solving string alignment in O(mn) - string

I need to solve the follow problem withing O(nm).
n = |T|
m = |P|
where T,P two strings
f is a scoring function.
the algorithm should return a substring T' of T such that score(P,T') value is the maximum.
score(A,B) is the max val for alignment A and B according f.
I know I can get it from DIST matrix which is a Monge matrix if f is discrete (meaning the diagonals of the matrix has weights not larger than C which is a constant, and the horizontal and vertical edges is 0 or some other constant), but in this case the f is a general function from (sigma * {-})x(sigma * {-}) to R (where '-' is a gap).
any ideas?

You've noticed that there are several algorithms that compute a shortest path in a graph whose arcs are (i, j) → (i + 1, j), (i + 1, j + 1), (i, j + 1). The most general form of this algorithm would allow every arc length to be specified separately, with the following meanings.
(i, j) → (i + 1, j): cost of aligning the (i+1)th letter of P with a gap in T
(i, j) → (i + 1, j + 1): cost of aligning the (i+1)th letter of P with the (j+1)th letter of T
(i, j) → (i, j + 1): cost of aligning a gap in P with the (j+1)th letter of T
Costs can be negative. To solve your substring problem, make the costs of all of the (i, j) → (i, j + 1) arcs zero so that we can delete from T without penalty.

Related

Convert DFA to RE

I constructed a finite automata for the language L of all strings made of the symbols 0, 1 and 2 (Σ = {0, 1, 2}) where the last symbol is not smaller than the first symbol. E.g., the strings 0, 2012, 01231 and 102 are in the language, but 10, 2021 and 201 are not in the language.
Then from that an GNFA so I can convert to RE.
My RE looks like this:
(0(0+1+2)* )(1(0(1+2)+1+2)* )(2((0+1)2+2))*)
I have no idea if this is correct, as I think I understand RE but not entirely sure.
Could someone please tell me if it’s correct and if not why?
There is a general method to convert any DFA into a regular expression, and is probably what you should be using to solve this homework problem.
For your attempt specifically, you can tell whether an RE is incorrect by finding a word that should be in the language, but that your RE doesn't accept, or a word that shouldn't be in the language that the RE does accept. In this case, the string 1002 should be in the language, but the RE doesn't match it.
There are two primary reasons why this string isn't matched. The first is that there should be a union rather than a concatenation between the three major parts of the language (words starting with 0, 1 and 2, respectively:
(0(0+1+2)*) (1(0(1+2)+1+2)*) (2((0+1)2+2))*) // wrong
(0(0+1+2)*) + (1(0(1+2)+1+2)*) + (2((0+1)2+2))*) // better
The second problem is that in the 1 and 2 cases, the digits smaller than the starting digit need to be repeatable:
(1(0 (1+2)+1+2)*) // wrong
(1(0*(1+2)+1+2)*) // better
If you do both of those things, the RE will be correct. I'll leave it as an exercise for you to follow that step for the 2 case.
The next thing you can try is find a way to make the RE more compact:
(1(0*(1+2)+1+2)*) // verbose
(1(0*(1+2))*) // equivalent, but more compact
This last step is just a matter of preference. You don't need the trailing +1+2 because 0* can be of zero length, so 0*(1+2) covers the +1+2 case.
You can use an algorithm but this DFA might be easy enough to convert as a one-off.
First, note that if the first symbol seen in the initial state is 0, you transition to state A and remain there. A is accepting. This means any string beginning with 0 is accepted. Thus, our regular expression might as well have a term like 0(0+1+2)* in it.
Second, note that if the first symbol seen in the initial state is 1, you transition to state B and remain in states B and D from that point on. You only leave B if you see 0 and you stay out of B as long as you keep seeing 0. The only way to end on D is if the last symbol you saw was 0. Therefore, strings beginning with 1 are accepted if and only if the strings don't end in 0. We can have a term like 1(0+1+2)*(1+2) in our regular expression as well to cover these cases.
