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Optimal designs are usually model-dependent and likely to be sub-optimal if the postulated model is not correctly specified. In practice, it is common that a researcher has a list of candidate models at hand and a design has to be found…

Statistics Theory · Mathematics 2023-03-29 Mingyao Ai , Holger Dette , Zhengfu Liu , Jun Yu

The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…

Quantum Physics · Physics 2024-07-11 Veronica Panizza , Philipp Hauke , Cristian Micheletti , Pietro Faccioli

Rising costs in recent years of developing new drugs and treatments have led to extensive research in optimization techniques in biomolecular design. Currently, the most widely used approach in biomolecular design is directed evolution,…

Machine Learning · Computer Science 2021-11-09 Alexander Whatley , Zhekun Luo , Xiangru Tang

Computer-assisted synthesis planning aims to help chemists find better reaction pathways faster. Finding viable and short pathways from sugar molecules to value-added chemicals can be modeled as a retrosynthesis planning problem with a…

Other Computer Science · Computer Science 2019-11-19 Peihong Jiang , Hieu Doan , Sandeep Madireddy , Rajeev Surendran Assary , Prasanna Balaprakash

De novo drug design is a crucial component of modern drug development, yet navigating the vast chemical space to find synthetically accessible, high-affinity candidates remains a significant challenge. Reinforcement Learning (RL) enhances…

Machine Learning · Computer Science 2025-12-25 R Yadunandan , Nimisha Ghosh

Quantum hardware and quantum-inspired algorithms are becoming increasingly popular for combinatorial optimization. However, these algorithms may require careful hyperparameter tuning for each problem instance. We use a reinforcement…

Machine Learning · Computer Science 2021-03-22 Dmitrii Beloborodov , A. E. Ulanov , Jakob N. Foerster , Shimon Whiteson , A. I. Lvovsky

The development of self-propelled particles at the micro- and the nanoscale has sparked a huge potential for future applications in active matter physics, microsurgery, and targeted drug delivery. However, while the latter applications…

Soft Condensed Matter · Physics 2022-08-24 Mahdi Nasiri , Benno Liebchen

We propose a bottom-up approach, based on Reinforcement Learning, to the design of a chain achieving efficient excitation-transfer performances. We assume distance-dependent interactions among particles arranged in a chain under…

Quantum Physics · Physics 2024-02-27 S. Sgroi , G. Zicari , A. Imparato , M. Paternostro

A reinforcement algorithm solves a classical optimization problem by introducing a feedback to the system which slowly changes the energy landscape and converges the algorithm to an optimal solution in the configuration space. Here, we use…

Disordered Systems and Neural Networks · Physics 2017-11-08 A. Ramezanpour

Machine learning has the potential to automate molecular design and drastically accelerate the discovery of new functional compounds. Towards this goal, generative models and reinforcement learning (RL) using string and graph…

Machine Learning · Computer Science 2022-02-02 Daniel Flam-Shepherd , Alexander Zhigalin , Alán Aspuru-Guzik

Offline reinforcement learning enables policy learning from pre-collected datasets without environment interaction, but existing Decision Transformer (DT) architectures struggle with long-horizon credit assignment and complex state-action…

Machine Learning · Computer Science 2025-12-18 Abraham Itzhak Weinberg

We propose a novel computational strategy for de novo design of molecules with desired properties termed ReLeaSE (Reinforcement Learning for Structural Evolution). Based on deep and reinforcement learning approaches, ReLeaSE integrates two…

Artificial Intelligence · Computer Science 2018-07-30 Mariya Popova , Olexandr Isayev , Alexander Tropsha

Quantum algorithm design plays a crucial role in exploiting the computational advantage of quantum devices. Here we develop a deep-reinforcement-learning based approach for quantum adiabatic algorithm design. Our approach is generically…

Quantum Physics · Physics 2020-05-20 Jian Lin , Zhong Yuan Lai , Xiaopeng Li

Machine learning based methods have shown potential for optimizing existing molecules with more desirable properties, a critical step towards accelerating new chemical discovery. Here we propose QMO, a generic query-based molecule…

Machine Learning · Computer Science 2022-04-21 Samuel Hoffman , Vijil Chenthamarakshan , Kahini Wadhawan , Pin-Yu Chen , Payel Das

Quantum control is concerned with the realisation of desired dynamics in quantum systems, serving as a linchpin for advancing quantum technologies and fundamental research. Analytic approaches and standard optimisation algorithms do not…

Quantum Physics · Physics 2025-05-29 Jan Ole Ernst , Aniket Chatterjee , Tim Franzmeyer , Axel Kuhn

Developing new drugs is laborious and costly, demanding extensive time investment. In this paper, we introduce a de-novo drug design strategy, which harnesses the capabilities of language models to devise targeted drugs for specific…

Biomolecules · Quantitative Biology 2025-05-20 Salma J. Ahmed , Emad A. Mohammed

We present a framework, which we call Molecule Deep $Q$-Networks (MolDQN), for molecule optimization by combining domain knowledge of chemistry and state-of-the-art reinforcement learning techniques (double $Q$-learning and randomized value…

Machine Learning · Computer Science 2020-06-22 Zhenpeng Zhou , Steven Kearnes , Li Li , Richard N. Zare , Patrick Riley

In this work, we introduce a method to fine-tune a Transformer-based generative model for molecular de novo design. Leveraging the superior sequence learning capacity of Transformers over Recurrent Neural Networks (RNNs), our model can…

Machine Learning · Computer Science 2024-03-11 Pengcheng Xu , Tao Feng , Tianfan Fu , Siddhartha Laghuvarapu , Jimeng Sun

Many multi-genic systemic diseases such as neurological disorders, inflammatory diseases, and the majority of cancers do not have effective treatments yet. Reinforcement learning powered systems pharmacology is a potentially effective…

Biomolecules · Quantitative Biology 2022-02-25 Ryan K. Tan , Yang Liu , Lei Xie

Quantum machine learning models use encoding circuits to map data into a quantum Hilbert space. While it is well known that the architecture of these circuits significantly influences core properties of the resulting model, they are often…

Quantum Physics · Physics 2025-03-03 Frederic Rapp , David A. Kreplin , Marco F. Huber , Marco Roth