cs1001.py , Tel Aviv University, Spring 2018/19 Recitation 10¶

We discussed iterators, generators, and the Karp-Rabin algorithm for string matching

Takeaways:¶
• A generator function is a function that contains the yield command and returns a genertor object.
• The Karp-Rabin algorithm is a probabilistic string matching algorithm (find all occurences of a string of length $m$ in a string of length $n$) running in linear time $O(m+n)$ (as opposed to the naive solution which has running time $O(nm)$).
• Make sure you read our KR summary.
• Make sure you understand the way the algorithm works, and in particular the "rolling hash mechanism", that is, how to compute the fingerprint of the next substring in $O(1)$ time, given the fingerprint of the current substring.
• Make sure you understand the "arithmetization" step used by the algorithm.

Code for printing several outputs in one cell (not part of the recitation):¶

In :
from IPython.core.interactiveshell import InteractiveShell
InteractiveShell.ast_node_interactivity = "all"

Iterators and Generators¶

Iterators¶

In :
l = "123"  #[1,2,3]
li = iter(l)
type(li)
li2 = iter(l)
Out:
str_iterator
In :
next(li)
Out:
'1'
In :
next(li)
Out:
'2'
In :
z = next(li)
print("z is", z)
z is 3
In :
next(li)
---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
<ipython-input-28-c9b8845252db> in <module>
----> 1 next(li)

StopIteration:
In :
next(li2)
Out:
'1'
In :
for elem in li2:
print(elem)
2
3

Generators¶

In :
def countdown_gen():
''' calling it creates an iterator for the values 5,4,3,2,1,'launch' '''
yield 5
yield 4
yield 3
yield 2
yield 1
yield 'launch'
In :
cd = countdown_gen()
cd #generator object (private case of iterator)
Out:
<generator object countdown_gen at 0x000002623F0CFE58>
In :
next(cd)
Out:
5
In :
next(cd)
Out:
4
In :
for e in cd:
print(e)
3
2
1
launch

With generators we can have infinite iterations

In [ ]:
def countdown_infinite():
i = 0
while True:
yield i
i += 1

[i for i in range(10)]

Solving this exam question about generators¶

Section (b)

In :
def SomePairs():
i=1
while True:
for j in range(i):
yield(i,j)
i=i+1

gen = SomePairs()
[next(gen) for _ in range(10)]
Out:
[(1, 0),
(2, 0),
(2, 1),
(3, 0),
(3, 1),
(3, 2),
(4, 0),
(4, 1),
(4, 2),
(4, 3)]

Section (c)

In :
def RevGen(PairsGen):
pairs = PairsGen()
while True:
pair = next(pairs)
yield(pair,pair)

gen = RevGen(SomePairs)
[next(gen) for _ in range(10)]
Out:
[(0, 1),
(0, 2),
(1, 2),
(0, 3),
(1, 3),
(2, 3),
(0, 4),
(1, 4),
(2, 4),
(3, 4)]

Section (d1)

In :
def UnionGenerators(gen1, gen2):
while True:
yield next(gen1)
yield next(gen2)

ug = UnionGenerators(SomePairs(), RevGen(SomePairs))

for _ in range(10):
next(ug)
Out:
(1, 0)
Out:
(0, 1)
Out:
(2, 0)
Out:
(0, 2)
Out:
(2, 1)
Out:
(1, 2)
Out:
(3, 0)
Out:
(0, 3)
Out:
(3, 1)
Out:
(1, 3)

Section (d2)

In [ ]:
def EqPairs():
i=0
while True:
yield (i,i)
i=i+1

def AllPairs():
return UnionGenerators(SomePairs(), UnionGenerators(EqPairs(), RevGen(SomePairs)))

gen = AllPairs()
[next(gen) for _ in range(10)]

The string-matching problem¶

Given a string $text$ of length $n$, and a short(er) string $pattern$ of length $m$ ($m\leq n$), report all occurrances of $pattern$ in $text$.

Example:

$text =$"abracadabra", $pattern =$"abr"

The requested output should be $[0,7]$, since $pattern$ appears in $text$ in indices $0,7$.

