturday, 5 September 2015

Notes from workshop on Computational Statistics and Machine Learning

I've just attended "Autonomous Citizens: Algorithms for Tomorrow's Society", a workshop as part of the Network on Computational Statistics and Machine Learning (NCSML). That's an ambitious title for a workshop! Autonomous Citizens are not going to hit the streets any time soon. The futuristic goals of Artificial Intelligence are still some way off. Robots are still clumsy, expensive and inflexible. But AI has changed dramatically since I was a student. Back in the days when computational power was more limited, AI was mostly about hand-coding knowledge into expert systems, grammars, state machines and rule bases. Now almost any form of intelligent behaviour from Google translation to Facebook face recognition makes heavy use of computational statistics to infer knowledge.

Posters: there were some really good posters and poster presenters who did a great job of explaining their work to me. In particular I'd like to read more about:
  • A Probabilistic Context-Sensitive Model of Subsequences (Jaroslav Fowkes, Charles Sutton): a method for finding frequent interesting subsequences. Other methods based on association mining give lots of frequent but uninteresting subsequences. Instead, define a generative model, then go on to use data and EM to infer the parameters of the model. 
  • Canonical Correlation Forests (Tom Rainforth, Frank Wood): a replacement for random forests that projects (a bootstrap sample of) the data into a different coordinate space using Canonical Correlation Analysis before making the decision nodes.
  • Algorithmic Design for Big Data (Murray Pollock et al): Retrospective Monte Carlo. Monte Carlo algorithms with reordered steps. There are stochastic steps and deterministic steps. The order can have a huge effect on efficiency. His analogy went as follows: imagine you've set a quiz with a right answer and a wrong answer. People submit responses and you need to choose a winner. You could first sort them all into two piles (correct, wrong) and then pick a winner from the correct pile (deterministic first, then stochastic). Or you could just randomly sample from all results until you get a winner (stochastic first). The second will be quicker.
  • MAP for Dirichlet Process Mixtures (Alexis Boukouvalas et al): a method for creating a Dirichlet Process Mixture model. This is useful as a k-means replacement where you don't know in advance what k should be, and where your clusters are not necessarily spherical.
Talks: these were mostly full talks (approx one hour), but then we had a short introduction to the Alan Turing Institute with Q&A at the end.

The first talk presented the idea of an Automated Statistician (Zoubin Ghahramani). Throw your time series data at the automated statistician and it'll give you back a report in natural language (English) explaining the trends and extending a prediction for the future. The idea is really nice. He has defined a language for representing a family of statistical models, a search procedure to find the best combination of models to fit your data, an evaluation method so that it knows when to stop searching, and a procedure to interpret/translate the models and explain the results. His language of models is based on Gaussian processes with a variety of interesting kernels, together with addition and multiplication as operators on models, and also allowing change points, so we can shift from one model combination to another at a given timepoint.

The next two talks were about robots, which are perhaps the ultimate autonomous citizens. Marc Deisenroth spoke about using reinforcement learning and Bayesian optimisation as two methods for speeding up learning in robots (presented with fun videos showing learning of pendulum swinging, valve control and walking motion). He works on minimising the expected cost of the policy function in reinforcement learning. His themes of using Gaussian processes, using knowledge of uncertainty to help determine which new points to sample were also reflected in the next talk by Jeremy Wyatt about robots that reason with uncertain and incomplete information. He uses epistemic predicates (know, assumption), and has probabilities associated with his robot's rule base so that it can represent uncertainty. If incoming data from sensors may be faulty, then that probability should be part of the decision making process.

Next was Steve Roberts, who described working with crowd sourced data (from sites such as zooniverse), real citizens rather then automated ones. He deals with unreliable worker responses and large datasets. People vary in their reliability, and he needs to increase accuracy of results and also use their time effectively. The data to be labelled has a prior probability distribution. Each person also has a confusion matrix, describing how they label objects. These confusion matrices can be inspected, and in fact form clusters representing characteristics of the people (optimist, pessimist, sensible, etc). There are many potential uses for understanding how people label the data. Along the way, he mentioned that Gibbs sampling is a good method but is too slow for his large data, so he uses Variational Bayes, because the approximations work for this scenario.

Finally, we heard from Howard Covington, who introduced the new Alan Turing Institute which aims to be the UK's national institute for Data Science. This is brand new, and currently only has 4 employees. There will eventually be a new building for this institute, in London, opposite the Crick Institute. It's good to see that computer science, maths and stats now have an discipline-specific institute and will have more visibility from this. However, it's an institute belonging to 5 universities: Oxford, Cambridge, UCL, Edinburgh and Warwick, each of which has contributed £5million. How the rest of us get to join in with the national institute is not yet clear (Howard Covington was vague: "later"). For now, we can join the scoping workshops that discuss the areas of research that are relevant to the institute. The website, which has only been up for 4 weeks so far, has a list of these, but no joining information. Presumably, email the coordinator of a workshop if you're interested. The Institute aims to have 200 staff in London (from Profs to PhDs, including administrators). They're looking for research fellows now (Autumn 2015), and PhDs soon. Faculty from the 5 unis will be seconded there for periods of time, paid for by the institute. There will be a formal launch party in November.

