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Policy Split: Incentivizing Dual-Mode Exploration in LLM Reinforcement with Dual-Mode Entropy Regularization METER: Evaluating Multi-Level Contextual Causal Reasoning in Large Language Models Think Before you Write: QA-Guided Reasoning for Character Descriptions in Books METRO: Towards Strategy Induction from Expert Dialogue Transcripts for Non-collaborative Dialogues Retrieval as Generation: A Unified Framework with Self-Triggered Information Planning Do LLMs Know Tool Irrelevance? Demystifying Structural Alignment Bias in Tool Invocations Enhancing Multimodal Large Language Models for Ancient Chinese Character Evolution Analysis via Glyph-Driven Fine-Tuning Exploring Knowledge Conflicts for Faithful LLM Reasoning: Benchmark and Method CocoaBench: Evaluating Unified Digital Agents in the Wild MathAgent: Adversarial Evolution of Constraint Graphs for Mathematical Reasoning Data Synthesis Efficient Training for Cross-lingual Speech Language Models Shared Emotion Geometry Across Small Language Models: A Cross-Architecture Study of Representation, Behavior, and Methodological Confounds A Systematic Analysis of the Impact of Persona Steering on LLM Capabilities Uncertainty-Aware Web-Conditioned Scientific Fact-Checking When Valid Signals Fail: Regime Boundaries Between LLM Features and RL Trading Policies When Verification Fails: How Compositionally Infeasible Claims Escape Rejection Mem$^2$Evolve: Towards Self-Evolving Agents via Co-Evolutionary Capability Expansion and Experience Distillation AOP-Smart: A RAG-Enhanced Large Language Model Framework for Adverse Outcome Pathway Analysis Advancing Polish Language Modeling through Tokenizer Optimization in the Bielik v3 7B and 11B Series TInR: Exploring Tool-Internalized Reasoning in Large Language Models Do BERT Embeddings Encode Narrative Dimensions? A Token-Level Probing Analysis of Time, Space, Causality, and Character in Fiction Generating Multiple-Choice Knowledge Questions with Interpretable Difficulty Estimation using Knowledge Graphs and Large Language Models Deep-Reporter: Deep Research for Grounded Multimodal Long-Form Generation Too Nice to Tell the Truth: Quantifying Agreeableness-Driven Sycophancy in Role-Playing Language Models Learning and Enforcing Context-Sensitive Control for LLMs Efficient Process Reward Modeling via Contrastive Mutual Information Computational Lesions in Multilingual Language Models Separate Shared and Language-specific Brain Alignment Bridging Linguistic Gaps: Cross-Lingual Mapping in Pre-Training and Dataset for Enhanced Multilingual LLM Performance Early Decisions Matter: Proximity Bias and Initial Trajectory Shaping in Non-Autoregressive Diffusion Language Models LLMs Should Incorporate Explicit Mechanisms for Human Empathy
MolSculpt: Sculpting 3D Molecular Geometries from Chemica...
Zhanpeng Chen, Weihao Gao, Shunyu Wang, Yanan Zhu, Hong Meng, Yu · 2025-12-09 · via cs.AI updates on arXiv.org

Generating precise 3D molecular geometries is crucial for drug discovery and material science. While prior efforts leverage 1D representations like SELFIES to ensure molecular validity, they fail to fully exploit the rich chemical knowledge entangled within 1D models, leading to a disconnect between 1D syntactic generation and 3D geometric realization. To bridge this gap, we propose MolSculpt, a novel framework that "sculpts" 3D molecular geometries from chemical syntax. MolSculpt is built upon a frozen 1D molecular foundation model and a 3D molecular diffusion model. We introduce a set of learnable queries to extract inherent chemical knowledge from the foundation model, and a trainable projector then injects this cross-modal information into the conditioning space of the diffusion model to guide the 3D geometry generation. In this way, our model deeply integrates 1D latent chemical knowledge into the 3D generation process through end-to-end optimization. Experiments demonstrate that MolSculpt achieves state-of-the-art (SOTA) performance in \textit{de novo} 3D molecule generation and conditional 3D molecule generation, showing superior 3D fidelity and stability on both the GEOM-DRUGS and QM9 datasets. Code is available at https://github.com/SakuraTroyChen/MolSculpt.