poPYtheSailor - 1 year ago 76

Python Question

I am running this code in python3.5 to find Concordance (logistic regression).

`for i in (ones2.index):`

for j in (zeros2.index):

pairs_tested = pairs_tested+1

if(ones2.iloc[i,1] > zeros2.iloc[j,1]):

conc = conc+1

elif(ones2.iloc[i,1]==zeros2.iloc[j,1]):

ties = ties+1

else:

disc = disc+1

# Calculate concordance, discordance and ties

concordance = conc/pairs_tested

discordance = disc/pairs_tested

ties_perc = ties/pairs_tested

print("Concordance = %r", concordance)

print("Discordance = %r", discordance)

print("Tied = %r", ties_perc)

print("Pairs = %r", pairs_tested)

There are 0.15mln rows in

Answer Source

Your code is doing 5.4 billion calculations due to the two for loops (0.15 mil * 36k):

I would do something like this: (Thanks to @Leon for helping me make this answer better)

```
from bisect import bisect_left, bisect_right
zeros_list = sorted([zeros2.iloc[j,1] for j in zeros2.index])
zeros2_length = len(zeros2_list)
for i in ones2.index:
cur_disc = bisect_left(zeros2_list, ones2.iloc[i,1])
cur_ties = bisect_right(zeros2_list, ones2.iloc[i,1]) - cur_disc
disc += cur_disc
ties += cur_ties
conc += zeros2_length - cur_ties - cur_disc
pairs_tested = zeros2_length * len(ones2.index)
concordance = conc/pairs_tested
discordance = disc/pairs_tested
ties_perc = ties/pairs_tested
print("Concordance = %r", concordance)
print("Discordance = %r", discordance)
print("Tied = %r", ties_perc)
print("Pairs = %r", pairs_tested
```

Or, the other way round, like this:

```
zeros_list = sorted([zeros2.iloc[j,1] for j in zeros2.index])
ones2_list = sorted([ones2.iloc[i,1] for i in ones2.index])
zeros2_length = len(zeros2_list)
ones2_length = len(ones2_list)
for i in zeros2.index:
cur_conc = bisect_left(ones2_list, zeros2.iloc[i,1])
cur_ties = bisect_right(ones2_list, zeros2.iloc[i,1]) - cur_conc
conc += cur_conc
ties += cur_ties
disc += ones2_length - cur_ties - cur_conc
# We could also achieve the above like this too:
# for i in zeros2_list:
# cur_conc = bisect_left(ones2_list, i)
# cur_ties = bisect_right(ones2_list, i) - cur_conc
# conc += cur_conc
# ties += cur_ties
# disc += ones2_length - cur_ties - cur_conc
pairs_tested = zeros2_length * ones2_length
concordance = conc/pairs_tested
discordance = disc/pairs_tested
ties_perc = ties/pairs_tested
print("Concordance = %r", concordance)
print("Discordance = %r", discordance)
print("Tied = %r", ties_perc)
print("Pairs = %r", pairs_tested
```