Next year, the NCSML workshop will be in Edinburgh.

Thursday, 30 July 2015

ISMB/ECCB 2015

ISMB/ECCB 2015 (and HitSEQ 2015) was held in Dublin, just across the Irish Sea from us here in Aberystwyth. So off we went, to find out the latest research in bioinformatics. There were many parallel tracks, but the recurring themes of the talks I attended were:
  • lots of work on human genomics, particularly disease, particularly cancer
  • single cell analysis, finding variation (SNVs) from clonal populations, haplotype resolution
  • sequencing technologies: RNA-seq, sequencing of methylation, Hi-C sequencing, ultra deep sequencing and lots of promise for long reads
  • reference sequences: most people were working with a reference rather than de-novo
  • training bioinformaticians, maintaining software, keeping a core of bioinfomaticians
  • the Burrows Wheeler transform - does it solve every large-data problem?
  • graphs, and ways of cleaning up graphs, adding weights to graphs, finding minimal/maximal components of graphs
There wasn't very much about the following topics, though they did make occasional appearances:
  • text mining
  • metagenomics
  • multi-omics
Too hard? Dropping out of favour? Or perhaps people working in these areas just don't attend this particular conference?

Aberystwyth PhD students with their posters: Stefani Dritsa, Sam Nicholls, Tom Hitch, Francesco Rubino

The keynote talks tended to be of the kind that long-established group PIs do well. They're the "Here's a summary of all the work my group has been doing for the past 5-10 years to answer this particular biological question" talk. While I admire their determination and group size, I feel that they're speaking only to a subgroup of the audience with this kind of talk, and that a keynote should somehow also aim to more generally inspire the audience to go out and do great work, have new ideas, think in new directions, and not just to have learned a little more about that specific subject area. The far more off-the-wall non-keynote talk by David Searls about a bioinformatic analysis of James Joyce's book Ulysses fascinated the audience, and provided exactly that. He received a huge round of applause.


The jobs notice boards were full (below are just 2 of the notice boards). More bioinformaticians are clearly needed!


Many of the conference talks are now online, but you need to be a member of ISCB to see them http://www.iscb.org/ismb-mm/media-ismbeccb2015. The papers are also collected in a special ISMB/ECCB issue of Bioinformatics.

Monday, 8 June 2015

Aber Bioinformatics Workshop

Last week we had the 2nd Aber Bioinformatics Workshop. It's an internal workshop for work-in-progress talks, posters and networking and the aim is for us all to keep up with what's going on in Aberystwyth in bioinformatics across departments and institutes. We had a wide range of talks on genomics and sequence analysis, metabolomics, optimising proteins, population and community modelling, data infrastructure and other topics. Here's the programme for the day.

Photo of all the attendees, taken by Sandy Spence
It was great to see that we now have so many people interested and working in bioinformatics, despite the difficulties in trying to understand all sides of the story (the biology, the computing, the statistics, etc). We talked about the range of modules and courses that were available to help people get up to speed with this, and how we should do more to let new PhD students know what is available. Also, now that we've had the workshop, hopefully we're more aware of the expertise and facilities available here in Aber, so we now know who to approach with questions and ideas.

At the end of the day we moved down to the pub, and continued to discuss more random topics: beetles, plant senescence, hens, temperature sensing wires for computer clusters, and concordance in Shakespeare texts. I'm sure this all helps in the long run.

Monday, 1 June 2015

Burglary at the railway refreshment rooms

The NLW have a fantastic collection of digitised historic newspaper articles available. They're going to release a new interface shortly with access to 15 million articles, and I was testing the search facility on the new interface today. I came across this gem of a story from the Aberystwyth Observer in 1907, which also happens to be available in their currently live beta collection.

BURGLARY AT THE RAILWAY REFRESHMENT ROOMS. The police are investigating two cases of robbery from the refreshment rooms at Borth and Dovey Junction. At these places thieves broke into the premises and got away with a quantity of wine and money. This is the second or third time that Dovey Junction has been visited during the last few years.

http://welshnewspapers.llgc.org.uk/en/page/view/3050081/ART41 (may need to zoom out and zoom in again before moving the page to see the article, which is at the edge of the page)

The thought of wine and money being held at remote Dovey Junction station is delightful, as is the fact that the reporter can't remember if it's the second or third time this has happened. Perhaps the reporter knows something about where the wine went.

Thursday, 21 May 2015

How much is enough?

