In order to process efficiently ever-higher dimensional data such as images, sentences, or audio recordings, one needs to find a proper way to reduce the dimensionality of such data. In this regard, SVD-based methods including PCA and Isomap have been extensively used. Recently, a neural network alternative called autoencoder has been proposed and is often preferred for its higher flexibility. This work aims to show that PCA is still a relevant technique for dimensionality reduction in the context of classification. To this purpose, we evaluated the performance of PCA compared to Isomap, a deep autoencoder, and a variational autoencoder. Experiments were conducted on three commonly used image datasets: MNIST, Fashion-MNIST, and CIFAR-10. The four different dimensionality reduction techniques were separately employed on each dataset to project data into a low-dimensional space. Then a k-NN classifier was trained on each projection with a cross-validated random search over the number of neighbours. Interestingly, our experiments revealed that k-NN achieved comparable accuracy on PCA and both autoencoders' projections provided a big enough dimension. However, PCA computation time was two orders of magnitude faster than its neural network counterparts.
When training a variational autoencoder (VAE) on a given dataset, determining the optimal number of latent variables is mostly done by grid search: a costly process in terms of computational time and carbon footprint. In this paper, we explore the intrinsic dimension estimation (IDE) of the data and latent representations learned by VAEs. We show that the discrepancies between the IDE of the mean and sampled representations of a VAE after only a few steps of training reveal the presence of passive variables in the latent space, which, in well-behaved VAEs, indicates a superfluous number of dim…
This paper proposes a theoretical framework on the mechanism of autoencoders. To the encoder part, under the main use of dimensionality reduction, we investigate its two fundamental properties: bijective maps and data disentangling. The general construction methods of an encoder that satisfies either or both of the above two properties are given. The generalization mechanism of autoencoders is modeled. Based on the theoretical framework above, we explain some experimental results of variational autoencoders, denoising autoencoders, and linear-unit autoencoders, with emphasis on the interpretat…
University of Toronto（多伦多大学）；Google Brain（谷歌大脑）；OpenAI
In this paper, we propose the "adversarial autoencoder" (AAE), which is a probabilistic autoencoder that uses the recently proposed generative adversarial networks (GAN) to perform variational inference by matching the aggregated posterior of the hidden code vector of the autoencoder with an arbitrary prior distribution. Matching the aggregated posterior to the prior ensures that generating from any part of prior space results in meaningful samples. As a result, the decoder of the adversarial autoencoder learns a deep generative model that maps the imposed prior to the data distribution. We sh…
Berkeley Center for Cosmological Physics（伯克利宇宙物理中心）；University of California（加利福尼亚大学）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）
Principal Component Analysis (PCA) minimizes the reconstruction error given a class of linear models of fixed component dimensionality. Probabilistic PCA adds a probabilistic structure by learning the probability distribution of the PCA latent space weights, thus creating a generative model. Autoencoders (AE) minimize the reconstruction error in a class of nonlinear models of fixed latent space dimensionality and outperform PCA at fixed dimensionality. Here, we introduce the Probabilistic Autoencoder (PAE) that learns the probability distribution of the AE latent space weights using a normaliz…
Max Planck Institute for Polymer Research（马克斯·普朗克聚合物研究所）；Koc University（科奇大学）
Extracting insight from the enormous quantity of data generated from molecular simulations requires the identification of a small number of collective variables whose corresponding low-dimensional free-energy landscape retains the essential features of the underlying system. Data-driven techniques provide a systematic route to constructing this landscape, without the need for extensive a priori intuition into the relevant driving forces. In particular, autoencoders are powerful tools for dimensionality reduction, as they naturally force an information bottleneck and, thereby, a low-dimensional…
University of Oxford（牛津大学）；Alan Turing Institute（艾伦·图灵研究所）；University of Birmingham（伯明翰大学）；University of Manchester（曼彻斯特大学）
Variational Autoencoders (VAEs) provide a flexible and scalable framework for non-linear dimensionality reduction. However, in application domains such as genomics where data sets are typically tabular and high-dimensional, a black-box approach to dimensionality reduction does not provide sufficient insights. Common data analysis workflows additionally use clustering techniques to identify groups of similar features. This usually leads to a two-stage process, however, it would be desirable to construct a joint modelling framework for simultaneous dimensionality reduction and clustering of feat…
Learning low-dimensional representations of ensemble forecast fields using autoencoder-based methods
Institute of Statistics, Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院统计研究所）；TUM School of Computation, Information and Technology, Technical University of Munich（慕尼黑工业大学计算、信息与技术学院）；Heidelberg Institute for Theoretical Studies（海德堡理论研究所）
The paper presents the application of Variational Autoencoders (VAE) for data dimensionality reduction and explorative analysis of mass spectrometry imaging data (MSI). The results confirm that VAEs are capable of detecting the patterns associated with the different tissue sub-types with performance than standard approaches.
