remedi 0.1.0__tar.gz

remedi-0.1.0/.github/workflows/python-app.yml

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+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.12"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        pip install .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest tests/

remedi-0.1.0/.github/workflows/release.yml

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+name: Release to PyPI
+
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch: # build-only dry run (no publish unless a tag triggered it)
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - name: Build sdist + wheel
+        run: uv build
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    # Only publish on a tag push; workflow_dispatch just builds above.
+    if: startsWith(github.ref, 'refs/tags/v')
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write # OIDC token for PyPI Trusted Publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1

remedi-0.1.0/.gitignore

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+__pycache__/
+datasets/
+figures/
+transformer_model/
+mace_model/
+.ruff_cache
+wandb
+.pytest_cache
+.vscode/
+eval_runs/
+training_runs/
+notebooks/
+backed_up_models/
+*.log
+raw_datasets/
+dataset
+uv.lock
+.claude
+.env
+CLAUDE.md
+*.model
+*.err
+*.out
+analysis_output/
+/submit_*.sh

remedi-0.1.0/.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+    -   id: check-added-large-files
+        args: ['--maxkb=1000']
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.6.9
+  hooks:
+  - id: ruff
+    args: ["--fix"]
+  - id: ruff-format

remedi-0.1.0/LICENSE

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+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
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remedi-0.1.0/NOTICE

@@ -0,0 +1,19 @@
+Rem3Di (remedi)
+Copyright 2026 The Rem3Di Authors
+
+This product includes software developed for the paper:
+  "Rem3Di: Learning smooth, chiral 3D molecular descriptors from atomistic
+   foundation models", NeurIPS 2025 Workshop on Symmetry and Geometry in
+   Neural Representations.
+
+Origin and attribution:
+  Source        https://github.com/molsuit/Rem3Di
+  Documentation https://molsuit.github.io/Rem3Di/
+  Paper         https://openreview.net/forum?id=jOmZsvXoK5
+
+If you use this software in academic or derivative work, please retain this
+notice and cite the paper above.
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use
+these files except in compliance with the License. See the LICENSE file for the
+full terms.

