Suiren-1.0 Technical Report: A Family of Molecular Foundation Models

Computational molecular property prediction requires representations that capture local chemistry, long-range interactions, and molecular topology. Conventional fingerprints provide efficient local substructure features, whereas learned graph and sequence models can represent broader context but often rely on pretraining or three-dimensional conformers. We introduce Wide Encoded Extended Connectivity Fingerprints (WEECFP) with Substructure Rotary Graph-distance Encoding (SuRGE), a tokenized hierarchical Morgan representation in which graph-distance-dependent rotations are applied at the input and within transformer self-attention. Across MoleculeNet and the Therapeutic Data Commons ADMET benchmarks, WEECFP-SuRGE is competitive with recent pretrained and geometry-aware methods without external pretraining or conformer generation. We also show that the rotated token representation remains structurally informative. A guided confirmed-handshake overlap procedure reconstructs the correct constitutional isomer for 92.6% of a 4,200-molecule self-library evaluation. Together, the predictive and reconstruction results indicate that WEECFP-SuRGE preserves local substructure identity while making relative topology available to the model.

Most machine learning models for molecular property prediction rely on a single molecular representation (either a sequence, a graph, or a 3D structure) and treat molecular geometry as static. We present MolFM-Lite, a multi-modal model that jointly encodes SELFIES sequences (1D), molecular graphs (2D), and conformer ensembles (3D) through cross-attention fusion, while conditioning predictions on experimental context via Feature-wise Linear Modulation (FiLM). Our main methodological contributions are: (1) a conformer ensemble attention mechanism that combines learnable attention with Boltzmann-weighted priors over multiple RDKit-generated conformers, capturing the thermodynamic distribution of molecular shapes; and (2) a cross-modal fusion layer where each modality can attend to others, enabling complementary information sharing. We evaluate on four MoleculeNet scaffold-split benchmarks using our model's own splits, and report all baselines re-evaluated under the same protocol. Comprehensive ablation studies across all four datasets confirm that each architectural component contributes independently, with tri-modal fusion providing 7-11% AUC improvement over single-modality baselines and conformer ensembles adding approximately 2% over single-conformer variants. Pre-training on ZINC250K (~250K molecules) using cross-modal contrastive and masked-atom objectives enables effective weight initialization at modest compute cost. We release all code, trained models, and data splits to support reproducibility.

Bioassay activity prediction is often data-limited because drug-discovery datasets rely on time-consuming and expensive wet-lab experiments for data generation and evaluation. This challenge has inspired recent research into molecular foundation models (MFMs), which aim to encode general-purpose chemical knowledge into molecular representations that generalize well in data-constrained scenarios. This paper presents Monroe, a new MFM with several innovations over the existing state of the art: increased scale allowing pre-training on over 81 million molecules from the PM6 quantum chemistry dataset; improved graph representation of stereochemistry; improved training losses including conformer denoising and embedding decorrelation; improved multi-task learning; and the use of a prior-data-fitted model (TabPFN) for downstream in-context prediction. Our evaluations use a principled pairwise comparison framework that measures statistically significant performance differences. Across established Polaris benchmarks, Monroe matches or exceeds existing MFMs, while on activity cliff benchmarks, designed to assess utility for molecular discovery, it achieves significant improvements over prior methods. Finally, ablation and transfer experiments show that PFN-based downstream predictors also substantially improve two leading existing models, MiniMol and CheMeleon, yielding new state-of-the-art variants we call MiniMol_PFN and CheMeleon_PFN, suggesting that our downstream adaptation strategy generalizes beyond Monroe. Source code is at github.com/blazejba/monroe.