aPPR helps you calculate approximate personalized pageranks from large graphs, including those that can only be queried via an API. aPPR additionally performs degree correction and regularization, allowing you to recover blocks from stochastic blockmodels.
To learn more about aPPR you can:
Installation
You can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("RoheLab/aPPR")Find the personalized pagerank of a node in an igraph graph
library(aPPR)
library(igraph)
set.seed(27)
erdos_renyi_graph <- sample_gnp(n = 100, p = 0.5)
erdos_tracker <- appr(
erdos_renyi_graph, # the graph to work with
seeds = "5", # name of seed node (character)
epsilon = 0.0005 # desired approximation quality (see ?appr)
)
erdos_tracker
#> Personalized PageRank Approximator
#> ----------------------------------
#>
#> - number of seeds: 1
#> - visits so far: 5
#> - unique nodes visited so far: 1 out of maximum of Inf
#> - bad nodes so far: 0
#>
#> - teleportation constant (alpha): 0.15
#> - desired approximation error (epsilon): 5e-04
#> - achieved bound on approximation error: 0.000416297883029663
#> - current length of to-visit list: 0
#>
#> PPR table (see $stats field):
#> # A tibble: 51 × 7
#> name r p in_degree out_degree degree_adjusted regularized
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 5 0.0205 0.147 50 50 0.00294 0.00147
#> 2 3 0.0167 0 51 51 0 0
#> 3 6 0.0167 0 59 59 0 0
#> 4 8 0.0167 0 41 41 0 0
#> 5 15 0.0167 0 46 46 0 0
#> 6 16 0.0167 0 52 52 0 0
#> 7 17 0.0167 0 48 48 0 0
#> 8 19 0.0167 0 54 54 0 0
#> 9 20 0.0167 0 51 51 0 0
#> 10 21 0.0167 0 55 55 0 0
#> # … with 41 more rowsYou can access the Personalized PageRanks themselves via the stats field of Tracker objects.
erdos_tracker$stats
#> # A tibble: 51 × 7
#> name r p in_degree out_degree degree_adjusted regularized
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 5 0.0205 0.147 50 50 0.00294 0.00147
#> 2 3 0.0167 0 51 51 0 0
#> 3 6 0.0167 0 59 59 0 0
#> 4 8 0.0167 0 41 41 0 0
#> 5 15 0.0167 0 46 46 0 0
#> 6 16 0.0167 0 52 52 0 0
#> 7 17 0.0167 0 48 48 0 0
#> 8 19 0.0167 0 54 54 0 0
#> 9 20 0.0167 0 51 51 0 0
#> 10 21 0.0167 0 55 55 0 0
#> # … with 41 more rowsSometimes you may wish to limit computation time by limiting the number of nodes to visit, which you can do as follows:
limited_visits_tracker <- appr(
erdos_renyi_graph,
seeds = "5",
epsilon = 1e-10,
max_visits = 20 # max unique nodes to visit during approximation
)
#> Warning: Maximum visits reached. Finishing aPPR calculation early.
limited_visits_tracker
#> Personalized PageRank Approximator
#> ----------------------------------
#>
#> - number of seeds: 1
#> - visits so far: 22
#> - unique nodes visited so far: 20 out of maximum of 20
#> - bad nodes so far: 0
#>
#> - teleportation constant (alpha): 0.15
#> - desired approximation error (epsilon): 1e-10
#> - achieved bound on approximation error: 0.00423832387327568
#> - current length of to-visit list: 100
#>
#> PPR table (see $stats field):
#> # A tibble: 100 × 7
#> name r p in_degree out_degree degree_adjusted regularized
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 5 0.212 0.118 50 50 0.00237 0.00119
#> 2 3 0.0140 0 51 51 0 0
#> 3 6 0.0140 0 59 59 0 0
#> 4 8 0.0140 0 41 41 0 0
#> 5 15 0.0136 0 46 46 0 0
#> 6 16 0.0138 0 52 52 0 0
#> 7 17 0.0138 0 48 48 0 0
#> 8 19 0.0137 0 54 54 0 0
#> 9 20 0.0135 0 51 51 0 0
#> 10 21 0.0138 0 55 55 0 0
#> # … with 90 more rowsFind the personalized pagerank of a Twitter user using rtweet
ftrevorc_ppr <- appr(
rtweet_graph(),
"ftrevorc",
epsilon = 1e-4,
max_visits = 5
)
#> Warning: Maximum visits reached. Finishing aPPR calculation early.
ftrevorc_ppr
#> Personalized PageRank Approximator
#> ----------------------------------
#>
#> - number of seeds: 1
#> - visits so far: 6
#> - unique nodes visited so far: 5 out of maximum of 5
#> - bad nodes so far: 10
#>
#> - teleportation constant (alpha): 0.15
#> - desired approximation error (epsilon): 1e-04
#> - achieved bound on approximation error: 0.00175980395529336
#> - current length of to-visit list: 5
#>
#> PPR table (see $stats field):
#> # A tibble: 210 × 7
#> name r p in_degree out_degree degree_adjusted regularized
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 7752257741314… 0.211 0.118 69 120 0.00172 5.50e-8
#> 2 17163639 0.00559 0 20033 1596 0 0
#> 3 9381208958721… 0.00559 0 372 179 0 0
#> 4 1359003756063… 0.00559 0 230 116 0 0
#> 5 76228303 0.00559 0 7253 2274 0 0
#> 6 1024298722828… 0.00559 0 382 829 0 0
#> 7 1264590946144… 0.00559 0 116 189 0 0
#> 8 1107711818997… 0.00559 0 3404 410 0 0
#> 9 1217315090 0.00559 0 20660 402 0 0
#> 10 1120701503763… 0.00559 0 354 243 0 0
#> # … with 200 more rowsLogging
aPPR uses logger for displaying information to the user. By default, aPPR is quite verbose. You can control verbosity by loading logger and setting the logging threshold.
library(logger)
# hide basically all messages (not recommended)
log_threshold(FATAL, namespace = "aPPR")
appr(
erdos_renyi_graph, # the graph to work with
seeds = "5", # name of seed node (character)
epsilon = 0.0005 # desired approximation quality (see ?appr)
)If you submit a bug report, please please please include a log file using the TRACE threshold. You can set up this kind of detailed logging via the following:
set.seed(528491) # be sure to set seed for bug reports
log_appender(
appender_file(
"/path/to/logfile.log" ## TODO: choose a path to log to
),
namespace = "aPPR"
)
log_threshold(TRACE, namespace = "aPPR")
tracker <- appr(
rtweet_graph(),
seed = c("hadleywickham", "gvanrossum"),
epsilon = 1e-6
)Ethical considerations
People have a right to choose how public and discoverable their information is. aPPR will often lead you to accounts that interesting, but also small and out of sight. Do not change the public profile or attention towards these the people running these accounts, or any other accounts, without their permission.
References
Chen, Fan, Yini Zhang, and Karl Rohe. “Targeted Sampling from Massive Block Model Graphs with Personalized PageRank.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 82, no. 1 (February 2020): 99–126. https://doi.org/10.1111/rssb.12349. arxiv
Andersen, Reid, Fan Chung, and Kevin Lang. “Local Graph Partitioning Using PageRank Vectors.” In 2006 47th Annual IEEE Symposium on Foundations of Computer Science (FOCS’06), 475–86. Berkeley, CA, USA: IEEE, 2006. https://doi.org/10.1109/FOCS.2006.44.