Graph auto-encoder predicts unobserved node features from biological networks and omics data.
problem Integrating biological networks and continuous node features for better prediction.
method Graph neural networks and feature auto-encoders trained on feature reconstruction.
result Graph feature auto-encoder outperforms auto-encoders trained on graph reconstruction for predicting unobserved node features.
We present two instances, L-GAE and L-VGAE, of the variational graph auto-encoding family (VGAE) based on separating feature propagation operations from graph convolution layers typically found in graph learning methods to a single linear matrix computation made prior to input in standard auto-encoder architectures. Th…
Principal components analysis (PCA) is the optimal linear auto-encoder of data, and it is often used to construct features. Enforcing sparsity on the principal components can promote better generalization, while improving the interpretability of the features. We study the problem of constructing optimal sparse linear a…
AutoDiff combines auto-encoder and diffusion model for realistic tabular data synthesis.
problem Generating realistic synthetic tabular data with heterogeneous features.
method Employing auto-encoder architecture to handle tabular data's complexity.
result Synthetic tables from AutoDiff show good statistical fidelity and perform well in machine learning tasks.
Auto-encoders are among the most popular neural network architecture for dimension reduction. They are composed of two parts: the encoder which maps the model distribution to a latent manifold and the decoder which maps the latent manifold to a reconstructed distribution. However, auto-encoders are known to provoke cha…
The key idea of variational auto-encoders (VAEs) resembles that of traditional auto-encoder models in which spatial information is supposed to be explicitly encoded in the latent space. However, the latent variables in VAEs are vectors, which can be interpreted as multiple feature maps of size 1x1. Such representations…
DIVA clusters dynamic data without needing cluster count, outperforming baselines.
problem Clustering complex, dynamic data without prior knowledge of cluster count.
method Nonparametric Dirichlet Process Mixtures with memoized online variational inference.
result DIVA outperforms state-of-the-art in classifying complex data with changing features.
MIAEAD detects anomalies in mixed data types.
problem Challenges of heterogeneity in feature subsets for anomaly detection.
method Multiple-Input Variational Auto-Encoder (MIVAE) for simultaneous feature subset anomaly scoring.
result MIVAE outperforms conventional methods and state-of-the-art unsupervised models in AUC score.
Mask-reconstruction pretraining helps in downstream tasks by capturing more semantic features.
problem How mask-reconstruction pretraining helps in downstream tasks and why it surpasses supervised learning.
method Theoretical analysis and experimental validation of mask-reconstruction pretraining (MRP) on auto-encoders.
result MRP provably captures more semantic features than supervised learning, leading to better performance in downstream tasks.
Automatic sleep staging is a challenging problem and state-of-the-art algorithms have not yet reached satisfactory performance to be used instead of manual scoring by a sleep technician. Much research has been done to find good feature representations that extract the useful information to correctly classify each epoch…
We introduce the variational graph auto-encoder (VGAE), a framework for unsupervised learning on graph-structured data based on the variational auto-encoder (VAE). This model makes use of latent variables and is capable of learning interpretable latent representations for undirected graphs. We demonstrate this model us…
In this paper, a multi-layer architecture (in a hierarchical fashion) by stacking various Kernel Ridge Regression (KRR) based Auto-Encoder for one-class classification is proposed and is referred as MKOC. MKOC has many layers of Auto-Encoders to project the input features into new feature space and the last layer was r…
Traditional set prediction models can struggle with simple datasets due to an issue we call the responsibility problem. We introduce a pooling method for sets of feature vectors based on sorting features across elements of the set. This can be used to construct a permutation-equivariant auto-encoder that avoids this re…
This paper studies an intelligent ultimate technique for health-monitoring and prognostic of common rotary machine components, particularly bearings. During a run-to-failure experiment, rich unsupervised features from vibration sensory data are extracted by a trained sparse auto-encoder. Then, the correlation of the ex…
We address the task of simultaneous feature fusion and modeling of discrete ordinal outputs. We propose a novel Gaussian process(GP) auto-encoder modeling approach. In particular, we introduce GP encoders to project multiple observed features onto a latent space, while GP decoders are responsible for reconstructing the…
