I want to store lots of data so that
they can be accessed by an index,
each data is just yes and no (so probably one bit is enough for each)
I am looking for the data structure which has the highest performance and occupy least space.
probably storing data in a flat memory, one bit per data is not a good choice on the other hand using different type of tree structures still use lots of memory (e.g. pointers in each node are required to make these tree even though each node has just one bit of data).
Does anyone have any Idea?
What's wrong with using a single block of memory and either storing 1 bit per byte (easy indexing, but wastes 7 bits per byte) or packing the data (slightly trickier indexing, but more memory efficient) ?
Well in Java the BitSet might be a good choice http://download.oracle.com/javase/6/docs/api/java/util/BitSet.html
If I understand your question correctly you should store them in an unsigned integer where you assign each value to a bit of the integer (flag).
Say you represent 3 values and they can be on or off. Then you assign the first to 1, the second to 2 and the third to 4. Your unsigned int can then be 0,1,2,3,4,5,6 or 7 depending on which values are on or off and you check the values using bitwise comparison.
Depends on the language and how you define 'index'. If you mean that the index operator must work, then your language will need to be able to overload the index operator. If you don't mind using an index macro or function, you can access the nth element by dividing the given index by the number of bits in your type (say 8 for char, 32 for uint32_t and variants), then return the result of arr[n / n_bits] & (1 << (n % n_bits))
Have a look at a Bloom Filter: http://en.wikipedia.org/wiki/Bloom_filter
It performs very well and is space-efficient. But make sure you read the fine print below ;-): Quote from the above wiki page.
An empty Bloom filter is a bit array
of m bits, all set to 0. There must
also be k different hash functions
defined, each of which maps or hashes
some set element to one of the m array
positions with a uniform random
distribution. To add an element, feed
it to each of the k hash functions to
get k array positions. Set the bits at
all these positions to 1. To query for
an element (test whether it is in the
set), feed it to each of the k hash
functions to get k array positions. If
any of the bits at these positions are
0, the element is not in the set – if
it were, then all the bits would have
been set to 1 when it was inserted. If
all are 1, then either the element is
in the set, or the bits have been set
to 1 during the insertion of other
elements. The requirement of designing
k different independent hash functions
can be prohibitive for large k. For a
good hash function with a wide output,
there should be little if any
correlation between different
bit-fields of such a hash, so this
type of hash can be used to generate
multiple "different" hash functions by
slicing its output into multiple bit
fields. Alternatively, one can pass k
different initial values (such as 0,
1, ..., k − 1) to a hash function that
takes an initial value; or add (or
append) these values to the key. For
larger m and/or k, independence among
the hash functions can be relaxed with
negligible increase in false positive
rate (Dillinger & Manolios (2004a),
Kirsch & Mitzenmacher (2006)).
Specifically, Dillinger & Manolios
(2004b) show the effectiveness of
using enhanced double hashing or
triple hashing, variants of double
hashing, to derive the k indices using
simple arithmetic on two or three
indices computed with independent hash
functions. Removing an element from
this simple Bloom filter is
impossible. The element maps to k
bits, and although setting any one of
these k bits to zero suffices to
remove it, this has the side effect of
removing any other elements that map
onto that bit, and we have no way of
determining whether any such elements
have been added. Such removal would
introduce a possibility for false
negatives, which are not allowed.
One-time removal of an element from a
Bloom filter can be simulated by
having a second Bloom filter that
contains items that have been removed.
However, false positives in the second
filter become false negatives in the
composite filter, which are not
permitted. In this approach re-adding
a previously removed item is not
possible, as one would have to remove
it from the "removed" filter. However,
it is often the case that all the keys
are available but are expensive to
enumerate (for example, requiring many
disk reads). When the false positive
rate gets too high, the filter can be
regenerated; this should be a
relatively rare event.
Related
The problem is to find out all the sequences of length k in a given DNA sequence which occur more than once. I found a approach of using a rolling hash function, where for each sequence of length k, hash is computed and is stored in a map. To check if the current sequence is a repetition, we compute it's hash and check if the hash already exist in the hash map. If yes, then we include this sequence in our result, otherwise add it to the hash map.
Rolling hash here means, when moving on to the next sequence by sliding the window by one, we use the hash of previous sequence in a way that we remove the contribution of the first character of previous sequence and add the contribution of the newly added char i.e. the last character of the new sequence.
