Consider the first number, say m. See how many times this number is repeated consecutively. If it is repeated k times in a row, it gives rise to two entries in the output list: first
the number k, then the number m. (This is similar to how we say “four 2s” when we see
[2,2,2,2].) Then we move on to the next number after this run of m. Repeat the process
until every number in the list is considered
Example:The process is perhaps best understood by looking at a few examples:
• readAloud([]) should return []
• readAloud([1,1,1]) should return [3,1]
• readAloud([-1,2,7]) should return [1,-1,1,2,1,7]
• readAloud([3,3,8,-10,-10,-10]) should return [2,3,1,8,3,-10]
• readAloud([3,3,1,1,3,1,1]) should return [2,3,2,1,1,3,2,1]
I have the following code:
def readAloud(lst: List[int]) -> List[int]:
answer:List[int]=[]
l=len(lst)
d=1
for i in range(l-1):
if(lst[i]==lst[i]):
d = d + 1
answer.append(d)
answer.append(lst[i])
if (lst[i-1] != lst[i]):
d=1
answer.append(d)
answer.append(lst[i])
return answer
Grouping adjacent elements is exactly what itertools.groupby is for.
from itertools import chain, groupby
def read_aloud(numbers):
r = ((sum(1 for _ in v), k) for k, v in groupby(numbers))
return list(chain.from_iterable(r))
Examples:
>>> read_aloud([])
[]
>>> read_aloud([1, 1, 1])
[3, 1]
>>> read_aloud([3, 3, 8, -10, -10, -10])
[2, 3, 1, 8, 3, -10]
>>> read_aloud([3, 3, 1, 1, 3, 1, 1])
[2, 3, 2, 1, 1, 3, 2, 1]
Here a solution (but this is not the only one :) )
def readAloud(lst):
answer = []
count = 1
prev_elt = lst[0]
for m in lst[1:] + [None]: # we add Node for the last values
if prev_elt == m:
count += 1
else:
answer.extend([count, prev_elt])
prev_elt = m
count = 1
return answer
print(readAloud([3,3,1,1,3,1,1]))
Related
I have a torch tensor edge_index of shape (2, N) that represents edges in a graph. For each (x, y) there is also a (y, x), where x and y are node IDs (ints). During the forward pass of my model I need to mask out certain edges. So, for example, I have:
n1 = [0, 3, 4] # list of node ids as x
n2 = [1, 2, 1] # list of node ids as y
edge_index = [[1, 2, 0, 1, 3, 4, 2, 3, 1, 4, 2, 4], # actual edges as (x, y) and (y, x)
[2, 1, 1, 0, 4, 3, 3, 2, 4, 1, 4, 2]]
# do something that efficiently removes (x, y) and (y, x) edges as formed by n1 and n2
Final edge_index should look like:
>>> edge_index
[[1, 2, 3, 4, 2, 4],
[2, 1, 4, 3, 4, 2]]
Preferably we need to efficiently make some kind of boolean mask that I can apply to edge index e.g. as edge_index[:, mask] or something like that.
Could also be done in numpy but I'd like to avoid converting back and forth.
Edit #1:
If that can't be done, then I can think of a way so that, instead of n1 and n2, I have access to the indices of the positions I need to exclude in one tensor e.g. _except=[2, 3, 6, 7, 8, 9] (by making a dict/index once in the beginning).
Is there a way to get the desired result by "telling" edge_index to drop the indices in except? edge_index[:, _except] gives me the ones I want to get rid of. I need its complement operation.
Edit #2:
I managed to do it like this:
mask = torch.ones(edge_index.shape[1], dtype=torch.bool)
for i in range(len(n1)):
mask = mask & ~(torch.tensor([n1[i], n2[i]], dtype=torch.long) == edge_index.T).all(dim=1) & ~(torch.tensor([n2[i], n1[i]], dtype=torch.long) == edge_index.T).all(dim=1)
edge_index[:, mask]
but it is too slow and I can't use it. How can I speed it up?
Edit #3: I managed to solve this Edit#1 efficiently with:
mask = torch.ones(edge_index.shape[1], dtype=torch.bool)
mask[_except] = False
edge_index[:, mask]
Still interested in solving the original problem if someone comes up with something...
