diff --git a/content/04.results.md b/content/04.results.md index 3b3d470..ec41a0f 100644 --- a/content/04.results.md +++ b/content/04.results.md @@ -14,7 +14,7 @@ LogMap returns a score rather than a binary answer - we took the best performing cutoff. The distribution of F1 scores with different thresholds are show in @fig:logmap-scatter-plot-combined. -![**LogMap Results**](images/logmap-scatter-plot-combined.pdf){#fig:logmap-scatter-plot-combined height=3in} +![**LogMap Results**](images/logmap-scatter-plot-combined.png){#fig:logmap-scatter-plot-combined height=3in} ### Anatomy Task Results @@ -27,7 +27,7 @@ Table: Results of *Drosophila* to *Danio rerio* anatomy matching In this task, GPT-4 scored highest in both accuracy and precision. -![**LogMap Results**](images/logmap-scatter-plot-fbbt-zfa.pdf){#fig:logmap-scatter-plot-fbbt-zfa height=3in} +![**LogMap Results**](images/logmap-scatter-plot-fbbt-zfa.png){#fig:logmap-scatter-plot-fbbt-zfa height=3in} We also assessed Fly to Worm: @@ -35,7 +35,7 @@ We also assessed Fly to Worm: Table: Results of *Drosophila* to *C elegans* anatomy matching {#tbl:main_results_fbbt_wbbt} -![**LogMap Results**](images/logmap-scatter-plot-fbbt-wbbt.pdf){#fig:logmap-scatter-plot-fbbt-wbbt height=3in} +![**LogMap Results**](images/logmap-scatter-plot-fbbt-wbbt.png){#fig:logmap-scatter-plot-fbbt-wbbt height=3in} ### Developmental Stage ontology task results @@ -43,7 +43,7 @@ Table: Results of *Drosophila* to *C elegans* anatomy matching Table: Results of human developmental stages (HsapDv) vs mouse developmental stages (MmusDv) {#tbl:main_results_hsapdv_mmusdv} -![**LogMap Results**](images/logmap-scatter-plot-hsapdv-mmusdv.pdf){#fig:logmap-scatter-plot-hsapdv-mmusdv height=3in} +![**LogMap Results**](images/logmap-scatter-plot-hsapdv-mmusdv.png){#fig:logmap-scatter-plot-hsapdv-mmusdv height=3in} ### Disease matching task results @@ -54,6 +54,6 @@ all heritable renal diseases from Mondo to all renal diseases from NCIT. Table: Results of MONDO vs NCIT (renal subset) {#tbl:main_results_mondo_ncit_renal_subset} -![**LogMap Results**](images/logmap-scatter-plot-mondo-ncit-renal-subset.pdf){#fig:logmap-scatter-plot-mondo-ncit-renal-subset height=3in} +![**LogMap Results**](images/logmap-scatter-plot-mondo-ncit-renal-subset.png){#fig:logmap-scatter-plot-mondo-ncit-renal-subset height=3in} In this task, the previous SOTA achieves slight gain in precision over GPT based methods. diff --git a/content/images/logmap-scatter-plot-combined.pdf b/content/images/logmap-scatter-plot-combined.pdf index 6a1609e..7036972 100644 Binary files a/content/images/logmap-scatter-plot-combined.pdf and b/content/images/logmap-scatter-plot-combined.pdf differ diff --git a/content/images/logmap-scatter-plot-combined.png b/content/images/logmap-scatter-plot-combined.png new file mode 100644 index 0000000..8a43903 Binary files /dev/null and b/content/images/logmap-scatter-plot-combined.png differ diff --git a/content/images/logmap-scatter-plot-fbbt-wbbt.pdf b/content/images/logmap-scatter-plot-fbbt-wbbt.pdf index 7b85d09..6c14b34 100644 Binary files a/content/images/logmap-scatter-plot-fbbt-wbbt.pdf and b/content/images/logmap-scatter-plot-fbbt-wbbt.pdf differ diff --git a/content/images/logmap-scatter-plot-fbbt-wbbt.png b/content/images/logmap-scatter-plot-fbbt-wbbt.png new file mode 100644 index 0000000..cbd1aa2 Binary files /dev/null and b/content/images/logmap-scatter-plot-fbbt-wbbt.png differ diff --git a/content/images/logmap-scatter-plot-fbbt-zfa.pdf b/content/images/logmap-scatter-plot-fbbt-zfa.pdf index 7cf1334..f35b5cd 100644 Binary files a/content/images/logmap-scatter-plot-fbbt-zfa.pdf and b/content/images/logmap-scatter-plot-fbbt-zfa.pdf differ diff --git a/content/images/logmap-scatter-plot-fbbt-zfa.png b/content/images/logmap-scatter-plot-fbbt-zfa.png new file mode 100644 index 0000000..4f841d9 Binary files /dev/null and b/content/images/logmap-scatter-plot-fbbt-zfa.png differ diff --git a/content/images/logmap-scatter-plot-hsapdv-mmusdv.pdf b/content/images/logmap-scatter-plot-hsapdv-mmusdv.pdf index f90dc69..00f6215 100644 Binary files a/content/images/logmap-scatter-plot-hsapdv-mmusdv.pdf and b/content/images/logmap-scatter-plot-hsapdv-mmusdv.pdf differ diff --git a/content/images/logmap-scatter-plot-hsapdv-mmusdv.png b/content/images/logmap-scatter-plot-hsapdv-mmusdv.png new file mode 100644 index 0000000..709b806 Binary files /dev/null and b/content/images/logmap-scatter-plot-hsapdv-mmusdv.png differ diff --git a/content/images/logmap-scatter-plot-mondo-ncit-renal-subset.pdf b/content/images/logmap-scatter-plot-mondo-ncit-renal-subset.pdf index cb6366b..6e4f178 100644 Binary files a/content/images/logmap-scatter-plot-mondo-ncit-renal-subset.pdf and b/content/images/logmap-scatter-plot-mondo-ncit-renal-subset.pdf differ diff --git a/content/images/logmap-scatter-plot-mondo-ncit-renal-subset.png b/content/images/logmap-scatter-plot-mondo-ncit-renal-subset.png new file mode 100644 index 0000000..26cac6b Binary files /dev/null and b/content/images/logmap-scatter-plot-mondo-ncit-renal-subset.png differ diff --git a/notebooks/Mapping-Evaluation-combined.ipynb b/notebooks/Mapping-Evaluation-combined.ipynb index 49a424a..5c12457 100644 --- a/notebooks/Mapping-Evaluation-combined.ipynb +++ b/notebooks/Mapping-Evaluation-combined.ipynb @@ -5,10 +5,10 @@ "id": "da02b833", "metadata": { "papermill": { - 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"iopub.execute_input": "2023-09-08T06:42:48.115659Z", - "iopub.status.busy": "2023-09-08T06:42:48.115250Z", - "iopub.status.idle": "2023-09-08T06:42:48.133435Z", - "shell.execute_reply": "2023-09-08T06:42:48.132472Z" + "iopub.execute_input": "2023-09-08T07:12:51.169209Z", + "iopub.status.busy": "2023-09-08T07:12:51.168563Z", + "iopub.status.idle": "2023-09-08T07:12:51.185491Z", + "shell.execute_reply": "2023-09-08T07:12:51.184624Z" }, "papermill": { - "duration": 0.033388, - "end_time": "2023-09-08T06:42:48.136141", + "duration": 0.031181, + "end_time": "2023-09-08T07:12:51.187977", "exception": false, - "start_time": "2023-09-08T06:42:48.102753", + "start_time": "2023-09-08T07:12:51.156796", "status": "completed" }, "tags": [] @@ -3078,16 +3078,16 @@ "id": "34971961", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:48.161187Z", - "iopub.status.busy": "2023-09-08T06:42:48.160797Z", - "iopub.status.idle": "2023-09-08T06:42:48.791178Z", - "shell.execute_reply": "2023-09-08T06:42:48.790297Z" + "iopub.execute_input": "2023-09-08T07:12:51.212428Z", + "iopub.status.busy": "2023-09-08T07:12:51.211998Z", + "iopub.status.idle": "2023-09-08T07:12:51.839376Z", + "shell.execute_reply": "2023-09-08T07:12:51.838439Z" }, "papermill": { - 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"iopub.status.busy": "2023-09-08T06:42:48.851190Z", - "iopub.status.idle": "2023-09-08T06:42:49.080559Z", - "shell.execute_reply": "2023-09-08T06:42:49.079702Z" + "iopub.execute_input": "2023-09-08T07:12:51.903720Z", + "iopub.status.busy": "2023-09-08T07:12:51.903062Z", + "iopub.status.idle": "2023-09-08T07:12:52.135215Z", + "shell.execute_reply": "2023-09-08T07:12:52.134345Z" }, "papermill": { - "duration": 0.245419, - "end_time": "2023-09-08T06:42:49.083196", + "duration": 0.250152, + "end_time": "2023-09-08T07:12:52.137812", "exception": false, - "start_time": "2023-09-08T06:42:48.837777", + "start_time": "2023-09-08T07:12:51.887660", "status": "completed" }, "tags": [] @@ -3245,16 +3245,16 @@ "id": "951219ed", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:49.109351Z", - "iopub.status.busy": "2023-09-08T06:42:49.108945Z", - "iopub.status.idle": "2023-09-08T06:42:49.848909Z", - "shell.execute_reply": "2023-09-08T06:42:49.847879Z" + "iopub.execute_input": "2023-09-08T07:12:52.163471Z", + "iopub.status.busy": "2023-09-08T07:12:52.162816Z", + "iopub.status.idle": "2023-09-08T07:12:52.865559Z", + "shell.execute_reply": "2023-09-08T07:12:52.864364Z" }, "papermill": { - "duration": 0.756664, - "end_time": "2023-09-08T06:42:49.852158", + "duration": 0.718714, + "end_time": "2023-09-08T07:12:52.868652", "exception": false, - "start_time": "2023-09-08T06:42:49.095494", + "start_time": "2023-09-08T07:12:52.149938", "status": "completed" }, "tags": [] @@ -3270,16 +3270,16 @@ "id": "a7de6bab", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:49.879674Z", - "iopub.status.busy": "2023-09-08T06:42:49.879228Z", - "iopub.status.idle": "2023-09-08T06:42:50.604446Z", - "shell.execute_reply": "2023-09-08T06:42:50.603563Z" + "iopub.execute_input": "2023-09-08T07:12:52.894745Z", + "iopub.status.busy": "2023-09-08T07:12:52.894293Z", + "iopub.status.idle": "2023-09-08T07:12:53.797379Z", + "shell.execute_reply": "2023-09-08T07:12:53.796459Z" }, "papermill": { - "duration": 0.742523, - "end_time": "2023-09-08T06:42:50.607065", + "duration": 0.919025, + "end_time": "2023-09-08T07:12:53.799948", "exception": false, - "start_time": "2023-09-08T06:42:49.864542", + "start_time": "2023-09-08T07:12:52.880923", "status": "completed" }, "tags": [] @@ -3324,6 +3324,7 @@ "plt.ylabel('F1')\n", "plt.title(f'{task} LogMap score threshold vs F1 (accuracy)')\n", "\n", + "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.png\", format='png')\n", "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.pdf\", format='pdf')\n", "\n", "# Show the plot\n", @@ -3336,16 +3337,16 @@ "id": "e12c93c4", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:50.635523Z", - "iopub.status.busy": "2023-09-08T06:42:50.634676Z", - "iopub.status.idle": "2023-09-08T06:42:50.641450Z", - "shell.execute_reply": "2023-09-08T06:42:50.640450Z" + "iopub.execute_input": "2023-09-08T07:12:53.827145Z", + "iopub.status.busy": "2023-09-08T07:12:53.826573Z", + "iopub.status.idle": "2023-09-08T07:12:53.832717Z", + "shell.execute_reply": "2023-09-08T07:12:53.831828Z" }, "papermill": { - "duration": 0.023883, - "end_time": "2023-09-08T06:42:50.644076", + "duration": 0.022602, + "end_time": "2023-09-08T07:12:53.835302", "exception": false, - "start_time": "2023-09-08T06:42:50.620193", + "start_time": "2023-09-08T07:12:53.812700", "status": "completed" }, "tags": [] @@ -3361,16 +3362,16 @@ "id": "a7e7524f", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:50.671622Z", - "iopub.status.busy": "2023-09-08T06:42:50.671207Z", - "iopub.status.idle": "2023-09-08T06:42:50.848184Z", - "shell.execute_reply": "2023-09-08T06:42:50.847188Z" + "iopub.execute_input": "2023-09-08T07:12:53.863344Z", + "iopub.status.busy": "2023-09-08T07:12:53.862951Z", + "iopub.status.idle": "2023-09-08T07:12:54.037307Z", + "shell.execute_reply": "2023-09-08T07:12:54.036282Z" }, "papermill": { - "duration": 0.194083, - "end_time": "2023-09-08T06:42:50.851168", + "duration": 0.191529, + "end_time": "2023-09-08T07:12:54.040187", "exception": false, - "start_time": "2023-09-08T06:42:50.657085", + "start_time": "2023-09-08T07:12:53.848658", "status": "completed" }, "tags": [] @@ -3387,16 +3388,16 @@ "id": "b03b2621", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:50.878981Z", - "iopub.status.busy": "2023-09-08T06:42:50.878584Z", - "iopub.status.idle": "2023-09-08T06:42:50.888695Z", - "shell.execute_reply": "2023-09-08T06:42:50.887472Z" + "iopub.execute_input": "2023-09-08T07:12:54.067444Z", + "iopub.status.busy": "2023-09-08T07:12:54.066716Z", + "iopub.status.idle": "2023-09-08T07:12:54.077610Z", + "shell.execute_reply": "2023-09-08T07:12:54.076607Z" }, "papermill": { - "duration": 0.02742, - "end_time": "2023-09-08T06:42:50.891438", + "duration": 0.027265, + "end_time": "2023-09-08T07:12:54.080230", "exception": false, - "start_time": "2023-09-08T06:42:50.864018", + "start_time": "2023-09-08T07:12:54.052965", "status": "completed" }, "tags": [] @@ -3422,16 +3423,16 @@ "id": "d66185bc", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:50.918712Z", - "iopub.status.busy": "2023-09-08T06:42:50.918171Z", - "iopub.status.idle": "2023-09-08T06:42:50.958627Z", - "shell.execute_reply": "2023-09-08T06:42:50.957532Z" + "iopub.execute_input": "2023-09-08T07:12:54.107610Z", + "iopub.status.busy": "2023-09-08T07:12:54.106643Z", + "iopub.status.idle": "2023-09-08T07:12:54.147676Z", + "shell.execute_reply": "2023-09-08T07:12:54.146873Z" }, "papermill": { - "duration": 0.057014, - "end_time": "2023-09-08T06:42:50.961427", + "duration": 0.057541, + "end_time": "2023-09-08T07:12:54.150482", "exception": false, - "start_time": "2023-09-08T06:42:50.904413", + "start_time": "2023-09-08T07:12:54.092941", "status": "completed" }, "tags": [] @@ -3457,16 +3458,16 @@ "id": "bc23aa02", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:50.989296Z", - "iopub.status.busy": "2023-09-08T06:42:50.988883Z", - "iopub.status.idle": "2023-09-08T06:42:51.012723Z", - "shell.execute_reply": "2023-09-08T06:42:51.011812Z" + "iopub.execute_input": "2023-09-08T07:12:54.178819Z", + "iopub.status.busy": "2023-09-08T07:12:54.178403Z", + "iopub.status.idle": "2023-09-08T07:12:54.202166Z", + "shell.execute_reply": "2023-09-08T07:12:54.201193Z" }, "papermill": { - "duration": 0.040516, - "end_time": "2023-09-08T06:42:51.015222", + "duration": 0.041187, + "end_time": "2023-09-08T07:12:54.204991", "exception": false, - "start_time": "2023-09-08T06:42:50.974706", + "start_time": "2023-09-08T07:12:54.163804", "status": "completed" }, "tags": [] @@ -3703,10 +3704,10 @@ "id": "fe33118f", "metadata": { "papermill": { - "duration": 0.01307, - "end_time": "2023-09-08T06:42:51.041860", + "duration": 0.013094, + "end_time": "2023-09-08T07:12:54.231676", "exception": false, - "start_time": "2023-09-08T06:42:51.028790", + "start_time": "2023-09-08T07:12:54.218582", "status": "completed" }, "tags": [] @@ -3720,10 +3721,10 @@ "id": "8b066d2c", "metadata": { "papermill": { - "duration": 0.013049, - "end_time": "2023-09-08T06:42:51.068103", + "duration": 0.014219, + "end_time": "2023-09-08T07:12:54.259104", "exception": false, - "start_time": "2023-09-08T06:42:51.055054", + "start_time": "2023-09-08T07:12:54.244885", "status": "completed" }, "tags": [] @@ -3737,10 +3738,10 @@ "id": "77ee339f", "metadata": { "papermill": { - "duration": 0.013464, - "end_time": "2023-09-08T06:42:51.094866", + "duration": 0.013485, + "end_time": "2023-09-08T07:12:54.286096", "exception": false, - "start_time": "2023-09-08T06:42:51.081402", + "start_time": "2023-09-08T07:12:54.272611", "status": "completed" }, "tags": [] @@ -3754,10 +3755,10 @@ "id": "e648f511", "metadata": { "papermill": { - "duration": 0.013413, - "end_time": "2023-09-08T06:42:51.121571", + "duration": 0.013483, + "end_time": "2023-09-08T07:12:54.313357", "exception": false, - "start_time": "2023-09-08T06:42:51.108158", + "start_time": "2023-09-08T07:12:54.299874", "status": "completed" }, "tags": [] @@ -3771,10 +3772,10 @@ "id": "8b53aa7d", "metadata": { "papermill": { - "duration": 0.013148, - "end_time": "2023-09-08T06:42:51.148090", + "duration": 0.01299, + "end_time": "2023-09-08T07:12:54.339474", "exception": false, - "start_time": "2023-09-08T06:42:51.134942", + "start_time": "2023-09-08T07:12:54.326484", "status": "completed" }, "tags": [] @@ -3804,8 +3805,8 @@ }, "papermill": { "default_parameters": {}, - "duration": 7.247808, - "end_time": "2023-09-08T06:42:51.583817", + "duration": 7.274585, + "end_time": "2023-09-08T07:12:54.874729", "environment_variables": {}, "exception": null, "input_path": "Mapping-Evaluation.ipynb", @@ -3813,7 +3814,7 @@ "parameters": { "task": "combined" }, - "start_time": "2023-09-08T06:42:44.336009", + "start_time": "2023-09-08T07:12:47.600144", "version": "2.4.0" } }, diff --git a/notebooks/Mapping-Evaluation-fbbt-wbbt.ipynb b/notebooks/Mapping-Evaluation-fbbt-wbbt.ipynb index ef1305b..588e36d 100644 --- a/notebooks/Mapping-Evaluation-fbbt-wbbt.ipynb +++ b/notebooks/Mapping-Evaluation-fbbt-wbbt.ipynb @@ -5,10 +5,10 @@ "id": "da02b833", "metadata": { "papermill": { - "duration": 0.008594, - "end_time": "2023-09-08T06:42:21.442286", + "duration": 0.008313, + "end_time": "2023-09-08T07:12:24.972486", "exception": false, - "start_time": "2023-09-08T06:42:21.433692", + "start_time": "2023-09-08T07:12:24.964173", "status": "completed" }, "tags": [] @@ -25,16 +25,16 @@ "id": "615ad1f2", "metadata": { "execution": { - 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"iopub.status.busy": "2023-09-08T06:42:23.628817Z", - "iopub.status.idle": "2023-09-08T06:42:23.838047Z", - "shell.execute_reply": "2023-09-08T06:42:23.837190Z" + "iopub.execute_input": "2023-09-08T07:12:27.153813Z", + "iopub.status.busy": "2023-09-08T07:12:27.153100Z", + "iopub.status.idle": "2023-09-08T07:12:27.367494Z", + "shell.execute_reply": "2023-09-08T07:12:27.366501Z" }, "papermill": { - "duration": 0.225243, - "end_time": "2023-09-08T06:42:23.840680", + "duration": 0.231989, + "end_time": "2023-09-08T07:12:27.370403", "exception": false, - "start_time": "2023-09-08T06:42:23.615437", + "start_time": "2023-09-08T07:12:27.138414", "status": "completed" }, "tags": [] @@ -3866,16 +3866,16 @@ "id": "951219ed", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:23.868140Z", - "iopub.status.busy": "2023-09-08T06:42:23.867740Z", - "iopub.status.idle": "2023-09-08T06:42:24.566094Z", - "shell.execute_reply": "2023-09-08T06:42:24.565098Z" + "iopub.execute_input": "2023-09-08T07:12:27.397794Z", + "iopub.status.busy": "2023-09-08T07:12:27.397092Z", + "iopub.status.idle": "2023-09-08T07:12:28.100796Z", + "shell.execute_reply": "2023-09-08T07:12:28.099747Z" }, "papermill": { - "duration": 0.715324, - "end_time": "2023-09-08T06:42:24.568883", + "duration": 0.720274, + "end_time": "2023-09-08T07:12:28.103493", "exception": false, - "start_time": "2023-09-08T06:42:23.853559", + "start_time": "2023-09-08T07:12:27.383219", "status": "completed" }, "tags": [] @@ -3891,16 +3891,16 @@ "id": "a7de6bab", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:24.596131Z", - "iopub.status.busy": "2023-09-08T06:42:24.595713Z", - "iopub.status.idle": "2023-09-08T06:42:25.297567Z", - "shell.execute_reply": "2023-09-08T06:42:25.296076Z" + "iopub.execute_input": "2023-09-08T07:12:28.130014Z", + "iopub.status.busy": "2023-09-08T07:12:28.129613Z", + "iopub.status.idle": "2023-09-08T07:12:28.975691Z", + "shell.execute_reply": "2023-09-08T07:12:28.974771Z" }, "papermill": { - "duration": 0.72022, - "end_time": "2023-09-08T06:42:25.302022", + "duration": 0.862606, + "end_time": "2023-09-08T07:12:28.978831", "exception": false, - "start_time": "2023-09-08T06:42:24.581802", + "start_time": "2023-09-08T07:12:28.116225", "status": "completed" }, "tags": [] @@ -3945,6 +3945,7 @@ "plt.ylabel('F1')\n", "plt.title(f'{task} LogMap score threshold vs F1 (accuracy)')\n", "\n", + "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.png\", format='png')\n", "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.pdf\", format='pdf')\n", "\n", "# Show the plot\n", @@ -3957,16 +3958,16 @@ "id": "e12c93c4", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:25.372500Z", - "iopub.status.busy": "2023-09-08T06:42:25.371945Z", - "iopub.status.idle": "2023-09-08T06:42:25.378493Z", - "shell.execute_reply": "2023-09-08T06:42:25.377548Z" + "iopub.execute_input": "2023-09-08T07:12:29.021289Z", + "iopub.status.busy": "2023-09-08T07:12:29.020679Z", + "iopub.status.idle": "2023-09-08T07:12:29.027206Z", + "shell.execute_reply": "2023-09-08T07:12:29.026339Z" }, "papermill": { - "duration": 0.030798, - "end_time": "2023-09-08T06:42:25.381399", + "duration": 0.031642, + "end_time": "2023-09-08T07:12:29.030087", "exception": false, - "start_time": "2023-09-08T06:42:25.350601", + "start_time": "2023-09-08T07:12:28.998445", "status": "completed" }, "tags": [] @@ -3982,16 +3983,16 @@ "id": "a7e7524f", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:25.410392Z", - "iopub.status.busy": "2023-09-08T06:42:25.409605Z", - "iopub.status.idle": "2023-09-08T06:42:25.587230Z", - "shell.execute_reply": "2023-09-08T06:42:25.585995Z" + "iopub.execute_input": "2023-09-08T07:12:29.059278Z", + "iopub.status.busy": "2023-09-08T07:12:29.058882Z", + "iopub.status.idle": "2023-09-08T07:12:29.248072Z", + "shell.execute_reply": "2023-09-08T07:12:29.247022Z" }, "papermill": { - "duration": 0.194978, - "end_time": "2023-09-08T06:42:25.590188", + "duration": 0.206963, + "end_time": "2023-09-08T07:12:29.251019", "exception": false, - "start_time": "2023-09-08T06:42:25.395210", + "start_time": "2023-09-08T07:12:29.044056", "status": "completed" }, "tags": [] @@ -4008,16 +4009,16 @@ "id": "b03b2621", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:25.619943Z", - "iopub.status.busy": "2023-09-08T06:42:25.619087Z", - "iopub.status.idle": "2023-09-08T06:42:25.629893Z", - "shell.execute_reply": "2023-09-08T06:42:25.628961Z" + "iopub.execute_input": "2023-09-08T07:12:29.279692Z", + "iopub.status.busy": "2023-09-08T07:12:29.279250Z", + "iopub.status.idle": "2023-09-08T07:12:29.289093Z", + "shell.execute_reply": "2023-09-08T07:12:29.288221Z" }, "papermill": { - "duration": 0.028553, - "end_time": "2023-09-08T06:42:25.632387", + "duration": 0.027294, + "end_time": "2023-09-08T07:12:29.291656", "exception": false, - "start_time": "2023-09-08T06:42:25.603834", + "start_time": "2023-09-08T07:12:29.264362", "status": "completed" }, "tags": [] @@ -4043,16 +4044,16 @@ "id": "d66185bc", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:25.661299Z", - "iopub.status.busy": "2023-09-08T06:42:25.660554Z", - "iopub.status.idle": "2023-09-08T06:42:25.701334Z", - "shell.execute_reply": "2023-09-08T06:42:25.700261Z" + "iopub.execute_input": "2023-09-08T07:12:29.320100Z", + "iopub.status.busy": "2023-09-08T07:12:29.319380Z", + "iopub.status.idle": "2023-09-08T07:12:29.360395Z", + "shell.execute_reply": "2023-09-08T07:12:29.359479Z" }, "papermill": { - "duration": 0.057824, - "end_time": "2023-09-08T06:42:25.703957", + "duration": 0.057937, + "end_time": "2023-09-08T07:12:29.363006", "exception": false, - "start_time": "2023-09-08T06:42:25.646133", + "start_time": "2023-09-08T07:12:29.305069", "status": "completed" }, "tags": [] @@ -4078,16 +4079,16 @@ "id": "bc23aa02", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:25.733882Z", - "iopub.status.busy": "2023-09-08T06:42:25.733492Z", - "iopub.status.idle": "2023-09-08T06:42:25.751107Z", - "shell.execute_reply": "2023-09-08T06:42:25.750257Z" + "iopub.execute_input": "2023-09-08T07:12:29.392606Z", + "iopub.status.busy": "2023-09-08T07:12:29.391906Z", + "iopub.status.idle": "2023-09-08T07:12:29.409287Z", + "shell.execute_reply": "2023-09-08T07:12:29.408122Z" }, "papermill": { - "duration": 0.035591, - "end_time": "2023-09-08T06:42:25.753601", + "duration": 0.035023, + "end_time": "2023-09-08T07:12:29.411874", "exception": false, - "start_time": "2023-09-08T06:42:25.718010", + "start_time": "2023-09-08T07:12:29.376851", "status": "completed" }, "tags": [] @@ -4149,10 +4150,10 @@ "id": "fe33118f", "metadata": { "papermill": { - "duration": 0.01355, - "end_time": "2023-09-08T06:42:25.781158", + "duration": 0.013985, + "end_time": "2023-09-08T07:12:29.439543", "exception": false, - "start_time": "2023-09-08T06:42:25.767608", + "start_time": "2023-09-08T07:12:29.425558", "status": "completed" }, "tags": [] @@ -4166,10 +4167,10 @@ "id": "8b066d2c", "metadata": { "papermill": { - "duration": 0.013402, - "end_time": "2023-09-08T06:42:25.808172", + "duration": 0.013336, + "end_time": "2023-09-08T07:12:29.466544", "exception": false, - "start_time": "2023-09-08T06:42:25.794770", + "start_time": "2023-09-08T07:12:29.453208", "status": "completed" }, "tags": [] @@ -4183,10 +4184,10 @@ "id": "77ee339f", "metadata": { "papermill": { - "duration": 0.013971, - "end_time": "2023-09-08T06:42:25.835788", + "duration": 0.01382, + "end_time": "2023-09-08T07:12:29.494308", "exception": false, - "start_time": "2023-09-08T06:42:25.821817", + "start_time": "2023-09-08T07:12:29.480488", "status": "completed" }, "tags": [] @@ -4200,10 +4201,10 @@ "id": "e648f511", "metadata": { "papermill": { - "duration": 0.013953, - "end_time": "2023-09-08T06:42:25.863602", + "duration": 0.013667, + "end_time": "2023-09-08T07:12:29.522046", "exception": false, - "start_time": "2023-09-08T06:42:25.849649", + "start_time": "2023-09-08T07:12:29.508379", "status": "completed" }, "tags": [] @@ -4217,10 +4218,10 @@ "id": "8b53aa7d", "metadata": { "papermill": { - "duration": 0.014054, - "end_time": "2023-09-08T06:42:25.891861", + "duration": 0.013392, + "end_time": "2023-09-08T07:12:29.549145", "exception": false, - "start_time": "2023-09-08T06:42:25.877807", + "start_time": "2023-09-08T07:12:29.535753", "status": "completed" }, "tags": [] @@ -4250,8 +4251,8 @@ }, "papermill": { "default_parameters": {}, - "duration": 6.854357, - "end_time": "2023-09-08T06:42:26.428622", + "duration": 7.005064, + "end_time": "2023-09-08T07:12:29.984098", "environment_variables": {}, "exception": null, "input_path": "Mapping-Evaluation.ipynb", @@ -4259,7 +4260,7 @@ "parameters": { "task": "fbbt-wbbt" }, - "start_time": "2023-09-08T06:42:19.574265", + "start_time": "2023-09-08T07:12:22.979034", "version": "2.4.0" } }, diff --git a/notebooks/Mapping-Evaluation-fbbt-zfa.ipynb b/notebooks/Mapping-Evaluation-fbbt-zfa.ipynb index 2bdb693..4f4aed3 100644 --- a/notebooks/Mapping-Evaluation-fbbt-zfa.ipynb +++ b/notebooks/Mapping-Evaluation-fbbt-zfa.ipynb @@ -5,10 +5,10 @@ "id": "da02b833", "metadata": { "papermill": { - "duration": 0.007979, - "end_time": "2023-09-08T06:42:12.804355", + "duration": 0.008079, + "end_time": "2023-09-08T07:12:15.697128", "exception": false, - "start_time": "2023-09-08T06:42:12.796376", + "start_time": "2023-09-08T07:12:15.689049", "status": "completed" }, "tags": [] @@ -25,16 +25,16 @@ "id": "615ad1f2", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:12.820220Z", - "iopub.status.busy": "2023-09-08T06:42:12.819808Z", - "iopub.status.idle": "2023-09-08T06:42:12.830674Z", - "shell.execute_reply": "2023-09-08T06:42:12.829762Z" + "iopub.execute_input": "2023-09-08T07:12:15.713338Z", + "iopub.status.busy": "2023-09-08T07:12:15.712926Z", + "iopub.status.idle": "2023-09-08T07:12:15.723500Z", + "shell.execute_reply": "2023-09-08T07:12:15.722605Z" }, "papermill": { - "duration": 0.021993, - "end_time": "2023-09-08T06:42:12.833442", + "duration": 0.022004, + "end_time": "2023-09-08T07:12:15.726241", "exception": false, - "start_time": "2023-09-08T06:42:12.811449", + "start_time": "2023-09-08T07:12:15.704237", "status": "completed" }, "tags": [ @@ -51,19 +51,19 @@ { "cell_type": "code", "execution_count": 2, - "id": "d553ca6b", + "id": "ad824be5", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:12.848688Z", - "iopub.status.busy": "2023-09-08T06:42:12.848285Z", - "iopub.status.idle": "2023-09-08T06:42:12.852380Z", - "shell.execute_reply": "2023-09-08T06:42:12.851500Z" + "iopub.execute_input": "2023-09-08T07:12:15.741714Z", + "iopub.status.busy": "2023-09-08T07:12:15.741302Z", + "iopub.status.idle": "2023-09-08T07:12:15.745841Z", + "shell.execute_reply": "2023-09-08T07:12:15.744727Z" }, "papermill": { - "duration": 0.014622, - "end_time": "2023-09-08T06:42:12.854964", + "duration": 0.015527, + "end_time": "2023-09-08T07:12:15.748665", "exception": false, - "start_time": "2023-09-08T06:42:12.840342", + "start_time": "2023-09-08T07:12:15.733138", "status": "completed" }, "tags": [ @@ -82,16 +82,16 @@ "id": "ff08a44a", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:12.870172Z", - "iopub.status.busy": "2023-09-08T06:42:12.869521Z", - "iopub.status.idle": "2023-09-08T06:42:13.627867Z", - "shell.execute_reply": "2023-09-08T06:42:13.626763Z" + "iopub.execute_input": "2023-09-08T07:12:15.764483Z", + "iopub.status.busy": "2023-09-08T07:12:15.763471Z", + "iopub.status.idle": "2023-09-08T07:12:16.616718Z", + "shell.execute_reply": "2023-09-08T07:12:16.615646Z" }, "papermill": { - "duration": 0.769062, - "end_time": "2023-09-08T06:42:13.630804", + "duration": 0.864249, + "end_time": "2023-09-08T07:12:16.619626", "exception": false, - "start_time": "2023-09-08T06:42:12.861742", + "start_time": "2023-09-08T07:12:15.755377", "status": "completed" }, "tags": [] @@ -107,16 +107,16 @@ "id": "ae1634aa", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:13.645951Z", - "iopub.status.busy": "2023-09-08T06:42:13.645484Z", - "iopub.status.idle": "2023-09-08T06:42:13.652242Z", - "shell.execute_reply": "2023-09-08T06:42:13.651350Z" + "iopub.execute_input": "2023-09-08T07:12:16.634740Z", + "iopub.status.busy": "2023-09-08T07:12:16.634251Z", + "iopub.status.idle": "2023-09-08T07:12:16.641038Z", + "shell.execute_reply": "2023-09-08T07:12:16.640200Z" }, "papermill": { - "duration": 