Disentangled Latent Spaces for Reduced Order Models using Deterministic Autoencoders
Institute for Fluid Dynamics and Ship Theory, Hamburg University of Technology（汉堡工业大学流体动力学与船舶理论研究所）；Institute of Mathematics, Hamburg University of Technology（汉堡工业大学数学研究所）
Virginia Polytechnic Institute and State University（弗吉尼亚理工学院暨州立大学）
A rapidly growing area of research is the use of machine learning approaches such as autoencoders for dimensionality reduction of data and models in scientific applications. We show that the canonical formulation of autoencoders suffers from several deficiencies that can hinder their performance. Using a meta-learning approach, we reformulate the autoencoder problem as a bi-level optimization procedure that explicitly solves the dimensionality reduction task. We prove that the new formulation corrects the identified deficiencies with canonical autoencoders, provide a practical way to solve it,…
Invertible flow-based generative models are an effective method for learning to generate samples, while allowing for tractable likelihood computation and inference. However, the invertibility requirement restricts models to have the same latent dimensionality as the inputs. This imposes significant architectural, memory, and computational costs, making them more challenging to scale than other classes of generative models such as Variational Autoencoders (VAEs). We propose a generative model based on probability flows that does away with the bijectivity requirement on the model and only assume…
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 over-regularization which can lead to failure to escape local maxima. This phenomenon, known as posterior collapse, prevents learning a meaningful latent encoding of the data. Recent methods have mitigated this issue by deterministically moment-matching an aggregated posterior distribution to an aggregate prior. However, abandoning a probabilistic framework (and thus relying…
NTT Network Technology Laboratories, NTT Corporation（NTT公司NTT网络技术实验室）；Faculty of Natural Sciences, International Christian University（国际基督教大学自然科学学院）
Anomaly detection using dimensionality reduction has been an essential technique for monitoring multidimensional data. Although deep learning-based methods have been well studied for their remarkable detection performance, their interpretability is still a problem. In this paper, we propose a novel algorithm for estimating the dimensions contributing to the detected anomalies by using variational autoencoders (VAEs). Our algorithm is based on an approximative probabilistic model that considers the existence of anomalies in the data, and by maximizing the log-likelihood, we estimate which dimen…
University of Waterloo（滑铁卢大学）；Vector Institute（向量研究所）
We consider the problem of sufficient dimensionality reduction (SDR), where the high-dimensional observation is transformed to a low-dimensional sub-space in which the information of the observations regarding the label variable is preserved. We propose DVSDR, a deep variational approach for sufficient dimensionality reduction. The deep structure in our model has a bottleneck that represent the low-dimensional embedding of the data. We explain the SDR problem using graphical models and use the framework of variational autoencoders to maximize the lower bound of the log-likelihood of the joint …
Department of Chemical and Biomolecular Engineering, University of Maryland（马里兰大学化学与生物分子工程系）
Conformational sampling of biomolecules using molecular dynamics simulations often produces large amount of high dimensional data that makes it difficult to interpret using conventional analysis techniques. Dimensionality reduction methods are thus required to extract useful and relevant information. Here we devise a machine learning method, Gaussian mixture variational autoencoder (GMVAE) that can simultaneously perform dimensionality reduction and clustering of biomolecular conformations in an unsupervised way. We show that GMVAE can learn a reduced representation of the free energy landscap…
Autoencoders gained popularity in the deep learning revolution given their ability to compress data and provide dimensionality reduction. Although prominent deep learning methods have been used to enhance autoencoders, the need to provide robust uncertainty quantification remains a challenge. This has been addressed with variational autoencoders so far. Bayesian inference via Markov Chain Monte Carlo (MCMC) sampling has faced several limitations for large models; however, recent advances in parallel computing and advanced proposal schemes have opened routes less traveled. This paper presents B…
Institut de Mathématiques de Toulouse（图卢兹数学研究所）；University of Toulouse（图卢兹大学）；Liebherr Aerospace Toulouse（利勃海尔航空航天图卢兹公司）；University Toulouse 3（图卢兹第三大学）
In this work, we explore dimensionality reduction techniques for univariate and multivariate time series data. We especially conduct a comparison between wavelet decomposition and convolutional variational autoencoders for dimension reduction. We show that variational autoencoders are a good option for reducing the dimension of high dimensional data like ECG. We make these comparisons on a real world, publicly available, ECG dataset that has lots of variability and use the reconstruction error as the metric. We then explore the robustness of these models with noisy data whether for training or…
