Molecular Optimization

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4 papers in the last four weeks, against 2 the four weeks before. 0.0% of all new papers.

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  1. PharmAgent: Constraint-Aware Search with Frozen Language Models for Molecular Optimization

    Oct 4, 2026Nihui Shao, Guanxing Chen, Jilong Shi +6Molecular Optimization

    City University of Hong Kong (Dongguan) · The Hong Kong Polytechnic University · Tencent AI Lab +2

  2. TMCS: Tool-Grounded Multi-Agent Reasoning for Compositional Chemical Problem Solving

    Sep 28, 2026Shengqin Wang, Jie Jin, Yu Cheng +4Chemical StructuresMulti-Agent Reasoning

    East China Normal University, Shanghai Innovation Institute, University College London, Huawei Noah’s Ark Lab

  3. M3OS: A Monte Carlo Graph Search-Orchestrated Multi-Agent LLM System for Evidence-Traced Molecular Optimization

    Sep 28, 2026Junjie Wang, Yaowei Jin, Ruohui Tang +7Molecular OptimizationMulti-Agent Large Language Model Systems

    Lingang Laboratory, Shanghai, 200031, China. · School of Information Science and Technology, ShanghaiTech University, Shanghai, 201210, China. · Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, 200240, China.

  4. BOReFT: Manifold Steering of Language Models for Black-box Optimization

    Sep 27, 2026Dhruv Agarwal, Rico Angell, Kavitha Srinivas +4Bayesian OptimizationBlack-Box Optimization

    University of Massachusetts Amherst · New York University · IBM Research +1

  5. Elite-Weighted Supervised Fine-tuning for Goal-Directed Molecular Optimization

    Aug 31, 2026Shiyun Wa, Yifei Wang, Anna G. Green +2Molecular OptimizationModel Fine-Tuning

    Research, Biogen, Cambridge, MA 02142, USA · Manning College of Information & Computer Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA

  6. A Modular Agentic Framework for Synthetically Constrained Multi-Objective Hit-to-Lead Optimization

    Aug 11, 2026Kelvin P. Idanwekhai, Enes Kelestemur, Benjamin Strickland +6Drug DiscoveryMolecular Optimization

    Department of Chemistry, UNC Chapel Hill, Chapel Hill, NC, USA · Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy at UNC, Chapel Hill, NC, USA · Department of Applied Physical Sciences, UNC Chapel Hill, NC, USA +1

  7. Out-Of-The-Loop Multi-Fidelity Bayesian Optimization

    Aug 4, 2026Gustavo Sutter, Hao Wang, Luis Ricardez-Sandoval +2Multi-FidelityBayesian Optimization

    Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada · Vector Institute, Toronto, ON, Canada · Department of Chemical Engineering, University of Waterloo, Waterloo, ON, Canada +2

  8. Oracle-Budgeted Molecular Optimization with Short-Term Graph Memory

    Jul 30, 2026Jiannan Yang, Veronika Thost, Xiang Ling +1Molecular OptimizationGraph-Structured Memories

    Computer Science Stony Brook University Stony Brook, New York, USA · Molecular AI Novo Nordisk Lexington, Massachusetts, USA · Biomedical Engineering Stony Brook University Stony Brook, New York, USA +1

  9. Q-Steer: Action-Value Guidance for Molecular Policy Optimization

    Jul 29, 2026Xinyu Wang, Jinbo Bi, Minghu SongMolecular OptimizationFrictive Policy Optimization

    Department of Computer Science and Engineering, University of Connecticut · 1Storrs, CT 06269, USA · Institute of Health and Medicine, Hefei Comprehensive National Science Center +1

  10. Transfer Learning Architectures for Scalable Multi-Fidelity Bayesian Optimization

    Jul 26, 2026Jaewook Lee, Ethan Errington, Christian D. Lorenz +1Bayesian OptimizationGaussian Process

    Department of Engineering, King’s College London, London, WC2R 2LS, United Kingdom.

