Deep Molecular Representation Learning via Fusing Physical and Chemical Information
Authors: Shuwen Yang, Ziyao Li, Guojie Song, Lingsheng Cai
NeurIPS 2021 | Conference PDF | Archive PDF | Plain Text | LLM Run Details
| Reproducibility Variable | Result | LLM Response |
|---|---|---|
| Research Type | Experimental | We evaluated Phys Chem on quantum mechanics (QM7, QM8 and QM9) and physical chemistry (LIPOP, FREESOLV and ESOL) datasets, as well as drug effectiveness datasets of the notorious SARS-CoV-2. [...] We split all datasets into 8:1:1 as training, validation and test sets. |
| Researcher Affiliation | Academia | 1Key Laboratory of Machine Perception and Intelligence (MOE), Peking University, Beijing, China 2Center for Data Science, Peking University, Beijing, China |
| Pseudocode | No | No pseudocode or clearly labeled algorithm block found in the paper. |
| Open Source Code | No | The paper does not provide any explicit statement or link indicating the availability of open-source code for the described methodology. |
| Open Datasets | Yes | The datasets are publicly available at http://moleculenet.ai/datasets-1. The datasets are available at https://opendata.ncats.nih.gov/covid19/ (CC BY 4.0 license) and are continuously extended. |
| Dataset Splits | Yes | We split all datasets into 8:1:1 as training, validation and test sets. |
| Hardware Specification | No | No specific hardware details (like GPU models, CPU types, or memory) used for running experiments are mentioned in the paper. |
| Software Dependencies | Yes | We use the 2020.03.1.0 version of the RDKit package at http://www.rdkit.org/. |
| Experiment Setup | Yes | Unless otherwise specified, we used L = 2 pairs of blocks for Phys Chem. In the initializer, we used a 2-layer GCN and a 2-layer LSTM. In each Phys Net block, we set df = 3, S = 4 and τ = 0.25. In each Chem Net block, we set the dimensions of atom and bond states as 128 and 64, correspondingly. In the representation readout block, we used T = 1 global attentive layers with 256-dimensional meta-atom states. |