Karp-Rabin Algorithm¶

• The algorithm works as follows:
• An initial "fingerprint" is computed for the pattern string and the first substring of length $m$ in the text
• If both fingerprints are equal, we assume a match
• Then, a "rolling hash" mechanism computes the next fingerprint in $O(1)$ time given the current fingerprint in the text
• At each stage again a comparison is made and equal fingerprints are considered a match
In :
def is_prime(N, show_witness=False):
""" probabilistic test for N's compositeness """
for i in range(0,100):
a = random.randint(1,N-1) # a is a random integer in [1..N-1]
if pow(a,N-1,N) != 1:
if show_witness:  # caller wishes to see a witness
print(N,"is composite","\n",a,"is a witness, i=",i+1)
return False
return True

def find_prime(n):
""" find random n-bit long prime """
while(True):
candidate = random.randrange(2**(n-1),2**n)
if is_prime(candidate):
return candidate

def fingerprint(string, basis, r):
""" used to computes karp-rabin fingerprint of the pattern
and of the first substring in the text
employs Horner method (modulo r) """
s = 0
for ch in string:
s = (s*basis + ord(ch)) % r # Horner
return s

def substring_fingerprints(string, m, basis, r):
""" return a list of all fingerprints of size m windows in string """
fp_list = []
b_power = pow(basis, m-1, r)

# compute first fingerprint
fp_list.append(fingerprint(string[0:m], basis, r))

# compute f_list[s], based on f_list[s-1]
for s in range(1,len(string)-m+1): # O(n-m-1), each iteration O(1)
next_fingerprint = \
((fp_list[s-1] - ord(string[s-1])*b_power) * basis \
+ ord(string[s+m-1])) % r
fp_list.append(next_fingerprint)

return fp_list

def find_matches_KR(text, pattern, r=None):
""" find all shifts of occurances of pattern in text """
if len(pattern) > len(text):
return [] #no matches

basis = 2**16 # assume 16 bits are enough for all chars
if r == None:
r = find_prime(32) # randomly pick a 32 bit long prime using
# good old find_prime from an earlier lecture

p = fingerprint(pattern, basis, r)
fp_list = substring_fingerprints(text, len(pattern), basis, r)

matches = [shift for shift in range(len(fp_list)) if fp_list[shift] == p]

return matches
In :
pattern = "abr"
In :
r = find_prime(32)
base = 2**16

r
Out:
2149219973
In :
fingerprint("abr", base, r)
Out:
1818795565
In :
base = 2**16
arit = ord("a")*(base**2) + ord("b")*(base**1) + ord("r")*(base**0)
arit
fp = arit%r
fp
Out:
416618250354
Out:
1818795565
In :
substring_fingerprints(text, 3, base, r)
Out:
[1818795565,
1816371474,
1759694964,
1818861084,
1811784715,
1818926620,
1808312063,
1818795565,
1816371474]
In :
find_matches_KR(text, pattern, r)
Out:
[0, 7]

Safe version¶

Makes sure no false positives occur. In the worst case, when all $n-m$ possible substrings are indeed matches, behaves as the naive solution in terms of time complexity.

In :
def find_matches_KR_safe(text, pattern, r=None):
""" a safe version of KR
checks every suspect for a match """
if len(pattern) > len(text):
return [] #no matches

basis = 2**16 # assume 16 bits are enough for all chars
if r == None:
r = find_prime(32) # randomly pick a 32 bit long prime using
# good old find_prime from an earlier lecture

p = fingerprint(pattern, basis, r)
fp_list = substring_fingerprints(text, len(pattern), basis, r)

matches = [shift for shift in range(len(fp_list)) \
if fp_list[shift] == p and \
text[shift:shift+len(pattern)]==pattern]

return matches

Competition between versions on single char string.¶

This is the worst-case scenario for the safe version. Changing $m$ has a greater effect on the safe version than on the standard KR.

