BUG: GroupBy.mean() is extremely slow with sparse arrays

[gokceneraslan]

• [x ] I have checked that this issue has not already been reported.

• [ x] I have confirmed this bug exists on the latest version of pandas.

• (optional) I have confirmed this bug exists on the master branch of pandas.

---

Code Sample, a copy-pastable example

import pandas as pd
import numpy as np

np.random.seed(0)
df = pd.DataFrame(np.random.rand(1000, 1000) > 0.8, dtype=int)
df['g'] = ['A' if x else 'B' for x in np.random.rand(1000) > 0.5]

%timeit -n 3 -r 5 df.groupby('g').mean()

sdf = df.set_index('g').astype('Sparse[int]').reset_index()
%timeit -n 3 -r 5 sdf.groupby('g').mean()

Output:

Dense:
11 ms ± 430 µs per loop (mean ± std. dev. of 5 runs, 3 loops each)

Sparse:
3.91 s ± 33.5 ms per loop (mean ± std. dev. of 5 runs, 3 loops each)

or subset of a real-word dataset:

import pandas as pd

df = pd.read_csv('https://github.com/pandas-dev/pandas/files/5176354/pbmc-sparse-df.csv.gz', 
                 index_col=0).astype(int).reset_index()
%timeit -n 3 -r 5 df.groupby('Cell type').mean()

sdf = df.set_index('Cell type').astype(pd.SparseDtype(int, fill_value=0)).reset_index()
%timeit -n 3 -r 5 sdf.groupby('Cell type').mean()

Output:

Dense:
9.2 ms ± 403 µs per loop (mean ± std. dev. of 5 runs, 3 loops each)

Sparse:
3.73 s ± 126 ms per loop (mean ± std. dev. of 5 runs, 3 loops each)

Problem description

GroupBy.mean() with the SparseArray seems extremely slow compared to dense matrices (here around 355 times).

Output of pd.show_versions()

INSTALLED VERSIONS

commit : f2ca0a2
python : 3.8.5.final.0
python-bits : 64
OS : Darwin
OS-release : 19.6.0
Version : Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64
machine : x86_64
processor : i386
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8

pandas : 1.1.1
numpy : 1.19.1
pytz : 2020.1
dateutil : 2.8.1
pip : 20.2.1
setuptools : 49.2.1.post20200802
Cython : None
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 2.11.2
IPython : 7.17.0
pandas_datareader: None
bs4 : None
bottleneck : None
fsspec : 0.8.0
fastparquet : None
gcsfs : None
matplotlib : 3.3.0
numexpr : 2.7.1
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : 1.0.0
pytables : None
pyxlsb : None
s3fs : None
scipy : 1.5.2
sqlalchemy : None
tables : 3.6.1
tabulate : None
xarray : None
xlrd : None
xlwt : None
numba : 0.50.1

I attached the file here for reproducibility.

pbmc-sparse-df.csv.gz

[TomAugspurger]

Can you create the DataFrame in memory? (see http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports).

[gokceneraslan]

import pandas as pd
import numpy as np

np.random.seed(0)
df = pd.DataFrame(np.random.rand(1000, 1000) > 0.8, dtype=int)
df['g'] = ['A' if x else 'B' for x in np.random.rand(1000) > 0.5]

%timeit -n 3 -r 5 df.groupby('g').mean()

sdf = df.set_index('g').astype('Sparse[int]').reset_index()
%timeit -n 3 -r 5 sdf.groupby('g').mean()

Output:

11 ms ± 430 µs per loop (mean ± std. dev. of 5 runs, 3 loops each)
3.91 s ± 33.5 ms per loop (mean ± std. dev. of 5 runs, 3 loops each)

[TomAugspurger]

Thanks (can you add that to the original post?)

Next thing we need to figure out: is this specific to Sparse, or is it a general issue with all extensionarrays? ExtensionArrays can't be sent to Cython, so we have to take the slower python path. Right now my hunch is that it applies to all EAs. Can you do some investigation?

[gokceneraslan]

I am not familiar with pandas codebase and Cython at all, so I probably cannot. But any help is appreciated.

[gokceneraslan]

I can c/p snakeviz profiles, if it helps:

Dense:

%snakeviz df.groupby('g').mean()

Sparse:

%snakeviz sdf.groupby('g').mean()

[arw2019]

There's a slowdown withInt64

   ...: %timeit -n 3 -r 5 df.groupby('g').mean() 
   ...:  
   ...: sdf = df.set_index('g').astype('Int64').reset_index() 
   ...: %timeit -n 3 -r 5 sdf.groupby('g').mean() 
   ...:                                                                                                                                                                                                           
8.06 ms ± 966 µs per loop (mean ± std. dev. of 5 runs, 3 loops each)
333 ms ± 10.6 ms per loop (mean ± std. dev. of 5 runs, 3 loops each)

[v1gnesh]

Yes! It's unbearably slow. Please help!
All memory-saving gains from using sparse is being wiped out by extremely long CPU time.

In my case, a sparse df (shape of (100317, 24) with all uint16) takes just 636.9 KB in memory.
Dense df (same shape) takes 4.6 MB in memory.

Sparse groupby took 527.5207s, whereas dense groupby finished in 0.2229s