NM Toxicity models integration

.pre-commit-config.yaml

@@ -1,38 +1,46 @@
 repos:
--   repo: local
-    hooks:
-    - id: update-requirements-txt
-      name: update-requirements-txt
-      description: 'Generate requirements.txt based on poetry.lock'
-      entry: poetry
-      args: [export, --without-hashes, --format, requirements.txt, --output, requirements.txt]
-      language: system
-      pass_filenames: false
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
-    hooks:
-    -   id: check-merge-conflict
-    -   id: debug-statements
-    -   id: check-yaml
--   repo: https://github.com/psf/black
-    rev: 23.1.0
-    hooks:
-    -   id: black
-        args:
-        - --line-length=79
-        - --target-version=py38
--   repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.1
-    hooks:
-    -   id: autoflake
-        args:
-        - --in-place
-        - --remove-all-unused-imports
-        - --remove-duplicate-keys
-        - --ignore-init-module-imports
--   repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.9.0
-    hooks:
-    -   id: reorder-python-imports
-        args:
-            - --py38-plus
+    # - repo: local
+    #   hooks:
+    #       - id: update-requirements-txt
+    #         name: update-requirements-txt
+    #         description: "Generate requirements.txt based on poetry.lock"
+    #         entry: poetry
+    #         args:
+    #             [
+    #                 export,
+    #                 --without-hashes,
+    #                 --format,
+    #                 requirements.txt,
+    #                 --output,
+    #                 requirements.txt,
+    #             ]
+    #         language: system
+    #         pass_filenames: false
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: check-merge-conflict
+          - id: debug-statements
+          - id: check-yaml
+    - repo: https://github.com/psf/black
+      rev: 23.1.0
+      hooks:
+          - id: black
+            args:
+                - --line-length=79
+                - --target-version=py38
+    - repo: https://github.com/PyCQA/autoflake
+      rev: v2.0.1
+      hooks:
+          - id: autoflake
+            args:
+                - --in-place
+                - --remove-all-unused-imports
+                - --remove-duplicate-keys
+                - --ignore-init-module-imports
+    - repo: https://github.com/asottile/reorder_python_imports
+      rev: v3.9.0
+      hooks:
+          - id: reorder-python-imports
+            args:
+                - --py38-plus

config/datasets/admet/toxisity_mouse_oral_ld50.yaml

@@ -0,0 +1,23 @@
+task:
+  - qsar-regression
+
+name: toxicity_mouse_oral_ld50
+description: The dataset contains information on the lethal dose (LD50) values of various chemical substances, tested on mice through oral administration, indicating the dose required to kill 50% of a mouse population under experimental conditions.
+
+markup_info: Информация о разметке
+date_time: 22.10.2024
+
+_target_: innofw.core.datamodules.pandas_datamodules.QsarDataModule
+
+train:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_mouse_oral_ld50/train.zip
+  target: ./data/toxicity_mouse_oral_ld50/train
+test:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_mouse_oral_ld50/test.zip
+  target: ./data/toxicity_mouse_oral_ld50/test
+infer:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_mouse_oral_ld50/test.zip
+  target: ./data/toxicity_mouse_oral_ld50/test
+smiles_col: smiles
+target_col: Toxicity Value
+val_size: 0.2

config/datasets/admet/toxisity_rabbit_skin_ld50.yaml

@@ -0,0 +1,23 @@
+task:
+  - qsar-regression
+
+name: toxicity_rabbit_skin_ld50
+description: The dataset provides information on the lethal dose (LD50) values for various chemical substances applied to rabbit skin, indicating the dose required to cause death in 50% of the rabbit population under experimental conditions.
+
+markup_info: Информация о разметке
+date_time: 22.10.2024
+
+_target_: innofw.core.datamodules.pandas_datamodules.QsarDataModule
+
+train:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rabbit_skin_ld50/train.zip
+  target: ./data/toxicity_rabbit_skin_ld50/train
+test:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rabbit_skin_ld50/test.zip
+  target: ./data/toxicity_rabbit_skin_ld50/test
+infer:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rabbit_skin_ld50/test.zip
+  target: ./data/toxicity_rabbit_skin_ld50/test
+smiles_col: smiles
+target_col: Toxicity Value
+val_size: 0.2

