Molecular Optimization

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7 papers in the last four weeks, against 2 the four weeks before. 0.1% of all new papers.

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Information-Dense Synthesis for Molecular Discovery
Oct 6, 2026Kasper K. Jakobsen, Eli N. WeinsteinMolecular Optimization Drug Discovery
Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, DK.
PharmAgent: Constraint-Aware Search with Frozen Language Models for Molecular Optimization
Oct 4, 2026Nihui Shao, Guanxing Chen, Jilong Shi +6Molecular Optimization Large Language Model-Guided Optimization
City University of Hong Kong (Dongguan) · The Hong Kong Polytechnic University · Tencent AI Lab +2
Latent JEPA: Abstract Future Prediction for Latent Reasoning in Chemistry
Oct 1, 2026Xinjian Zhao, Yaoyao Xu, Xuemin Chen +2Molecular Optimization Joint-Embedding Predictive Architecture
School of Data Science, The Chinese University of Hong Kong, Shenzhen · Shanghai Artificial Intelligence Laboratory
TMCS: Tool-Grounded Multi-Agent Reasoning for Compositional Chemical Problem Solving
Sep 28, 2026Shengqin Wang, Jie Jin, Yu Cheng +4Molecular Optimization Tool-Augmented Language Model Agents
East China Normal University, Shanghai Innovation Institute, University College London, Huawei Noah’s Ark Lab
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 Optimization Multi-Agent LLM 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.
One Sequence, Many Decodings: CAGenMol-2 Recasts Drug Design as Masked Molecular Inference
Sep 28, 2026Yanting Li, Enyan Dai, Lei Wang +2Molecular Optimization Masked Diffusion Models
The Hong Kong University of Science and Technology (Guangzhou) · Jinan University, Guangzhou
MolDesignBench: Evaluating LLM-based Agent for Scenario-grounded Molecular Design
Sep 23, 2026Yongjun Jeong, Hanbum Ko, Ye Rin Kim +6Molecular Optimization LLM Agent Evaluation
Department of Artificial Intelligence, Korea University · LG AI Research · Department of Statistics, Korea University
Ensemble-Conditioned Molecular Design
Sep 14, 2026Ross Irwin, Alessandro Tibo, Jon Paul Janet +1Molecular Optimization Structure-Based Drug Design
Molecular AI Discovery Sciences, R&D AstraZeneca Gothenburg, Sweden · Department of Computer Science and Engineering Chalmers University of Technology and University of Gothenburg Gothenburg, Sweden
Elite-Weighted Supervised Fine-tuning for Goal-Directed Molecular Optimization
Aug 31, 2026Shiyun Wa, Yifei Wang, Anna G. Green +2Supervised Fine-Tuning Molecular Optimization
Research, Biogen, Cambridge, MA 02142, USA · Manning College of Information & Computer Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
A Modular Agentic Framework for Synthetically Constrained Multi-Objective Hit-to-Lead Optimization
Aug 11, 2026Kelvin P. Idanwekhai, Enes Kelestemur, Benjamin Strickland +6Molecular Optimization LLM Agent Orchestration
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
PolymerGPT: Multi-property Optimization with a Decoder-Based GPT Model for Generative Polymer Design
Aug 2, 2026Charlie Pyle, Adarsh Gadari, C. Adrian Figg +3Molecular Optimization Molecular Generation
Texas A&M University · University of Pittsburgh · Department of Chemistry, Virginia Tech +2
Oracle-Budgeted Molecular Optimization with Short-Term Graph Memory
Jul 30, 2026Jiannan Yang, Veronika Thost, Xiang Ling +1Molecular Optimization Surrogate-Assisted Optimization
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
Q-Steer: Action-Value Guidance for Molecular Policy Optimization
Jul 29, 2026Xinyu Wang, Jinbo Bi, Minghu SongMolecular Optimization Large Language Model-Guided 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
OLEDLM: A Unified Language Model for OLED Molecular Design
Jul 22, 2026Fukang Wen, Yuchong Tang, Jingyuan Li +9Molecular Optimization Materials Science