Third, note that if the first symbol seen in the initial state is 2, you transition to state C and remain in states C and E from that point on. You leave state C if you see anything but 2 and stay out of B until you see a 2 again. The only way to end up on C is if the last symbol you saw was 2. Therefore, strings beginning with 2 are accepted if and only if the strings end in 2. We can have a term like 2(0+1+2)*(2) in our regular expression as well to cover these cases.
Finally, we see that there are no other cases to consider; our three terms cover all cases and the union of them fully describes our language:
0(0+1+2)* + 1(0+1+2)*(1+2) + 2(0+1+2)*2
It was easy to just write out the answer here because this DFA is sort of like three simple DFAs put together with a start state. More complicated DFAs might be easier to convert to REs using algorithms that don't require you understand or follow what the DFA is doing.
Note that if the start state is accepting (mentioned in a comment on another answer) the RE changes as follows:
e + 0(0+1+2)* + 1(0+1+2)*(1+2) + 2(0+1+2)*2
Basically, we just tack the empty string onto it since it is not already generated by any of the other parts of the aggregate expression.
You have the equivalent of what is known as a right-linear system. It's right-linear because the variables occur on the right hand sides only to the first degree and only on the right-hand sides of each term. The system that you have may be written - with a change in labels from 0,1,2 to u,v,w - as
S ≥ u A + v B + w C
A ≥ 1 + (u + v + w) A
B ≥ 1 + u D + (v + w) B
C ≥ 1 + (u + v) E + w C
D ≥ u D + (v + w) B
E ≥ (u + v) E + w C
The underlying algebra is known as a Kleene algebra. It is defined by the following identities that serve as its fundamental properties
(xy)z = x(yz), x1 = x = 1x,
(x + y) + z = x + (y + z), x + 0 = x = 0 + x,
y0z = 0, w(x + y)z = wxz + wyz,
x + y = y + x, x + x = x,
with a partial ordering relation defined by
x ≤ y ⇔ y ≥ x ⇔ ∃z(x + z = y) ⇔ x + y = y
With respect to this ordering relation, all finite subsets have least upper bounds, including the following
0 = ⋁ ∅, x + y = ⋁ {x, y}
The sum operator "+" is the least upper bound operator.
The system you have is a right-linear fixed point system, since it expresses the variables on the left as a (right-linear) function, as given on the right, of the variables. The object being specified by the system is the least solution with respect to the ordering; i.e. the least fixed point solution; and the regular expression sought out is the value that the main variable has in the least fixed point solution.
The last axiom(s) for Kleene algebras can be stated in any of a number of equivalent ways, including the following:
0* = 1
the least fixed point solution to x ≥ a + bx + xc is x = b* a c*.
There are other ways to express it. A consequence is that one has identities such as the following:
1 + a a* = a* = 1 + a* a
(a + b)* = a* (b a*)*
(a b)* a = a (b a)*
In general, right linear systems, such as the one corresponding to your problem may be written in vector-matrix form as 𝐪 ≥ 𝐚 + A 𝐪, with the least fixed point solution given in matrix form as 𝐪 = A* 𝐚. The central theorem of Kleene algebras is that all finite right-linear systems have least fixed point solutions; so that one can actually define matrix algebras over Kleene algebras with product and sum given respectively as matrix product and matrix sum, and that this algebra can be made into a Kleene algebra with a suitably-defined matrix star operation through which the least fixed point solution is expressed. If the matrix A decomposes into block form as
B C
D E
then the star A* of the matrix has the block form
(B + C E* D)* (B + C E* D)* C E*
(E + D B* C)* D B* (E + D B* C)*
So, what this is actually saying is that for a vector-matrix system of the form
x ≥ a + B x + C y
y ≥ b + D x + E y
the least fixed point solution is given by
x = (B + C E* D)* (a + C E* b)
y = (E + D B* C)* (D B* a + b)
The star of a matrix, if expressed directly in terms of its components, will generally be huge and highly redundant. For an n×n matrix, it has size O(n³) - cubic in n - if you allow for redundant sub-expressions to be defined by macros. Otherwise, if you in-line insert all the redundancy then I think it blows up to a highly-redundant mess that is exponential in n in size.