  11. Sample Efficient Generative Optimization for Molecular Design

    Jul 14, 2026Sarina Kopf, Cristina Nevado, Philippe SchwallerMolecular OptimizationMolecular Design

    LIAC, ISIC, EPFL, Lausanne, Switzerland · Department of Chemistry, University of Zurich, Zurich, Switzerland · Centre of Competence in Research (NCCR) Catalysis, Zurich, Switzerland

  12. On the Design Space of Discrete Diffusion Online Adaptation for Molecular Optimization

    Jul 3, 2026Trevor Chen, Ariel Dai, Jason Yang +8Molecular OptimizationGenerative Models

    1Caltech · ETH Zurich · ETH AI Center +1

  13. Diffeomorphic Optimization

    Jul 1, 2026Ludwig Winkler, Andrew Leaver-Fay, Joseph Kleinhenz +1Differentiable OptimizationProtein Design

    Microsoft Research AI4Science · Prescient Design, Genentech Roche

  14. Active-GRPO: Adaptive Imitation and Self-Improving Reasoning for Molecular Optimization

    Jul 1, 2026Xuefeng Liu, Mingxuan Cao, Qinan Huang +3Molecular OptimizationFlow-Grpo

    School of Medicine, Stanford University · 2Data Science Institute, University of Chicago · 3Pritzker School of Molecular Engineering, University of Chicago +2

  15. Beyond Drug Discovery: The Nanotechnology Molecular Optimization (NMO) Benchmark

    Jun 29, 2026Matthias Blaschke, Daniel Kienzle, Zsuzsanna Koczor-Benda +3Molecular OptimizationDrug Discovery

    University of Augsburg · CAAPS† · Germany +2

  16. Target-Aware Bandit Allocation for Scalable Surrogate Optimization in Chemical Space

    Jun 25, 2026Mohammad Haddadnia, Yuvan Chali, Abhilash Jayaraj +4Molecular OptimizationDrug Design

    Dana-Farber Cancer Institute, Boston, MA, USA · Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA · Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA +4

  17. Energy-efficient codon optimization on thermodynamic hardware

    Jun 15, 2026Andraz Jelincic, Ross C. WalkerThermodynamicsEnergy-Efficient

    1Extropic Corp., Boston, MA

  18. In-Context Learning for Latent Space Bayesian Optimization

    Jun 8, 2026Tuan A. Vu, Harri Lähdesmäki, Julien MartinelliBayesian OptimizationMolecular Optimization

    Aalto University

  19. Bayesian Optimization of a Multi-Product Chemical Reactor Using Composite Models and Partial Physics Knowledge

    Jun 7, 2026Liqiu Dong, Marta Zagórowska, Mehmet MercangözChemical Process SystemsBayesian Optimization

    Department of Chemical Engineering, Imperial College London, London, UK · DCSC, Delft University of Technology, Delft, Netherlands

  20. Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design

    May 30, 2026Zaifei Yang, Weiyu Chen, Yaqing Wang +1Drug DesignMolecular Optimization

    1The Hong Kong University of Science and Technology · 2City University of Hong Kong · Beijing Institute of Mathematical Sciences and Applications

  21. PhAME: Phenotype-Aware Molecular Editing via Latent Diffusion

    May 27, 2026Łukasz Janisiów, Sebastian Musiał, Bartosz Zieliński +2Molecular OptimizationDrug Design

    Faculty of Mathematics and Computer Science, Jagiellonian University · Doctoral School of Exact and Natural Sciences, Jagiellonian University · Jagiellonian Center for Artificial Intelligence, Jagiellonian University +2

  22. The Montparnasse Algorithm for RNA Design

    May 25, 2026Tristan CazenaveMessenger RnaMolecular Optimization

    LAMSADE, Universit´e Paris Dauphine - PSL, Paris, France

  23. Molecular Lead Optimization via Agentic Tool Planning

    May 21, 2026Lingxiao Li, Haobo Zhang, Ruohao Fan +2Molecular OptimizationDrug Discovery

    University of Michigan Ann Arbor, Michigan, USA · Department of Biochemistry and Molecular Medicine University of California, Davis Davis, California, USA · Department of Pharmacology and Toxicology Michigan State University East Lansing, Michigan, USA

  24. Fine-tuning Pocket-Aware Diffusion Models via Denoising Policy Optimization

    May 17, 2026Yuan Xue, Daniel Kudenko, Megha KhoslaDrug DesignMolecular Optimization

    L3S Research Center, Hanover, Germany · Delft University of Technology, Delft, Netherlands

  25. Evolutionary Extreme Learning Machine of ab-initio Energy Landscapes for Crystal Structure Prediction using Manta Ray Optimization with Levy Flight

    May 16, 2026Adrian Rubio-SolisCrystal Structure PredictionFree-Energy Landscape

    Hamlyn Centre for Robotic Surgery, Imperial College London (ICL) · London SW7 2AZ, UK United Kingdom

