From 786f1c6c921b58d3d07469a81a4577c85b43ec84 Mon Sep 17 00:00:00 2001
From: Fize Jacques <jacques.fize@cirad.fr>
Date: Wed, 5 May 2021 10:16:12 +0200
Subject: [PATCH] change in the documentation
---
doc/source/graph_generator.rst | 13 +++++---
doc/source/link_pred_eval.rst | 59 ++++++++++++++++++++++++++++++++++
evalNE_script.py | 11 +++----
3 files changed, 73 insertions(+), 10 deletions(-)
diff --git a/doc/source/graph_generator.rst b/doc/source/graph_generator.rst
index 52128c3..8273369 100644
--- a/doc/source/graph_generator.rst
+++ b/doc/source/graph_generator.rst
@@ -13,8 +13,11 @@ For example, if you want to generate a graph following the stochastic block mode
from lib.random import stochastic_block_model_graph
G = stochastic_block_model_graph(nb_nodes=300,nb_edges=1200,nb_com=5,percentage_edge_betw=0.01)
+Graph Models
+------------
+
Stochastic Block Model
-----------------------
+^^^^^^^^^^^^^^^^^^^^^^
This model partitions :math:`n` vertices in :math:`k` blocks, and places edges between pairs of nodes with a probability that depends on the vertices membership. The probability of a pair of nodes is computed based four parameter, the number of vertices :math:`|V|` and edges :math:`|E|`, the number of blocks :math:`|B|` and finally, the percentage of interlinks :math:`per_{betw}`, i.e number of selected pairs of nodes that belongs to different blocks.
First, we assign randomly a block :math:`b_i \in B` for each node :math:`v \in V`. In this model, all blocks are associated with the same number of nodes :math:`\frac{|V|}{|B|}`. Second, to compute the probability of a pair of nodes to be connected, we use the function :math:`f(u,v)` defined as follows:
@@ -46,7 +49,7 @@ To compute the :math:`p_{in}` and :math:`p_{out}`, we do the following:
Spatial Model
--------------
+^^^^^^^^^^^^^
This model generate a graph with $n$ vertices and $e$ edges selected randomly. Edges are selected using the deterrence function defined in the following formula:
.. math::
@@ -57,18 +60,20 @@ where :math:`u` and :math:`v` are two vertices and :math:`p_u` and :math:`p_v` c
Nodes coordinates can be generated randomly or randomly selected from existing places (here countries centroids).
ER Random Graph
----------------
+^^^^^^^^^^^^^^^
The model returns a Erdős-Rényi graph or a binomial graph. Basically,
the model generates a graph :math:`G_{n,m}` where :math:`n` corresponds to the number of vertices
and :math:`m` the number of edges in :math:`G_{n,m}`. In this model, each pair of nodes has the same
probability to be connected.
Configuration model
--------------------
+^^^^^^^^^^^^^^^^^^^
The configuration model generates a graph (graph with parallel edges and self loops) by randomly assigning edges to match a given degree distribution. In our case, generated graph degree distribution follows a powerlaw. We use the Molloy-Reed approach [molloy1995critical]_ to generate the graph.
.. [molloy1995critical] Molloy, M., & Reed, B. (1995). A critical point for random graphs with a given degree sequence. Random structures & algorithms, 6(2â€3), 161-180.
+
+
Generate a graph dataset based on different models and configurations
---------------------------------------------------------------------
diff --git a/doc/source/link_pred_eval.rst b/doc/source/link_pred_eval.rst
index 82573ee..2d75de6 100644
--- a/doc/source/link_pred_eval.rst
+++ b/doc/source/link_pred_eval.rst
@@ -1,2 +1,61 @@
Link Prediction Evaluation
==========================
+
+Link Prediction with state of the art methods
+---------------------------------------------
+
+In order to evaluate link predictions methods on a graph dataset, we use the `run_eval.py` script. Here
+a graph dataset is a dirctory that contains a file for each graph. For now, the accepted graph format are
+: edgelist (txt), gephi (.gexf) and graphml (.gml).
+
+To launch the evaluation, just run the following command in your terminal:
+
+.. code-block::shell
+
+ python run_eval.py <dataset_dir_path> <output_filename> [-f graph_format] [-t edge fraction used] [-v verbose]
+
+
+Select which link prediction methods to evaluate
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can change the methods evaluated in the `evalNE_script.py` file by changing different variables.