So, there's intelligence required and involved (literally meaning: AI) in finding or pruning optimal forms that avoid the blow-up as much as possible. That's a non-trivial job for any purported matrix solver and regular expression synthesis compiler.
An heuristic, for your system, is to solve for the variables that don't have a "1" on the right-hand side and in-line substitute the solutions - and to work from bottom-up in terms of the dependency chain of the variables. That would mean starting with D and E first
D ≥ u* (v + w) B
E ≥ (u + v)* w C
In-line substitute into the other inequations
S ≥ u A + v B + w C
A ≥ 1 + (u + v + w) A
B ≥ 1 + u u* (v + w) B + (v + w) B
C ≥ 1 + (u + v) (u + v)* w C + w C
Apply Kleene algebra identities (e.g. x x* y + y = x* y)
S ≥ u A + v B + w C
A ≥ 1 + (u + v + w) A
B ≥ 1 + u* (v + w) B
C ≥ 1 + (u + v)* w C
Solve for the next layer of dependency up: A, B and C:
A ≥ (u + v + w)*
B ≥ (u* (v + w))*
C ≥ ((u + v)* w)*
Apply some more Kleene algebra (e.g. (x* y)* = 1 + (x + y)* y) to get
B ≥ 1 + N (v + w)
C ≥ 1 + N w
where, for convenience we set N = (u + v + w)*. In-line substitute at the top-level:
S ≥ u N + v (1 + N (v + w)) + w (1 + N w).
The least fixed point solution, in the main variable S, is thus:
S = u N + v + v N (v + w) + w + w N w.
where
N = (u + v + w)*.
As you can already see, even with this simple example, there's a lot of chess-playing to navigate through the system to find an optimally-pruned solution. So, it's certainly not a trivial problem. What you're essentially doing is synthesizing a control-flow structure for a program in a structured programming language from a set of goto's ... essentially the core process of reverse-compiling from assembly language to a high level language.
One measure of optimization is that of minimizing the loop-depth - which here means minimizing the depth of the stars or the star height. For example, the expression x* (y x*)* has star-height 2 but reduces to (x + y)*, which has star height 1. Methods for reducing star-height come out of the research by Hashiguchi and his resolution of the minimal star-height problem. His proof and solution (dating, I believe, from the 1980's or 1990's) is complex and to this day the process still goes on of making something more practical of it and rendering it in more accessible form.
Hashiguchi's formulation was cast in the older 1950's and 1960's formulation, predating the axiomatization of Kleene algebras (which was in the 1990's), so to date, nobody has rewritten his solution in entirely algebraic form within the framework of Kleene algebras anywhere in the literature ... as far as I'm aware. Whoever accomplishes this will have, as a result, a core element of an intelligent regular expression synthesis compiler, but also of a reverse-compiler and programming language synthesis de-compiler. Essentially, with something like that on hand, you'd be able to read code straight from binary and the lid will be blown off the world of proprietary systems. [Bite tongue, bite tongue, mustn't reveal secret yet, must keep the ring hidden.]

Check whether a subset with sum divisible by m exists

Given a set of non-negative distinct integers, and a value m, determine if there is a subset of the given set with sum divisible by m.
The solution on geeksforgeeks states that-
If n > m there will always be a subset with sum divisible by m (which is easy to prove with pigeonhole principle). So we need to handle only cases of n <= m.
Can somebody please explain what this case means and what is its relation to pigeonhole principle? Also how is this case different from n <= m?
Making this a bit more verbose of this:
Label the numbers a1, a2, ... an in any order. Now consider the sums:
b1=a1
b2=a1+a2
b3=a1+a2+a3
...
bn=a1+a2+...+an
These are either all unique numbers or one of the as are 0 (which is divisible by m).
Now if any of the bs are divisible by m we are done.