University of São Paulo（圣保罗大学）；University of São Carlos（圣卡洛斯大学）；Budapest University of Technology and Economics（布达佩斯技术与经济大学）
Given two distinct datasets, an important question is if they have arisen from the the same data generating function or alternatively how their data generating functions diverge from one another. In this paper, we introduce an approach for measuring the distance between two datasets with high dimensionality using variational autoencoders. This approach is augmented by a permutation hypothesis test in order to check the hypothesis that the data generating distributions are the same within a significance level. We evaluate both the distance measurement and hypothesis testing approaches on genera…
High-content screening uses large collections of unlabeled cell image data to reason about genetics or cell biology. Two important tasks are to identify those cells which bear interesting phenotypes, and to identify sub-populations enriched for these phenotypes. This exploratory data analysis usually involves dimensionality reduction followed by clustering, in the hope that clusters represent a phenotype. We propose the use of stacked de-noising auto-encoders to perform dimensionality reduction for high-content screening. We demonstrate the superior performance of our approach over PCA, Local …
Power sector capacity expansion models (CEMs) that are used for studying future low-carbon grid scenarios must incorporate detailed representation of grid operations. Often CEMs are formulated to model grid operations over representative periods that are sampled from the original input data using clustering algorithms. However, such representative period selection (RPS) methods are limited by the declining efficacy of the clustering algorithm with increasing dimensionality of the input data and do not consider the relative importance of input data variations on CEM outcomes. Here, we propose a…
The variational autoencoder (VAE; Kingma, Welling (2014)) is a recently proposed generative model pairing a top-down generative network with a bottom-up recognition network which approximates posterior inference. It typically makes strong assumptions about posterior inference, for instance that the posterior distribution is approximately factorial, and that its parameters can be approximated with nonlinear regression from the observations. As we show empirically, the VAE objective can lead to overly simplified representations which fail to use the network's entire modeling capacity. We present…
International University of Business Agriculture and Technology（国际商业农业技术大学）；Islamic University of Technology（伊斯兰科技大学）
The central aim of this paper is to implement Deep Autoencoder and Neighborhood Components Analysis (NCA) dimensionality reduction methods in Matlab and to observe the application of these algorithms on nine unlike datasets from UCI machine learning repository. These datasets are CNAE9, Movement Libras, Pima Indians diabetes, Parkinsons, Knowledge, Segmentation, Seeds, Mammographic Masses, and Ionosphere. First of all, the dimension of these datasets has been reduced to fifty percent of their original dimension by selecting and extracting the most relevant and appropriate features or attribute…
University of New Mexico（新墨西哥大学）；The MIND Research Network（MIND研究网络）
Independent component analysis (ICA), as an approach to the blind source-separation (BSS) problem, has become the de-facto standard in many medical imaging settings. Despite successes and a large ongoing research effort, the limitation of ICA to square linear transformations have not been overcome, so that general INFOMAX is still far from being realized. As an alternative, we present feature analysis in medical imaging as a problem solved by Helmholtz machines, which include dimensionality reduction and reconstruction of the raw data under the same objective, and which recently have overcome …
Explainable AI for Multivariate Time Series Pattern Exploration: Latent Space Visual Analytics with Temporal Fusion Transformer and Variational Autoencoders in Power Grid Event Diagnosis
Autoencoders are able to learn useful data representations in an unsupervised matter and have been widely used in various machine learning and computer vision tasks. In this work, we present methods to train Invertible Neural Networks (INNs) as (variational) autoencoders which we call INN (variational) autoencoders. Our experiments on MNIST, CIFAR and CelebA show that for low bottleneck sizes our INN autoencoder achieves results similar to the classical autoencoder. However, for large bottleneck sizes our INN autoencoder outperforms its classical counterpart. Based on the empirical results, we…
Institute Industrial IT（工业信息技术研究所）；Fraunhofer IOSB-INA（弗劳恩霍夫应用光学与精密工程研究所-INA）
Unsupervised anomaly detection (AD) is a major topic in the field of Cyber-Physical Production Systems (CPPSs). A closely related concern is dimensionality reduction (DR) which is: 1) often used as a preprocessing step in an AD solution, 2) a sort of AD, if a measure of observation conformity to the learned data manifold is provided. We argue that the two aspects can be complementary in a CPPS anomaly detection solution. In this work, we focus on the nonlinear autoencoder (AE) as a DR/AD approach. The contribution of this work is: 1) we examine the suitability of AE reconstruction error as an …