1Tsinghua University · 5MathonAI Team · 2Beijing Institute of Mathematical Sciences and Applications +2
Boltzmann-Expected Molecular Design with Decoupled Annealing Flows
Jul 21, 2026Selma Moqvist, Richard Beckmann, Ross Irwin +2Molecular Optimization Molecular Graph Generation
Department of Computer Science and Engineering Chalmers University of Technology & University of Gothenburg SE-41296 Gothenburg, Sweden · Molecular AI Discovery Sciences, R&D AstraZeneca SE-43183 Mölndal, Sweden
DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Models
Jul 21, 2026Yiming Qin, Kai Yi, Miruna Cretu +3Protein-Ligand Binding Affinity Prediction Molecular Optimization
EPFL, Switzerland · MRC-LMB, UK · University of Cambridge, UK
Adopting Reinforcement Learning with Verifiable Rewards for Molecular Generation
Jul 21, 2026Mingxuan Ouyang, Hao Lan, Wanyu LinMolecular Optimization Reinforcement Learning with Verifiable Rewards
Sample Efficient Generative Optimization for Molecular Design
Jul 14, 2026Sarina Kopf, Cristina Nevado, Philippe SchwallerMolecular Optimization Surrogate-Assisted Optimization
LIAC, ISIC, EPFL, Lausanne, Switzerland · Department of Chemistry, University of Zurich, Zurich, Switzerland · Centre of Competence in Research (NCCR) Catalysis, Zurich, Switzerland
Generating Developable 3D Molecules via Pocket-Conditioned Diffusion and Property-Aware Optimization
Jul 14, 2026Ruoxi Gao, Jiangweizhi Peng, Ziqi Chen +10Molecular Optimization Structure-Based Drug Design
Computer Science and Engineering, The Ohio State University, Columbus, OH 43210. · Industrial and System Engineering, University of Minnesota, Minneapolis, MN 55455. · Google Cloud, Google LLC, Mountain View, CA 94043. +6
Gene Expression-Informed Jointly Controlled Generative Modeling for Precision Molecular Design
Jul 13, 2026Hang Yuan, Chen Li, Wenjun Ma +2Molecular Optimization Molecular Generation
School of Artificial Intelligence South China Normal University Foshan, Guangdong, China · D3 Center The University of Osaka Suita, Osaka, Japan · School of Computer Science South China Normal University Guangzhou, Guangdong, China
A Precedent-Guided Co-Scientist for Side-Effect-Aware Drug Redesign
Jul 3, 2026Yujin Kim, Charmgil HongMolecular Optimization Scientific Workflow Automation
Department of Computer Science and Electrical Engineering, Handong Global University, Pohang, Republic of Korea.
On the Design Space of Discrete Diffusion Online Adaptation for Molecular Optimization
Jul 3, 2026Trevor Chen, Ariel Dai, Jason Yang +8Molecular Optimization Diffusion Model Fine-Tuning
1Caltech · ETH Zurich · ETH AI Center +1
Active-GRPO: Adaptive Imitation and Self-Improving Reasoning for Molecular Optimization
Jul 1, 2026Xuefeng Liu, Mingxuan Cao, Qinan Huang +3Molecular Optimization Large Language Model-Guided Optimization
School of Medicine, Stanford University · 2Data Science Institute, University of Chicago · 3Pritzker School of Molecular Engineering, University of Chicago +2
Beyond Drug Discovery: The Nanotechnology Molecular Optimization (NMO) Benchmark
Jun 29, 2026Matthias Blaschke, Daniel Kienzle, Zsuzsanna Koczor-Benda +3Molecular Optimization Benchmark Design
University of Augsburg · CAAPS† · Germany +2
Target-Aware Bandit Allocation for Scalable Surrogate Optimization in Chemical Space
Jun 25, 2026Mohammad Haddadnia, Yuvan Chali, Abhilash Jayaraj +4Multi-Armed Bandits Molecular Optimization
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
Sesame: Structure-Aware Molecular Generation via Spatial Density-Map Conditioning
Jun 22, 2026Konstantin Yatsenko, Arvind ThiagarajanMolecular Optimization Structure-Based Drug Design
Tessel Biosciences, Inc., 750 Main Street, Cambridge, MA 02139
Reward Transport: Property Control in Flow Matching via Noise-Space Alignment