Input: AAAAACCCCCAAAAACCCCCCAAAAAGGGTTT
and k=10
Answer: {AAAAACCCCC, CCCCCAAAAA}
This algorithm looks perfect, but I can't go about making a perfect hash function so that collisions are avoided. It would be a great help if somebody can explain how to make a perfect hash under any circumstance and most importantly in this case.
This is actually a research problem.
Let's come to terms with some facts
Input = N, Input length = |N|
You have to move a size k, here k=10, sliding window over the input. Therefore you must live with O(|N|) or more.
Your rolling hash is a form of locality sensitive deterministic hashing, the downside of deterministic hashing is the benefit of hashing is greatly diminished as the more often you encounter similar strings the harder it will be to hash
The longer your input the less effective hashing will be
Given these facts "rolling hashes" will soon fail. You cannot design a rolling hash that will even work for 1/10th of a chromosome.
SO what alternatives do you have?
Bloom Filters. They are much more robust than simple hashing. The downside is sometimes they have a false positives. But this can be mitigated by using several filters.
Cuckoo Hashes similar to bloom filters, but use less memory and have locality sensitive "hashing" and worst case constant lookup time
Just stick every suffix in a suffix trie. Once this is done, just output every string at depth 10 that also has atleast 2 children with one of the children being a leaf.
Improve on the suffix trie with a suffix tree. Lookup is not as straightforward but memory consumption is less.
My favorite the FM-Index. In my opinion the cleanest solution uses the Burrows Wheeler Transform. This technique is also used in industryu tools like Bowtie and BWA
Heads-up: This is not a general solution, but a good trick that you can use when k is not large.
The trick is to encrypt the sequence into an integer by bit manipulation.
If your input k is relatively small, let's say around 10. Then you can encrypt your DNA sequence in an int via bit manipulation. Since for each character in the sequence, there are only 4 possibilities, A, C, G, T. You can simply make your own mapping which uses 2 bits to represent a letter.
For example: 00 -> A, 01 -> C, 10 -> G, 11 -> T.
In this way, if k is 10, you won't need a string with 10 characters as hash key. Instead, you can only use 20 bits in an integer to represent the previous key string.
Then when you do your rolling hash, you left shift the integer that stores your previous sequence for 2 bits, then use any bit operations like |= to set the last two bits with your new character. And remember to clear the 2 left most bits that you just shifted, meaning you are removing them from your sliding window.
By doing this, a string could be stored in an integer, and using that integer as hash key might be nicer and cheaper in terms of the complexity of the hash function computation. If your input length k is slightly longer than 16, you may be able to use a long value. Otherwise, you might be able to use a bitset or a bitarray. But to hash them becomes another issue.
Therefore, I'd say this solution is a nice attempt for this problem when the sequence length is relatively small, i.e. can be stored in a single integer or long integer.
You can build the suffix array and the LCP array. Iterate through the LCP array, every time you see a value greater or equal to k, report the string referred to by that position (using the suffix array to determine where the substring comes from).
After you report a substring because the LCP was greater or equal to k, ignore all following values until reaching one that is less than k (this avoids reporting repeated values).
The construction of both, the suffix array and the LCP, can be done in linear time. So overall the solution is linear with respect to the size of the input plus output.
What you could do is use Chinese Remainder Theorem and pick several large prime moduli. If you recall, CRT means that a system of congruences with coprime moduli has a unique solution mod the product of all your moduli. So if you have three moduli 10^6+3, 10^6+33, and 10^6+37, then in effect you have a modulus of size 10^18 more or less. With a sufficiently large modulus, you can more or less disregard the idea of a collision happening at all---as my instructor so beautifully put it, it's more likely that your computer will spontaneously catch fire than a collision to happen, since you can drive that collision probability to be as arbitrarily small as you like.
Imagine you have N distinct people and that you have a record of where these people are, exactly M of these records to be exact.
For example
1,50,299
1,2,3,4,5,50,287
1,50,299
So you can see that 'person 1' is at the same place with 'person 50' three times. Here M = 3 obviously since there's only 3 lines. My question is given M of these lines, and a threshold value (i.e person A and B have been at the same place more than threshold times), what do you suggest the most efficient way of returning these co-occurrences?
So far I've built an N by N table, and looped through each row, incrementing table(N,M) every time N co occurs with M in a row. Obviously this is an awful approach and takes 0(n^2) to O(n^3) depending on how you implent. Any tips would be appreciated!