In just three years, Variational Autoencoders (VAEs) have emerged as one of the most popular approaches to unsupervised learning of complicated distributions. VAEs are appealing because they are built on top of standard function approximators (neural networks), and can be trained with stochastic gradient descent. VAEs have already shown promise in generating many kinds of complicated data, including handwritten digits, faces, house numbers, CIFAR images, physical models of scenes, segmentation, and predicting the future from static images. This tutorial introduces the intuitions behind VAEs, e…
Reducing dimensionality is a key preprocessing step in many data analysis applications to address the negative effects of the curse of dimensionality and collinearity on model performance and computational complexity, to denoise the data or to reduce storage requirements. Moreover, in many applications it is desirable to reduce the input dimensions by choosing a subset of variables that best represents the entire set without any a priori information available. Unsupervised variable selection techniques provide a solution to this second problem. An autoencoder, if properly regularized, can solv…
University of Gothenburg（哥德堡大学）；Chalmers University of Technology（查尔姆斯理工大学）
High-dimensional data sets are often analyzed and explored via the construction of a latent low-dimensional space which enables convenient visualization and efficient predictive modeling or clustering. For complex data structures, linear dimensionality reduction techniques like PCA may not be sufficiently flexible to enable low-dimensional representation. Non-linear dimension reduction techniques, like kernel PCA and autoencoders, suffer from loss of interpretability since each latent variable is dependent of all input dimensions. To address this limitation, we here present path lasso penalize…
The joint optimization of the reconstruction and classification error is a hard non convex problem, especially when a non linear mapping is utilized. In order to overcome this obstacle, a novel optimization strategy is proposed, in which a Convolutional Autoencoder for dimensionality reduction and a classifier composed by a Fully Connected Network, are combined to simultaneously produce supervised dimensionality reduction and predictions. It turned out that this methodology can also be greatly beneficial in enforcing explainability of deep learning architectures. Additionally, the resulting La…
Machine Learning models are vulnerable to adversarial attacks that rely on perturbing the input data. This work proposes a novel strategy using Autoencoder Deep Neural Networks to defend a machine learning model against two gradient-based attacks: The Fast Gradient Sign attack and Fast Gradient attack. First we use an autoencoder to denoise the test data, which is trained with both clean and corrupted data. Then, we reduce the dimension of the denoised data using the hidden layer representation of another autoencoder. We perform this experiment for multiple values of the bound of adversarial p…
Cancer survival prediction is important for developing personalized treatments and inducing disease-causing mechanisms. Multi-omics data integration is attracting widespread interest in cancer research for providing information for understanding cancer progression at multiple genetic levels. Many works, however, are limited because of the high dimensionality and heterogeneity of multi-omics data. In this paper, we propose a novel method to integrate multi-omics data for cancer survival prediction, called Stacked AutoEncoder-based Survival Prediction Neural Network (SAEsurv-net). In the cancer …
High dimensionality, i.e. data having a large number of variables, tends to be a challenge for most machine learning tasks, including classification. A classifier usually builds a model representing how a set of inputs explain the outputs. The larger is the set of inputs and/or outputs, the more complex would be that model. There is a family of classification algorithms, known as lazy learning methods, which does not build a model. One of the best known members of this family is the kNN algorithm. Its strategy relies on searching a set of nearest neighbors, using the input variables as positio…
National Research Council of Canada（加拿大国家研究委员会）；Université Paris-Saclay（巴黎萨克雷大学）；CNRS（法国国家科学研究中心）
Autoencoders (AE) provide a useful method for nonlinear dimensionality reduction but are ill-suited for low data regimes. Conversely, Principal Component Analysis (PCA) is data-efficient but is limited to linear dimensionality reduction, posing a problem when data exhibits inherent nonlinearity. This presents a challenge in various scientific and engineering domains such as the nanophotonic component design, where data exhibits nonlinear features while being expensive to obtain due to costly real measurements or resource-consuming solutions of partial differential equations. To address this di…
Remote sensing framework for geological mapping via stacked autoencoders and clustering