0.017032, - "end_time": "2023-09-08T06:42:13.654779", + "duration": 0.017, + "end_time": "2023-09-08T07:12:16.643524", "exception": false, - "start_time": "2023-09-08T06:42:13.637747", + "start_time": "2023-09-08T07:12:16.626524", "status": "completed" }, "tags": [] @@ -131,10 +131,10 @@ "id": "3ed03b87", "metadata": { "papermill": { - "duration": 0.006624, - "end_time": "2023-09-08T06:42:13.668027", + "duration": 0.006635, + "end_time": "2023-09-08T07:12:16.656697", "exception": false, - "start_time": "2023-09-08T06:42:13.661403", + "start_time": "2023-09-08T07:12:16.650062", "status": "completed" }, "tags": [] @@ -149,16 +149,16 @@ "id": "2aa307e1", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:13.683919Z", - "iopub.status.busy": "2023-09-08T06:42:13.683168Z", - "iopub.status.idle": "2023-09-08T06:42:13.688305Z", - "shell.execute_reply": "2023-09-08T06:42:13.687407Z" + "iopub.execute_input": "2023-09-08T07:12:16.672244Z", + "iopub.status.busy": "2023-09-08T07:12:16.671858Z", + "iopub.status.idle": "2023-09-08T07:12:16.677036Z", + "shell.execute_reply": "2023-09-08T07:12:16.676137Z" }, "papermill": { - "duration": 0.015981, - "end_time": "2023-09-08T06:42:13.690905", + "duration": 0.016031, + "end_time": "2023-09-08T07:12:16.679651", "exception": false, - "start_time": "2023-09-08T06:42:13.674924", + "start_time": "2023-09-08T07:12:16.663620", "status": "completed" }, "tags": [] @@ -179,16 +179,16 @@ "id": "4ab16d0d", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:13.705591Z", - "iopub.status.busy": "2023-09-08T06:42:13.705232Z", - "iopub.status.idle": "2023-09-08T06:42:13.741537Z", - "shell.execute_reply": "2023-09-08T06:42:13.740670Z" + "iopub.execute_input": "2023-09-08T07:12:16.694810Z", + "iopub.status.busy": "2023-09-08T07:12:16.694429Z", + "iopub.status.idle": "2023-09-08T07:12:16.730997Z", + "shell.execute_reply": "2023-09-08T07:12:16.730152Z" }, "papermill": { - "duration": 0.046639, - "end_time": "2023-09-08T06:42:13.744214", + "duration": 0.047294, + "end_time": "2023-09-08T07:12:16.733640", "exception": false, - "start_time": "2023-09-08T06:42:13.697575", + "start_time": "2023-09-08T07:12:16.686346", "status": "completed" }, "tags": [] @@ -480,16 +480,16 @@ "id": "75b244e4", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:13.761292Z", - "iopub.status.busy": "2023-09-08T06:42:13.760609Z", - "iopub.status.idle": "2023-09-08T06:42:13.779211Z", - "shell.execute_reply": "2023-09-08T06:42:13.778288Z" + "iopub.execute_input": "2023-09-08T07:12:16.750802Z", + "iopub.status.busy": "2023-09-08T07:12:16.749907Z", + "iopub.status.idle": "2023-09-08T07:12:16.768843Z", + "shell.execute_reply": "2023-09-08T07:12:16.767970Z" }, "papermill": { - 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"iopub.execute_input": "2023-09-08T06:42:13.849366Z", - "iopub.status.busy": "2023-09-08T06:42:13.848559Z", - "iopub.status.idle": "2023-09-08T06:42:13.875378Z", - "shell.execute_reply": "2023-09-08T06:42:13.874513Z" + "iopub.execute_input": "2023-09-08T07:12:16.838367Z", + "iopub.status.busy": "2023-09-08T07:12:16.837988Z", + "iopub.status.idle": "2023-09-08T07:12:16.865401Z", + "shell.execute_reply": "2023-09-08T07:12:16.864471Z" }, "papermill": { - "duration": 0.039156, - "end_time": "2023-09-08T06:42:13.878190", + "duration": 0.039458, + "end_time": "2023-09-08T07:12:16.868138", "exception": false, - "start_time": "2023-09-08T06:42:13.839034", + "start_time": "2023-09-08T07:12:16.828680", "status": "completed" }, "tags": [] @@ -1517,16 +1517,16 @@ "id": "d122110e", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:13.898060Z", - "iopub.status.busy": "2023-09-08T06:42:13.897638Z", - "iopub.status.idle": "2023-09-08T06:42:13.925782Z", - "shell.execute_reply": "2023-09-08T06:42:13.924804Z" + "iopub.execute_input": "2023-09-08T07:12:16.887879Z", + "iopub.status.busy": "2023-09-08T07:12:16.887467Z", + "iopub.status.idle": "2023-09-08T07:12:16.915790Z", + "shell.execute_reply": "2023-09-08T07:12:16.914858Z" }, "papermill": { - 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"iopub.execute_input": "2023-09-08T06:42:13.991549Z", - "iopub.status.busy": "2023-09-08T06:42:13.991152Z", - "iopub.status.idle": "2023-09-08T06:42:14.009989Z", - "shell.execute_reply": "2023-09-08T06:42:14.009109Z" + "iopub.execute_input": "2023-09-08T07:12:16.979983Z", + "iopub.status.busy": "2023-09-08T07:12:16.979605Z", + "iopub.status.idle": "2023-09-08T07:12:16.998820Z", + "shell.execute_reply": "2023-09-08T07:12:16.997899Z" }, "papermill": { - "duration": 0.032386, - "end_time": "2023-09-08T06:42:14.012594", + "duration": 0.03271, + "end_time": "2023-09-08T07:12:17.001470", "exception": false, - "start_time": "2023-09-08T06:42:13.980208", + "start_time": "2023-09-08T07:12:16.968760", "status": "completed" }, "tags": [] @@ -2373,16 +2373,16 @@ "id": "eff5657b", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:14.034768Z", - "iopub.status.busy": "2023-09-08T06:42:14.034346Z", - "iopub.status.idle": "2023-09-08T06:42:14.053165Z", - "shell.execute_reply": "2023-09-08T06:42:14.052207Z" + "iopub.execute_input": "2023-09-08T07:12:17.023790Z", + "iopub.status.busy": "2023-09-08T07:12:17.023017Z", + "iopub.status.idle": "2023-09-08T07:12:17.042610Z", + "shell.execute_reply": "2023-09-08T07:12:17.041727Z" }, "papermill": { - "duration": 0.032903, - "end_time": "2023-09-08T06:42:14.055744", + "duration": 0.033442, + "end_time": "2023-09-08T07:12:17.045070", "exception": false, - "start_time": "2023-09-08T06:42:14.022841", + "start_time": "2023-09-08T07:12:17.011628", "status": "completed" }, "tags": [] @@ -2581,16 +2581,16 @@ "id": "9a787501", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:14.078875Z", - "iopub.status.busy": "2023-09-08T06:42:14.078329Z", - "iopub.status.idle": "2023-09-08T06:42:14.093472Z", - "shell.execute_reply": "2023-09-08T06:42:14.092494Z" + "iopub.execute_input": "2023-09-08T07:12:17.067731Z", + "iopub.status.busy": "2023-09-08T07:12:17.067062Z", + "iopub.status.idle": "2023-09-08T07:12:17.082080Z", + "shell.execute_reply": "2023-09-08T07:12:17.081168Z" }, "papermill": { - "duration": 0.029728, - "end_time": "2023-09-08T06:42:14.096171", + "duration": 0.028952, + "end_time": "2023-09-08T07:12:17.084687", "exception": false, - "start_time": "2023-09-08T06:42:14.066443", + "start_time": "2023-09-08T07:12:17.055735", "status": "completed" }, "tags": [] @@ -2637,16 +2637,16 @@ "id": "1647f393", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:14.119353Z", - "iopub.status.busy": "2023-09-08T06:42:14.118964Z", - "iopub.status.idle": "2023-09-08T06:42:14.411347Z", - "shell.execute_reply": "2023-09-08T06:42:14.410500Z" + "iopub.execute_input": "2023-09-08T07:12:17.107221Z", + "iopub.status.busy": "2023-09-08T07:12:17.106825Z", + "iopub.status.idle": "2023-09-08T07:12:17.399848Z", + "shell.execute_reply": "2023-09-08T07:12:17.398963Z" }, "papermill": { - "duration": 0.306821, - "end_time": "2023-09-08T06:42:14.413769", + "duration": 0.307263, + "end_time": "2023-09-08T07:12:17.402461", "exception": false, - "start_time": "2023-09-08T06:42:14.106948", + "start_time": "2023-09-08T07:12:17.095198", "status": "completed" }, "tags": [] @@ -2679,16 +2679,16 @@ "id": "0faf3d72", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:14.438334Z", - "iopub.status.busy": "2023-09-08T06:42:14.437907Z", - "iopub.status.idle": "2023-09-08T06:42:14.455475Z", - "shell.execute_reply": "2023-09-08T06:42:14.454484Z" + "iopub.execute_input": "2023-09-08T07:12:17.426760Z", + "iopub.status.busy": "2023-09-08T07:12:17.426344Z", + "iopub.status.idle": "2023-09-08T07:12:17.444337Z", + "shell.execute_reply": "2023-09-08T07:12:17.443330Z" }, "papermill": { - "duration": 0.033126, - "end_time": "2023-09-08T06:42:14.458004", + "duration": 0.033388, + "end_time": "2023-09-08T07:12:17.447058", "exception": false, - "start_time": "2023-09-08T06:42:14.424878", + "start_time": "2023-09-08T07:12:17.413670", "status": "completed" }, "tags": [] @@ -2899,16 +2899,16 @@ "id": "34971961", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:14.483170Z", - "iopub.status.busy": "2023-09-08T06:42:14.482469Z", - "iopub.status.idle": "2023-09-08T06:42:15.211292Z", - "shell.execute_reply": "2023-09-08T06:42:15.210124Z" + "iopub.execute_input": "2023-09-08T07:12:17.471906Z", + "iopub.status.busy": "2023-09-08T07:12:17.471198Z", + "iopub.status.idle": "2023-09-08T07:12:18.227520Z", + "shell.execute_reply": "2023-09-08T07:12:18.226635Z" }, "papermill": { - "duration": 0.74429, - "end_time": "2023-09-08T06:42:15.213924", + "duration": 0.77176, + "end_time": "2023-09-08T07:12:18.230325", "exception": false, - "start_time": "2023-09-08T06:42:14.469634", + "start_time": "2023-09-08T07:12:17.458565", "status": "completed" }, "tags": [] @@ -2918,54 +2918,54 @@ "data": { "text/html": [ "\n", - 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"iopub.status.busy": "2023-09-08T06:42:15.271346Z", - "iopub.status.idle": "2023-09-08T06:42:15.504840Z", - "shell.execute_reply": "2023-09-08T06:42:15.503968Z" + "iopub.execute_input": "2023-09-08T07:12:18.288224Z", + "iopub.status.busy": "2023-09-08T07:12:18.287297Z", + "iopub.status.idle": "2023-09-08T07:12:18.517156Z", + "shell.execute_reply": "2023-09-08T07:12:18.516289Z" }, "papermill": { - "duration": 