diff --git a/runs.ipynb b/runs.ipynb
index 9b3b81f5f..bb1f3e1a0 100644
--- a/runs.ipynb
+++ b/runs.ipynb
@@ -111,451 +111,31 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 3,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "net\n",
- "\u001b[33mNextflow 24.04.4 is available - Please consider updating your version to it\u001b[m\n",
- "N E X T F L O W ~ version 23.10.4\n",
- "Launching `target/nextflow/workflows/run_robustness_analysis/main.nf` [shrivelled_yalow] DSL2 - revision: 0f2d0d38c3\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "\u001b[2A\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "\u001b[3A\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[5A\n",
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- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[5A\n",
- "executor > local (6)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (8)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (9)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (10)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (11)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (12)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (13)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (14)\u001b[K\n",
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- "\u001b[6A\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (15)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (16)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (17)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (18)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (19)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (19)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (20)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (21)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (22)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (23)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (23)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (25)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (26)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (26)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (27)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (28)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (28)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (29)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (30)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (30)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (31)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (32)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (33)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (34)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (35)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (35)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (35)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (36)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (37)\u001b[K\n",
- "[43/b657d8] process > run_robustness_analysis:run... [100%] 30 of 30 ✔\u001b[K\n",
- "[fb/d3d8f4] process > run_robustness_analysis:run... [ 3%] 1 of 30, failed: 1\u001b[K\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[33m[d7/c872ed] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (figr_20_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
- "\u001b[7A\n",
- "executor > local (38)\u001b[K\n",
- "[43/b657d8] process > run_robustness_analysis:run... [100%] 30 of 30 ✔\u001b[K\n",
- "[e0/3a7f17] process > run_robustness_analysis:run... [ 6%] 2 of 30, failed: 2\u001b[K\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[33m[d7/c872ed] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (figr_20_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
- "\u001b[33m[80/13556a] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (celloracle_20_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
- "\u001b[8A\n",
- "executor > local (38)\u001b[K\n",
- "[43/b657d8] process > run_robustness_analysis:run... [100%] 30 of 30 ✔\u001b[K\n",
- "[e0/3a7f17] process > run_robustness_analysis:run... [ 6%] 2 of 30, failed: 2\u001b[K\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[33m[d7/c872ed] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (figr_20_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
- "\u001b[33m[80/13556a] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (celloracle_20_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
- "\u001b[8A\n",
- "executor > local (39)\u001b[K\n",
- "[43/b657d8] process > run_robustness_analysis:run... [100%] 30 of 30 ✔\u001b[K\n",
- "[55/60c6f2] process > run_robustness_analysis:run... [ 10%] 3 of 30, failed: 3\u001b[K\n",
- "[- ] process > run_robustness_analysis:run... -\u001b[K\n",
- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[33m[d7/c872ed] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (figr_20_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
- "\u001b[33m[80/13556a] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (celloracle_20_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
- "\u001b[33m[e0/3a7f17] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (figr_0_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
