Something pretty annoying in evolutionary computing is that mildly different and overlapping concepts tend to pick dramatically different names. My latest confusion because of this is that gene-expression-programming seems very similar to cartesian-genetic-programming.
(how) Are these fundamentally different concepts?
I've read that indirect encoding of GP instructions is an effective technique ( both GEP and CGP do that ). Has there been reached some sort of consensus that indirect encoding has outdated classic tree bases GP?
Well, it seems that there is some difference between gene expression programming (GEP) and cartesian genetic programming (CGP or what I view as classic genetic programming), but the difference might be more hyped up than it really ought to be. Please note that I have never used GEP, so all of my comments are based on my experience with CGP.
In CGP there is no distinction between genotype and a phenotype, in other words- if you're looking at the "genes" of a CGP you're also looking at their expression. There is no encoding here, i.e. the expression tree is the gene itself.
In GEP the genotype is expressed into a phenotype, so if you're looking at the genes you will not readily know what the expression is going to look like. The "inventor" of GP, Cândida Ferreira, has written a really good paper and there are some other resources which try to give a shorter overview of the whole concept.
Ferriera says that the benefits are "obvious," but I really don't see anything that would necessarily make GEP better than CGP. Apparently GEP is multigenic, which means that multiple genes are involved in the expression of a trait (i.e. an expression tree). In any case, the fitness is calculated on the expressed tree, so it doesn't seem like GEP is doing anything to increase the fitness. What the author claims is that GEP increases the speed at which the fitness is reached (i.e. in fewer generations), but frankly speaking you can see dramatic performance shifts from a CGP just by having a different selection algorithm, a different tournament structure, splitting the population into tribes, migrating specimens between tribes, including diversity into the fitness, etc.
Selection:
random
roulette wheel
top-n
take half
etc.
Tournament Frequency:
once per epoch
once per every data instance
once per generation.
Tournament Structure:
Take 3, kill 1 and replace it with the child of the other two.
Sort all individuals in the tournament by fitness, kill the lower half and replace it with the offspring of the upper half (where lower is worse fitness and upper is better fitness).
Randomly pick individuals from the tournament to mate and kill the excess individuals.
Tribes
A population can be split into tribes that evolve independently of each-other:
Migration- periodically, individual(s) from a tribe would be moved to another tribe
The tribes are logically separated so that they're like their own separate populations running in separate environments.
Diversity Fitness
Incorporate diversity into the fitness, where you count how many individuals have the same fitness value (thus are likely to have the same phenotype) and you penalize their fitness by a proportionate value: the more individuals with the same fitness value, the more penalty for those individuals. This way specimens with unique phenotypes will be encouraged, therefore there will be much less stagnation of the population.
Those are just some of the things that can greatly affect the performance of a CGP, and when I say greatly I mean that it's in the same order or greater than Ferriera's performance. So if Ferriera didn't tinker with those ideas too much, then she could have seen much slower performance of the CGPs... especially if she didn't do anything to combat stagnation. So I would be careful when reading performance statistics on GEP, because sometimes people fail to account for all of the "optimizations" available out there.
There seems to be some confusion in these answers that must be clarified. Cartesian GP is different from classic GP (aka tree-based GP), and GEP. Even though they share many concepts and take inspiration from the same biological mechanisms, the representation of the individuals (the solutions) varies.
In CGPthe representation (mapping between genotype and phenotype) is indirect, in other words, not all of the genes in a CGP genome will be expressed in the phenome (a concept also found in GEP and many others). The genotypes can be coded in a grid or array of nodes, and the resulting program graph is the expression of active nodes only.
In GEP the representation is also indirect, and similarly not all genes will be expressed in the phenotype. The representation in this case is much different from treeGP or CGP, but the genotypes are also expressed into a program tree. In my opinion GEP is a more elegant representation, easier to implement, but also suffers from some defects like: you have to find the appropriate tail and head size which is problem specific, the mnltigenic version is a bit of a forced glue between expression trees, and finally it has too much bloat.
Independently of which representation may be better than the other in some specific problem domain, they are general purpose, can be applied to any domain as long as you can encode it.
