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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Latest papers 66

Oct 6, 2026stat.ML

Information-Dense Synthesis for Molecular Discovery

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)

to

\mathcal{O}(\log d)

or

\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.

Kasper K. Jakobsen, Eli N. Weinstein

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

Molecular Optimization Drug Discovery

Oct 4, 2026cs.AI

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

Molecular optimization must improve target activity and satisfy developability constraints within limited evaluation budgets. Classical methods require tailored rules or training to incorporate chemical instructions and property feedback. Frozen language models can condition edits on this information, but need explicit constraint control and relevant experience. We therefore present PharmAgent, a constraint-aware molecular search method driven by adaptive external state. Its Lagrangian controller translates violations in accepted states into accumulated constraint pressure, keeping this history separate from current property measurements. Structure-indexed replay complements this feedback with relevant evaluated transitions that guide subsequent proposals. As a curriculum progressively activates constraints, candidates and the incumbent are compared under the same current objective, and the accepted state determines the next multiplier update. We derive an exact identity that characterizes how accepted-state violations accumulate in the controller's multipliers. Across five tasks with five independent runs, PharmAgent achieves a summed area under the target-score curves (AUC) of 3.9208 in target-only search, improving over MOLLEO by 37.3%. With online constraints, it achieves a property-adjusted AUC of 0.7076, improving over the strongest online baseline, ExLLM, by 53.8%. These results rank first among all evaluated methods in both target-only and constraint-aware search. The online comparison covers all five baseline frameworks. The full system leads every ablation variant in target quality, property-adjusted performance, and Pareto hypervolume. All five molecular cases reach feasible final states, documenting target gains and trade-offs.

Nihui Shao, Guanxing Chen, Jilong Shi +6

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

Molecular Optimization Large Language Model-Guided Optimization Drug Discovery Memory-Augmented Language Model Agents

Oct 1, 2026cs.LG

Latent JEPA: Abstract Future Prediction for Latent Reasoning in Chemistry

Large language models offer a promising foundation for chemical reasoning, bringing together chemical knowledge and multistep problem solving. Chemical intuition can provide an initial sense of plausible outcomes before the details of a solution are fully worked out. Inspired by how such expectations complement explicit analysis, we study how continuous latent thoughts can be trained to anticipate informative aspects of future solutions without verbalizing every intermediate step. We introduce Latent JEPA, a framework that combines autoregressive learning with joint-embedding prediction of one or more future views. For chemical reasoning, we develop textual and molecular prediction objectives that connect latent thoughts to both subsequent reasoning and molecular outcomes. Experiments on ChemCoTBench show gains in molecular optimization and on several editing and reaction metrics. Representation analyses show that future prediction makes latent thoughts more informative about molecular outcomes and strengthens their correspondence with chemical structure. These findings support abstract future prediction as a learning principle for connecting continuous latent reasoning with scientific outcomes.

Xinjian Zhao, Yaoyao Xu, Xuemin Chen +2

School of Data Science, The Chinese University of Hong Kong, Shenzhen · Shanghai Artificial Intelligence Laboratory

Molecular Optimization Joint-Embedding Predictive Architecture Predictive Representation Learning Molecular Representation Learning Latent Reasoning

Sep 28, 2026cs.AI

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

Despite the promise of Large Language Models (LLMs) in computational chemistry, rigorous combinatorial chemistry problems remain difficult because they require quantitatively constrained molecular modification, candidate validation, and systematic revision after failed attempts. Existing tool-augmented chemical agents demonstrate useful planning and tool use, but they rarely provide a unified loop for property-driven molecular optimization and workflow-level composition. To bridge this gap, we propose Tool-Grounded Multi-Agent Reasoning for Compositional Chemical Problem Solving (TMCS), a step-by-step multi-agent framework that formalizes chemical problem solving as an interpretable, tool-augmented workflow. At the task level, specialized agents leverage external tools, few-shot trajectory memory, and structured reflection to iteratively refine solutions. At the workflow level, TMCS chains generation, understanding, editing, description, and optimization into a closed-loop pipeline. Evaluations across multiple chemical tasks demonstrate that TMCS consistently enhances chemical reasoning across both open- and closed-source base models, achieving state-of-the-art performance.

Shengqin Wang, Jie Jin, Yu Cheng +4

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

Molecular Optimization Tool-Augmented Language Model Agents LLM Agents Multi-Agent Reasoning Large Language Model-Guided Scientific Discovery

Sep 28, 2026cs.LG

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

Small-molecule optimization integrates medicinal-chemistry reasoning and computational evidence through iterative, multi-objective decisions. When large language models (LLMs) reason over optimization histories stored primarily in conversational context, they must recover candidate identities, prior evaluations, and task constraints to guide subsequent decisions. We present M3OS, a multi-agent LLM system that decouples molecular-design reasoning from optimization-state management through Monte Carlo graph search. A persistent graph links evaluated candidates, parent-child transformations and evaluation evidence, while rewards and visit statistics guide LLM-assisted parent selection. Two branches combine tool-driven candidate generation with knowledge- and case-guided medicinal-chemistry editing. An execution harness controls graph updates through structured output extraction, molecular validation and task-bound evaluation. Agents receive role-specific contexts, while the graph preserves optimization trajectories beyond their active contexts. Across three molecular optimization benchmarks, M3OS achieves higher success rates than baselines, supporting the integration of persistent search state, specialized agents and controlled execution for multi-constraint optimization.

Junjie Wang, Yaowei Jin, Ruohui Tang +7

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.

Molecular Optimization Multi-Agent LLM Systems Large Language Model-Guided Optimization Memory-Augmented Language Model Agents

Sep 28, 2026cs.LG

One Sequence, Many Decodings: CAGenMol-2 Recasts Drug Design as Masked Molecular Inference

Drug design couples property evaluation, conditional generation, structure-based design, and local optimization, yet machine learning systems typically address these capabilities with separate task-specific models. We introduce CAGenMol-2, a masked diffusion molecular language model that represents molecules, continuous scalar properties, and 3D protein pockets within a single wrapped sequence. Within this pretrained interface, downstream operations are selected by which sequence regions are observed or masked at inference, allowing one checkpoint to perform property prediction, property- and pocket-conditioned generation, and partial-constraint design without task-specific architectures or backbone fine-tuning. We further propose Adaptive Fragment Optimization (AdaFO), a gradient-free mask-and-refill search that turns the masked decoder into an iterative local molecular optimizer. On CrossDocked2020, AdaFO increases Success Rate from 30.2% to 70.8%, the best reported under this protocol, while largely preserving drug-likeness and diversity. Finally, scaffold-preserving directional editing and CRBN/VHL case studies demonstrate its use in compound design workflows spanning local molecular editing, structure-based prioritization, and downstream simulation-based screening.

Yanting Li, Enyan Dai, Lei Wang +2

The Hong Kong University of Science and Technology (Guangzhou) · Jinan University, Guangzhou

Molecular Optimization Masked Diffusion Models Structure-Based Drug Design Molecular Generation Molecular Property Prediction

Sep 23, 2026cs.AI

MolDesignBench: Evaluating LLM-based Agent for Scenario-grounded Molecular Design

Real-world molecular design remains challenging for large language model (LLM)-based agents. It requires them to interpret design contexts, satisfy multiple constraints, identify infeasible specifications, and reason over multi-step tool outputs. Existing benchmarks do not capture this complexity, focusing instead on explicit and narrow constraints, only feasible problems, and single-path solutions. To address this gap, we propose MolDesignBench, a scenario-grounded benchmark that more closely reflects real-world molecular design for evaluating tool-augmented LLM agents. MolDesignBench comprises 2K generation and optimization instances that combine implicit requirements embedded in design narratives with explicit property and functional-group constraints, including infeasible cases, and require the effective use of 17 specialized chemistry tools. Experiments across diverse frontier LLMs reveal low success rates--with the best achieving only

\sim43

%--and frequent failures in implicit-constraint reasoning, infeasibility detection, and tool reasoning. The corresponding fine-grained failure-mode analysis identifies implicit constraint interpretation and infeasibility detection as the primary bottlenecks, establishing MolDesignBench as a rigorous testbed to guide future research on chemical agents. The benchmark, tool interface, and evaluation code are publicly available.

Yongjun Jeong, Hanbum Ko, Ye Rin Kim +6

Department of Artificial Intelligence, Korea University · LG AI Research · Department of Statistics, Korea University

Molecular Optimization LLM Agent Evaluation AI Agent Benchmarks Molecular Generation

Sep 14, 2026cs.LG

Ensemble-Conditioned Molecular Design

Molecular design is typically approached as a problem of finding molecules which can adopt a single bioactive conformation. In reality, molecules occupy a distribution over conformations, and many of the properties which determine whether a candidate is viable depend on that distribution rather than on any single conformer. We reframe molecular design as an optimisation of both the modes and properties of molecules' conformational ensembles, where modes can be represented as shapes, pharmacophore profiles or protein pockets, and properties are aggregate scalars computed over the whole distribution. To realise this we introduce ensemble-conditioned guidance, a framework which conditions 3D molecular generative models on both axes simultaneously. Mode conditions are composed adaptively at inference by combining the vector fields produced under each condition. Conditions may be targeted or avoided, mixed across modalities and combined in arbitrary numbers, allowing a wide range of design tasks to be expressed with a single trained model. We introduce adaptive symmetry learning to allow conditions from different reference frames to be composed, and extend our generative framework to enable flexible-size generation. We evaluate on new benchmarks for multi-mode conditioning and ensemble property optimisation, and apply the framework to two practical drug discovery tasks, dual-target binder design and active-state-selective agonist design, where in both cases conditioning on the additional state improves the desired outcome over single-state conditioning.

Ross Irwin, Alessandro Tibo, Jon Paul Janet +1

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

Molecular Optimization Structure-Based Drug Design 3D Molecular Generation Molecular Generation Conditional Generative Modeling

Aug 31, 2026cs.LG

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

Goal-directed optimization is essential for steering molecular generators to propose candidates with desired properties. However, it is often implemented with policy-gradient reinforcement learning, which requires a generation-trajectory log-probability whose form depends on the model architecture and generation procedure. This makes an optimizer difficult to reuse across architectures and conditional generative designs. Supervised fine-tuning needs none of that machinery, but its update is driven by a fixed dataset, so the reward never enters the update. We introduce Elite-Weighted Supervised Fine-tuning (EW-SFT), which uses reward to guide elite selection of high-scoring molecules, and updates the model by its own pretraining loss on that set. Ablations show that reward information is passed primarily through elite selection, rather than through continuous weighting within the selected set. Because the update consumes only scored molecules and the model's native loss, the same rule applies across autoregressive, masked-diffusion, and discrete-flow generators, and across de novo, motif-extension, and linker-design tasks. Under a fixed budget of 3D shape alignment oracle calls on two kinase reference compounds, EW-SFT consistently outperforms the corresponding native optimizers. It further improves goal-directed optimization under a 2D similarity oracle on four held-out references and achieves comparable performance on a sample-efficiency benchmark without a trajectory-level RL formulation. These results demonstrate that EW-SFT is a unified and effective optimizer across molecular generators, design constraints, references, and oracles.