- "\u001b[9A\n",
- "executor > local (39)\u001b[K\n",
- "[43/b657d8] process > run_robustness_analysis:run... [100%] 30 of 30 ✔\u001b[K\n",
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- "\u001b[33m[fb/d3d8f4] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (granie_10_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
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- "\u001b[33m[9a/4594a4] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_2:processWf:regression_2_process (collectri_10_scgen_pearson.regression_2)` terminated with an error exit status (137) -- Error is ignored\u001b[39m\u001b[K\n",
- "\u001b[K\n",
- "\u001b[K\n",
- "WARN: Killing running tasks (6)\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"!bash scripts/run_robust_analys.sh \"net\""
]
},
{
"cell_type": "code",
- "execution_count": 63,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
- "data": {
- "text/html": [
- "
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- "\n",
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- " \n",
- " \n",
- " | \n",
- " collectri | \n",
- " granie | \n",
- " figr | \n",
- " celloracle | \n",
- " scglue | \n",
- " scenicplus | \n",
- "
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- " \n",
- " \n",
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- "text/plain": [
- " collectri granie figr celloracle scglue scenicplus\n",
- "0 -0.224471 0.185105 0.186789 0.228927 0.234921 0.33327\n",
- "10 -0.315255 0.170255 0.139809 0.203669 0.132937 0.312483\n",
- "20 -0.369273 0.160628 0.125023 0.183348 0.156769 0.293282\n",
- "50 -0.421345 0.105859 0.067059 0.110983 0.081232 0.231999\n",
- "100 -0.456039 -0.028658 -0.090232 -0.003224 -0.10102 -0.018023"
- ]
- },
- "execution_count": 63,
- "metadata": {},
- "output_type": "execute_result"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_net/state.yaml to resources/results/robust_analy_reg2_net/state.yaml\n",
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_net/scores.yaml to resources/results/robust_analy_reg2_net/scores.yaml\n",
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_net/metric_configs.yaml to resources/results/robust_analy_reg2_net/metric_configs.yaml\n",
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_net/trace.txt to resources/results/robust_analy_reg2_net/trace.txt\n"
+ ]
}
],
"source": [
- "base_folder = 'output/robust_analy_net'\n",
- "\n",
- "result_file = f'{base_folder}/scores.yaml'\n",
- "with open(result_file, 'r') as file:\n",
- " data = yaml.safe_load(file)\n",
- "df_reg1 = pd.DataFrame({}, columns=grn_models)\n",
- "# Iterate over the data\n",
- "for entry in data:\n",
- " method_id = entry['method_id']\n",
- " reg_type, degree, method = method_id.split('-')\n",
- " if reg_type == 'reg1':\n",
- " col = 'ex(True)_tf(-1)'\n",
- " ex_true_tf_idx = entry['metric_ids'].index(col)\n",
- " ex_true_tf_value = entry['metric_values'][ex_true_tf_idx]\n",
- " df_reg1.loc[int(degree), method] = ex_true_tf_value\n",
- "\n",
- "df_reg1.sort_index()\n"
+ "!aws s3 sync s3://openproblems-data/resources/grn/results/robust_analy_reg2_net ./resources/results/robust_analy_reg2_net"
]
},
{
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- "\u001b[32;1mCompleted at: 25-Aug-2024 22:35:49\n",
- "Duration : 9m 39s\n",
- "CPU hours : 1.7\n",
- "Succeeded : 91\n",
- "\u001b[22;39m\u001b[K\n",
- "\n"
- ]
- }
- ],
- "source": [
- "!bash scripts/run_robust_analys.sh \"weight\""
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 43,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " collectri | \n",
- " granie | \n",
- " figr | \n",
- " celloracle | \n",
- " scglue | \n",
- " scenicplus | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 0 | \n",
- " -0.224471 | \n",
- " 0.185105 | \n",
- " 0.186789 | \n",
- " 0.228927 | \n",
- " 0.234921 | \n",
- " 0.33327 | \n",
- "
\n",
- " \n",
- " 10 | \n",
- " -0.224716 | \n",
- " 0.185143 | \n",
- " 0.18504 | \n",
- " 0.227575 | \n",
- " 0.225391 | \n",
- " 0.333008 | \n",
- "
\n",
- " \n",
- " 20 | \n",
- " -0.228165 | \n",
- " 0.183382 | \n",
- " 0.180036 | \n",
- " 0.224755 | \n",
- " 0.221201 | \n",
- " 0.332981 | \n",
- "
\n",
- " \n",
- " 50 | \n",
- " -0.235282 | \n",
- " 0.174765 | \n",
- " 0.164224 | \n",
- " 0.20491 | \n",
- " 0.167678 | \n",
- " 0.325849 | \n",
- "
\n",
- " \n",
- " 100 | \n",
- " -0.297882 | \n",
- " 0.146087 | \n",
- " 0.117188 | \n",
- " 0.167833 | \n",
- " 0.120502 | \n",
- " 0.304062 | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " collectri granie figr celloracle scglue scenicplus\n",
- "0 -0.224471 0.185105 0.186789 0.228927 0.234921 0.33327\n",
- "10 -0.224716 0.185143 0.18504 0.227575 0.225391 0.333008\n",
- "20 -0.228165 0.183382 0.180036 0.224755 0.221201 0.332981\n",
- "50 -0.235282 0.174765 0.164224 0.20491 0.167678 0.325849\n",
- "100 -0.297882 0.146087 0.117188 0.167833 0.120502 0.304062"
- ]
- },
- "execution_count": 43,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "base_folder = 'output/robust_analy_weight'\n",
- "\n",
- "result_file = f'{base_folder}/scores.yaml'\n",
- "with open(result_file, 'r') as file:\n",
- " data = yaml.safe_load(file)\n",
- "df_reg1 = pd.DataFrame({}, columns=grn_models)\n",
