A while ago I created a new website for my main Open Source project, the Watchmaker Framework for Evolutionary Computation.  While the new website was a definite improvement over the previous effort, it was still lacking something. It wasn’t distinctive. What I really needed was a logo, something that visually identified the project. But how do you represent evolution and/or a watchmaker in the form of a simple, distinct picture?

It was beyond my modest artistic skills so I headed to Reddit and floated the question of how to find a graphic designer who would be willing to contribute to an Open Source project. I wasn’t expecting much, after all I was asking somebody to work for free on a fairly obscure project.

The usual way to get somebody to make you a logo is to find a professional graphic designer and pay them, or to stump up some cash to fund a contest on worth1000.com or 99designs.com. The prices start at $204 at the latter. I got a few suggestions from the Reddit crowd that I should try this monetary compensation idea.

I also got several people offering to produce a logo for me free-of-charge, and even a few who spontaneously decided to create something and submit it as a suggestion (see some of the links in the Reddit thread).  I really wasn’t sure if there would be many graphic designers who were interested in helping out Open Source software projects but it seems there are plenty. What is lacking is somewhere on the web to connect these willing designers with needy projects.

One of the people who got in touch to offer his services was Charles Burdett. He sent me a link to his impressive portfolio. I quickly accepted Charles’ offer before he had a chance to change his mind. This meant turning down a number of other offers that I received. I’m extremely grateful to all of the people who were willing to help me out, and some of the concepts that people suggested would have made very good logos.

Charles came up with the concept that now adorns the Watchmaker project website – the clockwork Ichthyostega. To be honest, I don’t even know how to pronounce that but Wikipedia tells me that Ichthyostega was a creature from the Upper Devonian Period. It was an intermediate form between fish and amphibian, so a significant step in the evolution of life on this planet.

This logo fits in very nicely with the existing site design and, because it’s a simple outline drawing, it should be very versatile for use in different contexts. I’m very happy with the result and I’d like to thank Charles for all of his work on this. If you like this logo, or any of Charles’ other work, he is available for hire.

The Watchmaker Framework for Evolutionary Computation has reached version 0.7.1.  This is an incremental release that refines a couple of the changes made in the substantial 0.7.0 update.  It also adds support for Evolution Strategies to complement the existing support for generational and steady-state evolutionary/genetic algorithms.

In addition, the (still incomplete) user manual has a new section on the different selection strategies that are available.

• Downloads
• Full Changelog
• API Documentation
• User Manual

Jack’s new career in software development was going pretty well, but he didn’t appreciate the daily stand-up meetings.

The end of the year is here and, as is traditional among bloggers and mainstream media alike, I’ve lazily compiled a top 10 list to mark the occasion without having to exert myself. So here it is, according to Google Analytics, the top 10 articles of 2009 from this sporadically updated blog.

When I checked the stats, four of the top five most read articles this year were actually from 2008, with Why are you still not using Hudson? claiming first place. This list includes only those articles that were first posted in 2009.

1. 5 Ways to Become a Famous Programmer
2. Practical Evolutionary Computation: An Introduction
3. Random Number Generators: There Should be Only One
4. Practical Evolutionary Computation: Implementation
5. Debugging Java Web Start Applications
6. Using PHPUnit with Hudson
7. Understanding PHP – A journey into the darkness…
8. Programming the Semantic Web and Beautiful Data
9. Uncommons Maths 1.2
10. The Java Language Features that Nobody Uses

Happy New Year.

The Watchmaker Framework for Evolutionary Computation has reached version 0.7.0. If you’re new here, Watchmaker is a Java library for implementing evolutionary/genetic algorithms. This release is the most substantial update for some time.

Backwards-Incompatibilities

Firstly, I’ve refactored the evolution engine so that it is not as tightly tied to the standard generational model of evolution. What this means in practice is that the class formerly known as ConcurrentEvolutionEngine is now called GenerationalEvolutionEngine. For most users this should be the only backwards-incompatibility in this release. The constructor arguments are the same and all the old methods are still there so it should just be a case of updating your code to use the new name. If you were using SequentialEvolutionEngine, and I think this mostly affects the Mahout guys, this class no longer exists. Concurrency is no longer managed via different sub-classes. Instead you should also use GenerationalEvolutionEngine and call the new setSingleThreaded method to force all work to be done synchronously on the request thread.

If you use Watchmaker to evolve BitString objects, this release improves the performance of the provided mutation and cross-over operators. One side-effect of this is that the semantics of the BitStringMutation class have been modified, so you may need to adjust your parameters.

Steady-State Evolution

OK, on to the good stuff. The reason for the evolution engine changes was to make it easier for the framework to support different types of evolutionary algorithm. The benefits of these changes will become more apparent in subsequent releases but there is one example in this release.  The framework now has first-class support for steady-state evolution via the new SteadyStateEvolutionEngine.  In steady-state evolution the population is evolved one member at a time rather than all members in parallel. This was possible in previous versions of the Watchmaker Framework but only via a nasty hack.

