9 papers
HD-Prot: A Protein Language Model for Joint Sequence-Structure Modeling with Continuous Structure Tokens
Yi Zhou, Haohao Qu, Yunqing Liu +3
Proteins inherently possess a consistent sequence-structure duality. The abundance of protein sequence data, which can be readily represented as discrete tokens, has driven fruitfu…
Geometric Flow Matching for Molecular Conformation Generation via Manifold Decomposition
Yunqing Liu, Yi Zhou, Wenqi Fan
The generation of accurate 3D molecular conformations is a pivotal challenge in computational chemistry and drug discovery. Recently, diffusion and flow matching models have achiev…
Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation
Jiatong Li, Junxian Li, Weida Wang +6
Recently, Large Language Models (LLMs) have demonstrated great potential in natural language-driven molecule discovery. However, existing datasets and benchmarks for molecule-text…
MolReFlect: Towards In-Context Fine-grained Alignments between Molecules and Texts
Jiatong Li, Yunqing Liu, Wei Liu +6
Molecule discovery is a pivotal research field, impacting everything from medicine to materials. Recently, Large Language Models (LLMs) have been widely adopted in molecular unders…
Error Notebook-Guided, Training-Free Part Retrieval in 3D CAD Assemblies via Vision-Language Models
Yunqing Liu, Nan Zhang, Zhiming Tan
Effective specification-aware part retrieval within complex CAD assemblies is essential for automated engineering tasks. However, using LLMs/VLMs for this task is challenging: the…
ATLAS: Autoformalizing Theorems through Lifting, Augmentation, and Synthesis of Data
Xiaoyang Liu, Kangjie Bao, Jiashuo Zhang +5
Autoformalization, the automatic translation of mathematical content from natural language into machine-verifiable formal languages, has seen significant progress driven by advance…