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aPPR

Lifecycle: experimental CRAN status Codecov test coverage R build status

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.

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,    # convergence criterion (see below)
  verbose = FALSE
)
#> Error in igraph::`V<-`(`*tmp*`, value = `*vtmp*`): invalid indexing

erdos_tracker
#> Error in eval(expr, envir, enclos): object 'erdos_tracker' not found

Find the personalized pagerank of a Twitter user using rtweet

fchen365_ppr <- appr(
  rtweet_graph(),
  "fchen365",
  epsilon = 1e-3,
  verbose = TRUE
)

fchen365_ppr$stats
#> # A tibble: 94 x 7
#>    name                 r     p in_degree out_degree degree_adjusted regularized
#>    <chr>            <dbl> <dbl>     <dbl>      <dbl>           <dbl>       <dbl>
#>  1 7752257741314~ 0.0970  0.135        47         97         0.00288 0.000000116
#>  2 759249         0.00791 0         13313       1359         0       0          
#>  3 97505313       0.00791 0          1280       2551         0       0          
#>  4 35109534       0.00791 0          1743        345         0       0          
#>  5 1225146797049~ 0.00791 0             6         11         0       0          
#>  6 7804292688660~ 0.00791 0          4159       1244         0       0          
#>  7 14897792       0.00791 0         17836       5542         0       0          
#>  8 165678616      0.00791 0         58259       1206         0       0          
#>  9 9095302874905~ 0.00791 0           191        637         0       0          
#> 10 16549997       0.00791 0         72320       1540         0       0          
#> # ... with 84 more rows

Find the personalized pagerank of a Twitter user and cache the following network in the process

alexpghayes_ppr <- appr(
  twittercache_graph(),
  "alexpghayes",
  epsilon = 1e-4,
  verbose = TRUE
)

alexpghayes_ppr$stats
#> # A tibble: 1,243 x 7
#>    name                 r     p in_degree out_degree degree_adjusted regularized
#>    <chr>            <dbl> <dbl>     <dbl>      <dbl>           <dbl>       <dbl>
#>  1 7804292688660~ 9.71e-2 0.135      4069       1241       0.0000333 0.000000909
#>  2 628745609      6.19e-4 0           129        216       0         0          
#>  3 780934633      6.19e-4 0         19471       2878       0         0          
#>  4 20406724       6.19e-4 0         33816       8344       0         0          
#>  5 1152655010871~ 6.19e-4 0           552       1150       0         0          
#>  6 302667955      6.19e-4 0          3917       1724       0         0          
#>  7 2768346873     6.19e-4 0          6304       1376       0         0          
#>  8 3147524537     6.19e-4 0          1353        712       0         0          
#>  9 43261106       6.19e-4 0          1317        723       0         0          
#> 10 31241437       6.19e-4 0       4492431        215       0         0          
#> # ... with 1,233 more rows

README beyond this point is really just scratch for myself

Sink nodes and unreachable nodes

citation_graph <- sample_pa(100)

citation_tracker <- appr(citation_graph, seeds = "5")
#> Error in igraph::`V<-`(`*tmp*`, value = `*vtmp*`): invalid indexing
citation_tracker
#> Error in eval(expr, envir, enclos): object 'citation_tracker' not found

Why should I use aPPR?

  • curious about nodes important to the community around a particular user who you wouldn’t find without algorithmic help

  • 1 hop network is too small, 2-3 hop networks are too large (recall diameter of twitter graph is 3.7!!!)

  • want to study a particular community but don’t know exactly which accounts to investigate, but you do have a good idea of one or two important accounts in that community

aPPR calculates an approximation

comment on p = 0 versus p != 0

Advice on choosing epsilon

Number of unique visits as a function of epsilon, wait times, runtime proportion to 1 / (alpha * epsilon), etc, etc

speaking strictly in terms of the p != 0 nodes

1e-4 and 1e-5: finishes quickly, neighbors with high degree get visited 1e-6: visits most of 1-hop neighborhood. finishes in several hours for accounts who follow thousands of people with ~10 tokens. 1e-7: visits beyond the 1-hop neighbor by ???. takes a couple days to run with ~10 tokens. 1e-8: visits a lot beyond the 1-hop neighbor, presumably the important people in the 2-hop neighbor, ???

the most disparate a users interests, and the less connected their neighborhood, the longer it will take to run aPPR

Limitations

  • Connected graph assumption, what results look like when we violate this assumption
  • Sampling is one node at a time

Speed ideas

compute is not an issue relative to actually getting data

Compute time ~ access from Ram time << access from disk time << access from network time.

Make requests to API in bulk, memoize everything, cache / write to disk in a separate process?

General pattern: cache on disk, and also in RAM

Working with Tracker objects

See ?Tracker for details.

Ethical considerations

people have a right to choose how public / visible / discoverable their information is. if you come across interesting users who are not in the public eye, do not elevate them into the public eye or increase attention on their accounts without their permission.

References

  1. Chen, F., Zhang, Y. & Rohe, K. Targeted sampling from massive Blockmodel graphs with personalized PageRank. 2019. pdf

  2. Andersen, R., Chung, F. & Lang, K. Local Graph Partitioning using PageRank Vectors. 2006. pdf

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