Shiyun Wa, Yifei Wang, Anna G. Green +2

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

Supervised Fine-Tuning Molecular Optimization Molecular Generation

Aug 11, 2026cs.AI

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

Hit-to-lead optimization requires iterative design of hit analogs across competing potency, selectivity, physicochemical, pharmacokinetic, safety, and synthetic constraints. We present SABLE (Synthetically-accessible Agentic Bayesian Ligand Exploration), an open-source framework that employs natural-language orchestration to guide chemical structure optimization. SABLE uses an LLM to interpret user-defined goals and route tasks, while specialized tools perform reaction-templated analog enumeration, physicochemical and ADMET property prediction, structure-based affinity scoring, and Bayesian optimization. The resulting workflow is a computational twin of the analytical and prioritization stages of the design-make-test-analyze cycle, providing provenance of each numerical output. Across single, and multi-objective optimization studies, SABLE enriches candidate sets for user-defined computational objectives while evaluating only a subset of the enumerated search space. Its modular architecture allows tools and characterization backends to be replaced by editing a simple config file, without modifying operational logic. SABLE provides an extensible decision-support framework for prioritizing synthetically constrained analogs in early-stage drug discovery.

Kelvin P. Idanwekhai, Enes Kelestemur, Benjamin Strickland +6

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

Molecular Optimization LLM Agent Orchestration Structure-Based Drug Design

Aug 2, 2026cs.AI

PolymerGPT: Multi-property Optimization with a Decoder-Based GPT Model for Generative Polymer Design

Polymer property prediction and inverse generative design targeting desired properties are two crucial tasks in machine learning-assisted polymer design. While the former has received considerable attention, there have been limited methods developed for the latter. Existing methods focus on single-property optimization in the generative process, whereas accurate prediction of macroscopic material behavior requires simultaneous control of multiple physical properties. In this paper, we provide a transformative framework for direct optimization of a large collection of polymer properties. We propose PolymerGPT, a decoder-based GPT model that incorporates up to 37 commonly used polymer properties into the generative process via learned conditioning prefixes. It also supports a scaffold condition that specifies a desired scaffold for predicted structures. Our experimental results demonstrate that PolymerGPT achieves exceptional performance for unconditional and conditional generation while maintaining high validity, uniqueness, and novelty. Conditioning on five key properties yields generated structures whose predicted values closely match all target properties simultaneously.

Charlie Pyle, Adarsh Gadari, C. Adrian Figg +3

Texas A&M University · University of Pittsburgh · Department of Chemistry, Virginia Tech +2

Molecular Optimization Molecular Generation Conditional Generative Modeling

Jul 30, 2026cs.LG

Oracle-Budgeted Molecular Optimization with Short-Term Graph Memory

Molecular optimization is commonly performed under a limited oracle budget, which makes deciding what to evaluate as important as deciding what to generate. We introduce short-term graph memory, a plug-in module that preserves the generator architecture and native update rule while learning from previously evaluated molecules to prioritize subsequent oracle queries. The module maintains an online graph neural surrogate that pre-screens each round's candidate pool, so the fixed oracle budget is spent on molecules with higher predicted utility. Applied to a fragment-based generator on a standard molecular optimization benchmark, it improves the mean top-10 score at no extra oracle cost and never falls behind the base on any oracle; the gain extends to all four generators we tested at a tight budget of one thousand calls. We then analyze how surrogate-guided selection interacts with the exploration and exploitation behavior of different generators. Its benefit at larger budgets is consistent with two properties of the backbone: how broadly it searches, and how effectively its native search already exploits oracle feedback. We provide a simple way to spend a fixed oracle budget more selectively, and evidence on which generators benefit from it.

Jiannan Yang, Veronika Thost, Xiang Ling +1

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

Molecular Optimization Surrogate-Assisted Optimization Black-Box Optimization Molecular Generation

Jul 29, 2026cs.LG

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

Oracle-limited molecular optimization gives reward only after a complete molecule is generated, while each rollout requires many local next-token decisions. This delayed-feedback interface makes molecular policy optimization myopic: an optimizer can learn that a molecule was good without knowing which intermediate actions made it good. We introduce Q-Steer, a rollout-time action-value steering primitive for molecular language models. Q-Steer uses an offline-trained and frozen prefix-action value scorer, PAVS-Q, that estimates the downstream reward of taking a candidate next token under a partial SMILES prefix, then adds a normalized value bonus to sampling logits. The optimizer update rule and online oracle budget are unchanged; the claim is fixed-online-oracle performance, not equal total compute. On PMO23 with a fixed 10,000-call online budget, complete factorial studies across two molecular language-model backbones and four optimizers show that Q-Steer improves mean valid-unique score in all eight backbone-optimizer cells, with positive macro mean-score gains between +0.033 and +0.049 and 18-20 task wins per cell. Mechanism controls show that action identity matters: prefix-broadcast values are nearly neutral, while shuffled action values harm performance. These results support Q-Steer as a reusable rollout-time action-value wrapper that improves average molecular optimization reward across optimizer families and policy backbones without changing the online oracle budget.

Xinyu Wang, Jinbo Bi, Minghu Song

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

Molecular Optimization Large Language Model-Guided Optimization Policy Optimization

Jul 22, 2026cs.LG

OLEDLM: A Unified Language Model for OLED Molecular Design

The development of organic light-emitting diode (OLED) materials faces the compounded challenges of an astronomically large chemical space, stringent quantum-chemical constraints, and a scarcity of labeled data. Although the question of OLED generation is important, few models have been trained effectively for this specific domain. We propose an inverse molecular design framework based on causal language models: given target optoelectronic properties (e.g., excitation energy, oscillator strength), our model directly generates OLED SMILES sequences satisfying the specified constraints. We employ a multi-stage strategy: first, we establish a foundational chemical language model using a LLaMA-style transformer architecture. To the best of our knowledge, this represents the first successful adaptation of LLMs specifically for the OLED domain, bridging the gap between generic molecular generation and the stringent structural requirements of optoelectronic materials. Second, we fine-tune property predictors based on a BERT model pre-trained on our large-scale OLED dataset. Then, we perform Reinforcement Learning on our fine-tuned model, leveraging our property predictor, for better SMILES generation. Finally, through DFT verification, we demonstrate that our framework can efficiently navigate the OLED chemical space, generating novel candidates with high structural validity and optimized optoelectronic properties.

Fukang Wen, Yuchong Tang, Jingyuan Li +9

1Tsinghua University · 5MathonAI Team · 2Beijing Institute of Mathematical Sciences and Applications +2

Molecular Optimization Materials Science Molecular Generation

Jul 21, 2026stat.ML

Boltzmann-Expected Molecular Design with Decoupled Annealing Flows

Most 3D properties relevant to molecular design, including free energies and shape descriptors, are

\textit{expectations}

over the Boltzmann distribution over 3D configurations of a molecular graph. However, existing property-guided generative models tie each property to a single structure, ignoring the underlying ensemble. We recast 3D molecular design as

\textbf{Boltzmann-expected design}

and realise it with

\textbf{DECAF}

(Decoupled Annealing Flows), which factorise the joint distribution over graphs and coordinates into two conditional flow models: a graph-conditioned flow

p(x\mid\mathcal{G})

, acting as a

\textit{Boltzmann emulator}

, and a coordinate-conditioned flow

p(\mathcal{G}\mid x)

, proposing new graphs from 3D information. By alternating the two flows, DECAF optimises molecular graphs with a simulated-annealing acceptance rule whose scoring function is evaluated on ensembles drawn from

p(x\mid\mathcal{G})

, making ensemble statistics, not single-conformer properties, the design target. The resulting loop requires no retraining to change objectives. On GEOM-Drugs, we show that ensemble-aware optimisation produces graphs whose mean radius of gyration and solvent-accessible surface area consistently shift toward targets, while single-conformer optimisation degrades on larger drug-like molecules where Boltzmann distributions are broadest. DECAF extends to multi-objective trade-offs and, uniquely among 3D generative models, to

\textbf{higher-moment design}

: jointly optimising an ensemble property's variance and skewness to produce flexible molecules biased to a prescribed conformational regime: we verify the conformational distributions of these higher-moment designs with all-atom MD simulations.

Selma Moqvist, Richard Beckmann, Ross Irwin +2

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

Molecular Optimization Molecular Graph Generation 3D Molecular Generation Molecular Generation

Jul 21, 2026cs.LG

DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Models

Designing small molecule ligands that bind with high affinity to specific protein pockets is a fundamental goal in drug discovery, as small molecules constitute a major fraction of approved therapeutics. Recent breakthroughs in structure prediction, such as AlphaFold-3 and Boltz-2, enable accurate biomolecular interaction prediction and show promise as foundation models for downstream tasks, including binding affinity prediction. We propose to leverage these models and introduce DBMol, a new structure predictor-guided framework for de novo small molecule design. DBMol formulates an alternating optimization and projection process. In the optimization stage, DBMol starts from an initial molecule and uses gradient-based optimization to improve pocket-specific interactions and predicted binding affinity using a structure prediction model. In the projection stage, a flow-matching model maps the optimized molecular graph to discrete and chemically valid molecules. Experiments show that DBMol effectively optimizes the Boltz-2 affinity proxy and generates molecules with strong predicted affinity and specificity under Boltz-2 evaluation. To reduce self-confirmation bias, we further evaluate generated molecules using held-out metrics, including AF3-based evaluation. DBMol substantially improves pocket coverage while maintaining molecular diversity over unconditional generation, and is competitive under held-out metrics despite the absence of reference-ligand supervision. These results support the promise of structure prediction models as effective optimization signals for de novo molecular design.

