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🔬 Supplementary material

Supplemental material

This document provides additional information about the benchmarking setup, data, and results that were presented in the manuscript.

Benchmark setup

Code and benchmarking scenarios

Repository

Operating systems and hardware configurations

macOS

  • cpu architecture: arm64
  • cpu name: Apple M3 Max
  • cpu cores: 16
  • memory: 64 GB
  • kernel: Darwin Kernel Version 24.2.0: Fri Dec 6 19:02:12 PST 2024; root:xnu-11215.61.5~2/RELEASE_ARM64_T6031
  • system: Darwin
  • os-release: macOS-15.2-arm64-arm-64bit
  • python: 3.12.4
  • polars-bio: 0.8.3

Linux

c3-standard-22 machine was used for benchmarking.

  • cpu architecture: x86_64
  • cpu name: Intel(R) Xeon(R) Platinum 8481C CPU @ 2.70GHz
  • cpu cores: 22
  • memory: 88 GB
  • kernel: Linux-6.8.0-1025-gcp-x86_64-with-glibc2.35
  • system: Linux
  • os-release: #27~22.04.1-Ubuntu SMP Mon Feb 24 16:42:24 UTC 2025
  • python: 3.12.8
  • polars-bio: 0.8.3

Software

Data

AIList dataset was used for benchmarking.

Dataset# Name Size(x1000) Non-flatness
0 chainRn4 2,351 6
1 fBrain 199 1
2 exons 439 2
3 chainOrnAna1 1,957 6
4 chainVicPac2 7,684 8
5 chainXenTro3Link 50,981 7
6 chainMonDom5Link 128,187 7
7 ex-anno 1,194 2
8 ex-rna 9,945 7

Note

Test dataset in Parquet format can be downloaded from:

Single thread results

Results for overlap, nearest, count-overlaps, and coverage operations with single-thread performance on apple-m3-max and gcp-linux platforms.

apple-m3-max

1-2

overlap
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 0.035619 0.043113 0.0383 2.70x
bioframe 0.102257 0.104425 0.103354 1.00x
pyranges0 0.025425 0.032821 0.028001 3.69x
pyranges1 0.059608 0.064147 0.061763 1.67x
pybedtools 0.343204 0.352804 0.348434 0.30x
genomicranges 1.042893 1.044245 1.043488 0.10x
nearest
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 0.039943 0.045166 0.042109 4.45x
bioframe 0.185452 0.189631 0.187388 1.00x
pyranges0 0.092334 0.09634 0.093688 2.00x
pyranges1 0.133631 0.134179 0.133981 1.40x
pybedtools 0.756676 0.761866 0.75953 0.25x
count-overlaps
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 0.026706 0.029754 0.028142 4.69x
bioframe 0.131124 0.133729 0.132052 1.00x
pyranges0 0.039136 0.039774 0.039377 3.35x
pyranges1 0.061976 0.063181 0.062658 2.11x
pybedtools 0.665804 0.673844 0.668534 0.20x
genomicranges 0.994963 1.006435 0.999389 0.13x
coverage
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 0.0262 0.028749 0.027418 6.30x
bioframe 0.16949 0.176628 0.172842 1.00x
pyranges0 0.07376 0.076708 0.075369 2.29x
pyranges1 0.128027 0.133263 0.130247 1.33x
pybedtools 0.701817 0.708726 0.705839 0.24x
genomicranges 1.032651 1.049059 1.040799 0.17x

8-7

overlap
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 3.987391 4.648581 4.235518 7.17x
bioframe 29.793837 30.991576 30.375518 1.00x
pyranges0 15.632212 15.974075 15.857213 1.92x
pyranges1 31.622804 33.699074 32.680701 0.93x
pybedtools 916.711575 919.974811 918.154834 0.03x
genomicranges 479.214112 487.832054 484.579554 0.06x
nearest
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 2.116922 2.169534 2.139006 32.13x
bioframe 68.581465 68.992651 68.725495 1.00x
pyranges0 1.381964 1.508513 1.424446 48.25x
pyranges1 2.697684 2.728407 2.717532 25.29x
pybedtools 35.528719 35.876667 35.699544 1.93x
count-overlaps
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 1.445467 1.484052 1.46225 58.77x
bioframe 85.632767 86.26148 85.935955 1.00x
pyranges0 9.674847 9.833233 9.753982 8.81x
pyranges1 10.170249 10.254359 10.201813 8.42x
pybedtools 33.101592 33.966188 33.423595 2.57x
genomicranges 488.972732 490.395787 489.548184 0.18x
coverage
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 1.195279 1.205765 1.199323 20.45x
bioframe 24.423391 24.682901 24.525909 1.00x
pyranges0 11.093644 11.328071 11.220416 2.19x
pyranges1 11.987003 12.147925 12.066045 2.03x
pybedtools 59.699275 60.04087 59.84965 0.41x
genomicranges 500.041974 503.31936 502.043072 0.05x

