Genetic Argonaut

PPSN X - A Luso Highlight

2008-09-30T18:09:00.006-03:00

Jorge Tavares has posted his personal summary of PPSN X event. See it here.

He says everything was O.K. along the whole event and praises the PPSN approach concerning poster presentations.

It's interesting: Jorge's summary is the fourth, at least, to point a positive statement of PPSN. So far, PPSN X has received, as long as I am aware of, no negative reviews from the bloggers I know of (JJ, Togelius, and Jorge Tavares). Maybe, it could be a model for others conferences following the evolutionary computation venue.

PPSN X In Pictures

2008-09-25T11:35:00.005-03:00

Our friend, Juan Julián Merelo Guervós, has put on line the nice pictures he took while attending to PPSN X. See his gallery here.

I think the picture above shows Professor Hans-Paul Schwefel's back and the PPSN X attendees are gathering at the backyard of Schwefel's house. (Am I right, JJ?)

Evolving Virtual Creatures Through Simulated Evolution

2008-09-25T11:15:00.004-03:00

Interesting project this one:

"This application is an example of evolutionary computing that you can run on your own Windows PC at home (see the download section). It uses a process similar to biological evolution to gradually evolve a population of virtual creatures in a 3D graphical and physical environment. Much of the inspiration for this project came from the wonderful work of Karl Sims. In the mid 90's Dr. Sims did something very similar, using an evolutionary algorithm to evolve the body plans and control systems of virtual creatures whose bodies were composed of jointed blocks. His creatures were evolved in simulated land and water environments for their ability to swim, walk, jump, follow a light source, and compete against opponents for control of a resource. See the related projects section for links some videos from Dr. Sims and links to other virtual creature evolution projects).

With this program you can watch a process of simulated Darwinian evolution unfold before your eyes (although the process can take several days of computer time depending on your computer speed and your evolution settings). The user is given control of many of the parameters of the evolution such as the size of the creature population, the mutation rate, the ability for which the creatures will be evolved, and many other settings. Users are encouraged to send me any interesting creatures they should happen to produce for inclusion in the Zoo. There are already numerous strange and interesting virtual creatures on display there, with many more to come."

PPSN X - Even More Personal Highlights

2008-09-24T21:13:00.003-03:00

Our blog friend, Juan Julián Merelo Guervós, has written some very nice personal highlights on PPSN X, see them here and here.

He comments on the organization of the event and upon the quality of the papers accepted to be shown at PPSN.

Ride The Lightning

2008-09-24T21:05:00.003-03:00

A lightning struck near my backyard last Friday! It blown up my ADSL modem and my LCD monitor too, I even heard a sound like that one when someone explodes a balloon. It is what I get for living less than 2 degrees below the Equator line. Rain falls almost everyday and lightning follows it.

PPSN X - More Personal Highlights

2008-09-18T09:49:00.004-03:00

Our blog friend, Julian Togelius, who is attending PPSN X, has posted another view of his concerning that conference, see it here.

In this post, Julian draws a critique among the three major evolutionary computation conferences (CEC, GECCO, and PPSN) concerning the kind and quality level of papers sent to them.

For his previous reports, follow this link.

PPSN X - Personal Highlights

2008-09-16T23:51:00.004-03:00

Our blog friend and official viking, Julian Togelius, has posted his first impressions on PPSN X event. See his summaries here and here.

Our another blog friend, Juan Julián Merelo Guervós (call him JJ, for short), organized a singing contest among the attendees and is the official PPSN DJ chair.

PPSN X - Parallel Problem Solving from Nature 10th Edition

2008-09-15T03:45:00.004-03:00

It has already began the 10th edition of the PPSN conference which was started in 1990. See the current edition site here. For a log upon the past editions, see here

It is being held at the Technical University of Dortmund (TUD, former Uni-Dortmund) and you can check the accepted papers here. It seems there will be a wide range of topics on evolutionary computation.

By the way, check the blog entry by our blog friend Juan Julián Merelo Guervós on PPSN X here. Another blog entry here, by Jorge Tavares.

Professor Hans-Paul Schwefel is the PPSN X honorary chair

Let's wait for more blogging from Dortmund at the PPSN X. [Estoy confiando en ti, JJ! Don't disapoint me! :) ]

Evolving Architecture Through Simulated Evolution

2008-09-14T08:11:00.006-03:00

Very good post this one, see it here.