- "# Iterate over the data\n",
- "for entry in data:\n",
- " method_id = entry['method_id']\n",
- " reg_type, degree, method = method_id.split('-')\n",
- " if reg_type == 'reg1':\n",
- " col = 'ex(True)_tf(-1)'\n",
- " ex_true_tf_idx = entry['metric_ids'].index(col)\n",
- " ex_true_tf_value = entry['metric_values'][ex_true_tf_idx]\n",
- " df_reg1.loc[int(degree), method] = ex_true_tf_value\n",
- "\n",
- "df_reg1.sort_index()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Negative vs positive controls"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 36,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "\u001b[33mNextflow 24.04.4 is available - Please consider updating your version to it\u001b[m\n",
- "N E X T F L O W ~ version 23.10.4\n",
- "Launching `target/nextflow/workflows/run_robustness_analysis/main.nf` [magical_mercator] DSL2 - revision: 6bd5cda1f4\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
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- "\u001b[6A\n",
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- "\u001b[6A\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (31)\u001b[K\n",
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- "[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
- "\u001b[6A\n",
- "executor > local (32)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (33)\u001b[K\n",
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- "\u001b[6A\n",
- "executor > local (33)\u001b[K\n",
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- "\u001b[6A\n",
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- "\u001b[6A\n",
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- "\u001b[6A\n",
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- "\u001b[6A\n",
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+ "executor > local (71)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (36)\u001b[K\n",
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+ "executor > local (72)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
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+ "executor > local (73)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
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+ "executor > local (74)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
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+ "executor > local (75)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (39)\u001b[K\n",
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+ "executor > local (75)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
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+ "executor > local (76)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
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+ "executor > local (77)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (41)\u001b[K\n",
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+ "executor > local (78)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
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+ "executor > local (79)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
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+ "executor > local (80)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (43)\u001b[K\n",
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+ "executor > local (81)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (43)\u001b[K\n",
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+ "executor > local (81)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (44)\u001b[K\n",
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+ "executor > local (82)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (45)\u001b[K\n",
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+ "executor > local (83)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (45)\u001b[K\n",
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+ "executor > local (83)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (46)\u001b[K\n",
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+ "executor > local (84)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (46)\u001b[K\n",
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+ "executor > local (85)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (47)\u001b[K\n",
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+ "executor > local (86)\u001b[K\n",
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"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
- "executor > local (47)\u001b[K\n",
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+ "executor > local (86)\u001b[K\n",
+ "[46/d03fc1] process > run_robustness_analysis:run... [100%] 30 of 30 ✔\u001b[K\n",
+ "[4f/e10dd4] process > run_robustness_analysis:run... [ 90%] 27 of 30\u001b[K\n",
+ "[40/90153e] process > run_robustness_analysis:run... [ 85%] 23 of 27\u001b[K\n",
"[- ] process > run_robustness_analysis:pub... -\u001b[K\n",
"\u001b[6A\n",
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- "\u001b[32;1mCompleted at: 25-Aug-2024 22:13:05\n",
- "Duration : 5m 54s\n",
- "CPU hours : 1.0\n",
- "Succeeded : 55\n",
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+ "\u001b[32;1mCompleted at: 25-Aug-2024 22:35:49\n",
