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A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…

Machine Learning · Computer Science 2020-01-01 Elman Mansimov , Omar Mahmood , Seokho Kang , Kyunghyun Cho

Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in…

Computational Physics · Physics 2021-03-19 Jun Zhang , Yao-Kun Lei , Zhen Zhang , Junhan Chang , Maodong Li , Xu Han , Lijiang Yang , Yi Isaac Yang , Yi Qin Gao

Molecular graph representation learning is a fundamental problem in modern drug and material discovery. Molecular graphs are typically modeled by their 2D topological structures, but it has been recently discovered that 3D geometric…

Machine Learning · Computer Science 2022-05-31 Shengchao Liu , Hanchen Wang , Weiyang Liu , Joan Lasenby , Hongyu Guo , Jian Tang

Visual localization techniques rely upon some underlying scene representation to localize against. These representations can be explicit such as 3D SFM map or implicit, such as a neural network that learns to encode the scene. The former…

Computer Vision and Pattern Recognition · Computer Science 2024-06-13 Maxime Pietrantoni , Gabriela Csurka , Martin Humenberger , Torsten Sattler

Neural networks currently dominate the machine learning community and they do so for good reasons. Their accuracy on complex tasks such as image classification is unrivaled at the moment and with recent improvements they are reasonably easy…

Machine Learning · Computer Science 2019-01-21 Sascha Saralajew , Lars Holdijk , Maike Rees , Thomas Villmann

We introduce a new neural architecture and an unsupervised algorithm for learning invariant representations from temporal sequence of images. The system uses two groups of complex cells whose outputs are combined multiplicatively: one that…

Neural and Evolutionary Computing · Computer Science 2010-06-03 Karo Gregor , Yann LeCun

The Method of Continuous Molecular Fields is a universal approach to predict various properties of chemical compounds, in which molecules are represented by means of continuous fields (such as electrostatic, steric, electron density…

Chemical Physics · Physics 2013-11-07 Igor I. Baskin , Nelly I. Zhokhova

The graph structure is a commonly used data storage mode, and it turns out that the low-dimensional embedded representation of nodes in the graph is extremely useful in various typical tasks, such as node classification, link prediction ,…

Social and Information Networks · Computer Science 2020-08-03 Xing Li , Wei Wei , Xiangnan Feng , Xue Liu , Zhiming Zheng

The quest for efficient and robust deep learning models for molecular systems representation is increasingly critical in scientific exploration. The advent of message passing neural networks has marked a transformative era in graph-based…

Computational Physics · Physics 2026-01-05 Jian Chang , Shuze Zhu

The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through Graph Neural Networks (GNNs). It is well known that both atoms and…

Quantitative Methods · Quantitative Biology 2020-06-15 Hehuan Ma , Yatao Bian , Yu Rong , Wenbing Huang , Tingyang Xu , Weiyang Xie , Geyan Ye , Junzhou Huang

In this work we target a learnable output representation that allows continuous, high resolution outputs of arbitrary shape. Recent works represent 3D surfaces implicitly with a Neural Network, thereby breaking previous barriers in…

Computer Vision and Pattern Recognition · Computer Science 2020-10-28 Julian Chibane , Aymen Mir , Gerard Pons-Moll

In this paper, we propose to exploit the rich hierarchical features of deep convolutional neural networks to improve the accuracy and robustness of visual tracking. Deep neural networks trained on object recognition datasets consist of…

Computer Vision and Pattern Recognition · Computer Science 2018-08-14 Chao Ma , Jia-Bin Huang , Xiaokang Yang , Ming-Hsuan Yang

We present a new approach to 3D object representation where a neural network encodes the geometry of an object directly into the weights and biases of a second 'mapping' network. This mapping network can be used to reconstruct an object by…

Machine Learning · Computer Science 2020-04-07 Eric Mitchell , Selim Engin , Volkan Isler , Daniel D Lee

We present a novel technique for implicit neural representation of light fields at continuously defined viewpoints with high quality and fidelity. Our implicit neural representation maps 4D coordinates defining two-plane parameterization of…

Graphics · Computer Science 2023-05-11 Süleyman Aslan , Brandon Yushan Feng , Amitabh Varshney

Implicit neural representations (INRs), which leverage neural networks to represent signals by mapping coordinates to their corresponding attributes, have garnered significant attention. They are extensively utilized for image…

Computer Vision and Pattern Recognition · Computer Science 2025-04-08 Sheng Zheng , Chaoning Zhang , Dongshen Han , Fachrina Dewi Puspitasari , Xinhong Hao , Yang Yang , Heng Tao Shen

Properties of molecules are indicative of their functions and thus are useful in many applications. With the advances of deep learning methods, computational approaches for predicting molecular properties are gaining increasing momentum.…

Quantitative Methods · Quantitative Biology 2021-07-07 Zhengyang Wang , Meng Liu , Youzhi Luo , Zhao Xu , Yaochen Xie , Limei Wang , Lei Cai , Qi Qi , Zhuoning Yuan , Tianbao Yang , Shuiwang Ji

The quest for accurate prediction of drug molecule properties poses a fundamental challenge in the realm of Artificial Intelligence Drug Discovery (AIDD). An effective representation of drug molecules emerges as a pivotal component in this…

Machine Learning · Computer Science 2024-04-22 Zhuoyuan Wang , Jiacong Mi , Shan Lu , Jieyue He

Neural embeddings are a popular set of methods for representing words, phrases or text as a low dimensional vector (typically 50-500 dimensions). However, it is difficult to interpret these dimensions in a meaningful manner, and creating…

Computation and Language · Computer Science 2018-01-10 Neil R. Smalheiser , Gary Bonifield

Neural fields, also known as implicit neural representations, have emerged as a powerful means to represent complex signals of various modalities. Based on this Dupont et al. (2022) introduce a framework that views neural fields as data,…

Machine Learning · Computer Science 2023-02-10 Matthias Bauer , Emilien Dupont , Andy Brock , Dan Rosenbaum , Jonathan Richard Schwarz , Hyunjik Kim

Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and geometric aspects of the…

Biomolecules · Quantitative Biology 2021-05-18 Bowen Jing , Stephan Eismann , Patricia Suriana , Raphael J. L. Townshend , Ron Dror