Yiming Qin, Kai Yi, Miruna Cretu +3

EPFL, Switzerland · MRC-LMB, UK · University of Cambridge, UK

Protein-Ligand Binding Affinity Prediction Molecular Optimization Structure-Based Drug Design Molecular Generation Drug Discovery

Jul 21, 2026cs.LG

Adopting Reinforcement Learning with Verifiable Rewards for Molecular Generation

Leveraging large language models (LLMs) for molecular generation has shown remarkable potential in chemical and drug design. Current methods primarily rely on supervised training or fine-tuning with limited datasets, which are insufficient to capture complex molecular design objectives. While some approaches attempt to guide generation toward specific goals, they often lack direct optimization mechanisms, making it difficult to align generated molecules with desired properties. To tackle these challenges, we propose \textbf{LLMol}, a principled reinforcement learning framework that directly incorporates verifiable rewards for targeted molecule generation. The key insight is to formulate molecular design as a goal-conditioned sequence prediction task, where verifiable rewards serve as explicit supervision to drive generation toward desired objectives. LLMol follows a two-stage training paradigm combining supervised learning and reinforcement learning. In the first stage, large language models are supervised fine-tuned to capture chemical syntax and molecular distributions. In the second stage, we introduce Reinforcement Learning with Verifiable Rewards (RLVR), which directly integrates property-based reward signals to guide molecular generation toward task-specific objectives. To address the high variance and instability common in discrete sequence optimization, we adopt Group Relative Policy Optimization (GRPO), a stable on-policy algorithm that smooths reward signals and improves training robustness. This framework enables LLMol to effectively handle a range of molecular design tasks, including single-property targeting (e.g., penalized logP, QED) and structure-constrained optimization. Experimental results demonstrate that LLMol consistently outperforms existing methods, achieving higher success rates and improved efficiency across diverse molecular benchmarks.

Mingxuan Ouyang, Hao Lan, Wanyu Lin

Molecular Optimization Reinforcement Learning with Verifiable Rewards Molecular Generation

Jul 14, 2026cs.LG

Sample Efficient Generative Optimization for Molecular Design

Molecular optimization in drug discovery, materials design, and catalysis requires searching vast chemical spaces under tight evaluation budgets, since high-fidelity oracles and experimental measurements are costly. The practical impact of an optimization method therefore hinges on its sample efficiency: how few evaluations it needs to find strong candidates. We introduce Sample Efficient Generative Optimization (SEGO), a framework for Bayesian optimization on adaptively generated molecules. In SEGO, a probabilistic surrogate model forms a hypothesis about where hits lie in chemical space, a generative model is steered to propose candidates in that region, the most promising candidate is selected via an acquisition function, and the resulting oracle call is used both to sharpen the surrogate and to anchor the generator in real reward. SEGO attains state-of-the-art performance on the practical molecular optimization (PMO) benchmark using only one tenth of the oracle calls consumed by other methods, and on a multiparameter docking task it reaches ten hits in roughly half the oracle calls of existing approaches. These gains move molecular optimization closer to campaigns driven by direct experimental feedback.

Sarina Kopf, Cristina Nevado, Philippe Schwaller

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

Molecular Optimization Surrogate-Assisted Optimization Bayesian Optimization Molecular Generation Drug Discovery

Jul 14, 2026cs.LG

Generating Developable 3D Molecules via Pocket-Conditioned Diffusion and Property-Aware Optimization

Drug discovery and development is time-consuming and resource-intensive, motivating computational approaches such as diffusion models for de novo drug design. Many such models follow the structure-based drug design (SBDD) paradigm, generating molecules to fit a target binding pocket. However, existing diffusion-based SBDD methods typically couple pocket and ligand representation learning, model interactions only at the atom level, and prioritize binding affinity over other developability properties. Here, we introduce conDitar-dev, a conditional diffusion-based SBDD framework for generating ligands with strong binding affinities and favorable ADMET properties. It consists of three modules: msPRL, a pretrained multi-scale pocket representation learning module; conDitar, a pocket-conditioned diffusion model guided by msPRL representations; and paOPT, a generation-time method for optimizing ligand developability. On a newly curated benchmark of human disease targets, conDitar outperforms state-of-the-art SBDD baselines, achieving an average binding score of -8.85 kcal/mol. Across five ADMET properties, conDitar-dev improves performance by up to 73% over conDitar. To further validate the abilities of conDitar-dev to generate developable molecules, we have applied it to two validated druggable targets: programmed death-ligand 1 (PD-L1) and colony-stimulating factor 1 receptor (CSF1R) proteins. Top-ranked generatively designed molecules and their analogs have been experimentally synthesized and biologically tested. Two molecules generated directly by conDitar-dev for PD-L1 exhibited SPR-derived

K_D

values of 3.49 and 3.75

μ

M, respectively. Hit expansion based on conDitar-dev-designed molecules identified selective CSF1R inhibitors with IC

_{50}

values as low as 200 nM, while also uncovering opportunities for drug repositioning.

Ruoxi Gao, Jiangweizhi Peng, Ziqi Chen +10

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

Molecular Optimization Structure-Based Drug Design 3D Molecular Generation Molecular Generation Conditional Diffusion Models

Jul 13, 2026cs.LG

Gene Expression-Informed Jointly Controlled Generative Modeling for Precision Molecular Design

Precision molecular design aims to discover personalized drug candidates through joint control of multiple conditions, such as biological relevance and molecular design strategies. Biological relevance reflects cellular functional states under disease or perturbation conditions, while molecular design strategies provide complementary guidance in terms of structural intentions and property optimization. In this study, we propose JoPMol, a jointly controlled precision molecular generative model that integrates biological states encoded by gene expression profiles with molecular structure information expressed in text, and chemical properties quantified by numerical values within a unified modeling framework. This formulation enables coordinated generation and optimization of candidate molecules under joint condition control. Experimental results show that JoPMol outperforms state-of-the-art methods across multiple evaluation metrics. Moreover, JoPMol demonstrates strong generalization ability in both transfer tasks and biologically grounded simulation scenarios, validating its effectiveness for precision molecular design. The source code is publicly available at https://github.com/hala-yh/JoPMol.

Hang Yuan, Chen Li, Wenjun Ma +2

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

Molecular Optimization Molecular Generation Conditional Generative Modeling Drug Discovery

Jul 3, 2026cs.LG

A Precedent-Guided Co-Scientist for Side-Effect-Aware Drug Redesign

We propose PRECEDE, a precedent-guided co-scientist for side-effect-aware drug redesign that revises a parent compound to mitigate a specified side effect while preserving therapeutic function. Rather than isolated molecular generation, PRECEDE frames redesign as evidence-grounded reasoning over drug--side-effect associations, biomedical knowledge graphs, and precedents of safety-driven optimization, coordinated by an LLM orchestrator with explicit policies and human-review checkpoints. We position PRECEDE as a human-supervised AI-for-science workflow in which hypotheses remain auditable, falsifiable, and bounded by prior pharmacology.

Yujin Kim, Charmgil Hong

Department of Computer Science and Electrical Engineering, Handong Global University, Pohang, Republic of Korea.

Molecular Optimization Scientific Workflow Automation Large Language Model-Guided Scientific Discovery Drug Discovery

Jul 3, 2026cs.LG

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

Molecular optimization often starts from a pretrained generative model that captures a broad prior over valid molecular structures. At test time, however, the goal is not to sample from this prior, but to use a limited oracle budget to shift generation toward task-specific high-reward molecules. We study this adaptation problem for discrete diffusion models. Each online round couples several choices. The loop must decide which candidates to evaluate, how rewards become model updates, which feedback to reuse, and how far to move beyond the pretrained prior. These choices have mostly been studied in isolation, leaving open whether they complement one another, become redundant, or interfere inside a full online adaptation loop. We conduct controlled studies across six small-molecule binding-affinity tasks and three protein-fitness tasks. We find that acquisition, reward shaping, and model debiasing provide complementary routes to higher reward, especially for small molecules. Replay further stabilizes learning, while validity penalties keep small-molecule exploration on the valid molecular manifold. Together, these findings point to a practical recipe for feedback-efficient molecular optimization: online fine-tuning with acquisition, reward shaping, debiasing, replay, and validity control. This recipe outperforms offline fine-tuning and inference-time search baselines under matched oracle-call budgets and GPU-hour accounting. The gains are largest when high-reward candidates require larger shifts from the pretrained prior.

Trevor Chen, Ariel Dai, Jason Yang +8

1Caltech · ETH Zurich · ETH AI Center +1

Molecular Optimization Diffusion Model Fine-Tuning Diffusion Models

Jul 1, 2026cs.LG

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

Scientific reasoning is an increasingly important capability of large language models, yet improving the robustness and efficiency of training such reasoning remains a key open challenge. We study this problem in instruction-based molecular optimization, where answer-only supervised fine-tuning (SFT) collapses multi-step reasoning and reinforcement learning with verifiable rewards (RLVR) suffers from sparse feedback. Reference-guided Policy Optimization mitigates both by anchoring policy updates to dataset-provided references, but its effectiveness is tightly coupled to reference quality: weak or misaligned references impose a performance ceiling. To overcome this ceiling, we propose active reasoning, a paradigm in which the policy actively decides, on a per-instance basis, when to imitate a reference and when to reinforce its own discoveries, while continuously upgrading what it imitates. We instantiate this paradigm as Active Group Relative Policy Optimization (Active-GRPO), realized through two coupled mechanisms: active imitate-reinforce and active referencing. The former performs imitation learning when the reference still outperforms the policy's own candidates, and shifts to self-improvement via reinforcement learning once the policy has generated molecules that surpass the reference. The latter continuously upgrades the reference itself by replacing it with the best policy-generated candidate discovered so far, progressively raising the imitation target and ensuring that reference guidance remains informative-rather than restrictive-throughout training. Across TOMG-Bench MOLOPT, Active-GRPO improves average SRxSim from 0.0959 for GRPO and 0.1665 for RePO to 0.1773 under matched three-seed evaluation, with statistically significant gains on LogP, MR, and QED.

