Very Difficult Indexing Challenge: Do This in One Line - performance

I have data that has N rows with K elements per row. Each element has an integer value (index) between 0 and INDEX_SIZE.
I want to count for every two indexes:
n11[i,j]: in how many rows does index i appear and j appear together.
n10[i,j]: in how many rows does index i appear and j does not.
n01[i,j]: in how many rows does index i not appear and j appears.
n00[i,j]: in how many rows neither index i nor index j appear.
I'd like to do the following code with indexing, much much faster:
N = 10
K = 5
INDEX_SIZE = 100
# Random seed to get the same values every time:
np.random.seed(100)
data = np.random.random_integers(0, INDEX_SIZE-1, (N,K))
# These are for the good values:
n11 = np.zeros((INDEX_SIZE,INDEX_SIZE))
n10 = np.zeros((INDEX_SIZE,INDEX_SIZE))
n01 = np.zeros((INDEX_SIZE,INDEX_SIZE))
n00 = np.zeros((INDEX_SIZE,INDEX_SIZE))
for id1 in range(INDEX_SIZE):
for id2 in range(INDEX_SIZE):
for i in range(data.shape[0]):
if id1 in data[i,:] and id2 in data[i,:]:
n11[id1,id2] += 1
if id1 in data[i,:] and id2 not in data[i,:]:
n10[id1,id2] += 1
if id1 not in data[i,:] and id2 in data[i,:]:
n01[id1,id2] += 1
if id1 not in data[i,:] and id2 not in data[i,:]:
n00[id1,id2] += 1
# These are for the indexing code:
n11v2 = np.zeros((INDEX_SIZE,INDEX_SIZE))
n10v2 = np.zeros((INDEX_SIZE,INDEX_SIZE))
n01v2 = np.zeros((INDEX_SIZE,INDEX_SIZE))
n00v2 = np.zeros((INDEX_SIZE,INDEX_SIZE))
# Code with indexing here:
#
def diff(a,b):
return np.mean(np.abs(a-b))
print('Diff(n11,n11v2) = '+str(diff(n11,n11v2)))
print('Diff(n10,n10v2) = '+str(diff(n10,n10v2)))
print('Diff(n01,n01v2) = '+str(diff(n01,n01v2)))
print('Diff(n00,n00v2) = '+str(diff(n00,n00v2)))
How do I do this over all the rows at once? I believe the for loop can be replaced in one line per counter (so 4 lines in total). I tried itertools and looking up np.indices but could not make any progress. I can easily do this for a single row with a 2D boolean mask (iterating only over rows). But this is too slow.
EDIT: fixed random integer generation

Here is a solution using sparse matrices. It's not one line per output. (It's two but I'm saving four lines by not using the preallocation.) It's reasonably fast, though (~1 min for N=10^6, K=150, INDEX_SIZE=500).
## These are for the indexing code:
#n11v2 = np.zeros((INDEX_SIZE,INDEX_SIZE))
#n10v2 = np.zeros((INDEX_SIZE,INDEX_SIZE))
#n01v2 = np.zeros((INDEX_SIZE,INDEX_SIZE))
#n00v2 = np.zeros((INDEX_SIZE,INDEX_SIZE))
# Code with indexing here:
from scipy import sparse
spD = sparse.csr_matrix((np.ones(data.size, np.int32), data.ravel(),
np.arange(0, N*K+1, K, np.int32)), (N, INDEX_SIZE))
spD.sum_duplicates()
spD.data = np.ones_like(spD.data)
n11v2 = (spD.T#spD).A
m = np.einsum('ii->i', n11v2)[:, None]
n10v2 = m - n11v2
n01v2 = n10v2.T
n00v2 = N + n11v2 - m - m.T

Related

Create sparse matrix in parallel in Julia

I am trying to parallelize the creation of a sparse matrix in Julia. Inspired by this post this post I am trying this:
using Distributed
addprocs(4)
#everywhere using DistributedArrays
rows = [Int[] for _ in procs()]
cols = [Int[] for _ in procs()]
vals = [Float64[] for _ in procs()]
distribute(rows)
distribute(cols)
distribute(vals)
#sync #distributed for i = 1:1000
for j = 1:1000
v = exp(-(i - j)^2)
if v > 0.1
push!(localpart(rows)[1], i)
push!(localpart(cols)[1], j)
push!(localpart(vals)[1], v)
end
end
end
ROWS = vcat(rows...)
COLS = vcat(cols...)
VALS = vcat(vals...)
K = sparse(ROWS, COLS, VALS)
# K = 0×0 SparseMatrixCSC{Float64, Int64} with 0 stored entries
This outputs an empty matrix, and it does not get filled. But I found that if I call #fetchfrom 2 rows, the rows that it creates is not empty. So it seems that it is just not combining everything.
How can I fix this?
distribute(rows) does not modify rows to be distributed; it returns a new distributed array filled with the input. You have to work with its result, something like
rows = distribute([Int[] for _ in procs()])

get pairs / triple / quadruple... of elements from vector by function

I have a vector with a couple of elements and I want to write a function that returns me all combinations of x items from this vector.
The following code produces the right output for the case x=2 or x=3 or x=4.
However, I can not implement a solution for every possible x following this idea.
values = {'A','B','C','D','E'};
n = length(values);
data2 = {}; % case x=2
for i = 1:n
for j = i+1:n
data2{end+1} = {values{i}, values{j}};
fprintf('%s %s\n',values{i}, values{j})
end
end
data3 = {}; % case x=3
for i = 1:n
for j = i+1:n
for k = j+1:n
data3{end+1} = {values{i}, values{j}, values{k}};
fprintf('%s %s %s\n',values{i}, values{j}, values{k})
end
end
end
data4 = {}; % case x=4
for i = 1:n
for j = i+1:n
for k = j+1:n
for l = k+1:n
data4{end+1} = {values{i}, values{j}, values{k}, values{l}};
fprintf('%s %s %s %s\n',values{i}, values{j}, values{k}, values{l})
end
end
end
end
How would a function look like which would be able to return my data variable?
data = getCombinations(values, x) %values is vector with elements, x is integer value
EDIT
The following code comes pretty close:
data = perms(values)
data = data(:,1:x)
data = unique(data,'rows')
but it still produces output like A,B and B,A
EDIT2
This fixed it somehow but it is not very nice to look at and it does not work for text entries in cells but only for numbers
data = perms(values)
data = data(:,1:x)
data = sort(data,2)
data = unique(data,'rows')
EDIT3
This did it but it is not very nice to look at... Maybe there is a better solution?
function [data] = getCombinations(values,x)
i = 1:length(values);
d = perms(i);
d = d(:,1:x);
d = sort(d,2);
d = unique(d,'rows');
data = v(d);
end
If you don't want repetitions (and your example suggests you don't) then try nchoosek as nchoosek(1:n, x) to give indices:
values = {'A','B','C','D','E'};
n = length(values);
x = 3;
C = nchoosek(1:n, x);
data = values(C)
In the above, each row is a unique combination of 3 of the 5 elements of values.
