Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm

TL;DR

This paper introduces a kernel-based method combining RDKFingerprint, Sinkhorn-Knopp algorithm, and kernel PCA to analyze SMILES strings for molecular structure classification and regression, showing improved performance over baselines.

Contribution

It proposes a novel kernel matrix computation approach for SMILES strings using RDKFingerprint and Sinkhorn-Knopp, enhancing molecular analysis accuracy.

Findings

Outperforms baseline methods in drug subcategory classification.

Achieves better solubility and partition coefficient regression results.

Demonstrates effectiveness of kernel PCA in molecular data analysis.

Abstract

In molecular structure data, SMILES (Simplified Molecular Input Line Entry System) strings are used to analyze molecular structure design. Numerical feature representation of SMILES strings is a challenging task. This work proposes a kernel-based approach for encoding and analyzing molecular structures from SMILES strings. The proposed approach involves computing a kernel matrix using the Sinkhorn-Knopp algorithm while using kernel principal component analysis (PCA) for dimensionality reduction. The resulting low-dimensional embeddings are then used for classification and regression analysis. The kernel matrix is computed by converting the SMILES strings into molecular structures using the Morgan Fingerprint, which computes a fingerprint for each molecule. The distance matrix is computed using the pairwise kernels function. The Sinkhorn-Knopp algorithm is used to compute the final kernel matrix that satisfies the constraints of a probability distribution. This is achieved by iteratively adjusting the kernel matrix until the marginal distributions of the rows and columns match the desired marginal distributions. We provided a comprehensive empirical analysis of the proposed kernel method to evaluate its goodness with greater depth. The suggested method is assessed for drug subcategory prediction (classification task) and solubility AlogPS ``Aqueous solubility and Octanol/Water partition coefficient" (regression task) using the benchmark SMILES string dataset. The outcomes show the proposed method outperforms several baseline methods in terms of supervised analysis and has potential uses in molecular design and drug discovery. Overall, the suggested method is a promising avenue for kernel methods-based molecular structure analysis and design.