There is no need to create the table. Just create a hash/dictionary/whatever your language calls it. Then in pseudocode:
answer = []
for S in sets:
for (i, j) in pairs from S:
count[(i,j)]++
if threshold == count[(i,j)]:
answer.append((i,j))
If you have M sets of size of size K the running time will be O(M*K^2).
If you want you can actually keep the list of intersecting sets in a data structure parallel to count without changing the big-O.
Furthermore the same algorithm can be readily implemented in a distributed way using a map-reduce. For the count you just have to emit a key of (i, j) and a value of 1. In the reduce you count them. Actually generating the list of sets is similar.
The known concept for your case is Market Basket analysis. In this context, there are different algorithms. For example Apriori algorithm can be using for your case in a specific case for sets of size 2.
Moreover, in these cases to finding association rules with specific supports and conditions (which for your case is the threshold value) using from LSH and min-hash too.
you could use probability to speed it up, e.g. only check each pair with 1/50 probability. That will give you a 50x speed up. Then double check any pairs that make it close enough to 1/50th of M.
To double check any pairs, you can either go through the whole list again, or you could double check more efficiently if you do some clever kind of reverse indexing as you go. e.g. encode each persons row indices into 64 bit integers, you could use binary search / merge sort type techniques to see which 64 bit integers to compare, and use bit operations to compare 64 bit integers for matches. Other things to look up could be reverse indexing, binary indexed range trees / fenwick trees.
I have an operation A * A -> A, which is commutative and associative. This means the order I apply it in doesn't matter, as long as I use the same elements. Nice.
I have to apply it to a list of values. To be more precise, I have to use it as the operation to accumulate the values of the list. So far, so good.
I then have a series of requests to add an element to the list, or erase it from the list. After each insertion or deletion, I have to return the new accumulated value for the new list. Simple, right?
The problem is I don't have an inverse; that is no operation '/' able to remove b if I only know a * b and tell me the other operand must have been a. (in fact, there isn't even an identity element)
So, my only obvious option is to accumulate again at every deletion -in linear time.
Can I do better? I've thought a lot about it.
And the answer is, of course I can... if I really want: I need to implement a custom binary tree, maybe a red/black one to have good worst case guarantees. Have next to the value an additional cache storing the result of the whole subtree.
cache = value * left.cache * right.cache
Maintain this invariant after every operation; then the root cache is the result.
However, "implement a custom R/B tree while maintaining an additional invariant" isn't something I'm particularly comfortable at doing. Well I would do it, but not swear by its correctness. Plus, the constant before the log would probably be significant. It seems pretty unwieldy, to do a simple thing like keeping track of an accumulation.
Does anyone see a better solution?
For completeness: the operation is a union of filters. A filter is a couple (code, mask), and a value "passes the filter" if (C bitwise operators) (value ^ code) & mask == 0; that is, if its bit corresponding to bits set in mask are equal to the corresponding bits in code. The union therefore sets to 0 (ignored) the bits where masks or codes differ, and keeps the ones which are the same.
Bonus appreciation to anyone finding a way to exploit the specific properties of the operation to get a solution more efficient than it is possible for the general problem I abstracted! ;-)
For your specific problem you could keep track for each bit x:
The total number of times that bit x is set to 1 in a mask
The total number of times that bit x is set to 1 in a mask and bit x of code is equal to 0
The total number of times that bit x is set to 1 in a mask and bit x of code is equal to 1
With these 3 counts (for each bit) it is straightforward to compute the union of all the filters.
The complexity is O(R) (where R is the number of bits in mask) to add or remove a filter.
I am keen to try and implement minhashing to find near duplicate content. http://blog.cluster-text.com/tag/minhash/ has a nice write up, but there the question of just how many hashing algorithms you need to run across the shingles in a document to get reasonable results.
The blog post above mentioned something like 200 hashing algorithms. http://blogs.msdn.com/b/spt/archive/2008/06/10/set-similarity-and-min-hash.aspx lists 100 as a default.
Obviously there is an increase in the accuracy as the number of hashes increases, but how many hash functions is reasonable?
To quote from the blog
It is tough to get the error bar on our similarity estimate much
smaller than [7%] because of the way error bars on statistically
sampled values scale — to cut the error bar in half we would need four
times as many samples.
Does this mean that mean that decreasing the number of hashes to something like 12 (200 / 4 / 4) would result in an error rate of 28% (7 * 2 * 2)?
