Model history

Model validation reports:

• Validation report: extend_v1
• Validation report: extend_v2
• Validation report: bridge_v1

Read more about the validation methodology below.

Validation methodology

For each model validation, depending on the type of model, chempleter.inference.extend or chempleter.inference.bridge are used. Metrics and descriptors are calculated for N (500, by default) random samples. See chempleter.validate module for the source code.

Generation Quality Metrics

The following metrics assess the quality of the generated molecules:

Generation Quality Metrics

Metric	Description
Uniqueness	Fraction of generated molecules that are unique. Computed as the number of distinct SMILES strings divided by the total number of generated molecules.
Novelty	Fraction of generated molecules not present in the training dataset. Computed by comparing the set of generated SMILES to the reference SMILES dataset and calculating the proportion that are new.
SELFIES fidelity	Measures the encoding fidelity of the SELFIES representation. Computed as the average fraction of tokens in the generated SELFIES that are ignored when re-encoding the molecule back to SELFIES via from generated SMILES. Lower values indicate that a low fraction of generated tokens are ignored due to the decoding or the model is generating more valid molecules.

Descriptor statistics

The following descriptors (as implemented in RDKit) and their distirbutions summarize the physicochemical and structural properties of the generated molecules:

Descriptor Statistics

Descriptor	Description
MW	Molecular Weight. Average, min, and max over generated molecules.
LogP	Octanol-water partition coefficient. Indicates lipophilicity.
SA_Score	Synthetic Accessibility Score. Estimates ease of chemical synthesis (1 = easy, 10 = difficult).
QED	Quantitative Estimate of Drug-likeness (0–1). Higher is more drug-like.
Fsp3	Fraction of sp3 hybridized carbons.
RotatableBonds	Number of rotatable bonds. Indicates molecular flexibility.
RingCount	Number of rings present in the molecule.
TPSA	Topological Polar Surface Area. Correlates with permeability and solubility.
RadicalElectrons	Number of unpaired electrons (radicals) in the molecule.