Xuefeng Liu, Mingxuan Cao, Qinan Huang +3

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

Molecular Optimization Large Language Model-Guided Optimization Group Relative Policy Optimization Policy Optimization Imitation Learning RL Fine-Tuning

Jun 29, 2026cs.LG

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

Generative molecular design is shaped by simple proxy benchmarks for drug-like properties and models pretrained on large pharmaceutical datasets. This combination yields strong benchmark metrics but limits transferability to domains structurally distinct from drug discovery. To overcome this limitation and drive discovery toward real, scientifically grounded targets, we introduce the Nanotechnology Molecular Optimization (NMO) Benchmark, which bridges machine learning (ML) and quantum materials science. NMO acts simultaneously as a rigorous testbed for the ML community and a discovery engine for nanotechnology research. The suite replaces proxy oracles with quantum simulations and introduces strict protocols that prioritize scientific utility over leaderboard-oriented overfitting. The physics-based NMO tasks impose hard structural constraints and rugged fitness landscapes, posing fundamentally new requirements on generative models. Notably, advanced molecular optimization methods underperform much simpler approaches on the NMO tasks. We develop a new baseline method identifying the critical components to solve the NMO tasks, including a novel representation for modeling structural constraints and a domain-agnostic pretraining strategy to eliminate pharmaceutical dataset bias. Our results surpass state-of-the-art physical properties and reveal previously unknown structural motifs, offering new insights for the nanotechnology community and demonstrating that ML can drive genuine scientific discovery.

Matthias Blaschke, Daniel Kienzle, Zsuzsanna Koczor-Benda +3

University of Augsburg · CAAPS† · Germany +2

Molecular Optimization Benchmark Design Molecular Generation Molecular Representation Learning Computational Materials Science

Jun 25, 2026cs.LG

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

Identifying high-utility candidates from massive discrete spaces under expensive evaluations is a recurring challenge across the sciences, with structure-based drug discovery as a prominent example. While surrogate-based optimization can increase sample efficiency by reducing the number of expensive evaluations, modern molecular libraries have reached billions to trillions of compounds, making full-library surrogate inference itself a major computational bottleneck. We introduce BOBa, a bandit-guided surrogate optimization framework that eliminates full-library inference by adaptively allocating computation across partitions of the action space. By treating partitions as arms in a multi-armed bandit, BOBa concentrates inference and evaluations on empirically promising partitions while maintaining principled exploration. Experiments on real-world synthesis-on-demand libraries demonstrate that optimism-under-uncertainty bandits, combined with meaningful action space partitioning, are essential for effective allocation of inference and evaluations. Our findings reveal a tunable tradeoff between screening performance and surrogate inference cost, which supports practical optimization over current libraries, and establishes a viable route to ultra-large library virtual screening.

Mohammad Haddadnia, Yuvan Chali, Abhilash Jayaraj +4

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

Multi-Armed Bandits Molecular Optimization Surrogate-Assisted Optimization Virtual Screening Drug Discovery

Jun 22, 2026cs.LG

Sesame: Structure-Aware Molecular Generation via Spatial Density-Map Conditioning

Generative molecular models for drug design are a promising direction with much active research. In the next phase of computational drug design, such models will need to understand small molecule structure and protein-ligand interactions, and they will need to possess the machinery to generate molecules de novo. Incorporating each feature poses a critical challenge. Equally important, yet often treated as secondary, is the ability to grow a molecule from a partial starting point -- a scaffold or fragment supplied by a chemist -- which is the central operation of lead optimization. We present Sesame (Spatial Evoformer for a Structure-Aware Molecular Engine), a diffusion-based molecular generation model that leverages a novel spatial pairformer module to condition on partial molecular structure and the surrounding protein pocket, both expressed as continuous spatial density maps. This single conditioning mechanism supports both de novo generation and fragment-conditioned lead optimization, letting a medicinal chemist prune a hit to a scaffold and have Sesame grow it in productive ways. In addition to this module, we also introduce a diffusion framework for joint denoising of atom types, bond types, and positions, along with a trajectory finetuning scheme that trains on the model's own sampling rollouts to improve generation quality. Sesame is trained on a large corpus of ligand-only and protein-ligand datasets.

Konstantin Yatsenko, Arvind Thiagarajan

Tessel Biosciences, Inc., 750 Main Street, Cambridge, MA 02139

Molecular Optimization Structure-Based Drug Design 3D Molecular Generation Molecular Generation Conditional Generative Modeling Diffusion Models

Jun 13, 2026cs.LG

Reward Transport: Property Control in Flow Matching via Noise-Space Alignment

The coupling in flow matching -- the rule pairing noise vectors with data points -- is typically treated as a computational choice. We show that this coupling can instead serve as an alignment interface: by matching noise and data according to a target molecular property, it embeds controllable structure directly into the learned flow field. Building on this view, we introduce Reward Transport, which uses optimal transport coupling at training time to align a scalar noise-space coordinate with molecular rewards; at inference, varying this coordinate steers the generated distribution without requiring an oracle, reward model, gradient guidance, or additional computation. In the coupling-preserving limit, thresholding this coordinate recovers the Cross-Entropy Method's truncated reward distribution, providing a principled, continuously adjustable distribution-level control knob. Empirically, on ZINC-250K and GuacaMol, sweeping the scalar induces monotone control of logP and consistent QED control over its operating range; most tellingly, the same knob produces opposite structural responses for different targets, growing molecules for logP but shrinking them for QED, which rules out a generic size bias. The interface is complementary to classifier-free guidance and conditional flow matching, while a negative result under epsilon-prediction diffusion clarifies where coupling-level alignment is structurally absent. Code: https://github.com/KehanGuo2/reward-transport

Kehan Guo, Yili Shen, Yujun Zhou +4

University of Notre Dame · Carnegie Mellon University

Flow Matching Molecular Optimization Molecular Generation Flow-Based Generative Modeling

Jun 11, 2026cs.AI

APCyc: Property-Informed Design of Cyclic Peptides via Automated Cyclization

Cyclic peptides represent a promising class of therapeutic compounds in modern drug discovery, often offering improved stability and binding affinity. However, the de novo design of cyclic peptides remains challenging because methods must identify pocket-adaptive cyclization patterns and linkage sites while simultaneously controlling drug-relevant properties. This challenge is particularly pronounced for recent generative models trained predominantly on linear peptide data, which may fail to capture cyclization-specific constraints. To address the limitation, we introduce APCyc, a target-aware de novo cyclic peptide generation framework that explicitly models cyclization and jointly optimizes multiple essential physicochemical properties. By using an expanded residue vocabulary and explicitly encoding cyclization-site and linkage-type information, APCyc learns cyclization-aware representations and leverages Bayesian posterior guidance to steer sampling toward cyclic peptides satisfying multiple property objectives. Experimental results demonstrate that our model learns target-dependent cyclization preferences, and enables effective and controllable multi-property optimization for cyclic peptide design. The source code of this paper is available at https://github.com/HKUSTGZ-ML4Health-Lab/APCyc.

Yifan Zhao, Lang Qin, Jintai Chen

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

Molecular Optimization Molecular Generation Conditional Generative Modeling Drug Discovery

Jun 10, 2026cs.LG

Range-Aware Bayesian Optimization for Discovering Diverse Designs within Target Property Windows

In many materials and product design problems, desirable candidates exhibit properties that fall within an acceptable range rather than achieve a single optimum. Recovering multiple, distinct solutions that satisfy such specifications is also practically valuable, as some candidates may be preferred for reasons of cost, processability, or robustness that are difficult to encode directly in an objective function. Here, we develop a range-aware Bayesian optimization (BO) framework in which the acquisition function directly scores the posterior probability that a candidate satisfies a target range. The framework naturally extends to parallel pursuit of multiple distinct specifications over a shared candidate space. Across benchmark tasks, range-aware acquisition consistently recovers larger and more diverse sets of valid designs than standard BO baselines and recent goal-seeking methods. Its utility is further demonstrated in two practically motivated design case studies involving optimizing reaction conditions for polymer synthesis and sequence-defined oligomer discovery for prescribed optical absorption bands, supported by quantum chemical calculations. These results suggest that range-aware BO can provide a practical and sample-efficient foundation for specification-driven design, particularly when design flexibility and solution diversity are important considerations.

Shengli Jiang, Jason Wu, Charles M. Schroeder +1

Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA

Molecular Optimization Bayesian Optimization Safe Bayesian Optimization Constrained Optimization Quality-Diversity Optimization

Jun 8, 2026physics.chem-ph

My Chemical Harness: Evolutionary Molecular Design over Synthetic Pathways with Large Language Model Agents

Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes. We introduce My Chemical Harness, a route-native evolutionary framework for goal-directed molecular design in which the search population consists of executable synthetic pathways rather than isolated molecular graphs. Each route is built from purchasable building blocks and reaction templates, executed by deterministic chemistry tools, and scored through task-specific molecular oracles. Large language models (LLMs) are used only as strategy controllers that select high-level preferences over route length, move type, reaction families, motifs, and exploration pressure, while local code performs route construction, validation, deduplication, scoring, selection, and memory updates. This separation lets the LLM guide exploration without allowing it to introduce hallucinated products or unsupported reaction steps. On a soluble epoxide hydrolase proxy task, our LLM agent improves over single pass LLM and deterministic controllers, reaching state-of-the-art performance across the sEH score, synthetic accessibility score, and AiZynthFinder success rate metrics. These results suggest that constrained LLM agents can play a significant role in molecular discovery without requiring training, fine-tuning, or dedicated generative models.

César Ojeda, Darius A. Faroughy, Maryam Karimi +3

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

Molecular Optimization LLM Agents

Jun 8, 2026cs.LG

In-Context Learning for Latent Space Bayesian Optimization

Bayesian optimization (BO) is a central tool for sample-efficient design, and latent-space Bayesian optimization (LSBO) extends it to structured objects such as molecules and proteins. In parallel, tabular foundation models such as TabPFN and TabICL now achieve state-of-the-art regression performance and are increasingly used as BO surrogates. Because their Bayesian behavior is induced by large synthetic pretraining collections, the composition of this pretraining distribution is crucial. LSBO creates a distinctive mismatch: the induced map from latent code to objective value differs markedly from the regression tasks used to train current in-context models. We address this mismatch by complementing the pretraining stage of tabular foundation model surrogates with synthetic optimization tasks defined on the latent space of a molecular VAE. The continued-pretraining objective features a regularizer that anchors the model to the original checkpoint, preserving its broad regression prior while avoiding overspecialization to the adaptation tasks. On held-out molecular optimization benchmarks, the resulting model achieves strong performance, supporting the relevance of LSBO-specific adaptation for in-context surrogates.

