diff --git a/src/notebooks/6.0-benchmark_analysis.ipynb b/src/notebooks/6.0-benchmark_analysis.ipynb
index f0e7c13..276fd7b 100644
--- a/src/notebooks/6.0-benchmark_analysis.ipynb
+++ b/src/notebooks/6.0-benchmark_analysis.ipynb
@@ -288,7 +288,7 @@
" index = np.where(cn == np.amin(cn))\n",
" # if list is full of 0's (i.e sum == 0), then there are no shared neighbors \n",
" \n",
- " if np.sum(cn) == 0 or len(np.array(cn)[index]) > 1:\n",
+ " if np.sum(cn) == 0: #or len(np.array(cn)[index]) > 1:\n",
" continue \n",
" \n",
" for val in index:\n",
@@ -454,7 +454,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "Calculating scores for algorithms: 100%|██████████| 11/11 [00:03<00:00, 3.19it/s]\n"
+ "Calculating scores for algorithms: 100%|██████████| 11/11 [00:06<00:00, 1.67it/s]\n"
]
}
],
@@ -544,66 +544,66 @@
"
\n",
" \n",
" Common Neighbors | \n",
- " 50.0 | \n",
+ " 34.615 | \n",
" 0.132 | \n",
- " 2/4 | \n",
- " 44.444 | \n",
+ " 36/104 | \n",
+ " 31.765 | \n",
" 0.108 | \n",
- " 4/9 | \n",
+ " 27/85 | \n",
"
\n",
" \n",
" Cosine Similiarity | \n",
" 43.75 | \n",
" 0.132 | \n",
" 7/16 | \n",
- " 42.857 | \n",
+ " 38.889 | \n",
" 0.108 | \n",
- " 6/14 | \n",
+ " 14/36 | \n",
"
\n",
" \n",
" Jaccard index | \n",
" 43.75 | \n",
" 0.132 | \n",
" 7/16 | \n",
- " 40.0 | \n",
+ " 37.143 | \n",
" 0.108 | \n",
- " 6/15 | \n",
+ " 13/35 | \n",
"
\n",
" \n",
" Sorensen index | \n",
" 43.75 | \n",
" 0.132 | \n",
" 7/16 | \n",
- " 40.0 | \n",
+ " 37.143 | \n",
" 0.108 | \n",
- " 6/15 | \n",
+ " 13/35 | \n",
"
\n",
" \n",
" Hub Promoted Index | \n",
- " 60.0 | \n",
+ " 34.343 | \n",
" 0.132 | \n",
- " 3/5 | \n",
- " 46.154 | \n",
+ " 34/99 | \n",
+ " 37.209 | \n",
" 0.108 | \n",
- " 6/13 | \n",
+ " 16/43 | \n",
"
\n",
" \n",
" Hub Depressed Index | \n",
" 43.75 | \n",
" 0.132 | \n",
" 7/16 | \n",
- " 41.667 | \n",
+ " 35.211 | \n",
" 0.108 | \n",
- " 5/12 | \n",
+ " 25/71 | \n",
"
\n",
" \n",
" Leicht–Holme–Newman Index | \n",
" 43.75 | \n",
" 0.132 | \n",
" 7/16 | \n",
- " 46.667 | \n",
+ " 40.0 | \n",
" 0.108 | \n",
- " 7/15 | \n",
+ " 14/35 | \n",
"
\n",
" \n",
" Preferential Attachment | \n",
@@ -618,28 +618,28 @@
" Adamic-Adar | \n",
" 33.333 | \n",
" 0.132 | \n",
- " 2/6 | \n",
- " 36.364 | \n",
+ " 30/90 | \n",
+ " 32.143 | \n",
" 0.108 | \n",
- " 4/11 | \n",
+ " 18/56 | \n",
"
\n",
" \n",
" Resource Allocation Index | \n",
" 33.333 | \n",
" 0.132 | \n",
- " 2/6 | \n",
- " 36.364 | \n",
+ " 30/90 | \n",
+ " 32.143 | \n",
" 0.108 | \n",
- " 4/11 | \n",
+ " 18/56 | \n",
"
\n",
" \n",
