Predicting Side Effect of Drug Molecules using Recurrent Neural Networks

Identification and verification of molecular properties such as side effects is one of the most important and time-consuming steps in the process of molecule synthesis. For example, failure to identify side effects before submission to regulatory groups can cost millions of dollars and months of additional research to the companies. Failure to identify side effects during the regulatory review can also cost lives. The complexity and expense of this task have made it a candidate for a machine learning-based solution. Prior approaches rely on complex model designs and excessive parameter counts for side effect predictions. We believe reliance on complex models only shifts the difficulty away from chemists rather than alleviating the issue. Implementing large models is also expensive without prior access to high-performance computers. We propose a heuristic approach that allows for the utilization of simple neural networks, specifically the recurrent neural network, with a 98+% reduction in the number of required parameters compared to available large language models while still obtaining near identical results as top-performing models.

Energy-based Generative Models for Target-specific Drug Discovery

Drug targets are the main focus of drug discovery due to their key role in disease pathogenesis. Computational approaches are widely applied to drug development because of the increasing availability of biological molecular datasets. Popular generative approaches can create new drug molecules by learning the given molecule distributions. However, these approaches are mostly not for target-specific drug discovery. We developed an energy-based probabilistic model for computational target-specific drug discovery. Results show that our proposed TagMol can generate molecules with similar binding affinity scores as real molecules. GAT-based models showed faster and better learning relative to GCN baseline models.

Quantum Machine Learning for Material Synthesis and Hardware Security

Using quantum computing, this paper addresses two scientifically pressing and day-to-day relevant problems, namely, chemical retrosynthesis which is an important step in drug/material discovery and security of the semiconductor supply chain. We show that Quantum Long Short-Term Memory (QLSTM) is a viable tool for retrosynthesis. We achieve 65% training accuracy with QLSTM, whereas classical LSTM can achieve 100%. However, in testing, we achieve 80% accuracy with the QLSTM while classical LSTM peaks at only 70% accuracy! We also demonstrate an application of Quantum Neural Network (QNN) in the hardware security domain, specifically in Hardware Trojan (HT) detection using a set of power and area Trojan features. The QNN model achieves detection accuracy as high as 97.27%.