arXiv AI August 11, 2026 By Qingyuan Zeng, Pengxiang Cai, Zixin Guan, Ziyang Chen, Anglin Liu, Xinyao Lai, Jintai Chen

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

arXiv:2605. 25681v2 Announce Type: replace-cross Abstract: 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.

Summary generated by The Flow from the publisher's feed. The full article lives at arXiv AI.

diffusion

arXiv AI

Jun 2

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

arXiv:2606. 01220v1 Announce Type: cross Abstract: 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).

By Guang Lin, Shikui Tu, Lei Xu

diffusion reinforcement-learning fine-tuning benchmarks data-engineering

arXiv Machine Learning

Aug 4

Fused Bayesian Flow Networks for Dual-Target Molecular Design

arXiv:2608. 01007v1 Announce Type: new Abstract: Dual-target drug design aims to generate 3D molecules that can simultaneously interact with two target proteins, offering a promising route for discovering polypharmacological compounds against complex diseases.

By Jingyuan Zhou, Shikui Tu, Lei Xu

diffusion safety

arXiv Machine Learning

Jul 7

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

arXiv:2607. 02834v1 Announce Type: new Abstract: Molecular optimization often starts from a pretrained generative model that captures a broad prior over valid molecular structures.

By Trevor Chen, Ariel Dai, Jason Yang, Riccardo De Santi, Daniel Khalil, Wenda Chu, Nate Gruver, Pranav Murugan, Alexander F. G. Goldberg, Maruan Al-Shedivat, Yisong Yue

diffusion fine-tuning

arXiv Machine Learning

Aug 4

Refine Drugs, Don't Complete Them: Uniform-Source Discrete Flows for Fragment-Based Drug Discovery

arXiv:2509. 26405v2 Announce Type: replace Abstract: We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules.

By Benno Kaech, Luis Wyss, Karsten Borgwardt, Gianvito Grasso

fine-tuning benchmarks

arXiv Machine Learning

Jun 2

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

arXiv:2606. 01461v1 Announce Type: new Abstract: Developing effective anticancer therapeutics remains challenging due to tumor heterogeneity and the absence of well-defined molecular targets across cancer subtypes.

By Brenda Nogueira, Gisela A. Gonzalez-Montiel, Nitesh V. Chawla, Nuno Moniz

llms agents diffusion

arXiv AI

Jun 2

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

arXiv:2606. 00555v1 Announce Type: new Abstract: 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.

By Zaifei Yang, Weiyu Chen, Yaqing Wang, James Kwok

llms agents benchmarks

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