+To change the heuristics evaluated, change the following :
+
+.. code-block:: python
+
+ methods_heuristics = ['random_prediction',
+ 'common_neighbours',
+ 'jaccard_coefficient',
+ "adamic_adar_index",
+ "preferential_attachment",
+ "resource_allocation_index",
+ "stochastic_block_model",
+ "stochastic_block_model_degree_corrected",
+ "spatial_link_prediction"
+ ]
+
+The string corresponds to the name of the function available in `evalne.methods.similarity` modules.
+
+Thanks to **OpenNE**, we can also evaluated methods based on networks embedding. To remove or add such methods
+modify the following variables in the same file :
+
+.. code-block:: python
+
+ methods_ne = ["node2vec" ,"hope-opne", "gf", "sdne", "deepWalk", "line", "grarep"]
+ commands = [
+ "python -m openne --method node2vec --graph-format edgelist --epochs 100 --number-walks 10 --walk-length 80 --window-size 10",
+ "python -m openne --method hope --epochs 100",
+ "python -m openne --method gf --epochs 100",
+ "python -m openne --method sdne --epochs 100 --encoder-list [1024,128] --beta 5 --bs 500",
+ "python -m openne --method deepWalk --graph-format edgelist --epochs 100 --number-walks 10 --walk-length 80 --window-size 10",
+ "python -m openne --method line --graph-format edgelist --epochs 10",
+ "python -m openne --method grarep --epochs 100"
+ ]
+
+More specifically, in `methods` you add the name of the one method you want to use; and in `commands`, you add the openne
+command required to compute the embedding using this method.
+
+Link prediction based on the erosion model
+------------------------------------------
+
+To run the evaluation of our link prediction method based on erosion, you must use the `eval_mixed_model.py` script.
diff --git a/evalNE_script.py b/evalNE_script.py
index ceef756..0e62d47 100644
--- a/evalNE_script.py
+++ b/evalNE_script.py
@@ -58,7 +58,7 @@ log("Dataset Built !")
scoresheet = Scoresheet()
# Set the baselines
-methods = ['random_prediction',
+methods_heuristics = ['random_prediction',
'common_neighbours',
'jaccard_coefficient',
"adamic_adar_index",
@@ -70,7 +70,7 @@ methods = ['random_prediction',
]
# Evaluate heristics
-pbar = tqdm(methods,disable= (not args.verbose))
+pbar = tqdm(methods_heuristics,disable= (not args.verbose))
for method in pbar:
pbar.set_description("Evaluate "+method)
result = nee.evaluate_baseline(method=method,)
@@ -81,7 +81,7 @@ if args.network_embedding:
# Check if OpenNE is installed
import openne
# Set embedding methods from OpenNE
- methods = "node2vec hope-opne gf sdne deepWalk line grarep".split() #lap-opne
+ methods_ne = ["node2vec" ,"hope-opne", "gf", "sdne", "deepWalk", "line", "grarep"]
commands = [
"python -m openne --method node2vec --graph-format edgelist --epochs 100 --number-walks 10 --walk-length 80 --window-size 10",
"python -m openne --method hope --epochs 100",
@@ -90,19 +90,18 @@ if args.network_embedding:
"python -m openne --method deepWalk --graph-format edgelist --epochs 100 --number-walks 10 --walk-length 80 --window-size 10",
"python -m openne --method line --graph-format edgelist --epochs 10",
"python -m openne --method grarep --epochs 100"
- # "python -m openne --method lap --epochs 100",
]
edge_emb = [ 'hadamard'] #'average',
# Evaluate embedding methods
- pbar = tqdm(enumerate(methods), disable=(not args.verbose))
+ pbar = tqdm(enumerate(methods_ne), disable=(not args.verbose))
for i,method in pbar:
pbar.set_description("Evaluate "+method)
is_weighted = nx.is_weighted(G)
command = commands[i] + " --input {} --output {} --representation-size {}"
if is_weighted:
command = command + " --weighted"
- results = nee.evaluate_cmd(method_name=methods[i], method_type='ne', command=command,
+ results = nee.evaluate_cmd(method_name=methods_ne[i], method_type='ne', command=command,
edge_embedding_methods=edge_emb, input_delim=' ', output_delim=' ', verbose=args.verbose,write_weights=is_weighted)
scoresheet.log_results(results)
--
GitLab