Otherwise:
The remainders of some non-divisible number/m can be in the range of 1...(m-1). So there are m-1 numbers of possible remainders`.
Since numbers b1...bn weren't divisible by m they must have remainders in the range of 1...(m-1). So you must pair n numbers of bs (pigeons) with m-1 remainders (pigeonholes).
We have more pigeons than pigeonholes => there must be at least two pigeons in the same pigeonhole.
That means: there must be at least two bs with the same remainder: call them bi, bj (i<j). Since all of our bs are unique and bi % m == bj % m (the remainders of bi/m and bj/m are the same) => bi - bj = x * m (where x is a positive integer). Therefore bi - bj is divisible by m and bi - bj = ai+1 + ... + aj. Therefore ai+1 + ... + aj is divisible by m which is exactly what we wanted to proof.
Let us create a new set of numbers (i.e. a[ ] array) by doing prefix sum of given values (i.e. value[ ] array).
a[0] = value[0]
a[1] = value[0] + value[1]
a[n] = value[0] + value[1] + .... + value[n]
Now we have n new numbers. If any of them are divisible by m we are done.
If we divide the a[ ] array elements with m, we can get remainders in range of [1, m - 1].
But, we have a total of n values.
So, there exist two numbers 0<=i,j<=n in a such that a[i] mod(m) == a[j] mod(m).
Due to the above statement, we can say that a[i] - a[j] is divisible by m.
Now, let's consider i > j.
We also know that, a[i] = value[i] + value[i - 1] + ... + value[0] and a[j] = value[j] + value[j - 1] + ... + value[0].
So, a[i] - a[j] = value[i] + value[i - 1] + ... + value[i - j + 1] is also divisible by m.

Count the Number of Zero's between Range of integers

. Is there any Direct formula or System to find out the Numbers of Zero's between a Distinct Range ... Let two Integer M & N are given . if I have to find out the total number of zero's between this Range then what should I have to do ?
Let M = 1234567890 & N = 2345678901
And answer is : 987654304
Thanks in advance .
Reexamining the Problem
Here is a simple solution in Ruby, which inspects each integer from the interval [m,n], determines the string of its digits in the standard base 10 positional system, and counts the occuring 0 digits:
def brute_force(m, n)
if m > n
return 0
end
z = 0
m.upto(n) do |k|
z += k.to_s.count('0')
end
z
end
If you run it in an interactive Ruby shell you will get
irb> brute_force(1,100)
=> 11
which is fine. However using the interval bounds from the example in the question
m = 1234567890
n = 2345678901
you will recognize that this will take considerable time. On my machine it does need more than a couple of seconds, I had to cancel it so far.
So the real question is not only to come up with the correct zero counts but to do it faster than the above brute force solution.
Complexity: Running Time
The brute force solution needs to perform n-m+1 times searching the base 10 string for the number k, which is of length floor(log_10(k))+1, so it will not use more than
O(n (log(n)+1))
string digit accesses. The slow example had an n of roughly n = 10^9.
Reducing Complexity
Yiming Rong's answer is a first attempt to reduce the complexity of the problem.
If the function for calculating the number of zeros regarding the interval [m,n] is F(m,n), then it has the property
F(m,n) = F(1,n) - F(1,m-1)
so that it suffices to look for a most likely simpler function G with the property
G(n) = F(1,n).
Divide and Conquer
Coming up with a closed formula for the function G is not that easy. E.g.
the interval [1,1000] contains 192 zeros, but the interval [1001,2000] contains 300 zeros, because a case like k = 99 in the first interval would correspond to k = 1099 in the second interval, which yields another zero digit to count. k=7 would show up as 1007, yielding two more zeros.
What one can try is to express the solution for some problem instance in terms of solutions to simpler problem instances. This strategy is called divide and conquer in computer science. It works if at some complexity level it is possible to solve the problem instance and if one can deduce the solution of a more complex problem from the solutions of the simpler ones. This naturally leads to a recursive formulation.
