diff --git a/README.md b/README.md index ac7604a0b..a94eee130 100644 --- a/README.md +++ b/README.md @@ -318,14 +318,13 @@ trainer.test() ## Computational performances -We measured the efficiency of data generation in DeepRank2 using the tutorials' [PDB files](https://zenodo.org/record/8187806) (+/- 100 data points per data set). -Below results were obtained as an average of X runs, on Apple M1 Pro, using a single CPU. -Parameter settings as follows: resolution: atomic; `distance_cutoff`:5.5 Å; radius (for SRV only): 10 Å. - -| | [Features modules](https://deeprank2.readthedocs.io/en/latest/features.html) used | Comments | Data processing speed **[seconds/structure]** | Memory **[megabyte/structure]** | -|------|---------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------:|:--------------------------------:| -| PPIs | `components`, `contact`, `exposure`, `irc`, `secondary_structure`, `surfacearea`, 33 features in total. | `conservation` feature module was not used because PSSM files were not available for the data. | graph only: **3.58** (std 0.27)
graph+grid: **12.92** (std 1.39) | graph only: **0.54** (std 0.07)
graph+grid: **16.09** (std 0.44) | -| SRVs | `components`, `contact`, `exposure`, `irc`, `secondary_structure`, `surfacearea`, 26 features in total. | Same as above for `conservation`. | graph only: **1.82** (std 0.37)
graph+grid: **2.58** (std 0.66) | graph only: **0.05** (std 0.01)
graph+grid: **8.52** (std 8.50)| +We measured the efficiency of data generation in DeepRank2 using the tutorials' [PDB files](https://zenodo.org/record/8187806) (~100 data points per data set), averaging the results run on Apple M1 Pro, using a single CPU. +Parameter settings were: atomic resolution, `distance_cutoff` of 5.5 Å, radius (for SRV only) of 10 Å. The [features modules](https://deeprank2.readthedocs.io/en/latest/features.html) used were `components`, `contact`, `exposure`, `irc`, `secondary_structure`, `surfacearea`, for a total of 33 features for PPIs and 26 for SRVs. + +| | Data processing speed
[seconds/structure] | Memory
[megabyte/structure] | +|------|:--------------------------------------------------------:|:--------------------------------------------------------:| +| PPIs | graph only: **2.99** (std 0.23)
graph+grid: **11.35** (std 1.30) | graph only: **0.54** (std 0.07)
graph+grid: **16.09** (std 0.44) | +| SRVs | graph only: **2.20** (std 0.08)
graph+grid: **2.85** (std 0.10) | graph only: **0.05** (std 0.01)
graph+grid: **17.52** (std 0.59) | ## Package development