remedi-0.1.0/PKG-INFO

@@ -0,0 +1,161 @@
+Metadata-Version: 2.4
+Name: remedi
+Version: 0.1.0
+Summary: Smooth, chiral 3D molecular descriptors from atomistic foundation models
+Project-URL: Homepage, https://molsuit.github.io/Rem3Di/
+Project-URL: Documentation, https://molsuit.github.io/Rem3Di/
+Project-URL: Repository, https://github.com/molsuit/Rem3Di
+Project-URL: Paper, https://openreview.net/forum?id=jOmZsvXoK5
+Author: The Rem3Di Authors
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Keywords: cheminformatics,chirality,equivariant,mace,machine-learned-interatomic-potentials,molecular-descriptors
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.12
+Requires-Dist: ase>=3.24.0
+Requires-Dist: chemiscope>=1.0.3
+Requires-Dist: datashader>=0.19.0
+Requires-Dist: pyarrow
+Requires-Dist: pydantic
+Requires-Dist: pydantic-yaml
+Requires-Dist: pymatgen>=2026.3.23
+Requires-Dist: pytdc>=0.3.6
+Requires-Dist: rdkit>=2024.9.4
+Requires-Dist: umap-learn
+Requires-Dist: wandb
+Requires-Dist: zarr>=3.2
+Provides-Extra: cpu
+Requires-Dist: mace-torch>=0.3.16; extra == 'cpu'
+Requires-Dist: torch-sim-atomistic; extra == 'cpu'
+Requires-Dist: torch>=2.5.1; extra == 'cpu'
+Provides-Extra: cuda
+Requires-Dist: cuequivariance-ops-torch-cu12==0.9.1; extra == 'cuda'
+Requires-Dist: cuequivariance-torch==0.9.1; extra == 'cuda'
+Requires-Dist: cuequivariance==0.9.1; extra == 'cuda'
+Requires-Dist: mace-torch>=0.3.16; extra == 'cuda'
+Requires-Dist: nvidia-cusparselt-cu12; extra == 'cuda'
+Requires-Dist: nvmolkit>=0.5.0; extra == 'cuda'
+Requires-Dist: torch-sim-atomistic; extra == 'cuda'
+Requires-Dist: torch>=2.5.1; extra == 'cuda'
+Provides-Extra: eval
+Requires-Dist: bblean>=0.10.3; extra == 'eval'
+Requires-Dist: lightgbm>=4.6.0; extra == 'eval'
+Requires-Dist: molfeat; extra == 'eval'
+Requires-Dist: pandas; extra == 'eval'
+Requires-Dist: pyyaml; extra == 'eval'
+Requires-Dist: scikit-learn; extra == 'eval'
+Requires-Dist: scipy; extra == 'eval'
+Description-Content-Type: text/markdown
+
+# Rem3Di: REpresentation learning for Molecules with 3D Information
+
+<div align="center">
+  <b>Learning smooth, chiral 3D molecular representations from equivariant atomistic foundation models</b>
+  <br> <br>
+  <a href="https://www.linkedin.com/in/steffen-wedig/" target="_blank">Steffen&nbsp;Wedig</a> &emsp; <b>&middot;</b> &emsp;
+  <a href="https://www.felixburton.com" target="_blank">Felix&nbsp;Burton</a> &emsp; <b>&middot;</b> &emsp;
+  <a href="https://www.linkedin.com/in/rokas-elijošius-9148a8147/" target="_blank">Rokas&nbsp;Elijošius</a><sup>*</sup> &emsp; <b>&middot;</b> &emsp;
+  <a href="https://www.phy.cam.ac.uk/profile/dr-christoph-schran/" target="_blank">Christoph&nbsp;Schran</a><sup>*</sup> &emsp; <b>&middot;</b> &emsp;
+  <a href="https://www.larsschaaf.com" target="_blank">Lars&nbsp;L.&nbsp;Schaaf</a><sup>*</sup>
+  <br> <br>
+  <a href="https://openreview.net/forum?id=jOmZsvXoK5&referrer" target="_blank"><b><u>Paper Link</u></b></a>
+  &emsp;
+  <a href="https://molsuit.github.io/Rem3Di/" target="_blank"><img alt="Documentation" src="https://img.shields.io/badge/Documentation-online-blue"></a>
+  <br> <br>
+</div>
+
+<div align="center">
+    <img width="600" alt="Rem3Di" src="docs/header-rem3di.jpg"/>
+</div>
+
+
+## Documentation
+
+📖 Full usage docs — installation, quickstart, evaluating models, training downstream
+heads, training from scratch, and concepts — are online at
+**<https://molsuit.github.io/Rem3Di/>**.
+
+
+
+## Setup
+1. pip install from pyproject.toml
+2. Additionally clone and install a torch-sim fork from https://github.com/steffen-wedig/torch-sim
+
+
+## Raw dataset download
+We work with a number of different datasets for benchmarking Rem3Di.
+
+Scripts to download these datasets from can be found in scripts/dataset_download. All scripts take the target destination folder as their first argument.
+
+Example: Geom Drugs can be downloaded by:
+
+```bash