Tuan A. Vu, Harri Lähdesmäki, Julien Martinelli

Aalto University

Synthetic Data Pretraining Molecular Optimization Surrogate Modeling Bayesian Optimization Latent Space Optimization Tabular ICL

Jun 8, 2026physics.chem-ph

Closing the Prior-Posterior Loop: Self-Reflective Molecular Design with Analysis-Driven LLM Iteration

Can a general-purpose large language model design molecules with the precision of a seasoned chemist? Current LLM-based frameworks answer this question with scalar feedback loops - generate, score, reject - that amount to informed trial-and-error. Here we show that replacing a single number with the full physicochemical rationale from first-principles calculations transforms the LLM from a stochastic sampler into a causal reasoner. Our system couples retrieval-augmented generation with a self-reflection module that feeds orbital energies, atomic charges, and electron densities - rather than compressed scores - back into the design loop. On HOMO-LUMO gap targets from 2.0 to 5.0 eV, this structure-property-relationship (SPR) reflection achieves a deviation as low as 0.0014 eV with a 100% success rate under the SPR+RAG configuration, consistently outperforming scalar-feedback and non-reflective baselines in median and mean deviation. The framework generalizes seamlessly to dipole-moment design, synthetic accessibility optimization, and molecular docking, and proves robust across 7 distinct LLM backbones. These results establish a new paradigm: when the model understands not only that a molecule fails, but why, iterative molecular design becomes genuinely mechanistic.

Junyi Gong, Zijie Qiu, Ben Zhong Tang

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

Molecular Optimization LLM Self-Refinement Molecular Generation

Jun 5, 2026cs.LG

Generative Molecular Morphing for Flexible-Size Design via Unbalanced Optimal Transport

The success of generative molecular design hinges on a model's steerability toward high-reward samples. Because many molecular properties are intrinsically linked to molecular size, accurately capturing the joint distribution of properties and the number of atoms is essential. However, current diffusion and flow-based models fix the number of atoms, which ultimately limits their ability to navigate this complex relationship. To address this, we introduce Morph, a flexible-size generative model for conditional and unconditional 3D molecular design based on geometric graphs. By dynamically adapting size, Morph can seamlessly integrate existing structural priors, like scaffolds, and significantly enhances property steering. We show that Morph matches current fixed-size state-of-the-art models while offering the benefit of unparalleled sampling flexibility. We demonstrate out-of-distribution generation in regimes where previous models fail, paving the way for enhanced generative modeling for molecular design.

Malte Franke, Stefan P. Schmid, Zarko Ivkovic +2

ETH Zürich · NCCR Catalysis

Molecular Optimization Molecular Graph Generation 3D Molecular Generation Molecular Generation Conditional Generative Modeling

May 31, 2026cs.LG

Genotype-Conditioned Molecular Generation via Evidence-Grounded Multi-Objective Latent Perturbation in Diffusion Models

Developing effective anticancer therapeutics remains challenging due to tumor heterogeneity and the absence of well-defined molecular targets across cancer subtypes. Generative models conditioned on cancer genotypes offer a promising avenue for personalized drug discovery, yet existing approaches lack explicit optimization for simultaneous sensitivity, synthesizability, and mechanistic binding plausibility. We present a latent-space optimization approach for a pretrained genotype-to-drug diffusion model, introducing a learnable perturbation over the molecular latent space optimized via gradient ascent to maximize a composite reward combining predicted drug sensitivity (AUC), drug-likeness (QED), and synthetic accessibility (SAS). Critically, biological realism is enforced by grounding both reward design and evaluation in experimentally-derived cancer cell line data and validated pharmacologic signals, anchoring candidate generation in real-world clinical evidence. Mechanistic consistency plausibility is further assessed by a multi-agent LLM pipeline grounded in the diffusion model's attention mechanism. Experiments across 15 cancer cell lines from three held-out evaluation sets demonstrate consistent and noticeable improvements over competing baselines in sensitivity, drug-likeness, synthesizability, and chemical validity.

Brenda Nogueira, Gisela A. Gonzalez-Montiel, Nitesh V. Chawla +1

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

Molecular Optimization Oncology Molecular Generation Conditional Diffusion Models Drug Discovery

May 31, 2026cs.LG

Fine-Tuning Diffusion Models for Molecular Generation via Reinforcement Learning and Fast Sampling

Generating molecules that simultaneously satisfy drug-like properties and conform to the 3D structure of a target protein is a core challenge in structure-based drug design (SBDD). Existing generative approaches, however, often rely on costly post-hoc processing during Sampling or require carefully curated datasets during training, yet still achieve modest gains. These limitations are especially pronounced in multi-objective settings, where balancing conflicting criteria remains a core challenge. To address these challenges, We propose FTDiff, a reinforcement learning fine-tuning framework tailored for diffusion-based molecular generation under structural constraints. To ensure stable and sample-efficient optimization, FTDiff adopts a group relative policy optimization (GRPO) style strategy. Furthermore, FTDiff builds upon a time-free pretrained diffusion model and incorporates a fast sampling mechanism that reduces the number of denoising steps, significantly accelerating both training and inference while maintaining generation quality. By optimizing a fixed threshold-aware reward, FTDiff effectively guides the model to produce valid, diverse, and high- quality molecules that balance multiple drug design objectives. Extensive experiments on benchmark datasets demonstrate that FTDiff consistently outperforms prior methods, without requiring expensive post-hoc optimization or intricate data engineering.

Guang Lin, Shikui Tu, Lei Xu

Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China · Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen, Guangdong, China

Molecular Optimization Diffusion Model Fine-Tuning Structure-Based Drug Design 3D Molecular Generation RL for Diffusion Models Molecular Generation

May 30, 2026cs.AI

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

Structure-based drug design increasingly employs LLM agents to iteratively refine ligands against a target pocket, yet a viable ligand must satisfy two often-conflicting objectives -- binding affinity and druggability -- which single optimization steps rarely improve together. To quantify this difficulty, we introduce two diagnostic metrics: the first measures how often a single edit improves both objectives, and the second measures how often a gain on one objective comes with a loss on the other. Applying these diagnostics to current LLM-agent pipelines exposes a consistent failure mode: the agent performs molecular editing without knowing how the pocket-ligand complex responds to local modifications, thus rarely achieving joint improvement. Inspired by medicinal chemists, who probe the pocket-ligand complex with controlled analog edits before choosing an optimization direction, we propose \textbf{PROBE}, an optimization framework built around edit-response probing. PROBE first decomposes the ligand into editable sites and builds a pocket-specific \textbf{site map} that flags where joint gains are plausible, where the two objectives are likely in tension, and where liability substructures should be changed; it then performs controlled probe edits whose responses are distilled into an \textbf{EditManual}. Guided by the site map and EditManual, PROBE runs an iterative multi-agent loop in which an affinity agent, a druggability agent, and a co-optimization agent jointly produce edits. On the CrossDocked2020 benchmark, PROBE achieves state-of-the-art performance and substantially mitigates the failure modes exposed by our diagnostics metrics.

Zaifei Yang, Weiyu Chen, Yaqing Wang +1

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

Molecular Optimization Multi-Agent LLM Systems Large Language Model-Guided Optimization Structure-Based Drug Design

May 28, 2026cs.LG

Constrained Flow Optimization via Sequential Fine Tuning for Molecular Design

Adapting generative foundation models, in particular diffusion and flow models, to optimize given reward functions (e.g., binding affinity) while satisfying constraints (e.g., molecular synthesizability) is fundamental for their adoption in real-world scientific discovery applications such as molecular design or protein engineering. While recent works have introduced scalable methods for reward-guided fine-tuning of such models via reinforcement learning and control schemes, it remains an open problem how to algorithmically trade-off reward maximization and constraint satisfaction in a reliable and predictable manner. Motivated by this challenge, we first present a rigorous framework for Constrained Generative Optimization, which brings an optimization viewpoint to the introduced adaptation problem and retrieves the relevant task of constrained generation as a sub-case. Then, we introduce Constrained Flow Optimization (CFO), an algorithm that automatically and provably balances reward maximization and constraint satisfaction by reducing the original problem to sequential fine-tuning via established, scalable methods. We provide convergence guarantees for constrained generative optimization and constrained generation via CFO. Ultimately, we present an experimental evaluation of CFO on both synthetic, yet illustrative, settings, and a molecular design task. Across these evaluations, CFO achieves consistent increases in reward while ensuring high constraint satisfaction, showcasing its practical utility for constrained generative optimization.

Sven Gutjahr, Riccardo De Santi, Luca Schaufelberger +2

Department of Computer Science, ETH Zurich · ETH AI Center · NCCR Catalysis, Switzerland +1

Constrained Generative Modeling Molecular Optimization Generative Modeling Flow-Based Generative Modeling

May 28, 2026q-bio.QM

Mixing Vector Model for Copolymer Inference via Mixed Integer Linear Programming

A novel two-phase molecule inference framework, mol-infer, has recently been developed to infer chemical graphs with prescribed abstract structures and desired property values through mixed integer linear programming (MILP) under the two-layered model, with guaranteed optimality and exactness relative to the given learned prediction function and structural constraints. In this study, we extend this framework to copolymers by introducing a simple feature representation, called the mixing vector (MV) model. In the proposed model, a copolymer feature vector is represented as a convex combination of MILP-tractable monomer descriptors weighted by the mixing ratio of the constituent monomers. This representation does not require explicit sequence-class information and is therefore naturally compatible with MILP-based inverse design. Under this model, we construct prediction functions for several copolymer property datasets using artificial neural networks, reduced quadratic multiple linear regression, and random forests. The proposed representation achieves practically useful predictive performance across multiple physicochemical property datasets; in particular, the best test R^2 score exceeds 0.7 for nine of the ten datasets and exceeds 0.9 for six datasets. We also formulate a multi-monomer inverse-design problem under the MV representation with a prescribed mixing ratio and show that the resulting MILP instances remain tractable, even for three-monomer settings. Finally, we perform an external consistency check by re-evaluating the inferred candidates and comparing the re-computed property values with those predicted by the learned model. Overall, the proposed framework gives a tractable first step toward model-level exact inverse design of copolymers under the two-layered model.

Jianshen Zhu, Raveena Rai, Taiyo Sohkawa +4

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

Molecular Optimization Materials Property Prediction Materials Science Inverse Design

May 27, 2026cs.CE

Closed-Loop Molecular Design with Calibrated Deference

We present Cognitive Loop via In-Situ Optimization (CLIO), an agent that couples a continuously-updated belief-state graph with a recursive plan-then-act loop. The result is a reasoning agent that can contribute something qualitatively different, which we term \emph{calibrated deference}: the capacity to recognize when its own tools or assumptions are failing, to adapt its strategy in response, and to generate mechanistic hypotheses that guide experimental revision. We tested CLIO in a closed-loop human-AI campaign to design an aqueous organic redox flow battery (AORFB) negolyte, with CLIO leading proposal and interpretation in close partnership with chemists who synthesized, characterized, and weighed in on design choices. Across 17 candidates over three rounds, CLIO converged on a top phosphonate candidate; characterization confirmed a 130mV improvement in redox potential over the literature baseline. Characterization then revealed unexpectedly poor electrochemical reversibility -- a regression no property predictor had flagged. CLIO generated competing mechanistic hypotheses, prioritized discriminating diagnostics, traced the failure to phosphonate-potassium ion pairing, and prescribed a sulfonate replacement. The resulting compound showed substantially improved electrochemical reversibility and maintained a 90mV improvement in redox potential, closing the design-make-test-redesign loop.

