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ACM/IEEE Design Automation Conference (DAC)

Invited: Drug Discovery Approaches using Quantum Machine Learning

Junde Li, Mahabubul Alam, Congzhou Mike Sha, Jian Wang, Nikolay V. Dokholyan, Swaroop Ghosh

Published Nov 8, 2021• 34 citations
Publisher

Abstract

Traditional drug discovery pipelines can require multiple years and billions of dollars of investment. Deep generative and discriminative models are widely adopted to assist in drug development. Classical machines cannot efficiently reproduce the atypical patterns of quantum computers, which may improve the quality of learned tasks. We propose a suite of quantum machine learning techniques: incorporating generative adversarial networks (GAN), convolutional neural networks (CNN) and variational auto-encoders (VAE) to generate small drug molecules, classify binding pockets in proteins, and generate large drug molecules, respectively.

DOI
10.1109/dac18074.2021.9586268

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Traditional drug discovery pipelines can require multiple years and billions of dollars of investment. Deep generative and discriminative models are widely adopted to assist in drug development. Classical machines cannot efficiently reproduce the atypical patterns of quantum computers, which may improve the quality of learned tasks. We propose a suite of quantum machine learning techniques: incorporating generative adversarial networks (GAN), convolutional neural networks (CNN) and variational auto-encoders (VAE) to generate small drug molecules, classify binding pockets in proteins, and generate large drug molecules, respectively.
Traditional drug discovery pipeline takes several years and cost billions of dollars. Deep generative and predictive models are widely adopted to assist in drug development. Classical machines cannot efficiently produce atypical patterns of quantum computers which might improve the training quality of learning tasks. We propose a suite of quantum machine learning techniques e.g., generative adversarial network (GAN), convolutional neural network (CNN) and variational auto-encoder (VAE) to generate small drug molecules, classify binding pockets in proteins, and generate large drug molecules, respectively.
Existing drug discovery pipelines take 5–10 years and cost billions of dollars. Computational approaches aim to sample from regions of the whole molecular and solid-state compounds called chemical space, which could be on the order of106010^{60}1060. Deep generative models can model the underlying probability distribution of both the physical structures and property of drugs and relate them nonlinearly. By exploiting patterns in massive datasets, these models can distill salient features that characterize the molecules. Generative adversarial networks (GANs) discover drug candidates by generating molecular structures that obey chemical and physical properties and show affinity toward binding with the receptor for a target disease. However, classical GANs cannot explore certain regions of the chemical space and suffer from training instabilities. The practical utility of such models is limited due to the vast size of the search space, characterized by millions of parameters. A full quantum GAN may require more than 90 qubits even to generate small molecules with up to nine heavy atoms. The proposed quantum GAN with a hybrid generator (QGAN-HG) model is composed of a hybrid quantum generator that supports various number of qubits and quantum circuit layers, and a classical discriminator. The QGAN-HG with less than 20% of the original parameters can learn molecular distributions as efficiently as its classical counterpart. Another extended version of the proposed QGAN-HG, which utilizes multiple quantum subcircuits, considerably accelerates our standard QGAN-HG training process and avoids the potential gradient vanishing issue of deep neural networks.
Drug discovery for a given protein target is a complex, resource-intensive process, often requiring years of research and billions of dollars in investment. Computational techniques, particularly deep learning models, have accelerated molecular generation, but they remain constrained by classical computational limitations and reliance on known chemical patterns. To address these challenges, we propose a hybrid quantum conditional GAN with gradient penalty for drug design, integrating quantum computing to enhance exploration of the vast chemical space. The proposed approach leverages a hybrid classical and quantum generative model to create novel molecular structures while ensuring they adhere to chemical and pharmacological properties. By conditioning the generative model on protein target sequences, we improve molecular specificity, increasing the likelihood of discovering viable drug candidates. Our framework generates chemically valid, diverse, and target-specific molecules, offering a promising avenue for more efficient and precise data-driven drug discovery.
De novo drug design with desired biological activities is crucial for developing novel therapeutics for patients. The drug development process is time- and resource-consuming, and it has a low probability of success. Recent advances in machine learning and deep learning technology have reduced the time and cost of the discovery process and therefore, improved pharmaceutical research and development. In this paper, we explore the combination of two rapidly developing fields with lead candidate discovery in the drug development process. First, artificial intelligence has already been demonstrated to successfully accelerate conventional drug design approaches. Second, quantum computing has demonstrated promising potential in different applications, such as quantum chemistry, combinatorial optimizations, and machine learning. This article explores hybrid quantum-classical generative adversarial networks (GAN) for small molecule discovery. We substituted each element of GAN with a variational quantum circuit (VQC) and demonstrated the quantum advantages in the small drug discovery. Utilizing a VQC in the noise generator of a GAN to generate small molecules achieves better physicochemical properties and performance in the goal-directed benchmark than the classical counterpart. Moreover, we demonstrate the potential of a VQC with only tens of learnable parameters in the generator of GAN to generate small molecules. We also demonstrate the quantum advantage of a VQC in the discriminator of GAN. In this hybrid model, the number of learnable parameters is significantly less than the classical ones, and it can still generate valid molecules. The hybrid model with only tens of training parameters in the quantum discriminator outperforms the MLP-based one in terms of both generated molecule properties and the achieved KL divergence. However, the hybrid quantum-classical GANs still face challenges in generating unique and valid molecules compared to their classical counterparts.
The convergence of Quantum Computing and Generative Artificial Intelligence (AI) marks a transformative leap in the field of drug discovery. Traditional drug development pipelines are often slow, costly, and limited by classical computational constraints. This paper presents a novel hybrid approach—QuantumGeneraDrug—that integrates quantum generative models with deep learning architectures to accelerate molecule generation, optimize binding affinities, and reduce computation time. A comprehensive literature survey highlights the evolution of both quantum algorithms and generative AI models applied to pharmaceutical research. The proposed system demonstrates improved performance over existing frameworks in key metrics such as valid molecule rate, druglikeness (QED) score, binding affinity accuracy, and processing time per compound. Comparative results are illustrated using numerical tables and visualized via bar and pie charts. The study concludes that Quantum Generative AI holds immense promise for next-generation drug discovery, especially in tackling complex diseases and enabling personalized medicine.
The drug design process currently requires considerable time and resources to develop each new compound that enters the market. This work develops an application of hybrid quantum generative models based on the integration of parameterized quantum circuits into known molecular generative adversarial networks and proposes quantum cycle architectures that improve model performance and stability during training. Through extensive experimentation on benchmark drug design datasets, quantum machine 9 (QM9) and PubChemQC 9 (PC9), the introduced models are shown to outperform the previously achieved scores. Most prominently, the new scores indicate an increase of up to 30% in the quantitative estimation of druglikeness. The new hybrid quantum machine learning algorithms, as well as the achieved scores of pharmacokinetic properties, contribute to the development of fast and accurate drug discovery processes.