I need to compare a query bit sequence with a database of up to a million bit sequences. All bit sequences are 100 bits long. I need the lookup to be as fast as possible. Are there any packages out there for fast determination of the similarity between two bit sequences? --Edit-- The bit sequences are position sensitive.
I have seen a possible algorithm on Bit Twiddling Hacks but if there is a ready made package that would be better.
If the database is rather static, you may want to build a tree data structure on it.
Search the tree recursively or in multiple threads and per search keep an actual difference variable. If the actual difference becomes greater than what you would consider 'similar', abort the search.
E.g. Suppose we have the following tree:
root
0 1
0 1 0 1
0 1 0 1 0 1 0 1
If you want to look for patterns similar to 011, and only want to allow 1 different bit at most, search like this (recursively or multi-threaded):
Start at the root
Take the left branch (0), this is similar, so difference is still 0
Take the left branch (0), this is different, so difference becomes 1, which is still acceptable
take the left branch (0), this is different, so difference becomes 2, which is too high. Abort looking in this branch.
take the right branch (1), this is equal, so difference remains 1, continue to search in this branch (not shown here)
Take the right branch (1), this is equal, so difference remains 0, go on
take the left branch (0), this is different, so difference becomes 1, which is still acceptable, go on.
This goes on until you have found your bit patterns.
If your bit patterns are more dynamic and being updated in your application, you will have to update the tree.
If memory is a problem, consider going to 64-bit.
If you want to look up the, let's say 50, most matching patterns, and we can assume that the input data set is rather static (or can be dynamically updated), you can repeat the initial phase of the previous comment, so:
For every bit pattern, count the bits.
Store the bit patterns in a multi_map (if you use STL, Java probably has something similar)
Then, use the following algorithm:
Make 2 collections: one for storing the found patterns, one for storing possibly good patterns (this second collection should probably be map, mapping 'distances' to patterns)
Take your own pattern and count the bits, assume this is N
Look in the multimap at index N, all these patterns will have the same sum, but not necessarily be completely identical
Compare all the patterns at index N. If they are equal store the result in the first collection. If they are not equal, store the result in the second collection/map, using the difference as key.
Look in the multimap at index N-1, all these patterns will have a distance of 1 or more
Compare all the patterns at index N-1. If they have a distance of 1, store them in the first collection. If they have a larger distance, store the result in the second collection/map, using the difference as key.
Repeat for index N+1
Now look in the second collection/map and see if there is something stored with distance 1. If it is, remove them from the second collection/map and store them in the first collection.
Repeat this for distance 2, distance 3, ... until you have enough patterns.
If the number of required patterns is not too big, and the average distance is also not too big, then the number of real compares between patterns is probably only a few %.
Unfortunately, since the patterns will be distributed using a Gaussian curve, there will still be quite some patterns to check. I didn't do a mathematical check on it, but in practice, if you don't want too many patterns out of the millions, and the average distance is not too far, you should be able to find the set of most-close patterns by checking only a few percent of the total bit patterns.
Please keep me updated of your results.
I came up with a second alternative.
For every bit pattern of the million ones count the number of bits and store the bit patterns in an STL multi_map (if you're writing in C++).
Then count the number of bits in your pattern. Suppose you have N bits set in your bit pattern.
If you now want to allow at most D differences, look up all the bit patterns in the multi_map having N-D, N-D+1, ..., N-1, N, N+1, ... N+D-1, N+D bits.
Unfortunately, the division of bit patterns in the multi_map will follow a Gaussian pattern, which means that in practice you will still have to compare quite some bit patterns.
(Originally I thought this could be solved by counting even 0's and uneven 1's but this isn't true.)
Assuming that you want to allow 1 difference, you have to look up 3 slots in the multi_map out of the 100 possible slots, leaving you with 3% of the actual bit patterns to do a full compare.
Related
I am using neo4j to calculate some statistics on a data set. For that I am often using sum on a floating point value. I am getting different results depending on the circumstances. For example, a query that does this:
...