It deals with the optimization of an acoustic shell which delivers the best sound distribution along the space it covers. The author used a genetic algorithm to tune the parameters.

Evolving Fish Swimming Through Simulated Evolution

2008-09-14T07:44:00.004-03:00

Great story about a robot tuna which has its parameters set up by a genetic algorithm. See the link below:

MIT Ocean Engineering - RoboTuna.

It reminds me of an earlier post here:

Evolving Design Through Simulated Evolution.

An excerpt from the robot tuna case:

"The third and final phase is a search for the optimum swimming performance obtainable within the physical limits imposed by the design of the RoboTuna and the length of the existing testing tank. The current analytical intractability of the fluid dynamics of this problem indicated that the most pragmatic way to proceed would be to optimize the body wave controller experimentally. In simple terms, given the seven parameters which control the swimming body wave, this can be thought of as an experimental search through seven dimentional space. This large number of dimensions quickly creates a massive logistics problem (about 282,475,249 combinations of parameters).

Given that it takes approximately 5 minutes to make a single experimental run down the tank, it would take a time frame in the order of millions of years to perform a blind search through all the combinatorial possiblities in the persuit of an optimum (it is no coincidence that this is about the same amount of time it took for the biological tuna to evolve to its present form). Obviously a more efficient search mechanism is needed, in orger to find the optimum before either time ran out or the apparatus failed mechanically. After a survey of many existing multidimensional space search techniques, a robust, seft-optimizing system based on a Genetic Algorithm was developed."

Geophysics, Here I Go!

2008-09-07T17:54:00.000-03:00

Maybe, it is too much early for a definitive decison on which field I should choose. BUT, thinking a little of some key factors, I consider geophysics would be much more interesting to me than a bioinformatics adventure in the unknown.

Being pretty honest, I have curiosity about geophysics, what I have not felt so far when it comes to bioinformatics.

The figure of this post is a phenomenon strongly related to geophysics: An wave. It is The Great Wave off Kanagawa

Day Off - Updated

2008-09-05T01:06:00.006-03:00

Today, I went to the bioinformatics class which I am only attending without having enrolled in it. The professor did not come and gave us no excuses for his absence. I consider the more the professor shows he is committed to the subject, the more he can catch the attention and hearts of students.

I am almost to the point of not going to those classes anymore. I feel it will be fruitless to me and that it would be much more sensible to prepare me to do the admission exam on geophysics.

A little update here: As my blog friend, Juan Julián Merelo Guervós, said in the comments box, the bioinformatics professor's absence has to do with one of the Seven Deadly Sins: Sloth! :)

Well, it is very plausible. :)

The Seven Deadly Sins Of Bioinformatics

2008-09-03T19:50:00.003-03:00

As I am concerned with applying for a bioinformatics MSc., so I am looking for informations of that field, mainly those ones providing a critique panorama of its current (and, of course, future) trends and games. What I have most heard is that bioinformatics is the future, the 21st Century Job, it will help to replace the petrochemical industry bringing to us an alternative energy resource which is not only green, but, also, renewable, and so on. Despite all those positive remarks, I am not interested in them. I want to know critique statements about that field, what is hard to find out when talking to bioinformaticians here, since what they have told makes me feel as though I was in a Marlboro ad. :)

I have found a very interesting presentation about the deadly sins of bioinformatics, see this link:

The Seven Deadly Sins Of Bioinformatics.

The Seven Deadly Sins Of Bioinformatics are the following:

01. Parochialism And Insularity
02. Exceptionalism
03. Autonomy Or Death!
04. Vanity: Pride And Narcissism
05. Monolith Megalomania
06. Scientific Method Sloth
07. Instant Gratification

Gosh! A bioinformatics laboratory being the lair of at least one of those sins could become a hard place to social interaction.

By the way, the presentation is a nice overview of what is happening nowadays in bioinformatics, its current research situation and the views the computer science guys have of the biology guys (and vice-versa).

The Grad School

2008-09-03T01:20:00.001-03:00

That's it!

Next year, I shall be applying for some interesting course in Grad School. Despite the current fad in Brazil concerning the New Wave Of Public Exams to be admitted into one of the three major public Brazilian services (municipality, state, or federal), I would not feel comfortable after five years studying to get my BA. degree on computer/computing engineering to work in something that has little to nothing to do with engineering at all.

