From 494a2dedd9f797ce8385f78811ada87eeec225db Mon Sep 17 00:00:00 2001 From: RobRossmiller-TG <165701656+RobRossmiller-TG@users.noreply.github.com> Date: Wed, 4 Sep 2024 13:49:21 -0400 Subject: [PATCH 1/6] add normalization --- .../global/unweighted/tg_pagerank.gsql | 56 ++++++----- .../baseline/centrality/pagerank/Empty.json | 2 +- .../baseline/centrality/pagerank/Tree.json | 2 +- tests/run.sh | 1 - tests/test/baseline/algos/__init__.py | 2 +- tests/test/baseline/algos/common.py | 27 ++++++ .../test/baseline/algos/degree_centrality.py | 29 +----- tests/test/baseline/algos/pagerank.py | 93 +++++++++++++++---- tests/test/test_centrality.py | 1 + 9 files changed, 141 insertions(+), 72 deletions(-) diff --git a/algorithms/Centrality/pagerank/global/unweighted/tg_pagerank.gsql b/algorithms/Centrality/pagerank/global/unweighted/tg_pagerank.gsql index 88a4df6b..6d949980 100644 --- a/algorithms/Centrality/pagerank/global/unweighted/tg_pagerank.gsql +++ b/algorithms/Centrality/pagerank/global/unweighted/tg_pagerank.gsql @@ -1,10 +1,10 @@ -CREATE QUERY tg_pagerank (STRING v_type, STRING e_type, FLOAT max_change=0.001, INT maximum_iteration=25, FLOAT damping=0.85, INT top_k = 100, BOOL print_results = TRUE, STRING result_attribute = "", STRING file_path = "", BOOL display_edges = FALSE) SYNTAX V1 { +CREATE QUERY tg_pagerank (STRING v_type, STRING e_type, FLOAT max_change=0.001, INT maximum_iteration=25, FLOAT damping=0.85, INT top_k = 100, BOOL normalize=TRUE, BOOL print_results = TRUE, STRING result_attribute = "", STRING file_path = "", BOOL display_edges = FALSE) SYNTAX V1 { /* - First Author: unk - First Commit Date: unk + First Author: + First Commit Date: Recent Author: Rob Rossmiller - Recent Commit Date: Rob Rossmiller + Recent Commit Date: Sept 4, 2024 Repository: @@ -41,7 +41,7 @@ CREATE QUERY tg_pagerank (STRING v_type, STRING e_type, FLOAT max_change=0.001, file_path: file to write CSV output to top_k: - #top scores to output + //top scores to output display_edges: output edges for visualization max_change: @@ -52,39 +52,49 @@ CREATE QUERY tg_pagerank (STRING v_type, STRING e_type, FLOAT max_change=0.001, TYPEDEF TUPLE Vertex_Score; HeapAccum(top_k, score DESC) @@top_scores_heap; - SetAccum @@top_vertices; # vertices with top score - MaxAccum @@max_diff = 9999; # max score change in an iteration - SumAccum @sum_recvd_score = 0; # sum of scores each vertex receives FROM neighbors - SumAccum @sum_score = 1; # initial score for every vertex is 1. - SetAccum @@edge_set; # list of all edges, if display is needed + SetAccum @@top_vertices; // vertices with top score + MaxAccum @@max_diff = 9999; // max score change in an iteration + SumAccum @sum_recvd_score = 0; // sum of scores each vertex receives FROM neighbors + SumAccum @sum_score = 1; // initial score for every vertex is 1. + SetAccum @@edge_set; // list of all edges, if display is needed FILE f (file_path); + INT N=1; + + + // PageRank iterations + Start = {v_type}; // Start with all vertices of specified type(s) + IF normalize THEN + N = Start.size(); + tmp = SELECT s FROM Start:s + ACCUM s.@sum_score = 1.0/N; + END; - # PageRank iterations - Start = {v_type}; # Start with all vertices of specified type(s) WHILE @@max_diff > max_change LIMIT maximum_iteration DO @@max_diff = 0; + V = SELECT s FROM Start:s -(e_type:e)- v_type:t - ACCUM - t.@sum_recvd_score += s.@sum_score/(s.outdegree(e_type)) + ACCUM t.@sum_recvd_score += s.@sum_score/(s.outdegree(e_type)) POST-ACCUM - s.@sum_score = (1.0 - damping) + damping * s.@sum_recvd_score, + s.@sum_score = (1.0-damping)/N + damping * s.@sum_recvd_score, s.@sum_recvd_score = 0, @@max_diff += abs(s.@sum_score - s.@sum_score'); - END; # END WHILE loop + END; - # Output + // Output IF file_path != "" THEN f.println("Vertex_ID", "PageRank"); END; + V = SELECT s FROM Start:s - POST-ACCUM + POST-ACCUM IF result_attribute != "" THEN s.setAttr(result_attribute, s.