WITH foo
ORDER BY foo.fooId
RETURN SUM(foo.Weight)
Returns different result than the query that simply does the sum:
...
RETURN SUM(foo.Weight)
The differences are miniscule (293.07724195098984 vs 293.07724195099007). But it is enough to make simple equality checks fail. Another example would be a different instance of the database, loaded with the same data using the same loading process can produce the same issue (the dbs might not be 1:1, the load order of some relations might be different). I took the raw values that neo4j sums (by simply removing the SUM()) and verified that they are the same in all cases (different dbs and ordered/not ordered).
What are my options here? I don't mind losing some precision (I already tried to cut down the precision from 15 to 12 decimal places but that did not seem to work), but I need the results to match up.
Because of rounding errors, floats are not associative. (a+b)+c!=a+(b+c).
The result of every operation is rounded to fit the floats coding constraints and (a+b)+c is implemented as round(round(a+b) +c) while a+(b+c) as round(a+round(b+c)).
As an obvious illustration, consider the operation (2^-100 + 1 -1). If interpreted as a (2^-100 + 1)-1, it will return 0, as 1+2^-100 would require a precision too large for floats or double coding in IEEE754 and can only be coded as 1.0. While (2^-100 +(1-1)) correctly returns 2^-100 that can be coded by either floats or doubles.
This is a trivial example, but these rounding errors may exist after every operation and explain why floating point operations are not associative.
Databases generally do not return data in a garanteed order and depending on the actual order, operations will be done differently and that explains the behaviour that you have.
In general, for this reason, it not a good idea to do equality comparison on floats. Generally, it is advised to replace a==b by abs(a-b) is "sufficiently" small.
"sufficiently" may depend on your algorithm. float are equivalent to ~6-7 decimals and doubles to 15-16 decimals (and I think that it is what is used on your DB). Depending on the number of computations, you may have the last 1--3 decimals affected.
The best is probably to use
abs(a-b)<relative-error*max(abs(a),abs(b))
where relative-error must be adjusted to your problem. Probably something around 10^-13 can be correct, but you must experiment, as rounding errors depends on the number of computations, on the dispersion of the values and on what you may consider as "equal" for you problem.
Look at this site for a discussion on comparison methods. And read What Every Computer Scientist Should Know About Floating-Point Arithmetic by David Goldberg that discusses, among others, these problems.
This question is related to my previous question
Is it possible to get a legit range info when using a SMT constraint with Z3
So it seems that "efficiently" finding the maximum range info is not proper, given typical 32-bit vectors and so on. But on the other hand, I am thinking whether it is feasible to find certain "sub-maximum" range info, which hopefully becomes more efficient. Another thing is that we may want to have certain "safe" guarantee, say for all elements in the sub-maximum range, they must satisfy the constraint, but there could exist some other solutions that would satisfy the constraint as well.
I am currently exploring whether model counting technique could make sense in this setting. Any thoughts would be appreciated very much. Thanks.
General case
This is not just a question of efficiency. Consider a problem where you have two variables a and b, and a single constraint:
a != b
What's the range of b? (maximum or otherwise?)
You can say all values are legitimate. But that would be wrong, as obviously the choice of a impacts the choice of b. The more variables you have around, the more complicated the problem will become. I don't think the problem is even well defined in this case, so searching for a solution (efficient or otherwise) doesn't make much sense.
Single variable assumption
Having said that, I think you can come up with a solution if you assume there's precisely one variable in the system. (Or, alternatively, if you fix all the other variables to some predefined constants.) If you're willing to go down this path, then you can implement a binary search algorithm to find a reasonably sized range by simply proving the quantified formula
Exists([b], And(b >= minBound, b <= maxBound, Not(constraints)))
Once you get unsat for this, you have your range. So long as you get sat, you can adjust your minBound/maxBound to search within smaller ranges. In the worst case, this can turn into a linear walk, but you can "cut-down" this search by making sure you go down a significant size in each step. That could be a parameter to the whole search, depending on how large you want your intervals to be. It'll have to be a choice between trying to find a maximal range, and how long you want to spend in this search. Of course, if you cut-down too much, you can miss a big interval, but that's the cost of efficiency.