If you're ok with the way you suggested at Edit#1,
you get the complement result by:
edge_index[:, [i for i in range(edge_index.shape[1]) if not (i in _except)]]
hope this is fast enough for your requirement.
Edit 1:
from functools import reduce
ids = torch.stack([torch.tensor(n1), torch.tensor(n2)], dim=1)
ids = torch.cat([ids, ids[:, [1,0]]], dim=0)
res = edge_index.unsqueeze(0).repeat(6, 1, 1) == ids.unsqueeze(2).repeat(1, 1, 12)
mask = ~reduce(lambda x, y: x | (reduce(lambda p, q: p & q, y)), res, reduce(lambda p, q: p & q, res[0]))
edge_index[:, mask]
Edit 2:
ids = torch.stack([torch.tensor(n1), torch.tensor(n2)], dim=1)
ids = torch.cat([ids, ids[:, [1,0]]], dim=0)
res = edge_index.unsqueeze(0).repeat(6, 1, 1) == ids.unsqueeze(2).repeat(1, 1, 12)
mask = ~(res.sum(1) // 2).sum(0).bool()
edge_index[:, mask]
My goal is to get joint probability (here we use count for example) matrix from data samples. Now I can get the expected result, but I'm wondering how to optimize it. Here is my implementation:
def Fill2DCountTable(arraysList):
'''
:param arraysList: List of arrays, length=2
each array is of shape (k, sampleSize),
k == 1 (or None. numpy will align it) if it's single variable
else k for a set of variables of size k
:return: xyJointCounts, xMarginalCounts, yMarginalCounts
'''
jointUniques, jointCounts = np.unique(np.vstack(arraysList), axis=1, return_counts=True)
_, xReverseIndexs = np.unique(jointUniques[[0]], axis=1, return_inverse=True) ###HIGHLIGHT###
_, yReverseIndexs = np.unique(jointUniques[[1]], axis=1, return_inverse=True)
xyJointCounts = np.zeros((xReverseIndexs.max() + 1, yReverseIndexs.max() + 1), dtype=np.int32)
xyJointCounts[tuple(np.vstack([xReverseIndexs, yReverseIndexs]))] = jointCounts
xMarginalCounts = np.sum(xyJointCounts, axis=1) ###HIGHLIGHT###
yMarginalCounts = np.sum(xyJointCounts, axis=0)
return xyJointCounts, xMarginalCounts, yMarginalCounts
def Fill3DCountTable(arraysList):
# :param arraysList: List of arrays, length=3
jointUniques, jointCounts = np.unique(np.vstack(arraysList), axis=1, return_counts=True)
_, xReverseIndexs = np.unique(jointUniques[[0]], axis=1, return_inverse=True)
_, yReverseIndexs = np.unique(jointUniques[[1]], axis=1, return_inverse=True)
_, SReverseIndexs = np.unique(jointUniques[2:], axis=1, return_inverse=True)
SxyJointCounts = np.zeros((SReverseIndexs.max() + 1, xReverseIndexs.max() + 1, yReverseIndexs.max() + 1), dtype=np.int32)
SxyJointCounts[tuple(np.vstack([SReverseIndexs, xReverseIndexs, yReverseIndexs]))] = jointCounts
SMarginalCounts = np.sum(SxyJointCounts, axis=(1, 2))
SxJointCounts = np.sum(SxyJointCounts, axis=2)
SyJointCounts = np.sum(SxyJointCounts, axis=1)
return SxyJointCounts, SMarginalCounts, SxJointCounts, SyJointCounts
My use scenario is to do conditional independence test over variables. SampleSize is usually quite big (~10k) and each variable's categorical cardinality is relatively small (~10). I still find the speed not satisfying.
How to best optimize this code, or even logic outside the code? I may have some thoughts:
The ###HIGHLIGHT### lines. On a single X I may calculate (X;Y1), (Y2;X), (X;Y3|S1)... for many times, so what if I save cache variable's (and conditional set's) {uniqueValue: reversedIndex} dictionary and its marginal count, and then directly get marginalCounts (no need to sum) and replace to get reverseIndexs (no need to unique).