In :
import time

text = "a"*1000000
print("text = 'a'*",len(text))
print()
for pattern in ["a"*100, "a"*1000, "a"*10000, "a"*100000]:
print("pattern = 'a'*",len(pattern))
r = find_prime(32)
for f in [find_matches_KR, find_matches_KR_safe]:
t0=time.perf_counter()
res=f(text, pattern, r)
t1=time.perf_counter()
print (f.__name__, t1-t0 )
print("") #newline
text = 'a'* 1000000

pattern = 'a'* 100
find_matches_KR 1.4179207529959967
find_matches_KR_safe 1.6589124150050338

pattern = 'a'* 1000
find_matches_KR 1.3420768009964377
find_matches_KR_safe 1.775463817990385

pattern = 'a'* 10000
find_matches_KR 1.2947049719950883
find_matches_KR_safe 2.638186254000175

pattern = 'a'* 100000
find_matches_KR 1.4077826730062952
find_matches_KR_safe 13.829727393997018

Competition between versions on random strings.¶

Note that the standard and safe versions of KR has similar running times. Moreover, as $m$ increases, the running time slightly decreases since there are less candidates to consider.

In :
import random
def gen_str(size):
''' Generate a random lowercase English string of length size'''
s=""
for i in range(size):
s+=random.choice("abcdefghijklmnopqrstuvwxyz")
return s

n=1000000
m=1000
text = gen_str(n)
pattern = gen_str(m)
print("random str of len n=", n, " , random pattern of length m=",m)
r = find_prime(32)
for f in [find_matches_KR, find_matches_KR_safe]:
t0=time.perf_counter()
f(text, pattern, r)
t1=time.perf_counter()
print (f.__name__, t1-t0)

m=10000
pattern = gen_str(m)
print("random str of len n=", n, " , random pattern of length m=",m)
r = find_prime(32)
for f in [find_matches_KR, find_matches_KR_safe]:
t0=time.perf_counter()
f(text, pattern, r)
t1=time.perf_counter()
print (f.__name__, t1-t0)

m=100000
pattern = gen_str(m)
print("random str of len n=", n, " , random pattern of length m=",m)
r = find_prime(32)
for f in [find_matches_KR, find_matches_KR_safe]:
t0=time.perf_counter()
f(text, pattern, r)
t1=time.perf_counter()
print (f.__name__, t1-t0)
random str of len n= 1000000  , random pattern of length m= 1000
Out:
[]
find_matches_KR 1.4785060709982645
Out:
[]
find_matches_KR_safe 1.3623063810082385
random str of len n= 1000000  , random pattern of length m= 10000
Out:
[]
find_matches_KR 1.383506228987244
Out:
[]
find_matches_KR_safe 1.3038542309950572
random str of len n= 1000000  , random pattern of length m= 100000
Out:
[]
find_matches_KR 1.25419370700547
Out:
[]
find_matches_KR_safe 1.6594200499966973

Choice of $r$¶

By setting $r$ to be a power of the base we will obtain more false-positives. Specifically, for $r=base$, we will get many more false positives. Why is that?

Note that the computation of the fingerprint is of the form $fp = (x \cdot base + y) \mod r$ for some $x,y$ (where $y$ is the arithmetization of the last character in the current substring).

In the case where $base = r$ this is equivalent to $(x \cdot r + y) \mod r = y \mod r$, i.e., the fingerprint takes into account only the last character of the substring!

Clearly, choosing $r$ which is a multiple of $base$ is not a good idea. This may also serve as an intuition for why we choose $r$ to be prime - say for example we know that all the fingerprints we compute are even, then if our $r$ is a multiple of $2$, we will always have $fp \mod r$ an even number, and thus we will only utilize half of our range!

In :
# Many false positives

# Same result here since the "x" will be cancelled out

# The safe check still works, of course
Out:
[2, 4, 6, 9]
Out:
[2, 4, 6, 9]
Out:

In :
fingerprint("da", 2**16, r=2**16)
ord("d")*(2**16)**1 + ord("a")
ord("a")

fingerprint("ca", 2**16, r=2**16)
ord("c")*(2**16)**1 + ord("a")
(ord("c")*(2**16)**1 + ord("a") )%2**16
Out:
97
Out:
6553697
Out:
97
Out:
97
Out:
6488161
Out:
97
In :
base = 2**16
r = 2**16
fingerprint("bda", base, r)
ord("b")*(base**2) + ord("d")*(base**1) + ord("a")
(ord("b")*base + ord("d"))*base + ord("a")
((ord("b")*base + ord("d"))*base + ord("a"))%r == ord("a")%r

fingerprint("cda", base, r)
(ord("c")*base + ord("d"))*base + ord("a")
((ord("c")*base + ord("d"))*base + ord("a"))%r == ord("a")%r
Out:
97
Out:
420913348705
Out:
420913348705
Out:
True
Out:
97
Out:
425208316001
Out:
True

When $r = base^k$ for some $k$ we have a similar behaviour, though this time it means we only take the last $k$ characters of the rolling hash into account.

