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.

Machine-generated by The Flow from the publisher's headline and feed description — not written or checked by a human. 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

Sep 10

FuseDiff: Symmetry-Preserving Joint Diffusion for Dual-Target Structure-Based Drug Design

FuseDiff is an end‑to‑end diffusion model designed for dual‑target structure‑based drug design, jointly generating a ligand graph and two pocket‑specific binding poses conditioned on both target pockets. It employs a message‑passing backbone with Dual‑target Local Context Fusion (DLCF) to fuse ligand atom contexts from both pockets, preserving symmetry while enabling expressive joint modeling. The model enforces topological consistency across the two poses and allows target‑specific geometric adaptation, achieving state‑of‑the‑art docking performance and enabling systematic assessment of dual‑target pose quality before docking‑based pose search.

By Jianliang Wu, Anjie Qiao, Zhen Wang, Zhewei Wei, Sheng Chen

diffusion benchmarks

arXiv Machine Learning

Sep 2

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

arXiv:2609.00189v1 Announce Type: new Abstract: Goal-directed optimization is essential for steering molecular generators to propose candidates with desired properties. However, it is often implement...

By Shiyun Wa, Yifei Wang, Anna G. Green, Simone Sciabola, Ye Wang

diffusion reinforcement-learning fine-tuning benchmarks safety

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FuseDiff: Symmetry-Preserving Joint Diffusion for Dual-Target Structure-Based Drug Design

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