Alternatively pass in the values directly:
data = nchoosek(values, x);

Algorithm for equiprobable random square binary matrices with two non-adjacent non-zeros in each row and column

It would be great if someone could point me towards an algorithm that would allow me to :
create a random square matrix, with entries 0 and 1, such that
every row and every column contain exactly two non-zero entries,
two non-zero entries cannot be adjacent,
all possible matrices are equiprobable.
Right now I manage to achieve points 1 and 2 doing the following : such a matrix can be transformed, using suitable permutations of rows and columns, into a diagonal block matrix with blocks of the form
1 1 0 0 ... 0
0 1 1 0 ... 0
0 0 1 1 ... 0
.............
1 0 0 0 ... 1
So I start from such a matrix using a partition of [0, ..., n-1] and scramble it by permuting rows and columns randomly. Unfortunately, I can't find a way to integrate the adjacency condition, and I am quite sure that my algorithm won't treat all the matrices equally.
Update
I have managed to achieve point 3. The answer was actually straight under my nose : the block matrix I am creating contains all the information needed to take into account the adjacency condition. First some properties and definitions:
a suitable matrix defines permutations of [1, ..., n] that can be build like so: select a 1 in row 1. The column containing this entry contains exactly one other entry equal to 1 on a row a different from 1. Again, row a contains another entry 1 in a column which contains a second entry 1 on a row b, and so on. This starts a permutation 1 -> a -> b ....
For instance, with the following matrix, starting with the marked entry
v
1 0 1 0 0 0 | 1
0 1 0 0 0 1 | 2
1 0 0 1 0 0 | 3
0 0 1 0 1 0 | 4
0 0 0 1 0 1 | 5
0 1 0 0 1 0 | 6
------------+--
1 2 3 4 5 6 |
we get permutation 1 -> 3 -> 5 -> 2 -> 6 -> 4 -> 1.
the cycles of such a permutation lead to the block matrix I mentioned earlier. I also mentioned scrambling the block matrix using arbitrary permutations on the rows and columns to rebuild a matrix compatible with the requirements.
But I was using any permutation, which led to some adjacent non-zero entries. To avoid that, I have to choose permutations that separate rows (and columns) that are adjacent in the block matrix. Actually, to be more precise, if two rows belong to a same block and are cyclically consecutive (the first and last rows of a block are considered consecutive too), then the permutation I want to apply has to move these rows into non-consecutive rows of the final matrix (I will call two rows incompatible in that case).
So the question becomes : How to build all such permutations ?
The simplest idea is to build a permutation progressively by randomly adding rows that are compatible with the previous one. As an example, consider the case n = 6 using partition 6 = 3 + 3 and the corresponding block matrix
1 1 0 0 0 0 | 1
0 1 1 0 0 0 | 2
1 0 1 0 0 0 | 3
0 0 0 1 1 0 | 4
0 0 0 0 1 1 | 5
0 0 0 1 0 1 | 6
------------+--
1 2 3 4 5 6 |
Here rows 1, 2 and 3 are mutually incompatible, as are 4, 5 and 6. Choose a random row, say 3.
We will write a permutation as an array: [2, 5, 6, 4, 3, 1] meaning 1 -> 2, 2 -> 5, 3 -> 6, ... This means that row 2 of the block matrix will become the first row of the final matrix, row 5 will become the second row, and so on.
Now let's build a suitable permutation by choosing randomly a row, say 3:
p = [3, ...]
The next row will then be chosen randomly among the remaining rows that are compatible with 3 : 4, 5and 6. Say we choose 4:
p = [3, 4, ...]
Next choice has to be made among 1 and 2, for instance 1:
p = [3, 4, 1, ...]
And so on: p = [3, 4, 1, 5, 2, 6].
Applying this permutation to the block matrix, we get:
1 0 1 0 0 0 | 3
0 0 0 1 1 0 | 4
1 1 0 0 0 0 | 1
0 0 0 0 1 1 | 5
0 1 1 0 0 0 | 2
0 0 0 1 0 1 | 6
------------+--
1 2 3 4 5 6 |
Doing so, we manage to vertically isolate all non-zero entries. Same has to be done with the columns, for instance by using permutation p' = [6, 3, 5, 1, 4, 2] to finally get
0 1 0 1 0 0 | 3
0 0 1 0 1 0 | 4
0 0 0 1 0 1 | 1
1 0 1 0 0 0 | 5
0 1 0 0 0 1 | 2
1 0 0 0 1 0 | 6
------------+--
6 3 5 1 4 2 |
So this seems to work quite efficiently, but building these permutations needs to be done with caution, because one can easily be stuck: for instance, with n=6 and partition 6 = 2 + 2 + 2, following the construction rules set up earlier can lead to p = [1, 3, 2, 4, ...]. Unfortunately, 5 and 6 are incompatible, so choosing one or the other makes the last choice impossible. I think I've found all situations that lead to a dead end. I will denote by r the set of remaining choices:
p = [..., x, ?], r = {y} with x and y incompatible
p = [..., x, ?, ?], r = {y, z} with y and z being both incompatible with x (no choice can be made)
p = [..., ?, ?], r = {x, y} with x and y incompatible (any choice would lead to situation 1)
p = [..., ?, ?, ?], r = {x, y, z} with x, y and z being cyclically consecutive (choosing x or z would lead to situation 2, choosing y to situation 3)
p = [..., w, ?, ?, ?], r = {x, y, z} with xwy being a 3-cycle (neither x nor y can be chosen, choosing z would lead to situation 3)
p = [..., ?, ?, ?, ?], r = {w, x, y, z} with wxyz being a 4-cycle (any choice would lead to situation 4)
p = [..., ?, ?, ?, ?], r = {w, x, y, z} with xyz being a 3-cycle (choosing w would lead to situation 4, choosing any other would lead to situation 4)
Now it seems that the following algorithm gives all suitable permutations:
As long as there are strictly more than 5 numbers to choose, choose randomly among the compatible ones.
If there are 5 numbers left to choose: if the remaining numbers contain a 3-cycle or a 4-cycle, break that cycle (i.e. choose a number belonging to that cycle).
If there are 4 numbers left to choose: if the remaining numbers contain three cyclically consecutive numbers, choose one of them.