Jun 13, 2026Kehan Guo, Yili Shen, Yujun Zhou +4Flow Matching Molecular Optimization
University of Notre Dame · Carnegie Mellon University
APCyc: Property-Informed Design of Cyclic Peptides via Automated Cyclization
Jun 11, 2026Yifan Zhao, Lang Qin, Jintai ChenMolecular Optimization Molecular Generation
AI Thrust The Hong Kong University of Science and Technology (Guangzhou) Guangzhou, China · AI-Peptide Drug Design Joint Laboratory The Hong Kong University of Science and Technology (Guangzhou) Guangzhou, China
Range-Aware Bayesian Optimization for Discovering Diverse Designs within Target Property Windows
Jun 10, 2026Shengli Jiang, Jason Wu, Charles M. Schroeder +1Molecular Optimization Bayesian Optimization
Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA
My Chemical Harness: Evolutionary Molecular Design over Synthetic Pathways with Large Language Model Agents
Jun 8, 2026César Ojeda, Darius A. Faroughy, Maryam Karimi +3Molecular Optimization LLM Agents
Institute of Mathematics, Faculty of Science, University of Potsdam, Campus Golm, Building 9, Karl-Liebknecht-Str. 24–25, 14476 Potsdam-Golm, Germany · NHETC, Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA · Potsdam Transfer, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam. +1
In-Context Learning for Latent Space Bayesian Optimization
Jun 8, 2026Tuan A. Vu, Harri Lähdesmäki, Julien MartinelliSynthetic Data Pretraining Molecular Optimization
Aalto University
Closing the Prior-Posterior Loop: Self-Reflective Molecular Design with Analysis-Driven LLM Iteration
Jun 8, 2026Junyi Gong, Zijie Qiu, Ben Zhong TangMolecular Optimization LLM Self-Refinement
Faculty of Chemistry, Shenzhen MSU-BIT University · School of Science and Engineering, Chinese University of Hong Kong (Shenzhen) · Department of Chemistry, Hong Kong University of Science and Technology
Generative Molecular Morphing for Flexible-Size Design via Unbalanced Optimal Transport
Jun 5, 2026Malte Franke, Stefan P. Schmid, Zarko Ivkovic +2Molecular Optimization Molecular Graph Generation
ETH Zürich · NCCR Catalysis
Genotype-Conditioned Molecular Generation via Evidence-Grounded Multi-Objective Latent Perturbation in Diffusion Models
May 31, 2026Brenda Nogueira, Gisela A. Gonzalez-Montiel, Nitesh V. Chawla +1Molecular Optimization Oncology
Department of Computer Science and Engineering University of Notre Dame Notre Dame, IN, 46556 · Department of Chemistry and Biochemistry University of Notre Dame Notre Dame, IN, 46556 · Lucy Family Institute for Data & Society University of Notre Dame Notre Dame, IN, 46556
Fine-Tuning Diffusion Models for Molecular Generation via Reinforcement Learning and Fast Sampling
May 31, 2026Guang Lin, Shikui Tu, Lei XuMolecular Optimization Diffusion Model Fine-Tuning
Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China · Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen, Guangdong, China
Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design
May 30, 2026Zaifei Yang, Weiyu Chen, Yaqing Wang +1Molecular Optimization Multi-Agent LLM Systems
1The Hong Kong University of Science and Technology · 2City University of Hong Kong · Beijing Institute of Mathematical Sciences and Applications
Constrained Flow Optimization via Sequential Fine Tuning for Molecular Design
May 28, 2026Sven Gutjahr, Riccardo De Santi, Luca Schaufelberger +2Constrained Generative Modeling Molecular Optimization
Department of Computer Science, ETH Zurich · ETH AI Center · NCCR Catalysis, Switzerland +1
Mixing Vector Model for Copolymer Inference via Mixed Integer Linear Programming
May 28, 2026Jianshen Zhu, Raveena Rai, Taiyo Sohkawa +4Molecular Optimization Materials Property Prediction
Department of Information Science and Technology, Tokyo University of Science, Noda 278-8510, Japan · Discrete Mathematics and Computational Intelligence Laboratory, Department of Mathematics, Quaid-i-Azam University, Islamabad 45320, Pakistan · Graduate School of Informatics, Kyoto University, Kyoto 606-8501, Japan +3
