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Predicting molecular conformations (or 3D structures) from molecular graphs is a fundamental problem in many applications. Most existing approaches are usually divided into two steps by first predicting the distances between atoms and then…

机器学习 · 计算机科学 2025-01-07 Minkai Xu , Wujie Wang , Shitong Luo , Chence Shi , Yoshua Bengio , Rafael Gomez-Bombarelli , Jian Tang

Learning interpretable and disentangled representations of data is a key topic in machine learning research. Variational Autoencoder (VAE) is a scalable method for learning directed latent variable models of complex data. It employs a clear…

机器学习 · 计算机科学 2020-06-04 Andriy Serdega , Dae-Shik Kim

Variational autoencoders (VAEs) are a popular generative model used to approximate distributions. The encoder part of the VAE is used in amortized learning of latent variables, producing a latent representation for data samples. Recently,…

机器学习 · 统计学 2023-05-12 Daniel G. Edelberg , Roy R. Lederman

Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of…

生物大分子 · 定量生物学 2019-05-22 Sean M. Colby , Jamie R. Nuñez , Nathan O. Hodas , Courtney D. Corley , Ryan R. Renslow

Disordered materials such as glasses, unlike crystals, lack long range atomic order and have no periodic unit cells, yielding a high dimensional configuration space with widely varying properties. The complexity not only increases…

计算工程、金融与科学 · 计算机科学 2025-11-12 Qiyuan Chen , Ajay Annamareddy , Ying-Fei Li , Dane Morgan , Bu Wang

Modern generative models are usually designed to match target distributions directly in the data space, where the intrinsic dimension of data can be much lower than the ambient dimension. We argue that this discrepancy may contribute to the…

机器学习 · 计算机科学 2020-07-02 Zijun Zhang , Ruixiang Zhang , Zongpeng Li , Yoshua Bengio , Liam Paull

As big spatial data becomes increasingly prevalent, classical spatiotemporal (ST) methods often do not scale well. While methods have been developed to account for high-dimensional spatial objects, the setting where there are exceedingly…

应用统计 · 统计学 2019-08-27 Samuel I. Berchuck , Felipe A. Medeiros , Sayan Mukherjee

Variational autoencoders~(VAEs) have shown a promise in data-driven conversation modeling. However, most VAE conversation models match the approximate posterior distribution over the latent variables to a simple prior such as standard…

计算与语言 · 计算机科学 2019-02-27 Xiaodong Gu , Kyunghyun Cho , Jung-Woo Ha , Sunghun Kim

Cancer is a primary cause of human death, but discovering drugs and tailoring cancer therapies are expensive and time-consuming. We seek to facilitate the discovery of new drugs and treatment strategies for cancer using variational…

机器学习 · 计算机科学 2021-04-16 Hongyuan Dong , Jiaqing Xie , Zhi Jing , Dexin Ren

As deep Variational Auto-Encoder (VAE) frameworks become more widely used for modeling biomolecular simulation data, we emphasize the capability of the VAE architecture to concurrently maximize the timescale of the latent space while…

化学物理 · 物理学 2021-12-08 Hannah K. Wayment-Steele , Vijay S. Pande

Given an image dataset, we are often interested in finding data generative factors that encode semantic content independently from pose variables such as rotation and translation. However, current disentanglement approaches do not impose…

计算机视觉与模式识别 · 计算机科学 2019-09-27 Tristan Bepler , Ellen D. Zhong , Kotaro Kelley , Edward Brignole , Bonnie Berger

Recent advances in artificial intelligence have propelled the development of innovative computational materials modeling and design techniques. Generative deep learning models have been used for molecular representation, discovery, and…

化学物理 · 物理学 2021-02-12 Navid Shervani-Tabar , Nicholas Zabaras

Variational autoencoders (VAEs) are powerful generative models with the salient ability to perform inference. Here, we introduce a quantum variational autoencoder (QVAE): a VAE whose latent generative process is implemented as a quantum…

Bayesian optimisation in the latent space of a Variational AutoEncoder (VAE) is a powerful framework for optimisation tasks over complex structured domains, such as the space of scientifically interesting molecules. However, existing…

机器学习 · 计算机科学 2025-07-08 Henry B. Moss , Sebastian W. Ober , Tom Diethe

We develop a semi-supervised variational autoencoder (SSVAE) framework to reconstruct and generate neutron star (NS) equations of state (EOS). The SSVAE consists of an encoder network that maps high-dimensional EOS data into a…

天体物理仪器与方法 · 物理学 2026-05-28 Tianqi Zhao , Fanglida Yan , Alex Ross , James M. Lattimer

In this paper, we introduce ControlVAE, a novel model-based framework for learning generative motion control policies based on variational autoencoders (VAE). Our framework can learn a rich and flexible latent representation of skills and a…

图形学 · 计算机科学 2022-10-13 Heyuan Yao , Zhenhua Song , Baoquan Chen , Libin Liu

Multimodal generative models require a unified approach to handle both discrete data (e.g., text and code) and continuous data (e.g., image, audio, video). In this work, we propose Latent Language Modeling (LatentLM), which seamlessly…

计算与语言 · 计算机科学 2024-12-12 Yutao Sun , Hangbo Bao , Wenhui Wang , Zhiliang Peng , Li Dong , Shaohan Huang , Jianyong Wang , Furu Wei

A major challenge in quantum computing is its application to large real-world datasets due to scarce quantum hardware resources. One approach to enabling tractable quantum models for such datasets involves finding low-dimensional…

量子物理 · 物理学 2025-04-11 Gaoyuan Wang , Jonathan Warrell , Prashant S. Emani , Mark Gerstein

Based on the traditional VAE, a novel neural network model is presented, with the latest molecular representation, SELFIES, to improve the effect of generating new molecules. In this model, multi-layer convolutional network and Fisher…

生物大分子 · 定量生物学 2023-05-03 Li Kai , Li Ning , Zhang Wei , Gao Ming

Controllable data generation aims to synthesize data by specifying values for target concepts. Achieving this reliably requires modeling the underlying generative factors and their relationships. In real-world scenarios, these factors…

机器学习 · 计算机科学 2025-11-21 Qilong Zhao , Shiyu Wang , Zeeshan Memon , Yang Qiao , Guangji Bai , Bo Pan , Zhaohui Qin , Liang Zhao