I have three treatments (Wild type, Mutant1 and Mutant2); I request inputs on how to decide the sample size that would be statistically significant (alpha <0.05) with high statistical power (1-beta=0.8).
Questions
I understand that we need the information of effect size. We approach this problem if we don't know the expected effect size prior; a trial experiment to estimate the effect size. In such case if we want to estimate the effect size with trial experiment; what could be the sample size to start with; a high (n=10) or as low as n=3? Can n=3 among treatments provide a good estimate of effect size or n=10 is better to get this estimate. Let's be specific; if we have resource for n=10 max. and we are given option to choose between n=3 or n=10 for this trial
This question is better asked in https://stats.stackexchange.com.
I would discourage you from trying to estimate effects sizes from pilot experiments with low n. Your estimates will be quite noisy and this is rarely done (at least in my field of neuroscience). Instead, I would suggest you estimate your effect size from the literature. Have other people measured something similar to what you are planning to do? What are the sample sizes they use? What kind of effect sizes do they report.
If you were going to go ahead with the plan to run a pilot study, I would recommend pre-registering your experimental design (https://www.cos.io/initiatives/prereg). Something like:
We will test the effects of mutation 1 and mutation 2 on XXXX (compared to wild type) in a cohort of 30 mice (10 in each group). Based on the results of this study, we will then conduct a power analysis and reproduce the experiments in a sample size required to have a power of 0.8 at p=0.05.
Our criteria for excluding animals from the power analysis will be .....
The statistical test for estimating effect size will be......"
etc.
Related
Sorry I'm just starting this project and don't have any ideas or code, I'm asking more of a theoretical question than a programming one.
It seems that every google search provides the same responses and it's very hard to find an answer to this question:
Is there a way to calculate win percentages for texas holdem poker (the same way they do on poker after dark or other televised poker events) without using the monte carlo/exhaustive enumeration methods. Assuming all cards are face up and we know every card in the deck.
Every response on other forums just seems to be "use pokerstove" or something similar, I'm looking for the theory to write the code.
Thanks.
Is there a way to calculate win percentages for texas holdem poker
(the same way they do on poker after dark or other televised poker
events) without using the monte carlo/exhaustive enumeration methods.
In specific instances it is possible...
You can use a perfect lookup table preflop for two players heads-up preflop matchups: note that the "typical" 169 vs 169 approximation ain't good enough (say Jh Th vs 9h 8h ain't really "JTs vs 98s": I mean, that would quite a gross approximation).
Besides that if you have a lot of memory and if you can live with gigantic cache misses, you technically could precompute gigantic lookup tables (say on the server side) and do lookups for other cases (e.g. for every possible three players all-in matchups preflop), but you'd really need a lot of memory : )
Note that "full enumeration" at flop and turn ain't an issue: at flop there's only 2 more cards to come, so there are typically only C(45,2) [two players all-in at flop, we know 2*2 holecards + 3 community cards -- hence leaving 990 possibilities] or C(43,2) [three players all-in at at flop, we know 3*2 holecards + 3 community cards].
So an actual evaluator would not use one but several methods. For example:
lookup table for two players all-in preflop (the fastest)
full enum for any number of players all-in at flop or turn because it's tiny (max 990 possibilities) -- very fast
monte-carlo or full enum for three players or more all-in preflop -- incredibly slower
It is interesting to see here that in the most typical cases you'll get the result very, very fast: most actual all-ins involve two players, not three or more.
So you're either looking up in a "1 vs 1 preflop" lookup table or doing full C(45,2) or C(46,1) full enum (which are, in both case, amazingly fast).
It's really only the "three players or more all-in preflop" case which do take time.
The answer is no.
There is no closed form computation that you can do to compute poker equities. Using combinatorics, you can identify and solve many subproblems, which speeds up computation.
