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Designing molecules that must satisfy multiple, often conflicting objectives is a central challenge in molecular discovery. The enormous size of chemical space and the cost of high-fidelity simulations have driven the development of machine…

Machine Learning · Statistics 2025-12-22 Madhav R. Muthyala , Farshud Sorourifar , Tianhong Tan , You Peng , Joel A. Paulson

The discovery of therapeutic molecules is fundamentally a multi-objective optimization problem. One formulation of the problem is to identify molecules that simultaneously exhibit strong binding affinity for a target protein, minimal…

Quantitative Methods · Quantitative Biology 2023-10-17 Jenna C. Fromer , David E. Graff , Connor W. Coley

Machine learning methods have been used to accelerate the molecule optimization process. However, efficient search for optimized molecules satisfying several properties with scarce labeled data remains a challenge for machine learning…

Biomolecules · Quantitative Biology 2022-12-20 Xin Xia , Yansen Su , Chunhou Zheng , Xiangxiang Zeng

Multi-objective Bayesian optimization aims to find the Pareto front of trade-offs between a set of expensive objectives while collecting as few samples as possible. In some cases, it is possible to evaluate the objectives separately, and a…

Machine Learning · Statistics 2025-03-04 Jack M. Buckingham , Sebastian Rojas Gonzalez , Juergen Branke

Multi-objective Bayesian optimization (MOBO) provides a principled framework for navigating trade-offs in molecular design. However, its empirical advantages over scalarized alternatives remain underexplored. We benchmark a simple…

Machine Learning · Computer Science 2025-12-25 Anabel Yong , Austin Tripp , Layla Hosseini-Gerami , Brooks Paige

Deep learning models form one of the most powerful machine learning models for the extraction of important features. Most of the designs of deep neural models, i.e., the initialization of parameters, are still manually tuned. Hence,…

Machine Learning · Computer Science 2023-05-18 Mrittika Chakraborty , Wreetbhas Pal , Sanghamitra Bandyopadhyay , Ujjwal Maulik

Molecular optimization is a fundamental goal in the chemical sciences and is of central interest to drug and material design. In recent years, significant progress has been made in solving challenging problems across various aspects of…

Computational Engineering, Finance, and Science · Computer Science 2022-10-11 Wenhao Gao , Tianfan Fu , Jimeng Sun , Connor W. Coley

Expensive multi-objective optimization problems can be found in many real-world applications, where their objective function evaluations involve expensive computations or physical experiments. It is desirable to obtain an approximate Pareto…

Neural and Evolutionary Computing · Computer Science 2022-10-18 Xi Lin , Zhiyuan Yang , Xiaoyuan Zhang , Qingfu Zhang

Multi-objective optimization is a widely studied problem in diverse fields, such as engineering and finance, that seeks to identify a set of non-dominated solutions that provide optimal trade-offs among competing objectives. However, the…

Neural and Evolutionary Computing · Computer Science 2024-01-15 Arash Heidari , Sebastian Rojas Gonzalez , Tom Dhaene , Ivo Couckuyt

Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective…

Quantitative Methods · Quantitative Biology 2008-11-05 Jean-Charles Boisson , Laetitia Jourdan , El-Ghazali Talbi , Dragos Horvath

Multiobjective design optimization problems require multiobjective optimization techniques to solve, and it is often very challenging to obtain high-quality Pareto fronts accurately. In this paper, the recently developed flower pollination…

Optimization and Control · Mathematics 2014-08-25 Xin-She Yang , M. Karamanoglu , X. S. He

Flower pollination algorithm is a new nature-inspired algorithm, based on the characteristics of flowering plants. In this paper, we extend this flower algorithm to solve multi-objective optimization problems in engineering. By using the…

Neural and Evolutionary Computing · Computer Science 2014-04-04 Xin-She Yang , M. Karamanoglu , Xingshi He

Multi-modal multi-objective optimization is to locate (almost) equivalent Pareto optimal solutions as many as possible. Some evolutionary algorithms for multi-modal multi-objective optimization have been proposed in the literature. However,…

Neural and Evolutionary Computing · Computer Science 2020-10-02 Ryoji Tanabe , Hisao Ishibuchi

An important benefit of multi-objective search is that it maintains a diverse population of candidates, which helps in deceptive problems in particular. Not all diversity is useful, however: candidates that optimize only one objective while…

Neural and Evolutionary Computing · Computer Science 2019-08-06 Hormoz Shahrzad , Babak Hodjat , Camille Dollé , Andrei Denissov , Simon Lau , Donn Goodhew , Justin Dyer , Risto Miikkulainen

Multi-modal multi-objective optimization is to locate (almost) equivalent Pareto optimal solutions as many as possible. While decomposition-based evolutionary algorithms have good performance for multi-objective optimization, they are…

Neural and Evolutionary Computing · Computer Science 2020-10-01 Ryoji Tanabe , Hisao Ishibuchi

There are a lot of real-world black-box optimization problems that need to optimize multiple criteria simultaneously. However, in a multi-objective optimization (MOO) problem, identifying the whole Pareto front requires the prohibitive…

Machine Learning · Computer Science 2023-11-23 Ryota Ozaki , Kazuki Ishikawa , Youhei Kanzaki , Shinya Suzuki , Shion Takeno , Ichiro Takeuchi , Masayuki Karasuyama

Multi-objective optimization aims at finding trade-off solutions to conflicting objectives. These constitute the Pareto optimal set. In the context of expensive-to-evaluate functions, it is impossible and often non-informative to look for…

Machine Learning · Statistics 2020-02-20 David Gaudrie , Rodolphe Le Riche , Victor Picheny , Benoit Enaux , Vincent Herbert

The design of molecules and materials with tailored properties is challenging, as candidate molecules must satisfy multiple competing requirements that are often difficult to measure or compute. While molecular structures, produced through…

Chemical Physics · Physics 2023-02-07 Julia Westermayr , Joe Gilkes , Rhyan Barrett , Reinhard J. Maurer

Many real world applications can be framed as multi-objective optimization problems, where we wish to simultaneously optimize for multiple criteria. Bayesian optimization techniques for the multi-objective setting are pertinent when the…

Machine Learning · Computer Science 2019-06-24 Biswajit Paria , Kirthevasan Kandasamy , Barnabás Póczos

Multiobjective combinatorial optimization (MOCO) problems can be found in many real-world applications. However, exactly solving these problems would be very challenging, particularly when they are NP-hard. Many handcrafted heuristic…

Machine Learning · Computer Science 2022-05-10 Xi Lin , Zhiyuan Yang , Qingfu Zhang
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