E.g. we can formulate a solution for a restricted version of G, which is only working for some of the arguments. We call it g and it is defined for 9, 99, 999, etc. and will be equal to G for these arguments.
It can be calculated using this recursive function:
# zeros for 1..n, where n = (10^k)-1: 0, 9, 99, 999, ..
def g(n)
if n <= 9
return 0
end
n2 = (n - 9) / 10
return 10 * g(n2) + n2
end
Note that this function is much faster than the brute force method: To count the zeros in the interval [1, 10^9-1], which is comparable to the m from the question, it just needs 9 calls, its complexity is
O(log(n))
Again note that this g is not defined for arbitrary n, only for n = (10^k)-1.
Derivation of g
It starts with finding the recursive definition of the function h(n),
which counts zeros in the numbers from 1 to n = (10^k) - 1, if the decimal representation has leading zeros.
Example: h(999) counts the zero digits for the number representations:
001..009
010..099
100..999
The result would be h(999) = 297.
Using k = floor(log10(n+1)), k2 = k - 1, n2 = (10^k2) - 1 = (n-9)/10 the function h turns out to be
h(n) = 9 [k2 + h(n2)] + h(n2) + n2 = 9 k2 + 10 h(n2) + n2
with the initial condition h(0) = 0. It allows to formulate g as
g(n) = 9 [k2 + h(n2)] + g(n2)
with the intital condition g(0) = 0.
From these two definitions we can define the difference d between h and g as well, again as a recursive function:
d(n) = h(n) - g(n) = h(n2) - g(n2) + n2 = d(n2) + n2
with the initial condition d(0) = 0. Trying some examples leads to a geometric series, e.g. d(9999) = d(999) + 999 = d(99) + 99 + 999 = d(9) + 9 + 99 + 999 = 0 + 9 + 99 + 999 = (10^0)-1 + (10^1)-1 + (10^2)-1 + (10^3)-1 = (10^4 - 1)/(10-1) - 4. This gives the closed form
d(n) = n/9 - k
This allows us to express g in terms of g only:
g(n) = 9 [k2 + h(n2)] + g(n2) = 9 [k2 + g(n2) + d(n2)] + g(n2) = 9 k2 + 9 d(n2) + 10 g(n2) = 9 k2 + n2 - 9 k2 + 10 g(n2) = 10 g(n2) + n2
Derivation of G
Using the above definitions and naming the k digits of the representation q_k, q_k2, .., q2, q1 we first extend h into H:
H(q_k q_k2..q_1) = q_k [k2 + h(n2)] + r (k2-kr) + H(q_kr..q_1) + n2
with initial condition H(q_1) = 0 for q_1 <= 9.
Note the additional definition r = q_kr..q_1. To understand why it is needed look at the example H(901), where the next level call to H is H(1), which means that the digit string length shrinks from k=3 to kr=1, needing an additional padding with r (k2-kr) zero digits.
Using this, we can extend g to G as well:
G(q_k q_k2..q_1) = (q_k-1) [k2 + h(n2)] + k2 + r (k2-kr) + H(q_kr..q_1) + g(n2)
with initial condition G(q_1) = 0 for q_1 <= 9.
Note: It is likely that one can simplify the above expressions like in case of g above. E.g. trying to express G just in terms of G and not using h and H. I might do this in the future. The above is already enough to implement a fast zero calculation.
Test Result
recursive(1234567890, 2345678901) =
987654304
expected:
987654304
success
See the source and log for details.
Update: I changed the source and log according to the more detailed problem description from that contest (allowing 0 as input, handling invalid inputs, 2nd larger example).
You can use a standard approach to find m = [1, M-1] and n = [1, N], then [M, N] = n - m.
Standard approaches are easily available: Counting zeroes.

bipartite graph and dynamic programming

I am solving a problem, which has a weighted complete bipartite graph(X,Y,XxY), where X has n nodes and Y has m nodes and n is less than m. I want to have a perfect cross free matching graph, such that no two edges cross while matching set X to set Y and all the nodes in X are taken at the end.The sum of weights of the resulting graph should be minimal, I need to devise a dynammic programming algorithm. This is how I thought of it:
nodes in X and Y are arranged x0, xi can have a horizontal edge to Y0,Yi and so on, but Y has more nodes than X.