This paper aims to develop a new and robust approach to feature representation. Motivated by the success of Auto-Encoders, we first theoretical summarize the general properties of all algorithms that are based on traditional Auto-Encoders: 1) The reconstruction error of the input can not be lower than a lower bound, wh…
Recurrent auto-encoder model summarises sequential data through an encoder structure into a fixed-length vector and then reconstructs the original sequence through the decoder structure. The summarised vector can be used to represent time series features. In this paper, we propose relaxing the dimensionality of the dec…
A brain can detect outlier just by using only normal samples. Similarly, one-class classification (OCC) also uses only normal samples to train the model and trained model can be used for outlier detection. In this paper, a multi-layer architecture for OCC is proposed by stacking various Graph-Embedded Kernel Ridge Regr…
Drug similarity has been studied to support downstream clinical tasks such as inferring novel properties of drugs (e.g. side effects, indications, interactions) from known properties. The growing availability of new types of drug features brings the opportunity of learning a more comprehensive and accurate drug similar…
A crucial challenge in image-based modeling of biomedical data is to identify trends and features that separate normality and pathology. In many cases, the morphology of the imaged object exhibits continuous change as it deviates from normality, and thus a generative model can be trained to model this morphological con…
The paper identifies saddlepoints in unsupervised auto-encoding neural nets.
problem The risk landscape of unsupervised least squares in auto-encoding neural nets.
method Established an equivalence between unsupervised least squares and principal manifolds, discussed regularization strategies for auto-encoders.
result All non-trivial critical points in auto-encoding are saddlepoints, which are degenerate in overcomplete auto-encoding.
New method uses neural networks to interpolate stellar atmospheres with high precision.
problem Recover precise stellar model atmospheres from grids of models.
method Deep neural network with 1D convolutional auto-encoder for feature extraction.
result Higher precision compared to traditional methods.
The contractive auto-encoder learns a representation of the input data that captures the local manifold structure around each data point, through the leading singular vectors of the Jacobian of the transformation from input to representation. The corresponding singular values specify how much local variation is plausib…
Current approaches for predicting sets from feature vectors ignore the unordered nature of sets and suffer from discontinuity issues as a result. We propose a general model for predicting sets that properly respects the structure of sets and avoids this problem. With a single feature vector as input, we show that our m…
In this paper, we propose a new deep feature selection method based on deep architecture. Our method uses stacked auto-encoders for feature representation in higher-level abstraction. We developed and applied a novel feature learning approach to a specific precision medicine problem, which focuses on assessing and prio…
In this paper, we suggest a framework to make use of mutual information as a regularization criterion to train Auto-Encoders (AEs). In the proposed framework, AEs are regularized by minimization of the mutual information between input and encoding variables of AEs during the training phase. In order to estimate the ent…
We propose a new family of optimization criteria for variational auto-encoding models, generalizing the standard evidence lower bound. We provide conditions under which they recover the data distribution and learn latent features, and formally show that common issues such as blurry samples and uninformative latent feat…
In many important machine learning applications, the training distribution used to learn a probabilistic classifier differs from the testing distribution on which the classifier will be used to make predictions. Traditional methods correct the distribution shift by reweighting the training data with the ratio of the de…
TSInsight improves interpretability of deep time-series models.
problem Lack of interpretability methods for time-series data.
method Attach auto-encoder to classifier with sparsity-inducing norm, fine-tune based on gradients and reconstruction penalty.
result TSInsight effectively boosts interpretability of deep time-series models.
New auto-encoder handles varying noise levels without retraining.
problem Auto-encoders degrade in noisy conditions.
method Formalized auto-encoders as transform learning, derived new architecture.
result Models generalize well to different noise levels.
DGA and DVGA learn disentangled graph representations to improve graph analysis.
problem Holistic graph auto-encoders fail to capture latent factors effectively.
method Design disentangled graph convolutional network and component-wise flow, impose independence constraints.
result Improved disentangled graph representations enhance graph analysis tasks.
