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Automatic molecule generation plays an important role on drug discovery and has received a great deal of attention in recent years thanks to deep learning successful use. Graph-based neural network represents state of the art methods on…

计算工程、金融与科学 · 计算机科学 2024-08-26 Yanbo Wang , Qianqian Song

In recent years, deep generative models have been successfully adopted for various molecular design tasks, particularly in the life and material sciences. A critical challenge for pre-trained generative molecular design (GMD) models is to…

机器学习 · 计算机科学 2024-06-03 A N M Nafiz Abeer , Sanket Jantre , Nathan M Urban , Byung-Jun Yoon

Sequence-to-sequence (Seq2seq) models have played an important role in the recent success of various natural language processing methods, such as machine translation, text summarization, and speech recognition. However, current Seq2seq…

计算与语言 · 计算机科学 2018-06-05 Myeongjun Jang , Seungwan Seo , Pilsung Kang

Variational Autoencoders (VAEs) have experienced recent success as data-generating models by using simple architectures that do not require significant fine-tuning of hyperparameters. However, VAEs are known to suffer from…

机器学习 · 统计学 2020-07-22 Wei Cheng , Gregory Darnell , Sohini Ramachandran , Lorin Crawford

Molecule generation is a task made very difficult by the complex ways in which we represent molecules computationally. A common technique used in molecular generative modeling is to use SMILES strings with recurrent neural networks built…

生物大分子 · 定量生物学 2024-02-28 Divahar Sivanesan

A specific challenge with deep learning approaches for molecule generation is generating both syntactically valid and chemically plausible molecular string representations. To address this, we propose a novel generative latent-variable…

生物大分子 · 定量生物学 2024-07-22 Ulrich A. Mbou Sob , Qiulin Li , Miguel Arbesú , Oliver Bent , Andries P. Smit , Arnu Pretorius

Existing vector quantization (VQ) based autoregressive models follow a two-stage generation paradigm that first learns a codebook to encode images as discrete codes, and then completes generation based on the learned codebook. However, they…

计算机视觉与模式识别 · 计算机科学 2023-05-22 Mengqi Huang , Zhendong Mao , Zhuowei Chen , Yongdong Zhang

Variational Autoencoders (VAEs) typically rely on a probabilistic decoder with a predefined likelihood, most commonly an isotropic Gaussian, to model the data conditional on latent variables. While convenient for optimization, this choice…

机器学习 · 统计学 2025-04-29 Chen Xu , Qiang Wang , Lijun Sun

The variational autoencoder (VAE) is a popular combination of deep latent variable model and accompanying variational learning technique. By using a neural inference network to approximate the model's posterior on latent variables, VAEs…

机器学习 · 计算机科学 2019-01-30 Junxian He , Daniel Spokoyny , Graham Neubig , Taylor Berg-Kirkpatrick

Variational auto-encoder (VAE) is a powerful unsupervised learning framework for image generation. One drawback of VAE is that it generates blurry images due to its Gaussianity assumption and thus L2 loss. To allow the generation of high…

计算机视觉与模式识别 · 计算机科学 2017-05-23 Lei Cai , Hongyang Gao , Shuiwang Ji

Variational autoencoders (VAEs) are fundamental for generative modeling and image reconstruction, yet their performance often struggles to maintain high fidelity in reconstructions. This study introduces a hybrid model, quantum variational…

计算机视觉与模式识别 · 计算机科学 2025-03-10 Farina Riaz , Fakhar Zaman , Hajime Suzuki , Sharif Abuadbba , David Nguyen

Variational autoencoders (VAEs) have received much attention recently as an end-to-end architecture for text generation with latent variables. In this paper, we investigate several multi-level structures to learn a VAE model to generate…

计算与语言 · 计算机科学 2019-06-21 Dinghan Shen , Asli Celikyilmaz , Yizhe Zhang , Liqun Chen , Xin Wang , Jianfeng Gao , Lawrence Carin

Building a scalable machine learning system for unsupervised anomaly detection via representation learning is highly desirable. One of the prevalent methods is using a reconstruction error from variational autoencoder (VAE) via maximizing…

机器学习 · 计算机科学 2020-05-08 Seonho Park , George Adosoglou , Panos M. Pardalos

Variational Autoencoders (VAE) and their variants have been widely used in a variety of applications, such as dialog generation, image generation and disentangled representation learning. However, the existing VAE models have some…

机器学习 · 计算机科学 2020-06-23 Huajie Shao , Shuochao Yao , Dachun Sun , Aston Zhang , Shengzhong Liu , Dongxin Liu , Jun Wang , Tarek Abdelzaher

Variational Autoencoders (VAEs) are powerful generative models capable of learning compact latent representations. However, conventional VAEs often generate relatively blurry images due to their assumption of an isotropic Gaussian latent…

计算机视觉与模式识别 · 计算机科学 2025-04-21 Andrew Kiruluta

Variational autoencoders (VAEs), as an important aspect of generative models, have received a lot of research interests and reached many successful applications. However, it is always a challenge to achieve the consistency between the…

机器学习 · 计算机科学 2022-05-10 Xiaoyu Chen , Chen Gong , Qiang He , Xinwen Hou , Yu Liu

Despite their ubiquity, variational autoencoders (VAEs) inherently suffer from posterior collapse, a failure mode in which latent variables are effectively ignored. This failure arises because explicit prior imposition drives optimization…

机器学习 · 计算机科学 2026-05-18 Hazhir Aliahmadi , Irina Babayan , Greg van Anders

Variational autoencoders (VAEs) frequently suffer from posterior collapse, where the latent variables become uninformative as the approximate posterior degenerates to the prior. While recent work has characterized collapse as a phase…

机器学习 · 计算机科学 2026-05-19 Zegu Zhang , Jian Zhang

As one of the most popular generative models, Variational Autoencoder (VAE) approximates the posterior of latent variables based on amortized variational inference. However, when the decoder network is sufficiently expressive, VAE may lead…

机器学习 · 计算机科学 2021-10-26 Dazhong Shen , Chuan Qin , Chao Wang , Hengshu Zhu , Enhong Chen , Hui Xiong

Recently, molecule generation using deep learning has been actively investigated in drug discovery. In this field, Transformer and VAE are widely used as powerful models, but they are rarely used in combination due to structural and…

生物大分子 · 定量生物学 2024-04-08 Yasuhiro Yoshikai , Tadahaya Mizuno , Shumpei Nemoto , Hiroyuki Kusuhara