  26. MolDeTox: Evaluating Language Model's Stepwise Fragment Editing for Molecular Detoxification

    May 12, 2026Jueon Park, Wonjune Jang, Jiwoo Lee +2ToxicityDetoxification

    Korea University · Myongji University · AIGEN Sciences

  27. FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization

    May 11, 2026Qingchuan Zhang, He Cao, Hao Li +6Molecular OptimizationPrecise Editing

    University of Science and Technology of China · International Digital Economy Academy · Peking University +5

  28. From Single-Step Edit Response to Multi-Step Molecular Optimization

    May 11, 2026Haojie Rao, Kun Li, Yida Xiong +5Molecular OptimizationPrecise Editing

    School of Computer Science, Wuhan University, Wuhan, China · School of Computer Science, Wuhan University Wuhan, China · Department of Data Science and Artificial Intelligence, Monash University, Victoria, Australia +5

  29. MolWorld: Molecule World Models for Actionable Molecular Optimization

    May 9, 2026Yang Qiao, Bo Pan, Hao-Wei Pang +3Molecular OptimizationMolecules

    Emory University · Atlanta, GA, USA · Merck & Co., Inc. +1

  30. From Feasible to Practical: Pareto-Optimal Synthesis Planning

    May 8, 2026Friedrich Hastedt, Dongda Zhang, Antonio del Rio ChanonaPareto FrontierMolecular Optimization

    Department of Chemical Engineering, Imperial College London, UK · Department of Chemical Engineering, University of Manchester, UK

  31. Hyper-Dimensional Fingerprints as Molecular Representations

    Apr 30, 2026Jonas Teufel, Luca Torresi, André Eberhard +1Molecular Representation LearningMolecular Optimization

    Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT), Kaiserstraße 12, Karlsruhe, Germany. · Karlsruhe Institute of Technology (KIT), Institute of Anthropomatics and Robotics (IAR), Kaiserstraße 12, Karlsruhe, Germany.

  32. Human-in-the-Loop Meta Bayesian Optimization for Fusion Energy and Scientific Applications

    Apr 30, 2026Ricardo Luna Gutierrez, Sahand Ghorbanpour, Ejaz Rahman +5Nuclear FusionPhysics-Informed Learning

    1Hewlett Packard Enterprise · University of Rochester

  33. C-MORAL: Controllable Multi-Objective Molecular Optimization with Reinforcement Alignment for LLMs

    Apr 24, 2026Rui Gao, Youngseung Jeon, Swastik Roy +2Molecular OptimizationOptimization Modeling

    University of California, Los Angeles · Amazon

  34. LLM-Guided Dynamic Action Spaces for Synthesizable Molecular Optimization

    Apr 9, 2026Tao Li, Kaiyuan Hou, Tuan Vinh +4Molecular OptimizationReaction

    Department of Computer Science, Emory University · School of Computer Science, Carnegie Mellon University · MRC Brain Network Dynamics Unit, University of Oxford +3

  35. Q-BIOLAT: Binary Latent Protein Fitness Landscapes for QUBO-Based Optimization

    Mar 29, 2026Truong-Son HyQuadratic Unconstrained Binary OptimizationProtein

    Department of Computer Science, University of Alabama at Birmingham, Birmingham, Alabama, USA

  36. MMAI Gym for Science: Training Liquid Foundation Models for Drug Discovery

    Mar 3, 2026Maksim Kuznetsov, Zulfat Miftahutdinov, Rim Shayakhmetov +17Drug DiscoveryMolecular Optimization

    Insilico Medicine · Liquid AI

  37. Bayesian Optimization for General Reaction Conditions

    Feb 26, 2025Stefan P. Schmid, Ella Miray Rajaonson, Cher Tian Ser +6Bayesian OptimizationMolecular Optimization

    Institute of Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich CH-8093, Switzerland · NCCR Catalysis, Switzerland · Department of Chemistry, University of Toronto, Toronto, Canada +13

  38. Small Molecule Optimization with Large Language Models

    Jul 26, 2024Philipp Guevorguian, Menua Bedrosian, Tigran Fahradyan +3Molecular OptimizationDrug Discovery

    YerevaNN research lab, Yerevan, Armenia.

  39. BEACON: A Bayesian Optimization Inspired Strategy for Efficient Novelty Search

    Jun 5, 2024Wei-Ting Tang, Ankush Chakrabarty, Joel A. PaulsonBayesian OptimizationSearch Algorithms

    University of Wisconsin-Madison, Department of Chemical and Biological Engineering, Madison, WI, USA. · The Ohio State University, Department of Chemical and Biomolecular Engineering, Columbus, OH, USA. · Insulet Corporation, Acton, MA, USA.