If there are 3 numbers left to choose: if the remaining numbers contain two cyclically consecutive numbers, choose one of them.
I am quite sure that this allows me to generate all suitable permutations and, hence, all suitable matrices.
Unfortunately, every matrix will be obtained several times, depending on the partition that was chosen.
Intro
Here is some prototype-approach, trying to solve the more general task of
uniform combinatorial sampling, which for our approach here means: we can use this approach for everything which we can formulate as SAT-problem.
It's not exploiting your problem directly and takes a heavy detour. This detour to the SAT-problem can help in regards to theory (more powerful general theoretical results) and efficiency (SAT-solvers).
That being said, it's not an approach if you want to sample within seconds or less (in my experiments), at least while being concerned about uniformity.
Theory
The approach, based on results from complexity-theory, follows this work:
GOMES, Carla P.; SABHARWAL, Ashish; SELMAN, Bart. Near-uniform sampling of combinatorial spaces using XOR constraints. In: Advances In Neural Information Processing Systems. 2007. S. 481-488.
The basic idea:
formulate the problem as SAT-problem
add randomly generated xors to the problem (acting on the decision-variables only! that's important in practice)
this will reduce the number of solutions (some solutions will get impossible)
do that in a loop (with tuned parameters) until only one solution is left!
search for some solution is being done by SAT-solvers or #SAT-solvers (=model-counting)
if there is more than one solution: no xors will be added but a complete restart will be done: add random-xors to the start-problem!
The guarantees:
when tuning the parameters right, this approach achieves near-uniform sampling
this tuning can be costly, as it's based on approximating the number of possible solutions
empirically this can also be costly!
Ante's answer, mentioning the number sequence A001499 actually gives a nice upper bound on the solution-space (as it's just ignoring adjacency-constraints!)
The drawbacks:
inefficient for large problems (in general; not necessarily compared to the alternatives like MCMC and co.)
need to change / reduce parameters to produce samples
those reduced parameters lose the theoretical guarantees
but empirically: good results are still possible!
Parameters:
In practice, the parameters are:
N: number of xors added
L: minimum number of variables part of one xor-constraint
U: maximum number of variables part of one xor-constraint
N is important to reduce the number of possible solutions. Given N constant, the other variables of course also have some effect on that.
Theory says (if i interpret correctly), that we should use L = R = 0.5 * #dec-vars.
This is impossible in practice here, as xor-constraints hurt SAT-solvers a lot!
Here some more scientific slides about the impact of L and U.
They call xors of size 8-20 short-XORS, while we will need to use even shorter ones later!
Implementation
Final version
Here is a pretty hacky implementation in python, using the XorSample scripts from here.
The underlying SAT-solver in use is Cryptominisat.
The code basically boils down to:
Transform the problem to conjunctive normal-form
as DIMACS-CNF
Implement the sampling-approach:
Calls XorSample (pipe-based + file-based)
Call SAT-solver (file-based)
Add samples to some file for later analysis
Code: (i hope i did warn you already about the code-quality)
from itertools import count
from time import time
import subprocess
import numpy as np
import os
import shelve
import uuid
import pickle
from random import SystemRandom
cryptogen = SystemRandom()
""" Helper functions """
# K-ARY CONSTRAINT GENERATION
# ###########################
# SINZ, Carsten. Towards an optimal CNF encoding of boolean cardinality constraints.
# CP, 2005, 3709. Jg., S. 827-831.
def next_var_index(start):
next_var = start
while(True):
yield next_var
next_var += 1
class s_index():
def __init__(self, start_index):
self.firstEnvVar = start_index
def next(self,i,j,k):
return self.firstEnvVar + i*k +j
def gen_seq_circuit(k, input_indices, next_var_index_gen):
cnf_string = ''
s_index_gen = s_index(next_var_index_gen.next())
# write clauses of first partial sum (i.e. i=0)
cnf_string += (str(-input_indices[0]) + ' ' + str(s_index_gen.next(0,0,k)) + ' 0\n')
for i in range(1, k):
cnf_string += (str(-s_index_gen.next(0, i, k)) + ' 0\n')
# write clauses for general case (i.e. 0 < i < n-1)
for i in range(1, len(input_indices)-1):
cnf_string += (str(-input_indices[i]) + ' ' + str(s_index_gen.next(i, 0, k)) + ' 0\n')
cnf_string += (str(-s_index_gen.next(i-1, 0, k)) + ' ' + str(s_index_gen.next(i, 0, k)) + ' 0\n')
for u in range(1, k):
cnf_string += (str(-input_indices[i]) + ' ' + str(-s_index_gen.next(i-1, u-1, k)) + ' ' + str(s_index_gen.next(i, u, k)) + ' 0\n')
cnf_string += (str(-s_index_gen.next(i-1, u, k)) + ' ' + str(s_index_gen.next(i, u, k)) + ' 0\n')
cnf_string += (str(-input_indices[i]) + ' ' + str(-s_index_gen.next(i-1, k-1, k)) + ' 0\n')
# last clause for last variable
cnf_string += (str(-input_indices[-1]) + ' ' + str(-s_index_gen.next(len(input_indices)-2, k-1, k)) + ' 0\n')
return (cnf_string, (len(input_indices)-1)*k, 2*len(input_indices)*k + len(input_indices) - 3*k - 1)
# K=2 clause GENERATION
# #####################
def gen_at_most_2_constraints(vars, start_var):
constraint_string = ''
used_clauses = 0
used_vars = 0
index_gen = next_var_index(start_var)
circuit = gen_seq_circuit(2, vars, index_gen)
constraint_string += circuit[0]
used_clauses += circuit[2]
used_vars += circuit[1]
start_var += circuit[1]
return [constraint_string, used_clauses, used_vars, start_var]
def gen_at_least_2_constraints(vars, start_var):
k = len(vars) - 2
vars = [-var for var in vars]
constraint_string = ''
used_clauses = 0
used_vars = 0
index_gen = next_var_index(start_var)
circuit = gen_seq_circuit(k, vars, index_gen)
constraint_string += circuit[0]
used_clauses += circuit[2]
used_vars += circuit[1]
start_var += circuit[1]
return [constraint_string, used_clauses, used_vars, start_var]
# Adjacency conflicts
# ###################
def get_all_adjacency_conflicts_4_neighborhood(N, X):
conflicts = set()
for x in range(N):
for y in range(N):
if x < (N-1):
conflicts.add(((x,y),(x+1,y)))
if y < (N-1):
conflicts.add(((x,y),(x,y+1)))
cnf = '' # slow string appends
for (var_a, var_b) in conflicts:
var_a_ = X[var_a]
var_b_ = X[var_b]
cnf += '-' + var_a_ + ' ' + '-' + var_b_ + ' 0 \n'
return cnf, len(conflicts)
# Build SAT-CNF
#############
def build_cnf(N, verbose=False):
var_counter = count(1)
N_CLAUSES = 0
X = np.zeros((N, N), dtype=object)
for a in range(N):
for b in range(N):
X[a,b] = str(next(var_counter))
# Adjacency constraints
CNF, N_CLAUSES = get_all_adjacency_conflicts_4_neighborhood(N, X)
# k=2 constraints
NEXT_VAR = N*N+1
for row in range(N):
constraint_string, used_clauses, used_vars, NEXT_VAR = gen_at_most_2_constraints(X[row, :].astype(int).tolist(), NEXT_VAR)
N_CLAUSES += used_clauses
CNF += constraint_string
constraint_string, used_clauses, used_vars, NEXT_VAR = gen_at_least_2_constraints(X[row, :].astype(int).tolist(), NEXT_VAR)
N_CLAUSES += used_clauses
CNF += constraint_string
for col in range(N):
constraint_string, used_clauses, used_vars, NEXT_VAR = gen_at_most_2_constraints(X[:, col].astype(int).tolist(), NEXT_VAR)
N_CLAUSES += used_clauses
CNF += constraint_string
constraint_string, used_clauses, used_vars, NEXT_VAR = gen_at_least_2_constraints(X[:, col].astype(int).tolist(), NEXT_VAR)
N_CLAUSES += used_clauses
CNF += constraint_string
# build final cnf
CNF = 'p cnf ' + str(NEXT_VAR-1) + ' ' + str(N_CLAUSES) + '\n' + CNF
return X, CNF, NEXT_VAR-1
# External tools
# ##############
def get_random_xor_problem(CNF_IN_fp, N_DEC_VARS, N_ALL_VARS, s, min_l, max_l):