For every node in X (i) I consider two options either horizontal neighbor which is j in set Y, or diagonal neighbors (i, j-1), (i,j+1) and choose the edge which minimizes the cost.and I keep track of the nodes in X and Y that are already taken.time complexity O(nm)
Is there a better way I can implement this. Any help is appreciated. This is a question I got in my midterm but I left it in choice.
Let w(x, y) be edge weight between nodes x in X and y in Y, and let M(i, j) be solution (minimum cross free matching graph) for vertices {x_0, x_1, ..., x_i} subset X and {y_0, y_1, ..., y_j} subset Y, where i < |X| and j < |Y|.
E.g. M(0, j) = min( w(x_0, y_a) ) for 0 <= a <= j. M(i, i-1) = infinity since there is no matching when 'right' set is smaller.
For i, j there are two possibilities: x_i is connected to y_j or not. Because of that recursion holds:
M(i, j) = min( w(i,j) + M(i-1, j-1), M(i, j-1) )

How to implement Frobenius pseudoprime algorithm?

Someone told me that the Frobenius pseudoprime algorithm take three times longer to run than the Miller–Rabin primality test but has seven times the resolution. So then if one where to run the former ten times and the later thirty times, both would take the same time to run, but the former would provide about 233% more analyse power. In trying to find out how to perform the test, the following paper was discovered with the algorithm at the end:
A Simple Derivation for the Frobenius Pseudoprime Test
There is an attempt at implementing the algorithm below, but the program never prints out a number. Could someone who is more familiar with the math notation or algorithm verify what is going on please?
Edit 1: The code below has corrections added, but the implementation for compute_wm_wm1 is missing. Could someone explain the recursive definition from an algorithmic standpoint? It is not "clicking" for me.
Edit 2: The erroneous code has been removed, and an implementation of the compute_wm_wm1 function has been added below. It appears to work but may require further optimization to be practical.
from random import SystemRandom
from fractions import gcd
random = SystemRandom().randrange
def find_prime_number(bits, test):
number = random((1 << bits - 1) + 1, 1 << bits, 2)
while True:
for _ in range(test):
if not frobenius_pseudoprime(number):
break
else:
return number
number += 2
def frobenius_pseudoprime(integer):
assert integer & 1 and integer >= 3
a, b, d = choose_ab(integer)
w1 = (a ** 2 * extended_gcd(b, integer)[0] - 2) % integer
m = (integer - jacobi_symbol(d, integer)) >> 1
wm, wm1 = compute_wm_wm1(w1, m, integer)
if w1 * wm != 2 * wm1 % integer:
return False
b = pow(b, (integer - 1) >> 1, integer)
return b * wm % integer == 2
def choose_ab(integer):
a, b = random(1, integer), random(1, integer)
d = a ** 2 - 4 * b
while is_square(d) or gcd(2 * d * a * b, integer) != 1:
a, b = random(1, integer), random(1, integer)
d = a ** 2 - 4 * b
return a, b, d
def is_square(integer):
if integer < 0:
return False
if integer < 2:
return True
x = integer >> 1
seen = set([x])
while x * x != integer:
x = (x + integer // x) >> 1
if x in seen:
return False
seen.add(x)
return True
def extended_gcd(n, d):
x1, x2, y1, y2 = 0, 1, 1, 0
while d:
n, (q, d) = d, divmod(n, d)
x1, x2, y1, y2 = x2 - q * x1, x1, y2 - q * y1, y1
return x2, y2
def jacobi_symbol(n, d):
j = 1
while n:
while not n & 1:
n >>= 1
if d & 7 in {3, 5}:
j = -j
n, d = d, n
if n & 3 == 3 == d & 3:
j = -j
n %= d
return j if d == 1 else 0
def compute_wm_wm1(w1, m, n):
a, b = 2, w1
for shift in range(m.bit_length() - 1, -1, -1):
if m >> shift & 1:
a, b = (a * b - w1) % n, (b * b - 2) % n
else:
a, b = (a * a - 2) % n, (a * b - w1) % n
return a, b
print('Probably prime:\n', find_prime_number(300, 10))
You seem to have misunderstood the algorithm completely due to not being familiar with the notation.