Closed-Loop Molecular Design with Calibrated Deference
May 27, 2026Newman Cheng, Gordon Broadbent, Jason Dong +11Molecular Optimization AI Agents for Scientific Discovery
Microsoft Discovery & Quantum, Redmond, WA, USA. · Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA. · CanAm Bioresearch Inc., Winnipeg, MB, Canada. +1
PhAME: Phenotype-Aware Molecular Editing via Latent Diffusion
May 27, 2026Łukasz Janisiów, Sebastian Musiał, Bartosz Zieliński +2Molecular Optimization Classifier-Free Guidance
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
An Evolutionary Approach for Designing Stable and Highly Expressible Low-Immunogenicity Therapeutic mRNA Sequences
May 27, 2026Dhawa Sang Dong, Mausam Gurung, Suraj KandelMolecular Optimization Large Language Model-Guided Optimization
Department of Artificial Intelligence School of Engineering, Kathmandu University Dhulikhel, Nepal · Department of Electronics and Computer Engineering Kathmandu Engineering College, Trivubhan University Kathmandu, Nepal · Hetauda School of Management and Social Science Trivubhan University Hetauda, Nepal
MolLingo: Molecule-Native Representations for LLM-Powered Scientific Agents
May 27, 2026Thao Nguyen, Heng JiMolecular Optimization Multi-Agent LLM Systems
Siebel School of Computing and Data Science, University of Illinois Urbana-Champaign
DGLD: Domain-Gated Latent Diffusion for the Discovery of Novel Energetic Materials
May 26, 2026Yehudit Aperstein, Alexander ApartsinMolecular Optimization Latent Diffusion Models
Department of Intelligent Systems, Afeka Tel-Aviv College of Engineering, Israel. · School of Computer Science, Faculty of Sciences, HIT-Holon Institute of Technology, Israel.
Don't Retrain, Just Reuse: Recovering Dual-Target Molecules from Single-Target Diffusion Models
May 25, 2026Qingyuan Zeng, Pengxiang Cai, Zixin Guan +5Molecular Optimization Molecular Generation
The Hong Kong University of Science and Technology (Guangzhou) · Guangzhou University of Chinese Medicine
Molecular Lead Optimization via Agentic Tool Planning
May 21, 2026Lingxiao Li, Haobo Zhang, Ruohao Fan +2Molecular Optimization Large Language Model-Guided Optimization
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
Fine-tuning Pocket-Aware Diffusion Models via Denoising Policy Optimization
May 17, 2026Yuan Xue, Daniel Kudenko, Megha KhoslaMolecular Optimization Diffusion Model Fine-Tuning
L3S Research Center, Hanover, Germany · Delft University of Technology, Delft, Netherlands
Controllable Molecular Generative Foundation Models
May 14, 2026Yihan Zhu, Yuhan Liu, Weijiang Li +2Molecular Optimization Molecular Graph Generation
University of Notre Dame
Towards Discovery of Polymers for Insulin Delivery via Physics-Grounded Agentic Workflows
May 12, 2026Martins OtunMolecular Optimization Large Language Model-Guided Optimization
1Algonix AI Ltd., Scotland, United Kingdom
ToolMol: Evolutionary Agentic Framework for Multi-objective Drug Discovery
May 12, 2026Andrew Y. Zhou, Sharvaree Vadgama, Sumanth Varambally +3Molecular Optimization AI Agents for Scientific Discovery
Department of Computer Science and Engineering, UC San Diego, La Jolla, California, United States · Department of Computer Science, Stanford University, Stanford, California · Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California
MolDeTox: Evaluating Language Model's Stepwise Fragment Editing for Molecular Detoxification
May 12, 2026Jueon Park, Wonjune Jang, Jiwoo Lee +2Molecular Optimization LLM Evaluation
Korea University · Myongji University · AIGEN Sciences
SLIM: Sparse Latent Steering for Interpretable and Property-Directed LLM-Based Molecular Editing
May 11, 2026Mingxu Zhang, Yuhan Li, Lujundong Li +3Molecular Optimization LLM Interpretability
