Genetic Algorithms

Genetic Algorithms, Pyevolve, Python

The Interactive Robotic Painting Machine !

I’m glad to announce a project created by Benjamin Grosser called “Interactive Robotic Painting Machine“. The machine uses Python and Pyevolve as it’s Genetic Algorithm core, the concept is very interesting:

What I’ve built to consider these questions is an interactive robotic painting machine that uses artificial intelligence to paint its own body of work and to make its own decisions. While doing so, it listens to its environment and considers what it hears as input into the painting process. In the absence of someone or something else making sound in its presence, the machine, like many artists, listens to itself. But when it does hear others, it changes what it does just as we subtly (or not so subtly) are influenced by what others tell us.

Read more about the project in the Benjamin Grosser website.

 

by Christian S. Perone
Genetic Algorithms, News, Science

Health and Genetic Algorithms

From R&D Mag – Developing a potential life-saving mathematical tool -:

Math and medicine are coming together to help people who have suffered an abdominal aortic aneurysm, which with 15,000 is the 13th-leading cause of death in the United States.

At the heart of the effort are genetic algorithms written by Oak Ridge National Laboratory researchers that allow physicians to more efficiently assess and organize the often vast amounts of information contained in patient reports. Ultimately, with this tool—a sophisticated way to quickly extract key phrases—doctors will be able to characterize features and findings in reports and provide better patient care.

(…)

This work builds on previous studies involving genetic algorithms developed for mammography. That system allows doctors to quickly identify trends specific to an individual patient and match images and text to a database of known cancerous and pre-cancerous conditions.

Read full article here.

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Developing a potential life-saving mathematical tool

by Christian S. Perone
Article, Genetic Algorithms, genetic programming, News, Science

Darwin on the track

From The Economist article:

WHILE watching the finale of the Formula One grand-prix season on television last weekend, your correspondent could not help thinking how Darwinian motor racing has become. Each year, the FIA, the international motor sport’s governing body, sets new design rules in a bid to slow the cars down, so as to increase the amount of overtaking during a race—and thereby make the event more interesting to spectators and television viewers alike. The aim, of course, is to keep the admission and television fees rolling in. Over the course of a season, Formula One racing attracts a bigger audience around the world than any other sport.

Read the full article here.

by Christian S. Perone
Genetic Algorithms, Pyevolve, Python

The future can be written in RPython now

Following the recent article arguing why PyPy is the future of Python, I must say, PyPy is not the future of Python, is the present. When I have tested it last time (PyPy-c 1.1.0) with Pyevolve into the optimization of a simple Sphere function, it was at least 2x slower than Unladen Swallow Q2, but in that time, PyPy was not able to JIT. Now, with this new release of PyPy and the JIT’ing support, the scenario has changed.

PyPy has evolved a lot (actually, you can see this evolution here), a nice work was done on the GC system, saving (when compared to CPython) 8 bytes per object allocated, which is very interesting for applications that makes heavy use of object allocation (GP system are a strong example of this, since when they are implemented on object oriented languages, each syntax tree node is an object). Efforts are also being done to improve support for CPython extensions (written in C/C++), one of them is a little tricky: the use of RPyC, to proxy through TCP the remote calls to CPython; but the other seems by far more effective, which is the creation of the CPyExt subsystem. By using CPyExt, all you need is to have your CPython API functions implemented in CPyExt, a lot of people is working on this right now and you can do it too, it’s a long road to have a good API coverage, but when you think about advantages, this road becomes small.

In order to benchmark CPython, Jython, CPython+Psyco, Unladen Swallow and PyPy, I’ve used the Rastrigin function optimization (an example of that implementation is here in the Example 7 of Pyevolve 0.6rc1):

f(x) = 10n + \sum_{i=1}^{n}{x_{i}^{2}} -10\cos(2\pi x_{i})

Due to its large search space and number of local minima, Rastrigin function is often used to measure the performance of Genetic Algorithms. Rastrigin function has a global minimum at x=0 where the f(x) = 0; in order to increase the search space and required resources, I’ve used 40 variables (n=40)  and 10k generations.

Here are the information about versions used in this benchmark:

No warmup was performed in JVM or in PyPy. PyPy translator was executed using the “-Ojit” option in order to get the JIT version of the Python interpreter. The JVM was executed using the server mode, I’ve tested the client and server mode for Sun JVM and IcedTea6, the best results were observed from the server mode using Sun JVM, however when I’ve compared the client mode of IcedTea6 with the client mode of Sun JVM, the best results observed were from IcedTea6 (the same as using server mode in IcedTea6). Unladen Swallow was compiled using the project wiki instructions for building an optimized binary.

