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NM Toxicity models integration (#234)
* add mouse oral experiment * add toxisity_rabbit_skin_ld50 model * add toxisity_rat_intravenous_ld50 * add toxisity_rat_oral_ld50 * add toxisity_rat_skin_ld50 * fix typo * add admet examples * fix typo * fix dataset and model path
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|---|---|---|
| @@ -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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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|---|---|---|
| @@ -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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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10
config/experiments/regression/GR_221024_catboost_toxisity_mouse_oral_ld50.yaml
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| # @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} |
10 changes: 10 additions & 0 deletions
10
config/experiments/regression/GR_221024_catboost_toxisity_rabbit_skin_ld50.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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} |
10 changes: 10 additions & 0 deletions
10
config/experiments/regression/GR_221024_catboost_toxisity_rat_intravenous_ld50.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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} |
10 changes: 10 additions & 0 deletions
10
config/experiments/regression/GR_221024_catboost_toxisity_rat_oral_ld50.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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} |
10 changes: 10 additions & 0 deletions
10
config/experiments/regression/GR_221024_catboost_toxisity_rat_skin_ld50.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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} |
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| 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 |
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| 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| python train.py experiments=regression/GR_221024_catboost_toxicity_mouse_oral_ld50 |
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| python train.py experiments=regression/GR_221024_catboost_toxicity_mouse_oral_ld50 |
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| 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 |
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| 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 |
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|---|---|---|
| @@ -0,0 +1 @@ | ||
| python train.py experiments=regression/GR_221024_catboost_toxicity_rabbit_skin_ld50 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| python train.py experiments=regression/GR_221024_catboost_toxicity_rabbit_skin_ld50 |
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examples/admet/toxisity_rat_intravenous_ld50/infer_catboost.bat
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| 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 |
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| 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 |
1 change: 1 addition & 0 deletions
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examples/admet/toxisity_rat_intravenous_ld50/train_catboost.bat
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| python train.py experiments=regression/GR_221024_catboost_toxicity_rat_intravenous_ld50 |
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| python train.py experiments=regression/GR_221024_catboost_toxicity_rat_intravenous_ld50 |
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| 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 |
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| 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 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| python train.py experiments=regression/GR_221024_catboost_toxicity_rat_oral_ld50 |
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| Original file line number | Diff line number | Diff line change |
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| python train.py experiments=regression/GR_221024_catboost_toxicity_rat_oral_ld50 |
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| 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 |
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| 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 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| python train.py experiments=regression/GR_221024_catboost_toxicity_rat_skin_ld50 |
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| python train.py experiments=regression/GR_221024_catboost_toxicity_rat_skin_ld50 |