@sum_score) END, + IF file_path != "" THEN f.println(s, s.@sum_score) END, - + IF print_results THEN @@top_scores_heap += Vertex_Score(s, s.@sum_score) END; @@ -92,14 +102,16 @@ CREATE QUERY tg_pagerank (STRING v_type, STRING e_type, FLOAT max_change=0.001, IF print_results THEN PRINT @@top_scores_heap; IF display_edges THEN + FOREACH vert IN @@top_scores_heap DO @@top_vertices += vert.Vertex_ID; END; Top = {@@top_vertices}; - Top = SELECT s FROM Top:s -(e_type:e)- v_type:t - WHERE @@top_vertices.contains(t) - ACCUM @@edge_set += e; + Top = SELECT s + FROM Top:s -(e_type:e)- v_type:t + WHERE @@top_vertices.contains(t) + ACCUM @@edge_set += e; PRINT @@edge_set; PRINT Top; diff --git a/tests/data/baseline/centrality/pagerank/Empty.json b/tests/data/baseline/centrality/pagerank/Empty.json index ade4c388..8e4e0dac 100644 --- a/tests/data/baseline/centrality/pagerank/Empty.json +++ b/tests/data/baseline/centrality/pagerank/Empty.json @@ -1 +1 @@ -[{"@@top_scores_heap": [{"Vertex_ID": "P", "score": 0}, {"Vertex_ID": "N", "score": 0}, {"Vertex_ID": "F", "score": 0}, {"Vertex_ID": "C", "score": 0}, {"Vertex_ID": "J", "score": 0}, {"Vertex_ID": "R", "score": 0}, {"Vertex_ID": "A", "score": 0}, {"Vertex_ID": "T", "score": 0}, {"Vertex_ID": "D", "score": 0}, {"Vertex_ID": "E", "score": 0}, {"Vertex_ID": "L", "score": 0}, {"Vertex_ID": "S", "score": 0}, {"Vertex_ID": "I", "score": 0}, {"Vertex_ID": "H", "score": 0}, {"Vertex_ID": "G", "score": 0}, {"Vertex_ID": "B", "score": 0}, {"Vertex_ID": "Q", "score": 0}, {"Vertex_ID": "O", "score": 0}, {"Vertex_ID": "K", "score": 0}, {"Vertex_ID": "M", "score": 0}]}] +[{"@@top_scores_heap": []}] \ No newline at end of file diff --git a/tests/data/baseline/centrality/pagerank/Tree.json b/tests/data/baseline/centrality/pagerank/Tree.json index 39d09eec..b49c40c9 100644 --- a/tests/data/baseline/centrality/pagerank/Tree.json +++ b/tests/data/baseline/centrality/pagerank/Tree.json @@ -1 +1 @@ -[{"@@top_scores_heap": [{"Vertex_ID": "A", "score": 0.04753738488500107}, {"Vertex_ID": "B", "score": 0.06909959193353464}, {"Vertex_ID": "C", "score": 0.07220759154455524}, {"Vertex_ID": "D", "score": 0.07130204500748627}, {"Vertex_ID": "E", "score": 0.07480080379154676}, {"Vertex_ID": "F", "score": 0.0785393029006319}, {"Vertex_ID": "G", "score": 0.0785393029006319}, {"Vertex_ID": "H", "score": 0.07804404762676867}, {"Vertex_ID": "I", "score": 0.07804404762676867}, {"Vertex_ID": "J", "score": 0.054902205374844214}, {"Vertex_ID": "K", "score": 0.02869374578323252}, {"Vertex_ID": "L", "score": 0.02975219252757403}, {"Vertex_ID": "M", "score": 0.02975219252757403}, {"Vertex_ID": "N", "score": 0.02975219252757403}, {"Vertex_ID": "O", "score": 0.02975219252757403}, {"Vertex_ID": "P", "score": 0.029611982345715077}, {"Vertex_ID": "Q", "score": 0.029611982345715077}, {"Vertex_ID": "R", "score": 0.029611982345715077}, {"Vertex_ID": "S", "score": 0.029611982345715077}, {"Vertex_ID": "T", "score": 0.030833231131841908}]}] \ No newline at end of file +[{"@@top_scores_heap": [{"Vertex_ID": "A", "score": 0.04753738488500107}, {"Vertex_ID": "B", "score": 0.06909959193353465}, {"Vertex_ID": "C", "score": 0.07220759154455525}, {"Vertex_ID": "D", "score": 0.07130204500748626}, {"Vertex_ID": "E", "score": 0.07480080379154676}, {"Vertex_ID": "F", "score": 0.0785393029006319}, {"Vertex_ID": "G", "score": 0.0785393029006319}, {"Vertex_ID": "H", "score": 0.07804404762676867}, {"Vertex_ID": "I", "score": 0.07804404762676867}, {"Vertex_ID": "J", "score": 0.054902205374844214}, {"Vertex_ID": "K", "score": 0.02869374578323252}, {"Vertex_ID": "L", "score": 0.02975219252757403}, {"Vertex_ID": "M", "score": 0.02975219252757403}, {"Vertex_ID": "N", "score": 0.02975219252757403}, {"Vertex_ID": "O", "score": 0.02975219252757403}, {"Vertex_ID": "P", "score": 0.02961198234571507}, {"Vertex_ID": "Q", "score": 0.02961198234571507}, {"Vertex_ID": "R", "score": 0.02961198234571507}, {"Vertex_ID": "S", "score": 