ersiliaos/eos2db3 repository overview

⁠Chemical space 2D projections against ChemDiv

This tool performs PCA, UMAP and tSNE projections taking a 100k ChemDiv diversity set as a chemical space of reference. The Ersilia Compound Embeddings are used as descriptors. Four PCA components and two UMAP and tSNE components are returned.

This model was incorporated on 2024-11-09.Last packaged on 2026-03-09.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos2db3
• Slug: chemical-space-projections-chemdiv

⁠Domain

• Task: Representation
• Subtask: Projection
• Biomedical Area: Any
• Target Organism: Any
• Tags: Embedding

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 8
• Output Consistency: Fixed
• Interpretation: Coordinates of 2D projections, namely PCA, UMAP and tSNE.

Below are the Output Columns of the model:

⁠Source and Deployment

• Source: Local
• Source Type: Internal
• DockerHub: https://hub.docker.com/r/ersiliaos/eos2db3⁠
• Docker Architecture: AMD64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos2db3.zip⁠

⁠Resource Consumption

• Model Size (Mb): 1470
• Environment Size (Mb): 1010
• Image Size (Mb): 5423.93

Computational Performance (seconds):

• 10 inputs: 72.47
• 100 inputs: 62.01
• 10000 inputs: 1502.98

⁠References

• Source Code: https://github.com/ersilia-os/compound-embedding⁠
• Publication: https://www.chemdiv.com/catalog/diversity-libraries/representative-diversity-libraries-out-of-1-6m-stock/⁠
• Publication Type: Other
• Publication Year: 2024
• Ersilia Contributor: miquelduranfrigola⁠

⁠License

This package is licensed under a GPL-3.0⁠ license. The model contained within this package is licensed under a GPL-3.0-or-later⁠ 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 eos2db3

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

# serve the model
ersilia serve eos2db3
# 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!