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We present two deep generative models based on Variational Autoencoders to improve the accuracy of drug response prediction. Our models, Perturbation Variational Autoencoder and its semi-supervised extension, Drug Response Variational Autoencoder (Dr.VAE), learn latent representation of the underlying gene states before and after drug application that depend on: (i) drug-induced biological change of each gene and (ii) overall treatment response outcome. Our VAE-based models outperform the current published benchmarks in the field by anywhere from 3 to 11% AUROC and 2 to 30% AUPR. In addition, we found that better reconstruction accuracy does not necessarily lead to improvement in classification accuracy and that jointly trained models perform better than models that minimize reconstruction error independently.

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自動編碼器是一種人工神經網絡,用于以無監督的方式學習有效的數據編碼。自動編碼器的目的是通過訓練網絡忽略信號“噪聲”來學習一組數據的表示(編碼),通常用于降維。與簡化方面一起,學習了重構方面,在此,自動編碼器嘗試從簡化編碼中生成盡可能接近其原始輸入的表示形式,從而得到其名稱。基本模型存在幾種變體,其目的是迫使學習的輸入表示形式具有有用的屬性。自動編碼器可有效地解決許多應用問題,從面部識別到獲取單詞的語義。

Modern neural network training relies heavily on data augmentation for improved generalization. After the initial success of label-preserving augmentations, there has been a recent surge of interest in label-perturbing approaches, which combine features and labels across training samples to smooth the learned decision surface. In this paper, we propose a new augmentation method that leverages the first and second moments extracted and re-injected by feature normalization. We replace the moments of the learned features of one training image by those of another, and also interpolate the target labels. As our approach is fast, operates entirely in feature space, and mixes different signals than prior methods, one can effectively combine it with existing augmentation methods. We demonstrate its efficacy across benchmark data sets in computer vision, speech, and natural language processing, where it consistently improves the generalization performance of highly competitive baseline networks.

Graph structured data are abundant in the real world. Among different graph types, directed acyclic graphs (DAGs) are of particular interest to machine learning researchers, as many machine learning models are realized as computations on DAGs, including neural networks and Bayesian networks. In this paper, we study deep generative models for DAGs, and propose a novel DAG variational autoencoder (D-VAE). To encode DAGs into the latent space, we leverage graph neural networks. We propose an asynchronous message passing scheme that allows encoding the computations on DAGs, rather than using existing simultaneous message passing schemes to encode local graph structures. We demonstrate the effectiveness of our proposed D-VAE through two tasks: neural architecture search and Bayesian network structure learning. Experiments show that our model not only generates novel and valid DAGs, but also produces a smooth latent space that facilitates searching for DAGs with better performance through Bayesian optimization.

Both generative adversarial network models and variational autoencoders have been widely used to approximate probability distributions of datasets. Although they both use parametrized distributions to approximate the underlying data distribution, whose exact inference is intractable, their behaviors are very different. In this report, we summarize our experiment results that compare these two categories of models in terms of fidelity and mode collapse. We provide a hypothesis to explain their different behaviors and propose a new model based on this hypothesis. We further tested our proposed model on MNIST dataset and CelebA dataset.

We present new intuitions and theoretical assessments of the emergence of disentangled representation in variational autoencoders. Taking a rate-distortion theory perspective, we show the circumstances under which representations aligned with the underlying generative factors of variation of data emerge when optimising the modified ELBO bound in $\beta$-VAE, as training progresses. From these insights, we propose a modification to the training regime of $\beta$-VAE, that progressively increases the information capacity of the latent code during training. This modification facilitates the robust learning of disentangled representations in $\beta$-VAE, without the previous trade-off in reconstruction accuracy.

We propose a flipped-Adversarial AutoEncoder (FAAE) that simultaneously trains a generative model G that maps an arbitrary latent code distribution to a data distribution and an encoder E that embodies an "inverse mapping" that encodes a data sample into a latent code vector. Unlike previous hybrid approaches that leverage adversarial training criterion in constructing autoencoders, FAAE minimizes re-encoding errors in the latent space and exploits adversarial criterion in the data space. Experimental evaluations demonstrate that the proposed framework produces sharper reconstructed images while at the same time enabling inference that captures rich semantic representation of data.

