Towards 3D Molecule-Text Interpretation in Language Models
Authors: Sihang Li, Zhiyuan Liu, Yanchen Luo, Xiang Wang, Xiangnan He, Kenji Kawaguchi, Tat-Seng Chua, Qi Tian
ICLR 2024 | Conference PDF | Archive PDF | Plain Text | LLM Run Details
| Reproducibility Variable | Result | LLM Response |
|---|---|---|
| Research Type | Experimental | In this section, we conduct extensive experiments, including molecule-text retrieval, molecule captioning, and open-text molecular QA tasks, to demonstrate the effectiveness of 3D-Mo LM for 3D molecule-text interpretation. |
| Researcher Affiliation | Collaboration | 1University of Science and Technology of China 2National University of Singapore 3Mo E Key Laboratory of Brain-inspired Intelligent Perception and Cognition, USTC 4Institute of Dataspace, Hefei Comprehensive National Science Center 5Huawei Cloud |
| Pseudocode | No | The paper does not contain structured pseudocode or algorithm blocks. |
| Open Source Code | Yes | We release our codes and datasets at https://github.com/lsh0520/3D-Mo LM. |
| Open Datasets | Yes | We release our codes and datasets at https://github.com/lsh0520/3D-Mo LM. |
| Dataset Splits | Yes | This curated subset is subsequently partitioned into train / validation / test sets containing 12K / 1K / 2K pairs, respectively. |
| Hardware Specification | Yes | The computation overhead is 40 GPU hours on NVIDIA A100 with BFloat16 Mixed precision. |
| Software Dependencies | No | The paper mentions software like RDKit, GPT-3.5, GPT-4, and Llama2, but does not specify their version numbers for reproducibility. |
| Experiment Setup | Yes | The Q-former attached with a frozen 3D molecular encoder is pertrained for 50 epochs and the number of query tokens in it is set to 8. Adam W (Loshchilov & Hutter, 2018) optimizer is adopted with a weight decay of 0.05 and a learning rate scheduler of a combination of linear warmup with 1000 steps and cosine decay, in which the peak and minimal learning rates are 1e-4 and 5e-6, respectively. And the batch size and maximal text length are 64 and 256, respectively. |