Newman Cheng, Gordon Broadbent, Jason Dong +11

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

Molecular Optimization AI Agents for Scientific Discovery Human-in-the-Loop AI

May 27, 2026cs.LG

PhAME: Phenotype-Aware Molecular Editing via Latent Diffusion

Small-molecule drug discovery requires simultaneous optimization of numerous properties of candidate molecules. These properties can be investigated through the analysis of high-dimensional biological signatures, such as cell morphology and transcriptomic perturbations, which provide a rich perspective on the underlying biological mechanisms. However, existing generative methods, which use those signatures for optimization, fail to meet two key requirements: providing precise guidance toward desired phenotypic signatures while maintaining structural proximity to a known hit. We introduce PhAME (Phenotype-Aware Molecular Editing), a latent diffusion framework that overcomes this challenge by recasting molecular optimization as editing in the latent space of a pretrained graph-based VAE. Our central contribution is a compositional classifier-free guidance scheme with two independent scales, one for the phenotype-conditioning and one for similarity to the seed structure, allowing practitioners to control the tradeoff between these two objectives. Empirical evaluations across diverse benchmarks, including docking score optimization and multimodal phenotypic generation, demonstrate that PhAME achieves state-of-the-art results while maintaining high chemical validity and novelty.

Łukasz Janisiów, Sebastian Musiał, Bartosz Zieliński +2

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

Molecular Optimization Classifier-Free Guidance Latent Diffusion Models Drug Discovery

May 27, 2026cs.CL

An Evolutionary Approach for Designing Stable and Highly Expressible Low-Immunogenicity Therapeutic mRNA Sequences

Messenger RNA (mRNA) sequences as therapeutics require optimized design to ensure efficient translation, structural stability, and minimal immunogenicity. This study presents a two-stage in-silico framework that integrates deep learning and evolutionary computation for rational mRNA optimization instead of existing state-of-the-art models. In the first stage, a pretrained CodonTransformer (BERT-like Large Language Model) generates biologically coherent mRNA sequences encoding the target antigen. In the second stage, a genetic algorithm (GA) evolves these candidate sequences through codon-aware crossover and synonymous mutation guided by human codon usage preferences. Fitness functions for evaluation combined translation-related metrics (CAI, tAI, codon-pair bias), mRNA structural stability (local and global MFE via RNAfold, GC content), and reduced immunogenicity (CpG/UpA motif frequency). Over successive generations (38th, 40th, and 42nd), the GA improved (achieved CAI values of 0.73 to 0.74 and tAI values of 0.63 to 0.64) CAI and tAI by over 6% and codon-pair bias is high and consistent (0.97 ) and improved ribosomal accessibility at the 5' end, with an unpaired_30 fraction reaching 0.87; Global Minimum Free Energy (MFE) converged to a balanced range of -346 to -356 kcal/mol, achieving approximately 84% base-paired structural stability, and reduced immune-stimulatory motifs - lowering the average immune penalty to 27.3 in the final generation. Linear Design produces hyper-stable transcripts (MFE < - 2000 kcal/mol) that risk translation inefficiency due to extreme rigidity, and BiLSTM-CRF focuses solely on high CAI (0.96 to 0.98) without structural constraints, our framework achieves an optimal translation-stability equilibrium, highlighting the proposed BERT-GA framework as an effective, data-driven approach for the design and optimization of in-silico mRNA sequences.

Dhawa Sang Dong, Mausam Gurung, Suraj Kandel

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

Molecular Optimization Large Language Model-Guided Optimization Molecular Generation

May 27, 2026cs.AI

MolLingo: Molecule-Native Representations for LLM-Powered Scientific Agents

We present MolLingo, a multi-agent system that emulates the reasoning process of a chemist to automate molecular design. Existing LLM-based approaches either operate as standalone generative models without access to external tools or lack the multi-agent coordination and shared memory needed for iterative, evidence-driven reasoning across the molecular design pipeline. MolLingo addresses this by coordinating a Literature Agent, a Chemist Agent, and an Orchestrator through a shared memory module, with each agent equipped with domain-specific tools. To enable effective molecular reasoning, we introduce BRICS-based Fragment Enumeration (BFE), a synthesis-aware molecular fragmentation method that decomposes molecules into chemically meaningful building blocks represented as block-based SMILES paired with common chemical names. This representation bridges molecular structure and LLM semantic space, enabling block-level reasoning and editing that is difficult with raw SMILES alone. As a case study in early-stage therapeutic design, MolLingo further grounds the Chemist Agent's reasoning in binding site geometry and residue-level protein context derived from molecular docking to optimize molecules for stronger target binding. Across four benchmarks, MolLingo consistently outperforms frontier LLMs and specialized baselines, including a fourfold docking score improvement over GPT-5.4 despite using the same underlying model, consistent drug property optimization gains across multiple LLM backbones, and state-of-the-art results on TOMG-Bench, surpassing both frontier LLMs and the RL-based optimization method RePO. Our results suggest that LLMs are already capable molecular design assistants when guided through chemically meaningful representations and biologically grounded structural context. Code is available at: https://anonymous.4open.science/status/MolLingo-7450.

Thao Nguyen, Heng Ji

Siebel School of Computing and Data Science, University of Illinois Urbana-Champaign

Molecular Optimization Multi-Agent LLM Systems Structure-Based Drug Design Large Language Model-Guided Scientific Discovery

May 26, 2026physics.chem-ph

DGLD: Domain-Gated Latent Diffusion for the Discovery of Novel Energetic Materials

Energetic-materials performance gains translate directly into reduced propellant mass, smaller warheads, and more efficient civilian gas-generators, yet no new HMX-class compound has been disclosed in fifteen years. Designing one is a sparse-label problem: of ~66 k labelled CHNO molecules only ~3 k carry experimental or DFT-quality measurements, and naive generative models trained on the full mixture either memorise the high-performance tail or extrapolate without calibration. We introduce Domain-Gated Latent Diffusion (DGLD): a label-quality gate at training time, multi-task score-model guidance at sample time, and a four-stage chemistry-validation funnel ending in first-principles DFT audit. The result is 12 DFT-confirmed novel leads. The headline compound, 3,4,5-trinitro-1,2-isoxazole (L1), reaches \r{ho}"cal" =2.09 g/cm3 and D"K-J,cal" =8.25 km/s and is structurally dissimilar from all 65 980 training molecules (nearest-neighbour Tanimoto 0.27). A co-headline lead, E1 (4-nitro-1,2,3,5-oxatriazole), exceeds L1 on calibrated detonation velocity (D_"K-J,cal" =9.00 km/s) from a chemotype family disjoint from L1's. DGLD is the only method to land in the productive quadrant (simultaneously novel and on-target) at DFT level. SMILES-LSTM memorises 18.3% of its outputs exactly; SELFIES-GA's best novel candidate loses 3.5 km/s under DFT audit; REINVENT 4 generates novel high-N heterocycles but peaks at D=9.02 km/s. Code, checkpoints, and 918 mined hard negatives are released on Zenodo (DOI 10.5281/zenodo.19821953); the next compound to enter the HMX-class band can be discovered, validated, and recommended for synthesis at the cost of a few GPU-days.

Yehudit Aperstein, Alexander Apartsin

Department of Intelligent Systems, Afeka Tel-Aviv College of Engineering, Israel. · School of Computer Science, Faculty of Sciences, HIT-Holon Institute of Technology, Israel.

Molecular Optimization Latent Diffusion Models Materials Science Molecular Generation

May 25, 2026cs.LG

Don't Retrain, Just Reuse: Recovering Dual-Target Molecules from Single-Target Diffusion Models

Designing a single molecule that modulates two targets is a promising strategy for polypharmacology, but it remains substantially harder than standard single-target generation because one candidate must satisfy two binding requirements while preserving drug-likeness and synthesizability. Existing dual-target generative methods typically introduce dual-target capability by either retraining the generator or intervening in the diffusion process during sampling. The former can be costly and difficult to stabilize when dual-target supervision is sparse, while the latter may be sensitive to denoising-time target balancing and competing update directions. These limitations motivate a generator-preserving alternative that keeps the pretrained prior intact: can dual-target candidates instead be recovered from the input space of a frozen single-target diffusion model, without modifying its parameters or denoising dynamics? We formulate this task as a constrained multi-objective optimization problem and propose REUSE, a hierarchical evolutionary input-space search framework that combines pair-conditioned exploration with structured multi-stage selection to enforce dual-target affinity, chemical quality, and diversity. Experiments show that, compared with methods that modify the diffusion process, REUSE consistently improves dual-target affinity and balance, achieving a 20.9-percentage-point gain in Dual High Affinity over the strongest prior baseline while maintaining competitive molecular quality.

Qingyuan Zeng, Pengxiang Cai, Zixin Guan +5

The Hong Kong University of Science and Technology (Guangzhou) · Guangzhou University of Chinese Medicine

Molecular Optimization Molecular Generation Drug Discovery

May 21, 2026cs.LG

Molecular Lead Optimization via Agentic Tool Planning

Drug discovery is a lengthy and resource-intensive process composed of multiple stages. Among these stages, lead optimization plays a critical role in transforming early hit compounds into viable drug candidates. This stage requires improving ADMET-related properties through subtle structural refinement while preserving key molecular substructures responsible for binding affinity to disease targets. Recent advances in artificial intelligence have shown promise in accelerating various aspects of drug discovery; however, most existing approaches to lead optimization rely on one-step molecular optimization, which fail to account for the long-term consequences of sequential design decisions. To address this limitation, we propose TRACE, a trajectory-aware, LLM-reasoning agent for molecular lead optimization that formulates tool selection as a sequential decision-making problem over action trajectories. Given a lead molecule and an optimization objective, TRACE makes trajectory-aware decisions over molecular optimization tools, enabling forward-looking refinement under structural constraints. Experiments on multiple ADMET optimization tasks show that our agent achieves higher optimization success, larger property improvements, and higher validity, while preserving molecular similarity compared to baseline models.

