Evaluating Effects of Augmented SELFIES for Molecular Understanding Using QK-LSTM

Identifying molecular properties, including side effects, is a critical yet time-consuming step in drug development. Failing to detect these side effects before regulatory submission can result in significant financial losses and production delays, and overlooking them during the regulatory review can lead to catastrophic consequences. This challenge presents an opportunity for innovative machine learning approaches, particularly hybrid quantum-classical models like the Quantum Kernel-Based Long Short-Term Memory (QK-LSTM) network. The QK-LSTM integrates quantum kernel functions into the classical LSTM framework, enabling the capture of complex, non-linear patterns in sequential data. By mapping input data into a high-dimensional quantum feature space, the QK-LSTM model reduces the need for large parameter sets, allowing for model compression without sacrificing accuracy in sequence-based tasks. Recent advancements have been made in the classical domain using augmented variations of the Simplified Molecular Line-Entry System (SMILES). However, to the best of our knowledge, no research has explored the impact of augmented SMILES in the quantum domain, nor the role of augmented Self-Referencing Embedded Strings (SELFIES) in either classical or hybrid quantum-classical settings. This study presents the first analysis of these approaches, providing novel insights into their potential for enhancing molecular property prediction and side effect identification. Results reveal that augmenting SELFIES yields in statistically significant improvements from SMILES by a 5.97% improvement for the classical domain and a 5.91% improvement for the hybrid quantum-classical domain.

@article{beaudoin2025_2504.20789,
  title={ Evaluating Effects of Augmented SELFIES for Molecular Understanding Using QK-LSTM },
  author={ Collin Beaudoin and Swaroop Ghosh },
  journal={arXiv preprint arXiv:2504.20789},
  year={ 2025 }
}