+ "Duration : 9m 39s\n",
+ "CPU hours : 1.7\n",
+ "Succeeded : 91\n",
"\u001b[22;39m\u001b[K\n",
"\n"
]
}
],
"source": [
- "!bash scripts/run_pc_vs_nc.sh \"pc_vs_nc\""
+ "!bash scripts/run_robust_analys.sh \"weight\""
]
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 9,
"metadata": {},
"outputs": [
{
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " collectri | \n",
- " granie | \n",
- " figr | \n",
- " celloracle | \n",
- " scglue | \n",
- " scenicplus | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " Default | \n",
- " -0.224471 | \n",
- " 0.185105 | \n",
- " 0.186789 | \n",
- " 0.228927 | \n",
- " 0.234921 | \n",
- " 0.33327 | \n",
- "
\n",
- " \n",
- " Negative control compound | \n",
- " -0.249304 | \n",
- " 0.200482 | \n",
- " 0.211147 | \n",
- " 0.234089 | \n",
- " 0.250881 | \n",
- " 0.358298 | \n",
- "
\n",
- " \n",
- " Positive control compounds | \n",
- " -0.242072 | \n",
- " 0.175922 | \n",
- " 0.179734 | \n",
- " 0.215799 | \n",
- " 0.218924 | \n",
- " 0.316465 | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " collectri granie figr celloracle scglue \\\n",
- "Default -0.224471 0.185105 0.186789 0.228927 0.234921 \n",
- "Negative control compound -0.249304 0.200482 0.211147 0.234089 0.250881 \n",
- "Positive control compounds -0.242072 0.175922 0.179734 0.215799 0.218924 \n",
- "\n",
- " scenicplus \n",
- "Default 0.33327 \n",
- "Negative control compound 0.358298 \n",
- "Positive control compounds 0.316465 "
- ]
- },
- "execution_count": 7,
- "metadata": {},
- "output_type": "execute_result"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight/scores.yaml to resources/results/robust_analy_reg2_weight/scores.yaml\n",
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight/state.yaml to resources/results/robust_analy_reg2_weight/state.yaml\n",
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight/metric_configs.yaml to resources/results/robust_analy_reg2_weight/metric_configs.yaml\n",
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight/trace.txt to resources/results/robust_analy_reg2_weight/trace.txt\n"
+ ]
}
],
"source": [
- "base_folder = 'output/robust_analy_pc_vs_nc'\n",
- "\n",
- "result_file = f'{base_folder}/scores.yaml'\n",
- "with open(result_file, 'r') as file:\n",
- " data = yaml.safe_load(file)\n",
- "df_reg1 = pd.DataFrame({}, columns=grn_models)\n",
- "# Iterate over the data\n",
- "for entry in data:\n",
- " method_id = entry['method_id']\n",
- " reg_type, rest = method_id.split('--')\n",
- " subsample, method = rest.split('-')\n",
- " if reg_type == 'reg1':\n",
- " col = 'ex(True)_tf(-1)'\n",
- " ex_true_tf_idx = entry['metric_ids'].index(col)\n",
- " ex_true_tf_value = entry['metric_values'][ex_true_tf_idx]\n",
- " df_reg1.loc[int(subsample), method] = ex_true_tf_value\n",
- "\n",
- "df_reg1 = df_reg1.sort_index()\n",
- "df_reg1.index = ['Default', 'Negative control compound', 'Positive control compounds']\n",
- "df_reg1"
+ "!aws s3 sync s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight ./resources/results/robust_analy_reg2_weight"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Negative vs positive controls"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "!bash scripts/run_pc_vs_nc.sh \"pc_vs_nc\""
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "!aws s3 sync s3://openproblems-data/resources/grn/results/robust_analy_reg2_pc_vs_nc ./resources/results/robust_analy_reg2_pc_vs_nc"
]
},
{
@@ -2800,114 +1719,22 @@
},
{
"cell_type": "code",
- "execution_count": 60,
+ "execution_count": 10,
"metadata": {},
"outputs": [
{
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " collectri | \n",
- " granie | \n",
- " figr | \n",
- " celloracle | \n",
- " scglue | \n",
- " scenicplus | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " Degree 0% | \n",
- " -0.224471 | \n",
- " 0.185105 | \n",
- " 0.186789 | \n",
- " 0.228927 | \n",
- " 0.234921 | \n",
- " 0.33327 | \n",
- "
\n",
- " \n",
- " Degree 10% | \n",
- " -0.274131 | \n",
- " 0.121877 | \n",
- " 0.150885 | \n",
- " 0.170756 | \n",
- " 0.182001 | \n",
- " 0.288634 | \n",
- "
\n",
- " \n",
- " Degree 20% | \n",
- " -0.288105 | \n",
- " 0.083203 | \n",
- " 0.093822 | \n",
- " 0.106046 | \n",
- " 0.130437 | \n",
- " 0.215896 | \n",
- "
\n",
- " \n",
- " Degree 50% | \n",
- " -0.333019 | \n",
- " -0.008502 | \n",
- " -0.037703 | \n",
- " -0.009838 | \n",
- " -0.061216 | \n",
- " -0.009351 | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " collectri granie figr celloracle scglue scenicplus\n",
- "Degree 0% -0.224471 0.185105 0.186789 0.228927 0.234921 0.33327\n",
- "Degree 10% -0.274131 0.121877 0.150885 0.170756 0.182001 0.288634\n",
- "Degree 20% -0.288105 0.083203 0.093822 0.106046 0.130437 0.215896\n",
- "Degree 50% -0.333019 -0.008502 -0.037703 -0.009838 -0.061216 -0.009351"
- ]
- },
- "execution_count": 60,
- "metadata": {},
- "output_type": "execute_result"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign/trace.txt to resources/results/robust_analy_reg2_sign/trace.txt\n",
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign/state.yaml to resources/results/robust_analy_reg2_sign/state.yaml\n",
