Complex networks, complex processes

I’m writing a book on my sabbatical. Or trying to, anyway. So I thought I’d publicise the fact so people can hassle me to keep at it. I’ve been working on complex systems for a couple of years, especially on complex networks: things like the way people move through a road and rail network, or how diseases spread through social networks. It’s a bit of a change from my previous work on sensor data interpretation, although not as much as you might think: I’m wondering whether we could combine sensing and simulation, to use sensors to confirm predictions or to drive and condition further simulations. Getting into this area has been — and is — a head-wreck. It’s both highly mathematical and highly computational. I understand the computing; the maths, not so much. Many computer scientists would have the same reaction, but conversely, so would many mathematicians: the maths would be familiar, the computing a challenge. So effectively in order to make progress you have to climb two learning curves simultaneously: some unusual and challenging mathematics about stochastic processes, simulated using cluster or cloud computing which poses a lot of challenges even for someone used to programming. This is made harder by the research literature, though, which tends towards sparse mathematical descriptions, which is frustrating at two levels: the computing is probably interesting (to people like me), and it’s hard to re-create the results when the computational approach underlying the graphs and results is unclear. So with this in mind, and because I’ve never done it before, I’ve decided to write a textbook: Complex networks, complex processes. (No, I’m not very imaginative when it comes to titles…) The idea is to link the maths to the code, providing everything a research would need to get started with the maths and the computing. Since this is likely to be a book with, shall we say, limited circulation, I’ve decided not to bother with a publisher and instead make it completely open. You can look at the current state on the web here, download the sources, copy and run the code, or anything needed to get started. It’s a work in progress and it’s not very usual to advertise books before they’re in a fit state to be read, but I suppose that’s just a part of open science: make the process visible, warts and all. It also means I’ll hopefully get comments and encouragement to keep at it when it starts to fall by the wayside of other things I have to do. The goal is to get the majority done while I’m on research leave (until September), and comments on style, content, and progress will be most welcome.

Fully-funded PhD scholarship available

I have a fully-funded PhD scholarship available, tenable from September 2015, to work on data science in medicine.

University of St Andrews

School of Computer Science School of Medicine Funded PhD studentship The Schools of Computer Science and Medicine are looking to recruit a talented student to work on improving clinical trials of tuberculosis and other conditions using computational techniques. TB and related conditions are extremely costly in human and financial terms, and trials of new drugs and therapies are complicated by difficult environmental conditions and other factors. Improvements to the trials process will potentially translate directly into improved interventions, and so will help save lives. We seek to apply data-driven techniques to the design, analysis, and management of such trials. These techniques might include complex networks, computational epidemiology, machine learning, Bayesian analysis, and other cutting-edge approaches to data analytics. The ideal candidate will have an interest in data science applied to medical and biological problems, and an enthusiasm for working as part of a challenging multi-disciplinary project within St Andrews’ new Institute for Data-Intensive Research (IDIR). The studentship will be held jointly between the two Schools, with supervisors from Computer Science (Prof Simon Dobson, Dr Tom Kelsey) and Medicine (Prof Stephen Gillespie, Dr Ruth Bowness).  We offer a stimulating and supportive environment within a small and intimate university in a beautiful setting. The scholarship is fully funded to cover tuition fees and stipend for a registration period normally expected to be three-and-a-half years. Informal inquiries can be made in the first instance to Prof Simon Dobson. Applications will be considered until mid-March.

Goodbye to All That

Robert Graves (1929)

The autobiography of one of the four main English-language poets of the First World War (the others being Wilfred Owen, Siegfried Sassoon, and Rupert Brooke) offers a fascinating insight into the first-hand experience of war – if a less fascinating insight into the poet’s life.

Graves is clear about the trauma, dirt, terror, and suffering of the war. His description of a battle at Loos sums-up the mindlessness of the experience: waiting, anticipation, false starts, screwing-up courage only to be knocked back. It’s hard to imagine anyone going through that and not being exhausted by the adrenaline. On the way he meets Sassoon, as well as Thomas Hardy, TE Lawrence, and various other figures of the literary times.

The rest of the book is less satisfying: his boyhood at Charterhouse perhaps prepared him for the capricious nature of war, in a way, while his later experiences at Oxford and elsewhere added little to my appreciation, apart from summoning-up a vague jealousy at some of his descriptions of intellectual society just after the War: it’s hard to imagine many of the conversations he describes happening now, with their deep classical allusions and assumptions of erudition on all sides.