One way to generate 200 hash values is to generate one hash value using a good hash algorithm and generate 199 values cheaply by XORing the good hash value with 199 sets of random-looking bits having the same length as the good hash value (i.e. if your good hash is 32 bits, build a list of 199 32-bit pseudo random integers and XOR each good hash with each of the 199 random integers).
Do not simply rotate bits to generate hash values cheaply if you are using unsigned integers (signed integers are fine) -- that will often pick the same shingle over and over. Rotating the bits down by one is the same as dividing by 2 and copying the old low bit into the new high bit location. Roughly 50% of the good hash values will have a 1 in the low bit, so they will have huge hash values with no prayer of being the minimum hash when that low bit rotates into the high bit location. The other 50% of the good hash values will simply equal their original values divided by 2 when you shift by one bit. Dividing by 2 does not change which value is smallest. So, if the shingle that gave the minimum hash with the good hash function happens to have a 0 in the low bit (50% chance of that) it will again give the minimum hash value when you shift by one bit. As an extreme example, if the shingle with the smallest hash value from the good hash function happens to have a hash value of 0, it will always have the minimum hash value no matter how much you rotate the bits. This problem does not occur with signed integers because minimum hash values have extreme negative values, so they tend to have a 1 at the highest bit followed by zeros (100...). So, only hash values with a 1 in the lowest bit will have a chance at being the new lowest hash value after rotating down by one bit. If the shingle with minimum hash value has a 1 in the lowest bit, after rotating down one bit it will look like 1100..., so it will almost certainly be beat out by a different shingle that has a value like 10... after the rotation, and the problem of the same shingle being picked twice in a row with 50% probability is avoided.
Pretty much.. but 28% would be the "error estimate", meaning reported measurements would frequently be inaccurate by +/- 28%.
That means that a reported measurement of 78% could easily come from only 50% similarity..
Or that 50% similarity could easily be reported as 22%. Doesn't sound accurate enough for business expectations, to me.
Mathematically, if you're reporting two digits the second should be meaningful.
Why do you want to reduce the number of hash functions to 12? What "200 hash functions" really means is, calculate a decent-quality hashcode for each shingle/string once -- then apply 200 cheap & fast transformations, to emphasise certain factors/ bring certain bits to the front.
I recommend combining bitwise rotations (or shuffling) and an XOR operation. Each hash function can combined rotation by some number of bits, then XORing by a randomly generated integer.
This both "spreads" the selectivity of the min() function around the bits, and as to what value min() ends up selecting for.
The rationale for rotation, is that "min(Int)" will, 255 times out of 256, select only within the 8 most-significant bits. Only if all top bits are the same, do lower bits have any effect in the comparison.. so spreading can be useful to avoid undue emphasis on just one or two characters in the shingle.
The rationale for XOR is that, on it's own, bitwise rotation (ROTR) can 50% of the time (when 0 bits are shifted in from the left) converge towards zero, and that would cause "separate" hash functions to display an undesirable tendency to coincide towards zero together -- thus an excessive tendency for them to end up selecting the same shingle, not independent shingles.
There's a very interesting "bitwise" quirk of signed integers, where the MSB is negative but all following bits are positive, that renders the tendency of rotations to converge much less visible for signed integers -- where it would be obvious for unsigned. XOR must still be used in these circumstances, anyway.
Java has 32-bit hashcodes builtin. And if you use Google Guava libraries, there are 64-bit hashcodes available.
Thanks to #BillDimm for his input & persistence in pointing out that XOR was necessary.
What you want can be be easily obtained from universal hashing. Popular textbooks like Corman et al as very readable information in section 11.3.3 pp 265-268. In short, you can generate family of hash functions using following simple equation:
h(x,a,b) = ((ax+b) mod p) mod m
x is key you want to hash
a is any odd number you can choose between 1 to p-1 inclusive.
b is any number you can choose between 0 to p-1 inclusive.
p is a prime number that is greater than max possible value of x
m is a max possible value you want for hash code + 1
By selecting different values of a and b you can generate many hash codes that are independent of each other.
An optimized version of this formula can be implemented as follows in C/C++/C#/Java:
(unsigned) (a*x+b) >> (w-M)
Here,
- w is size of machine word (typically 32)
- M is size of hash code you want in bits
- a is any odd integer that fits in to machine word
- b is any integer less than 2^(w-M)
Above works for hashing a number. To hash a string, get the hash code that you can get using built-in functions like GetHashCode and then use that value in above formula.