# .cnf not part of arg!
p = subprocess.Popen(['./gen-wff', CNF_IN_fp,
str(N_DEC_VARS), str(N_ALL_VARS),
str(s), str(min_l), str(max_l), 'xored'],
stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
result = p.communicate()
os.remove(CNF_IN_fp + '-str-xored.xor') # file not needed
return CNF_IN_fp + '-str-xored.cnf'
def solve(CNF_IN_fp, N_DEC_VARS):
seed = cryptogen.randint(0, 2147483647) # actually no reason to do it; but can't hurt either
p = subprocess.Popen(["./cryptominisat5", '-t', '4', '-r', str(seed), CNF_IN_fp], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
result = p.communicate()[0]
sat_line = result.find('s SATISFIABLE')
if sat_line != -1:
# solution found!
vars = parse_solution(result)[:N_DEC_VARS]
# forbid solution (DeMorgan)
negated_vars = list(map(lambda x: x*(-1), vars))
with open(CNF_IN_fp, 'a') as f:
f.write( (str(negated_vars)[1:-1] + ' 0\n').replace(',', ''))
# assume solve is treating last constraint despite not changing header!
# solve again
seed = cryptogen.randint(0, 2147483647)
p = subprocess.Popen(["./cryptominisat5", '-t', '4', '-r', str(seed), CNF_IN_fp], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
result = p.communicate()[0]
sat_line = result.find('s SATISFIABLE')
if sat_line != -1:
os.remove(CNF_IN_fp) # not needed anymore
return True, False, None
else:
return True, True, vars
else:
return False, False, None
def parse_solution(output):
# assumes there is one
vars = []
for line in output.split("\n"):
if line:
if line[0] == 'v':
line_vars = list(map(lambda x: int(x), line.split()[1:]))
vars.extend(line_vars)
return vars
# Core-algorithm
# ##############
def xorsample(X, CNF_IN_fp, N_DEC_VARS, N_VARS, s, min_l, max_l):
start_time = time()
while True:
# add s random XOR constraints to F
xored_cnf_fp = get_random_xor_problem(CNF_IN_fp, N_DEC_VARS, N_VARS, s, min_l, max_l)
state_lvl1, state_lvl2, var_sol = solve(xored_cnf_fp, N_DEC_VARS)
print('------------')
if state_lvl1 and state_lvl2:
print('FOUND')
d = shelve.open('N_15_70_4_6_TO_PLOT')
d[str(uuid.uuid4())] = (pickle.dumps(var_sol), time() - start_time)
d.close()
return True
else:
if state_lvl1:
print('sol not unique')
else:
print('no sol found')
print('------------')
""" Run """
N = 15
N_DEC_VARS = N*N
X, CNF, N_VARS = build_cnf(N)
with open('my_problem.cnf', 'w') as f:
f.write(CNF)
counter = 0
while True:
print('sample: ', counter)
xorsample(X, 'my_problem', N_DEC_VARS, N_VARS, 70, 4, 6)
counter += 1
Output will look like (removed some warnings):
------------
no sol found
------------
------------
no sol found
------------
------------
no sol found
------------
------------
sol not unique
------------
------------
FOUND
Core: CNF-formulation
We introduce one variable for every cell of the matrix. N=20 means 400 binary-variables.
Adjancency:
Precalculate all symmetry-reduced conflicts and add conflict-clauses.
Basic theory:
a -> !b
<->
!a v !b (propositional logic)
Row/Col-wise Cardinality:
This is tough to express in CNF and naive approaches need an exponential number
of constraints.
We use some adder-circuit based encoding (SINZ, Carsten. Towards an optimal CNF encoding of boolean cardinality constraints) which introduces new auxiliary-variables.
Remark:
sum(var_set) <= k
<->
sum(negated(var_set)) >= len(var_set) - k
These SAT-encodings can be put into exact model-counters (for small N; e.g. < 9). The number of solutions equals Ante's results, which is a strong indication for a correct transformation!
There are also interesting approximate model-counters (also heavily based on xor-constraints) like approxMC which shows one more thing we can do with the SAT-formulation. But in practice i have not been able to use these (approxMC = autoconf; no comment).
Other experiments
I did also build a version using pblib, to use more powerful cardinality-formulations
for the SAT-CNF formulation. I did not try to use the C++-based API, but only the reduced pbencoder, which automatically selects some best encoding, which was way worse than my encoding used above (which is best is still a research-problem; often even redundant-constraints can help).
Empirical analysis
For the sake of obtaining some sample-size (given my patience), i only computed samples for N=15. In this case we used:
N=70 xors
L,U = 4,6
I also computed some samples for N=20 with (100,3,6), but this takes a few mins and we reduced the lower bound!
Visualization
Here some animation (strengthening my love-hate relationship with matplotlib):
Edit: And a (reduced) comparison to brute-force uniform-sampling with N=5 (NXOR,L,U = 4, 10, 30):
(I have not yet decided on the addition of the plotting-code. It's as ugly as the above one and people might look too much into my statistical shambles; normalizations and co.)
