Zhuoyang Jiang

Yanting Li, Zhuoyang Jiang, Enyan Dai et al.

Goal-directed molecular generation requires satisfying heterogeneous constraints such as protein--ligand compatibility and multi-objective drug-like properties, yet existing methods often optimize these constraints in isolation, failing to reconcile conflicting objectives (e.g., affinity vs. safety), and struggle to navigate the non-differentiable chemical space without compromising structural validity. To address these challenges, we propose CAGenMol, a condition-aware discrete diffusion framework over molecular sequences that formulates molecular design as conditional denoising guided by heterogeneous structural and property signals. By coupling discrete diffusion with reinforcement learning, the model aligns the generation trajectory with non-differentiable objectives while preserving chemical validity and diversity. The non-autoregressive nature of diffusion language model further enables iterative refinement of molecular fragments at inference time. Experiments on structure-conditioned, property-conditioned, and dual-conditioned benchmarks demonstrate consistent improvements over state-of-the-art methods in binding affinity, drug-likeness, and success rate, highlighting the effectiveness of our framework.

Zhuoyang Jiang, Yaosen Min, Peiran Jin et al.

We present Connection-Aware Motif Sequencing (CamS), a graph-to-sequence representation that enables decoder-only Transformers to learn molecular graphs via standard next-token prediction (NTP). For molecular property prediction, SMILES-based NTP scales well but lacks explicit topology, whereas graph-native masked modeling captures connectivity but risks disrupting the pivotal chemical details (e.g., activity cliffs). CamS bridges this gap by serializing molecular graphs into structure-rich causal sequences. CamS first mines data-driven connection-aware motifs. It then serializes motifs via scaffold-rooted breadth-first search (BFS) to establish a stable core-to-periphery order. Crucially, CamS enables hierarchical modeling by concatenating sequences from fine to coarse motif scales, allowing the model to condition global scaffolds on dense, uncorrupted local structural evidence. We instantiate CamS-LLaMA by pre-training a vanilla LLaMA backbone on CamS sequences. It achieves state-of-the-art performance on MoleculeNet and the activity-cliff benchmark MoleculeACE, outperforming both SMILES-based language models and strong graph baselines. Interpretability analysis confirms that our multi-scale causal serialization effectively drives attention toward cliff-determining differences.