+mkdir raw_datasets
+bash scripts/dataset_download/download_geomdrugs.sh ./raw_datasets
+```
+
+## Generating a MoleculeDataset for Training
+TL;DR: We generate molecular datasets containing molecular structures and their mace descriptors from various sources, examples can be found in ```scripts/dataset_creation```.
+
+
+### Dataset Overview
+MoleculeDatasets (```remedi/data_handling/dataset/molecule_dataset.py```) is the object that contains all embedding and structural data for our molecular datasets. The datasets can further contain system wide, molecular labels, or atomwise labels, which can be used for training regression models. Our datasets are backed by zarr arrays(Design motivitation: multithreaded read access from disk, when dataset size exceeds memory limit). As the size of molecules varies, the MoleculeDataset contain pointer values that point to the molecules atom limits.
+
+### Dataset Generation
+Dataset generation is implemented batchwise to increase performance, as GPU memory can be fully utilized in this way. The pipeline goes through the following stages.
+
+1. MoleculeGenerators yield batches of smiles or processed ase atoms, in case the molecular structures are available in the datasets. For a new data source, like a new dataset that stores molecular data in its own way, you need to implement a new MoleculeGenerator.
+2. Configurable Orchestrator will execute the pipeline. E.g. perform conformal sampling, relaxation. Lastly, the mace descriptors will be configured
+3. Everything (Embeddings, structures, optional system wide or atom wise regression labels) will be shoved into the right zarr arrays in the MoleculeDataset.
+
+## Running Pretraining
+1. Create a training dir with a training_config.yaml and architecture_config.yaml **or** generate the architecture_config.yaml with the scripts/write_config_file.py script. In the train dir
+2. Run pretrainig via scripts/scripts/run_denoising_pretraining.py --train_dir "dir"
+
+One note re. training: For training we create new dataset object (class TrainingMoleculeDataset). This contains additionally logic how multiple dataloader workers can simulatounsly retireve data from the same zarr files.
+
+
+## Using Pretrained Model
+
+
+
+```python
+import torch
+from remedi.configuration.architecture_config import EncoderOnlyArchitectureConfig
+from remedi.evaluation.evaluation_utils import evaluate_molecular_descriptor_on_dataset
+from remedi.data_handling.dataset.training_dataset import (
+    TrainingMoleculeDataset,
+    pos_emb_getitem,
+)
+ds = TrainingMoleculeDataset(training_config.dataset_path, get_item=pos_emb_getitem)
+model = EncoderOnlyArchitectureConfig.from_directory(model_dir).build()
+model.encoder.load_state_dict(torch.load(f"{model_dir}/encoder.pth"))
+model.preprocessor.atomic_preprocessor.load_state_dict(
+    torch.load(f"{model_dir}/atomic_preprocessor.pth")
+)
+model.preprocessor.geometric_preprocessor.load_state_dict(
+    torch.load(f"{model_dir}/geometric_preprocessor.pth")
+)
+remedi_descriptors = evaluate_molecular_descriptor_on_dataset(model, ds)
+```
+
+## Citation
+
+If you use any of this code in your work, please cite our paper
+(<a href="https://openreview.net/forum?id=jOmZsvXoK5&referrer" target="_blank">OpenReview</a>):
+
+> Wedig, Steffen, et al. <a href="https://openreview.net/forum?id=jOmZsvXoK5&referrer" target="_blank">"REM3DI: Learning smooth, chiral 3D molecular representations from equivariant atomistic foundation models."</a> NeurIPS 2025 Workshop on Symmetry and Geometry in Neural Representations. 2025.
+
+```bibtex
+@inproceedings{wedig2025rem3di,
+  title={REM3DI: Learning smooth, chiral 3D molecular representations from equivariant atomistic foundation models},
+  author={Wedig, Steffen and Elijo{\v{s}}ius, Rokas and Schran, Christoph and Schaaf, Lars Leon},
+  booktitle={NeurIPS 2025 Workshop on Symmetry and Geometry in Neural Representations},
+  year={2025}
+}
+```