Lingxiao Li, Haobo Zhang, Ruohao Fan +2

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

Molecular Optimization Large Language Model-Guided Optimization LLM Agent Planning Drug Discovery

May 17, 2026cs.LG

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

Structure-based drug design has been accelerated by pocket-aware 3D generative models, yet most methods primarily fit the training distribution and may fall short of satisfying multiple properties required in real-world therapeutic drug discovery. Recently, increasing attention has focused on structure-based molecule optimization (SBMO), which targets fine-grained control over multiple specified molecular properties. In this paper, we present DEPPA, a novel SBMO approach building upon Denoising Diffusion Policy Optimization for fine-tuning a pre-trained pocket-aware diffusion model via reinforcement learning. DEPPA enables optimization over multiple properties, including binding affinity, drug-likeness, synthesizability and diversity. We formulate the reverse denoising process of the pretrained pocket-aware diffusion model as a multi-step Markov Decision Process, where the desired properties that serve as reward signals are evaluated on the final generated ligand molecules. DEPPA incorporates a coarse denoising scheduler during the RL fine-tuning to achieve efficient and effective molecule optimization. Experimental results on the CrossDocked2020 benchmark demonstrate that DEPPA outperforms baselines in binding affinity (Vina Score -8.5 kcal/mol), drug-likeness and diversity while exhibiting competitive performance in synthesizability. The source code is available at https://github.com/xy9485/DePPA .

Yuan Xue, Daniel Kudenko, Megha Khosla

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

Molecular Optimization Diffusion Model Fine-Tuning Structure-Based Drug Design 3D Molecular Generation RL for Diffusion Models Molecular Generation+1

May 14, 2026cs.LG

Controllable Molecular Generative Foundation Models

Despite the success of foundation models in language and vision, molecular graph generation still lacks a unified framework for heterogeneous design tasks with reliable controllability. While reinforcement learning (RL) offers a natural post-training mechanism for task-specific optimization, applying it to graph generative models is hindered by the vast atom-wise action spaces and chemically invalid intermediate states. We propose \textbf{Co}ntrollable \textbf{Mole}cular Generative Foundation Models (CoMole), built with a unified motif-aware graph diffusion pipeline. By learning a motif-aware graph space, CoMole transfers pretrained structural priors into controllable generation, where RL optimizes conditional reverse policies over chemically meaningful decisions. We theoretically characterize the bottleneck of atom-level RL and justify motif-aware policy optimization. Across three heterogeneous benchmarks spanning materials and drug discovery, CoMole ranks first in controllability on all nine targets, reduces MAE by up to 48.2% relative to the strongest baselines, and maintains validity above 0.94 without rule-based correction or post-hoc filtering. We further show that CoMole transfers controllability to unseen properties by optimizing only task embeddings with the generator frozen, achieving performance competitive with strong task-specific baselines.

Yihan Zhu, Yuhan Liu, Weijiang Li +2

University of Notre Dame

Molecular Optimization Molecular Graph Generation Graph Foundation Models RL for Diffusion Models Molecular Generation Conditional Generative Modeling

May 12, 2026q-bio.QM

Towards Discovery of Polymers for Insulin Delivery via Physics-Grounded Agentic Workflows

Cold-chain storage limits access to insulin for hundreds of millions of people; a thermally protective patch polymer could help, but the design space is too large for exhaustive experiment. Starting from that problem, we narrow to an agentic workflow: a large language model (LLM) calls physics-based tools through the Model Context Protocol (MCP), searching the discrete PSMILES space under a budget of OpenMM Packmol-matrix evaluations. The LLM acts as an implicit acquisition function conditioned on a persistent "discovery world": hypotheses, literature claims, and simulation outcomes updated each iteration. Under matched oracle budgets, the best autonomous campaign reaches an insulin-polymer interaction energy of -2263 kJ/mol, outperforming reinforcement-learning baselines by 68% and Bayesian optimization by 19%. Three independent campaigns converge on one structural motif (dense hydrogen-bond donors and acceptors per repeat unit) while physics checks reject infeasible packings and name-structure mismatches before they steer the next step. The science stage is CPU-bound and runs on commodity hardware. More broadly, the same architecture and workflow designed here applies to other protein-stabilization tasks whenever a tractable screening oracle is available.

Martins Otun

1Algonix AI Ltd., Scotland, United Kingdom

Molecular Optimization Large Language Model-Guided Optimization Agentic Workflows Large Language Model-Guided Scientific Discovery

May 12, 2026cs.LG

ToolMol: Evolutionary Agentic Framework for Multi-objective Drug Discovery

Advances in large language models (LLMs) have recently opened new and promising avenues for small-molecule drug discovery. Yet existing LLM-based approaches for molecular generation often suffer from high rates of invalid and low-quality ligand candidates, a result of the syntactic limitations of current models with regard to molecular strings. In this paper, we introduce

\texttt{ToolMol}

, an evolutionary agentic framework for de novo drug design.

\texttt{ToolMol}

combines a multi-objective genetic algorithm with an agentic LLM operator that iteratively updates the ligand population. We build a comprehensive toolbox of RDKit-backed functions that allows our agentic operator to consisently make precise ligand modifications.

\texttt{ToolMol}

achieves state-of-the-art performance on multi-objective property optimization tasks, discovering drug-like and synthesizable ligands that have

>10\%

stronger predicted binding affinity compared to existing methods, evaluated on three protein targets.

\texttt{ToolMol}

ligands additionally achieve state-of-the-art results in gold-standard Absolute Binding Free Energy scores, gaining over existing methods by over

35\%

. By studying chain-of-thought reasoning traces, we observe that tool-calling enables the model to more faithfully execute its planned modifications, efficiently exploiting the strong chemical prior knowledge in LLMs.

Andrew Y. Zhou, Sharvaree Vadgama, Sumanth Varambally +3

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

Molecular Optimization AI Agents for Scientific Discovery Multi-Objective Evolutionary Optimization AI-Assisted Scientific Research LLM Tool Use Molecular Generation+1

May 12, 2026cs.AI

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

Large Language Models (LLMs) and Vision Language Models (VLMs) have recently shown promising capabilities in various scientific domain. In particular, these advances have opened new opportunities in drug discovery, where the ability to understand and modify molecular structures is critical for optimizing drug properties such as efficacy and toxicity. However, existing models and benchmarks often overlook toxicity-related challenges, focusing primarily on general property optimization without adequately addressing safety concerns. In addition, even existing toxicity repair benchmarks suffer from limited data diversity, low structural validity of generated molecules, and heavy reliance on proxy models for toxicity assessment. To address these limitations, we propose MolDeTox, a novel benchmark for molecular detoxification, designed to enable fine-grained and reliable evaluation of toxicity-aware molecular optimization across stepwise tasks. We evaluate a wide range of general-purpose LLMs and VLMs under diverse settings, and demonstrate that understanding and generating molecules at the fragment-level improves structural validity and enhances the quality of generated molecules. Moreover, through detailed task-level performance analysis, MolDeTox provides an interpretable benchmark that enables a deeper understanding of the detoxification process. Our dataset is available at : https://huggingface.co/datasets/MolDeTox/MolDeTox

Jueon Park, Wonjune Jang, Jiwoo Lee +2

Korea University · Myongji University · AIGEN Sciences

Molecular Optimization LLM Evaluation

May 11, 2026cs.LG

SLIM: Sparse Latent Steering for Interpretable and Property-Directed LLM-Based Molecular Editing

Large language models possess strong chemical reasoning capabilities, making them effective molecular editors. However, property-relevant information is implicitly entangled across their dense hidden states, providing no explicit handle for property control: a substantial fraction of edits fail to improve or even degrade target properties. To address these issues, we propose SLIM (Sparse Latent Interpretable Molecular editing), a plug-and-play framework that decomposes the editor's hidden states into sparse, property-aligned features via a Sparse Autoencoder with learnable importance gates. Steering in this sparse feature space precisely activates property-relevant dimensions, improving editing success rate without modifying model parameters. The same sparse basis further supports interpretable analysis of editing behavior. Experiments on the MolEditRL benchmark across four model architectures and eight molecular properties show consistent gains over baselines, with improvements of up to 42.4 points.

Mingxu Zhang, Yuhan Li, Lujundong Li +3

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

Molecular Optimization LLM Interpretability Large Language Model-Guided Optimization

May 11, 2026cs.LG

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

Molecular optimization seeks to improve a molecule through small structural edits while preserving similarity to the starting compound. Recent language-model approaches typically treat this task as prompt-conditioned sequence generation. However, relying on natural language introduces an inherent data-scaling bottleneck, often leads to chemical hallucinations, and ignores the strong context dependence of fragment effects. We present FORGE, a two-stage framework that reformulates molecular optimization as context-aware local editing. By utilizing automatically mined, verified low-to-high edit pairs instead of expensive human text annotations, Stage 1 ranks candidate fragments by their property contribution under the full molecular context to inject chemical prior, and Stage 2 generates explicit fragment replacements. Built on a compact 0.6B language model, FORGE further adapts to unseen black-box objectives through in-context demonstrations. Across Prompt-MolOpt, PMO-1k and ChemCoTBench, FORGE consistently outperforms prior methods, including substantially larger language models and graph methods. These results highlight the value of explicit fragment-level supervision as a more easily obtainable, scalable, and hallucination-less alternative to natural language training.

Qingchuan Zhang, He Cao, Hao Li +6

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

Molecular Optimization Large Language Model-Guided Optimization Molecular Generation

May 11, 2026cs.AI

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

Conditional molecular optimization aims to edit a molecule to realize a specified property shift. In practice, structurally similar molecule data is scarce, while decisions are inherently action-level: at each step, the system must select one local structural edit from a candidate set that is strictly filtered by chemical feasibility rules. This level mismatch between supervision and decision makes oracle-in-the-loop search unstable in molecular optimization. Regressing on property differences between molecule pairs improves data efficiency but relies on oracle-in-the-loop search, entangling transformation effects with global context and providing limited guidance for selecting the next feasible edit, often resorting to oracle-in-the-loop search. For this reason, we propose a response-oriented discrete edit optimization approach comprising two tightly coupled components: a single-step molecular edit response predictor (SMER) and a multi-step planner that composes local predictions into optimization trajectories via guided tree search (SMER-Opt). The approach learns a directional evaluation model over edit actions to support constraint-aware planning. It mines weakly related molecule pairs and decomposes their structural differences into minimal edit units, turning endpoint property annotations into process-level supervision and yielding reusable, transferable action primitives. A directional edit evaluator then scores feasible candidate edits by their likelihood of moving the molecule toward the desired property change, substantially reducing dependence on external evaluator queries at decision time. Code is available at https://anonymous.4open.science/r/SMER.