Theory
Statistical analysis is probably hard to do as the underlying problem is of such combinatoric nature. It's even not entirely obvious how that final cell-PDF should look like. In the case of N=odd, it's probably non-uniform and looks like a chess-board (i did brute-force check N=5 to observe this).
One thing we can be sure about (imho): symmetry!
Given a cell-PDF matrix, we should expect, that the matrix is symmetric (A = A.T).
This is checked in the visualization and the euclidean-norm of differences over time is plotted.
We can do the same on some other observation: observed pairings.
For N=3, we can observe the following pairs:
0,1
0,2
1,2
Now we can do this per-row and per-column and should expect symmetry too!
Sadly, it's probably not easy to say something about the variance and therefore the needed samples to speak about confidence!
Observation
According to my simplified perception, current-samples and the cell-PDF look good, although convergence is not achieved yet (or we are far away from uniformity).
The more important aspect are probably the two norms, nicely decreasing towards 0.
(yes; one could tune some algorithm for that by transposing with prob=0.5; but this is not done here as it would defeat it's purpose).
Potential next steps
Tune parameters
Check out the approach using #SAT-solvers / Model-counters instead of SAT-solvers
Try different CNF-formulations, especially in regards to cardinality-encodings and xor-encodings
XorSample is by default using tseitin-like encoding to get around exponentially grow
for smaller xors (as used) it might be a good idea to use naive encoding (which propagates faster)
XorSample supports that in theory; but the script's work differently in practice
Cryptominisat is known for dedicated XOR-handling (as it was build for analyzing cryptography including many xors) and might gain something by naive encoding (as inferring xors from blown-up CNFs is much harder)
More statistical-analysis
Get rid of XorSample scripts (shell + perl...)
Summary
The approach is very general
This code produces feasible samples
It should be not hard to prove, that every feasible solution can be sampled
Others have proven theoretical guarantees for uniformity for some params
does not hold for our params
Others have empirically / theoretically analyzed smaller parameters (in use here)
(Updated test results, example run-through and code snippets below.)
You can use dynamic programming to calculate the number of solutions resulting from every state (in a much more efficient way than a brute-force algorithm), and use those (pre-calculated) values to create equiprobable random solutions.
Consider the example of a 7x7 matrix; at the start, the state is:
0,0,0,0,0,0,0
meaning that there are seven adjacent unused columns. After adding two ones to the first row, the state could be e.g.:
0,1,0,0,1,0,0
with two columns that now have a one in them. After adding ones to the second row, the state could be e.g.:
0,1,1,0,1,0,1
After three rows are filled, there is a possibility that a column will have its maximum of two ones; this effectively splits the matrix into two independent zones:
1,1,1,0,2,0,1 -> 1,1,1,0 + 0,1
These zones are independent in the sense that the no-adjacent-ones rule has no effect when adding ones to different zones, and the order of the zones has no effect on the number of solutions.
In order to use these states as signatures for types of solutions, we have to transform them into a canonical notation. First, we have to take into account the fact that columns with only 1 one in them may be unusable in the next row, because they contain a one in the current row. So instead of a binary notation, we have to use a ternary notation, e.g.:
2,1,1,0 + 0,1
where the 2 means that this column was used in the current row (and not that there are 2 ones in the column). At the next step, we should then convert the twos back into ones.
Additionally, we can also mirror the seperate groups to put them into their lexicographically smallest notation:
2,1,1,0 + 0,1 -> 0,1,1,2 + 0,1
Lastly, we sort the seperate groups from small to large, and then lexicographically, so that a state in a larger matrix may be e.g.:
0,0 + 0,1 + 0,0,2 + 0,1,0 + 0,1,0,1
Then, when calculating the number of solutions resulting from each state, we can use memoization using the canonical notation of each state as a key.
Creating a dictionary of the states and the number of solutions for each of them only needs to be done once, and a table for larger matrices can probably be used for smaller matrices too.
Practically, you'd generate a random number between 0 and the total number of solutions, and then for every row, you'd look at the different states you could create from the current state, look at the number of unique solutions each one would generate, and see which option leads to the solution that corresponds with your randomly generated number.
Note that every state and the corresponding key can only occur in a particular row, so you can store the keys in seperate dictionaries per row.
TEST RESULTS
A first test using unoptimized JavaScript gave very promising results. With dynamic programming, calculating the number of solutions for a 10x10 matrix now takes a second, where a brute-force algorithm took several hours (and this is the part of the algorithm that only needs to be done once). The size of the dictionary with the signatures and numbers of solutions grows with a diminishing factor approaching 2.5 for each step in size; the time to generate it grows with a factor of around 3.