How much is enough? This question seems to crop up very frequently when analysing data. For example:
  • "How much data do I need to label in order to train a machine learning algorithm to recognise place names that locate newspaper articles?"
  • "Is my metagenome assembly good enough or do we need longer/fewer contigs?"
  • "What BLAST/RAPSearch threshold is close enough?"
  • "Are the k-mers long enough or short enough? (for taxon identification, for sequence assembly)"
Sadly there's no absolute answer to any of these. It depends. It depends on what your data looks like and what you want from the result. It also depends on how much time you have. It depends what question you really wanted to answer. What's the final goal of the work?

Sometimes there are numbers to report, measures that give us an idea of whether the process was good enough, after we've done the expensive computation. We can report various statistics about how good the result is, such as the N50 and its friends for sequence assembly, or the predictive accuracy for a newspaper article place name labeller. Which statistics to report are highly questionable. Does a single figure such as the N50 really tell us anything useful about the assembled sequence? It can't tell us which parts were good and which parts were messy. Do we really need lots of long contigs if we're assembling a metagenome? Perhaps the assembly is just an input to many further pipeline stages, and actually, choppy short contigs will do just fine for the next stage.

PAC learning theory was an attempt in 1984 by Leslie Valiant to address the questions about what was theoretically possible with data and machine learning. For what kinds of problem can we learn good hypotheses in a reasonable amount of time (hypotheses that are Probably Approximately Correct)? This led on to the question of how much data is enough to make a good job of machine learning? Some nice blog posts describing PAC learning theory and how much data is needed to ensure low error do a far better job than I could of explaining the theory. However, the basic theory assumes nice clean noise-free data and assume that the problem is actually learnable (it also tends to overestimate the amount of data we'd actually need). In the real world the data is far from clean, and the problem might never be learnable in the format that we've described or in the language we're using to create hypotheses. We're looking for a hypothesis in a space of hypotheses, but we don't know if the space is sensible. We could be like the drunk looking for his keys under the lamppost because the light is better there.

Perhaps there will be more theoretical advances in the future that tell us what kinds of genomic analysis are theoretically possible, and how much data they'd need, and what parameters to provide before we start. It's likely that this theory, like PAC theory, will only be able to tell us part of the story.

So if theory can't tell us how much is enough, then we have to empirically test and measure. But if we're still not sure how much is enough, then we're probably just not asking the right question.

Wednesday, 22 April 2015

Computer Science and Lindy Hop

It would seem that Lindy Hop is the dance of computing people, physicists and engineers. If you go to any swing dance camp, an unreasonable proportion of the people in the room will be somehow involved in IT. We have Lindy hoppers who have used Androids with sensors and fourier transforms to look at the pulse of the dance, use Lindy to illustrate quantum computing, and there is even a specific Lindy dance class for engineers. Sam Carroll described how digital media savvy the community was and is, in her Step Stealing work.

Okay, so people need money to go to dance camps, and computing professions generally pay well. And it gets us away from our desks and having fun with other people and music. However, these can't be the only reasons.

I think that I enjoy Lindy for lots of the same reasons that I enjoy computing. They're both about creating complex structures that are somehow beautiful. By complex structures I mean structures that are complicated enough that they make me feel pleased when I finally successfully make them work. By beautiful I mean code/dance/ideas that become elegant because of their appropriateness in that particular situation. And in both computing and Lindy I enjoy the reusable patterns. Reusable patterns in rhythm are like reusable patterns in computing: once you've understood them, they stay with you and can often tell you something more abstract about what you're trying to do.

So I think that computing and Lindy have more in common than just having fun. They also share reusable beautiful complexity.


Added note: If you want to try it out, come and join our Vintage Swinging in the Rain party on Friday 24th April, 8pm, Marine Hotel, Aberystwyth. There's a short dance class for beginners at about 8:30, and live music from The Paper Moon Band.

Wednesday, 15 April 2015

Employers at BCSWomen Lovelace Colloquium 2015

I think this year's Lovelace Colloquium was notable for the strong employer presence, both in sponsorship and in having employer stalls. This seems to be a year when computer science students are generally in demand. A conference of computing undergraduates presenting their work consists of ambitious students, who are ideal targets for recruiters. And the fact that it's a room full of bright women undergraduates is a very good thing for companies looking to increase their diversity.



Some of the companies who sponsored this year's Lovelace have been strong supporters for many years, including Google, FDM, EMC, UTC Aerospace, Interface3 and VMWare. They understood this a long time ago. But newer to this event were a whole variety of other companies, some small, some large, including Twitter, Slack, GCHQ, Scott Logic, JP Morgan, Bloomberg and Kotikan. We hope they enjoyed it too, and return in future years.





Kate Ho provided the keynote speech. She started her own software (games) company right after her PhD, and has gone from strength to strength, running a variety of startup companies since then. Her three tips: have side projects, be distinctive, keep a diary, were all good advice, both for technical work and for career development.

The friendliness of the Lovelace Colloquium never ceases to surprise and motivate me. Part of this is driven by Hannah's organisation style, pre-conference and during-conference, where nothing is too much trouble and everyone is made to feel at home. But I think it's also genuinely a room full of people having fun, getting to know others and make connections, and finding inspiration for their future careers.