Island Model Evolution

The major new feature in 0.7.0 is support for island model evolution. Instead of evolving a single population, you evolve multiple populations in parallel.  The idea is that the different populations will randomly proceed in different directions making it less likely that the evolution will get stuck at a local optimum. What makes this different from simply evolving a single population multiple times is that there is periodic migration of individuals between islands.  The motivation behind the migration is that combining independently evolved individuals with different traits will hopefully result in even fitter offspring. There’s a lot more detail that I’m glossing over that I intend to cover in a later post, but if you want to get started right away the IslandEvolution class is the place to start.

Sigma-Scaling Selection

0.7.0 also includes a new selection strategy. SigmaScaling uses the population’s fitness standard deviation to regulate the selection pressure, making premature convergence less likely.

More Information

• Full Changelog
• API Documentation
• (Incomplete) User Manual
• Download

Demo Applets

• Sudoku Solver
• Evolution of the Mona Lisa
• Travelling Salesman
• Biomorphs

Following the unfortunate demise of Jeff Atwood and Phil Haack’s blogs, the resultant schadenfreude on Reddit, and Jeff’s subsequent discussion of StackOverflow’s back-up process, I’m going to share with you everything that I know about back-up procedures. This won’t be a long post, I’m not a sysadmin.

You might keep frequent on-site back-ups to reduce the inconvenience of routine problems such as hardware failure, but it’s the off-site back-ups that ultimately determine how resilient you are in the face of real problems (fire, flood, etc.).  In that final analysis only the off-site back-ups matter. Making more, or more frequent, on-site back-ups will not help if your off-site back-ups are non-existent, broken (a.k.a. untested), or not frequent enough. There’s really only one question you need to ask yourself when deciding how frequently you need to back-up: how much data am I willing to lose?

If you are taking fortnightly dumps off-site but three days of data loss would kill your business then your back-up plan is worse than useless.  Sitting very still with all your fingers crossed would be a more effective disaster-prevention policy.

Tomek Kaczanowski has written a blog post showing how to use ReportNG with Gradle (an alternative build system for Java/Groovy/Scala). I’ve never used Gradle but it seems to have two things in its favour.  Firstly, it uses Groovy syntax rather than the cumbersome XML employed by Ant. Secondly, it’s not Maven. Maybe I should try it out some day?

The Watchmaker Framework for Evolutionary Computation has a new website at http://watchmaker.uncommons.org. The Java.net web hosting is slow and restrictive, so I’ve decided to self-host the project pages.

The project will continue to use the other Java.net tools such as Subversion, Issuezilla and the project forum for the foreseeable future, though I am weighing up the benefits and drawbacks of a possible relocation to GitHub.

I have no plans to move my other projects that are currently on Java.net (Uncommons Maths and ReportNG being the main ones).

Part of the new Watchmaker website is the development roadmap, which should answer some of the questions I’ve been asked about where the project is heading. Most of the work for version 0.7.0 is done and in Subversion, there are just a couple of rough edges to be worked out. I hope to do a release before the new year. Version 1.0 seems as far away as it did 3 and a half years ago.

I recently signed-up for GitHub. Compared to Java.net or Sourceforge, it provides a much lower barrier of entry for code hosting.  There’s no need to wait an indeterminate period of time for somebody to approve your project, you just upload it. And because it’s a DVCS, it’s easy for other people to fork your projects and submit patches. Open Source project hosting has become so straightforward, thanks to sites like GitHub and the Bazaar-based Launchpad, that it encourages developers to open up code that they might otherwise have kept to themselves. After all, why bother with local repositories and back-ups when you can get somebody else to do it for you and get free web-hosting and issue-tracking too?

I have a number of trivial and incomplete projects hosted in local Subversion repositories. I am slowly adding to GitHub those that have any worthwhile substance to them. I’m making no promises about the quality of this code, and I don’t intend to spend much time supporting it, but I’m putting it out there in case somebody might have a use for it.

First up is Zeitgeist. This is a small Java library/application for identifying common topics among a set of news articles downloaded from RSS feeds. It’s sort of like what Google News does. There is a basic HTML publisher included that generates a web page for displaying the current top news stories, including relevant pictures.

You give the program a list of RSS feeds that cover a certain topic (maybe world news, or music news, or a particular sport) and it uses non-negative matrix factorisation to detect similarities in the article contents and to group the articles by topic. The original idea comes from Programming Collective Intelligence.

The default HTML output looks a bit like the image below, but you could customise it with CSS or by hacking the default templates to modify what information is included (for example, you could add an excerpt instead of just displaying headlines).

The algorithm is not infallible and how well it works depends a lot on the feeds that you select. It’s also non-deterministic, so if you run it multiple times with the same input you will get variations in the output.  Perhaps Zeitgeist is not that useful in it’s current form but it could be used for adding on-topic news headlines to a website or as the basis for something more advanced.

When I released version 0.9.9 of ReportNG last week, I didn’t call it version 1.0 because I thought I’d probably have to fix some problem caused by the changes I’d made. I was right. It turns out that I broke the one tiny piece of JavaScript that the HTML reports use. Well that’s fixed now and, because none of the three people who downloaded 0.9.9 have complained about anything else, and because I’m not keen on double-figure components in version numbers (as in 0.9.10), I’ve decided that this can be version 1.0.  You can get it here (or from the Java.net Maven repository if that’s how you roll).