26 papers · ranked by Valyu relevance
Aman Singh, Tokunbo Ogunfunmi, Sotiris Kotsiantis
Autoencoders are a self-supervised learning system where, during training, the output is an approximation of the input. Typically, autoencoders have three parts: Encoder (which produces a compressed latent space representation of the input data), the Latent Space (which retains the knowledge in the input data with…
Nicola Milano, Monica Casella, Raffaella Esposito, Davide Marocco + 1 more
'Gianluca Borghini'] Latent variables analysis is an important part of psychometric research. In this context, factor analysis and other related techniques have been widely applied for the investigation of the internal structure of psychometric tests. However, these methods perform a linear dimensionality reduction…
Shichen Cao, Jingjing Li, Kenric P. Nelson, Mark A. Kon + 1 more
'Pierre Alquier'] We present a coupled variational autoencoder (VAE) method, which improves the accuracy and robustness of the model representation of handwritten numeral images. The improvement is measured in both increasing the likelihood of the reconstructed images and in reducing divergence between the posterior…
Yoshihiro Nagano, Ryo Karakida, Masato Okada
Deep neural networks are good at extracting low-dimensional subspaces (latent spaces) that represent the essential features inside a high-dimensional dataset. Deep generative models represented by variational autoencoders (VAEs) can generate and infer high-quality datasets, such as images. In particular, VAEs can…
Sabrina Rashid, Sohrab Shah, Ziv Bar-Joseph, Ravi Pandya
Intra-tumor heterogeneity is one of the key confounding factors in deciphering tumor evolution. Malignant cells exhibit variations in their gene expression, copy numbers, and mutation even when originating from a single progenitor cell. Single cell sequencing of tumor cells has recently emerged as a viable option for…
Margarita Geleta, Daniel Mas Montserrat, Xavier Giro-i-Nieto, Alexander G. Ioannidis
Modern biobanks provide numerous high-resolution genomic sequences of diverse populations. These datasets enable a better understanding of genotype-phenotype interactions with genome-wide association studies (GWAS) and power a new personalized precision medicine with polygenic risk scores (PRS). In order to account for…
Ehsan Abbasnejad, Anthony Dick, Anton van den Hengel
This paper presents an infinite variational autoencoder (VAE) whose capacity adapts to suit the input data. This is achieved using a mixture model where the mixing coefficients are modeled by a Dirichlet process, allowing us to integrate over the coefficients when performing inference. Critically, this then allows us…
Ahmed M. Daoud, Osama M. Elkomy, Walid I. Khedr, Khalid M. Hosny
In this paper, we propose a new hybrid model, called AVE, that integrates the strengths of Autoencoder (AE) and Variational Autoencoder (VAE) to enhance outlier detection for numerous high-dimensional datasets. The proposed architecture leverages the reconstruction strengths of AE and the regularized latent space of…
Andrea Asperti
In this article, we highlight what appears to be major issue of Variational Autoencoders (VAEs), evinced from an extensive experimentation with different networks architectures and datasets: the variance of generated data is significantly lower than that of training data. Since generative models are usually evaluated…
Gautam Ramachandra
In recent years Variation Autoencoders have become one of the most popular unsupervised learning of complicated distributions. Variational Autoencoder (VAE) provides more efficient reconstructive performance over a traditional autoencoder. Variational auto enocders make better approximaiton than MCMC. The VAE defines a…
Chao Zhang
Variational Autoencoder (VAE) is a generative model from the computer vision community; it learns a latent representation of the images and generates new images in an unsupervised way. Recently, Vanilla VAE has been applied to analyse single-cell datasets, in the hope of harnessing the representation power of latent…
Alan Jeffares, Liyuan Liu
Variational Autoencoders (VAEs) are well-established as a principled approach to probabilistic unsupervised learning with neural networks. Typically, an encoder network defines the parameters of a Gaussian distributed latent space from which we can sample and pass realizations to a decoder network. This model is…
Christopher Heje Grønbech, Maximillian Fornitz Vording, Pascal Timshel, Casper Kaae Sønderby + 2 more
Models for analysing and making relevant biological inferences from massive amounts of complex single-cell transcriptomic data typically require several individual dataprocessing steps, each with their own set of hyperparameter choices. With deep generative models one can work directly with count data, make…