Deep metric learning has been demonstrated to be highly effective in learning semantic representation and encoding information that can be used to measure data similarity, by relying on the embedding learned from metric learning. At the same time, variational autoencoder (VAE) has widely been used to approximate inference and proved to have a good performance for directed probabilistic models. However, for traditional VAE, the data label or feature information are intractable. Similarly, traditional representation learning approaches fail to represent many salient aspects of the data. In this project, we propose a novel integrated framework to learn latent embedding in VAE by incorporating deep metric learning. The features are learned by optimizing a triplet loss on the mean vectors of VAE in conjunction with standard evidence lower bound (ELBO) of VAE. This approach, which we call Triplet based Variational Autoencoder (TVAE), allows us to capture more fine-grained information in the latent embedding. Our model is tested on MNIST data set and achieves a high triplet accuracy of 95.60% while the traditional VAE (Kingma & Welling, 2013) achieves triplet accuracy of 75.08%.

We introduce an effective model to overcome the problem of mode collapse when training Generative Adversarial Networks (GAN). Firstly, we propose a new generator objective that finds it better to tackle mode collapse. And, we apply an independent Autoencoders (AE) to constrain the generator and consider its reconstructed samples as "real" samples to slow down the convergence of discriminator that enables to reduce the gradient vanishing problem and stabilize the model. Secondly, from mappings between latent and data spaces provided by AE, we further regularize AE by the relative distance between the latent and data samples to explicitly prevent the generator falling into mode collapse setting. This idea comes when we find a new way to visualize the mode collapse on MNIST dataset. To the best of our knowledge, our method is the first to propose and apply successfully the relative distance of latent and data samples for stabilizing GAN. Thirdly, our proposed model, namely Generative Adversarial Autoencoder Networks (GAAN), is stable and has suffered from neither gradient vanishing nor mode collapse issues, as empirically demonstrated on synthetic, MNIST, MNIST-1K, CelebA and CIFAR-10 datasets. Experimental results show that our method can approximate well multi-modal distribution and achieve better results than state-of-the-art methods on these benchmark datasets. Our model implementation is published here: //github.com/tntrung/gaan

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 Auto-Encoder (VAE). This regularizer encourages the encoded training distribution to match the prior. We compare our algorithm with several other techniques and show that it is a generalization of adversarial auto-encoders (AAE). Our experiments show that WAE shares many of the properties of VAEs (stable training, encoder-decoder architecture, nice latent manifold structure) while generating samples of better quality, as measured by the FID score.

Amortized inference has led to efficient approximate inference for large datasets. The quality of posterior inference is largely determined by two factors: a) the ability of the variational distribution to model the true posterior and b) the capacity of the recognition network to generalize inference over all datapoints. We analyze approximate inference in variational autoencoders in terms of these factors. We find that suboptimal inference is often due to amortizing inference rather than the limited complexity of the approximating distribution. We show that this is due partly to the generator learning to accommodate the choice of approximation. Furthermore, we show that the parameters used to increase the expressiveness of the approximation play a role in generalizing inference rather than simply improving the complexity of the approximation.

Unsupervised learning is of growing interest because it unlocks the potential held in vast amounts of unlabelled data to learn useful representations for inference. Autoencoders, a form of generative model, may be trained by learning to reconstruct unlabelled input data from a latent representation space. More robust representations may be produced by an autoencoder if it learns to recover clean input samples from corrupted ones. Representations may be further improved by introducing regularisation during training to shape the distribution of the encoded data in latent space. We suggest denoising adversarial autoencoders, which combine denoising and regularisation, shaping the distribution of latent space using adversarial training. We introduce a novel analysis that shows how denoising may be incorporated into the training and sampling of adversarial autoencoders. Experiments are performed to assess the contributions that denoising makes to the learning of representations for classification and sample synthesis. Our results suggest that autoencoders trained using a denoising criterion achieve higher classification performance, and can synthesise samples that are more consistent with the input data than those trained without a corruption process.

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