0.02961198234571507}, {"Vertex_ID": "T", "score": 0.030833231131841908}]}] \ No newline at end of file diff --git a/tests/run.sh b/tests/run.sh index 60b79622..40d6cbb6 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -1,6 +1,5 @@ clear python3 test/setup.py && - # python3 test/baseline/create_baselines.py && # pytest test/test_centrality.py::TestCentrality::test_degree_centrality1 #test/test_ml.py pytest test/test_centrality.py::TestCentrality::test_pagerank # pytest test/test_ml.py diff --git a/tests/test/baseline/algos/__init__.py b/tests/test/baseline/algos/__init__.py index 1e3b52ae..4de5b269 100644 --- a/tests/test/baseline/algos/__init__.py +++ b/tests/test/baseline/algos/__init__.py @@ -1,3 +1,3 @@ -from .degree_centrality import * +from .degree_centrality import DegreeCentralityBaseline from .fastrp import FastRPBaseline from .pagerank import PagerankBaseline diff --git a/tests/test/baseline/algos/common.py b/tests/test/baseline/algos/common.py index 9761acd6..2efc68c6 100644 --- a/tests/test/baseline/algos/common.py +++ b/tests/test/baseline/algos/common.py @@ -1,4 +1,9 @@ +import csv +import json + import networkx as nx +import numpy as np +from tqdm import tqdm def create_graph(edges, weights=False, directed=False) -> nx.Graph: @@ -13,3 +18,25 @@ def create_graph(edges, weights=False, directed=False) -> nx.Graph: else: g.add_edges_from(edges) return g + + +def create_baseline(paths, algo): + t = tqdm(paths, desc=f"Creating {algo} baselines") + for p, out_path, fn, m in t: + t.set_postfix_str(out_path.split("/")[-1].split(".")[0]) + with open(p) as f: + edges = np.array(list(csv.reader(f))) + + directed = True if "Directed" in out_path else False + weights = True if "Weighted" in out_path else False + g = create_graph(edges, weights, directed) + + # from matplotlib import pyplot as plt + # pos = nx.drawing.layout.kamada_kawai_layout(g) + # nx.draw(g, pos) + # nx.draw_networkx_labels(g, pos, {n: n for n in g.nodes}) + # plt.savefig(f"{out_path.split('/')[-1]}.png") + + res = fn(g, m) + with open(out_path, "w") as f: + json.dump(res, f) # , indent=2) diff --git a/tests/test/baseline/algos/degree_centrality.py b/tests/test/baseline/algos/degree_centrality.py index 1337116f..8272f3c1 100644 --- a/tests/test/baseline/algos/degree_centrality.py +++ b/tests/test/baseline/algos/degree_centrality.py @@ -1,14 +1,10 @@ -import csv -import json from collections import Counter from functools import partial import networkx as nx -import numpy as np -from .common import create_graph -from tqdm import tqdm from .base import Baseline +from .common import create_baseline def run_degree_baseline_complete(g: nx.Graph, _): @@ -59,27 +55,6 @@ def __init__(self, data_path_root, baseline_path_root): self.data_path_root = data_path_root self.baseline_path_root = baseline_path_root - def create_baseline(self, paths): - t = tqdm(paths, desc="Creating degree centrality baselines") - for p, out_path, fn, m in t: - t.set_postfix_str(out_path.split("/")[-1].split(".")[0]) - with open(p) as f: - edges = np.array(list(csv.reader(f))) - - directed = True if "Directed" in out_path else False - weights = True if "Weighted" in out_path else False - g = create_graph(edges, weights, directed) - - # from matplotlib import pyplot as plt - # pos = nx.drawing.layout.kamada_kawai_layout(g) - # nx.draw(g, pos) - # nx.draw_networkx_labels(g, pos, {n: n for n in g.nodes}) - # plt.savefig(f"{out_path.split('/')[-1]}.png") - - res = fn(g, m) - with open(out_path, "w") as f: - json.dump(res, f) # , indent=2) - def run(self): # (data, output_path, fun, metric) paths = [ @@ -258,4 +233,4 @@ def run(self): partial(weighted_deg_cent, dir="out"), ), ] - self.create_baseline(paths) + create_baseline(paths, "degree centrality") diff --git a/tests/test/baseline/algos/pagerank.py b/tests/test/baseline/algos/pagerank.py index 7a8e4f1e..a2f1fa48 100644 --- a/tests/test/baseline/algos/pagerank.py +++ b/tests/test/baseline/algos/pagerank.py @@ -1,12 +1,48 @@ -import csv -import json - import networkx as nx import numpy as np -from tqdm import tqdm +import pandas as pd +from pyTigerGraph.datasets import Datasets +from scipy.sparse import csc_matrix, csr, csr_matrix, spdiags +from sklearn import random_projection +from sklearn.preprocessing import normalize, scale from .base import Baseline -from .common import create_graph +from .common import create_baseline + + +def pr(g: nx.DiGraph, d=0.85): + N = g.number_of_nodes() + nodes = {n: 1 / N for n in g.nodes} + + dangling_nodes = [n for n in g.nodes if g.out_degree(n) == 0] + max_change = 0.001 + max_diff = 9999 + + print(sum(nodes.values9)) + i = 0 + # PageRank iterations + while max_diff > max_change or i >= 25: + max_diff = 0 + i += 1 + + prev = nodes + for n in nodes: + # traverse + for x in g.neighbors(n): + pass + return + + return nodes[35], nodes[35] / 2 + m: csr = nx.adjacency_matrix(g) + M = m.todense() + N = M.shape[1] + w = np.ones(N) / N + M_hat = d * M + v = M_hat @ w + (1 - d) + while np.linalg.norm(w - v) >= 1e-10: + w = v + v = M_hat @ w + (1 - d) + return v def run_pagerank(g: nx.Graph, metric): @@ -25,22 +61,35 @@ def __init__(self, data_path_root, baseline_path_root): self.data_path_root = data_path_root self.baseline_path_root = baseline_path_root - def create_baseline(self, paths): - t = tqdm(paths, desc="Creating pagerank baselines") - for p, out_path, fn, m in t: - t.set_postfix_str(out_path.split("/")[-1].split(".")[0]) - with open(p) as f: - edges = np.array(list(csv.reader(f))) + def run(self): + ds_name = "CoraV2" + # run pagerank on cora + dataset = Datasets(ds_name) + edges = pd.read_csv(dataset.tmp_dir + f"/{ds_name}/edges.csv", header=None) + edges.columns = ["src", "tgt"] + print(edges) - directed = True if "Directed" in out_path else False - weights = True if "Weighted" in out_path else False - g = create_graph(edges, weights, directed) + g = nx.DiGraph() + g.add_edges_from(edges.to_numpy()) + rank = {int(k): v for k, v in nx.pagerank(g).items()} + rank[0] = sum(rank.values()) + rank = dict(sorted(rank.items(), key=lambda x: x[0])) + import json - res = fn(g, m) - with open(out_path, "w") as f: - json.dump(res, f) # , indent=2) + with open("nx.json", "w") as f: + json.dump(rank, f, indent=2) - def run(self): + from matplotlib import pyplot as plt + + # pos = nx.drawing.layout.kamada_kawai_layout(g) + # pos = nx.drawing.layout.arf_layout(g) + # nx.draw(g, pos) + # nx.draw_networkx_labels(g, pos, {n: n for n in g.nodes}) + # plt.savefig(f"{out_path.split('/')[-1]}.png") + # plt.show() + # custom pagerank + print(pr(g)) + return # (data, output_path, fun, metric) paths = [ ( @@ -98,5 +147,11 @@ def run(self): run_pagerank, nx.pagerank, ), + ( + f"{self.data_path_root}/unweighted_edges/empty_graph_edges.csv", + f"{self.baseline_path_root}/centrality/pagerank/Empty.json", + run_pagerank, + nx.pagerank, + ), ] - self.create_baseline(paths) + create_baseline(paths, algo="pagerank") diff --git a/tests/test/test_centrality.py b/tests/test/test_centrality.py index ed6159f8..b437c7a5 100644 --- a/tests/test/test_centrality.py +++ b/tests/test/test_centrality.py @@ -49,6 +49,7 @@ def check_result( b["score"] ): q_type = "Template Query" if template_flag else "Generic Query" + pytest.exit(f'{q_type}: {r["score"]} != {b["score"]}') pytest.fail(f'{q_type}: {r["score"]} != {b["score"]}') @pytest.mark.parametrize("test_name", undirected_graphs) From fc850dc358516c2dc085233b9de3d5244a8a1a2a Mon Sep 17 00:00:00 2001 From: RobRossmiller-TG <165701656+RobRossmiller-TG@users.noreply.github.com> Date: Fri, 6 Sep 2024 15:49:27 -0400 Subject: [PATCH 2/6] merge to template tests --- tests/run.sh | 3 ++- tests/test/baseline/create_baselines.py | 4 ++-- tests/test/setup.py | 26 +++++-------------------- tests/test/test_centrality.py | 1 + tests/test/util.py | 25 ++++++++++++------------ 5 files