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.
arXiv:2609.08333v1 Announce Type: cross Abstract: In molecular discovery, molecule size is coupled to composition, structure, and other target properties. Yet most 3D generators require molecule size...
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.
The paper proposes a new framework called ensemble-conditioned guidance that reframes molecular design as an optimisation over both the modes and properties of a molecule’s conformational ensemble. It allows 3D generative models to be conditioned simultaneously on multiple axes—such as shapes, pharmacophore profiles, or protein pockets—by adaptively combining vector fields from each condition. The authors introduce adaptive symmetry learning for composable conditions across reference frames, extend the framework to support flexible-size generation, and demonstrate its effectiveness on new benchmarks and practical drug‑discovery tasks, showing improved outcomes when conditioning on additional states compared to single‑state approaches.
arXiv:2606. 07239v1 Announce Type: new Abstract: The success of generative molecular design hinges on a model's steerability toward high-reward samples.
arXiv:2607. 05736v1 Announce Type: new Abstract: Molecular property prediction often relies on isolated data modalities, where continuous 3D graph neural networks (GNNs) struggle to efficiently capture long-range topological dependencies and exact macroscopic heuristics.
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...
arXiv:2607. 03513v1 Announce Type: cross Abstract: We present AquaGen, the first all-atom, explicit solvent, periodic-boundary-condition-aware generative model that produces molecular configurations from the Boltzmann distribution at a fraction of the cost of molecular dynamics (MD).
arXiv:2606. 08375v1 Announce Type: new Abstract: All-atom generative modeling of 3D biomolecular complexes has emerged as the dominant paradigm for predicting the structure of proteins and protein-ligand systems.
The paper introduces juniper, a discrete denoising diffusion model that performs compositional backmapping from coarse‑grained (CG) beads to detailed molecular graphs. By conditioning on the octanol–water partition free energy, the model generates valid and unique molecules that closely match the target free‑energy distribution for two‑bead systems. This approach enables the conversion of CG screening results into candidate atomistic molecules for further study or synthesis.
Transport-Coupled Bayesian Flows for Molecular Graph Generation (TopBF) addresses a key mismatch in existing diffusion models for molecular graph generation by eliminating the need for hard discretization during sampling. The framework generates graphs directly in continuous parameter distributions, learns graph topology via a Quasi-Wasserstein optimal‑transport coupling with geodesic costs, and enables property‑conditioned generation without retraining. Experiments on QM9 and ZINC250k show that TopBF achieves higher structural fidelity and more efficient generation compared to prior methods.
arXiv:2607. 15682v1 Announce Type: new Abstract: Sampling from an unnormalized Boltzmann density requires proposals that move probability mass globally while retaining enough path-probability information for statistical correction.
arXiv:2605. 31498v2 Announce Type: replace Abstract: A long standing challenge in computational chemistry and biophysics is efficiently sampling the Boltzmann distribution of molecules.