model_cards/article.md

# Model documentation & parameters

**Algorithm Version**: Which model version (either protein-target-driven or gene-expression-profile-driven) to use and which checkpoint to rely on.

**Inference type**: Whether the model should be conditioned on the target (default) or whether the model is used in an  `Unbiased` manner.

**Protein target**: An AAS of a protein target used for conditioning. Only use if `Inference type` is `Conditional` and if the `Algorithm version` is a Protein model.

**Gene expression target**: A list of 2128 floats, representing the embedding of gene expression profile to be used for conditioning. Only use if `Inference type` is `Conditional` and if the `Algorithm version` is a Omic model.

**Decoding temperature**: The temperature parameter in the SMILES/SELFIES decoder. Higher values lead to more explorative choices, smaller values culminate in mode collapse.

**Maximal sequence length**: The maximal number of SMILES tokens in the generated molecule.

**Number of samples**: How many samples should be generated (between 1 and 50).


# Model card -- PaccMannRL

**Model Details**: PaccMannRL is a language model for conditional molecular design. It consists of a domain-specific encoder (for protein targets or gene expression profiles) and a generic molecular decoder. Both components are finetuned together using RL to convert the context representation into a molecule with high affinity toward the context (i.e., binding affinity to the protein or high inhibitory effect for the cell profile).

**Developers**: Jannis Born, Matteo Manica and colleagues from IBM Research.

**Distributors**: Original authors' code wrapped and distributed by GT4SD Team (2023) from IBM Research.

**Model date**: Published in 2021.

**Model version**: Models trained and distribuetd by the original authors.
- **Protein_v0**: Molecular decoder pretrained on 1.5M molecules from ChEMBL. Protein encoder pretrained on 404k proteins from UniProt. Encoder and decoder finetuned on 41 SARS-CoV-2-related protein targets with a binding affinity predictor trained on BindingDB.
- **Omic_v0**: Molecular decoder pretrained on 1.5M molecules from ChEMBL. Gene expression encoder pretrained on 12k gene expression profiles from TCGA. Encoder and decoder finetuned on a few hundred cancer cell profiles from GDSC with a IC50 predictor trained on GDSC.

**Model type**: A language-based molecular generative model that can be optimized with RL to generate molecules with high affinity toward a context.

**Information about training algorithms, parameters, fairness constraints or other applied approaches, and features**: 
- **Protein**: Parameters as provided on [(GitHub repo)](https://github.com/PaccMann/paccmann_sarscov2).
- **Omics**: Parameters as provided on [(GitHub repo)](https://github.com/PaccMann/paccmann_rl).

**Paper or other resource for more information**: 
- **Protein**: [PaccMannRL: De novo generation of hit-like anticancer molecules from transcriptomic data via reinforcement learning (2021; *iScience*)](https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6).
- **Omics**: [Data-driven molecular design for discovery and synthesis of novel ligands: a case study on SARS-CoV-2 (2021; *Machine Learning: Science and Technology*)](https://iopscience.iop.org/article/10.1088/2632-2153/abe808/meta).

**License**: MIT

**Where to send questions or comments about the model**: Open an issue on [GT4SD repository](https://github.com/GT4SD/gt4sd-core).

**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**: High reward on generating molecules with high affinity toward context. 

**Datasets**: ChEMBL, UniProt, GDSC and BindingDB (see above).

**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

**Omics**:
```bib
@article{born2021paccmannrl,
  title = {PaccMann\textsuperscript{RL}: De novo generation of hit-like anticancer molecules from transcriptomic data via reinforcement learning},
  journal = {iScience},
  volume = {24},
  number = {4},
  pages = {102269},
  year = {2021},
  issn = {2589-0042},
  doi = {https://doi.org/10.1016/j.isci.2021.102269},
  url = {https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6},
  author = {Born, Jannis and Manica, Matteo and Oskooei, Ali and Cadow, Joris and Markert, Greta and {Rodr{\'{i}}guez Mart{\'{i}}nez}, Mar{\'{i}}a}
}
```

**Proteins**:
```bib
@article{born2021datadriven,
  author = {Born, Jannis and Manica, Matteo and Cadow, Joris and Markert, Greta and Mill, Nil Adell and Filipavicius, Modestas and Janakarajan, Nikita and Cardinale, Antonio and Laino, Teodoro and {Rodr{\'{i}}guez Mart{\'{i}}nez}, Mar{\'{i}}a},
  doi = {10.1088/2632-2153/abe808},
  issn = {2632-2153},
  journal = {Machine Learning: Science and Technology},
  number = {2},
  pages = {025024},
  title = {{Data-driven molecular design for discovery and synthesis of novel ligands: a case study on SARS-CoV-2}},
  url = {https://iopscience.iop.org/article/10.1088/2632-2153/abe808},
  volume = {2},
  year = {2021}
}
```