remedi-0.1.0/README.md

@@ -0,0 +1,107 @@
+# Rem3Di: REpresentation learning for Molecules with 3D Information
+
+<div align="center">
+  <b>Learning smooth, chiral 3D molecular representations from equivariant atomistic foundation models</b>
+  <br> <br>
+  <a href="https://www.linkedin.com/in/steffen-wedig/" target="_blank">Steffen&nbsp;Wedig</a> &emsp; <b>&middot;</b> &emsp;
+  <a href="https://www.felixburton.com" target="_blank">Felix&nbsp;Burton</a> &emsp; <b>&middot;</b> &emsp;
+  <a href="https://www.linkedin.com/in/rokas-elijošius-9148a8147/" target="_blank">Rokas&nbsp;Elijošius</a><sup>*</sup> &emsp; <b>&middot;</b> &emsp;
+  <a href="https://www.phy.cam.ac.uk/profile/dr-christoph-schran/" target="_blank">Christoph&nbsp;Schran</a><sup>*</sup> &emsp; <b>&middot;</b> &emsp;
+  <a href="https://www.larsschaaf.com" target="_blank">Lars&nbsp;L.&nbsp;Schaaf</a><sup>*</sup>
+  <br> <br>
+  <a href="https://openreview.net/forum?id=jOmZsvXoK5&referrer" target="_blank"><b><u>Paper Link</u></b></a>
+  &emsp;
+  <a href="https://molsuit.github.io/Rem3Di/" target="_blank"><img alt="Documentation" src="https://img.shields.io/badge/Documentation-online-blue"></a>
+  <br> <br>
+</div>
+
+<div align="center">
+    <img width="600" alt="Rem3Di" src="docs/header-rem3di.jpg"/>
+</div>
+
+
+## Documentation
+
+📖 Full usage docs — installation, quickstart, evaluating models, training downstream
+heads, training from scratch, and concepts — are online at
+**<https://molsuit.github.io/Rem3Di/>**.
+
+
+
+## Setup
+1. pip install from pyproject.toml
+2. Additionally clone and install a torch-sim fork from https://github.com/steffen-wedig/torch-sim
+
+
+## Raw dataset download
+We work with a number of different datasets for benchmarking Rem3Di.
+
+Scripts to download these datasets from can be found in scripts/dataset_download. All scripts take the target destination folder as their first argument.
+
+Example: Geom Drugs can be downloaded by:
+
+```bash
+mkdir raw_datasets
+bash scripts/dataset_download/download_geomdrugs.sh ./raw_datasets
+```
+
+## Generating a MoleculeDataset for Training
+TL;DR: We generate molecular datasets containing molecular structures and their mace descriptors from various sources, examples can be found in ```scripts/dataset_creation```.
+
+
+### Dataset Overview
+MoleculeDatasets (```remedi/data_handling/dataset/molecule_dataset.py```) is the object that contains all embedding and structural data for our molecular datasets. The datasets can further contain system wide, molecular labels, or atomwise labels, which can be used for training regression models. Our datasets are backed by zarr arrays(Design motivitation: multithreaded read access from disk, when dataset size exceeds memory limit). As the size of molecules varies, the MoleculeDataset contain pointer values that point to the molecules atom limits.
+
+### Dataset Generation
+Dataset generation is implemented batchwise to increase performance, as GPU memory can be fully utilized in this way. The pipeline goes through the following stages.
+
+1. MoleculeGenerators yield batches of smiles or processed ase atoms, in case the molecular structures are available in the datasets. For a new data source, like a new dataset that stores molecular data in its own way, you need to implement a new MoleculeGenerator.
+2. Configurable Orchestrator will execute the pipeline. E.g. perform conformal sampling, relaxation. Lastly, the mace descriptors will be configured
+3. Everything (Embeddings, structures, optional system wide or atom wise regression labels) will be shoved into the right zarr arrays in the MoleculeDataset.
+
+## Running Pretraining
+1. Create a training dir with a training_config.yaml and architecture_config.yaml **or** generate the architecture_config.yaml with the scripts/write_config_file.py script. In the train dir
+2. Run pretrainig via scripts/scripts/run_denoising_pretraining.py --train_dir "dir"
+
+One note re. training: For training we create new dataset object (class TrainingMoleculeDataset). This contains additionally logic how multiple dataloader workers can simulatounsly retireve data from the same zarr files.
+
+
+## Using Pretrained Model
+
+
+
+```python
+import torch
+from remedi.configuration.architecture_config import EncoderOnlyArchitectureConfig
+from remedi.evaluation.evaluation_utils import evaluate_molecular_descriptor_on_dataset
+from remedi.data_handling.dataset.training_dataset import (
+    TrainingMoleculeDataset,
+    pos_emb_getitem,
+)
+ds = TrainingMoleculeDataset(training_config.dataset_path, get_item=pos_emb_getitem)
+model = EncoderOnlyArchitectureConfig.from_directory(model_dir).build()
+model.encoder.load_state_dict(torch.load(f"{model_dir}/encoder.pth"))
+model.preprocessor.atomic_preprocessor.load_state_dict(
+    torch.load(f"{model_dir}/atomic_preprocessor.pth")
+)
+model.preprocessor.geometric_preprocessor.load_state_dict(
+    torch.load(f"{model_dir}/geometric_preprocessor.pth")
+)
+remedi_descriptors = evaluate_molecular_descriptor_on_dataset(model, ds)
+```
+
+## Citation
+
+If you use any of this code in your work, please cite our paper
+(<a href="https://openreview.net/forum?id=jOmZsvXoK5&referrer" target="_blank">OpenReview</a>):
+
+> Wedig, Steffen, et al. <a href="https://openreview.net/forum?id=jOmZsvXoK5&referrer" target="_blank">"REM3DI: Learning smooth, chiral 3D molecular representations from equivariant atomistic foundation models."</a> NeurIPS 2025 Workshop on Symmetry and Geometry in Neural Representations. 2025.
+
+```bibtex
+@inproceedings{wedig2025rem3di,
+  title={REM3DI: Learning smooth, chiral 3D molecular representations from equivariant atomistic foundation models},
+  author={Wedig, Steffen and Elijo{\v{s}}ius, Rokas and Schran, Christoph and Schaaf, Lars Leon},
+  booktitle={NeurIPS 2025 Workshop on Symmetry and Geometry in Neural Representations},
+  year={2025}
+}
+```

remedi-0.1.0/configs/dataset_creation/benchmarks_local.yaml

@@ -0,0 +1,24 @@
+# Local benchmark dataset-build config — invoked by
+# `scripts/dataset_creation/build_benchmark_dataset.py`. Builds every
+# registered MoleculeNet + TDC ADMET benchmark; re-running is idempotent
+# (datasets whose zarr subdir already exists are skipped).
+
+output_root: /path/to/datasets/benchmarks
+moleculenet_raw_root: /path/to/molecule_net
+tdc_cache: /path/to/datasets/tdc_cache
+polaris_raw_root: /path/to/raw_datasets/polaris
+
+batch_size: 256
+n_sampled_conformers: 1
+max_embed_attempts: 200
+max_mmff_steps: 100
+mmff_non_bonded_thresh: 100.0
+
+tdc_train_valid_seed: 1
+
+filter:
+  max_atoms: 100
+  element_set: mace_off
+  strip_salts: true
+  neutralize: true
+  dedupe: true