How to further use matrix parallelization to do CITest in batch, i.e. calculate (X;Y|S1), (X;Y|S2), (X;Y|S3)... simultaneously?
Will torch be faster than numpy, on same CPU? Or on GPU?
It's an open question. Thank you for any possible ideas. Big thanks for your help :)
================== A test example is as follows ==================
xs = np.array( [2, 4, 2, 3, 3, 1, 3, 1, 2, 1] )
ys = np.array( [5, 5, 5, 4, 4, 4, 4, 4, 6, 5] )
Ss = np.array([ [1, 0, 0, 0, 1, 0, 0, 0, 1, 1],
[1, 1, 1, 0, 1, 0, 1, 0, 1, 0] ])
xyJointCounts, xMarginalCounts, yMarginalCounts = Fill2DCountTable([xs, ys])
SxyJointCounts, SMarginalCounts, SxJointCounts, SyJointCounts = Fill3DCountTable([xs, ys, Ss])
get 2D from (X;Y): xMarginalCounts=[3 3 3 1], yMarginalCounts=[5 4 1], and xyJointCounts (added axes name FYI):
xy| 4 5 6
--|-------
1 | 2 1 1
2 | 0 2 1
3 | 3 0 0
4 | 0 1 0
get 3D from (X;Y|{Z1,Z2}): SxyJointCounts is of shape 4x4x3, where the first 4 means the cardinality of {Z1,Z2} (00, 01, 10, 11 with respective SMarginalCounts=[3 3 1 3]). SxJointCounts is of shape 4x4 and SyJointCounts is of shape 4x3.
This question already has answers here:
Is there an efficient way to generate N random integers in a range that have a given sum or average?
(6 answers)
Closed 2 years ago.
I would like to generate a list of 15 integers with sum 12, minimum value is 0 and maximum is 6.
I tried following code
def generate(low,high,total,entity):
while sum(entity)!=total:
entity=np.random.randint(low, high, size=15)
return entity
But above function is not working properly. It is too much time consuming.
Please let me know the efficient way to generate such numbers?
The above will, strictly speaking work. But for 15 numbers between 0 and 6, the odds of generating 12 is not that high. In fact we can calculate the number of possibilities with:
F(s, 1) = 1 for 0≤s≤6
and
F(s, n) = Σ6i=0F(s-i, n-1).
We can calculate that with a value:
from functools import lru_cache
#lru_cache()
def f(s, n, mn, mx):
if n < 1:
return 0
if n == 1:
return int(mn <= s <= mx)
else:
if s < mn:
return 0
return sum(f(s-i, n-1, mn, mx) for i in range(mn, mx+1))
That means that there are 9'483'280 possibilities, out of 4'747'561'509'943 total possibilities to generate a sum of 12, or 0.00019975%. It will thus take approximately 500'624 iterations to come up with such solution.
We thus should better aim to find a straight-forward way to generate such sequence. We can do that by each time calculating the probability of generating a number: the probability of generating i as number as first number in a sequence of n numbers that sums up to s is F(s-i, n-1, 0, 6)/F(s, n, 0, 6). This will guarantee that we generate a uniform list over the list of possibilities, if we would each time draw a uniform number, then it will not match a uniform distribution over the entire list of values that match the given condition:
We can do that recursively with:
from numpy import choice
def sumseq(n, s, mn, mx):
if n > 1:
den = f(s, n, mn, mx)
val, = choice(
range(mn, mx+1),
1,
p=[f(s-i, n-1, mn, mx)/den for i in range(mn, mx+1)]
)
yield val
yield from sumseq(n-1, s-val, mn, mx)
elif n > 0:
yield s
With the above function, we can generate numpy arrays:
>>> np.array(list(sumseq(15, 12, 0, 6)))
array([0, 0, 0, 0, 0, 4, 0, 3, 0, 1, 0, 0, 1, 2, 1])
>>> np.array(list(sumseq(15, 12, 0, 6)))
array([0, 0, 1, 0, 0, 1, 4, 1, 0, 0, 2, 1, 0, 0, 2])
>>> np.array(list(sumseq(15, 12, 0, 6)))
array([0, 1, 0, 0, 2, 0, 3, 1, 3, 0, 1, 0, 0, 0, 1])
>>> np.array(list(sumseq(15, 12, 0, 6)))
array([5, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1])
>>> np.array(list(sumseq(15, 12, 0, 6)))
array([0, 0, 0, 0, 4, 2, 3, 0, 0, 0, 0, 0, 3, 0, 0])
You could try it implementing it a little bit differently.