In general, GEP is simpler from GP. Let's say you allow the following nodes in your program: constants, variables, +, -, *, /, if, ...
For each of such nodes with GP you must create the following operations:
- randomize
- mutate
- crossover
- and probably other genetic operators as well
In GEP for each of such nodes only one operation is needed to be implemented: deserialize, which takes array of numbers (like double in C or Java), and returns the node. It resembles object deserialization in languages like Java or Python (the difference is that deserialization in programming languages uses byte arrays, where here we have arrays of numbers). Even this 'deserialize' operation doesn't have to be implemented by the programmer: it can be implemented by a generic algorithm, just like it's done in Java or Python deserialization.
This simplicity from one point of view may make searching of best solution less successful, but from other side: requires less work from programmer and simpler algorithms may execute faster (easier to optimize, more code and data fits in CPU cache, and so on). So I would say that GEP is slightly better, but of course the definite answer depends on problem, and for many problems the opposite may be true.
Related
Can someone help me understand the definitions of phenotype and genotype in relation to evolutionary algorithms?
Am I right in thinking that the genotype is a representation of the solution. And the phenotype is the solution itself?
Thanks
Summary: For simple systems, yes, you are completely right. As you get into more complex systems, things get messier.
That is probably all most people reading this question need to know. However, for those who care, there are some weird subtleties:
People who study evolutionary computation use the words "genotype" and "phenotype" frustratingly inconsistently. The only rule that holds true across all systems is that the genotype is a lower-level (i.e. less abstracted) encoding than the phenotype. A consequence of this rule is that there can generally be multiple genotypes that map to the same phenotype, but not the other way around. In some systems, there are really only the two levels of abstraction that you mention: the representation of a solution and the solution itself. In these cases, you are entirely correct that the former is the genotype and the latter is the phenotype.
This holds true for:
Simple genetic algorithms where the solution is encoded as a bitstring.
Simple evolutionary strategies problems, where a real-value vector is evolved and the numbers are plugged directly into a function which is being optimized
A variety of other systems where there is a direct mapping between solution encodings and solutions.
But as we get to more complex algorithms, this starts to break down. Consider a simple genetic program, in which we are evolving a mathematical expression tree. The number that the tree evaluates to depends on the input that it receives. So, while the genotype is clear (it's the series of nodes in the tree), the phenotype can only be defined with respect to specific inputs. That isn't really a big problem - we just select a set of inputs and define phenotype based on the set of corresponding outputs. But it gets worse.
As we continue to look at more complex algorithms, we reach cases where there are no longer just two levels of abstraction. Evolutionary algorithms are often used to evolve simple "brains" for autonomous agents. For instance, say we are evolving a neural network with NEAT. NEAT very clearly defines what the genotype is: a series of rules for constructing the neural network. And this makes sense - that it the lowest-level encoding of an individual in this system. Stanley, the creator of NEAT, goes on to define the phenotype as the neural network encoded by the genotype. Fair enough - that is indeed a more abstract representation. However, there are others who study evolved brain models that classify the neural network as the genotype and the behavior as the phenotype. That is also completely reasonable - the behavior is perhaps even a better phenotype, because it's the thing selection is actually based on.
Finally, we arrive at the systems with the least definable genotypes and phenotypes: open-ended artificial life systems. The goal of these systems is basically to create a rich world that will foster interesting evolutionary dynamics. Usually the genotype in these systems is fairly easy to define - it's the lowest level at which members of the population are defined. Perhaps it's a ring of assembly code, as in Avida, or a neural network, or some set of rules as in geb. Intuitively, the phenotype should capture something about what a member of the population does over its lifetime. But each member of the population does a lot of different things. So ultimately, in these systems, phenotypes tend to be defined differently based on what is being studied in a given experiment. While this may seem questionable at first, it is essentially how phenotypes are discussed in evolutionary biology as well. At some point, a system is complex enough that you just need to focus on the part you care about.
This is for self-study of N-dimensional system of linear homogeneous ordinary differential equations of the form:
dx/dt=Ax
where A is the coefficient matrix of the system.