I am still a little hesitating upon geophysics or bioinformatics, both of them are amazing fields, but I must take into account the local academic environment and establishment of one and other at my university. The geophysics MSc. is a well established programme and it holds a very good critical mass of geophysicits - in addition, they make big engineering projects (sincerely, those guys are much closer to big engineering than the engineers themselves here).

The bioinformatics MSc. is just in its beginning and, to be honest, I dislike some engineering professors involved in it (for example, once, one of those professors, during a professor meeting, ordered another one to shut his mouth, because the other guy did not have any projects that would bring money to the department, then he could not say his opinion. Veeeeery democratic, isn't it?).

I am aware that I should not "complain" about those engineering professors, but just being completely blind not to see they have little interest in building a local excellence, what the guys from geophysics have already made, and, in my humble opinion, those professors only want to get the money coming from government agencies sponsoring biotech academic projects - it is a new fad happening in Brazil's universities. The professors from the biological sciences center have big bioinformatics ambitions, even telling us that we should seek some way to start up a bioinformatics business of our own. However, when looking at the local bioinformatics business opportunities, we feel anything but unmotivated. The bioscience guys have contributed on interesting genome endevour, such as the gene sequencing of Xylella fastidiosa. I am still thinking if I get into the bioinformatics grad school or not.

One of the key factors that leads me toward geophysics is the fact that in Brazil there are big oil/petroleum companies, such as Petrobras. Bioinformatics is still an activity being mainly sponsored by the Federal Brazilian Government (EMBRAPA, MCT, etc.) and its private ventures are very few. Sure, while it may seem a fruitless bioinformatics field for someone, it could be, by the other hand, a business opportunity before the eyes of another person, a chance to start a business from scratch - I am well aware of those two facets. The main consideration living in my mind these days is that I must make a choice and this choice will affect, likely, my whole life. So, I need to do a sensible choice, what is not easy. There are so many stuffs to ponder.

Early this year, I went to visit the geosciences center and the professor which accepted to be my advisor, as long as I apply for geophysics, treated me in a very very good manner. I liked the way we talked to each other, I felt as though I was his friend since a long time. He invited me to enter his office, to take a sit, and explain my situation. He heard everything, taking heed of each word I said. Few engineering professors treated me like he did.

On the other hand, when visiting the guys responsible for the bioinformatics MSc. programme, I felt like a a being from another planet. The woman who talked to me, told me very inaccurate informations concerning the bioinfo grad programme. Being honest, I disliked the way we interacted. A little more and she would be treading the grounds of impoliteness. I did not get a nice first impression of it.

I feel that I will end up applying for geophysics. BUT, let's see what will happen in the near future and see what field will receive the laurels of evolutionary computation...

--------------------------------------------------------

Personal Observations Upon Brazilian Public Service Admission Exams:

It's interesting how lawyers are well paid in Brazilian public services. Often, their salary range from US$ 3000.00 to US$ 6500.00 per month! At Petrobras - one of the most well-paying Brazilian corporations -, an engineer holding just a BA. degree can earn US$ 2150.00 per month! The funniest stuff is that an engineer can agregate knowledge and innovation to a given product, what helps to increase the product's value, while a public service lawyer is only eating away the contributors' money and, at least when it comes to Brazil, they do not deliver a good job, since their profession at service public level is full of corruption, bribery, lobby, ill will, and etc. Of course, there are very good lawyers in Brazil, but the majority is working for the private sector.

That's Brazil!

P.S: I wonder what an American entrepreneur and/or American venture would think about devoting one's life to eat away the contributors money instead of start a new business. My bet: A waste of time and, sure, money! :)

--------------------------------------------------------

Estimation of Distribution Algorithms Video Tutorial

2008-08-11T08:44:00.004-03:00

Martin Pelikan has uploaded his nice tutorial upon Estimation of Distribution Algorithms, see it here. The tutorial was given at GECCO 2008.

Even More GECCO 2008 HIghlights

2008-07-23T12:59:00.003-03:00

David Oranchak has made the best GECCO 2008 coverage I have read so far. See it here.

Some excerpts:

According to Nic McPhee’s twitters, GECCO 2008 had 471 attendees from 46 countries. This universal appeal of scientific research is one of things I liked about last year’s GECCO conference, too. This year’s conference, though, was almost as bad as last year’s when it came to feeding the attendees. Food was given out during the two hour poster session where I was presenting my poster, but all the food was gone in less than 20 minutes, and it was not replenished. Boo!