In :
find_matches_KR("Humpty Dumpty", "Humpty", r=2**(16*5))
Out:
[0, 7]
In :
fingerprint("Humpty", 2**16, r=2**(16*5))
fingerprint("Dumpty", 2**16, r=2**(16*5))
fingerprint("Xumpty", 2**16, r=2**(16*5))
Out:
2158299737877522940025
Out:
2158299737877522940025
Out:
2158299737877522940025
In :
substring_fingerprints("Humpty Dumpty", 6, 2**16, r=2**(16*5))
Out:
[2158299737877522940025,
2010726629729956855840,
2066067987872461357124,
2139856371159933386869,
2232065040410175930477,
590314951159640293488,
1254411530052683432052,
2158299737877522940025]
In :
# Why don't we return the last index?
find_matches_KR("Humpty Dumpty", "Humpty", r=2**(16*6))
Out:


Question 2 in this exercise¶

(We did not see this in class, but you should make sure you understand this exercise)¶

In :
def fingerprint(string, basis=2**16, r=2**32-3):
""" used to computes karp-rabin fingerprint of the pattern
employs Horner method (modulo r) """
partial_sum = 0
for x in string:
partial_sum = (partial_sum*basis + ord(x)) % r
return partial_sum

def slide(prev_fp, prev_char, next_char, b_power, basis=2**16, r=2**32-3):
new_fp=((prev_fp - ord(prev_char)*b_power)*basis + ord(next_char)) % r
return new_fp

Section (a)¶

Build a generator which, given a string text and a length parameter generates all KR fingerprints of desired length in text. Instructions:

• Make use of both $fingerprint$ and $slide$
• The generator can call $fingerprint$ only once
In :
def kr_gen(text, length, basis=2**16, r=2**32-3):
fp = fingerprint(text[:length])
yield fp
b_power = pow(basis, length - 1, r)
for s in range(1, len(text) - length + 1):
fp = slide(fp, text[s - 1], text[s - 1 + length], b_power)
yield fp
In :
gen = kr_gen("abracadabra", 3)
next(gen)
next(gen)
Out:
6422933
Out:
7471495
In :
next(gen)
next(gen)
next(gen)
next(gen)
next(gen)
next(gen)
next(gen)
next(gen)
next(gen)
next(gen)
Out:
6357433
Out:
6488452
Out:
6357389
Out:
6553988
Out:
6357390
Out:
6422933
Out:
7471495
---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
<ipython-input-23-6fd1aa460113> in <module>
6 next(gen)
7 next(gen)
----> 8 next(gen)
9 next(gen)
10 next(gen)

StopIteration:

Section (b)¶

Build a generator which, given two strings $text1, text2$ and a length parameter $\ell$ generates all pairs of indices $(i,j)$ such that $text1[i:i+\ell] == text2[j:j+\ell]$.

Instructions:

• Use $kr\_gen$ from the previous section
• The generator must work in space smaller than the size of the strings. In particular, at no point can you save the array of fingerprints of any entire string
In :
def generate_shared_substrings(text1, text2, length):
g1 = kr_gen(text1, length)
i1 = 0
for fp1 in g1:
g2 = kr_gen(text2, length)
i2 = 0
for fp2 in g2:
if fp1 == fp2:
yield(i1, i2)
i2 += 1
i1 += 1
In :
g = generate_shared_substrings("abcdef","xcdefx",3)
next(g)
next(g)
Out:
(2, 1)
Out:
(3, 2)
In :
next(g)
---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
<ipython-input-51-e734f8aca5ac> in <module>
----> 1 next(g)

StopIteration: