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,