import random
def generate(low,high,goal_sum,size=15):
output = []
for i in range(size):
new_int = random.randint(low,high)
if sum(output) + new_int <= goal_sum:
output.append(new_int)
else:
output.append(0)
random.shuffle(output)
return output
Also, if you use np.random.randint, your high will actually be high-1
Well, there is a simple and natural solution - use distribution which by definition provides you array of values with the fixed sum. Simplest one is Multinomial Distribution. The only code to add is to check and reject (and repeat sampling) if some sampled value is above maximum.
Along the lines
import numpy as np
def sample_sum_interval(n, p, maxv):
while True:
q = np.random.multinomial(n, p)
v = np.where(q > maxv)
if len(v[0]) == 0: # if len(v) > 0, some values are outside the range, reject
return q
return None
np.random.seed(32345)
k = 15
n = 12
maxv = 6
p = np.full((k), np.float64(1.0)/np.float64(k), dtype=np.float64) # probabilities
q = sample_sum_interval(n, p, maxv)
print(q)
print(np.sum(q))
q = sample_sum_interval(n, p, maxv)
print(q)
print(np.sum(q))
q = sample_sum_interval(n, p, maxv)
print(q)
print(np.sum(q))
UPDATE
I quickly looked at #WillemVanOnsem proposed method, and I believe it is different from multinomial used by myself.
If we look at multinomial PMF, and assume equal probabilities for all k numbers,
p1 = ... = pk = 1/k, then we could write PMF as
PMF(x1,...xk)=n!/(x1!...xk!) p1x1...pkxk =
n!/(x1!...xk!) k-x1...k-xk = n!/(x1!...xk!) k-Sumixi = n!/(x1!...xk!) k-n
Obviously, probabilities of particular x1...xk combinations would be different from each other due to factorials in denominator (modulo permutations, of course), which is different from #WillemVanOnsem approach where all of them would have equal probabilities to appear, I believe.
Moral of the story - those methods produce different distributions.
I have an 1 dimensional sorted array and would like to find all pairs of elements whose difference is no larger than 5.
A naive approach would to be to make N^2 comparisons doing something like
diffs = np.tile(x, (x.size,1) ) - x[:, np.newaxis]
D = np.logical_and(diffs>0, diffs<5)
indicies = np.argwhere(D)
Note here that the output of my example are indices of x. If I wanted the values of x which satisfy the criteria, I could do x[indicies].
This works for smaller arrays, but not arrays of the size with which I work.
An idea I had was to find where there are gaps larger than 5 between consecutive elements. I would split the array into two pieces, and compare all the elements in each piece.
Is this a more efficient way of finding elements which satisfy my criteria? How could I go about writing this?
Here is a small example:
x = np.array([ 9, 12,
21,
36, 39, 44, 46, 47,
58,
64, 65,])
the result should look like
array([[ 0, 1],
[ 3, 4],
[ 5, 6],
[ 5, 7],
[ 6, 7],
[ 9, 10]], dtype=int64)
Here is a solution that iterates over offsets while shrinking the set of candidates until there are none left:
import numpy as np
def f_pp(A, maxgap):
d0 = np.diff(A)
d = d0.copy()
IDX = []
k = 1
idx, = np.where(d <= maxgap)
vidx = idx[d[idx] > 0]
while vidx.size:
IDX.append(vidx[:, None] + (0, k))
if idx[-1] + k + 1 == A.size:
idx = idx[:-1]
d[idx] = d[idx] + d0[idx+k]
k += 1
idx = idx[d[idx] <= maxgap]
vidx = idx[d[idx] > 0]
return np.concatenate(IDX, axis=0)
data = np.cumsum(np.random.exponential(size=10000)).repeat(np.random.randint(1, 20, (10000,)))
pairs = f_pp(data, 1)
#pairs = set(map(tuple, pairs))
from timeit import timeit
kwds = dict(globals=globals(), number=100)
print(data.size, 'points', pairs.shape[0], 'close pairs')
print('pp', timeit("f_pp(data, 1)", **kwds)*10, 'ms')
Sample run:
99963 points 1020651 close pairs
pp 43.00256529124454 ms
Your idea of slicing the array is a very efficient approach. Since your data are sorted you can just calculate the difference and split it:
d=np.diff(x)
ind=np.where(d>5)[0]
pieces=np.split(x,ind)
Here pieces is a list, where you can then use in a loop with your own code on every element.