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign/scores.yaml to resources/results/robust_analy_reg2_sign/scores.yaml\n",
+ "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign/metric_configs.yaml to resources/results/robust_analy_reg2_sign/metric_configs.yaml\n"
+ ]
}
],
"source": [
- "base_folder = 'output/robust_analy_sign'\n",
- "\n",
- "result_file = f'{base_folder}/scores.yaml'\n",
- "with open(result_file, 'r') as file:\n",
- " data = yaml.safe_load(file)\n",
- "df_reg1 = pd.DataFrame({}, columns=grn_models)\n",
- "# Iterate over the data\n",
- "for entry in data:\n",
- " method_id = entry['method_id']\n",
- " reg_type, degree, method = method_id.split('-')\n",
- " if reg_type == 'reg1':\n",
- " col = 'ex(True)_tf(-1)'\n",
- " ex_true_tf_idx = entry['metric_ids'].index(col)\n",
- " ex_true_tf_value = entry['metric_values'][ex_true_tf_idx]\n",
- " df_reg1.loc[int(degree), method] = ex_true_tf_value\n",
- "\n",
- "df_reg1 = df_reg1.sort_index()\n",
- "df_reg1 = df_reg1.drop(100)\n",
- "df_reg1.index = ['Degree 0%', 'Degree 10%', 'Degree 20%', 'Degree 50%']\n",
- "\n",
- "df_reg1"
+ "!aws s3 sync s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign ./resources/results/robust_analy_reg2_sign"
]
},
{
@@ -2919,7 +1746,7 @@
},
{
"cell_type": "code",
- "execution_count": 48,
+ "execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
@@ -2955,7 +1782,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
@@ -2966,14 +1793,14 @@
},
{
"cell_type": "code",
- "execution_count": 49,
+ "execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
- "Processing groups: 100%|██████████| 4/4 [00:09<00:00, 2.36s/it]\n"
+ "Processing groups: 100%|██████████| 4/4 [00:55<00:00, 13.82s/it]\n"
]
}
],
@@ -2992,7 +1819,7 @@
},
{
"cell_type": "code",
- "execution_count": 50,
+ "execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
@@ -3001,18 +1828,38 @@
},
{
"cell_type": "code",
- "execution_count": 51,
+ "execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
- "n_iter = 100"
+ "n_iter = 10"
]
},
{
"cell_type": "code",
- "execution_count": 52,
+ "execution_count": 9,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "ename": "KeyboardInterrupt",
+ "evalue": "",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
+ "Cell \u001b[0;32mIn[9], line 5\u001b[0m\n\u001b[1;32m 3\u001b[0m net_corr \u001b[38;5;241m=\u001b[39m net_corr\u001b[38;5;241m.\u001b[39mreset_index()\u001b[38;5;241m.\u001b[39mmelt(id_vars\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m'\u001b[39m, var_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msource\u001b[39m\u001b[38;5;124m'\u001b[39m, value_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mweight\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 4\u001b[0m net_corr\u001b[38;5;241m.\u001b[39mrename(columns\u001b[38;5;241m=\u001b[39m{\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m'\u001b[39m: \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtarget\u001b[39m\u001b[38;5;124m'\u001b[39m}, inplace\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[0;32m----> 5\u001b[0m \u001b[43mnet_corr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_csv\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43moutput/causal/grns/net_corr_\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mi\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m.csv\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/util/_decorators.py:333\u001b[0m, in \u001b[0;36mdeprecate_nonkeyword_arguments..decorate..wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 327\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(args) \u001b[38;5;241m>\u001b[39m num_allow_args:\n\u001b[1;32m 328\u001b[0m warnings\u001b[38;5;241m.\u001b[39mwarn(\n\u001b[1;32m 329\u001b[0m msg\u001b[38;5;241m.\u001b[39mformat(arguments\u001b[38;5;241m=\u001b[39m_format_argument_list(allow_args)),\n\u001b[1;32m 330\u001b[0m \u001b[38;5;167;01mFutureWarning\u001b[39;00m,\n\u001b[1;32m 331\u001b[0m stacklevel\u001b[38;5;241m=\u001b[39mfind_stack_level(),\n\u001b[1;32m 332\u001b[0m )\n\u001b[0;32m--> 333\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/core/generic.py:3967\u001b[0m, in \u001b[0;36mNDFrame.to_csv\u001b[0;34m(self, path_or_buf, sep, na_rep, float_format, columns, header, index, index_label, mode, encoding, compression, quoting, quotechar, lineterminator, chunksize, date_format, doublequote, escapechar, decimal, errors, storage_options)\u001b[0m\n\u001b[1;32m 3956\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(\u001b[38;5;28mself\u001b[39m, ABCDataFrame) \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mto_frame()\n\u001b[1;32m 3958\u001b[0m formatter \u001b[38;5;241m=\u001b[39m DataFrameFormatter(\n\u001b[1;32m 3959\u001b[0m frame\u001b[38;5;241m=\u001b[39mdf,\n\u001b[1;32m 3960\u001b[0m header\u001b[38;5;241m=\u001b[39mheader,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 3964\u001b[0m decimal\u001b[38;5;241m=\u001b[39mdecimal,\n\u001b[1;32m 3965\u001b[0m )\n\u001b[0;32m-> 3967\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mDataFrameRenderer\u001b[49m\u001b[43m(\u001b[49m\u001b[43mformatter\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_csv\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 