The machine used was an Intel(R) Core(TM) 2 Duo E4500 (2×2.20Ghz) with 2GB of RAM.

The result of the benchmark (measured using wall time) in seconds for each setup (these results are the best of 3 sequential runs):

As you can see, PyPy with JIT got a speedup of 2.57x when compared to CPython 2.6.5 and 2.0x  faster than Unladen Swallow current trunk.

PyPy is not only the future of Python, but is becoming the present right now. PyPy will not bring us only an implementation of Python in Python (which in itself is the valuable result of great efforts), but also will bring the performance back (which many doubted at the beginning, wondering how could it be possible for an implementation of Python in Python be faster than an implementation in C ? And here is where the translation and JIT magic enters). When the time comes that Python interpreter can be entire written in a high level language (actually almost the same language, which is really weird), Python community can put their focus on improving the language itself instead of spending time solving the complexity of the lower level languages, is this not the great point of those efforts ?

By the way, just to note, PyPy isn’t only a translator for the Python interpreter written in RPython, it’s a translator of RPython, what means that PyPy isn’t only the future of Python, but probably, the future of many interpreters.

by Christian S. Perone
Genetic Algorithms, genetic programming, News, Pyevolve, Python

Pyevolve 0.6rc1 released !

I’m proud to announce the Pyevolve 0.6rc1 ! This is the first release candidate, but it’s pretty stable for production use (as from this 0.6 version we are very closer to a stable codebase, thanks to community).

See the documentation site and the What’s New.

I would like to thank the people who directly or indirectly have contributed with this release: Boris Gorelik, Amit Saha, Jelle Feringa, Henrik Rudstrom, Matteo de Felice, SIGEVOlution Board, Mike Benoit, Ryan Campbell, Jonas A. Gustavsson, Soham Sadhu, Ernesto Costa, Ido Ben-Tsion, Frank Goodman, Vishal Belsare, Benjamin Bush; and a lot of people who gave us feedback of the experience with the use of Pyevolve on their applications.

For downloads, go to the Downloads section at Documentation site.

If you see something wrong with this release candidate, please create a ticket reporting your problem at Pyevolve Trac, so we can provide fixes to the official release.

Happy coding !

– Christian S. Perone

by Christian S. Perone
Genetic Algorithms, genetic programming, News, Science

New issue of SIGEVOlution (Volume 4 Issue 3)

The new issue of SIGEVOlution (the newsletter of ACM Special Interest Group on Genetic and Evolutionary Computation) was released:

In this release you can read about:

Issues in applying computational intelligence
By Arthur Kordon

JavaXCSF
By Patrick O. Stalph, Martin V. Butz

And a lot of information about new PhD theses, new journal issues and about events to come.

by Christian S. Perone
Genetic Algorithms, News, Science

News: Using genetic algorithms to optimise current and future health planning

From a publication of 28/10/2010, of the authors Saoshi Sasaki, Alexis J Comber, Hiroshi Suzuki and Chris Brunsdon:

Background

Ambulance response time is a crucial factor in patient survival. The number of emergency cases (EMS cases) requiring an ambulance is increasing due to changes in population demographics. This is decreasing ambulance response times to the emergency scene. This paper predicts EMS cases for 5-year intervals from 2020, to 2050 by correlating current EMS cases with demographic factors at the level of the census area and predicted population changes. It then applies a modified grouping genetic algorithm to compare current and future optimal locations and numbers of ambulances. Sets of potential locations were evaluated in terms of the (current and predicted) EMS case distances to those locations.

Results

Future EMS demands were predicted to increase by 2030 using the model (R2=0.71). The optimal locations of ambulances based on future EMS cases were compared with current locations and with optimal locations modelled on current EMS case data. Optimising the location of ambulance stations locations reduced the average response times by 57 seconds. Current and predicted future EMS demand at modelled locations were calculated and compared.

Conclusions

The reallocation of ambulances to optimal locations improved response times and could contribute to higher survival rates from life-threatening medical events. Modelling EMS case ‘demand’ over census areas allows the data to be correlated to population characteristics and optimal ‘supply’ locations to be identified. Comparing current and future optimal scenarios allows more nuanced planning decisions to be made. This is a generic methodology that could be used to provide evidence in support of public health planning and decision making.

Read the original paper here.

by Christian S. Perone