arXiv Machine Learning
Jul 23

Boltzmann-Expected Molecular Design with Decoupled Annealing Flows

arXiv:2607. 19519v1 Announce Type: cross Abstract: 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.

By Selma Moqvist, Richard Beckmann, Ross Irwin, Roc\'io Mercado, Simon Olsson
Hugging Face Trending Papers
Sep 8

Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules

The paper introduces Equivariant-Free Transformer-Autoencoded Latent Flow Matching (EF‑TALFM), a two‑stage generative framework that uses a single fixed‑dimensional latent vector to produce variable‑size 3D molecules. The first stage samples the latent vector via flow matching, and the second stage employs an autoregressive Transformer decoder that determines molecule size while generating atom types, coordinates, and chemical states. EF‑TALFM outperforms prior methods on the PCQM4Mv2 benchmark, achieving higher uniqueness, novelty, and computational throughput, and its internal ranking improves the hit rate for target HOMO–LUMO gaps while maintaining novelty.

arXiv Machine Learning
Jul 13

Autoregressive latent diffusion for 3D molecule generation

arXiv:2607. 09277v1 Announce Type: new Abstract: Three-dimensional (3D) molecule generation has been dominated by diffusion models, which achieve strong generation quality but typically require the molecular size to be specified a priori.

By Federico Ottomano, Gaopeng Ren, Yingzhen Li, Kim E. Jelfs, Alex M. Ganose
arXiv AI
Jul 21

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints

arXiv:2607. 18144v1 Announce Type: cross Abstract: Structure-based drug design (SBDD) leverages the 3D structure of protein targets, often complemented by other spatial constraints, to generate candidate binding molecules.

By Thomas MacDougall, Maksim Kuznetsov, Roman Schutski, Rim Shayakhmetov, Maxim Malkov, Vladimir Aladinskiy, Alex Aliper, Alex Zhavoronkov