I wanted to know the computational complexity of ontologies. I am using the NIFSTD ontology and want to make a hierarchy based on some specific queries computation time (big O).
I have read that SPARQL itself is Pspace-complete. As you know, ontologies are usually based on RDF and are queried with the SPARQL.
I wanted the cost of searching for a concept in the ontology (select) and searching with a condition (where {...}).
In addition, is the computational complexity of opening and reading and ontology O(n) where n equals the size of the ontology file?
Thanks in Advance,
Aref
Searching for a concept where the IRI is known is very fast - most APIs have indexes for these, so you can assume O(1) for this.
Searching with a where condition depends entirely on the condition. The more complex the condition, the higher the cost - the upper limit is the same as the worst case complexity you mentioned.
Another factor to be taken into account is whether you want to include any inference regime in your analysis or not; if so, then there's another source of unknown complexity there - OWL 2 DL inferencing has exponential worst case complexity, but what the actual difficulty of reasoning on a given ontology is depends on many factors, and it is not easy to predict. Still an open research question.
The cost of loading an ontology is roughly proportional to its size, although some axioms require more processing than others. Big variations between different APIs are to be expected; I would consider O(n) an acceptable approximation.
Related
For large values of n, an algorithm that takes 20000n^2 steps has better time complexity (takes less time) than one that takes 0.001n^5 steps
I believe this statement is true. But, why?
If there are more steps wouldn't that take more time?
Computational complexity is considered in the asymptotic sense because the important question is usually of scaling. Even with your clear case, the ^5 algorithm begins to take longer around 275 items - which isn't very many. See this figure from wolfram alpha:
Quoting from the wikipedia article linked above:
Usually asymptotic estimates are used because different implementations of the same algorithm may differ in efficiency. However the efficiencies of any two "reasonable" implementations of a given algorithm are related by a constant multiplicative factor called a hidden constant.
All that said, if you have two comparable algorithms and the one with less complexity has a significant constant coefficient and you're only going to process 10 items, then it very well may be a good idea to choose the less efficient one. Some common libraries even switch algorithms depending upon the size of the data being processed; this is called a hybrid algorithm and Python's sorted implementation, Timsort uses it to switch between insertion sort and merge sort.
I want to increase performance of my sparql queries. I have to run all type of sparql query.
I have total 17,500,000 triples in the graph and i have other graph containg only knowledge. this graph containing same as and subclassOf property. Total triples of this graph is around 50,000,000, I am using on the fly inferencing in the sparql query.
I am using virtuoso as a database. It has inferencing functionality.
When I run query with inferencing, it is taking 80 secs for simple query. and without using inferencing it is taking 10 secs.
Sparql Query:
DEFINE input:inference 'myrule'
select DISTINCT ?uri1 ?uri2
from <GRAPH_NAME>
where {?uri1 rdf:type ezdi:Aspirin.
?patient ezdi:is_treated_with ?uri1.
?patient rdf:type ezdi:Patient.
?uri2 rdf:type ezdi:Hypertension .
?patient ezdi:is_suffering_with ?uri2.
?patient rdf:type ezdi:Patient } ORDER BY ?patient
I have done all the indexing providing by the virtuoso. System has 32 GB RAM.
And I have done NumberOfBuffer setting virtuoso.ini file.
I dont know what is the issue with inferencing. But I have to use Inferencing in the sparql Query.
If u know something then plz share ur idea.
Thank You
An ontology of 5M triples is quite large, though strictly speaking, that's not problematic. Performance with regards to reasoning is far more closely tied to the expressivity of your ontology than it's size. You could create an ontology with several order of magnitude fewer triples that would be harder to reasoning with.
With that said, there's not much I can specifically suggest. Virtuoso specific tuning is best left to their developers, so you might get some traction on their mailing list.
It appears that you're using some custom inferencing "my_rule" -- though in the comments you also claim RDFS & sameAs. You probably need to figure out what reasoning you're actually using, what profile (RDFS or OWL2 QL, RL, EL, DL) that your ontology falls into, and learn a little bit about how reasoning actually works. Further, equality reasoning is difficult, which you claim to be using in addition to RDFS. It might be possible that Virtuoso can compute the equivalence relations eagerly which could reduce the overhead of the query, but again, that is something you should take up with them on their mailing list.
Reasoning is not easy by any means, and there's no silver bullet for magically making reasoning faster beyond using a simpler, ie less expressive, ontology or less data, or both.
Lastly, you might try other databases which are designed for reasoning, such as OWLIM or Stardog. Not all databases are created equal, and it's entirely possible you've encoded something in your TBox which Virtuoso might not handle well, but could be handled easily by another system.
There are many factors which could lead to the performance issue you describe. The most common is to make an error in the NumberOfBuffers setting in the INI file -- which we cannot see, and so cannot diagnose, here.
Questions specifically regarding Virtuoso are generally best raised on the public OpenLink Discussion Forums, the Virtuso Users mailing list, or through a confidential Support Case. If you bring this there, we should be able to help you in more detail.
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.
Big 0 attempts to answer the question of inefficiency in algorithmic complexity. N+1 describes inefficiency as it relates to database queries in terms of separate queries to populate each item in a collection.
I'm currently trying to get my head around each of these concepts in different contexts at work, and I'm wondering now if somebody could explain whether these two concepts relate to each other in any way? Could somebody provide a description that would apply to both of them?
Big O notation for complexity is defined using number of operations of a Turing machine and can therefore describe any algorithm. The N+1 select problem describes inefficient relational algorithm (query), which needs always N+1 operations for every record. As that query is an algorithm, you can analyse its complexity.
O(N+1)=O(N)
This means you have linear complexity. Now if we used the correct algorithm, we would need only one operation (select) per record for each of two tables. The complexity would be:
O(2)=O(1)
This algorithm has constant complexity. This shows, that by analysing the complexity of both algorithms you would see which one suffers from the N+1 selects problem.
Is this clear?
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.