config/datasets/admet/toxisity_rat_intravenous_ld50.yaml

@@ -0,0 +1,23 @@
+task:
+  - qsar-regression
+
+name: toxicity_rat_intravenous_ld50
+description: The dataset contains information on the lethal dose (LD50) values for various chemical substances administered intravenously to rats, indicating the dose required to kill 50% of the rat population under experimental conditions.
+
+markup_info: Информация о разметке
+date_time: 22.10.2024
+
+_target_: innofw.core.datamodules.pandas_datamodules.QsarDataModule
+
+train:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rat_intravenous_ld50/train.zip
+  target: ./data/toxicity_rat_intravenous_ld50/train
+test:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rat_intravenous_ld50/test.zip
+  target: ./data/toxicity_rat_intravenous_ld50/test
+infer:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rat_intravenous_ld50/test.zip
+  target: ./data/toxicity_rat_intravenous_ld50/test
+smiles_col: smiles
+target_col: Toxicity Value
+val_size: 0.2

config/datasets/admet/toxisity_rat_oral_ld50.yaml

@@ -0,0 +1,23 @@
+task:
+  - qsar-regression
+
+name: toxicity_rat_oral_ld50
+description: The dataset contains information on the lethal dose (LD50) values of various chemical substances, tested on rat through oral administration, indicating the dose required to kill 50% of a rat population under experimental conditions.
+
+markup_info: Информация о разметке
+date_time: 22.10.2024
+
+_target_: innofw.core.datamodules.pandas_datamodules.QsarDataModule
+
+train:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rat_oral_ld50/train.zip
+  target: ./data/toxicity_rat_oral_ld50/train
+test:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rat_oral_ld50/test.zip
+  target: ./data/toxicity_rat_oral_ld50/test
+infer:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rat_oral_ld50/test.zip
+  target: ./data/toxicity_rat_oral_ld50/test
+smiles_col: smiles
+target_col: Toxicity Value
+val_size: 0.2

config/datasets/admet/toxisity_rat_skin_ld50.yaml

@@ -0,0 +1,22 @@
+task:
+  - qsar-regression
+
+name: toxicity_rat_skin_ld50
+description: The dataset provides information on the lethal dose (LD50) values for various chemical substances applied to rat skin, indicating the dose required to cause death in 50% of the rat population under experimental conditions.
+markup_info: Информация о разметке
+date_time: 18.06.2019
+
+_target_: innofw.core.datamodules.pandas_datamodules.QsarDataModule
+
+train:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rat_skin_ld50/train.zip
+  target: ./data/toxicity_rat_skin_ld50/train
+test:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rat_skin_ld50/test.zip
+  target: ./data/toxicity_rat_skin_ld50/test
+infer:
+  source: https://api.blackhole.ai.innopolis.university/public-datasets/toxisity_rat_skin_ld50/test.zip
+  target: ./data/toxicity_rat_skin_ld50/test
+smiles_col: smiles
+target_col: Toxicity Value
+val_size: 0.2

config/experiments/regression/GR_221024_catboost_toxisity_mouse_oral_ld50.yaml

@@ -0,0 +1,10 @@
+# @package _global_
+defaults:
+  - override /models: regression/catboost_regression
+  - override /datasets: admet/toxicity_mouse_oral_ld50
+  - override /callbacks: regression
+
+project: "toxicity_mouse_oral_ld50"
+task: "qsar-regression"
+random_seed: 42
+# original_work_dir: ${hydra:runtime.cwd}

config/experiments/regression/GR_221024_catboost_toxisity_rabbit_skin_ld50.yaml

@@ -0,0 +1,10 @@
+# @package _global_
+defaults:
+  - override /models: regression/catboost_regression
+  - override /datasets: admet/toxicity_rabbit_skin_ld50
+  - override /callbacks: regression
+
+project: "toxicity_rabbit_skin_ld50"
+task: "qsar-regression"
+random_seed: 42
+# original_work_dir: ${hydra:runtime.cwd}

config/experiments/regression/GR_221024_catboost_toxisity_rat_intravenous_ld50.yaml