def frobenius_pseudoprime(integer):
assert integer & 1 and integer >= 3
a, b, d = choose_ab(integer)
w1 = (a ** 2 // b - 2) % integer
That comes from the line
W0 ≡ 2 (mod n) and W1 ≡ a2b−1 − 2 (mod n)
But the b-1 doesn't mean 1/b here, but the modular inverse of b modulo n, i.e. an integer c with b·c ≡ 1 (mod n). You can most easily find such a c by continued fraction expansion of b/n or, equivalently, but with slightly more computation, by the extended Euclidean algorithm. Since you're probably not familiar with continued fractions, I recommend the latter.
m = (integer - d // integer) // 2
comes from
n − (∆/n) = 2m
and misunderstands the Jacobi symbol as a fraction/division (admittedly, I have displayed it here even more like a fraction, but since the site doesn't support LaTeX rendering, we'll have to make do).
The Jacobi symbol is a generalisation of the Legendre symbol - denoted identically - which indicates whether a number is a quadratic residue modulo an odd prime (if n is a quadratic residue modulo p, i.e. there is a k with k^2 ≡ n (mod p) and n is not a multiple of p, then (n/p) = 1, if n is a multiple of p, then (n/p) = 0, otherwise (n/p) = -1). The Jacobi symbol lifts the restriction that the 'denominator' be an odd prime and allows arbitrary odd numbers as 'denominators'. Its value is the product of the Legendre symbols with the same 'numerator' for all primes dividing n (according to multiplicity). More on that, and how to compute Jacobi symbols efficiently in the linked article.
The line should correctly read
m = (integer - jacobi_symbol(d,integer)) // 2
The following lines I completely fail to understand, logically, here should follow the calculation of
Wm and Wm+1 using the recursion
W2j ≡ Wj2 − 2 (mod n)
W2j+1 ≡ WjWj+1 − W1 (mod n)
An efficient method of using that recursion to compute the required values is given around formula (11) of the PDF.
w_m0 = w1 * 2 // m % integer
w_m1 = w1 * 2 // (m + 1) % integer
w_m2 = (w_m0 * w_m1 - w1) % integer
The remainder of the function is almost correct, except of course that it now gets the wrong data due to earlier misunderstandings.
if w1 * w_m0 != 2 * w_m2:
The (in)equality here should be modulo integer, namely if (w1*w_m0 - 2*w_m2) % integer != 0.
return False
b = pow(b, (integer - 1) // 2, integer)
return b * w_m0 % integer == 2
Note, however, that if n is a prime, then
b^((n-1)/2) ≡ (b/n) (mod n)
where (b/n) is the Legendre (or Jacobi) symbol (for prime 'denominators', the Jacobi symbol is the Legendre symbol), hence b^((n-1)/2) ≡ ±1 (mod n). So you could use that as an extra check, if Wm is not 2 or n-2, n can't be prime, nor can it be if b^((n-1)/2) (mod n) is not 1 or n-1.
Probably computing b^((n-1)/2) (mod n) first and checking whether that's 1 or n-1 is a good idea, since if that check fails (that is the Euler pseudoprime test, by the way) you don't need the other, no less expensive, computations anymore, and if it succeeds, it's very likely that you need to compute it anyway.
Regarding the corrections, they seem correct, except for one that made a glitch I previously overlooked possibly worse:
if w1 * wm != 2 * wm1 % integer:
That applies the modulus only to 2 * wm1.