3968\u001b[0m \u001b[43m \u001b[49m\u001b[43mpath_or_buf\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3969\u001b[0m \u001b[43m \u001b[49m\u001b[43mlineterminator\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mlineterminator\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3970\u001b[0m \u001b[43m \u001b[49m\u001b[43msep\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msep\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3971\u001b[0m \u001b[43m \u001b[49m\u001b[43mencoding\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mencoding\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3972\u001b[0m \u001b[43m \u001b[49m\u001b[43merrors\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43merrors\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3973\u001b[0m \u001b[43m \u001b[49m\u001b[43mcompression\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcompression\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3974\u001b[0m \u001b[43m \u001b[49m\u001b[43mquoting\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mquoting\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3975\u001b[0m \u001b[43m \u001b[49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3976\u001b[0m \u001b[43m \u001b[49m\u001b[43mindex_label\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mindex_label\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3977\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3978\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunksize\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunksize\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3979\u001b[0m \u001b[43m \u001b[49m\u001b[43mquotechar\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mquotechar\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3980\u001b[0m \u001b[43m \u001b[49m\u001b[43mdate_format\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdate_format\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3981\u001b[0m \u001b[43m \u001b[49m\u001b[43mdoublequote\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdoublequote\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3982\u001b[0m \u001b[43m \u001b[49m\u001b[43mescapechar\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mescapechar\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3983\u001b[0m \u001b[43m \u001b[49m\u001b[43mstorage_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstorage_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3984\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/io/formats/format.py:1014\u001b[0m, in \u001b[0;36mDataFrameRenderer.to_csv\u001b[0;34m(self, path_or_buf, encoding, sep, columns, index_label, mode, compression, quoting, quotechar, lineterminator, chunksize, date_format, doublequote, escapechar, errors, storage_options)\u001b[0m\n\u001b[1;32m 993\u001b[0m created_buffer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m 995\u001b[0m csv_formatter \u001b[38;5;241m=\u001b[39m CSVFormatter(\n\u001b[1;32m 996\u001b[0m path_or_buf\u001b[38;5;241m=\u001b[39mpath_or_buf,\n\u001b[1;32m 997\u001b[0m lineterminator\u001b[38;5;241m=\u001b[39mlineterminator,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1012\u001b[0m formatter\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfmt,\n\u001b[1;32m 1013\u001b[0m )\n\u001b[0;32m-> 1014\u001b[0m \u001b[43mcsv_formatter\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msave\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1016\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m created_buffer:\n\u001b[1;32m 1017\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(path_or_buf, StringIO)\n",
+ "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/io/formats/csvs.py:270\u001b[0m, in \u001b[0;36mCSVFormatter.save\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 251\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m get_handle(\n\u001b[1;32m 252\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfilepath_or_buffer,\n\u001b[1;32m 253\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmode,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 258\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m handles:\n\u001b[1;32m 259\u001b[0m \u001b[38;5;66;03m# Note: self.encoding is irrelevant here\u001b[39;00m\n\u001b[1;32m 260\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mwriter \u001b[38;5;241m=\u001b[39m csvlib\u001b[38;5;241m.\u001b[39mwriter(\n\u001b[1;32m 261\u001b[0m handles\u001b[38;5;241m.