For example, let's say you need 200 16-bit hash code for string s, then following code can be written as implementation:
public int[] GetHashCodes(string s, int count, int seed = 0)
{
var hashCodes = new int[count];
var machineWordSize = sizeof(int);
var hashCodeSize = machineWordSize / 2;
var hashCodeSizeDiff = machineWordSize - hashCodeSize;
var hstart = s.GetHashCode();
var bmax = 1 << hashCodeSizeDiff;
var rnd = new Random(seed);
for(var i=0; i < count; i++)
{
hashCodes[i] = ((hstart * (i*2 + 1)) + rnd.Next(0, bmax)) >> hashCodeSizeDiff;
}
}
Notes:
I'm using hash code word size as half of machine word size which in most cases would be 16-bit. This is not ideal and has far more chance of collision. This can be used by upgrading all arithmetic to 64-bit.
Normally you want to select a and b both randomly within above said ranges.
Just use 1 hash function! (and save the 1/(f ε^2) smallest values.)
Check out this article for the state of the art practical and theoretical bounds. It has this nice graph (below), explaining why you probably want to use just one 2-independent hash function and save the k smallest values.
When estimating set sizes the paper shows that you can get a relative error of approximately ε = 1/sqrt(f k) where f is the jaccard similarity and k is the number of values kept. So if you want error ε, you need k=1/(fε^2) or if your sets have similarity around 1/3 and you want a 10% relative error, you should keep the 300 smallest values.
It seems like another way to get N number of good hashed values would be to salt the same hash with N different salt values.
In practice, if applying the salt second, it seems you could hash the data, then "clone" the internal state of your hasher, add the first salt and get your first value. You'd reset this clone to the clean cloned state, add the second salt, and get your second value. Rinse and repeat for all N items.
Likely not as cheap as XOR against N values, but seems like there's possibility for better quality results, at a minimal extra cost, especially if the data being hashed is much larger than the salt value.
Given an integer, I need to find a match from a small set. The integer will almost always not be in the set. For most search algorithms, that is the worst case (taking the longest). But for this application, search time will be dominated by how quickly the search fails. So I want an algorithm who's best case is 'not found'.
Does such a thing exist?
The integers are far from random, being array indexes -- say 0..10k (15-bits). The sets will contain 0..7 integers, which is few enough for a simple linear search. But that would be worst case in almost every case.
The only thing I can think of would be a Bloom Filter. It would work something like this: Define F(int) = Set Bit (i AND 1Fh) (that is, a 32-bit integer with one bit set). With each set I would store the OR'd together values of F(each element) (a 32-bit integer with max n-bits set for n elements). The search would then be IF (F(i) AND F(set))>0 then perform linear search.
Thus the search would never be performed unless at least one set element had the same low 5-bits as the test integer i. A second test could be added based on the next lowest 5-bits.
Better ideas anyone?
The fastest algorithm I can imagine, which would succeed or fail immediately, is a huge array 0..MaxInt of Boolean, all False except True at Array[Set Member]. Search would be a simple array lookup:
Found = Array[Test]
But the memory footprint is absurd. A common optimization is a Hash Array.
As a test, I have implemented a Perfect Hash using bits of the Set Members. The function PHash(int) returns an integer 0..15 which is the array index where the match will be found if one exists. The search is then:
IF Array[PHash(Test)] = Test
THEN Found at Index PHash(Test)
ELSE Not Found
It will probably surprise no one that profiling shows this to be slower than a linear search.
(sigh)
Of course, no single Hash can reduce 15-bit integers to distinct 4-bit integers. I use many different hash functions. To produce the Set, I find which function produces distinct 4-bit hashes for that Set, then store the Set as the Hash Function Pointer plus a 16 element Array. Each Array element is either X or one Set Member, where X is not in the set range. (Failure to find a Perfect Hash would throw an exception, which has not yet happened.) None of this overhead matters in profiling as it is done once at program start.
To find a Test integer in a Set, I call Set.HashFunction(Test), then compare Test to that Set.Array Element. That final compare is the same as each step of a linear search. To be faster, the Hash Function must be faster than the remaining compares of the linear search. So this could be a faster algorithm, but only for large enough set sizes.
I have not experimented to find that set size. Anyway it would depend upon the speed of each hash function.