ersiliaos/eos4rw4 repository overview

⁠Continuous and data-driven descriptor (CDDD)

Encodes a molecule as 512 continuous descriptors taken from the bottleneck of a translation network. Winter and colleagues trained a recurrent encoder-decoder to rewrite a randomised SMILES as the canonical SMILES of the same structure, forcing the latent vector to carry the molecule rather than the string, and pre-trained it on roughly 72 million compounds merged from ZINC and PubChem. Ersilia serves the ONNX port of the encoder. Molecules it cannot embed (invalid SMILES, non-organic, very small or very large compounds) return empty values.

This model was incorporated on 2025-11-29.Last packaged on 2026-10-15.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos4rw4
• Slug: cddd-onnx

⁠Domain

• Task: Representation
• Subtask: Featurization
• Biomedical Area: Any
• Target Organism: Any
• Tags: Embedding, Descriptor, Chemical language model

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 512
• Output Consistency: Fixed
• Interpretation: 512 continuous descriptors learned by translating between molecular string representations. Empty values mean an invalid SMILES or a molecule outside the encoders domain (atoms other than B, C, N, O, F, P, S, Cl, Br, I; MW 12-600; 4-49 heavy atoms; logP -5 to 7).

Below are the Output Columns of the model:

10 of 512 columns are shown

⁠Source and Deployment

• Source: Local
• Source Type: External
• DockerHub: https://hub.docker.com/r/ersiliaos/eos4rw4⁠
• Docker Architecture: AMD64, ARM64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos4rw4.zip⁠

⁠Resource Consumption

• Model Size (Mb): 1413
• Environment Size (Mb): 996
• Image Size (Mb): 3804.97

Computational Performance (seconds):

• 10 inputs: 30.94
• 100 inputs: 18.9
• 10000 inputs: 168.6

⁠References

• Source Code: https://github.com/sergsb/cddd-onnx⁠
• Publication: https://doi.org/10.1039/c8sc04175j⁠
• Publication Type: Peer reviewed
• Publication Year: 2019
• Ersilia Contributor: GemmaTuron⁠

⁠License

This package is licensed under a GPL-3.0⁠ license. The model contained within this package is licensed under a MIT⁠ license.

Notice: Ersilia grants access to models as is, directly from the original authors, please refer to the original code repository and/or publication if you use the model in your research.

⁠Use

To use this model locally, you need to have the Ersilia CLI⁠ installed. The model can be fetched using the following command:

# fetch model from the Ersilia Model Hub
ersilia fetch eos4rw4

Then, you can serve, run and close the model as follows:

# serve the model
ersilia serve eos4rw4
# generate an example file
ersilia example -n 3 -f my_input.csv
# run the model
ersilia run -i my_input.csv -o my_output.csv
# close the model
ersilia close

⁠About Ersilia

The Ersilia Open Source Initiative⁠ is a tech non-profit organization fueling sustainable research in the Global South. Please cite⁠ the Ersilia Model Hub if you've found this model to be useful. Always let us know⁠ if you experience any issues while trying to run it. If you want to contribute to our mission, consider donating⁠ to Ersilia!