0.250015, - "end_time": "2023-09-08T06:42:15.507538", + "duration": 0.245306, + "end_time": "2023-09-08T07:12:18.519922", "exception": false, - "start_time": "2023-09-08T06:42:15.257523", + "start_time": "2023-09-08T07:12:18.274616", "status": "completed" }, "tags": [] @@ -3066,16 +3066,16 @@ "id": "951219ed", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:15.533968Z", - "iopub.status.busy": "2023-09-08T06:42:15.533300Z", - "iopub.status.idle": "2023-09-08T06:42:16.448874Z", - "shell.execute_reply": "2023-09-08T06:42:16.447720Z" + "iopub.execute_input": "2023-09-08T07:12:18.545532Z", + "iopub.status.busy": "2023-09-08T07:12:18.545115Z", + "iopub.status.idle": "2023-09-08T07:12:19.494844Z", + "shell.execute_reply": "2023-09-08T07:12:19.493689Z" }, "papermill": { - "duration": 0.931901, - "end_time": "2023-09-08T06:42:16.451788", + "duration": 0.965725, + "end_time": "2023-09-08T07:12:19.497656", "exception": false, - "start_time": "2023-09-08T06:42:15.519887", + "start_time": "2023-09-08T07:12:18.531931", "status": "completed" }, "tags": [] @@ -3091,16 +3091,16 @@ "id": "a7de6bab", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:16.477844Z", - "iopub.status.busy": "2023-09-08T06:42:16.477285Z", - "iopub.status.idle": "2023-09-08T06:42:17.229743Z", - "shell.execute_reply": "2023-09-08T06:42:17.228857Z" + "iopub.execute_input": "2023-09-08T07:12:19.524546Z", + "iopub.status.busy": "2023-09-08T07:12:19.523806Z", + "iopub.status.idle": "2023-09-08T07:12:20.492225Z", + "shell.execute_reply": "2023-09-08T07:12:20.491308Z" }, "papermill": { - "duration": 0.768486, - "end_time": "2023-09-08T06:42:17.232298", + "duration": 0.984466, + "end_time": "2023-09-08T07:12:20.494958", "exception": false, - "start_time": "2023-09-08T06:42:16.463812", + "start_time": "2023-09-08T07:12:19.510492", "status": "completed" }, "tags": [] @@ -3145,6 +3145,7 @@ "plt.ylabel('F1')\n", "plt.title(f'{task} LogMap score threshold vs F1 (accuracy)')\n", "\n", + "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.png\", format='png')\n", "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.pdf\", format='pdf')\n", "\n", "# Show the plot\n", @@ -3157,16 +3158,16 @@ "id": "e12c93c4", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:17.259994Z", - "iopub.status.busy": "2023-09-08T06:42:17.259433Z", - "iopub.status.idle": "2023-09-08T06:42:17.266711Z", - "shell.execute_reply": "2023-09-08T06:42:17.265857Z" + "iopub.execute_input": "2023-09-08T07:12:20.522632Z", + "iopub.status.busy": "2023-09-08T07:12:20.521717Z", + "iopub.status.idle": "2023-09-08T07:12:20.531092Z", + "shell.execute_reply": "2023-09-08T07:12:20.530173Z" }, "papermill": { - "duration": 0.024142, - "end_time": "2023-09-08T06:42:17.269429", + "duration": 0.02628, + "end_time": "2023-09-08T07:12:20.533891", "exception": false, - "start_time": "2023-09-08T06:42:17.245287", + "start_time": "2023-09-08T07:12:20.507611", "status": "completed" }, "tags": [] @@ -3182,16 +3183,16 @@ "id": "a7e7524f", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:17.296374Z", - "iopub.status.busy": "2023-09-08T06:42:17.295965Z", - "iopub.status.idle": "2023-09-08T06:42:17.483220Z", - "shell.execute_reply": "2023-09-08T06:42:17.482172Z" + "iopub.execute_input": "2023-09-08T07:12:20.561083Z", + "iopub.status.busy": "2023-09-08T07:12:20.560384Z", + "iopub.status.idle": "2023-09-08T07:12:20.760034Z", + "shell.execute_reply": "2023-09-08T07:12:20.758973Z" }, "papermill": { - "duration": 0.203805, - "end_time": "2023-09-08T06:42:17.485980", + "duration": 0.216535, + "end_time": "2023-09-08T07:12:20.763250", "exception": false, - "start_time": "2023-09-08T06:42:17.282175", + "start_time": "2023-09-08T07:12:20.546715", "status": "completed" }, "tags": [] @@ -3208,16 +3209,16 @@ "id": "b03b2621", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:17.513276Z", - "iopub.status.busy": "2023-09-08T06:42:17.512407Z", - "iopub.status.idle": "2023-09-08T06:42:17.522929Z", - "shell.execute_reply": "2023-09-08T06:42:17.521995Z" + "iopub.execute_input": "2023-09-08T07:12:20.793534Z", + "iopub.status.busy": "2023-09-08T07:12:20.792950Z", + "iopub.status.idle": "2023-09-08T07:12:20.806372Z", + "shell.execute_reply": "2023-09-08T07:12:20.805157Z" }, "papermill": { - "duration": 0.027217, - "end_time": "2023-09-08T06:42:17.525910", + "duration": 0.033095, + "end_time": "2023-09-08T07:12:20.809926", "exception": false, - "start_time": "2023-09-08T06:42:17.498693", + "start_time": "2023-09-08T07:12:20.776831", "status": "completed" }, "tags": [] @@ -3243,16 +3244,16 @@ "id": "d66185bc", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:17.554110Z", - "iopub.status.busy": "2023-09-08T06:42:17.553186Z", - "iopub.status.idle": "2023-09-08T06:42:17.594636Z", - "shell.execute_reply": "2023-09-08T06:42:17.593761Z" + "iopub.execute_input": "2023-09-08T07:12:20.839842Z", + "iopub.status.busy": "2023-09-08T07:12:20.839355Z", + "iopub.status.idle": "2023-09-08T07:12:20.887718Z", + "shell.execute_reply": "2023-09-08T07:12:20.886276Z" }, "papermill": { - "duration": 0.058025, - "end_time": "2023-09-08T06:42:17.597323", + "duration": 0.067029, + "end_time": "2023-09-08T07:12:20.891170", "exception": false, - "start_time": "2023-09-08T06:42:17.539298", + "start_time": "2023-09-08T07:12:20.824141", "status": "completed" }, "tags": [] @@ -3278,16 +3279,16 @@ "id": "bc23aa02", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:17.624749Z", - "iopub.status.busy": "2023-09-08T06:42:17.624346Z", - "iopub.status.idle": "2023-09-08T06:42:17.642248Z", - "shell.execute_reply": "2023-09-08T06:42:17.641252Z" + "iopub.execute_input": "2023-09-08T07:12:20.921874Z", + "iopub.status.busy": "2023-09-08T07:12:20.921300Z", + "iopub.status.idle": "2023-09-08T07:12:20.946407Z", + "shell.execute_reply": "2023-09-08T07:12:20.945260Z" }, "papermill": { - "duration": 0.034769, - "end_time": "2023-09-08T06:42:17.644996", + "duration": 0.043891, + "end_time": "2023-09-08T07:12:20.949229", "exception": false, - "start_time": "2023-09-08T06:42:17.610227", + "start_time": "2023-09-08T07:12:20.905338", "status": "completed" }, "tags": [] @@ -3384,10 +3385,10 @@ "id": "fe33118f", "metadata": { "papermill": { - "duration": 0.012952, - "end_time": "2023-09-08T06:42:17.671249", + "duration": 0.013184, + "end_time": "2023-09-08T07:12:20.976620", "exception": false, - "start_time": "2023-09-08T06:42:17.658297", + "start_time": "2023-09-08T07:12:20.963436", "status": "completed" }, "tags": [] @@ -3401,10 +3402,10 @@ "id": "8b066d2c", "metadata": { "papermill": { - "duration": 0.012832, - "end_time": "2023-09-08T06:42:17.697054", + "duration": 0.013149, + "end_time": "2023-09-08T07:12:21.002939", "exception": false, - "start_time": "2023-09-08T06:42:17.684222", + "start_time": "2023-09-08T07:12:20.989790", "status": "completed" }, "tags": [] @@ -3418,10 +3419,10 @@ "id": "77ee339f", "metadata": { "papermill": { - "duration": 0.012755, - "end_time": "2023-09-08T06:42:17.722720", + "duration": 0.01396, + "end_time": "2023-09-08T07:12:21.030286", "exception": false, - "start_time": "2023-09-08T06:42:17.709965", + "start_time": "2023-09-08T07:12:21.016326", "status": "completed" }, "tags": [] @@ -3435,10 +3436,10 @@ "id": "e648f511", "metadata": { "papermill": { - "duration": 0.013326, - "end_time": "2023-09-08T06:42:17.749176", + "duration": 0.013291, + "end_time": "2023-09-08T07:12:21.057227", "exception": false, - "start_time": "2023-09-08T06:42:17.735850", + "start_time": "2023-09-08T07:12:21.043936", "status": "completed" }, "tags": [] @@ -3452,10 +3453,10 @@ "id": "8b53aa7d", "metadata": { "papermill": { - "duration": 0.013133, - "end_time": "2023-09-08T06:42:17.775466", + "duration": 0.012906, + "end_time": "2023-09-08T07:12:21.083186", "exception": false, - "start_time": "2023-09-08T06:42:17.762333", + "start_time": "2023-09-08T07:12:21.070280", "status": "completed" }, "tags": [] @@ -3485,8 +3486,8 @@ }, "papermill": { "default_parameters": {}, - "duration": 7.719363, - "end_time": "2023-09-08T06:42:18.313134", + "duration": 8.435502, + "end_time": "2023-09-08T07:12:21.616832", "environment_variables": {}, "exception": null, "input_path": "Mapping-Evaluation.ipynb", @@ -3494,7 +3495,7 @@ "parameters": { "task": "fbbt-zfa" }, - "start_time": "2023-09-08T06:42:10.593771", + "start_time": "2023-09-08T07:12:13.181330", "version": "2.4.0" } }, diff --git a/notebooks/Mapping-Evaluation-hsapdv-mmusdv.ipynb b/notebooks/Mapping-Evaluation-hsapdv-mmusdv.ipynb index ebfb06e..b302ac9 100644 --- a/notebooks/Mapping-Evaluation-hsapdv-mmusdv.ipynb +++ b/notebooks/Mapping-Evaluation-hsapdv-mmusdv.ipynb @@ -5,10 +5,10 @@ "id": "da02b833", "metadata": { "papermill": { - "duration": 0.0084, - "end_time": "2023-09-08T06:42:29.597471", + "duration": 0.008537, + "end_time": "2023-09-08T07:12:33.192792", "exception": false, - "start_time": "2023-09-08T06:42:29.589071", + "start_time": "2023-09-08T07:12:33.184255", "status": "completed" }, "tags": [] @@ -25,16 +25,16 @@ "id": "615ad1f2", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:29.615196Z", - "iopub.status.busy": "2023-09-08T06:42:29.614749Z", - "iopub.status.idle": "2023-09-08T06:42:29.626421Z", - "shell.execute_reply": "2023-09-08T06:42:29.625286Z" + "iopub.execute_input": "2023-09-08T07:12:33.208733Z", + "iopub.status.busy": "2023-09-08T07:12:33.208284Z", + "iopub.status.idle": "2023-09-08T07:12:33.218998Z", + "shell.execute_reply": "2023-09-08T07:12:33.218047Z" }, "papermill": { - "duration": 