For example, if you are considering all five card hands, there are 52 choose 5 = 2,598,960 different hands. But knowing that suits are equivalent and using combinatorial methods (either analytic or computational), you can reduce the space of all hands to 134,459 classes each weighted according to the number of different hands in each equivalent class.
There are also various ways of using exhaustive evaluations tailored to your application. If you need to perform some subset of evaluations repeatedly, you can use caches or precomputed lookup tables targeted to your specific needs.
I am in the process of writing a genetic algorithm to solve Sudoku puzzles and was hoping for some input. The algorithm solves puzzles occasionally (about 1 out of 10 times on the same puzzle with max 1,000,000 iterations) and I am trying to get a little input about mutation rates, repopulation, and splicing. Any input is greatly appreciated as this is brand new to me and I feel like I am not doing things 100% correct.
A quick overview of the algorithm
Fitness Function
Counts the number of unique values of numbers 1 through 9 in each column, row, and 3*3 sub box. Each of these unique values in the subsets are summed and divided by 9 resulting in a floating value between 0 and 1. The sum of these values is divided by 27 providing a total fitness value ranging between 0 and 1. 1 indicates a solved puzzle.
Population Size:
100
Selection:
Roulette Method. Each node is randomly selected where nodes containing higher fitness values have a slightly better chance of selection
Reproduction:
Two randomly selected chromosomes/boards swap a randomly selected subset (row, column, or 3*3 subsets) The selection of subset(which row, column, or box) is random. The resulting boards are introduced into population.
Reproduction Rate: 12% of population per cycle
There are six reproductions per iteration resulting in 12 new chromosomes per cycle of the algorithm.
Mutation: mutation occurs at a rate of 2 percent of population after 10 iterations of no improvement of highest fitness.
Listed below are the three mutation methods which have varying weights of selection probability.
1: Swap randomly selected numbers. The method selects two random numbers and swaps them throughout the board. This method seems to have the greatest impact on growth early in the algorithms growth pattern. 25% chance of selection
2: Introduce random changes: Randomly select two cells and change their values. This method seems to help keep the algorithm from converging. %65 chance of selection
3: count the number of each value in the board. A solved board contains a count of 9 of each number between 1 and 9. This method takes any number that occurs less than 9 times and randomly swaps it with a number that occurs more than 9 times. This seems to have a positive impact on the algorithm but only used sparingly. %10 chance of selection
My main question is at what rate should I apply the mutation method. It seems that as I increase mutation I have faster initial results. However as the result approaches a correct result, I think the higher rate of change is introducing too many bad chromosomes and genes into the population. However, with the lower rate of change the algorithm seems to converge too early.
One last question is whether there is a better approach to mutation.
You can anneal the mutation rate over time to get the sort of convergence behavior you're describing. But I actually think there are probably bigger gains to be had by modifying other parts of your algorithm.
Roulette wheel selection applies a very high degree of selection pressure in general. It tends to cause a pretty rapid loss of diversity fairly early in the process. Binary tournament selection is usually a better place to start experimenting. It's a more gradual form of pressure, and just as importantly, it's much better controlled.
With a less aggressive selection mechanism, you can afford to produce more offspring, since you don't have to worry about producing so many near-copies of the best one or two individuals. Rather than 12% of the population producing offspring (possible less because of repetition of parents in the mating pool), I'd go with 100%. You don't necessarily need to literally make sure every parent participates, but just generate the same number of offspring as you have parents.
Some form of mild elitism will probably then be helpful so that you don't lose good parents. Maybe keep the best 2-5 individuals from the parent population if they're better than the worst 2-5 offspring.
With elitism, you can use a bit higher mutation rate. All three of your operators seem useful. (Note that #3 is actually a form of local search embedded in your genetic algorithm. That's often a huge win in terms of performance. You could in fact extend #3 into a much more sophisticated method that looped until it couldn't figure out how to make any further improvements.)