I have learned that you can check for stability by determining if the real parts of all the eigenvalues of A are negative. You can check for oscillations if there are any purely imaginary eigenvalues of A.
The author in the book I'm reading then introduces the Routh-Hurwitz criterion for detecting stability and oscillations of the system. This seems to be a more efficient computational short-cut than calculating eigenvalues.
What are the advantages of using Routh-Hurwitz criteria for stability and oscillations, when you can just find the eigenvalues quickly nowadays? For instance, will it be useful when I start to study nonlinear dynamics? Is there some additional use that I am completely missing?
Wikipedia entry on RH stability analysis has stuff about control systems, and ends up with a lot of equations in the s-domain (Laplace transforms), but for my applications I will be staying in the time-domain for the most part, and just focusing fairly narrowly on stability and oscillations in linear (or linearized) systems.
My motivation: it seems easy to calculate eigenvalues on my computer, and the Routh-Hurwitz criterion comes off as sort of anachronistic, the sort of thing that might save me a lot of time if I were doing this by hand, but not very helpful for doing analysis of small-fry systems via Matlab.
Edit: I've asked this at Math Exchange, which seems more appropriate:
https://math.stackexchange.com/questions/690634/use-of-routh-hurwitz-if-you-have-the-eigenvalues
There is an accepted answer there.
This is just legacy educational curriculum which fell way behind of the actual computational age. Routh-Hurwitz gives a very nice theoretical basis for parametrization of root positions and linked to much more abstract math.
However, for control purposes it is just a nice trick that has no practical value except maybe simple transfer functions with one or two unknown parameters. It had real value when computing the roots of the polynomials were expensive or even manual. Today, even root finding of polynomials is based on forming the companion matrix and computing the eigenvalues. In fact you can basically form a meshgrid and check the stability surface by plotting the largest real part in a few minutes.
Decision problems are not suited for use in evolutionary algorithms since a simple right/wrong fitness measure cannot be optimized/evolved. So, what are some methods/techniques for converting decision problems to optimization problems?
For instance, I'm currently working on a problem where the fitness of an individual depends very heavily on the output it produces. Depending on the ordering of genes, an individual either produces no output or perfect output - no "in between" (and therefore, no hills to climb). One small change in an individual's gene ordering can have a drastic effect on the fitness of an individual, so using an evolutionary algorithm essentially amounts to a random search.
Some literature references would be nice if you know of any.
Application to multiple inputs and examination of percentage of correct answers.
True, a right/wrong fitness measure cannot evolve towards more rightness, but an algorithm can nonetheless apply a mutable function to whatever input it takes to produce a decision which will be right or wrong. So, you keep mutating the algorithm, and for each mutated version of the algorithm you apply it to, say, 100 different inputs, and you check how many of them it got right. Then, you select those algorithms that gave more correct answers than others. Who knows, eventually you might see one which gets them all right.
There are no literature references, I just came up with it.
Well i think you must work on your fitness function.
When you say that some Individuals are more close to a perfect solution can you identify this solutions based on their genetic structure?
If you can do that a program could do that too and so you shouldn't rate the individual based on the output but on its structure.
I was recently talking with someone in Resource Management and we discussed the problem of assigning developers to projects when there are many variables to consider (of possibly different weights), e.g.:
The developer's skills & the technology/domain of the project
The developer's travel preferences & the location of the project
The developer's interests and the nature of the project
The basic problem the RM person had to deal with on a regular basis was this: given X developers where each developers has a unique set of attributes/preferences, assign them to Y projects where each project has its own set of unique attributes/requirements.
It seems clear to me that this is a very mathematical problem; it reminds me of old optimization problems from algebra and/or calculus (I don't remember which) back in high school: you know, find the optimal dimensions for a container to hold the maximum volume given this amount of material—that sort of thing.
My question isn't about the math, but rather whether there are any software projects/libraries out there designed to address this kind of problem. Does anyone know of any?
My question isn't about the math, but rather whether there are any software projects/libraries out there designed to address this kind of problem. Does anyone know of any?
In my humble opinion, I think that this is putting the cart before the horse. You first need to figure out what problem you want to solve. Then, you can look for solutions.