The best algorithm is highly dependent on the nature of your data which I'm unaware. For example another possibility is to write a nested loop:
pairs=[]
for i in range(x.size):
j=i+1
while x[j]-x[i]<=5 and j<x.size:
pairs.append([i,j])
j+=1
If you want it to be more clever, you can edit the outer loop in a way to jump when j hits a gap.
I have an array of points along a line:
a = np.array([18, 56, 32, 75, 55, 55])
I have another array that corresponds to the indices I want to use to access the information in a (they will always have equal lengths). Neither array a nor array b are sorted.
b = np.array([0, 2, 3, 2, 2, 2])
I want to group a into multiple sub-arrays such that the following would be possible:
c[0] -> array([18])
c[2] -> array([56, 75, 55, 55])
c[3] -> array([32])
Although the above example is simple, I will be dealing with millions of points, so efficient methods are preferred. It is also essential later that any sub-array of points can be accessed in this fashion later in the program by automated methods.
Here's one approach -
def groupby(a, b):
# Get argsort indices, to be used to sort a and b in the next steps
sidx = b.argsort(kind='mergesort')
a_sorted = a[sidx]
b_sorted = b[sidx]
# Get the group limit indices (start, stop of groups)
cut_idx = np.flatnonzero(np.r_[True,b_sorted[1:] != b_sorted[:-1],True])
# Split input array with those start, stop ones
out = [a_sorted[i:j] for i,j in zip(cut_idx[:-1],cut_idx[1:])]
return out
A simpler, but lesser efficient approach would be to use np.split to replace the last few lines and get the output, like so -
out = np.split(a_sorted, np.flatnonzero(b_sorted[1:] != b_sorted[:-1])+1 )
Sample run -
In [38]: a
Out[38]: array([18, 56, 32, 75, 55, 55])
In [39]: b
Out[39]: array([0, 2, 3, 2, 2, 2])
In [40]: groupby(a, b)
Out[40]: [array([18]), array([56, 75, 55, 55]), array([32])]
To get sub-arrays covering the entire range of IDs in b -
def groupby_perID(a, b):
# Get argsort indices, to be used to sort a and b in the next steps
sidx = b.argsort(kind='mergesort')
a_sorted = a[sidx]
b_sorted = b[sidx]
# Get the group limit indices (start, stop of groups)
cut_idx = np.flatnonzero(np.r_[True,b_sorted[1:] != b_sorted[:-1],True])
# Create cut indices for all unique IDs in b
n = b_sorted[-1]+2
cut_idxe = np.full(n, cut_idx[-1], dtype=int)
insert_idx = b_sorted[cut_idx[:-1]]
cut_idxe[insert_idx] = cut_idx[:-1]
cut_idxe = np.minimum.accumulate(cut_idxe[::-1])[::-1]
# Split input array with those start, stop ones
out = [a_sorted[i:j] for i,j in zip(cut_idxe[:-1],cut_idxe[1:])]
return out
Sample run -
In [241]: a
Out[241]: array([18, 56, 32, 75, 55, 55])
In [242]: b
Out[242]: array([0, 2, 3, 2, 2, 2])
In [243]: groupby_perID(a, b)
Out[243]: [array([18]), array([], dtype=int64),
array([56, 75, 55, 55]), array([32])]