The Hong Kong University of Science and Technology (Guangzhou) · Nanjing University of Aeronautics and Astronautics · The 63rd Research Institute, National University of Defense Technology, Nanjing
FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization
May 11, 2026Qingchuan Zhang, He Cao, Hao Li +6Molecular Optimization Large Language Model-Guided Optimization
University of Science and Technology of China · International Digital Economy Academy · Peking University +5
From Single-Step Edit Response to Multi-Step Molecular Optimization
May 11, 2026Haojie Rao, Kun Li, Yida Xiong +5Molecular Optimization Constrained Optimization
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
MolWorld: Molecule World Models for Actionable Molecular Optimization
May 9, 2026Yang Qiao, Bo Pan, Hao-Wei Pang +3Molecular Optimization World Models
Emory University · Atlanta, GA, USA · Merck & Co., Inc. +1
SPADE: Faster Drug Discovery by Learning from Sparse Data
May 6, 2026Rahul Nandakumar, Ben Fauber, Deepayan ChakrabartiMolecular Optimization AI-Assisted Scientific Research
McCombs School of Business University of Texas at Austin Austin, TX · NVIDIA
Computational Design and Experimental Validation of Photoactive PARP1 Inhibitors
Apr 27, 2026Simon Axelrod, Miroslav Kašpar, Kristýna Jelínková +8Molecular Optimization Structure-Based Drug Design
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138 · Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139 · Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
C-MORAL: Controllable Multi-Objective Molecular Optimization with Reinforcement Alignment for LLMs
Apr 24, 2026Rui Gao, Youngseung Jeon, Swastik Roy +2RL for Language Models Molecular Optimization
University of California, Los Angeles · Amazon
Multi-Objective Reinforcement Learning for Generating Covalent Inhibitor Candidates
Apr 21, 2026Renee GilMolecular Optimization Molecular Generation
Independent Researcher
KinetiDiff: Docking-Guided Diffusion for De Novo ACVR1 Inhibitor Design in Fibrodysplasia Ossificans Progressiva
Apr 17, 2026Aaryan PatelMolecular Optimization Diffusion Guidance
Saugus High School, Santa Clarita, CA
LLM-Guided Dynamic Action Spaces for Synthesizable Molecular Optimization
Apr 9, 2026Tao Li, Kaiyuan Hou, Tuan Vinh +4Molecular Optimization Large Language Model-Guided Optimization
Department of Computer Science, Emory University · School of Computer Science, Carnegie Mellon University · MRC Brain Network Dynamics Unit, University of Oxford +3

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Information-Dense Synthesis for Molecular Discovery

Kasper K. Jakobsen, Eli N. Weinstein

Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, DK.

Molecular Optimization Drug Discovery

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Machine learning can accelerate molecular discovery by designing molecules and planning experiments. However, many scientific challenges demand molecules with very rare properties, and in this sparse setting, existing algorithms offer little gain over random guessing. We propose a method to efficiently search large regions of molecular space using algorithmically controlled stochastic synthesis. Rather than design, make and test individual molecules, we design and make complex mixtures, test them as a pool, then deconvolute the molecule-activity map. We optimize synthesis to encode maximal information. Theoretically, this approach can reduce the number of experiments required to find the optimal molecule among

d

candidates from

\mathcal{O}(d)

\mathcal{O}(\log d)

\mathcal{O}(1)

. In simulation, on estimated protein fitness landscapes, it finds active molecules with an order of magnitude fewer experiments than existing Bayesian optimization methods.

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