In the defense applications track, we saw a talk about evolving swarm behaviors for unmanned aerial vehicles (UAVs). Some of the swarming, self-organizing, and attacking behaviors are inspired by behaviors of insects such as bees and wasps. Several interesting micro-UAV technologies were mentioned, such as the Black Widow, UAVs with flapping wings (including bat wings), and parasitic (!!!) UAVs such as SilentEyes (it is launched from larger UAVs). Don’t do anything suspicious, or a swarm of these damned things will form a stinging cloud around you.

There were many more interesting papers, too numerous to describe, showcasing the widespread and diverse applications of evolutionary computing. Some examples include evolving circuits with high testability, automatic defect classification in electronic wafer manufacturing, quantifying quality degradation on voice-over-IP networks, detection of malware (including zero-day virus attacks) using techniques inspired by biological immune systems, evolving color schemes for people with color blindness, investment portfolio optimization, modeling the Milky Way galaxy using BOINC volunteer computing, developing no-loss strategies for tic-tac-toe, finding deadlocks in large concurrent java programs, radar jamming, evolving functions that can detect computer program code plagiarism by students (beware, cheaters!), automatic route planning that takes traffic into consideration, automatic composition of rock music using genetic algorithms (seriously?), interactive evolution of facial composites of suspects in criminal investigations, detection of moving objects in videos, using a bacterial foraging algorithm to detect circles on images (wait, what?), evolving a World Computer Chess Champion-beating chess program by mimicking the behavior of a mentor, and prediction of whether a company will have financial losses.

Excellent coverage!!

Evolving Robot Gait Through Simulated Evolution

2008-07-23T04:22:00.003-03:00

Interesting story brought to me via my news webservice:

Students - And Robots - Learn In Professor´s Robotics Lab.

The genetic algorithm applied is the CGA - Cyclic Genetic Algorithm. Not to be confused with the cGA - Compact Genetic Algorithm, an EDA.

The main ideas behind CGA are the following:

Parker made modifications to the standard genetic algorithm to invent the cyclic genetic algorithm (CGA), a method by which cycles of behavior can be learned. The CGA is a method where the computer can self-generate code. In real life, this means that a robot who encounters mud, for instance, might adapt with a different gait. A robot that loses a leg could learn to walk without it.

To demonstrate, Parker changed the parameters on the computer to tell one robot that it was suddenly carrying a heavy load. The robot took on a new walk - slow, deliberate and heavy on stability. In further tests, he showed how the CGA could adapt the robot control codes for partial and full loss of one or two of its legs. "The original CGA method was very limited because it couldn´t react to sensory input," Parker said.

More formaly it can be put as:

"Cyclic Genetic Algorithms were developed to allow for the representation of a cycle of actions in the chromosome. They differ from the standard GA in that the chromosome is in the form of a circle with two tails. The tails of the CGA chromosome are provided to allow for pre and post-cycle procedures. They provide a means for completing tasks before and after entering the cycle. For gait sequence generation, the pre-cycle can position the legs in a ready to walk posture and the post-cycle can return the robot to a stable at rest posture. In our application, we used only the pre-cycle tail. TheCGA genes can be one of several possibilities. They can be as simple as normal genes that represent traits of the individual or they can be as complicated as cyclic sub-chromosomes that can be trained separately by a CGA. For our purposes, the genes represent tasks that are to be completed in a set amount of time. The trained chromosome will contain the cycle of primitive instructions that will be continually repeated by our robot's simple controller to produce a gait.

CGAs can have both fixed and variable length chromosomes. In either case, the system must be able to allot the proper number of tasks to each phase and be flexible enough to allow the CGA to form a complete cycle. When fixed length are used, the tasks at each gene can be repeated. The number of repetitions is encoded in the gene. In this way, fixed length chromosomes can take on the desirable characteristics of variable yet maintain the increased control of training fixed.

More GECCO 2008 Highlights

2008-07-21T13:16:00.002-03:00

Martin Pelikan has posted his presentations at GECCO 2008. See it here.

It's a nice overview on estimation of distribution algorithms showed at GECCO this year.

GECCO 2008 Highlights

2008-07-20T14:21:00.003-03:00

Nice GECCO 2008 overview from Epistasis blog author Jason Moore, see it here.

Darwinmania

2008-07-17T11:31:00.004-03:00

Very interesting articles from New York Times blogger Olivia Judson! In three parts, see them:

Darwinmania!