Example1 (Good case) There's a single constraint that says b != 5. Then your search will be quick and depending on which branch you'll go, you'll either find [0, 4] or [6, 255] assuming 8-bit words.
Example2 (Bad case) There's a single constraint that says b is even. Then your search will exhibit worst-case behavior, and if your "cut-down" size is 1, you'll possibly iterate 255 times before you settle down on [0, 0]; assuming z3 gives you the maximum odd number in each call.
I hope that illustrates the point. In general, though, I'd assume you'd be closer to the "good case" for practical applications and even if your cut-down size is minimal you can most likely converge in a few iterations. Of course, this entirely depends on your problem domain, but I'd expect it to hold for software analysis in general.
I am working on a data set of more than 22,000 records, and when I tried it with the apriori model, it's taking way too much time even for small number of records like 20. Is there a problem in my code or Is there a faster way to convert the asscocians into a list quickly? The code I used is below.
for i in range(0, 20):
transactions.append([str(dataset.values[i,j]) for j in range(0, 543)])
from apyori import apriori
associations = apriori(transactions, min_support=0.004, min_confidence=0.3, min_lift=3, min_length=2)
result = list(associations)
It's difficult to assess without your data, but the complexity of Apriori is based on a number of factors, including your support threshold, number of transactions, number of items, average/max transaction length, etc.
In cases where even a small number of transactions is taking a long time to run it's often a matter of too low of a minimum support. When support is very low (near 0) the algorithm is effectively still brute forcing, since it has to look at all possible combinations of items, of every length. This is the equivalent of a mathematical power set, which is exponential. For just 41 items you're actually trying 2^41 -1 possible combinations, which is just over 1.1 TRILLION possibilities.
I recommend starting with a "high" min_support at first (e.g. 0.20) and then working your way down slowly. It's easier to test things that take seconds at first than ones that'll take a long time.
Other important note: There is no min_length parameter in Apyori. I'm not sure where everyone's getting that from (you're not alone in thinking there is one), unless it's this one random blog post I found. The parameters are as follows (straight from the code):
Keyword arguments:
min_support -- The minimum support of relations (float).
min_confidence -- The minimum confidence of relations (float).
min_lift -- The minimum lift of relations (float).
max_length -- The maximum length of the relation (integer).
For what it's worth, I wrote unofficial docs for Apyori that can be found here.
I'm building an app using database.
I have a words table and everytime user types something, this app will record and update word the database.
And the frequency field will be auto increase after user enter one matched word.
But the trouble is user type day by day and i afraid the search performance will be reduce after times and also the Int field will reach to the limit (max limit Int) someday.
So, i limit the database to around less than 50.000 records.
I delete less-used records after a certain time.
But i don't know how to deal with frequency Int field of each word?
How to know exactly frequency usage of each word without increasing the field forever?
I recommend that you use a logarithmic scale for the frequency values. That's what is often done in situations like this. See Wikipedia to learn about logarithmic scales.
For example, if you have a word MAN that has a frequency of 15, the value you store in the database would be log(15) ~= 1.17609125906.
If you then find 4 new occurrences of MAN, then you want to add 4 to the field. You cannot add the log values directly because log(x)+log(y)=log(x*y). (See the Logarithm Rules section of this article for more information on log rules.)
Instead -- assuming you use a base 10 logarithm, you would use this formula:
SET frequency = log(10^frequency+4)
Depending on the length of your words, the few bytes for the frequency don't matter. With an unsigned four bytes integer, you can count up to more than two billion, which is way above the number of words what the user can type in in their whole lifespan.
So may want to go for two or three bytes, but the savings may be negligible.
Anyway, there are the following approaches for preventing overflow:
You can detect it, and then undo the operations, scale everything down by some factor of two, and then redo.
You can periodically check all your numbers and do the scaling when approaching the limit.
You can do a probabilistic update like below.