Haojie Rao, Kun Li, Yida Xiong +5

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

Molecular Optimization Constrained Optimization

May 9, 2026cs.LG

MolWorld: Molecule World Models for Actionable Molecular Optimization

Molecular optimization in drug discovery aims to discover molecules with improved target properties, but practical lead optimization often requires more than high predicted scores. A useful candidate should also be actionable: it should be reachable from known molecules through valid local structural transformations, so that it can be interpreted as a plausible revision within an evolving chemical series. Existing de novo and single-molecule optimization methods do not explicitly model such reachability, especially when both the target molecules and the intermediate molecules connecting them to known compounds are unknown. In this work, we formulate actionable molecular optimization as sequential expansion of a molecule-transfer graph, where nodes are molecules and edges encode valid local transformations. We propose MolWorld, a molecule world model-guided framework that treats the current molecule-transfer graph as an evolving search state. At each iteration, MolWorld selects local anchor contexts, generates candidate molecules conditioned on these contexts, evaluates their properties, and uses a learned world model to update the evolving molecule world by retaining admissible candidates and inserting them into the molecule-transfer graph. The expanded molecule world then guides subsequent optimization. Experiments on property optimization and docking-based tasks show that MolWorld discovers high-property molecules while maintaining substantially stronger structural connectivity, supporting actionable and sequential molecular design.

Yang Qiao, Bo Pan, Hao-Wei Pang +3

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

Molecular Optimization World Models Molecular Generation Drug Discovery

May 6, 2026cs.LG

SPADE: Faster Drug Discovery by Learning from Sparse Data

Drug discovery seeks molecules (ligands) that bind strongly and selectively to a target protein. However, fewer than 5% of candidate ligands pass the bar for even the early stages of drug discovery. Furthermore, we want methods that work for novel proteins for which we have no prior data. Starting from scratch, we have to iteratively select and test candidate ligands such that we find enough ligands of the desired quality in as few tests as possible. Our proposed algorithm, named SPADE, introduces a novel approach to ligand selection that requires only 40 tests on average to find 10 high-quality ligands. In one-vs-one comparisons, SPADE outperforms deep learning and Bayesian optimization methods on more proteins, achieving median improvements of 7%-32% in sample efficiency. SPADE is also 10x faster than its closest competitor at scoring candidate drugs. Dataset and code is available at https://anonymous.4open.science/r/SPADE_Fast_Drug_Discovery_by_Learning_from_Sparse_Data-F028/README.md

Rahul Nandakumar, Ben Fauber, Deepayan Chakrabarti

McCombs School of Business University of Texas at Austin Austin, TX · NVIDIA

Molecular Optimization AI-Assisted Scientific Research Active Learning Drug Discovery Data-Efficient Learning

Apr 27, 2026physics.chem-ph

Computational Design and Experimental Validation of Photoactive PARP1 Inhibitors

Light-activated drugs are a promising way to treat localized diseases for which existing treatments have severe side effects. However, their development is complicated by the set of photophysical and biological properties that must be simultaneously optimized. Here we used computational techniques to find a set of promising candidates for the photoactive inhibition of the poly(ADP-ribose) polymerase 1 (PARP1) cancer target. Using our recently developed methods based on atomistic simulation and machine learning (ML), we screened a set of 5 million hypothetical photoactive ligands. Our workflow used protein-ligand docking to identify candidates with differential PARP1 binding under light and dark conditions; ML force fields and quantum chemistry calculations to predict p

K_\mathrm{a}

, absorption spectra, and thermal half-lives; graph-based surrogate models to screen additional compounds; excited-state nonadiabatic dynamics with ML force fields to estimate quantum yields; and free energy perturbation (FEP) to refine binding predictions. From these predictions, we prioritized a small set of synthetically feasible candidates expected to have red-shifted absorption spectra, thermal half-lives on the order of seconds to minutes, and isomer-dependent PARP1 binding under visible-light control. We synthesized 10 candidates and experimentally characterized their photobehavior and PARP1 inhibition constants. Among the validated compounds, \textbf{1} showed a 15-fold increase in inhibition of PARP1 upon green-light irradiation at 519 nm (208.8

\pm

28.3

μ

M vs 14.4

\pm

1.9

μ

M). These results validate the computation-guided screening strategy for identifying red-shifted PARP1 photoinhibitors, while also underscoring current limitations such as rapid thermal relaxation in aqueous media.

Simon Axelrod, Miroslav Kašpar, Kristýna Jelínková +8

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

Molecular Optimization Structure-Based Drug Design Drug Discovery

Apr 24, 2026cs.LG

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

Large language models (LLMs) show promise for molecular optimization, but aligning them with selective and competing drug-design constraints remains challenging. We propose C-Moral, a reinforcement learning post-training framework for controllable multi-objective molecular optimization. C-Moral combines group-based relative optimization, property score alignment for heterogeneous objectives, and bottleneck-sensitive non-linear reward aggregation to improve stability across competing molecular properties. Experiments on C-MuMOInstruct and S

^2

-Bench MolOpt show that C-Moral achieves the best performance among compared methods on both benchmarks. On C-MuMOInstruct, C-Moral achieves the best Success Optimized Rate (SOR) of 48.9% on in-domain tasks and 39.5% on out-of-domain tasks while preserving scaffold similarity. On S

^2

-Bench MolOpt, it also achieves the strongest results across LogP, MR, and QED optimization tasks. These results suggest that C-Moral is an effective way to align molecular LLMs with continuous and constrained molecular design objectives. Our code and models are publicly available at https://github.com/Rwigie/C-MORAL.

Rui Gao, Youngseung Jeon, Swastik Roy +2

University of California, Los Angeles · Amazon

RL for Language Models Molecular Optimization Large Language Model-Guided Optimization Multi-Objective Language Model Alignment Drug Discovery

Apr 21, 2026cs.LG

Multi-Objective Reinforcement Learning for Generating Covalent Inhibitor Candidates

Rational design of covalent inhibitors requires simultaneously optimizing multiple properties, such as binding affinity, target selectivity, or electrophilic reactivity. This presents a multi-objective problem not easily addressed by screening alone. Here we present a machine learning pipeline for generating covalent inhibitor candidates using multi-objective reinforcement learning (RL), applied to two targets: epidermal growth factor receptor (EGFR) and acetylcholinesterase (ACHE). A SMILES-based pretrained LSTM serves as the generative model, optimized via policy gradient RL with Pareto crowding distance to balance competing scoring functions including synthetic accessibility, predicted covalent activity, residue affinity, and an approximated docking score. The pipeline rediscovers known covalent inhibitors at rates of up to 0.50% (EGFR) and 0.74% (ACHE) in 10,000-structure runs, with candidate structures achieving warhead-to-residue distances as short as 5.5 angstrom (EGFR) and 3.2 angstrom (ACHE) after further docking-based screening. More notably, the pipeline spontaneously generates structures bearing warhead motifs absent from the training data - including allenes, 3-oxo-

β

-sultams, and

α

-methylene-

β

-lactones - all of which have independent literature support as covalent warheads. These results suggest that RL-guided generation can explore covalent chemical space beyond its training distribution, and may be useful as a tool for medicinal chemists working on covalent drug discovery.

Renee Gil

Independent Researcher

Molecular Optimization Molecular Generation RL for Generative Models Drug Discovery

Apr 17, 2026physics.chem-ph

KinetiDiff: Docking-Guided Diffusion for De Novo ACVR1 Inhibitor Design in Fibrodysplasia Ossificans Progressiva

We present KinetiDiff, a structure-based framework for de novo kinase inhibitor design that integrates a Geometry-Complete Diffusion Model with real-time AutoDock Vina gradient guidance. By injecting physics-based docking gradients into the diffusion denoising loop, KinetiDiff steers molecule generation toward high-affinity conformations for ACVR1 (ALK2), the causative kinase in Fibrodysplasia Ossificans Progressiva. From 10,000 diffusion samples, the framework produced 9,997 valid molecules. The best candidate achieved

-11.05

kcal/mol (pKd = 8.10), a 19.2% improvement over the crystallographic reference. The top 100 candidates all exceed the reference, with 100% Lipinski compliance, median synthetic accessibility of 2.67, and internal diversity of 0.790. Systematic ablation across four guidance strategies--Vina-Direct (physics), HNN-Denovo (neural proxy), multi-objective, and unguided--demonstrates that real-time docking guidance dominates on all metrics. We evaluate HNN-Denovo as a computationally efficient alternative (60-fold speedup per step), revealing a domain-mismatch limitation (r = 0.224 correlation with Vina) that explains its inferior performance. These results establish gradient-guided geometric diffusion as a practical approach for generating potent, synthetically accessible inhibitors against rare-disease kinase targets.

Aaryan Patel

Saugus High School, Santa Clarita, CA

Molecular Optimization Diffusion Guidance Structure-Based Drug Design Molecular Generation Drug Discovery

Apr 9, 2026cs.LG

LLM-Guided Dynamic Action Spaces for Synthesizable Molecular Optimization

Synthesizable molecular optimization seeks to improve target properties while ensuring that molecular modifications follow feasible synthetic pathways. Existing synthesis-aware methods typically rely on exploring a large space of candidate transformations defined by reaction templates and purchasable building blocks. This search becomes even more challenging when property improvement requires multiple reaction steps, as the space expands further along the pathway. To address this challenge, we introduce MolReAct, which reformulates molecular optimization as search over compact reaction spaces proposed by a tool-augmented large language model (LLM). At each step, the LLM combines its prior chemical knowledge with cheminformatics tools to identify a molecule-specific set of compatible reactions, preserving synthesizability while making multi-step optimization feasible. Given this compact action space, we further leverage Group Relative Policy Optimization (GRPO) with the terminal oracle reward to improve long-term decision-making over multiple reaction steps. Across diverse molecular optimization tasks, MolReAct achieves the highest Top-10 score on 11 of 14 tasks and the best sample efficiency on 12 of 14 tasks, outperforming existing baselines under limited oracle budgets. Beyond these gains, MolReAct also provides each optimized molecule with a template-grounded synthetic pathway.

Tao Li, Kaiyuan Hou, Tuan Vinh +4

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

Molecular Optimization Large Language Model-Guided Optimization