changed, 23 insertions(+), 36 deletions(-) diff --git a/tests/run.sh b/tests/run.sh index 40d6cbb6..37f58816 100755 --- a/tests/run.sh +++ b/tests/run.sh @@ -1,6 +1,7 @@ clear python3 test/setup.py && # pytest test/test_centrality.py::TestCentrality::test_degree_centrality1 #test/test_ml.py - pytest test/test_centrality.py::TestCentrality::test_pagerank + # pytest test/test_centrality.py::TestCentrality::test_pagerank # pytest test/test_ml.py + pytest test/test_centrality.py::TestCentrality echo 'done' diff --git a/tests/test/baseline/create_baselines.py b/tests/test/baseline/create_baselines.py index 98635ed0..12825784 100644 --- a/tests/test/baseline/create_baselines.py +++ b/tests/test/baseline/create_baselines.py @@ -5,8 +5,8 @@ def run(): - PagerankBaseline(data_path_root, baseline_path_root).run() - # DegreeCentralityBaseline(data_path_root, baseline_path_root).run() + # PagerankBaseline(data_path_root, baseline_path_root).run() + DegreeCentralityBaseline(data_path_root, baseline_path_root).run() # FastRPBaseline(data_path_root, baseline_path_root).run() diff --git a/tests/test/setup.py b/tests/test/setup.py index d41a0a4c..32d5aecc 100644 --- a/tests/test/setup.py +++ b/tests/test/setup.py @@ -1,13 +1,12 @@ import json import os import re -import time from glob import glob import pyTigerGraph as tg from dotenv import load_dotenv from pyTigerGraph.datasets import Datasets -from tqdm import tqdm, trange +from tqdm import tqdm import util from baseline import create_baselines @@ -17,17 +16,6 @@ pattern = re.compile(r'"name":\s*"tg_.*"') -# def add_reverse_edge_to_schema(ds: Datasets): -# with open(f"{dataset.tmp_dir}/{ds.name}/create_schema.gsql") as f: -# schema: str = f.read() -# with open(f"{dataset.tmp_dir}/{ds.name}/create_schema.gsql", "w") as f: -# schema = schema.replace( -# "ADD DIRECTED EDGE Cite (from Paper, to Paper, time Int, is_train Bool, is_val Bool);", -# 'ADD DIRECTED EDGE Cite (from Paper, to Paper, time Int, is_train Bool, is_val Bool) WITH REVERSE_EDGE="reverse_Cite";', -# ) -# f.write(schema) -# -# def get_query_path(q_name): pth = glob(f"../algorithms/**/{q_name}.gsql", recursive=True) return pth[0] @@ -40,9 +28,6 @@ def get_template_queries() -> list[str]: name = p.replace("../", "").split(".")[0].split("/") pkg = ".".join(x for x in name[:-1]) name = ".".join(x for x in name) - # if ".degree_cent" not in name: - # if "louvain" not in name: - # continue paths.append((name, p)) packages.append(pkg) @@ -51,9 +36,6 @@ def get_template_queries() -> list[str]: if __name__ == "__main__": - # print(get_template_queries()) - create_baselines.run() - exit(0) host_name = os.environ["HOST_NAME"] user_name = os.environ["USER_NAME"] password = os.environ["PASS"] @@ -75,7 +57,9 @@ def get_template_queries() -> list[str]: dataset = Datasets("graph_algorithms_testing") conn.ingestDataset(dataset, getToken=True) - conn.getToken() + + if os.environ.get("USE_TKN", "true").lower() == "true": + conn.getToken() conn.graphname = graph_name # install the queries @@ -109,7 +93,7 @@ def get_template_queries() -> list[str]: pkg_queries = [] queries = [q[0] for q in queries] - reg = re.compile(r"- (.*)\(.*\)") # find insatlled pacakge query names + reg = re.compile(r"- (.*)\(.*\)") # find installed pacakge query names for pkg in packages: r = conn.gsql(f"SHOW PACKAGE {pkg}") for p in reg.findall(r): diff --git a/tests/test/test_centrality.py b/tests/test/test_centrality.py index b437c7a5..cf8ac52c 100644 --- a/tests/test/test_centrality.py +++ b/tests/test/test_centrality.py @@ -347,6 +347,7 @@ def test_degree_centrality4(self, test_name): # ) # self.check_result(baseline, result, template_flag) # + @pytest.mark.skip(reason="Still testing pagerank") @pytest.mark.parametrize("test_name", undirected_graphs + directed_graphs) def test_pagerank(self, test_name): params = { diff --git a/tests/test/util.py b/tests/test/util.py index 109b80cb..8d143335 100644 --- a/tests/test/util.py +++ b/tests/test/util.py @@ -6,18 +6,19 @@ load_dotenv() -def get_featurizer(graph_name="graph_algorithms_testing"): - host_name = os.getenv("HOST_NAME") - user_name = os.getenv("USER_NAME") - password = os.getenv("PASS") - conn = tg.TigerGraphConnection( - host=host_name, - username=user_name, - password=password, - graphname=graph_name, - ) - if os.environ.get("USE_TKN", "true").lower() == "true": - conn.getToken() +def get_featurizer(conn:tg.TigerGraphConnection=None, graph_name="graph_algorithms_testing"): + if conn is None: + host_name = os.getenv("HOST_NAME") + user_name = os.getenv("USER_NAME") + password = os.getenv("PASS") + conn = tg.TigerGraphConnection( + host=host_name, + username=user_name, + password=password, + graphname=graph_name, + ) + if os.environ.get("USE_TKN", "true").lower() == "true": + conn.getToken() f = conn.gds.featurizer() return f From 1e57628a0d90cfc8fc94f18193bc2e025e424073 Mon Sep 17 00:00:00 2001 From: RobRossmiller-TG <165701656+RobRossmiller-TG@users.noreply.github.com> Date: Fri, 6 Sep 2024 15:51:39 -0400 Subject: [PATCH 3/6] put old baselines back --- tests/data/baseline/centrality/pagerank/Empty.json | 2 +- tests/data/baseline/centrality/pagerank/Hub_Spoke.json | 2 +- tests/data/baseline/centrality/pagerank/Hub_Spoke_Directed.json | 2 +- tests/data/baseline/centrality/pagerank/Line.json | 2 +- tests/data/baseline/centrality/pagerank/Line_Directed.json | 2 +- tests/data/baseline/centrality/pagerank/Ring.json | 2 +- tests/data/baseline/centrality/pagerank/Ring_Directed.json | 2 +- tests/data/baseline/centrality/pagerank/Tree.json | 2 +- tests/data/baseline/centrality/pagerank/Tree_Directed.json | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/tests/data/baseline/centrality/pagerank/Empty.json b/tests/data/baseline/centrality/pagerank/Empty.json index 8e4e0dac..5bc65dd7 100644 --- a/tests/data/baseline/centrality/pagerank/Empty.json +++ b/tests/data/baseline/centrality/pagerank/Empty.json @@ -1 +1 @@ -[{"@@top_scores_heap": []}] \ No newline at end of file +[{"@@top_scores_heap": [{"Vertex_ID": "B", "score": 1}, {"Vertex_ID": "H", "score": 1}, {"Vertex_ID": "I", "score": 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a/tests/data/baseline/centrality/pagerank/Hub_Spoke_Directed.json +++ b/tests/data/baseline/centrality/pagerank/Hub_Spoke_Directed.json @@ -1 +1 @@ -[{"@@top_scores_heap": [{"Vertex_ID": "A", "score": 0.04796147421875003}, {"Vertex_ID": "B", "score": 0.050107290830592136}, {"Vertex_ID": "C", "score": 0.050107290830592136}, {"Vertex_ID": "D", "score": 0.050107290830592136}, {"Vertex_ID": "E", "score": 0.050107290830592136}, {"Vertex_ID": "F", "score": 0.050107290830592136}, {"Vertex_ID": "G", "score": 0.050107290830592136}, {"Vertex_ID": "H", "score": 0.050107290830592136}, {"Vertex_ID": "I", "score": 0.050107290830592136}, {"Vertex_ID": "J", "score": 0.050107290830592136}, {"Vertex_ID": "K", "score": 0.050107290830592136}, {"Vertex_ID": "L", "score": 0.050107290830592136}, {"Vertex_ID": "M", "score": 0.050107290830592136}, {"Vertex_ID": "N", "score": 0.050107290830592136}, {"Vertex_ID": "O", "score": 0.050107290830592136}, {"Vertex_ID": "P", "score": 0.050107290830592136}, 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a/tests/data/baseline/centrality/pagerank/Tree_Directed.json b/tests/data/baseline/centrality/pagerank/Tree_Directed.json index fb466ceb..58e261d5 100644 --- a/tests/data/baseline/centrality/pagerank/Tree_Directed.json +++ b/tests/data/baseline/centrality/pagerank/Tree_Directed.json @@ -1 +1 @@ -[{"@@top_scores_heap": [{"Vertex_ID": "A", "score": 0.030283038177750167}, {"Vertex_ID": "B", "score": 0.043153655387605856}, {"Vertex_ID": "C", "score": 0.043153655387605856}, {"Vertex_ID": "D", "score": 0.04862366075639622}, {"Vertex_ID": "E", "score": 0.04862366075639622}, {"Vertex_ID": "F", "score": 0.04862366075639622}, {"Vertex_ID": "G", "score": 0.04862366075639622}, {"Vertex_ID": "H", "score": 