Probabilistic update
Instead of simply incrementing the frequency every time by one, you do it only with a probability which gets lower and lower as the counter grows. For example, you can do the increment with a probability of 1.0 / (oldValue + 1) or 2 ** -oldValue. The latter leads to a logarithmic growth, but, unlike the idea in the other answer, it works.
There are obviously some disadvantages due to the randomness and precision loss, but when all you care about is the relative frequency, it should be good enough.
I have an application in which I have to store a couple of millions of integers, I have to store them in a Look up table, obviously I cannot store such amount of data in memory and in my requirements I am very limited I have to store the data in an embebedded system so I am very limited in the space, so I would like to ask you about recommended methods that I can use for the reduction of the look up table. I cannot use function approximation such as neural networks, the values needs to be in a table. The range of the integers is not known at the moment. When I say integers I mean a 32 bit value.
Basically the idea is use some copmpression method to reduce the amount of memory but without losing many precision. This thing needs to run in hardware so the computation overhead cannot be very high.
In my algorithm I have to access to one value of the table do some operations with it and after update the value. In the end what I should have is a function which I pass an index to it and then I get a value, and after I have to use another function to write a value in the table.
I found one called tile coding , this one is based on several look up tables, does anyone know any other method?.
Thanks.
I'd look at the types of numbers you need to store and pull out the information that's common for many of them. For example, if they're tightly clustered, you can take the mean, store it, and store the offsets. The offsets will have fewer bits than the original numbers. Or, if they're more or less uniformly distributed, you can store the first number and then store the offset to the next number.
It would help to know what your key is to look up the numbers.
I need more detail on the problem. If you cannot store the real value of the integers but instead an approximation, that means you are going to reduce (throw away) some of the data (detail), correct? I think you are looking for a hash, which can be an artform in itself. For example say you have 32 bit values, one hash would be to take the 4 bytes and xor them together, this would result in a single 8 bit value, reducing your storage by a factor of 4 but also reducing the real value of original data. Typically you could/would go further and perhaps and only use a few of those 8 bits , say the lower 4 and reduce the value further.
I think my real problem is either you need the data or you dont, if you need the data you need to compress it or find more memory to store it. If you dont, then use a hash of some sort to reduce the number of bits until you reach the amount of memory you have for storage.
Read http://www.cs.ualberta.ca/~sutton/RL-FAQ.html
"Function approximation" refers to the
use of a parameterized functional form
to represent the value function
(and/or the policy), as opposed to a
simple table."
Perhaps that applies. Also, update your question with additional facts -- don't merely answer in the comments.
Edit.
A bit array can easily store a bit for each of your millions of numbers. Let's say you have numbers in the range of 1 to 8 million. In a single megabyte of storage you can have a 1 bit for each number in your set and a 0 for each number not in your set.
If you have numbers in the range of 1 to 32 million, you'll require 4Mb of memory for a big table of all 32M distinct numbers.
See my answer to Modern, high performance bloom filter in Python? for a Python implementation of a bit array of unlimited size.
If you are merely looking for the presence of the number in question a bloom filter, might be what you are looking for. Honestly though your question is fairly vague and confusing. It would help to explain what Q values are, and what you do with them once you find them in the table.
If your set of integers is homongenous, then you could try a hash table, because there is a trick you can use to cut the size of the stored integers, in your case, in half.
Assume the integer, n, because its set is homogenous can be the hash. Assume you have 0x10000 (16k) buckets. Each bucket index, iBucket = n&FFFF. Each item in a bucket need only store 16 bits, since the first 16 bits are the bucket index. The other thing you have to do to keep the data small is to put the count of items in the bucket, and use an array to hold the items in the bucket. Using a linked list will be too large and slow. When you iterate the array looking for a match, remember you only need to compare the 16 bits that are stored.
So assuming a bucket is a pointer to the array and a count. On a 32 bit system, this is 64 bits max. If the number of ints was small enough we might be able to do some fancy things and use 32 bits for a bucket. 16k * 8 bytes = 524k, 2 million shorts = 4mb. So this gets you a method to lookup the ints and about 40% compression.