اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدRe-balancing Variational Autoencoder Loss for Molecule Sequence Generation
95
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
Molecule generation is to design new molecules with specific chemical properties and further to optimize the desired chemical properties. Following previous work, we encode molecules into continuous vectors in the latent space and then decode the vectors into molecules under the variational autoencoder (VAE) framework. We investigate the posterior collapse problem of current RNN-based VAEs for molecule sequence generation. For the first time, we find that underestimated reconstruction loss leads to posterior collapse, and provide both theoretical and experimental evidence. We propose an effective and efficient solution to fix the problem and avoid posterior collapse. Without bells and whistles, our method achieves SOTA reconstruction accuracy and competitive validity on the ZINC 250K dataset. When generating 10,000 unique valid SMILES from random prior sampling, it costs JT-VAE1450s while our method only needs 9s. Our implementation is at https://github.com/chaoyan1037/Re-balanced-VAE.
قيم البحث
اقرأ أيضاً
In this paper, we treat the image generation task using an autoencoder, a representative latent model. Unlike many studies regularizing the latent variables distribution by assuming a manually specified prior, we approach the image generation task us
ing an autoencoder by directly estimating the latent distribution. To this end, we introduce latent density estimator which captures latent distribution explicitly and propose its structure. Through experiments, we show that our generative model generates images with the improved visual quality compared to previous autoencoder-based generative models.
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 autoencoders (VAEs
) and multi-layer perceptrons (MLPs) to predict anti-cancer drug responses. Our model takes as input gene expression data of cancer cell lines and anti-cancer drug molecular data and encodes these data with our {sc {GeneVae}} model, which is an ordinary VAE model, and a rectified junction tree variational autoencoder ({sc JTVae}) model, respectively. A multi-layer perceptron processes these encoded features to produce a final prediction. Our tests show our system attains a high average coefficient of determination ($R^{2} = 0.83$) in predicting drug responses for breast cancer cell lines and an average $R^{2} = 0.845$ for pan-cancer cell lines. Additionally, we show that our model can generates effective drug compounds not previously used for specific cancer cell lines.
Recent progress in quantum algorithms and hardware indicates the potential importance of quantum computing in the near future. However, finding suitable application areas remains an active area of research. Quantum machine learning is touted as a pot
ential approach to demonstrate quantum advantage within both the gate-model and the adiabatic schemes. For instance, the Quantum-assisted Variational Autoencoder has been proposed as a quantum enhancement to the discrete VAE. We extend on previous work and study the real-world applicability of a QVAE by presenting a proof-of-concept for similarity search in large-scale high-dimensional datasets. While exact and fast similarity search algorithms are available for low dimensional datasets, scaling to high-dimensional data is non-trivial. We show how to construct a space-efficient search index based on the latent space representation of a QVAE. Our experiments show a correlation between the Hamming distance in the embedded space and the Euclidean distance in the original space on the Moderate Resolution Imaging Spectroradiometer (MODIS) dataset. Further, we find real-world speedups compared to linear search and demonstrate memory-efficient scaling to half a billion data points.
This paper proposes Dirichlet Variational Autoencoder (DirVAE) using a Dirichlet prior for a continuous latent variable that exhibits the characteristic of the categorical probabilities. To infer the parameters of DirVAE, we utilize the stochastic gr
adient method by approximating the Gamma distribution, which is a component of the Dirichlet distribution, with the inverse Gamma CDF approximation. Additionally, we reshape the component collapsing issue by investigating two problem sources, which are decoder weight collapsing and latent value collapsing, and we show that DirVAE has no component collapsing; while Gaussian VAE exhibits the decoder weight collapsing and Stick-Breaking VAE shows the latent value collapsing. The experimental results show that 1) DirVAE models the latent representation result with the best log-likelihood compared to the baselines; and 2) DirVAE produces more interpretable latent values with no collapsing issues which the baseline models suffer from. Also, we show that the learned latent representation from the DirVAE achieves the best classification accuracy in the semi-supervised and the supervised classification tasks on MNIST, OMNIGLOT, and SVHN compared to the baseline VAEs. Finally, we demonstrated that the DirVAE augmented topic models show better performances in most cases.
Gravitational wave detectors such as LIGO and Virgo are susceptible to various types of instrumental and environmental disturbances known as glitches which can mask and mimic gravitational waves. While there are 22 classes of non-Gaussian noise gradi
ents currently identified, the number of classes is likely to increase as these detectors go through commissioning between observation runs. Since identification and labelling new noise gradients can be arduous and time-consuming, we propose $beta$-Annelead VAEs to learn representations from spectograms in an unsupervised way. Using the same formulation as cite{alemi2017fixing}, we view Bottleneck-VAEs~cite{burgess2018understanding} through the lens of information theory and connect them to $beta$-VAEs~cite{higgins2017beta}. Motivated by this connection, we propose an annealing schedule for the hyperparameter $beta$ in $beta$-VAEs which has advantages of: 1) One fewer hyperparameter to tune, 2) Better reconstruction quality, while producing similar levels of disentanglement.
الأسئلة المقترحة
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
