Geometric representation-conditioned molecule generation provides an effective paradigm that decouples molecule representation modeling from structure generation. By decoupling molecule generation into two stages-first generating a meaningful molecule representation, and then generating a 3D molecule conditioned on this representation-the efficiency and quality of the generation process can be significantly enhanced. However, its effectiveness is fundamentally limited by the quality of the representation space: pretrained molecular encoders, such as UniMol, produce representations that are non-smooth and not fully exploited during the generative training process. In this work, we propose LENSEs, a framework that better exploits the potential of molecule representations in representation-conditioned generation methods. In particular, LENSEs introduces three complementary mechanisms: (1) a representation head, simultaneously trained during generative tasks, that extracts multi-level representations from the pretrained encoder; (2) a molecule perceptual loss that optimizes the generator in a semantic-informative representation space; and (3) a node-level representation alignment (REPA) loss that explicitly aligns the generator's hidden states with encoder representations, reducing the semantic gap between pretraining and generation. We demonstrate the effectiveness of these improvements through extensive molecule generation tasks. Specifically, on the challenging molecule generation dataset GEOM-DRUG, LENSEs achieves 97.28% validity and 98.51% molecule stability, surpassing existing advanced methods. Further analyses through Lipschitz constant reduction (4.6x) and QM9 probing tasks also demonstrate the smoother, more informative refined representations, establishing generative training with alignment objectives as a potential pretraining paradigm for molecular encoders.
Three-dimensional (3D) molecule generation has been dominated by diffusion models, which achieve strong generation quality but typically require the molecular size to be specified a priori. Recent autoregressive approaches have substantially narrowed the performance gap while naturally supporting variable-length generation and conditioning on partial molecular context. However, balancing unconditional and context-conditioned generation remains challenging. We introduce KRONOS, a latent autoregressive diffusion framework that generates molecules in the latent space of a pre-trained autoencoder, jointly modeling molecular graph topology and geometry, while retaining the flexibility of autoregressive generation. We further introduce a mixed training strategy inspired by Fill-in-the Middle (FIM) paradigm, enabling both unconditional and fragment-conditioned molecular generation within a single left-to-right autoregressive model. Experiments on QM9 and GEOM-Drugs demonstrate that KRONOS achieves leading unconditional generation performance among autoregressive methods, while remaining competitive with diffusion models. Moreover, fragment-conditioned generation is achieved with negligible impact on unconditional generation performance, demonstrating that both generation paradigms can be supported within a single architecture.
Large language models (LLMs) are increasingly used for molecular tasks, but it remains unclear which molecular representation to use. We present a systematic benchmark evaluating LLM molecular competence across nine representations and eight chemical tasks. We benchmark 16 LLMs across five model families, including reasoning and non-reasoning variants, chemistry-specialized LLMs, and closed frontier models. Performance is strongly representation-dependent and no single representation wins across tasks, though CML is the best, followed by MolJSON, InChI, and then canonical SMILES. Explicit structured text representations (CML and MolJSON) dominate structural tasks; IUPAC dominates semantic tasks, winning molecule retrieval for all 16 LLMs; and SMILES variants are rarely optimal despite their prevalence in pretraining. Chemistry-specialized models perform well with SMILES at the cost of large degradations with structured text representations, suggesting SMILES-only evaluation rewards specialization that does not generalize. Using LLM-as-a-judge, we find that IUPAC produces the highest fraction of correct molecule generations. A mechanistic study via tokenization audits, linear probes and attention shows that representations are encoded differently inside the model; for example, structured representations require higher attention across the molecular span. Our results argue against representation-invariant evaluation and motivate task-aware representation routing for LLM-based chemistry.
Property-conditional molecular generation should produce valid, diverse molecules while responding to continuous target values at low sampling cost. We introduce DriftingMol, a two-stage framework that adapts drifting models to a SELFIES latent molecular space. A frozen SELFIES beta-VAE provides the latent space, and the hidden representation of its decoder serves as the drift feature map. In decoder-coupled drift, decoder weights remain fixed, but drift gradients are backpropagated through the decoder feature map to a DiT generator, inducing a pullback metric aligned with molecular decoding. On ZINC250K, the default setting achieves QED Spearman correlation 0.493 with 94.7% uniqueness, while the strongest decoder-coupled condition reaches 0.510. Under protocol-matched four-property conditioning, decoder-coupled drift reaches mean Spearman correlation up to 0.598. Across 15 controlled variants, models that preserve the gradient path through decoder features achieve higher correlations than the tested latent-space, random-feature, and external-feature drift variants, while detached or stop-gradient decoder controls yield near-zero QED correlation and very low uniqueness. These results indicate that decoder-coupled drift is a useful low-cost mechanism for property-biased molecular generation, requiring one generator evaluation and one frozen decoder pass.