In this note we present a generative model of natural images consisting of a deep hierarchy of layers of latent random variables, each of which follows a new type of distribution that we call rectified Gaussian. These rectified Gaussian units allow spike-and-slab type sparsity, while retaining the differentiability nec…
Variational Auto-Encoders have often been used for unsupervised pretraining, feature extraction and out-of-distribution and anomaly detection in the medical field. However, VAEs often lack the ability to produce sharp images and learn high-level features. We propose to alleviate these issues by adding a new branch to c…
Recent work suggests that some auto-encoder variants do a good job of capturing the local manifold structure of the unknown data generating density. This paper contributes to the mathematical understanding of this phenomenon and helps define better justified sampling algorithms for deep learning based on auto-encoder v…
What do auto-encoders learn about the underlying data generating distribution? Recent work suggests that some auto-encoder variants do a good job of capturing the local manifold structure of data. This paper clarifies some of these previous observations by showing that minimizing a particular form of regularized recons…
Due to the rapid innovation of technology and the desire to find and employ biomarkers for neurodegenerative disease, high-dimensional data classification problems are routinely encountered in neuroimaging studies. To avoid over-fitting and to explore relationships between disease and potential biomarkers, feature lear…
Fisher auto-encoders use Fisher divergence for more robust generative modeling.
problem Model uncertainty in generative models.
method Minimizing Fisher divergence between true and modeled joint distributions.
result Fisher auto-encoders can more accurately quantify model uncertainty.
We propose the Wasserstein Auto-Encoder (WAE)---a new algorithm for building a generative model of the data distribution. WAE minimizes a penalized form of the Wasserstein distance between the model distribution and the target distribution, which leads to a different regularizer than the one used by the Variational Aut…
In this work, we study value function approximation in reinforcement learning (RL) problems with high dimensional state or action spaces via a generalized version of representation policy iteration (RPI). We consider the limitations of proto-value functions (PVFs) at accurately approximating the value function in low d…
Graph clustering, aiming to partition nodes of a graph into various groups via an unsupervised approach, is an attractive topic in recent years. To improve the representative ability, several graph auto-encoder (GAE) models, which are based on semi-supervised graph convolution networks (GCN), have been developed and th…
This paper presents an unsupervised method to learn a neural network, namely an explainer, to interpret a pre-trained convolutional neural network (CNN), i.e., the explainer uses interpretable visual concepts to explain features in middle conv-layers of a CNN. Given feature maps of a conv-layer of the CNN, the explaine…
Generative source separation methods such as non-negative matrix factorization (NMF) or auto-encoders, rely on the assumption of an output probability density. Generative Adversarial Networks (GANs) can learn data distributions without needing a parametric assumption on the output density. We show on a speech source se…
One of the major advantages in using Deep Learning for Finance is to embed a large collection of information into investment decisions. A way to do that is by means of compression, that lead us to consider a smaller feature space. Several studies are proving that non-linear feature reduction performed by Deep Learning …
Paper proposes a novel auto-encoder for latent density estimation.
problem Challenges of learning generative probabilistic models due to curse of dimensionality.
method Joint dimensionality reduction and non-parametric density estimation framework using a novel estimator.
result Proposed model achieves promising results on various datasets.
We propose a robust classifier to predict buying intentions based on user behaviour within a large e-commerce website. In this work we compare traditional machine learning techniques with the most advanced deep learning approaches. We show that both Deep Belief Networks and Stacked Denoising auto-Encoders achieved a su…
Develops a new non-adversarial framework for better generative models.
problem Inaccurate approximation of target distribution in latent space.
method Tessellated Wasserstein Auto-Encoders (TWAE) using centroidal Voronoi tessellation (CVT) to tessellate latent space.
result Significantly enhances generative performance in terms of FID compared to existing models.
Automatic recognition of human activities from time-series sensor data (referred to as HAR) is a growing area of research in ubiquitous computing. Most recent research in the field adopts supervised deep learning paradigms to automate extraction of intrinsic features from raw signal inputs and addresses HAR as a multi-…
BPVAE enhances VAE robustness to OOD inputs.
problem VAEs struggle with OOD detection, assigning higher likelihoods to some OOD samples.
method Combines VAE with two independent priors: training dataset and simple dataset.
result BPVAE outperforms standard VAEs in OOD detection and generalization.