0.025246, - "end_time": "2023-09-08T06:42:29.630042", + "duration": 0.021966, + "end_time": "2023-09-08T07:12:33.221802", "exception": false, - "start_time": "2023-09-08T06:42:29.604796", + "start_time": "2023-09-08T07:12:33.199836", "status": "completed" }, "tags": [ @@ -51,19 +51,19 @@ { "cell_type": "code", "execution_count": 2, - "id": "dd7622d6", + "id": "eecbc3e3", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:29.647651Z", - "iopub.status.busy": "2023-09-08T06:42:29.647176Z", - "iopub.status.idle": "2023-09-08T06:42:29.651531Z", - "shell.execute_reply": "2023-09-08T06:42:29.650588Z" + "iopub.execute_input": "2023-09-08T07:12:33.236935Z", + "iopub.status.busy": "2023-09-08T07:12:33.236546Z", + "iopub.status.idle": "2023-09-08T07:12:33.240869Z", + "shell.execute_reply": "2023-09-08T07:12:33.239899Z" }, "papermill": { - "duration": 0.017089, - "end_time": "2023-09-08T06:42:29.654292", + "duration": 0.014899, + "end_time": "2023-09-08T07:12:33.243518", "exception": false, - "start_time": "2023-09-08T06:42:29.637203", + "start_time": "2023-09-08T07:12:33.228619", "status": "completed" }, "tags": [ @@ -82,16 +82,16 @@ "id": "ff08a44a", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:29.672531Z", - "iopub.status.busy": "2023-09-08T06:42:29.672070Z", - "iopub.status.idle": "2023-09-08T06:42:30.346653Z", - "shell.execute_reply": "2023-09-08T06:42:30.345654Z" + "iopub.execute_input": "2023-09-08T07:12:33.258197Z", + "iopub.status.busy": "2023-09-08T07:12:33.257751Z", + "iopub.status.idle": "2023-09-08T07:12:33.879996Z", + "shell.execute_reply": "2023-09-08T07:12:33.878864Z" }, "papermill": { - 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"duration": 0.00725, - "end_time": "2023-09-08T06:42:30.389920", + "duration": 0.006843, + "end_time": "2023-09-08T07:12:33.920401", "exception": false, - "start_time": "2023-09-08T06:42:30.382670", + "start_time": "2023-09-08T07:12:33.913558", "status": "completed" }, "tags": [] @@ -149,16 +149,16 @@ "id": "2aa307e1", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:30.405531Z", - "iopub.status.busy": "2023-09-08T06:42:30.405090Z", - "iopub.status.idle": "2023-09-08T06:42:30.410190Z", - "shell.execute_reply": "2023-09-08T06:42:30.409273Z" + "iopub.execute_input": "2023-09-08T07:12:33.935750Z", + "iopub.status.busy": "2023-09-08T07:12:33.935084Z", + "iopub.status.idle": "2023-09-08T07:12:33.940125Z", + "shell.execute_reply": "2023-09-08T07:12:33.939227Z" }, "papermill": { - "duration": 0.015978, - "end_time": "2023-09-08T06:42:30.412790", + "duration": 0.015649, + "end_time": "2023-09-08T07:12:33.942751", "exception": false, - "start_time": "2023-09-08T06:42:30.396812", + "start_time": "2023-09-08T07:12:33.927102", "status": "completed" }, "tags": [] @@ -179,16 +179,16 @@ "id": "4ab16d0d", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:30.429808Z", - "iopub.status.busy": "2023-09-08T06:42:30.428918Z", - "iopub.status.idle": "2023-09-08T06:42:30.466005Z", - "shell.execute_reply": "2023-09-08T06:42:30.465055Z" + "iopub.execute_input": "2023-09-08T07:12:33.957934Z", + "iopub.status.busy": "2023-09-08T07:12:33.957237Z", + "iopub.status.idle": "2023-09-08T07:12:33.991067Z", + "shell.execute_reply": "2023-09-08T07:12:33.990193Z" }, "papermill": { - "duration": 0.049058, - "end_time": "2023-09-08T06:42:30.469129", + "duration": 0.04428, + "end_time": "2023-09-08T07:12:33.993739", "exception": false, - "start_time": "2023-09-08T06:42:30.420071", + "start_time": "2023-09-08T07:12:33.949459", "status": "completed" }, "tags": [] @@ -480,16 +480,16 @@ "id": "75b244e4", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:30.486401Z", - "iopub.status.busy": "2023-09-08T06:42:30.485973Z", - "iopub.status.idle": "2023-09-08T06:42:30.515014Z", - "shell.execute_reply": "2023-09-08T06:42:30.512714Z" + "iopub.execute_input": "2023-09-08T07:12:34.010366Z", + "iopub.status.busy": "2023-09-08T07:12:34.009681Z", + "iopub.status.idle": "2023-09-08T07:12:34.026064Z", + "shell.execute_reply": "2023-09-08T07:12:34.025264Z" }, "papermill": { - 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"iopub.execute_input": "2023-09-08T06:42:30.598079Z", - "iopub.status.busy": "2023-09-08T06:42:30.597662Z", - "iopub.status.idle": "2023-09-08T06:42:30.635326Z", - "shell.execute_reply": "2023-09-08T06:42:30.634437Z" + "iopub.execute_input": "2023-09-08T07:12:34.100738Z", + "iopub.status.busy": "2023-09-08T07:12:34.100332Z", + "iopub.status.idle": "2023-09-08T07:12:34.136974Z", + "shell.execute_reply": "2023-09-08T07:12:34.136144Z" }, "papermill": { - "duration": 0.051327, - "end_time": "2023-09-08T06:42:30.637976", + "duration": 0.049418, + "end_time": "2023-09-08T07:12:34.139622", "exception": false, - "start_time": "2023-09-08T06:42:30.586649", + "start_time": "2023-09-08T07:12:34.090204", "status": "completed" }, "tags": [] @@ -2645,16 +2645,16 @@ "id": "d122110e", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:30.658995Z", - "iopub.status.busy": "2023-09-08T06:42:30.658616Z", - "iopub.status.idle": "2023-09-08T06:42:30.695286Z", - "shell.execute_reply": "2023-09-08T06:42:30.694406Z" + "iopub.execute_input": "2023-09-08T07:12:34.161867Z", + "iopub.status.busy": "2023-09-08T07:12:34.161467Z", + "iopub.status.idle": "2023-09-08T07:12:34.198551Z", + "shell.execute_reply": "2023-09-08T07:12:34.197714Z" }, "papermill": { - 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"iopub.execute_input": "2023-09-08T06:42:30.767191Z", - "iopub.status.busy": "2023-09-08T06:42:30.766798Z", - "iopub.status.idle": "2023-09-08T06:42:30.790632Z", - "shell.execute_reply": "2023-09-08T06:42:30.789757Z" + "iopub.execute_input": "2023-09-08T07:12:34.270174Z", + "iopub.status.busy": "2023-09-08T07:12:34.269772Z", + "iopub.status.idle": "2023-09-08T07:12:34.294487Z", + "shell.execute_reply": "2023-09-08T07:12:34.293532Z" }, "papermill": { - "duration": 0.03984, - "end_time": "2023-09-08T06:42:30.793283", + "duration": 0.040711, + "end_time": "2023-09-08T07:12:34.297235", "exception": false, - "start_time": "2023-09-08T06:42:30.753443", + "start_time": "2023-09-08T07:12:34.256524", "status": "completed" }, "tags": [] @@ -4486,16 +4486,16 @@ "id": "eff5657b", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:30.819850Z", - "iopub.status.busy": "2023-09-08T06:42:30.818987Z", - "iopub.status.idle": "2023-09-08T06:42:30.843873Z", - "shell.execute_reply": "2023-09-08T06:42:30.843000Z" + "iopub.execute_input": "2023-09-08T07:12:34.324022Z", + "iopub.status.busy": "2023-09-08T07:12:34.323292Z", + "iopub.status.idle": "2023-09-08T07:12:34.347965Z", + "shell.execute_reply": "2023-09-08T07:12:34.347113Z" }, "papermill": { - "duration": 0.040721, - "end_time": "2023-09-08T06:42:30.846312", + "duration": 0.040752, + "end_time": "2023-09-08T07:12:34.350446", "exception": false, - "start_time": "2023-09-08T06:42:30.805591", + "start_time": "2023-09-08T07:12:34.309694", "status": "completed" }, "tags": [] @@ -5075,16 +5075,16 @@ "id": "9a787501", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:30.874478Z", - "iopub.status.busy": "2023-09-08T06:42:30.874092Z", - "iopub.status.idle": "2023-09-08T06:42:30.888472Z", - "shell.execute_reply": "2023-09-08T06:42:30.887561Z" + "iopub.execute_input": "2023-09-08T07:12:34.379101Z", + "iopub.status.busy": "2023-09-08T07:12:34.378721Z", + "iopub.status.idle": "2023-09-08T07:12:34.393616Z", + "shell.execute_reply": "2023-09-08T07:12:34.392722Z" }, "papermill": { - "duration": 0.031602, - "end_time": "2023-09-08T06:42:30.891136", + "duration": 0.032281, + "end_time": "2023-09-08T07:12:34.396080", "exception": false, - "start_time": "2023-09-08T06:42:30.859534", + "start_time": "2023-09-08T07:12:34.363799", "status": "completed" }, "tags": [] @@ -5131,16 +5131,16 @@ "id": "1647f393", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:30.918795Z", - "iopub.status.busy": "2023-09-08T06:42:30.918413Z", - "iopub.status.idle": "2023-09-08T06:42:30.947669Z", - "shell.execute_reply": "2023-09-08T06:42:30.946668Z" + "iopub.execute_input": "2023-09-08T07:12:34.423666Z", + "iopub.status.busy": "2023-09-08T07:12:34.423256Z", + "iopub.status.idle": "2023-09-08T07:12:34.453690Z", + "shell.execute_reply": "2023-09-08T07:12:34.452880Z" }, "papermill": { - "duration": 0.046317, - "end_time": "2023-09-08T06:42:30.950408", + "duration": 0.047186, + "end_time": "2023-09-08T07:12:34.456340", "exception": false, - "start_time": "2023-09-08T06:42:30.904091", + "start_time": "2023-09-08T07:12:34.409154", "status": "completed" }, "tags": [] @@ -5172,16 +5172,16 @@ "id": "0faf3d72", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:30.978984Z", - "iopub.status.busy": "2023-09-08T06:42:30.978596Z", - "iopub.status.idle": "2023-09-08T06:42:31.001676Z", - "shell.execute_reply": "2023-09-08T06:42:31.000791Z" + "iopub.execute_input": "2023-09-08T07:12:34.485328Z", + "iopub.status.busy": "2023-09-08T07:12:34.484570Z", + "iopub.status.idle": "2023-09-08T07:12:34.507757Z", + "shell.execute_reply": "2023-09-08T07:12:34.506920Z" }, "papermill": { - "duration": 0.040461, - "end_time": "2023-09-08T06:42:31.004428", + "duration": 0.040737, + "end_time": "2023-09-08T07:12:34.510564", "exception": false, - "start_time": "2023-09-08T06:42:30.963967", + "start_time": "2023-09-08T07:12:34.469827", "status": "completed" }, "tags": [] @@ -5748,16 +5748,16 @@ "id": "34971961", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:31.034542Z", - "iopub.status.busy": "2023-09-08T06:42:31.034153Z", - "iopub.status.idle": "2023-09-08T06:42:31.649719Z", - "shell.execute_reply": "2023-09-08T06:42:31.648861Z" + "iopub.execute_input": "2023-09-08T07:12:34.540829Z", + "iopub.status.busy": "2023-09-08T07:12:34.540089Z", + "iopub.status.idle": "2023-09-08T07:12:35.155055Z", + "shell.execute_reply": "2023-09-08T07:12:35.154208Z" }, "papermill": { - "duration": 0.633448, - "end_time": "2023-09-08T06:42:31.652392", + "duration": 0.632948, + "end_time": "2023-09-08T07:12:35.157671", "exception": false, - "start_time": "2023-09-08T06:42:31.018944", + "start_time": "2023-09-08T07:12:34.524723", "status": "completed" }, "tags": [] @@ -5767,54 +5767,54 @@ "data": { "text/html": [ "\n", - 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"iopub.status.busy": "2023-09-08T06:42:31.720045Z", - "iopub.status.idle": "2023-09-08T06:42:31.944892Z", - "shell.execute_reply": "2023-09-08T06:42:31.944054Z" + "iopub.execute_input": "2023-09-08T07:12:35.226472Z", + "iopub.status.busy": "2023-09-08T07:12:35.225659Z", + "iopub.status.idle": "2023-09-08T07:12:35.449896Z", + "shell.execute_reply": "2023-09-08T07:12:35.448995Z" }, "papermill": { - "duration": 0.243123, - "end_time": "2023-09-08T06:42:31.947504", + "duration": 0.243245, + "end_time": "2023-09-08T07:12:35.452439", "exception": false, - "start_time": "2023-09-08T06:42:31.704381", + "start_time": "2023-09-08T07:12:35.209194", "status": "completed" }, "tags": [] @@ -5915,16 +5915,16 @@ "id": "951219ed", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:31.979556Z", - "iopub.status.busy": "2023-09-08T06:42:31.978886Z", - "iopub.status.idle": "2023-09-08T06:42:32.677590Z", - "shell.execute_reply": "2023-09-08T06:42:32.676567Z" + "iopub.execute_input": "2023-09-08T07:12:35.484083Z", + "iopub.status.busy": "2023-09-08T07:12:35.483689Z", + "iopub.status.idle": "2023-09-08T07:12:36.181231Z", + "shell.execute_reply": "2023-09-08T07:12:36.180136Z" }, "papermill": { - "duration": 0.717691, - "end_time": "2023-09-08T06:42:32.680393", + "duration": 0.716558, + "end_time": "2023-09-08T07:12:36.184146", "exception": false, - "start_time": "2023-09-08T06:42:31.962702", + "start_time": "2023-09-08T07:12:35.467588", "status": "completed" }, "tags": [] @@ -5940,16 +5940,16 @@ "id": "a7de6bab", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:32.711252Z", - "iopub.status.busy": "2023-09-08T06:42:32.710868Z", - "iopub.status.idle": "2023-09-08T06:42:33.406095Z", - "shell.execute_reply": "2023-09-08T06:42:33.405183Z" + "iopub.execute_input": "2023-09-08T07:12:36.216227Z", + "iopub.status.busy": "2023-09-08T07:12:36.215813Z", + "iopub.status.idle": "2023-09-08T07:12:37.100877Z", + "shell.execute_reply": "2023-09-08T07:12:37.099974Z" }, "papermill": { - "duration": 0.713677, - "end_time": "2023-09-08T06:42:33.408736", + "duration": 0.903617, + "end_time": "2023-09-08T07:12:37.103457", "exception": false, - "start_time": "2023-09-08T06:42:32.695059", + "start_time": "2023-09-08T07:12:36.199840", "status": "completed" }, "tags": [] @@ -5994,6 +5994,7 @@ "plt.ylabel('F1')\n", "plt.title(f'{task} LogMap score threshold vs F1 (accuracy)')\n", "\n", + "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.png\", format='png')\n", "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.pdf\", format='pdf')\n", "\n", "# Show the plot\n", @@ -6006,16 +6007,16 @@ "id": "e12c93c4", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:33.441877Z", - "iopub.status.busy": "2023-09-08T06:42:33.441381Z", - "iopub.status.idle": "2023-09-08T06:42:33.447266Z", - "shell.execute_reply": "2023-09-08T06:42:33.446447Z" + "iopub.execute_input": "2023-09-08T07:12:37.136663Z", + "iopub.status.busy": "2023-09-08T07:12:37.136103Z", + "iopub.status.idle": "2023-09-08T07:12:37.142385Z", + "shell.execute_reply": "2023-09-08T07:12:37.141476Z" }, "papermill": { - "duration": 0.025535, - "end_time": "2023-09-08T06:42:33.449938", + "duration": 0.026463, + "end_time": "2023-09-08T07:12:37.145324", "exception": false, - "start_time": "2023-09-08T06:42:33.424403", + "start_time": "2023-09-08T07:12:37.118861", "status": "completed" }, "tags": [] @@ -6031,16 +6032,16 @@ "id": "a7e7524f", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:33.483089Z", - "iopub.status.busy": "2023-09-08T06:42:33.482395Z", - "iopub.status.idle": "2023-09-08T06:42:33.661668Z", - "shell.execute_reply": "2023-09-08T06:42:33.660615Z" + "iopub.execute_input": "2023-09-08T07:12:37.177918Z", + "iopub.status.busy": "2023-09-08T07:12:37.177240Z", + "iopub.status.idle": "2023-09-08T07:12:37.353722Z", + "shell.execute_reply": "2023-09-08T07:12:37.352806Z" }, "papermill": { - 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"duration": 0.035288, - "end_time": "2023-09-08T06:42:38.748508", + "duration": 0.036675, + "end_time": "2023-09-08T07:12:42.445110", "exception": false, - "start_time": "2023-09-08T06:42:38.713220", + "start_time": "2023-09-08T07:12:42.408435", "status": "completed" }, "tags": [] @@ -3625,16 +3625,16 @@ "id": "9a787501", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:38.773634Z", - "iopub.status.busy": "2023-09-08T06:42:38.773256Z", - "iopub.status.idle": "2023-09-08T06:42:38.787880Z", - "shell.execute_reply": "2023-09-08T06:42:38.786864Z" + "iopub.execute_input": "2023-09-08T07:12:42.471837Z", + "iopub.status.busy": "2023-09-08T07:12:42.470779Z", + "iopub.status.idle": "2023-09-08T07:12:42.485468Z", + "shell.execute_reply": "2023-09-08T07:12:42.484616Z" }, "papermill": { - "duration": 0.029975, - "end_time": "2023-09-08T06:42:38.790580", + "duration": 0.03036, + "end_time": "2023-09-08T07:12:42.488013", "exception": false, - "start_time": "2023-09-08T06:42:38.760605", + "start_time": "2023-09-08T07:12:42.457653", "status": "completed" }, "tags": [] @@ -3681,16 +3681,16 @@ "id": "1647f393", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:38.815880Z", - "iopub.status.busy": "2023-09-08T06:42:38.815068Z", - "iopub.status.idle": "2023-09-08T06:42:38.980231Z", - "shell.execute_reply": "2023-09-08T06:42:38.979291Z" + "iopub.execute_input": "2023-09-08T07:12:42.513296Z", + "iopub.status.busy": "2023-09-08T07:12:42.512648Z", + "iopub.status.idle": "2023-09-08T07:12:42.680899Z", + "shell.execute_reply": "2023-09-08T07:12:42.680074Z" }, "papermill": { - "duration": 0.180707, - "end_time": "2023-09-08T06:42:38.982915", + "duration": 0.18379, + "end_time": "2023-09-08T07:12:42.683509", "exception": false, - "start_time": "2023-09-08T06:42:38.802208", + "start_time": "2023-09-08T07:12:42.499719", "status": "completed" }, "tags": [] @@ -3723,16 +3723,16 @@ "id": "0faf3d72", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:39.008965Z", - "iopub.status.busy": "2023-09-08T06:42:39.008583Z", - "iopub.status.idle": "2023-09-08T06:42:39.030668Z", - "shell.execute_reply": "2023-09-08T06:42:39.029749Z" + "iopub.execute_input": "2023-09-08T07:12:42.710045Z", + "iopub.status.busy": "2023-09-08T07:12:42.709058Z", + "iopub.status.idle": "2023-09-08T07:12:42.731379Z", + "shell.execute_reply": "2023-09-08T07:12:42.730496Z" }, "papermill": { - "duration": 0.038297, - "end_time": "2023-09-08T06:42:39.033287", + "duration": 0.03848, + "end_time": "2023-09-08T07:12:42.734041", "exception": false, - "start_time": "2023-09-08T06:42:38.994990", + "start_time": "2023-09-08T07:12:42.695561", "status": "completed" }, "tags": [] @@ -4265,16 +4265,16 @@ "id": "34971961", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:39.060959Z", - "iopub.status.busy": "2023-09-08T06:42:39.060259Z", - "iopub.status.idle": "2023-09-08T06:42:39.682222Z", - "shell.execute_reply": "2023-09-08T06:42:39.681320Z" + "iopub.execute_input": "2023-09-08T07:12:42.762288Z", + "iopub.status.busy": "2023-09-08T07:12:42.761870Z", + "iopub.status.idle": "2023-09-08T07:12:43.381098Z", + "shell.execute_reply": "2023-09-08T07:12:43.380131Z" }, "papermill": { - "duration": 0.638516, - "end_time": "2023-09-08T06:42:39.684867", + "duration": 0.636981, + "end_time": "2023-09-08T07:12:43.383866", "exception": false, - "start_time": "2023-09-08T06:42:39.046351", + "start_time": "2023-09-08T07:12:42.746885", "status": "completed" }, "tags": [] @@ -4284,54 +4284,54 @@ "data": { "text/html": [ "\n", - 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"iopub.status.busy": "2023-09-08T06:42:39.759465Z", - "iopub.status.idle": "2023-09-08T06:42:39.997629Z", - "shell.execute_reply": "2023-09-08T06:42:39.996768Z" + "iopub.execute_input": "2023-09-08T07:12:43.446569Z", + "iopub.status.busy": "2023-09-08T07:12:43.446130Z", + "iopub.status.idle": "2023-09-08T07:12:43.676335Z", + "shell.execute_reply": "2023-09-08T07:12:43.675372Z" }, "papermill": { - "duration": 0.256352, - "end_time": "2023-09-08T06:42:40.000235", + "duration": 0.247522, + "end_time": "2023-09-08T07:12:43.679152", "exception": false, - "start_time": "2023-09-08T06:42:39.743883", + "start_time": "2023-09-08T07:12:43.431630", "status": "completed" }, "tags": [] @@ -4432,16 +4432,16 @@ "id": "951219ed", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:40.029466Z", - "iopub.status.busy": "2023-09-08T06:42:40.028762Z", - "iopub.status.idle": "2023-09-08T06:42:40.813263Z", - "shell.execute_reply": "2023-09-08T06:42:40.811916Z" + "iopub.execute_input": "2023-09-08T07:12:43.707683Z", + "iopub.status.busy": "2023-09-08T07:12:43.707294Z", + "iopub.status.idle": "2023-09-08T07:12:44.396281Z", + "shell.execute_reply": "2023-09-08T07:12:44.395220Z" }, "papermill": { - "duration": 