These are the number of solutions, states, signatures (total size of the dictionaries), and maximum number of signatures per row (largest dictionary per row) that are created:
size unique solutions states signatures max/row
4x4 2 9 6 2
5x5 16 73 26 8
6x6 722 514 107 40
7x7 33,988 2,870 411 152
8x8 2,215,764 13,485 1,411 596
9x9 179,431,924 56,375 4,510 1,983
10x10 17,849,077,140 218,038 13,453 5,672
11x11 2,138,979,146,276 801,266 38,314 14,491
12x12 304,243,884,374,412 2,847,885 104,764 35,803
13x13 50,702,643,217,809,908 9,901,431 278,561 96,414
14x14 9,789,567,606,147,948,364 33,911,578 723,306 238,359
15x15 2,168,538,331,223,656,364,084 114,897,838 1,845,861 548,409
16x16 546,386,962,452,256,865,969,596 ... 4,952,501 1,444,487
17x17 155,420,047,516,794,379,573,558,433 12,837,870 3,754,040
18x18 48,614,566,676,379,251,956,711,945,475 31,452,747 8,992,972
19x19 17,139,174,923,928,277,182,879,888,254,495 74,818,773 20,929,008
20x20 6,688,262,914,418,168,812,086,412,204,858,650 175,678,000 50,094,203
(Additional results obtained with C++, using a simple 128-bit integer implementation. To count the states, the code had to be run using each state as a seperate signature, which I was unable to do for the largest sizes. )
EXAMPLE
The dictionary for a 5x5 matrix looks like this:
row 0: 00000 -> 16 row 3: 101 -> 0
1112 -> 1
row 1: 20002 -> 2 1121 -> 1
00202 -> 4 1+01 -> 0
02002 -> 2 11+12 -> 2
02020 -> 2 1+121 -> 1
0+1+1 -> 0
row 2: 10212 -> 1 1+112 -> 1
12012 -> 1
12021 -> 2 row 4: 0 -> 0
12102 -> 1 11 -> 0
21012 -> 0 12 -> 0
02121 -> 3 1+1 -> 1
01212 -> 1 1+2 -> 0
The total number of solutions is 16; if we randomly pick a number from 0 to 15, e.g. 13, we can find the corresponding (i.e. the 14th) solution like this:
state: 00000
options: 10100 10010 10001 01010 01001 00101
signature: 00202 02002 20002 02020 02002 00202
solutions: 4 2 2 2 2 4
This tells us that the 14th solution is the 2nd solution of option 00101. The next step is:
state: 00101
options: 10010 01010
signature: 12102 02121
solutions: 1 3
This tells us that the 2nd solution is the 1st solution of option 01010. The next step is:
state: 01111
options: 10100 10001 00101
signature: 11+12 1112 1+01
solutions: 2 1 0
This tells us that the 1st solution is the 1st solution of option 10100. The next step is:
state: 11211
options: 01010 01001
signature: 1+1 1+1
solutions: 1 1
This tells us that the 1st solutions is the 1st solution of option 01010. The last step is:
state: 12221
options: 10001
And the 5x5 matrix corresponding to randomly chosen number 13 is:
0 0 1 0 1
0 1 0 1 0
1 0 1 0 0
0 1 0 1 0
1 0 0 0 1
And here's a quick'n'dirty code example; run the snippet to generate the signature and solution count dictionary, and generate a random 10x10 matrix (it takes a second to generate the dictionary; once that is done, it generates random solutions in half a millisecond):
function signature(state, prev) {
var zones = [], zone = [];
for (var i = 0; i < state.length; i++) {
if (state[i] == 2) {
if (zone.length) zones.push(mirror(zone));
zone = [];
}
else if (prev[i]) zone.push(3);
else zone.push(state[i]);
}
if (zone.length) zones.push(mirror(zone));
zones.sort(function(a,b) {return a.length - b.length || a - b;});
return zones.length ? zones.join("2") : "2";
function mirror(zone) {
var ltr = zone.join('');
zone.reverse();
var rtl = zone.join('');
return (ltr < rtl) ? ltr : rtl;
}
}
function memoize(n) {
var memo = [], empty = [];
for (var i = 0; i <= n; i++) memo[i] = [];
for (var i = 0; i < n; i++) empty[i] = 0;
memo[0][signature(empty, empty)] = next_row(empty, empty, 1);
return memo;
function next_row(state, prev, row) {
if (row > n) return 1;
var solutions = 0;
for (var i = 0; i < n - 2; i++) {
if (state[i] == 2 || prev[i] == 1) continue;
for (var j = i + 2; j < n; j++) {
if (state[j] == 2 || prev[j] == 1) continue;
var s = state.slice(), p = empty.slice();
++s[i]; ++s[j]; ++p[i]; ++p[j];
var sig = signature(s, p);
var sol = memo[row][sig];
if (sol == undefined)
memo[row][sig] = sol = next_row(s, p, row + 1);
solutions += sol;
}
}
return solutions;
}
}
function random_matrix(n, memo) {
var matrix = [], empty = [], state = [], prev = [];
for (var i = 0; i < n; i++) empty[i] = state[i] = prev[i] = 0;
var total = memo[0][signature(empty, empty)];
var pick = Math.floor(Math.random() * total);
document.write("solution " + pick.toLocaleString('en-US') +
" from a total of " + total.toLocaleString('en-US') + "<br>");
for (var row = 1; row <= n; row++) {
var options = find_options(state, prev);
for (var i in options) {
var state_copy = state.slice();
for (var j in state_copy) state_copy[j] += options[i][j];
var sig = signature(state_copy, options[i]);
var solutions = memo[row][sig];
if (pick < solutions) {
matrix.push(options[i].slice());
prev = options[i].slice();
state = state_copy.slice();
break;
}
else pick -= solutions;
}
}
return matrix;
function find_options(state, prev) {
var options = [];
for (var i = 0; i < n - 2; i++) {
if (state[i] == 2 || prev[i] == 1) continue;
for (var j = i + 2; j < n; j++) {
if (state[j] == 2 || prev[j] == 1) continue;
var option = empty.slice();
++option[i]; ++option[j];
options.push(option);
}
}
return options;
}
}
var size = 10;
var memo = memoize(size);
var matrix = random_matrix(size, memo);
for (var row in matrix) document.write(matrix[row] + "<br>");
The code snippet below shows the dictionary of signatures and solution counts for a matrix of size 10x10. I've used a slightly different signature format from the explanation above: the zones are delimited by a '2' instead of a plus sign, and a column which has a one in the previous row is marked with a '3' instead of a '2'. This shows how the keys could be stored in a file as integers with 2×N bits (padded with 2's).
function signature(state, prev) {
var zones = [], zone = [];
for (var i = 0; i < state.length; i++) {
if (state[i] == 2) {
if (zone.length) zones.push(mirror(zone));
zone = [];
}
else if (prev[i]) zone.push(3);
else zone.push(state[i]);
}
if (zone.length) zones.push(mirror(zone));
zones.sort(function(a,b) {return a.length - b.length || a - b;});
return zones.length ? zones.join("2") : "2";
function mirror(zone) {
var ltr = zone.join('');
zone.reverse();
var rtl = zone.join('');
return (ltr < rtl) ? ltr : rtl;
}
}
function memoize(n) {
var memo = [], empty = [];
for (var i = 0; i <= n; i++) memo[i] = [];
for (var i = 0; i < n; i++) empty[i] = 0;
memo[0][signature(empty, empty)] = next_row(empty, empty, 1);
return memo;
function next_row(state, prev, row) {
if (row > n) return 1;
var solutions = 0;
for (var i = 0; i < n - 2; i++) {
if (state[i] == 2 || prev[i] == 1) continue;
for (var j = i + 2; j < n; j++) {
if (state[j] == 2 || prev[j] == 1) continue;
var s = state.slice(), p = empty.slice();
++s[i]; ++s[j]; ++p[i]; ++p[j];
var sig = signature(s, p);
var sol = memo[row][sig];
if (sol == undefined)
memo[row][sig] = sol = next_row(s, p, row + 1);
solutions += sol;
}
}
return solutions;
}
}
var memo = memoize(10);
for (var i in memo) {
document.write("row " + i + ":<br>");
for (var j in memo[i]) {
document.write(""" + j + "": " + memo[i][j] + "<br>");
}
}
Just few thoughts. Number of matrices satisfying conditions for n <= 10:
3 0
4 2
5 16
6 722
7 33988
8 2215764
9 179431924
10 17849077140
Unfortunatelly there is no sequence with these numbers in OEIS.