Concerning the recursion for the Wj, I think it is best to explain with a working implementation, first in toto for easy copy and paste:
def compute_wm_wm1(w1,m,n):
a, b = 2, w1
bits = int(log(m,2)) - 2
if bits < 0:
bits = 0
mask = 1 << bits
while mask <= m:
mask <<= 1
mask >>= 1
while mask > 0:
if (mask & m) != 0:
a, b = (a*b-w1)%n, (b*b-2)%n
else:
a, b = (a*a-2)%n, (a*b-w1)%n
mask >>= 1
return a, b
Then with explanations in between:
def compute_wm_wm1(w1,m,n):
We need the value of W1, the index of the desired number, and the number by which to take the modulus as input. The value W0 is always 2, so we don't need that as a parameter.
Call it as
wm, wm1 = compute_wm_wm1(w1,m,integer)
in frobenius_pseudoprime (aside: not a good name, most of the numbers returning True are real primes).
a, b = 2, w1
We initialise a and b to W0 and W1 respectively. At each point, a holds the value of Wj and b the value of Wj+1, where j is the value of the bits of m so far consumed. For example, with m = 13, the values of j, a and b develop as follows:
consumed remaining j a b
1101 0 w_0 w_1
1 101 1 w_1 w_2
11 01 3 w_3 w_4
110 1 6 w_6 w_7
1101 13 w_13 w_14
The bits are consumed left-to-right, so we have to find the first set bit of m and place our 'pointer' right before it
bits = int(log(m,2)) - 2
if bits < 0:
bits = 0
mask = 1 << bits
I subtracted a bit from the computed logarithm just to be entirely sure that we don't get fooled by a floating point error (by the way, using log limits you to numbers of at most 1024 bits, about 308 decimal digits; if you want to treat larger numbers, you have to find the base-2 logarithm of m in a different way, using log was the simplest way, and it's just a proof of concept, so I used that here).
while mask <= m:
mask <<= 1
Shift the mask until it's greater than m,so the set bit points just before m's first set bit. Then shift one position back, so we point at the bit.
mask >>= 1
while mask > 0:
if (mask & m) != 0:
a, b = (a*b-w1)%n, (b*b-2)%n
If the next bit is set, the value of the initial portion of consumed bits of m goes from j to 2*j+1, so the next values of the W sequence we need are W2j+1 for a and W2j+2 for b. By the above recursion formula,
W_{2j+1} = W_j * W_{j+1} - W_1 (mod n)
W_{2j+2} = W_{j+1}^2 - 2 (mod n)
Since a was Wj and b was Wj+1, a becomes (a*b - W_1) % n and b becomes (b * b - 2) % n.
else:
a, b = (a*a-2)%n, (a*b-w1)%n
If the next bit is not set, the value of the initial portion of consumed bits of m goes from j to 2*j, so a becomes W2j = (Wj2 - 2) (mod n), and b becomes
W2j+1 = (Wj * Wj+1 - W1) (mod n).
mask >>= 1
Move the pointer to the next bit. When we have moved past the final bit, mask becomes 0 and the loop ends. The initial portion of consumed bits of m is now all of m's bits, so the value is of course m.
Then we can
return a, b
Some additional remarks:
def find_prime_number(bits, test):
while True:
number = random(3, 1 << bits, 2)
for _ in range(test):
if not frobenius_pseudoprime(number):
break
else:
return number
Primes are not too frequent among the larger numbers, so just picking random numbers is likely to take a lot of attempts to hit one. You will probably find a prime (or probable prime) faster if you pick one random number and check candidates in order.
Another point is that such a test as the Frobenius test is disproportionally expensive to find that e.g. a multiple of 3 is composite. Before using such a test (or a Miller-Rabin test, or a Lucas test, or an Euler test, ...), you should definitely do a bit of trial division to weed out most of the composites and do the work only where it has a fighting chance of being worth it.
Oh, and the is_square function isn't prepared to deal with arguments less than 2, divide-by-zero errors lurk there,
def is_square(integer):
if integer < 0:
return False
if integer < 2:
return True
x = integer // 2
should help.

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