0.802806, - "end_time": "2023-09-08T06:42:40.816691", + "duration": 0.706433, + "end_time": "2023-09-08T07:12:44.399128", "exception": false, - "start_time": "2023-09-08T06:42:40.013885", + "start_time": "2023-09-08T07:12:43.692695", "status": "completed" }, "tags": [] @@ -4457,16 +4457,16 @@ "id": "a7de6bab", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:40.847547Z", - "iopub.status.busy": "2023-09-08T06:42:40.847097Z", - "iopub.status.idle": "2023-09-08T06:42:41.618513Z", - "shell.execute_reply": "2023-09-08T06:42:41.617657Z" + "iopub.execute_input": "2023-09-08T07:12:44.428624Z", + "iopub.status.busy": "2023-09-08T07:12:44.428203Z", + "iopub.status.idle": "2023-09-08T07:12:45.336359Z", + "shell.execute_reply": "2023-09-08T07:12:45.335486Z" }, "papermill": { - "duration": 0.789424, - "end_time": "2023-09-08T06:42:41.620966", + "duration": 0.926353, + "end_time": "2023-09-08T07:12:45.339080", "exception": false, - "start_time": "2023-09-08T06:42:40.831542", + "start_time": "2023-09-08T07:12:44.412727", "status": "completed" }, "tags": [] @@ -4511,6 +4511,7 @@ "plt.ylabel('F1')\n", "plt.title(f'{task} LogMap score threshold vs F1 (accuracy)')\n", "\n", + "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.png\", format='png')\n", "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.pdf\", format='pdf')\n", "\n", "# Show the plot\n", @@ -4523,16 +4524,16 @@ "id": "e12c93c4", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:41.651617Z", - "iopub.status.busy": "2023-09-08T06:42:41.651102Z", - "iopub.status.idle": "2023-09-08T06:42:41.658068Z", - "shell.execute_reply": "2023-09-08T06:42:41.657161Z" + "iopub.execute_input": "2023-09-08T07:12:45.369158Z", + "iopub.status.busy": "2023-09-08T07:12:45.368602Z", + "iopub.status.idle": "2023-09-08T07:12:45.374683Z", + "shell.execute_reply": "2023-09-08T07:12:45.373946Z" }, "papermill": { - "duration": 0.025379, - "end_time": "2023-09-08T06:42:41.660662", + "duration": 0.02409, + "end_time": "2023-09-08T07:12:45.377275", "exception": false, - "start_time": "2023-09-08T06:42:41.635283", + "start_time": "2023-09-08T07:12:45.353185", "status": "completed" }, "tags": [] @@ -4548,16 +4549,16 @@ "id": "a7e7524f", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:41.690210Z", - "iopub.status.busy": "2023-09-08T06:42:41.689801Z", - "iopub.status.idle": "2023-09-08T06:42:41.870025Z", - "shell.execute_reply": "2023-09-08T06:42:41.869152Z" + "iopub.execute_input": "2023-09-08T07:12:45.408182Z", + "iopub.status.busy": "2023-09-08T07:12:45.407223Z", + "iopub.status.idle": "2023-09-08T07:12:45.581171Z", + "shell.execute_reply": "2023-09-08T07:12:45.580111Z" }, "papermill": { - "duration": 0.198137, - "end_time": "2023-09-08T06:42:41.872902", + "duration": 0.19252, + "end_time": "2023-09-08T07:12:45.584235", "exception": false, - "start_time": "2023-09-08T06:42:41.674765", + "start_time": "2023-09-08T07:12:45.391715", "status": "completed" }, "tags": [] @@ -4574,16 +4575,16 @@ "id": "b03b2621", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:41.903710Z", - "iopub.status.busy": "2023-09-08T06:42:41.903323Z", - "iopub.status.idle": "2023-09-08T06:42:41.914256Z", - "shell.execute_reply": "2023-09-08T06:42:41.913338Z" + "iopub.execute_input": "2023-09-08T07:12:45.614625Z", + "iopub.status.busy": "2023-09-08T07:12:45.614213Z", + "iopub.status.idle": "2023-09-08T07:12:45.624437Z", + "shell.execute_reply": "2023-09-08T07:12:45.623427Z" }, "papermill": { - "duration": 0.0293, - "end_time": "2023-09-08T06:42:41.916818", + "duration": 0.028137, + "end_time": "2023-09-08T07:12:45.627001", "exception": false, - "start_time": "2023-09-08T06:42:41.887518", + "start_time": "2023-09-08T07:12:45.598864", "status": "completed" }, "tags": [] @@ -4609,16 +4610,16 @@ "id": "d66185bc", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:41.946927Z", - "iopub.status.busy": "2023-09-08T06:42:41.946544Z", - "iopub.status.idle": "2023-09-08T06:42:41.987454Z", - "shell.execute_reply": "2023-09-08T06:42:41.986504Z" + "iopub.execute_input": "2023-09-08T07:12:45.657053Z", + "iopub.status.busy": "2023-09-08T07:12:45.656372Z", + "iopub.status.idle": "2023-09-08T07:12:45.697040Z", + "shell.execute_reply": "2023-09-08T07:12:45.696162Z" }, "papermill": { - "duration": 0.058826, - "end_time": "2023-09-08T06:42:41.990100", + "duration": 0.058287, + "end_time": "2023-09-08T07:12:45.699583", "exception": false, - "start_time": "2023-09-08T06:42:41.931274", + "start_time": "2023-09-08T07:12:45.641296", "status": "completed" }, "tags": [] @@ -4644,16 +4645,16 @@ "id": "bc23aa02", "metadata": { "execution": { - "iopub.execute_input": "2023-09-08T06:42:42.020917Z", - "iopub.status.busy": "2023-09-08T06:42:42.020520Z", - "iopub.status.idle": "2023-09-08T06:42:42.036570Z", - "shell.execute_reply": "2023-09-08T06:42:42.035585Z" + "iopub.execute_input": "2023-09-08T07:12:45.730222Z", + "iopub.status.busy": "2023-09-08T07:12:45.729806Z", + "iopub.status.idle": "2023-09-08T07:12:45.746164Z", + "shell.execute_reply": "2023-09-08T07:12:45.744897Z" }, "papermill": { - "duration": 0.034695, - "end_time": "2023-09-08T06:42:42.039200", + "duration": 0.03493, + "end_time": "2023-09-08T07:12:45.748899", "exception": false, - "start_time": "2023-09-08T06:42:42.004505", + "start_time": "2023-09-08T07:12:45.713969", "status": "completed" }, "tags": [] @@ -4735,10 +4736,10 @@ "id": "fe33118f", "metadata": { "papermill": { - "duration": 0.014207, - "end_time": "2023-09-08T06:42:42.067972", + "duration": 0.014741, + "end_time": "2023-09-08T07:12:45.778747", "exception": false, - "start_time": "2023-09-08T06:42:42.053765", + "start_time": "2023-09-08T07:12:45.764006", "status": "completed" }, "tags": [] @@ -4752,10 +4753,10 @@ "id": "8b066d2c", "metadata": { "papermill": { - "duration": 0.01484, - "end_time": "2023-09-08T06:42:42.097201", + "duration": 0.015998, + "end_time": "2023-09-08T07:12:45.809698", "exception": false, - "start_time": "2023-09-08T06:42:42.082361", + "start_time": "2023-09-08T07:12:45.793700", "status": "completed" }, "tags": [] @@ -4769,10 +4770,10 @@ "id": "77ee339f", "metadata": { "papermill": { - "duration": 0.014992, - "end_time": "2023-09-08T06:42:42.126990", + "duration": 0.014918, + "end_time": "2023-09-08T07:12:45.839483", "exception": false, - "start_time": "2023-09-08T06:42:42.111998", + "start_time": "2023-09-08T07:12:45.824565", "status": "completed" }, "tags": [] @@ -4786,10 +4787,10 @@ "id": "e648f511", "metadata": { "papermill": { - "duration": 0.014629, - "end_time": "2023-09-08T06:42:42.156347", + "duration": 0.015735, + "end_time": "2023-09-08T07:12:45.870757", "exception": false, - "start_time": "2023-09-08T06:42:42.141718", + "start_time": "2023-09-08T07:12:45.855022", "status": "completed" }, "tags": [] @@ -4803,10 +4804,10 @@ "id": "8b53aa7d", "metadata": { "papermill": { - "duration": 0.021463, - "end_time": "2023-09-08T06:42:42.202167", + "duration": 0.014922, + "end_time": "2023-09-08T07:12:45.900564", "exception": false, - "start_time": "2023-09-08T06:42:42.180704", + "start_time": "2023-09-08T07:12:45.885642", "status": "completed" }, "tags": [] @@ -4836,8 +4837,8 @@ }, "papermill": { "default_parameters": {}, - "duration": 7.139322, - "end_time": "2023-09-08T06:42:42.844058", + "duration": 6.957497, + "end_time": "2023-09-08T07:12:46.340854", "environment_variables": {}, "exception": null, "input_path": "Mapping-Evaluation.ipynb", @@ -4845,7 +4846,7 @@ "parameters": { "task": "mondo-ncit-renal-subset" }, - "start_time": "2023-09-08T06:42:35.704736", + "start_time": "2023-09-08T07:12:39.383357", "version": "2.4.0" } }, diff --git a/notebooks/Mapping-Evaluation.ipynb b/notebooks/Mapping-Evaluation.ipynb index d085b49..e0752ee 100644 --- a/notebooks/Mapping-Evaluation.ipynb +++ b/notebooks/Mapping-Evaluation.ipynb @@ -2758,6 +2758,7 @@ "plt.ylabel('F1')\n", "plt.title(f'{task} LogMap score threshold vs F1 (accuracy)')\n", "\n", + "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.png\", format='png')\n", "plt.savefig(f\"../content/images/logmap-scatter-plot-{task}.pdf\", format='pdf')\n", "\n", "# Show the plot\n", diff --git a/notebooks/logmap-scatter-plot-combined.pdf b/notebooks/logmap-scatter-plot-combined.pdf index 55c3dd9..f86d899 100644 Binary files a/notebooks/logmap-scatter-plot-combined.pdf and b/notebooks/logmap-scatter-plot-combined.pdf differ diff --git a/notebooks/logmap-scatter-plot-fbbt-wbbt.pdf b/notebooks/logmap-scatter-plot-fbbt-wbbt.pdf index eabf57e..612948d 100644 Binary files a/notebooks/logmap-scatter-plot-fbbt-wbbt.pdf and b/notebooks/logmap-scatter-plot-fbbt-wbbt.pdf differ diff --git a/notebooks/logmap-scatter-plot-fbbt-zfa.pdf b/notebooks/logmap-scatter-plot-fbbt-zfa.pdf index 0f2309e..19dae6e 100644 Binary files a/notebooks/logmap-scatter-plot-fbbt-zfa.pdf and b/notebooks/logmap-scatter-plot-fbbt-zfa.pdf differ diff --git a/notebooks/logmap-scatter-plot-hsapdv-mmusdv.pdf b/notebooks/logmap-scatter-plot-hsapdv-mmusdv.pdf index 0815b0e..99ee20b 100644 Binary files a/notebooks/logmap-scatter-plot-hsapdv-mmusdv.pdf and b/notebooks/logmap-scatter-plot-hsapdv-mmusdv.pdf differ diff --git a/notebooks/logmap-scatter-plot-mondo-ncit-renal-subset.pdf b/notebooks/logmap-scatter-plot-mondo-ncit-renal-subset.pdf index 130624b..4555ecb 100644 Binary files a/notebooks/logmap-scatter-plot-mondo-ncit-renal-subset.pdf and b/notebooks/logmap-scatter-plot-mondo-ncit-renal-subset.pdf differ