update to year 3, version 3

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 Lukas Friedrich, Merck KGaA Darmstadt 
+Copyright (c) 2020 Lukas Friedrich, Merck KGaA Darmstadt and  Jaak Simm, University of Leuven
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

config/example_parameters.json

@@ -14,7 +14,11 @@
     "nfolds": 5
   },
   "credibility_range": {
-    "PANEL": {
+    "NON-CATALOG-PANEL": {
+      "min": 3.0,
+      "max": 10.0
+    },
+    "CATALOG-PANEL": {
       "min": 3.0,
       "max": 10.0
     },
@@ -40,7 +44,7 @@
         "num_total": 50,
         "num_uncensored_total": 25
       },
-      "PANEL": {
+      "NON-CATALOG-PANEL": {
         "num_total": 50,
         "num_uncensored_total": 25
       },
@@ -58,7 +62,7 @@
         "num_active_total": 25,
         "num_inactive_total": 25
       },
-      "PANEL": {
+      "NON-CATALOG-PANEL": {
         "num_active_total": 25,
         "num_inactive_total": 25
       },
@@ -69,16 +73,25 @@
       "AUX_HTS": {
         "num_active_total": 10,
         "num_inactive_total": 10000
+      },
+      "AUX_PL": {
+        "num_active_total": 10,
+        "num_inactive_total": 10000
+      }
+    },
+    "CATALOG-PANEL": {
+        "num_total": 400,
+        "num_active_fold_min": 10,
+        "num_inactive_fold_min": 10
       }
-    }
   },
   "evaluation_quorum": {
     "regression": {
       "ADME": {
         "num_fold_min": 50,
         "num_uncensored_fold_min": 25
       },
-      "PANEL": {
+      "NON-CATALOG-PANEL": {
         "num_fold_min": 50,
         "num_uncensored_fold_min": 25
       },
@@ -89,14 +102,18 @@
       "AUX_HTS": {
         "num_fold_min": 50,
         "num_uncensored_fold_min": 25
+      },
+      "AUX_PL": {
+        "num_fold_min": 50,
+        "num_uncensored_fold_min": 25
       }
     },
     "classification": {
       "ADME": {
         "num_active_fold_min": 10,
         "num_inactive_fold_min": 10
       },
-      "PANEL": {
+      "NON-CATALOG-PANEL": {
         "num_active_fold_min": 10,
         "num_inactive_fold_min": 10
       },
@@ -111,7 +128,8 @@
     }
   },
   "initial_task_weights": {
-    "AUX_HTS": 0.1
+    "AUX_HTS": 0.1,
+    "AUX_PL": 0.1
   },
   "global_thresholds": {
     "AUX_HTS": 3.0
@@ -122,6 +140,9 @@
   "count_task": {
     "count_data_points": 25
   },
+  "regression_evaluation_task_filter": {
+    "min_standard_deviation": 0.5
+  },
   "lsh": {
     "nfolds": 5,
     "bits": [
@@ -143,4 +164,4 @@
       17552
     ]
   }
-}
+}

config/run_parameters/agg_val.json

@@ -0,0 +1,12 @@
+{
+    "assay_file": "input/w_cat/T0.csv",
+    "activity_file": "input/w_cat/T1.csv",
+    "mapping_table": "tests/w_cat/mapping_table/T5.csv",
+    "config_file": "data_prep/config/example_parameters.json",
+    "key_file": "data_prep/config/example_key.json",
+    "output_dir": "tests",
+    "run_name": "w_cat",
+    "number_cpu": 64,
+    "ref_hash": null,
+    "non_interactive": true
+}

config/run_parameters/apply_thres.json

@@ -0,0 +1,12 @@
+{
+    "assay_file": "tests/w_cat/results_tmp/aggregation/T0_upd.csv",
+    "activity_file": "tests/w_cat/results_tmp/aggregation/T4r.csv",
+    "catalog_file": "input/w_cat/T_cat.csv",
+    "config_file": "data_prep/config/example_parameters.json",
+    "key_file": "data_prep/config/example_key.json",
+    "output_dir": "tests",
+    "run_name": "w_cat",
+    "number_cpu": 4,
+    "ref_hash": null,
+    "non_interactive": true
+}

config/run_parameters/calc_desc.json

@@ -0,0 +1,10 @@
+{
+    "structure_file": "tests/w_cat/results_tmp/standardization/T2_standardized.csv",
+    "config_file": "data_prep/config/example_parameters.json",
+    "key_file": "data_prep/config/example_key.json",
+    "output_dir": "tests",
+    "run_name": "w_cat",
+    "number_cpu": 64,
+    "ref_hash": null,
+    "non_interactive": false
+}