gcp-linux

1-2

overlap
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 0.045943 0.064732 0.054234 1.66x
bioframe 0.084137 0.099481 0.090107 1.00x
pyranges0 0.056206 0.065654 0.061844 1.46x
pyranges1 0.09908 0.119018 0.106228 0.85x
pybedtools 0.38246 0.406379 0.39153 0.23x
genomicranges 1.19939 1.224621 1.208255 0.07x
nearest
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 0.057012 0.073822 0.064665 2.49x
bioframe 0.158764 0.165707 0.161273 1.00x
pyranges0 0.172297 0.176259 0.17363 0.93x
pyranges1 0.217619 0.234088 0.22335 0.72x
pybedtools 0.845945 0.84898 0.847447 0.19x
count-overlaps
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 0.035631 0.043555 0.04066 2.74x
bioframe 0.108015 0.116522 0.111266 1.00x
pyranges0 0.077336 0.080282 0.07844 1.42x
pyranges1 0.100883 0.106671 0.103181 1.08x
pybedtools 0.745958 0.759006 0.754393 0.15x
genomicranges 1.154942 1.164158 1.158506 0.10x
coverage
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 0.036476 0.040001 0.037897 5.10x
bioframe 0.189201 0.20046 0.193401 1.00x
pyranges0 0.141659 0.14424 0.143188 1.35x
pyranges1 0.206033 0.224902 0.213089 0.91x
pybedtools 0.773732 0.780424 0.776934 0.25x
genomicranges 1.186341 1.194172 1.189255 0.16x

8-7

overlap
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 6.235223 9.61441 7.723144 6.54x
bioframe 50.319263 50.956633 50.537202 1.00x
pyranges0 36.371926 36.581642 36.448645 1.39x
pyranges1 63.336711 63.455435 63.40654 0.80x
pybedtools 1149.001487 1152.127068 1150.070659 0.04x
genomicranges 597.951648 599.960895 599.002871 0.08x
nearest
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 3.576373 3.679698 3.633697 15.54x
bioframe 56.301865 56.776617 56.464305 1.00x
pyranges0 2.45308 2.60494 2.505172 22.54x
pyranges1 4.975662 5.011008 4.997007 11.30x
pybedtools 44.181913 44.79409 44.386971 1.27x
count-overlaps
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 2.052196 2.104447 2.075706 38.15x
bioframe 79.174164 79.234115 79.194209 1.00x
pyranges0 18.797436 18.851941 18.824498 4.21x
pyranges1 20.399172 20.436149 20.418562 3.88x
pybedtools 35.850631 36.142479 36.041115 2.20x
genomicranges 612.985873 613.52087 613.229997 0.13x
coverage
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 1.829478 1.838981 1.834999 15.44x
bioframe 28.29136 28.361417 28.326821 1.00x
pyranges0 18.611247 20.021441 19.473105 1.45x
pyranges1 22.118838 22.210733 22.161329 1.28x
pybedtools 74.477086 74.868659 74.618066 0.38x
genomicranges 623.865655 623.94955 623.896645 0.05x

Parallel performance

Results for parallel operations with 1, 2, 4, 6 and 8 threads.

apple-m3-max

8-7

overlap
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 3.247022 3.803021 3.370889 1.00x
polars_bio-2 1.798569 1.848162 1.811417 1.86x
polars_bio-4 1.140229 1.158243 1.147355 2.94x
polars_bio-6 0.959703 0.968725 0.962915 3.50x
polars_bio-8 0.694637 0.710492 0.701048 4.81x
nearest
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 2.186354 2.248171 2.220822 1.00x
polars_bio-2 1.162969 1.222115 1.187505 1.87x
polars_bio-4 0.708508 0.735763 0.720115 3.08x
polars_bio-6 0.632877 0.652955 0.642816 3.45x
polars_bio-8 0.456674 0.476473 0.465284 4.77x
count-overlaps
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 1.502551 1.534006 1.515078 1.00x
polars_bio-2 0.811236 0.821365 0.815682 1.86x
polars_bio-4 0.440628 0.46778 0.455358 3.33x
polars_bio-6 0.331317 0.338207 0.334638 4.53x
polars_bio-8 0.280465 0.282707 0.281311 5.39x
coverage
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 1.181806 1.185549 1.183889 1.00x
polars_bio-2 0.644288 0.645076 0.644587 1.84x
polars_bio-4 0.362752 0.363411 0.363036 3.26x
polars_bio-6 0.258583 0.272702 0.264111 4.48x
polars_bio-8 0.222888 0.234884 0.229052 5.17x