@@ -0,0 +1,10 @@
+# @package _global_
+defaults:
+  - override /models: regression/catboost_regression
+  - override /datasets: admet/toxicity_rat_intravenous_ld50
+  - override /callbacks: regression
+
+project: "toxicity_rat_intravenous_ld50"
+task: "qsar-regression"
+random_seed: 42
+# original_work_dir: ${hydra:runtime.cwd}

config/experiments/regression/GR_221024_catboost_toxisity_rat_oral_ld50.yaml

@@ -0,0 +1,10 @@
+# @package _global_
+defaults:
+  - override /models: regression/catboost_regression
+  - override /datasets: admet/toxicity_rat_oral_ld50
+  - override /callbacks: regression
+
+project: "toxicity_rat_oral_ld50"
+task: "qsar-regression"
+random_seed: 42
+# original_work_dir: ${hydra:runtime.cwd}

config/experiments/regression/GR_221024_catboost_toxisity_rat_skin_ld50.yaml

@@ -0,0 +1,10 @@
+# @package _global_
+defaults:
+  - override /models: regression/catboost_regression
+  - override /datasets: admet/toxicity_rat_skin_ld50
+  - override /callbacks: regression
+
+project: "toxicity_rat_skin_ld50"
+task: "qsar-regression"
+random_seed: 42
+# original_work_dir: ${hydra:runtime.cwd}

examples/admet/toxisity_mouse_oral_ld50/infer_catboost.bat

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_mouse_oral_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_mouse_oral_ld50.pickle

examples/admet/toxisity_mouse_oral_ld50/infer_catboost.sh

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_mouse_oral_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_mouse_oral_ld50.pickle

examples/admet/toxisity_mouse_oral_ld50/train_catboost.bat

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_mouse_oral_ld50

examples/admet/toxisity_mouse_oral_ld50/train_catboost.sh

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_mouse_oral_ld50

examples/admet/toxisity_rabbit_skin_ld50/infer_catboost.bat

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_rabbit_skin_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_rabbit_skin_ld50.pickle

examples/admet/toxisity_rabbit_skin_ld50/infer_catboost.sh

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_rabbit_skin_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_rabbit_skin_ld50.pickle

examples/admet/toxisity_rabbit_skin_ld50/train_catboost.bat

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_rabbit_skin_ld50

examples/admet/toxisity_rabbit_skin_ld50/train_catboost.sh

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_rabbit_skin_ld50

examples/admet/toxisity_rat_intravenous_ld50/infer_catboost.bat

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_rat_intravenous_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_rat_intravenous_ld50.pickle

examples/admet/toxisity_rat_intravenous_ld50/infer_catboost.sh

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_rat_intravenous_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_rat_intravenous_ld50.pickle

examples/admet/toxisity_rat_intravenous_ld50/train_catboost.bat

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_rat_intravenous_ld50

examples/admet/toxisity_rat_intravenous_ld50/train_catboost.sh

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_rat_intravenous_ld50

examples/admet/toxisity_rat_oral_ld50/infer_catboost.bat

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_rat_oral_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_rat_oral_ld50.pickle

examples/admet/toxisity_rat_oral_ld50/infer_catboost.sh

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_rat_oral_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_rat_oral_ld50.pickle

examples/admet/toxisity_rat_oral_ld50/train_catboost.bat

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_rat_oral_ld50

examples/admet/toxisity_rat_oral_ld50/train_catboost.sh

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_rat_oral_ld50

examples/admet/toxisity_rat_skin_ld50/infer_catboost.bat

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_rat_skin_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_rat_skin_ld50.pickle

examples/admet/toxisity_rat_skin_ld50/infer_catboost.sh

@@ -0,0 +1 @@
+python infer.py experiments=regression/GR_221024_catboost_toxicity_rat_skin_ld50 ckpt_path=https://api.blackhole.ai.innopolis.university/pretrained/catboost_toxisity_rat_skin_ld50.pickle

examples/admet/toxisity_rat_skin_ld50/train_catboost.bat

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_rat_skin_ld50

examples/admet/toxisity_rat_skin_ld50/train_catboost.sh

@@ -0,0 +1 @@
+python train.py experiments=regression/GR_221024_catboost_toxicity_rat_skin_ld50