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README.md
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- **Description:**
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- The model computes antimicrobial predictive probabilities for **40 bacterial strains** contained in [Maier et al., 2018](https://www.nature.com/articles/nature25979), using a two-step process:
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1. Generate molecular embeddings with a pre-trained **GINet** representation model (`model.pth`, `config.yaml`).
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2. Predict antimicrobial properties with a **trained XGBoost** classifier (`MolE-XGBoost-08.03.2024_14.20.pkl`).
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- The scores reflect the likelihood that a compound inhibits the growth of a given bacterial strain.
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- **Training data:** 100000 randomly sampled compounds from ChemBERTa for the pretraining of MolE and data from *Maier et al., 2018* containing the influence of 1197 marketed drugs on the growth of 40 bacterial strains for the XGBoost classifier
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- **Publication:** [Nature Communications (2025)](https://www.nature.com/articles/s41467-025-58804-4)
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- **Description:**
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- The model computes antimicrobial predictive probabilities for **40 bacterial strains** contained in [Maier et al., 2018](https://www.nature.com/articles/nature25979), using a two-step process:
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| 57 |
1. Generate molecular embeddings with a pre-trained **GINet** representation model (`model.pth`, `config.yaml`).
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2. Predict antimicrobial properties with a **trained XGBoost** classifier (`MolE-XGBoost-08.03.2024_14.20.pkl`). The scores reflect the likelihood that a compound inhibits the growth of a given bacterial strain.
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- **Training data:** 100000 randomly sampled compounds from ChemBERTa for the pretraining of MolE and data from *Maier et al., 2018* containing the influence of 1197 marketed drugs on the growth of 40 bacterial strains for the XGBoost classifier
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- **Publication:** [Nature Communications (2025)](https://www.nature.com/articles/s41467-025-58804-4)
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