CIMtools

CIMtools implements specialized cross-validation strategies for cheminformatics QSPR models by applying 'transformation-out' and 'solvent-out' cross-validation to reduce optimistic bias and improve performance estimation on unseen reaction types and solvent conditions.

Key Features:

• Transformation-out cross-validation: Excludes specific transformation classes from training to test model performance on unseen reaction types.
• Solvent-out cross-validation: Excludes specific solvents from training to evaluate model generalizability across different solvent conditions.
• Bias mitigation for k-fold CV: Addresses optimistic bias associated with conventional k-fold cross-validation by incorporating the nature of chemical objects into validation.
• QSPR modeling for reactions: Targets quantitative structure–property relationship (QSPR) models focused on reaction rate prediction and reaction kinetics.
• ISIDA Fragmentor integration: Provides a Python wrapper for ISIDA Fragmentor for fragment-based descriptor generation.
• RDtool atom-to-atom mapper integration: Provides a Python wrapper for RDtool atom-to-atom mapper for atom-mapping of reactions.

Scientific Applications:

• Rate constant prediction (bimolecular elimination): Predicts rate constants for bimolecular elimination reactions.
• Rate constant prediction (nucleophilic substitution): Predicts rate constants for nucleophilic substitution reactions.
• Rate constant prediction (Diels–Alder cycloaddition): Predicts rate constants for Diels–Alder cycloaddition reactions.
• Reaction kinetics and mechanistic studies: Provides more reliable model evaluation for studies of reaction kinetics and mechanisms.
• Generalization testing: Enables assessment of model performance on novel structural transformations and reactions under new conditions.

Methodology:

Applies transformation-out and solvent-out cross-validation to QSPR models, implements exclusion of specific transformation classes or solvents from training, and interfaces via a Python wrapper with ISIDA Fragmentor and RDtool atom-to-atom mapper.