Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules
Updated 4 h ago · first seen 11 Sept 2026
paper_01M294FTPMG85ZQN746EBY5N0J
- Published
- 11 Sept 2026
- T1 · 4 h ago
- arXiv
- 2609.08333
- T1 · 4 h ago
- Category
- physics.chem-ph
- T1 · 4 h ago
Abstract
-cross Abstract: In molecular discovery, molecule size is coupled to composition, structure, and other target properties. Yet most 3D generators require molecule size to be specified before generation. Here, we introduce Equivariant-Free Transformer-Autoencoded Latent Flow Matching, a two-stage generative framework that relies entirely on a single fixed-dimensional molecule-level latent representation to generate variable-size molecules. The second-stage flow matching model samples this latent vector, and an autoregressive Transformer decoder then determines molecule size while generating atom types, coordinates, and chemically informative states. Canonical atom ordering and rigid-pose alignment enable standard Transformers without equivariant layers, while joint decoding of molecular geometry and an enriched chemical state enables reliable, deterministic, chemistry-guided graph recovery without requiring a learned dense pairwise bond decoder. The same fixed-dimensional latent supports unconditional and property-conditioned flow matching, while optional property supervision adds an internal ranking readout, with no separate predictor or reference calculations. On PCQM4Mv2, EF-TALFM achieves the highest fraction of molecules that are unique, training-set novel, pass sanitization and PoseBusters sanity checks, 89.4\%, compared with 75.6\% for UAE-3D and 69.8\% for FlowMol. EF-TALFM also achieves higher measured computational throughput for training and sampling. Across ten target HOMO--LUMO gaps, internal ranking doubles the density functional theory (DFT)-verified hit rate within $0.1\,\mathrm{eV}$, while preserving 97\% novelty among unique verified hits. These results demonstrate that fixed-dimensional molecule-level generation followed by symmetry-resolved autoregressive realization provides a practical architecture for open-ended and property-directed 3D molecular design.
Authors 4
Weichi Yao, Cameron Gruich, Bryan R. Goldsmith, Yixin Wang
Specification
- Official page
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
- Arxiv announce type
- replace
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
- arXiv id
- 2609.08333
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
- Categories
- physics.chem-ph, cs.LG, q-bio.QM
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
- Primary category
- physics.chem-ph
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
- Published
- 11 Sept 2026
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
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Provenance
Attributed facts
9
Source tiers
T19
Freshest observation
4 h ago
Conflicts
None
No models linked to this paper yet.
- Authors
- Weichi Yao, Cameron Gruich, Bryan R. Goldsmith
As of
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Claim history
Official pageofficial_url1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| https://arxiv.org/abs/2609.08333 | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Abstractabstract1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| -cross Abstract: In molecular discovery, molecule size is coupled to composition, structure, and other target properties. Yet most 3D generators require molecule size to be specified before generation. Here, we introduce Equivariant-Free Transformer-Autoencoded Latent Flow Matching, a two-stage generative framework that relies entirely on a single fixed-dimensional molecule-level latent representation to generate variable-size molecules. The second-stage flow matching model samples this latent vector, and an autoregressive Transformer decoder then determines molecule size while generating atom types, coordinates, and chemically informative states. Canonical atom ordering and rigid-pose alignment enable standard Transformers without equivariant layers, while joint decoding of molecular geometry and an enriched chemical state enables reliable, deterministic, chemistry-guided graph recovery without requiring a learned dense pairwise bond decoder. The same fixed-dimensional latent supports unconditional and property-conditioned flow matching, while optional property supervision adds an internal ranking readout, with no separate predictor or reference calculations. On PCQM4Mv2, EF-TALFM achieves the highest fraction of molecules that are unique, training-set novel, pass sanitization and PoseBusters sanity checks, 89.4\%, compared with 75.6\% for UAE-3D and 69.8\% for FlowMol. EF-TALFM also achieves higher measured computational throughput for training and sampling. Across ten target HOMO--LUMO gaps, internal ranking doubles the density functional theory (DFT)-verified hit rate within $0.1\,\mathrm{eV}$, while preserving 97\% novelty among unique verified hits. These results demonstrate that fixed-dimensional molecule-level generation followed by symmetry-resolved autoregressive realization provides a practical architecture for open-ended and property-directed 3D molecular design. | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Arxiv announce typearxiv_announce_type1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| replace | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
arXiv idarxiv_id1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| 2609.08333 | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Categoriescategories1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| physics.chem-ph, cs.LG, q-bio.QM | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
PDFpdf_url1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| https://arxiv.org/pdf/2609.08333 | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Primary categoryprimary_category1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| physics.chem-ph | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Publishedpublished_at1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| 11 Sept 2026 | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Claims are temporal and append-only: a new observation closes the previous claim (valid_to) instead of overwriting it. Conflicting claims from different sources are kept side by side and flagged — never averaged. Methodology →
New paper: Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules
arxiv
| Source | Document | Type | Tier | Last observed | Snapshots |
|---|---|---|---|---|---|
| arXiv (Atom API + RSS) | rss.arxiv.org/rss/cs.LG | feed | T1· Official | 4 h ago | 1 |
Tier 1 = official/primary, 2 = quality secondary, 3 = community, 4 = unverified. Every snapshot is archived; see all sources and the methodology.