📢We are excited to share SynCoGen—the first generative model that co-generates 🔷building-block graphs,🔷reaction edges and 🔷full 3-D coordinates, so every molecule comes with both a synthesis plan and a physically plausible shape.

📜 Preprint: 🧑🏻‍💻 Code: Soon!.If you're interested, I'd be happy to chat at the ICML GenBio workshop! Kudos to my amazing co-authors @MirunaCretu2, Dmytro Shevchuk, Pietro Lio, Rob Batey, Mike Tyers, Michal Koziarski, Vignesh Ram Somnath, and Cheng-Hao Liu!.

📊 Results: .SynCoGen outperforms SOTA 3D molecular generation models on both structural quality and synthesizability while automatically proposing bench-ready reaction plans. Without any retraining, the model can also inpaint missing fragments between fixed substructures!

⚙️ How it works:.• Flow matching on atom coordinates. • Masked graph diffusion over building-block identities & reactions. -Only the number of building blocks is sampled, atom count is flexible!.• Single time variable ties the discrete and continuous streams together.

💡New dataset: SynSpace. How is SynCoGen trained?. • 600 k synthesis-aware building-block / reaction graphs. • 3.3 M conformers . from 93 commercially available blocks & 19 robust cross-coupling templates. Each sample pairs a 3D structure + reaction route by construction.

🚀 SynCoGen closes this gap with a hybrid denoising process that considers both 3D geometry and retrosynthetic feasibility!.

⚛️ On the other hand, most 3D small molecule co-generation methods involve discrete diffusion over individual atom types—not explicitly considering molecular synthesizability or plausible synthesis routes.

🧪 Motivation: Physicochemical traits are dictated by the spatial arrangement of atoms, yet most synthesis-aware generators stop at 2D graphs.

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