I don't see an obvious better/worse set of weights for your three mutation operators. I think at that point, you're firmly within the realm of experimental parameter tuning. Another idea is to inject a bit of knowledge into the process and, for example, say that early on in the process, you choose between them randomly. Later, as the algorithm is converging, favor the mutation operators that you think are more likely to help finish "almost-solved" boards.
I once made a fairly competent Sudoku solver, using GA. Blogged about the details (including different representations and mutation) here:
http://fakeguido.blogspot.com/2010/05/solving-sudoku-with-genetic-algorithms.html
Nominally a good problem to have, but I'm pretty sure it is because something funny is going on...
As context, I'm working on a problem in the facial expression/recognition space, so getting 100% accuracy seems incredibly implausible (not that it would be plausible in most applications...). I'm guessing there is either some consistent bias in the data set that it making it overly easy for an SVM to pull out the answer, =or=, more likely, I've done something wrong on the SVM side.
I'm looking for suggestions to help understand what is going on--is it me (=my usage of LibSVM)? Or is it the data?
The details:
About ~2500 labeled data vectors/instances (transformed video frames of individuals--<20 individual persons total), binary classification problem. ~900 features/instance. Unbalanced data set at about a 1:4 ratio.
Ran subset.py to separate the data into test (500 instances) and train (remaining).
Ran "svm-train -t 0 ". (Note: apparently no need for '-w1 1 -w-1 4'...)
Ran svm-predict on the test file. Accuracy=100%!
Things tried:
Checked about 10 times over that I'm not training & testing on the same data files, through some inadvertent command-line argument error
re-ran subset.py (even with -s 1) multiple times and did train/test only multiple different data sets (in case I randomly upon the most magical train/test pa
ran a simple diff-like check to confirm that the test file is not a subset of the training data
svm-scale on the data has no effect on accuracy (accuracy=100%). (Although the number of support vectors does drop from nSV=127, bSV=64 to nBSV=72, bSV=0.)
((weird)) using the default RBF kernel (vice linear -- i.e., removing '-t 0') results in accuracy going to garbage(?!)
(sanity check) running svm-predict using a model trained on a scaled data set against an unscaled data set results in accuracy = 80% (i.e., it always guesses the dominant class). This is strictly a sanity check to make sure that somehow svm-predict is nominally acting right on my machine.
Tentative conclusion?:
Something with the data is wacked--somehow, within the data set, there is a subtle, experimenter-driven effect that the SVM is picking up on.
(This doesn't, on first pass, explain why the RBF kernel gives garbage results, however.)
Would greatly appreciate any suggestions on a) how to fix my usage of LibSVM (if that is actually the problem) or b) determine what subtle experimenter-bias in the data LibSVM is picking up on.
Two other ideas:
Make sure you're not training and testing on the same data. This sounds kind of dumb, but in computer vision applications you should take care that: make sure you're not repeating data (say two frames of the same video fall on different folds), you're not training and testing on the same individual, etc. It is more subtle than it sounds.
Make sure you search for gamma and C parameters for the RBF kernel. There are good theoretical (asymptotic) results that justify that a linear classifier is just a degenerate RBF classifier. So you should just look for a good (C, gamma) pair.
Notwithstanding that the devil is in the details, here are three simple tests you could try:
Quickie (~2 minutes): Run the data through a decision tree algorithm. This is available in Matlab via classregtree, or you can load into R and use rpart. This could tell you if one or just a few features happen to give a perfect separation.
Not-so-quickie (~10-60 minutes, depending on your infrastructure): Iteratively split the features (i.e. from 900 to 2 sets of 450), train, and test. If one of the subsets gives you perfect classification, split it again. It would take fewer than 10 such splits to find out where the problem variables are. If it happens to "break" with many variables remaining (or even in the first split), select a different random subset of features, shave off fewer variables at a time, etc. It can't possibly need all 900 to split the data.
Deeper analysis (minutes to several hours): try permutations of labels. If you can permute all of them and still get perfect separation, you have some problem in your train/test setup. If you select increasingly larger subsets to permute (or, if going in the other direction, to leave static), you can see where you begin to lose separability. Alternatively, consider decreasing your training set size and if you get separability even with a very small training set, then something is weird.