0.05094809395836327}, {"Vertex_ID": "I", "score": 0.05094809395836327}, {"Vertex_ID": "J", "score": 0.05094809395836327}, {"Vertex_ID": "K", "score": 0.05094809395836327}, {"Vertex_ID": "L", "score": 0.05094809395836327}, {"Vertex_ID": "M", "score": 0.05094809395836327}, {"Vertex_ID": "N", "score": 0.05094809395836327}, {"Vertex_ID": "O", "score": 0.05094809395836327}, {"Vertex_ID": "P", "score": 0.051935549088716185}, {"Vertex_ID": "Q", "score": 0.051935549088716185}, {"Vertex_ID": "R", "score": 0.051935549088716185}, {"Vertex_ID": "S", "score": 0.051935549088716185}, {"Vertex_ID": "T", "score": 0.07358805999968221}]}] \ No newline at end of file +[{"@@top_scores_heap": [{"Vertex_ID": "T", "score": 1}, {"Vertex_ID": "S", "score": 1}, {"Vertex_ID": "K", "score": 1}, {"Vertex_ID": "L", "score": 1}, {"Vertex_ID": "O", "score": 1}, {"Vertex_ID": "R", "score": 1}, {"Vertex_ID": "N", "score": 1}, {"Vertex_ID": "M", "score": 1}, {"Vertex_ID": "P", "score": 1}, {"Vertex_ID": "Q", "score": 1}, {"Vertex_ID": "I", "score": 0.2523586}, {"Vertex_ID": "H", "score": 0.2523586}, {"Vertex_ID": "J", "score": 0.2523586}, {"Vertex_ID": "E", "score": 0.2408437}, {"Vertex_ID": "D", "score": 0.2408437}, {"Vertex_ID": "G", "score": 0.2408437}, {"Vertex_ID": "F", "score": 0.2408437}, {"Vertex_ID": "C", "score": 0.21375}, {"Vertex_ID": "B", "score": 0.21375}, {"Vertex_ID": "A", "score": 0.15}]}] \ No newline at end of file From 8aa56b0cdbfe04552150e67c7be0896ae04f5c29 Mon Sep 17 00:00:00 2001 From: RobRossmiller-TG <165701656+RobRossmiller-TG@users.noreply.github.com> Date: Fri, 6 Sep 2024 15:53:11 -0400 Subject: [PATCH 4/6] rm pagerank baseline --- tests/test/baseline/algos/pagerank.py | 157 -------------------------- 1 file changed, 157 deletions(-) delete mode 100644 tests/test/baseline/algos/pagerank.py diff --git a/tests/test/baseline/algos/pagerank.py b/tests/test/baseline/algos/pagerank.py deleted file mode 100644 index a2f1fa48..00000000 --- a/tests/test/baseline/algos/pagerank.py +++ /dev/null @@ -1,157 +0,0 @@ -import networkx as nx -import numpy as np -import pandas as pd -from pyTigerGraph.datasets import Datasets -from scipy.sparse import csc_matrix, csr, csr_matrix, spdiags -from sklearn import random_projection -from sklearn.preprocessing import normalize, scale - -from .base import Baseline -from .common import create_baseline - - -def pr(g: nx.DiGraph, d=0.85): - N = g.number_of_nodes() - nodes = {n: 1 / N for n in g.nodes} - - dangling_nodes = [n for n in g.nodes if g.out_degree(n) == 0] - max_change = 0.001 - max_diff = 9999 - - print(sum(nodes.values9)) - i = 0 - # PageRank iterations - while max_diff > max_change or i >= 25: - max_diff = 0 - i += 1 - - prev = nodes - for n in nodes: - # traverse - for x in g.neighbors(n): - pass - return - - return nodes[35], nodes[35] / 2 - m: csr = nx.adjacency_matrix(g) - M = m.todense() - N = M.shape[1] - w = np.ones(N) / N - M_hat = d * M - v = M_hat @ w + (1 - d) - while np.linalg.norm(w - v) >= 1e-10: - w = v - v = M_hat @ w + (1 - d) - return v - - -def run_pagerank(g: nx.Graph, metric): - res = metric(g) - - out = [] - for k, v in res.items(): - out.append({"Vertex_ID": k, "score": v}) - - out = [{"@@top_scores_heap": out}] - return out - - -class PagerankBaseline(Baseline): - def __init__(self, data_path_root, baseline_path_root): - self.data_path_root = data_path_root - self.baseline_path_root = baseline_path_root - - def run(self): - ds_name = "CoraV2" - # run pagerank on cora - dataset = Datasets(ds_name) - edges = pd.read_csv(dataset.tmp_dir + f"/{ds_name}/edges.csv", header=None) - edges.columns = ["src", "tgt"] - print(edges) - - g = nx.DiGraph() - g.add_edges_from(edges.to_numpy()) - rank = {int(k): v for k, v in nx.pagerank(g).items()} - rank[0] = sum(rank.values()) - rank = dict(sorted(rank.items(), key=lambda x: x[0])) - import json - - with open("nx.json", "w") as f: - json.dump(rank, f, indent=2) - - from