International Institute of Information Technology, Hyderabad（海得拉巴国际信息技术学院）；The University of Sydney（悉尼大学）；Curtin University（科廷大学）；University of New South Wales（新南威尔士大学）
Dimensionality reduction is a crucial first step for many unsupervised learning tasks including anomaly detection and clustering. Autoencoder is a popular mechanism to accomplish dimensionality reduction. In order to make dimensionality reduction effective for high-dimensional data embedding nonlinear low-dimensional manifold, it is understood that some sort of geodesic distance metric should be used to discriminate the data samples. Inspired by the success of geodesic distance approximators such as ISOMAP, we propose to use a minimum spanning tree (MST), a graph-based algorithm, to approximat…
Deep Invertible Autoencoders for Dimensionality Reduction of Dynamical Systems
MOX Laboratory, Department of Mathematics, Politecnico di Milano（米兰理工学院数学系MOX实验室）；Department of Applied Mathematics, University of Twente（埃因霍温理工大学应用数学系）
Time series sequence prediction and modelling has proven to be a challenging endeavor in real world datasets. Two key issues are the multi-dimensionality of data and the interaction of independent dimensions forming a latent output signal, as well as the representation of multi-dimensional temporal data inside of a predictive model. This paper proposes a multi-branch deep neural network approach to tackling the aforementioned problems by modelling a latent state vector representation of data windows through the use of a recurrent autoencoder branch and subsequently feeding the trained latent v…
College of Electrical Engineering and Computer Science, National Taiwan University（台湾大学电机资讯学院）
The vector representations of fixed dimensionality for words (in text) offered by Word2Vec have been shown to be very useful in many application scenarios, in particular due to the semantic information they carry. This paper proposes a parallel version, the Audio Word2Vec. It offers the vector representations of fixed dimensionality for variable-length audio segments. These vector representations are shown to describe the sequential phonetic structures of the audio segments to a good degree, with very attractive real world applications such as query-by-example Spoken Term Detection (STD). In t…
Feature selection reduces the dimensionality of data by identifying a subset of the most informative features. In this paper, we propose an innovative framework for unsupervised feature selection, called fractal autoencoders (FAE). It trains a neural network to pinpoint informative features for global exploring of representability and for local excavating of diversity. Architecturally, FAE extends autoencoders by adding a one-to-one scoring layer and a small sub-neural network for feature selection in an unsupervised fashion. With such a concise architecture, FAE achieves state-of-the-art perf…
Anomaly detection is referred to as a process in which the aim is to detect data points that follow a different pattern from the majority of data points. Anomaly detection methods suffer from several well-known challenges that hinder their performance such as high dimensionality. Autoencoders are unsupervised neural networks that have been used for the purpose of reducing dimensionality and also detecting network anomalies in large datasets. The performance of autoencoders debilitates when the training set contains noise and anomalies. In this paper, a new gradient-reversal method is proposed …
Goethe University Frankfurt（法兰克福歌德大学）；University of Montreal（蒙特利尔大学）
Regularized training of an autoencoder typically results in hidden unit biases that take on large negative values. We show that negative biases are a natural result of using a hidden layer whose responsibility is to both represent the input data and act as a selection mechanism that ensures sparsity of the representation. We then show that negative biases impede the learning of data distributions whose intrinsic dimensionality is high. We also propose a new activation function that decouples the two roles of the hidden layer and that allows us to learn representations on data with very high in…
The recent increase in dimensionality of data has thrown a great challenge to the existing dimensionality reduction methods in terms of their effectiveness. Dimensionality reduction has emerged as one of the significant preprocessing steps in machine learning applications and has been effective in removing inappropriate data, increasing learning accuracy, and improving comprehensibility. Feature redundancy exercises great influence on the performance of classification process. Towards the better classification performance, this paper addresses the usefulness of truncating the highly correlated…
In this paper, we investigate the usage of autoencoders in modeling textual data. Traditional autoencoders suffer from at least two aspects: scalability with the high dimensionality of vocabulary size and dealing with task-irrelevant words. We address this problem by introducing supervision via the loss function of autoencoders. In particular, we first train a linear classifier on the labeled data, then define a loss for the autoencoder with the weights learned from the linear classifier. To reduce the bias brought by one single classifier, we define a posterior probability distribution on the…
