Duplicate from jannisborn/gt4sd-moler

.gitattributes

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+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
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+*.lfs.* filter=lfs diff=lfs merge=lfs -text
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+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
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.gitignore

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+__pycache__/

LICENSE

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+MIT License
+
+Copyright (c) 2022 Generative Toolkit 4 Scientific Discovery
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+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.

README.md

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+---
+title: GT4SD - MoLeR
+emoji: 💡
+colorFrom: green
+colorTo: blue
+sdk: gradio
+sdk_version: 3.9.1
+app_file: app.py
+pinned: false
+python_version: 3.8.13
+pypi_version: 20.2.4
+duplicated_from: jannisborn/gt4sd-moler
+---
+
+Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

app.py

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+import logging
+import pathlib
+
+import gradio as gr
+import pandas as pd
+from gt4sd.algorithms.generation.moler import MoLeR, MoLeRDefaultGenerator
+
+from gt4sd.algorithms.registry import ApplicationsRegistry
+from utils import draw_grid_generate
+
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+
+TITLE = "MoLeR"
+
+
+def run_inference(
+    algorithm_version: str,
+    scaffolds: str,
+    beam_size: int,
+    number_of_samples: int,
+    seed: int,
+):
+    config = MoLeRDefaultGenerator(
+        algorithm_version=algorithm_version,
+        scaffolds=scaffolds,
+        beam_size=beam_size,
+        num_samples=4,
+        seed=seed,
+        num_workers=1,
+    )
+    model = MoLeR(configuration=config)
+    samples = list(model.sample(number_of_samples))
+
+    seed_mols = [] if scaffolds == "" else scaffolds.split(".")
+    return draw_grid_generate(seed_mols, samples)
+
+
+if __name__ == "__main__":
+
+    # Preparation (retrieve all available algorithms)
+    all_algos = ApplicationsRegistry.list_available()
+    algos = [
+        x["algorithm_version"]
+        for x in list(filter(lambda x: TITLE in x["algorithm_name"], all_algos))
+    ]
+
+    # Load metadata
+    metadata_root = pathlib.Path(__file__).parent.joinpath("model_cards")
+
+    examples = pd.read_csv(metadata_root.joinpath("examples.csv"), header=None).fillna(
+        ""
+    )
+
+    with open(metadata_root.joinpath("article.md"), "r") as f:
+        article = f.read()
+    with open(metadata_root.joinpath("description.md"), "r") as f:
+        description = f.read()
+
+    demo = gr.Interface(
+        fn=run_inference,
+        title="MoLeR (MOlecule-LEvel Representation)",
+        inputs=[
+            gr.Dropdown(algos, label="Algorithm version", value="v0"),
+            gr.Textbox(
+                label="Scaffolds",
+                placeholder="CC(C#C)N(C)C(=O)NC1=CC=C(Cl)C=C1",
+                lines=1,
+            ),
+            gr.Slider(minimum=1, maximum=5, value=1, step=1, label="Beam_size"),
+            gr.Slider(
+                minimum=1, maximum=50, value=10, label="Number of samples", step=1
+            ),
+            gr.Number(value=42, label="Seed", precision=0),
+        ],
+        outputs=gr.HTML(label="Output"),
+        article=article,
+        description=description,
+        examples=examples.values.tolist(),
+    )
+    demo.launch(debug=True, show_error=True)

model_cards/article.md

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+# Model documentation & parameters
+
+**Algorithm Version**: Which model checkpoint to use (trained on different datasets).
+
+**Scaffolds**: One or multiple scaffolds (or seed molecules), provided as '.'-separated SMILES. If empty, no scaffolds are used.
+
+**Number of samples**: How many samples should be generated (between 1 and 50).
+
+**Beam size**: Beam size used in beam search decoding (the higher the slower but better).
+
+**Seed**: The random seed used for initialization.
+
+
+# Model card
+
+**Model Details**: MoLeR is a graph-based molecular generative model that can be conditioned (primed) on scaffolds. The model decorates scaffolds with realistic structural motifs.
+
+**Developers**: Krzysztof Maziarz and co-authors from Microsoft Research and Novartis (full reference at bottom).
+
+**Distributors**: Developer's code wrapped and distributed by GT4SD Team (2023) from IBM Research.
+
+**Model date**: Released around March 2022.
+
+**Model version**: Model provided by original authors, see [their GitHub repo](https://github.com/microsoft/molecule-generation).
+
+**Model type**: An encoder-decoder-based GNN for molecular generation.
+
+**Information about training algorithms, parameters, fairness constraints or other applied approaches, and features**: Trained by the original authors with the default parameters provided [on GitHub](https://github.com/microsoft/molecule-generation).
+
+**Paper or other resource for more information**: [Learning to Extend Molecular Scaffolds with Structural Motifs (ICLR 2022)](https://openreview.net/forum?id=ZTsoE8G3GG).
+
+**License**: MIT
+
+**Where to send questions or comments about the model**: Open an issue on original author's [GitHub repository](https://github.com/microsoft/molecule-generation).
+
+**Intended Use. Use cases that were envisioned during development**: Chemical research, in particular drug discovery.
+
+**Primary intended uses/users**: Researchers and computational chemists using the model for model comparison or research exploration purposes.
+
+**Out-of-scope use cases**: Production-level inference, producing molecules with harmful properties.
+
+**Factors**: Not applicable.
+
+**Metrics**: Validation loss on decoding correct molecules. Evaluated on several downstream tasks.
+
+**Datasets**: 1.5M drug-like molecules from GuacaMol benchmark. Finetuning on 20 molecular optimization tasks from GuacaMol.
+
+**Ethical Considerations**: Unclear, please consult with original authors in case of questions.
+
+**Caveats and Recommendations**: Unclear, please consult with original authors in case of questions.
+
+Model card prototype inspired by [Mitchell et al. (2019)](https://dl.acm.org/doi/abs/10.1145/3287560.3287596?casa_token=XD4eHiE2cRUAAAAA:NL11gMa1hGPOUKTAbtXnbVQBDBbjxwcjGECF_i-WC_3g1aBgU1Hbz_f2b4kI_m1in-w__1ztGeHnwHs)
+
+## Citation
+
+```bib
+@inproceedings{maziarz2021learning,
+  author={Krzysztof Maziarz and Henry Richard Jackson{-}Flux and Pashmina Cameron and
+    Finton Sirockin and Nadine Schneider and Nikolaus Stiefl and Marwin H. S. Segler and Marc Brockschmidt},
+  title     = {Learning to Extend Molecular Scaffolds with Structural Motifs},
+  booktitle = {The Tenth International Conference on Learning Representations, {ICLR}},
+  year      = {2022}
+}
+```
+

