Attending to graph transformers

L Müller, M Galkin, C Morris, L Rampášek - arxiv preprint arxiv …, 2023 - arxiv.org
Recently, transformer architectures for graphs emerged as an alternative to established
techniques for machine learning with graphs, such as (message-passing) graph neural …

Artificial intelligence for science in quantum, atomistic, and continuum systems

X Zhang, L Wang, J Helwig, Y Luo, C Fu, Y **e… - arxiv preprint arxiv …, 2023 - arxiv.org
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural
sciences. Today, AI has started to advance natural sciences by improving, accelerating, and …

Data-driven quantum chemical property prediction leveraging 3D conformations with Uni-Mol+

S Lu, Z Gao, D He, L Zhang, G Ke - Nature communications, 2024 - nature.com
Quantum chemical (QC) property prediction is crucial for computational materials and drug
design, but relies on expensive electronic structure calculations like density functional theory …

Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey

T Kuang, P Liu, Z Ren - Big Data Mining and Analytics, 2024 - ieeexplore.ieee.org
The precise prediction of molecular properties is essential for advancements in drug
development, particularly in virtual screening and compound optimization. The recent …

Coati: Multimodal contrastive pretraining for representing and traversing chemical space

B Kaufman, EC Williams, C Underkoffler… - Journal of Chemical …, 2024 - ACS Publications
Creating a successful small molecule drug is a challenging multiparameter optimization
problem in an effectively infinite space of possible molecules. Generative models have …

Generating QM1B with PySCF

A Mathiasen, H Helal, K Klaser… - Advances in …, 2023 - proceedings.neurips.cc
The emergence of foundation models in Computer Vision and Natural Language Processing
have resulted in immense progress on downstream tasks. This progress was enabled by …

Automated 3D pre-training for molecular property prediction

X Wang, H Zhao, W Tu, Q Yao - Proceedings of the 29th ACM SIGKDD …, 2023 - dl.acm.org
Molecular property prediction is an important problem in drug discovery and materials
science. As geometric structures have been demonstrated necessary for molecular property …

Applications of Transformers in Computational Chemistry: Recent Progress and Prospects

R Wang, Y Ji, Y Li, ST Lee - The Journal of Physical Chemistry …, 2024 - ACS Publications
The powerful data processing and pattern recognition capabilities of machine learning (ML)
technology have provided technical support for the innovation in computational chemistry …

GeoMFormer: A general architecture for geometric molecular representation learning

T Chen, S Luo, D He, S Zheng, TY Liu… - arxiv preprint arxiv …, 2024 - arxiv.org
Molecular modeling, a central topic in quantum mechanics, aims to accurately calculate the
properties and simulate the behaviors of molecular systems. The molecular model is …

Highly accurate quantum chemical property prediction with uni-mol+

S Lu, Z Gao, D He, L Zhang, G Ke - arxiv preprint arxiv:2303.16982, 2023 - arxiv.org
Recent developments in deep learning have made remarkable progress in speeding up the
prediction of quantum chemical (QC) properties by removing the need for expensive …