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We consider feature representation learning problem of molecular graphs. Graph Neural Networks have been widely used in feature representation learning of molecular graphs. However, most existing methods deal with molecular graphs…

机器学习 · 计算机科学 2022-06-08 Zhaoning Yu , Hongyang Gao

This work presents the use of graph learning for the prediction of multi-step experimental outcomes for applications across experimental research, including material science, chemistry, and biology. The viability of geometric learning for…

机器学习 · 计算机科学 2024-08-13 Amanda A. Volk , Robert W. Epps , Jeffrey G. Ethier , Luke A. Baldwin

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

生物大分子 · 定量生物学 2023-10-10 Apakorn Kengkanna , Masahito Ohue

Deep learning is the mainstream technique for many machine learning tasks, including image recognition, machine translation, speech recognition, and so on. It has outperformed conventional methods in various fields and achieved great…

机器学习 · 计算机科学 2018-06-01 Na Lei , Zhongxuan Luo , Shing-Tung Yau , David Xianfeng Gu

Graph Nerual Networks (GNNs) are effective models in graph embedding. It extracts shallow features and neighborhood information by aggregating neighbor information to learn the embedding representation of different nodes. However, the local…

社会与信息网络 · 计算机科学 2023-12-14 Kejia Zhang

Machine Learning (ML) has the potential to accelerate discovery of new materials and shed light on useful properties of existing materials. A key difficulty when applying ML in Materials Science is that experimental datasets of material…

The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are…

机器学习 · 计算机科学 2023-09-06 Minghao Guo , Veronika Thost , Samuel W Song , Adithya Balachandran , Payel Das , Jie Chen , Wojciech Matusik

Graph neural networks, trained on experimental or calculated data are becoming an increasingly important tool in computational materials science. Networks, once trained, are able to make highly accurate predictions at a fraction of the cost…

材料科学 · 物理学 2024-06-19 Johannes Allotey , Keith T. Butler , Jeyan Thiyagalingam

Deep learning has proven to yield fast and accurate predictions of quantum-chemical properties to accelerate the discovery of novel molecules and materials. As an exhaustive exploration of the vast chemical space is still infeasible, we…

机器学习 · 统计学 2020-01-10 Niklas W. A. Gebauer , Michael Gastegger , Kristof T. Schütt

Graph neural network architectures are advantageous for predicting core-electron binding energies which depend on local bond environment effects, as the number of message passing layers defines the topological (bond) radius of the model's…

Advances in machine learning have led to graph neural network-based methods for drug discovery, yielding promising results in molecular design, chemical synthesis planning, and molecular property prediction. However, current graph neural…

定量方法 · 定量生物学 2021-07-13 Jiahua Rao , Shuangjia Zheng , Yuedong Yang

We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes…

Graphs neural networks (GNNs) learn node features by aggregating and combining neighbor information, which have achieved promising performance on many graph tasks. However, GNNs are mostly treated as black-boxes and lack human intelligible…

机器学习 · 计算机科学 2020-06-05 Hao Yuan , Jiliang Tang , Xia Hu , Shuiwang Ji

When confronted with a substance of unknown identity, researchers often perform mass spectrometry on the sample and compare the observed spectrum to a library of previously-collected spectra to identify the molecule. While popular, this…

化学物理 · 物理学 2019-05-07 Jennifer N. Wei , David Belanger , Ryan P. Adams , D. Sculley

Rapid determination of molecular structures can greatly accelerate workflows across many chemical disciplines. However, elucidating structure using only one-dimensional (1D) NMR spectra, the most readily accessible data, remains an…

化学物理 · 物理学 2024-08-16 Frank Hu , Michael S. Chen , Grant M. Rotskoff , Matthew W. Kanan , Thomas E. Markland

Speckle patterns produced by coherent X-ray have a close relationship with the internal structure of materials but quantitative inversion of the relationship to determine structure from speckle patterns is challenging. Here, we investigate…

Machine learning plays an increasingly important role in many areas of chemistry and materials science, e.g. to predict materials properties, to accelerate simulations, to design new materials, and to predict synthesis routes of new…

Graph Neural Networks (GNNs) are a form of deep learning that enable a wide range of machine learning applications on graph-structured data. The learning of GNNs, however, is known to pose challenges for memory-constrained devices such as…

机器学习 · 计算机科学 2023-05-01 Jeroen Bollen , Jasper Steegmans , Jan Van den Bussche , Stijn Vansummeren

The representations of neural networks are often compared to those of biological systems by performing regression between the neural network responses and those measured from biological systems. Many different state-of-the-art deep neural…

神经元与认知 · 定量生物学 2023-12-13 Abdulkadir Canatar , Jenelle Feather , Albert Wakhloo , SueYeon Chung

Data-driven prediction of molecular properties presents unique challenges to the design of machine learning methods concerning data structure/dimensionality, symmetry adaption, and confidence management. In this paper, we present a…

机器学习 · 计算机科学 2019-01-31 Yu-Hang Tang , Wibe A. de Jong