Method #1 is fast & should be insightful. There are some other methods I could recommend, but #1 and #2 are easy and it would be odd if they don't give any insights.
Assumed infinite storage where size/volume/physics (metrics,gigabytes/terrabytes) won't matter only the number of elements and their labels, statistically pattern should emerge already at 30 subsets, but can you agree that less than 1000 subsets is too little to test, and at least 10000 distinct subsets / "elements", "entries" / entities is "a large data set". Or larger?
Thanks
I'm not sure I understand your question, but it sounds like you are attempting to ask about how many elements of data set you need to sample in order to ensure a certain degree of accuracy (30 is a magic number from the Central Limit Theorem that comes in to play frequently).
If that is the case, the sample size you need depends on the confidence level and confidence interval. If you want a 95% confidence level and a 5% confidence interval (i.e. you want to be 95% confident that the proportion you determine from your sample is within 5% of the proportion in the full data set), you end up needing a sample size of no more than 385 elements. The greater the confidence level and the smaller the confidence interval that you want to generate, the larger the sample size you need.
Here is a nice discussion on the mathematics of determining sample size
and a handy sample size calculator if you just want to run the numbers.
I'm working with a couple of AI algorithms at school and I find people use the words Fuzzy Logic to explain any situation that they can solve with a couple of cases. When I go back to the books I just read about how instead of a state going from On to Off it's a diagonal line and something can be in both states but in different "levels".
I've read the wikipedia entry and a couple of tutorials and even programmed stuff that "uses fuzzy logic" (an edge detector and a 1-wheel self-controlled robot) and still I find it very confusing going from Theory to Code... for you, in the less complicated definition, what is fuzzy logic?
Fuzzy logic is logic where state membership is, essentially, a float with range 0..1 instead of an int 0 or 1. The mileage you get out of it is that things like, for example, the changes you make in a control system are somewhat naturally more fine-tuned than what you'd get with naive binary logic.
An example might be logic that throttles back system activity based on active TCP connections. Say you define "a little bit too many" TCP connections on your machine as 1000 and "a lot too many" as 2000. At any given time, your system has a "too many TCP connections" state from 0 (<= 1000) to 1 (>= 2000), which you can use as a coefficient in applying whatever throttling mechanisms you have available. This is much more forgiving and responsive to system behavior than naive binary logic that only knows how to determine "too many", and throttle completely, or "not too many", and not throttle at all.
I'd like to add to the answers (that have been modded up) that, a good way to visualize fuzzy logic is follows:
Traditionally, with binary logic you would have a graph whose membership function is true or false whereas in a fuzzy logic system, the membership function is not.
1|
| /\
| / \
| / \
0|/ \
------------
a b c d
Assume for a second that the function is "likes peanuts"
a. kinda likes peanuts
b. really likes peanuts
c. kinda likes peanuts
d. doesn't like peanuts
The function itself doesn't have to be triangular and often isn't (it's just easier with ascii art).
A fuzzy system will likely have many of these, some even overlapping (even opposites) like so:
1| A B
| /\ /\ A = Likes Peanuts
| / \/ \ B = Doesn't Like Peanuts
| / /\ \
0|/ / \ \
------------
a b c d
so now c is "kind likes peanuts, kinda doesn't like peanuts" and d is "really doesn't like peanuts"
And you can program accordingly based on that info.
Hope this helps for the visual learners out there.
The best definition of fuzzy logic is given by its inventor Lotfi Zadeh:
“Fuzzy logic means of representing problems to computers in a way akin to the way human solve them and the essence of fuzzy logic is that everything is a matter of degree.”