\u001b[39mhandle,\n\u001b[1;32m 262\u001b[0m lineterminator\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mlineterminator,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 267\u001b[0m quotechar\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mquotechar,\n\u001b[1;32m 268\u001b[0m )\n\u001b[0;32m--> 270\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_save\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/io/formats/csvs.py:275\u001b[0m, in \u001b[0;36mCSVFormatter._save\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 273\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_need_to_save_header:\n\u001b[1;32m 274\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_save_header()\n\u001b[0;32m--> 275\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_save_body\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/io/formats/csvs.py:313\u001b[0m, in \u001b[0;36mCSVFormatter._save_body\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 311\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m start_i \u001b[38;5;241m>\u001b[39m\u001b[38;5;241m=\u001b[39m end_i:\n\u001b[1;32m 312\u001b[0m \u001b[38;5;28;01mbreak\u001b[39;00m\n\u001b[0;32m--> 313\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_save_chunk\u001b[49m\u001b[43m(\u001b[49m\u001b[43mstart_i\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mend_i\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/io/formats/csvs.py:324\u001b[0m, in \u001b[0;36mCSVFormatter._save_chunk\u001b[0;34m(self, start_i, end_i)\u001b[0m\n\u001b[1;32m 321\u001b[0m data \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(res\u001b[38;5;241m.\u001b[39m_iter_column_arrays())\n\u001b[1;32m 323\u001b[0m ix \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdata_index[slicer]\u001b[38;5;241m.\u001b[39m_get_values_for_csv(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_number_format)\n\u001b[0;32m--> 324\u001b[0m \u001b[43mlibwriters\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwrite_csv_rows\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 325\u001b[0m \u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 326\u001b[0m \u001b[43m \u001b[49m\u001b[43mix\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 327\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mnlevels\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 328\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcols\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 329\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwriter\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 330\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
+ "File \u001b[0;32mwriters.pyx:56\u001b[0m, in \u001b[0;36mpandas._libs.writers.write_csv_rows\u001b[0;34m()\u001b[0m\n",
+ "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
+ ]
+ }
+ ],
"source": [
"for i in range(n_iter):\n",
" net_corr = net.sample(len(tfs), axis=1)\n",
@@ -3023,7 +1870,7 @@
},
{
"cell_type": "code",
- "execution_count": 53,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -4969,16 +3816,15 @@
},
{
"cell_type": "code",
- "execution_count": 22,
+ "execution_count": 13,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "download: s3://openproblems-data/resources/grn/results/single_omics/state.yaml to resources/results/single_omics/state.yaml\n",
- "download: s3://openproblems-data/resources/grn/results/single_omics/scores.yaml to resources/results/single_omics/scores.yaml\n",
- "download: s3://openproblems-data/resources/grn/results/single_omics/trace.txt to resources/results/single_omics/trace.txt\n"
+ "download: s3://openproblems-data/resources/grn/results/single_omics/trace.txt to resources/results/single_omics/trace.txt\n",
+ "download: s3://openproblems-data/resources/grn/results/single_omics/scores.yaml to resources/results/single_omics/scores.yaml\n"
]
}
],
@@ -4986,15 +3832,6 @@
"!aws s3 sync s3://openproblems-data/resources/grn/results/single_omics ./resources/results/single_omics"
]
},
- {
- "cell_type": "code",
- "execution_count": 10,
- "metadata": {},
- "outputs": [],
- "source": [
- "!aws s3 sync s3://openproblems-data/resources/grn/results/grn_evaluation_GB_figr ./resources/results/grn_evaluation_GB_figr "
- ]
- },
{
"cell_type": "code",
"execution_count": null,
diff --git a/scripts/run_benchmark_single_omics.sh b/scripts/run_benchmark_single_omics.sh
index 0ab78cf33..5cc756408 100644
--- a/scripts/run_benchmark_single_omics.sh
+++ b/scripts/run_benchmark_single_omics.sh
@@ -1,12 +1,12 @@
#!/bin/bash
# RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
-RUN_ID="single_omics"
-resources_dir="s3://openproblems-data/resources_test/grn"
-publish_dir="s3://openproblems-data/resources_test/grn/results/${RUN_ID}"
+RUN_ID="single_omics_test"
+# resources_dir="s3://openproblems-data/resources_test/grn"
+# publish_dir="s3://openproblems-data/resources_test/grn/results/${RUN_ID}"
-# resources_dir="./resources_test/"
-# publish_dir="output/${RUN_ID}"
+resources_dir="./resources_test/"
+publish_dir="output/${RUN_ID}"
reg_type=ridge
subsample=-2
diff --git a/scripts/run_pc_vs_nc.sh b/scripts/run_pc_vs_nc.sh
index 52e851695..055d43f98 100644
--- a/scripts/run_pc_vs_nc.sh
+++ b/scripts/run_pc_vs_nc.sh
@@ -4,19 +4,18 @@
subsamples=(-2 -3 -4)
-RUN_ID="robust_analy_$1"
-resources_dir="resources"
-publish_dir="output/${RUN_ID}"
+RUN_ID="robust_analy_reg2_$1"
+# resources_dir="resources"
+resources_dir="s3://openproblems-data/resources/grn"
-# resources_dir="s3://openproblems-data/resources/grn"
-# publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}"
+publish_dir="${resources_dir}/${RUN_ID}"
grn_models_folder="${resources_dir}/grn_models"
reg_type=ridge
max_workers=10
-layer=pearson
+layer=scgen_pearson
param_file="./params/${RUN_ID}.yaml"
@@ -30,7 +29,6 @@ grn_names=(
)
-
# Start writing to the YAML file
cat > $param_file << HERE
param_list:
@@ -66,12 +64,12 @@ output_state: "state.yaml"