Sergei Popov, Mikhail Lazarev, Vladislav Belavin, Denis Derkach + 2 more
'Andrey Ustyuzhanin' 'Muhammad Aleem'] There are many problems in physics, biology, and other natural sciences in which symbolic regression can provide valuable insights and discover new laws of nature. Widespread deep neural networks do not provide interpretable solutions. Meanwhile, symbolic expressions give us a…
Pavel Kohout, Michal Vasina, Marika Majerova, Veronika Novakova + 5 more
Enzymes play a crucial role in sustainable industrial applications, with their optimization posing a formidable challenge due to the intricate interplay among residues. Computational methodologies predominantly rely on evolutionary insights, leveraging homologous sequences to pinpoint conserved and functionally…
Kuo-Hao Fanchiang, Cheng-Chien Kuo, Anastasios Doulamis
Dry-type power transformers play a critical role in the power system. Detecting various overheating faults in the running state of the power transformer is necessary to avoid the collapse of the power system. In this paper, we propose a novel deep variational autoencoder-based anomaly detection method to recognize the…
Florian Eichin, Maren Hackenberg, Caroline Broichhagen, Antje Kilias + 3 more
Live imaging techniques, such as two-photon imaging, promise novel insights into cellular activity patterns at a high spatial and temporal resolution. While current deep learning approaches typically focus on specific supervised tasks in the analysis of such data, e.g., learning a segmentation mask as a basis for…
Xianxu Hou, Ke Sun, Linlin Shen, Guoping Qiu
We present a new method for improving the performances of variational autoencoder (VAE). In addition to enforcing the deep feature consistent principle thus ensuring the VAE output and its corresponding input images to have similar deep features, we also implement a generative adversarial training mechanism to force…
Yiran Dong, Chuanhou Gao
variational autoencoder Authors: ['Yiran Dong' 'Chuanhou Gao'] Abstract—In this paper, we develop the notion of evidence lower bound difference (ELBD), based on which an efficient score algorithm is presented to implement feature selection on latent variables of VAE and its variants. Further, we propose weak…
Ran Liu, Mehdi Azabou, Max Dabagia, Chi-Heng Lin + 4 more
Meaningful and simplified representations of neural activity can yield insights into how and what information is being processed within a neural circuit. However, without labels, finding representations that reveal the link between the brain and behavior can be challenging. Here, we introduce a novel unsupervised…
Wei, Yuan-Hao, Yan-Jie Sun
This study advances the Variational Autoencoder (VAE) framework by addressing challenges in Independent Component Analysis (ICA) under both determined and underdetermined conditions, focusing on enhancing the independence and interpretability of latent variables. Traditional VAEs map observed data to latent variables…
Samuel Renaud, Rachael Mansbach
Current antibacterial treatments cannot overcome the rapidly growing resistance of bacteria to antibiotic drugs, and novel treatment methods are required. One option is the development of new antimicrobial peptides (AMPs), to which bacterial resistance build-up is comparatively slow. Deep generative models have…
David Buterez, Jon Paul Janet, Steven Kiddle, Pietro Liò
We investigate the potential of graph neural networks for transfer learning and improving molecular property prediction on sparse and expensive to acquire high-fidelity data by leveraging low-fidelity measurements as an inexpensive proxy for a targeted property ofinterest. This problem arises in discovery processes…
Vladimir Kondratyev, Marian Dryzhakov, Timur Gimadiev, Dmitriy Slutskiy
In this work, we provide further development of the junction tree variational autoencoder (JT VAE) architecture in terms of implementation and application of the internal feature space of the model. Pretraining of JT VAE on a large dataset and further optimization with a regression model led to a latent space that can…
Authors not listed
Deep generative models are transforming early-stage drug discovery, yet most current approaches are not well suited for realistic, small-data settings and often rely on simplified molecular representations such as linear strings, overlooking the inherent graph-based structure of molecules. To address this, we first…
Tagir Akhmetshin, Arkadii Lin, Timur Madzhidov, Alexandre Varnek
Autoencoders represent a promising technique for the inverse quantitative structure-activity relationship (QSAR) task. However, undesirable bias, such as atom ordering, affects the neighbourhood behaviour of autoencoders’ latent space and, consequently, usage of the latent vectors as variables in machine-learning…