From 9038e14b1a9c351c92f6e0eae1ce2b1978248135 Mon Sep 17 00:00:00 2001
From: Utaemon Toyota <toyota@cl.uni-heidelberg.de>
Date: Tue, 26 Feb 2019 20:36:52 +0100
Subject: [PATCH] add README and add argparse to cora.py
---
EP/Cora_node_classification/README.md | 6 +++++-
EP/Cora_node_classification/cora.py | 25 +++++++++++++++++--------
2 files changed, 22 insertions(+), 9 deletions(-)
diff --git a/EP/Cora_node_classification/README.md b/EP/Cora_node_classification/README.md
index 526942e..adfa8e5 100644
--- a/EP/Cora_node_classification/README.md
+++ b/EP/Cora_node_classification/README.md
@@ -8,6 +8,7 @@ Graph Embedding Propagation
# Cora Node Classification
To evaluate the trained graph and the embeddings the task of node classification will be executed. First, the data of cora will be imported into a networkX graph, which will be saved in a pickle file to use it for the training of the embeddings with our EP-SP algorithm. Afterwards the trained embedding will be evaluated with LibLinear L2-Logistic Regression provided from sklearn.
+Graph building is provided on cora.py, the evaluation on node_classification.py.
# Required Data
- Cora dataset saved in cora_data for building the graph
@@ -33,7 +34,10 @@ For node_classification.py
# Running instructions
For cora.py
-...
+python3 cora.py [-n] [-e] [-o]
+ -n / --nodes Path to cora file containing nodes
+ -e / --edges Path to cora file containing edges
+ -o / --output Path where the graph should be saved
For node_classification.py
python3 node_classification.py [-g] [-e] [-s] [-i] [-n]
diff --git a/EP/Cora_node_classification/cora.py b/EP/Cora_node_classification/cora.py
index 95c21df..1eed9f8 100644
--- a/EP/Cora_node_classification/cora.py
+++ b/EP/Cora_node_classification/cora.py
@@ -1,14 +1,20 @@
"""
+@project: Software Projekt @ Heidelberg University, Institute for Computational Linguistics
+@requirements: cora data, numpy, networkX, pickle
@info
-Getting a networkx graph from Cora. Graph can be saved in txt file. CARE: numpy-arrays are converted to lists due to errors (NumPy array is not JSON serializable).
+Getting a networkx graph from Cora. Graph will be saved in a pickle file.
@usage
-get_graph(path_nodes="/cora_data/cora.content", path_edges="/cora_data/cora.cites")
--> return graph with nodes and edges
-To write the graph informations in file:
-def write_graph_to_file(path_nodes="/cora_data/cora.content", path_edges="/cora_data/cora.cites", path_output_graph = "")
+python3 cora.py [-n] [-e] [-o]
+ -n / --nodes Path to cora file containing nodes
+ -e / --edges Path to cora file containing edges
+ -o / --output Path where the graph should be saved
+
+As a module (used in node_classification.py) you can access the graph with
+read_pickle_graph("path_to_cora_graph")
"""
+import argparse
import networkx as nx
import numpy as np
import pickle as pkl
@@ -116,8 +122,11 @@ def read_pickle_graph(path = "graph.pkl"):
graph = pkl.load(f)
return graph
-
if __name__ == "__main__":
# execute only if run as a script
- get_graph(path_nodes="/cora_data/cora.content", path_edges="/cora_data/cora.cites")
- get_init_emb(rand_type="normal_random", dimension = 128, quantity=1433)
+ parser = argparse.ArgumentParser(description="Skript for building cora graph.")
+ parser.add_argument("-n", "--nodes", default="/cora_data/cora.content", help="path to file containing cora nodes")
+ parser.add_argument("-e", "--edges", default="/home/utaemon/SP/cora/cora.cites", help="path to file containing edges/citations")
+ parser.add_argument("-o", "--output", default="", help="path where the graph should be saved")
+ args = parser.parse_args()
+ write_pickle_graph_file(path_nodes=args.nodes, path_edges=args.edges, path_output_graph=args.output)
--
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