publish_dir: "$publish_dir"
HERE
-nextflow run . \
- -main-script target/nextflow/workflows/run_robustness_analysis/main.nf \
- -profile docker \
- -with-trace \
- -c src/common/nextflow_helpers/labels_ci.config \
- -params-file ${param_file}
+# nextflow run . \
+# -main-script target/nextflow/workflows/run_robustness_analysis/main.nf \
+# -profile docker \
+# -with-trace \
+# -c src/common/nextflow_helpers/labels_ci.config \
+# -params-file ${param_file}
# ./tw-windows-x86_64.exe launch `
# https://github.com/openproblems-bio/task_grn_benchmark.git `
diff --git a/scripts/run_robust_analys.sh b/scripts/run_robust_analys.sh
index 721254210..f8348c950 100644
--- a/scripts/run_robust_analys.sh
+++ b/scripts/run_robust_analys.sh
@@ -3,12 +3,12 @@
# RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
degrees=(0 10 20 50 100)
-noise_type="$1" #"net"
+noise_type="$1" #"net", "weight", "sign"
echo $noise_type
-RUN_ID="robust_analy_$1"
-resources_dir="resources"
-# resources_dir="s3://openproblems-data/resources/grn"
+RUN_ID="robust_analy_reg2_$1"
+# resources_dir="resources"
+resources_dir="s3://openproblems-data/resources/grn"
publish_dir="${resources_dir}/results/${RUN_ID}"
diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml
index d8fc3904e..64ba87ad7 100644
--- a/src/api/comp_method.yaml
+++ b/src/api/comp_method.yaml
@@ -23,7 +23,7 @@ functionality:
__merge__: file_prediction.yaml
required: false
direction: output
- default: output/grn.csv
+ example: output/grn.csv
- name: --temp_dir
type: string
direction: input
diff --git a/src/methods/multi_omics/scenicplus/config.vsh.yaml b/src/methods/multi_omics/scenicplus/config.vsh.yaml
index 77a37d0a0..c5671553a 100644
--- a/src/methods/multi_omics/scenicplus/config.vsh.yaml
+++ b/src/methods/multi_omics/scenicplus/config.vsh.yaml
@@ -33,7 +33,7 @@ functionality:
platforms:
- type: docker
- image: apassemi/scenicplus:1.0.0
+ image: apassemi/scenicplus:1.0.1
setup:
- type: python
packages: [ flatbuffers ]
diff --git a/src/methods/multi_omics/scenicplus/script.py b/src/methods/multi_omics/scenicplus/script.py
index 6d5160ba6..69c7f5753 100644
--- a/src/methods/multi_omics/scenicplus/script.py
+++ b/src/methods/multi_omics/scenicplus/script.py
@@ -607,7 +607,7 @@
os.path.join(out_dir, 'cistarget-db', 'v10nr_clust_public.zip')
)
with zipfile.ZipFile(os.path.join(out_dir, 'cistarget-db', 'v10nr_clust_public.zip'), 'r') as zip_ref:
- zip_ref.extractall(os.path.join(out_dir))
+ zip_ref.extractall(os.path.join(out_dir, 'cistarget-db'))
# Download chromosome sizes
if not os.path.exists(os.path.join(out_dir, 'cistarget-db', 'hg38.chrom.sizes')):
diff --git a/src/methods/multi_omics/scglue/main.py b/src/methods/multi_omics/scglue/main.py
index 7e6ac4ac9..fc6b450f3 100644
--- a/src/methods/multi_omics/scglue/main.py
+++ b/src/methods/multi_omics/scglue/main.py
@@ -141,7 +141,6 @@ def cis_inference(par):
if attr["qval"] < 0.05
)
-
scglue.genomics.Bed(atac.var).write_bed(f"{par['temp_dir']}/peaks.bed", ncols=3)
scglue.genomics.write_links(
gene2peak,
@@ -150,8 +149,6 @@ def cis_inference(par):
f"{par['temp_dir']}/gene2peak.links", keep_attrs=["score"]
)
-
-
motif_bed = scglue.genomics.read_bed(par['motif_file']) ## http://download.gao-lab.org/GLUE/cisreg/JASPAR2022-hg38.bed.gz
tfs = pd.Index(motif_bed["name"]).intersection(rna.var_names)
rna[:, np.union1d(genes, tfs)].write_loom(f"{par['temp_dir']}/rna.loom")
diff --git a/src/metrics/regression_1/main.py b/src/metrics/regression_1/main.py
index 48781be5c..52cadf53b 100644
--- a/src/metrics/regression_1/main.py
+++ b/src/metrics/regression_1/main.py
@@ -176,6 +176,7 @@ def main(par):
tf_all = np.loadtxt(par['tf_all'], dtype=str)
gene_names = perturbation_data.var.index.to_numpy()
net = pd.read_csv(par['prediction'])
+ # net['weight'] = net.weight.abs()
# subset to keep only those links with source as tf
if par['apply_tf']:
net = net[net.source.isin(tf_all)]
diff --git a/src/robustness_analysis/script.py b/src/robustness_analysis/script.py
index 6c17fc94d..ad3eca2b4 100644
--- a/src/robustness_analysis/script.py
+++ b/src/robustness_analysis/script.py
@@ -23,7 +23,7 @@
assert 'weight' in prediction.columns
print('Add noise to weight')
std_dev = prediction['weight'].std()
- noise = np.random.normal(0, degree * std_dev, size=prediction['weight'].shape)
+ noise = np.random.normal(loc=0, scale=degree * std_dev, size=prediction['weight'].shape)
prediction['weight'] += noise
elif type == 'links': # shuffle source-target-weight
diff --git a/src/workflows/run_benchmark_single_omics/main.nf b/src/workflows/run_benchmark_single_omics/main.nf
index d0ef0391d..2f5182517 100644
--- a/src/workflows/run_benchmark_single_omics/main.nf
+++ b/src/workflows/run_benchmark_single_omics/main.nf
@@ -24,16 +24,16 @@ workflow run_wf {
// ]
methods = [
- ennet,
- grnboost2,
- scsgl,
- tigress
+ portia,
+ // ennet
+ grnboost2
+ // scsgl,
+ // tigress
]
// construct list of metrics
metrics = [
- regression_1,
- regression_2
+ regression_1
]
/****************************
@@ -87,7 +87,8 @@ workflow run_wf {
method_id: comp.config.functionality.name,
prediction: output.prediction
]
- }
+ },
+ auto: [publish: "state"]
)
// run all metrics