arXiv:2607. 19083v1 Announce Type: new Abstract: Equivariant graph neural networks provide a powerful modeling language for three-dimensional scientific data, but their reuse is often limited by implementations tied to specific tasks, outputs, and training regimes.
arXiv:2602. 21565v3 Announce Type: replace Abstract: Generative Flow Networks (GFlowNets) learn to sample diverse candidates in proportion to a reward function, making them well-suited for scientific discovery, where exploring multiple promising solutions is crucial.
The paper introduces Gromov-Monge Flow Matching, a method that incorporates permutation-equivariance into generative graph models by aligning graph pairs up to node relabeling using the Gromov–Monge distance. It shows theoretically that quotient couplings can be lifted to aligned representatives without extra cost and that symmetrization yields equivariant flow-matching minimizers, even for categorical endpoints. Practically, the authors build minibatch couplings with Gromov–Wasserstein relaxations and optional outer assignments, improving sample quality in continuous graph and categorical molecular generation while remaining compatible with standard equivariant architectures.
arXiv:2606. 03232v1 Announce Type: cross Abstract: Graph Neural Networks (GNNs) have revolutionized Neural Force Fields for atomistic simulations, achieving near-quantum accuracy at reduced cost, yet adapting these models to new chemical systems requires expensive retraining of foundation models.
arXiv:2606. 30961v1 Announce Type: cross Abstract: Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species.
arXiv:2605. 01625v3 Announce Type: replace Abstract: Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology.
arXiv:2510.07289v2 Announce Type: replace Abstract: Molecular graph representation learning is widely used in chemical and biomedical research. While pre-trained 2D graph encoders have demonstrated s...
Zatom-2 is a multitask generative model for atomistic data that has been pretrained on about five million structures from the OMol25 and OMat24 datasets. It uses a multiscale Transformer with conditional flow matching to support tasks such as generation, structure prediction, and energy/force prediction for both molecules and materials. The model outperforms its predecessor, Zatom-1, on molecular distribution fidelity and benchmark generation tasks, and improves protein backbone designability from 67.8% to 74.8% after finetuning on 2,000 protein domains.
arXiv:2605. 02937v2 Announce Type: replace-cross Abstract: Deep learning in de novo protein design has achieved atomic-level fidelity.
arXiv:2511. 19264v2 Announce Type: replace-cross Abstract: Generative Flow Networks (GFlowNets) construct molecules through sequential decisions, but their internal policies remain opaque, limiting adoption in drug discovery, where chemists need interpretable rationales for proposed structures.
arXiv:2608. 04257v1 Announce Type: new Abstract: Blood-brain barrier permeability (BBBP) prediction is a critical screening task in central nervous system drug discovery, where candidate molecules must be assessed for whether they can cross, or should be prevented from crossing, the blood-brain barrier.
arXiv:2607. 06224v1 Announce Type: new Abstract: Designing microbial strains that produce high-value chemicals at commercially viable titers remains a central challenge in metabolic engineering.
arXiv:2607. 12380v1 Announce Type: new Abstract: Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its own graph, equivariant, or frame-based architecture.