" Shortest Path | \n",
- " 0.0 | \n",
+ " 11.111 | \n",
" 0.132 | \n",
- " 0/1 | \n",
- " 0.0 | \n",
+ " 18/162 | \n",
+ " 14.844 | \n",
" 0.108 | \n",
- " 0/10 | \n",
+ " 57/384 | \n",
"
\n",
" \n",
"\n",
@@ -647,43 +647,43 @@
],
"text/plain": [
" openbio_precision openbio_val_by_chance \\\n",
- "Common Neighbors 50.0 0.132 \n",
+ "Common Neighbors 34.615 0.132 \n",
"Cosine Similiarity 43.75 0.132 \n",
"Jaccard index 43.75 0.132 \n",
"Sorensen index 43.75 0.132 \n",
- "Hub Promoted Index 60.0 0.132 \n",
+ "Hub Promoted Index 34.343 0.132 \n",
"Hub Depressed Index 43.75 0.132 \n",
"Leicht–Holme–Newman Index 43.75 0.132 \n",
"Preferential Attachment 5.0 0.132 \n",
"Adamic-Adar 33.333 0.132 \n",
"Resource Allocation Index 33.333 0.132 \n",
- "Shortest Path 0.0 0.132 \n",
+ "Shortest Path 11.111 0.132 \n",
"\n",
" # openbio_pairs custom_precision \\\n",
- "Common Neighbors 2/4 44.444 \n",
- "Cosine Similiarity 7/16 42.857 \n",
- "Jaccard index 7/16 40.0 \n",
- "Sorensen index 7/16 40.0 \n",
- "Hub Promoted Index 3/5 46.154 \n",
- "Hub Depressed Index 7/16 41.667 \n",
- "Leicht–Holme–Newman Index 7/16 46.667 \n",
+ "Common Neighbors 36/104 31.765 \n",
+ "Cosine Similiarity 7/16 38.889 \n",
+ "Jaccard index 7/16 37.143 \n",
+ "Sorensen index 7/16 37.143 \n",
+ "Hub Promoted Index 34/99 37.209 \n",
+ "Hub Depressed Index 7/16 35.211 \n",
+ "Leicht–Holme–Newman Index 7/16 40.0 \n",
"Preferential Attachment 1/20 9.302 \n",
- "Adamic-Adar 2/6 36.364 \n",
- "Resource Allocation Index 2/6 36.364 \n",
- "Shortest Path 0/1 0.0 \n",
+ "Adamic-Adar 30/90 32.143 \n",
+ "Resource Allocation Index 30/90 32.143 \n",
+ "Shortest Path 18/162 14.844 \n",
"\n",
" custom_val_by_chance # custom_pairs \n",
- "Common Neighbors 0.108 4/9 \n",
- "Cosine Similiarity 0.108 6/14 \n",
- "Jaccard index 0.108 6/15 \n",
- "Sorensen index 0.108 6/15 \n",
- "Hub Promoted Index 0.108 6/13 \n",
- "Hub Depressed Index 0.108 5/12 \n",
- "Leicht–Holme–Newman Index 0.108 7/15 \n",
+ "Common Neighbors 0.108 27/85 \n",
+ "Cosine Similiarity 0.108 14/36 \n",
+ "Jaccard index 0.108 13/35 \n",
+ "Sorensen index 0.108 13/35 \n",
+ "Hub Promoted Index 0.108 16/43 \n",
+ "Hub Depressed Index 0.108 25/71 \n",
+ "Leicht–Holme–Newman Index 0.108 14/35 \n",
"Preferential Attachment 0.108 4/43 \n",
- "Adamic-Adar 0.108 4/11 \n",
- "Resource Allocation Index 0.108 4/11 \n",
- "Shortest Path 0.108 0/10 "
+ "Adamic-Adar 0.108 18/56 \n",
+ "Resource Allocation Index 0.108 18/56 \n",
+ "Shortest Path 0.108 57/384 "
]
},
"execution_count": 15,