For example, if you formulate the problem by assigning some kind of numerical compatibility score to every developer/project pair with the goal of maximizing the total sum of compatibility scores, then you have a maximum-weight matching problem which can be solved with the Hungarian algorithm. Conveniently, this algorithm is implemented as part of Google's or-tools library.
On the other hand, let's say that you find that computing compatibility scores to be infeasible or unreasonable. Instead, let's say that each developer ranks all the projects from best to worst (e.g.: in terms of preference) and, similarly, each project ranks each developer from best to worst (e.g.: in terms of suitability to the project). In this case, you have an instance of the Stable Marriage problem, which is solved by the Gale-Shapley algorithm. I don't have a pointer to an established library for G-S, but it's simple enough that it seems that lots of people just code their own.
Yes, there are mathematical methods for solving a type of problem which this problem can be shoehorned into. It is the natural consequence of thinking of developers as "resources", like machine parts, largely interchangeable, their individuality easily reduced to simple numerical parameters. You can make up rules such as
The fitness value is equal to the subject skill parameter multiplied by the square root of the reliability index.
and never worry about them again. The same rules can be applied to different developers, different subjects, different scales of projects (with a SLOC scaling factor of, say, 1.5). No insight or real leadership is needed, the equations make everything precise and "assured". The best thing about this approach is that when the resources fail to perform the way your equations say they should, you can just reduce their performance scores to make them fit. And if someone has already written the tool, then you don't even have to worry about the math.
(It is interesting to note that Resource Management people always seem to impose such metrics on others in an organization -- thereby making their own jobs easier-- and never on themselves...)
An article has been making the rounds lately discussing the use of genetic algorithms to optimize "build orders" in StarCraft II.
http://lbrandy.com/blog/2010/11/using-genetic-algorithms-to-find-starcraft-2-build-orders/
The initial state of a StarCraft match is pre-determined and constant. And like chess, decisions made in this early stage of the match have long-standing consequences to a player's ability to perform in the mid and late game. So the various opening possibilities or "build orders" are under heavy study and scrutiny. Until the circulation of the above article, computer-assisted build order creation probably wasn't as popularity as it has been recently.
My question is... Is a genetic algorithm really the best way to model optimizing build orders?
A build order is a sequence of actions. Some actions have prerequisites like, "You need building B before you can create building C, but you can have building A at any time." So a chromosome may look like AABAC.
I'm wondering if a genetic algorithm really is the best way to tackle this problem. Although I'm not too familiar with the field, I'm having a difficult time shoe-horning the concept of genes into a data structure that is a sequence of actions. These aren't independent choices that can be mixed and matched like a head and a foot. So what value is there to things like reproduction and crossing?
I'm thinking whatever chess AIs use would be more appropriate since the array of choices at any given time could be viewed as tree-like in a way.
Although I'm not too familiar with the field, I'm having a difficult time shoe-horning the concept of genes into a data structure that is a sequence of actions. These aren't independent choices that can be mixed and matched like a head and a foot. So what value is there to things like reproduction and crossing?
Hmm, that's a very good question. Perhaps the first few moves in Starcraft can indeed be performed in pretty much any order, since contact with the enemy is not as immediate as it can be in Chess, and therefore it is not as important to remember the order of the first few moves as it is to know which of the many moves are included in those first few. But the link seems to imply otherwise, which means the 'genes' are indeed not all that amenable to being swapped around, unless there's something cunning in the encoding that I'm missing.
On the whole, and looking at the link you supplied, I'd say that genetic algorithms are a poor choice for this situation, which could be accurately mathematically modelled in some parts and the search tree expanded out in others. They may well be better than an exhaustive search of the possibility space, but may not be - especially given that there are multiple populations and poorer ones are just wasting processing time.
However, what I mean by "a poor choice" is that it is inefficient relative to a more appropriate approach; that's not to say that it couldn't still produce 98% optimal results in under a second or whatever. In situations such as this where the brute force of the computer is useful, it is usually more important that you have modelled the search space correctly than to have used the most effective algorithm.
As TaslemGuy pointed out, Genetic Algorithms aren't guaranteed to be optimal, even though they usually give good results.