There is one similar (A001499), without condition for neighbouring one's. Number of nxn matrices in this case is 'of order' as A001499's number of (n-1)x(n-1) matrices. That is to be expected since number
of ways to fill one row in this case, position 2 one's in n places with at least one zero between them is ((n-1) choose 2). Same as to position 2 one's in (n-1) places without the restriction.
I don't think there is an easy connection between these matrix of order n and A001499 matrix of order n-1, meaning that if we have A001499 matrix than we can construct some of these matrices.
With this, for n=20, number of matrices is >10^30. Quite a lot :-/
This solution use recursion in order to set the cell of the matrix one by one. If the random walk finish with an impossible solution then we rollback one step in the tree and we continue the random walk.
The algorithm is efficient and i think that the generated data are highly equiprobable.
package rndsqmatrix;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.stream.IntStream;
public class RndSqMatrix {
/**
* Generate a random matrix
* #param size the size of the matrix
* #return the matrix encoded in 1d array i=(x+y*size)
*/
public static int[] generate(final int size) {
return generate(size, new int[size * size], new int[size],
new int[size]);
}
/**
* Build a matrix recursivly with a random walk
* #param size the size of the matrix
* #param matrix the matrix encoded in 1d array i=(x+y*size)
* #param rowSum
* #param colSum
* #return
*/
private static int[] generate(final int size, final int[] matrix,
final int[] rowSum, final int[] colSum) {
// generate list of valid positions
final List<Integer> positions = new ArrayList();
for (int y = 0; y < size; y++) {
if (rowSum[y] < 2) {
for (int x = 0; x < size; x++) {
if (colSum[x] < 2) {
final int p = x + y * size;
if (matrix[p] == 0
&& (x == 0 || matrix[p - 1] == 0)
&& (x == size - 1 || matrix[p + 1] == 0)
&& (y == 0 || matrix[p - size] == 0)
&& (y == size - 1 || matrix[p + size] == 0)) {
positions.add(p);
}
}
}
}
}
// no valid positions ?
if (positions.isEmpty()) {
// if the matrix is incomplete => return null
for (int i = 0; i < size; i++) {
if (rowSum[i] != 2 || colSum[i] != 2) {
return null;
}
}
// the matrix is complete => return it
return matrix;
}
// random walk
Collections.shuffle(positions);
for (int p : positions) {
// set '1' and continue recursivly the exploration
matrix[p] = 1;
rowSum[p / size]++;
colSum[p % size]++;
final int[] solMatrix = generate(size, matrix, rowSum, colSum);
if (solMatrix != null) {
return solMatrix;
}
// rollback
matrix[p] = 0;
rowSum[p / size]--;
colSum[p % size]--;
}
// we can't find a valid matrix from here => return null
return null;
}
public static void printMatrix(final int size, final int[] matrix) {
for (int y = 0; y < size; y++) {
for (int x = 0; x < size; x++) {
System.out.print(matrix[x + y * size]);
System.out.print(" ");
}
System.out.println();
}
}
public static void printStatistics(final int size, final int count) {
final int sumMatrix[] = new int[size * size];
for (int i = 0; i < count; i++) {
final int[] matrix = generate(size);
for (int j = 0; j < sumMatrix.length; j++) {
sumMatrix[j] += matrix[j];
}
}
printMatrix(size, sumMatrix);
}
public static void checkAlgorithm() {
final int size = 8;
final int count = 2215764;
final int divisor = 122;
final int sumMatrix[] = new int[size * size];
for (int i = 0; i < count/divisor ; i++) {
final int[] matrix = generate(size);
for (int j = 0; j < sumMatrix.length; j++) {
sumMatrix[j] += matrix[j];
}
}
int total = 0;
for(int i=0; i < sumMatrix.length; i++) {
total += sumMatrix[i];
}
final double factor = (double)total / (count/divisor);
System.out.println("Factor=" + factor + " (theory=16.0)");
}
public static void benchmark(final int size, final int count,
final boolean parallel) {
final long begin = System.currentTimeMillis();
if (!parallel) {
for (int i = 0; i < count; i++) {
generate(size);
}
} else {
IntStream.range(0, count).parallel().forEach(i -> generate(size));
}
final long end = System.currentTimeMillis();
System.out.println("rate="
+ (double) (end - begin) / count + "ms/matrix");
}
public static void main(String[] args) {
checkAlgorithm();
benchmark(8, 10000, true);
//printStatistics(8, 2215764/36);
printStatistics(8, 2215764);
}
}
The output is:
Factor=16.0 (theory=16.0)
rate=0.2835ms/matrix
552969 554643 552895 554632 555680 552753 554567 553389
554071 554847 553441 553315 553425 553883 554485 554061
554272 552633 555130 553699 553604 554298 553864 554028
554118 554299 553565 552986 553786 554473 553530 554771
554474 553604 554473 554231 553617 553556 553581 553992
554960 554572 552861 552732 553782 554039 553921 554661
553578 553253 555721 554235 554107 553676 553776 553182
553086 553677 553442 555698 553527 554850 553804 553444
Here is a very fast approach of generating the matrix row by row, written in Java:
public static void main(String[] args) throws Exception {
int n = 100;
Random rnd = new Random();
byte[] mat = new byte[n*n];
byte[] colCount = new byte[n];
//generate row by row
for (int x = 0; x < n; x++) {
//generate a random first bit
int b1 = rnd.nextInt(n);
while ( (x > 0 && mat[(x-1)*n + b1] == 1) || //not adjacent to the one above
(colCount[b1] == 2) //not in a column which has 2
) b1 = rnd.nextInt(n);
//generate a second bit, not equal to the first one
int b2 = rnd.nextInt(n);
while ( (b2 == b1) || //not the same as bit 1
(x > 0 && mat[(x-1)*n + b2] == 1) || //not adjacent to the one above
(colCount[b2] == 2) || //not in a column which has 2
(b2 == b1 - 1) || //not adjacent to b1
(b2 == b1 + 1)
) b2 = rnd.nextInt(n);
//fill the matrix values and increment column counts
mat[x*n + b1] = 1;
mat[x*n + b2] = 1;
colCount[b1]++;
colCount[b2]++;
}
String arr = Arrays.toString(mat).substring(1, n*n*3 - 1);
System.out.println(arr.replaceAll("(.{" + n*3 + "})", "$1\n"));
}
It essentially generates each a random row at a time. If the row will violate any of the conditions, it is generated again (again randomly). I believe this will satisfy condition 4 as well.
Adding a quick note that it will spin forever for N-s where there is no solutions (like N=3).

finding unions of line segments on a number line

I have a number-line between 0 to 1000. I have many line segments on the number line. All line segments' x1 is >= 0 and all x2 are < 1000. All x1 and x2 are integers.