An Original Confession

Let’s Get Rid of Darwinism

Those articles are intended to celebrate the 150th anniversary of the first announcement of [Darwin's] discovery of natural selection, the main driving force of evolution.

Excellent!!

Evolving Design Through Simulated Evolution

2008-07-04T15:53:00.007-03:00

Amazing article from Elisava:

Bionics And Design: Witnesses To The Evolution Of This Approach.

Some quotes from the text:

"[...] Natural history research, even that which seems to be no more than the fruit of pure and empty curiosity, can have very real uses, which would be enough to justify it even to those who only want research into useful things, if before condemning we could have the patience to wait for time to show the use we could make of its [...]."

Rene-Antoine Ferchault de Reaumur, A History of Wasps - 1719.

"It is the story of the development of the branch of mathematics called the calculus of variations, which concerns questions of optimization —finding forms or patterns that maximize or minimize a particular quantity Is the igloo the optimal housing form for minimal heat loss to the outside? Do bees really use the least possible ammount of wax in constructing their hexagonal cells?"

Stefan Hildebrandt & Anthony Tromba - 1985

"The oldest shells in the universe are the crusts of the cooling stars... We can compare them to an egg-shell: they are formed on the surface of moving liquid drops. In long-ago prehistory, about 400 million years ago, living nature took advantage of the fact that a curved structure is 50 to 100 times stronger than a flat structure of the same thickness. This means that the protecting envelope around fragile micro-organisms can as much reduce the expense of material and weight as obtain a greater degree of protection[...]."

Heinz Isler - 1989

"I believe that flowers —vivacious or woody plants— not only present the most frequent type of shell, but that they are also those of the greatest beauty. They offer a complementary perfection: they are kinetic structures. According to need, they can vary their form to open or close the flower, or even to aid the process of pollinization[...]."

Heinz Isler - 1989

"Nature offers us a range of secrets that will not be revealed except with much patience and love [...]."

Le Ricolais - 1935-1969

Darwin And Wallace - 150 Years

2008-07-01T19:19:00.004-03:00

Nice overview of the joint presentation held in 1858 - 150 years ago - to show up the first skunks upon evolution through natural selection, see here. The main enthusiasts involved in such a discussion were Charles Darwin and Alfred Russel Wallace. Both of them sent a representative to read their respective writings upon the subject. It's funny to know that the main hall of the famous Linnean Society of London was filled with persons holding a layman skill on evolution and science in general, very different from what a contemporary mind would expect, that is, "experts" following the 19th Century biology Zeitgeist.

It is such important day for evolutionary computation, since in 1858 was the "first generation" of its subsequent development!

I wonder what those two men would say if they saw what their ideas - and others' too - has helped to create and solve...

On Penguins And Submarines, Airplanes, And So On!

2008-06-30T18:25:00.007-03:00

Interesting finding here:

Aerodynamics In The Animal World. Yes, I know: Another Google automatic translation. But, it is better to read something slightly comprehensible than nothing at all. The main ideas are very clear, I think. :)

The article has to do with the aerodynamics on animal bodies, such as the Penguin's, and how it deals with aerodynamical problems - turbulence, acceleration issues, and etc.

The Penguin's streamlined body could be an inspiration when it comes to submarine body design, helping to create even quieter, faster, and more efficient submarines. Let alone it could also be applied on other areas strongly relying on aerodynamics, such as airplanes, rockets, and etc.

See a short movie of the Ṕenguin's flight here.

Ingo Rechenberg And Micro Air Vehicles

2008-06-28T12:06:00.003-03:00

A very nice point to read:

Evolution? Innovation!

Yeah! I know... it is an automatic translation from Google. But I think the main ideas are comprehensible.

The current work of Ingo Rechenberg has to with MAVs: Micro Air Vehicles. He is engaged in producing the first functional MAV for real world problems, such as detecting illegal substances and explosives.

So, let's wait for what Der Bioniker will show us on the next years!

Lawrence J. Fogel Highlighted By The American Society For Cybernetics

2008-05-13T12:55:00.005-03:00

Lawrence J. Fogel has been highlighted by the American Society For Cybernetics. See it here. For a complete list of cyberneticians, see here.

Lawrence Fogel is the father of the so called evolutionary programming, which his son, David B. Fogel, later improved and extended to work on real valued domains.

Via Natural Selection, Inc.