Least satisfying is that to autobiography of a poet reveals so little about his poetic frame of mind. Graves doesn’t explore the what it means to be a poet, although he alludes to the “poetic tendency” often enough. It’s a surprisingly unrevealing book at a personal level: perhaps less intimately revealing than his poetry itself, in fact, but worth reading for its historical context.

3/5. Finished Saturday 24 January, 2015.

(Originally published on Goodreads.)

2015 CPHC/BCS Distinguished Dissertations competition

The 2015 CPHC/BCS Distinguished Dissertations competition is now open for submissions via the submissions site. Closing date Wednesday 1 April 2015. Further details can be found below and on the competition web page. The Council of Professors and Heads of Computing (CPHC), in conjunction with BCS, The Chartered Institute for IT, annually selects for publication the best British PhD/DPhil dissertations in computer science. The scheme aims to make more visible the significant contribution made by the UK - in particular by post-graduate students - to computer science. Publication also serves to provide a model for future students. The selection panel on behalf of BCS/CPHC consists of experienced computer scientists, not more than one from any institution, each normally serving on the panel for three years. Any dissertation is eligible which is submitted for a doctorate in the British Isles in what is commonly understood as Computer Science. (Theses which are basically in some other discipline but which make use, even very extensive use, of computing will not be regarded as eligible.)  However, there is a limit of THREE dissertations per year per university, and one per research group within any university. To be considered, a dissertation should:

  • make a noteworthy contribution to the subject;
  • reach a high standard of exposition;
  • place its results clearly in the context of computer science as a whole; and
  • enable a computer scientist with significantly different interests to grasp its essentials.
It is reasonable to submit a thesis to the scheme if it has all of the above qualities in good measure, and if it is comparable in standard with the top 10% of dissertations in the subject. Long dissertations are not encouraged; if the main text is more than 80,000 words, there should be good justification. The dissertation should be submitted electronically (as a PDF file) by the author’s examiners, or by the Head of Department with the examiner’s advice. The submitted version of the dissertation must be the final version after any required corrections have been made. The competition period for the 2015 competition is for theses accepted from 1 January 2014 until the closing date of 1 April 2015. A dissertation cannot be submitted to the competition more than once. The dissertation should be accompanied by a written nomination comprising the following information:
  • a justification, of about 300 words, by one of the examiners — preferably the external — explaining the dissertation’s claim to  distinction (against the criteria listed above);
  • the name of the primary supervisor and the research group within the university to which the student was primarily affiliated;
  • an assurance that within the competition period the examiners have recommended to the author’s institution that the doctorate should be awarded;
  • the names and contact details of three suggested reviewers who are not in the same Department as the nominated thesis and who are independent of the supervision and examining of the thesis; and
  • an indication should be given if the dissertation is being considered for publication elsewhere.
The nominated reviewers must have confirmed that they are willing to provide a review. In addition the author’s written agreement that their thesis may be considered for the Distinguished Dissertation competition should be emailed by the author to Submissions should be made on-line via The first author name submitted should be that of the thesis author; the individual submitting the nomination should list themselves as the second author. The title and abstract should be those of the thesis being nominated. The first file uploaded should be the 300 word nomination; the thesis document should be uploaded as an attachment. If any problems are experienced, or you have any questions, please email for assistance. The deadline for submission is 1 April 2015.

American Prometheus: The Triumph and Tragedy of J. Robert Oppenheimer

Kai Bird (2005)

Hard to imagine a better scientific and political biography.

I had a rough understanding of Oppenheimer’s story: his management of the Manhattan project, his victimisation during the McCarthy witchhunts, and his directorship of the Institute for Advanced Study. What I hadn’t realised was his own scientific standing: his association with Born, Bathe, Dirac, Heisenberg, and others, and the fact that his own contributions rank alongside theirs, including his first formulation of the equations describing black holes. Despite not entering at all into the technicalities, the authors make clear how deeply embedded he was into the initial descriptions and elaborations of quantum mechanics.

The book is squally strong when dealing with the development of the bomb and with the aftermath, the lead-up to Oppenheimer’s trial as a security risk brought about in part by his principled opposition to the development of the “Super”, or hydrogen bomb. The treatment is well-balanced, making no attempt to hide the part Oppenheimer played in his own downfall (although still being somewhat at a loss to describe many elements of his behaviour).

The picture that emerges is of a profound scientist and humanist who was destroyed at least in part by his own fragilities and complexities: aspects of his character that undoubtedly helped in his greatness as we as leading to his downfall. That this element of Greek tragedy would have been deeply appreciated by Oppenheimer himself only adds to the sense of a contribution spoiled by the actions of men who failed to understand what drove him and what he could give.

5/5. Finished Thursday 1 January, 2015.

(Originally published on Goodreads.)