The meaning of solving problems with computers akin to the way human solve can easily be explained with a simple example from a basketball game; if a player wants to guard another player firstly he should consider how tall he is and how his playing skills are. Simply if the player that he wants to guard is tall and plays very slow relative to him then he will use his instinct to determine to consider if he should guard that player as there is an uncertainty for him. In this example the important point is the properties are relative to the player and there is a degree for the height and playing skill for the rival player. Fuzzy logic provides a deterministic way for this uncertain situation.
There are some steps to process the fuzzy logic (Figure-1). These steps are; firstly fuzzification where crisp inputs get converted to fuzzy inputs secondly these inputs get processed with fuzzy rules to create fuzzy output and lastly defuzzification which results with degree of result as in fuzzy logic there can be more than one result with different degrees.
Figure 1 – Fuzzy Process Steps (David M. Bourg P.192)
To exemplify the fuzzy process steps, the previous basketball game situation could be used. As mentioned in the example the rival player is tall with 1.87 meters which is quite tall relative to our player and can dribble with 3 m/s which is slow relative to our player. Addition to these data some rules are needed to consider which are called fuzzy rules such as;
if player is short but not fast then guard,
if player is fast but not short then don’t guard
If player is tall then don’t guard
If player is average tall and average fast guard
Figure 2 – how tall
Figure 3- how fast
According to the rules and the input data an output will be created by fuzzy system such as; the degree for guard is 0.7, degree for sometimes guard is 0.4 and never guard is 0.2.
Figure 4-output fuzzy sets
On the last step, defuzzication, is using for creating a crisp output which is a number which may determine the energy that we should use to guard the player during game. The centre of mass is a common method to create the output. On this phase the weights to calculate the mean point is totally depends on the implementation. On this application it is considered to give high weight to guard or not guard but low weight given to sometimes guard. (David M. Bourg, 2004)
Figure 5- fuzzy output (David M. Bourg P.204)
Output = [0.7 * (-10) + 0.4 * 1 + 0.2 * 10] / (0.7 + 0.4 + 0.2) ≈ -3.5
As a result fuzzy logic is using under uncertainty to make a decision and to find out the degree of decision. The problem of fuzzy logic is as the number of inputs increase the number of rules increase exponential.
For more information and its possible application in a game I wrote a little article check this out
To build off of chaos' answer, a formal logic is nothing but an inductively defined set that maps sentences to a valuation. At least, that's how a model theorist thinks of logic. In the case of a sentential boolean logic:
(basis clause) For all A, v(A) in {0,1}
(iterative) For the following connectives,
v(!A) = 1 - v(A)
v(A & B) = min{v(A), v(B)}
v(A | B) = max{v(A), v(B)}
(closure) All sentences in a boolean sentential logic are evaluated per above.
A fuzzy logic changes would be inductively defined:
(basis clause) For all A, v(A) between [0,1]
(iterative) For the following connectives,
v(!A) = 1 - v(A)
v(A & B) = min{v(A), v(B)}
v(A | B) = max{v(A), v(B)}
(closure) All sentences in a fuzzy sentential logic are evaluated per above.
Notice the only difference in the underlying logic is the permission to evaluate a sentence as having the "truth value" of 0.5. An important question for a fuzzy logic model is the threshold that counts for truth satisfaction. This is to ask: for a valuation v(A), for what value D it is the case the v(A) > D means that A is satisfied.
If you really want to found out more about non-classical logics like fuzzy logic, I would recommend either An Introduction to Non-Classical Logic: From If to Is or Possibilities and Paradox
Putting my coder hat back on, I would be careful with the use of fuzzy logic in real world programming, because of the tendency for a fuzzy logic to be undecidable. Maybe it's too much complexity for little gain. For instance a supervaluational logic may do just fine to help a program model vagueness. Or maybe probability would be good enough. In short, I need to be convinced that the domain model dovetails with a fuzzy logic.
Maybe an example clears up what the benefits can be:
Let's say you want to make a thermostat and you want it to be 24 degrees.
This is how you'd implement it using boolean logic:
Rule1: heat up at full power when
it's colder than 21 degrees.