model_cards/description.md

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+<img align="right" src="https://raw.githubusercontent.com/GT4SD/gt4sd-core/main/docs/_static/gt4sd_logo.png" alt="logo" width="120" >
+
+MoLeR ([Maziarz et al., (2022), *ICLR*](https://openreview.net/forum?id=ZTsoE8G3GG)) is a graph-based molecular generative model that can be conditioned (primed) on scaffolds. This model is provided and distributed by the **GT4SD** (Generative Toolkit for Scientific Discovery).
+
+For **examples** and **documentation** of the model parameters, please see below.
+Moreover, we provide a **model card** ([Mitchell et al. (2019)](https://dl.acm.org/doi/abs/10.1145/3287560.3287596?casa_token=XD4eHiE2cRUAAAAA:NL11gMa1hGPOUKTAbtXnbVQBDBbjxwcjGECF_i-WC_3g1aBgU1Hbz_f2b4kI_m1in-w__1ztGeHnwHs)) at the bottom of this page.

model_cards/examples.csv

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+v0,,1,4,0
+v0,CC(=O)NC1=NC2=CC(OCC3=CC=CN(CC4=CC=C(Cl)C=C4)C3=O)=CC=C2N1,1,10,0
+v0,C12C=CC=NN1C(C#CC1=C(C)C=CC3C(NC4=CC(C(F)(F)F)=CC=C4)=NOC1=3)=CN=2.CCO,3,5,5
+
+

requirements.txt

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+-f https://download.pytorch.org/whl/cpu/torch_stable.html
+-f https://data.pyg.org/whl/torch-1.12.1+cpu.html
+# pip==20.2.4
+torch==1.12.1
+torch-scatter
+torch-spline-conv
+torch-sparse
+torch-geometric
+torchvision==0.13.1
+torchaudio==0.12.1
+gt4sd>=1.0.0
+molgx>=0.22.0a1
+molecule_generation
+nglview
+PyTDC==0.3.7
+gradio==3.12.0
+markdown-it-py>=2.1.0
+mols2grid>=0.2.0
+numpy==1.23.5
+pandas>=1.0.0
+terminator @ git+https://github.com/IBM/regression-transformer@gt4sd
+guacamol_baselines @ git+https://github.com/GT4SD/guacamol_baselines.git@v0.0.2
+moses @ git+https://github.com/GT4SD/moses.git@v0.1.0
+paccmann_chemistry @ git+https://github.com/PaccMann/paccmann_chemistry@0.0.4
+paccmann_generator @ git+https://github.com/PaccMann/paccmann_generator@0.0.2
+paccmann_gp @ git+https://github.com/PaccMann/paccmann_gp@0.1.1
+paccmann_omics @ git+https://github.com/PaccMann/paccmann_omics@0.0.1.1
+paccmann_predictor @ git+https://github.com/PaccMann/paccmann_predictor@sarscov2
+reinvent_models @ git+https://github.com/GT4SD/reinvent_models@v0.0.1

utils.py

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+import json
+import logging
+import os
+from collections import defaultdict
+from typing import Dict, List, Tuple
+
+import mols2grid
+import pandas as pd
+from rdkit import Chem
+from terminator.selfies import decoder
+
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+
+
+def draw_grid_generate(
+    seeds: List[str],
+    samples: List[str],
+    n_cols: int = 3,
+    size=(140, 200),
+) -> str:
+    """
+    Uses mols2grid to draw a HTML grid for the generated molecules
+
+    Args:
+        samples: The generated samples.
+        n_cols: Number of columns in grid. Defaults to 5.
+        size: Size of molecule in grid. Defaults to (140, 200).
+
+    Returns:
+        HTML to display
+    """
+
+    result = defaultdict(list)
+    result.update(
+        {
+            "SMILES": seeds + samples,
+            "Name": [f"Seed_{i}" for i in range(len(seeds))]
+            + [f"Generated_{i}" for i in range(len(samples))],
+        },
+    )
+
+    result_df = pd.DataFrame(result)
+    obj = mols2grid.display(
+        result_df,
+        tooltip=list(result.keys()),
+        height=1100,
+        n_cols=n_cols,
+        name="Results",
+        size=size,
+    )
+    return obj.data