matplotlib import pyplot as plt - - # pos = nx.drawing.layout.kamada_kawai_layout(g) - # pos = nx.drawing.layout.arf_layout(g) - # nx.draw(g, pos) - # nx.draw_networkx_labels(g, pos, {n: n for n in g.nodes}) - # plt.savefig(f"{out_path.split('/')[-1]}.png") - # plt.show() - # custom pagerank - print(pr(g)) - return - # (data, output_path, fun, metric) - paths = [ - ( - f"{self.data_path_root}/unweighted_edges/complete_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Complete.json", - run_pagerank, - nx.pagerank, - ), - ( - f"{self.data_path_root}/unweighted_edges/line_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Line.json", - run_pagerank, - nx.pagerank, - ), - ( - f"{self.data_path_root}/unweighted_edges/ring_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Ring.json", - run_pagerank, - nx.pagerank, - ), - ( - f"{self.data_path_root}/unweighted_edges/hubspoke_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Hub_Spoke.json", - run_pagerank, - nx.pagerank, - ), - ( - f"{self.data_path_root}/unweighted_edges/tree_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Tree.json", - run_pagerank, - nx.pagerank, - ), - # directed - ( - f"{self.data_path_root}/unweighted_edges/line_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Line_Directed.json", - run_pagerank, - nx.pagerank, - ), - ( - f"{self.data_path_root}/unweighted_edges/ring_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Ring_Directed.json", - run_pagerank, - nx.pagerank, - ), - ( - f"{self.data_path_root}/unweighted_edges/hubspoke_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Hub_Spoke_Directed.json", - run_pagerank, - nx.pagerank, - ), - ( - f"{self.data_path_root}/unweighted_edges/tree_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Tree_Directed.json", - run_pagerank, - nx.pagerank, - ), - ( - f"{self.data_path_root}/unweighted_edges/empty_graph_edges.csv", - f"{self.baseline_path_root}/centrality/pagerank/Empty.json", - run_pagerank, - nx.pagerank, - ), - ] - create_baseline(paths, algo="pagerank") From 3b74f2abdfedf9c2ab549886de790468f3bc88d8 Mon Sep 17 00:00:00 2001 From: RobRossmiller-TG <165701656+RobRossmiller-TG@users.noreply.github.com> Date: Fri, 6 Sep 2024 15:54:57 -0400 Subject: [PATCH 5/6] placeholder --- tests/test/baseline/algos/pagerank.py | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 tests/test/baseline/algos/pagerank.py diff --git a/tests/test/baseline/algos/pagerank.py b/tests/test/baseline/algos/pagerank.py new file mode 100644 index 00000000..603635cf --- /dev/null +++ b/tests/test/baseline/algos/pagerank.py @@ -0,0 +1,26 @@ +import networkx as nx +import pandas as pd +from pyTigerGraph.datasets import Datasets + +from .base import Baseline +from .common import create_baseline + + +def run_pagerank(g: nx.Graph, metric): + res = metric(g) + + out = [] + for k, v in res.items(): + out.append({"Vertex_ID": k, "score": v}) + + out = [{"@@top_scores_heap": out}] + return out + + +class PagerankBaseline(Baseline): + def __init__(self, data_path_root, baseline_path_root): + self.data_path_root = data_path_root + self.baseline_path_root = baseline_path_root + + def run(self): + return From 0c4f35f3c944970279c8fb1af3563a01f7bb28b4 Mon Sep 17 00:00:00 2001 From: RobRossmiller-TG <165701656+RobRossmiller-TG@users.noreply.github.com> Date: Fri, 6 Sep 2024 15:56:15 -0400 Subject: [PATCH 6/6] fail instead of exit --- tests/test/test_centrality.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test/test_centrality.py b/tests/test/test_centrality.py index cf8ac52c..dc33799b 100644 --- a/tests/test/test_centrality.py +++ b/tests/test/test_centrality.py @@ -49,7 +49,6 @@ def check_result( b["score"] ): q_type = "Template Query" if template_flag else "Generic Query" - pytest.exit(f'{q_type}: {r["score"]} != {b["score"]}') pytest.fail(f'{q_type}: {r["score"]} != {b["score"]}') @pytest.mark.parametrize("test_name", undirected_graphs)