gcp-linux

8-7

overlap
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 6.325617 8.185275 7.005925 1.00x
polars_bio-2 3.920645 4.617084 4.198055 1.67x
polars_bio-4 3.036273 3.060781 3.0452 2.30x
polars_bio-6 2.127994 2.134505 2.131016 3.29x
polars_bio-8 1.731485 1.789347 1.752986 4.00x
nearest
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 4.047329 4.439016 4.198198 1.00x
polars_bio-2 2.624132 2.722843 2.682361 1.57x
polars_bio-4 1.809028 1.917798 1.871763 2.24x
polars_bio-6 1.309557 1.362131 1.333989 3.15x
polars_bio-8 1.066945 1.113168 1.087907 3.86x
count-overlaps
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 2.426441 2.456318 2.439266 1.00x
polars_bio-2 1.22516 1.272066 1.245401 1.96x
polars_bio-4 0.711421 0.744023 0.724315 3.37x
polars_bio-6 0.563797 0.607321 0.580574 4.20x
polars_bio-8 0.459308 0.493886 0.479126 5.09x
coverage
Library Min (s) Max (s) Mean (s) Speedup
polars_bio 2.212958 2.23035 2.222531 1.00x
polars_bio-2 1.132056 1.15405 1.146413 1.94x
polars_bio-4 0.645737 0.661564 0.652277 3.41x
polars_bio-6 0.50589 0.511256 0.50839 4.37x
polars_bio-8 0.439503 0.450924 0.447075 4.97x

End to end tests

Results for an end-to-end test with calculating overlaps and saving results to a CSV file.

apple-m3-max

1-2

e2e-overlap-csv
Library Min (s) Max (s) Mean (s) Speedup Peak memory (MB)
polars_bio 0.042378 0.130957 0.071929 3.10x 285.468
polars_bio_streaming 0.035498 0.037438 0.036653 6.09x 274.093
bioframe 0.208548 0.251457 0.223219 1.00x 300.75
pyranges0 0.409707 0.415361 0.412135 0.54x 329.968
pyranges1 0.47518 0.491508 0.482739 0.46x 324.468

8-7

e2e-overlap-csv
Library Min (s) Max (s) Mean (s) Speedup Peak memory (MB)
polars_bio 22.781745 23.916568 23.161559 16.64x 14677.0468
polars_bio_streaming 18.501279 18.797602 18.676707 20.63x 555.109
bioframe 383.108514 387.500069 385.309331 1.00x 33806.062
pyranges0 276.421312 279.839508 277.845198 1.39x 29777.312
pyranges1 355.703878 367.680249 360.875151 1.07x 34526.859

gcp-linux

1-2

e2e-overlap-csv
Library Min (s) Max (s) Mean (s) Speedup Peak memory (MB)
polars_bio 0.072393 0.151871 0.09916 2.80x 314.234
polars_bio_streaming 0.064092 0.067914 0.066202 4.19x 288.621
bioframe 0.258278 0.31288 0.277225 1.00x 287.101
pyranges0 0.591745 0.599954 0.595204 0.47x 307.218
pyranges1 0.683388 0.702289 0.690362 0.40x 327.863

8-7

e2e-overlap-csv
Library Min (s) Max (s) Mean (s) Speedup Peak memory (MB)
polars_bio 44.539766 45.543038 45.196903 12.55x 14575.14
polars_bio_streaming 34.007093 35.972075 35.309756 16.06x 480.207
bioframe 566.167037 567.617695 567.13069 1.00x 43295.378
pyranges0 417.291061 421.875539 419.571591 1.35x 22915.917
pyranges1 538.365637 548.624613 543.918168 1.04x 43408.699

Memory profiles

2025-03-26T05:56:30.333935 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:30.776036 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:30.985503 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:31.253535 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:31.510558 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:31.758246 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:32.018335 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:32.468350 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:33.003015 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:33.336517 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:33.855791 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:34.145515 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:34.416296 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:34.869871 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:35.131625 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:35.629111 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:35.897464 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:36.180110 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:36.573390 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/ 2025-03-26T05:56:37.080391 image/svg+xml Matplotlib v3.9.4, https://matplotlib.org/