I need to find all of the unions of the line segments.
In this image, the line segments are in blue and the unions are in red:
Is there an existing algorithm for this type of problem?
You can use marzullo's algorithm (see Wikipedia for more details).
Here is a Python implementation I wrote:
def ip_ranges_grouping(range_lst):
## Based on Marzullo's algorithm
## Input: list of IP ranges
## Returns a new merged list of IP ranges
table = []
for rng in range_lst:
start,end = rng.split('-')
table.append((ip2int(start),1))
table.append((ip2int(end),-1))
table.sort(key=lambda x: x[0])
for i in range(len(table) - 1):
if((table[i][0] == table[i+1][0]) and ((table[i][1] == -1) and (table[i+1][1] == 1))):
table[i],table[i+1] = table[i+1],table[i]
merged = []
end = count = 0
while (end < len(table)):
start = end
count += table[end][1]
while(count > 0): # upon last index, count == 0 and loop terminates
end += 1
count += table[end][1]
merged.append(int2ip(table[start][0]) + '-' + int2ip(table[end][0]))
end += 1
return merged
Considering that the coordinates of your segments are bounded ([0, 1000]) integers, you could use an array of size 1000 initialized with zeroes. You then run through your set of segments and set 1 on every cell of the array that the segment covers. You then only have to run through the array to check for contigous sequences of 1.
--- -----
--- ---
1111100111111100
The complexity depends on the number of segments but also on their length.
Here is another method, which also work for floating point segments. Sort the segments. You then only have to travel the sorted segments and compare the boundaries of each adjacent segments. If they cross, they are in the same union.
If the segments are not changed dynamically, it is a simple problem. Just sorting all the segments by the left end, then scanning the sorted elements:
struct Seg {int L,R;};
int cmp(Seg a, Seg b) {return a.L < b.L;}
int union_segs(int n, Seg *segs, Segs *output) {
sort(segs, segs + n, cmp);
int right_most = -1;
int cnt = 0;
for (int i = 0 ; i < n ; i++) {
if (segs[i].L > right_most) {
right_most = segs[i].R;
++cnt;
output[cnt].L = segs[i].L;
output[cnt].R = segs[i].R;
}
if (segs[i].R > right_most) {
right_most = segs[i].R;
output[cnt].R = segs[i].R;
}
}
return cnt+1;
}
The time complexity is O(nlogn) (sorting) + O(n) (scan).
If the segments are inserted and deleted dynamically, and you want to query the union at any time, you will need some more complicated data structures such as range tree.

Vectorize matrix operation in R

I have a R x C matrix filled to the k-th row and empty below this row. What i need to do is to fill the remaining rows. In order to do this, i have a function that takes 2 entire rows as arguments, process these rows and output 2 fresh rows (these outputs will fill the empty rows of the matrix, in batches of 2). I have a fixed matrix containing all 'pairs' of rows to be processed, but my for loop is not helping performance:
# the processRows function:
processRows = function(r1, r2)
{
# just change a little bit the two rows and return it in a compact way
nr1 = r1 * 0.1
nr2 = -r2 * 0.1
matrix (c(nr1, nr2), ncol = 2)
}
# M is the matrix
# nrow(M) and k are even, so nLeft is even
M = matrix(1:48, ncol = 3)
# half to fill (can be more or less, but k is always even)
k = nrow(M)/2
# simulate empty rows to be filled
M[-(1:k), ] = 0
cat('before fill')
print(M)
# number of empty rows to fill
nLeft = nrow(M) - k
nextRow = k + 1
# each row in idxList represents a 'pair' of rows to be processed
# any pairwise combination of non-empty rows could happen
# make it reproducible
set.seed(1)
idxList = matrix (sample(1:k, k), ncol = 2, byrow = TRUE)
for ( i in 1 : (nLeft / 2))
{
row1 = M[idxList[i, 1],]
row2 = M[idxList[i, 2],]
# the two columns in 'results' will become 2 rows in M
results = processRows(row1, row2)
# fill the matrix
M[nextRow, ] = results[, 1]
nextRow = nextRow + 1
M[nextRow, ] = results[, 2]
nextRow = nextRow + 1
}
cat('after fill')
print(M)
Okay, here is your code first. We run this so that we have a copy of the "true" matrix, the one we hope to reproduce, faster.
#### Original Code (aka Gold Standard) ####
M = matrix(1:48, ncol = 3)
k = nrow(M)/2
M[-(1:k), ] = 0
nLeft = nrow(M) - k
nextRow = k + 1
idxList = matrix(1:k, ncol = 2)
for ( i in 1 : (nLeft / 2))
{
row1 = M[idxList[i, 1],]
row2 = M[idxList[i, 2],]
results = matrix(c(2*row1, 3*row2), ncol = 2)
M[nextRow, ] = results[, 1]
nextRow = nextRow + 1
M[nextRow, ] = results[, 2]
nextRow = nextRow + 1
}
Now here is the vectorized code. The basic idea is if you have 4 rows you are processing. Rather than passing them as vectors one at a time, do it at once. That is:
(1:3) * 2
(1:3) * 2
(1:3) * 2
(1:3) * 2
is the same (but slower) as:
c(1:3, 1:3, 1:3, 1:3) * 2
So first, we will use your same setup code, then create the rows to be processed as two long vectors (where all 4 original rows are just strung together as in my simple example above). Then, we take those results, and transform them into matrices with the appropriate dimensions. The last trick is to assign the results back in in just two steps. You can assign to multiple rows of a matrix at once, so we use seq() to get odd and even numbers so assign the first and second column of the results to, respectively.
#### Vectorized Code (testing) ####
M2 = matrix(1:48, ncol = 3)
k2 = nrow(M2)/2
M2[-(1:k2), ] = 0
nLeft2 = nrow(M2) - k2
nextRow2 = k2 + 1
idxList2 = matrix(1:k2, ncol = 2)
## create two long vectors of all rows to be processed
row12 <- as.vector(t(M2[idxList2[, 1],]))
row22 <- as.vector(t(M2[idxList2[, 2],]))
## get all results
results2 = matrix(c(2*row12, 3*row22), ncol = 2)
## add results back
M2[seq(nextRow2, nextRow2 + nLeft2-1, by = 2), ] <- matrix(results2[,1], nLeft2/2, byrow=TRUE)
M2[seq(nextRow2+1, nextRow2 + nLeft2, by = 2), ] <- matrix(results2[,2], nLeft2/2, byrow=TRUE)
## check that vectorized code matches your examples
all.equal(M, M2)
Which on my machine gives:
> all.equal(M, M2)
[1] TRUE

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