To get optimal results you would have to search through every possible combination of actions until you find the optimal path through the tree-like representation. However, doing this for StarCraft is difficult, since there are so many different paths to reach a goal. In chess you move a pawn from e2 to e4 and then the opponent moves. In StarCraft you can move a unit at instant x or x+1 or x+10 or ...
A chess engine can look at many different aspects of the board (e.g. how many pieces does it have and how many does the opponent have), to guide it's search. It can ignore most of the actions available if it knows that they are strictly worse than others.
For a build-order creator only time really matters. Is it better to build another drone to get minerals faster, or is it faster to start that spawning pool right away? Not as straightforward as with chess.
These kinds of decisions happen pretty early on, so you will have to search each alternative to conclusion before you can decide on the better one, which will take a long time.
If I were to write a build-order optimizer myself, I would probably try to formulate a heuristic that estimates how good (close the to the goal state) the current state is, just as chess engines do:
Score = a*(Buildings_and_units_done/Buildings_and_units_required) - b*Time_elapsed - c*Minerals - d*Gas + e*Drone_count - f*Supply_left
This tries to keep the score tied to the completion percentage as well as StarCraft common knowledge (keep your ressources low, build drones, don't build more supply than you need). The variables a to f would need tweaking, of course.
After you've got a heuristic that can somewhat estimate the worth of a situation, I would use Best-first search or maybe IDDFS to search through the tree of possibilities.
Edit:
I recently found a paper that actually describes build order optimization in StarCraft, in real time even. The authors use depth-first search with branch and bound and heuristics that estimate the minimum amount of effort required to reach the goal based on the tech tree (e.g. zerglings need a spawning pool) and the time needed to gather the required minerals.
Genetic Algorithm can be, or can sometimes not be, the optimal or non-optimal solution. Based on the complexity of the Genetic Algorithm, how much mutation there is, the forms of combinations, and how the chromosomes of the genetic algorithm is interpreted.
So, depending on how your AI is implemented, Genetic Algorithms can be the best.
You are looking at a SINGLE way to implement genetic algorithms, while forgetting about genetic programming, the use of math, higher-order functions, etc. Genetic algorithms can be EXTREMELY sophisticated, and by using clever combining systems for crossbreeding, extremely intelligent.
For instance, neural networks are optimized by genetic algorithms quite often.
Look up "Genetic Programming." It's similar, but uses tree-structures instead of lines of characters, which allows for more complex interactions that breed better. For more complex stuff, they typically work out better.
There's been some research done using hierarchical reinforcement learning to build a layered ordering of actions that efficiently maximizes a reward. I haven't found much code implementing the idea, but there are a few papers describing MAXQ-based algorithms that have been used to explicitly tackle real-time strategy game domains, such as this and this.
This Genetic algorithm only optimizes the strategy for one very specific part of the game: The order of the first few build actions of the game. And it has a very specific goal as well: To have as many roaches as quickly as possible.
The only aspects influencing this system seem to be (I'm no starcraft player):
build time of the various units and
buildings
allowed units and buildings given the available units and buildings
Larva regeneration rate.
This is a relatively limited, relatively well defined problem with a large search space. As such it is very well suited for genetic algorithms (and quite a few other optimization algorithm at that). A full gene is a specific set of build orders that ends in the 7th roach. From what I understand you can just "play" this specific gene to see how fast it finishes, so you have a very clear fitness test.
You also have a few nice constraints on the build order, so you can combine different genes slightly smarter than just randomly.
A genetic algorithm used in this way is a very good tool to find a more optimal build order for the first stage of a game of starcraft. Due to its random nature it is also good at finding a surprising strategy, which might have been an additional goal of the author.
To use a genetic algorithm as the algorithm in an RTS game you'd have to find a way to encode reactions to situations rather than just plain old build orders. This also involves correctly identifying situations which can be a difficult task in itself. Then you'd have to let these genes play thousands of games of starcraft, against each other and (possibly) against humans, selecting and combining winners (or longer-lasting losers). This is also a good application of genetic algorithms, but it involves solving quite a few very hard problems before you even get to the genetic algorithm part.