config/run_parameters/filter_clf.json

@@ -0,0 +1,12 @@
+{
+    "classification_activity_file": "tests/w_cat/results_tmp/thresholding/T4c.csv",
+    "classification_weight_table": "tests/w_cat/results_tmp/thresholding/T3c.csv",
+    "catalog_file": "input/w_cat/T_cat.csv",
+    "mapping_table_T5": "tests/w_cat/mapping_table/T5.csv",
+    "config_file": "data_prep/config/example_parameters.json",
+    "key_file": "data_prep/config/example_key.json",
+    "output_dir": "tests",
+    "run_name": "w_cat",
+    "ref_hash": null,
+    "non_interactive": true
+}

config/run_parameters/filter_reg.json

@@ -0,0 +1,10 @@
+{
+    "regression_activity_file": "tests/w_cat/results_tmp/aggregation/T4r.csv",
+    "regression_weight_table": "tests/w_cat/results_tmp/aggregation/T0_upd.csv",
+    "config_file": "data_prep/config/example_parameters.json",
+    "key_file": "data_prep/config/example_key.json",
+    "output_dir": "tests",
+    "run_name": "w_cat",
+    "ref_hash": null,
+    "non_interactive": true
+}

config/run_parameters/fold_assign.json

@@ -0,0 +1,10 @@
+{
+    "structure_file": "tests/w_cat/results_tmp/descriptors/T2_descriptors.csv",
+    "config_file": "data_prep/config/example_parameters.json",
+    "key_file": "data_prep/config/example_key.json",
+    "output_dir": "tests",
+    "run_name": "w_cat",
+    "number_cpu": 64,
+    "ref_hash": null,
+    "non_interactive": false
+}

config/run_parameters/make_matrices.json

@@ -0,0 +1,14 @@
+{
+    "structure_file": "tests/w_cat/mapping_table/T6.csv",
+    "activity_file_clf": "tests/w_cat/results_tmp/classification/T10c.csv",
+    "weight_table_clf": "tests/w_cat/results_tmp/classification/T8c.csv",
+    "activity_file_reg": "tests/w_cat/results_tmp/regression/T10r.csv",
+    "weight_table_reg": "tests/w_cat/results_tmp/regression/T8r.csv",
+    "config_file": "data_prep/config/example_parameters.json",
+    "key_file": "data_prep/config/example_key.json",
+    "output_dir": "tests",
+    "run_name": "w_cat",
+    "using_auxiliary": "yes",
+    "ref_hash": null,
+    "non_interactive": true
+}

config/run_parameters/pipeline.json

@@ -0,0 +1,19 @@
+{
+    "structure_file": "input/w_cat/T2.csv",
+    "activity_files": [
+        "input/w_cat/T1.csv"
+    ],
+    "weight_tables": [
+        "input/w_cat/T0.csv"
+    ],
+    "catalog_file": "input/w_cat/T_cat.csv",
+    "config_file": "data_prep/config/example_parameters.json",
+    "key_file": "data_prep/config/example_key.json",
+    "output_dir": "tests/",
+    "run_name": "w_cat_entire",
+    "using_auxiliary": "no",
+    "number_cpu": 128,
+    "ref_hash": null,
+    "non_interactive": true,
+    "folding_method": "scaffold"
+}

melloddy_pipeline_env.yml

@@ -8,26 +8,30 @@ channels:
 dependencies:
   - mkl
   - mkl_random
-  - numpy=1.19
+  - numpy=1.20.1
   - openssl
-  - pandas=1.1
+  - pandas=1.3.3
   - python=3.8.2
-  - rdkit=2020.09.1.0
-  - scipy=1.5.2
+  - rdkit=2021.03.5
+  - scipy=1.7.1
   - sqlite
   - tqdm
   - nose2
   - pytest
-  - scikit-learn=0.23.2
-  - pytorch::pytorch=1.4.0
-  - pytorch::torchvision=0.5.0
-  - cudatoolkit=10.1
+  - scikit-learn=0.24.2
+  - pytorch::pytorch=1.8.1
+  - cudatoolkit=10.2.89
   - tensorboard
   - notebook
   - ipykernel
   - jupyterlab
   - ipykernel
   - matplotlib
   - seaborn
-  - dask=2.30.0
+  - dask=2021.8.1
+  - torchinfo=1.5.3
+  - pip
+  - pip:
+    - pandera
+    - pynvml==11.0.0