Rule2:
cool down at full power when it's
warmer than 27 degrees.
Such a system will only once and a while be 24 degrees, and it will be very inefficient.
Now, using fuzzy logic, it would be like something like this:
Rule1: For each degree that it's colder than 24 degrees, turn up the heater one notch (0 at 24).
Rule2: For each degree that it's warmer than 24 degress, turn up the cooler one notch (0 at 24).
This system will always be somewhere around 24 degrees, and it only once and will only once and a while make a tiny adjustment. It will also be more energy-efficient.
Well, you could read the works of Bart Kosko, one of the 'founding fathers'. 'Fuzzy Thinking: The New Science of Fuzzy Logic' from 1994 is readable (and available quite cheaply secondhand via Amazon). Apparently, he has a newer book 'Noise' from 2006 which is also quite approachable.
Basically though (in my paraphrase - not having read the first of those books for several years now), fuzzy logic is about how to deal with the world where something is perhaps 10% cool, 50% warm, and 10% hot, where different decisions may be made on the degree to which the different states are true (and no, it wasn't entirely an accident that those percentages don't add up to 100% - though I'd accept correction if needed).
A very good explanation, with a help of Fuzzy Logic Washing Machines.
I know what you mean about it being difficult to go from concept to code. I'm writing a scoring system that looks at the values of sysinfo and /proc on Linux systems and comes up with a number between 0 and 10, 10 being the absolute worst. A simple example:
You have 3 load averages (1, 5, 15 minute) with (at least) three possible states, good, getting bad, bad. Expanding that, you could have six possible states per average, adding 'about to' to the three that I just noted. Yet, the result of all 18 possibilities can only deduct 1 from the score. Repeat that with swap consumed, actual VM allocated (committed) memory and other stuff .. and you have one big bowl of conditional spaghetti :)
Its as much a definition as it is an art, how you implement the decision making process is always more interesting than the paradigm itself .. whereas in a boolean world, its rather cut and dry.
It would be very easy for me to say if load1 < 2 deduct 1, but not very accurate at all.
If you can teach a program to do what you would do when evaluating some set of circumstances and keep the code readable, you have implemented a good example of fuzzy logic.
Fuzzy Logic is a problem-solving methodology that lends itself to implementation in systems ranging from simple, small, embedded micro-controllers to large, networked, multi-channel PC or workstation-based data acquisition and control systems. It can be implemented in hardware, software, or a combination of both. Fuzzy Logic provides a simple way to arrive at a definite conclusion based upon vague, ambiguous, imprecise, noisy, or missing input information. Fuzzy Logic approach to control problems mimics how a person would make decisions, only much faster.
Fuzzy logic has proved to be particularly useful in expert system and other artificial intelligence applications. It is also used in some spell checkers to suggest a list of probable words to replace a misspelled one.
To learn more, just check out: http://en.wikipedia.org/wiki/Fuzzy_logic.
The following is sort of an empirical answer.
A simple (possibly simplistic answer) is that "fuzzy logic" is any logic that returns values other than straight true / false, or 1 / 0. There are a lot of variations on this and they tend to be highly domain specific.
For example, in my previous life I did search engines that used "content similarity searching" as opposed to then common "boolean search". Our similarity system used the Cosine Coefficient of weighted-attribute vectors representing the query and the documents and produced values in the range 0..1. Users would supply "relevance feedback" which was used to shift the query vector in the direction of desirable documents. This is somewhat related to the training done in certain AI systems where the logic gets "rewarded" or "punished" for results of trial runs.
Right now Netflix is running a competition to find a better suggestion algorithm for their company. See http://www.netflixprize.com/. Effectively all of the algorithms could be characterized as "fuzzy logic"
Fuzzy logic is calculating algorithm based on human like way of thinking. It is particularly useful when there is a large number of input variables. One online fuzzy logic calculator for two variables input is given:
http://www.cirvirlab.com/simulation/fuzzy_logic_calculator.php