Interaction between pharmacological agents can trigger unexpected adverse events. Capturing richer and more comprehensive information about drug-drug interactions (DDI) is one of the key tasks in public health and drug development. Recently, several knowledge graph embedding approaches have received increasing attention in the DDI domain due to their capability of projecting drugs and interactions into a low-dimensional feature space for predicting links and classifying triplets. However, existing methods only apply a uniformly random mode to construct negative samples. As a consequence, these samples are often too simplistic to train an effective model. In this paper, we propose a new knowledge graph embedding framework by introducing adversarial autoencoders (AAE) based on Wasserstein distances and Gumbel-Softmax relaxation for drug-drug interactions tasks. In our framework, the autoencoder is employed to generate high-quality negative samples and the hidden vector of the autoencoder is regarded as a plausible drug candidate. Afterwards, the discriminator learns the embeddings of drugs and interactions based on both positive and negative triplets. Meanwhile, in order to solve vanishing gradient problems on the discrete representation--an inherent flaw in traditional generative models--we utilize the Gumbel-Softmax relaxation and the Wasserstein distance to train the embedding model steadily. We empirically evaluate our method on two tasks, link prediction and DDI classification. The experimental results show that our framework can attain significant improvements and noticeably outperform competitive baselines.
HRL Laboratories, LLC（HRL实验室有限责任公司）；University of Virginia（弗吉尼亚大学）
In this paper we study generative modeling via autoencoders while using the elegant geometric properties of the optimal transport (OT) problem and the Wasserstein distances. We introduce Sliced-Wasserstein Autoencoders (SWAE), which are generative models that enable one to shape the distribution of the latent space into any samplable probability distribution without the need for training an adversarial network or defining a closed-form for the distribution. In short, we regularize the autoencoder loss with the sliced-Wasserstein distance between the distribution of the encoded training samples…
This work presents a reformulation of the recently proposed Wasserstein autoencoder framework on a non-Euclidean manifold, the Poincaré ball model of the hyperbolic space. By assuming the latent space to be hyperbolic, we can use its intrinsic hierarchy to impose structure on the learned latent space representations. We demonstrate the model in the visual domain to analyze some of its properties and show competitive results on a graph link prediction task.
Swiss Data Science Center (SDSC), EPFL/ETHZ（瑞士数据科学中心（SDSC），洛桑联邦理工学院/苏黎世联邦理工学院）；Signal Processing Laboratory (LTS4), EPFL（信号处理实验室（LTS4），洛桑联邦理工学院）
In order to perform network analysis tasks, representations that capture the most relevant information in the graph structure are needed. However, existing methods do not learn representations that can be interpreted in a straightforward way and that are robust to perturbations to the graph structure. In this work, we address these two limitations by proposing node2coords, a representation learning algorithm for graphs, which learns simultaneously a low-dimensional space and coordinates for the nodes in that space. The patterns that span the low dimensional space reveal the graph's most import…
School of Computer Science and Engineering, Central South University（中南大学计算机科学与工程学院）；School of Computer Science and Technology, Nanjing Tech University（南京工业大学计算机科学与技术学院）
Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial agents. Therefore, screening of microbe-drug associations can benefit greatly drug research and development. With the increase of microbial genomic and pharmacological datasets, we are greatly motivated to develop an effective computational method to identify new microbe-drug associations. In this paper, we proposed a novel method, Graph2MDA, to predict microbe-…
Imperial College London（帝国理工学院）；Twitter（推特）；USI Lugano（卢加诺大学）
Recent research efforts have shown the possibility to discover anticancer drug-like molecules in food from their effect on protein-protein interaction networks, opening a potential pathway to disease-beating diet design. We formulate this task as a graph classification problem on which graph neural networks (GNNs) have achieved state-of-the-art results. However, GNNs are difficult to train on sparse low-dimensional features according to our empirical evidence. Here, we present graph augmented features, integrating graph structural information and raw node attributes with varying ratios, to eas…
The University of Sydney Business School（悉尼大学商学院）；The University of Sydney（悉尼大学）
This paper introduces Wasserstein Adversarially Regularized Graph Autoencoder (WARGA), an implicit generative algorithm that directly regularizes the latent distribution of node embedding to a target distribution via the Wasserstein metric. The proposed method has been validated in tasks of link prediction and node clustering on real-world graphs, in which WARGA generally outperforms state-of-the-art models based on Kullback-Leibler (KL) divergence and typical adversarial framework.
Indian Statistical Institute, Kolkata（印度统计研究所（加尔各答））
The introduction of Variational Autoencoders (VAE) has been marked as a breakthrough in the history of representation learning models. Besides having several accolades of its own, VAE has successfully flagged off a series of inventions in the form of its immediate successors. Wasserstein Autoencoder (WAE), being an heir to that realm carries with it all of the goodness and heightened generative promises, matching even the generative adversarial networks (GANs). Needless to say, recent years have witnessed a remarkable resurgence in statistical analyses of the GANs. Similar examinations for Aut…
Harbin Institute of Technology at Weihai（哈尔滨工业大学（威海））；University of Edinburgh（爱丁堡大学）；Sun Yat-sen University（中山大学）；University of Arizona（亚利桑那大学）
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, respectiv…
Drug-drug interactions (DDIs) are a major cause of preventable hospitalizations and deaths. Predicting the occurrence of DDIs helps drug safety professionals allocate investigative resources and take appropriate regulatory action promptly. Traditional DDI prediction methods predict DDIs based on the similarity between drugs. Recently, researchers revealed that predictive performance can be improved by better modeling the interactions between drug pairs with bilinear forms. However, the shallow models leveraging bilinear forms suffer from limitations on capturing complicated nonlinear interacti…
VinAI Research（VinAI研究院）；University of Texas, Austin（德克萨斯大学奥斯汀分校）
Relational regularized autoencoder (RAE) is a framework to learn the distribution of data by minimizing a reconstruction loss together with a relational regularization on the latent space. A recent attempt to reduce the inner discrepancy between the prior and aggregated posterior distributions is to incorporate sliced fused Gromov-Wasserstein (SFG) between these distributions. That approach has a weakness since it treats every slicing direction similarly, meanwhile several directions are not useful for the discriminative task. To improve the discrepancy and consequently the relational regulari…
Probabilistic models with hierarchical-latent-variable structures provide state-of-the-art results amongst non-autoregressive, unsupervised density-based models. However, the most common approach to training such models based on Variational Autoencoders (VAEs) often fails to leverage deep-latent hierarchies; successful approaches require complex inference and optimisation schemes. Optimal Transport is an alternative, non-likelihood-based framework for training generative models with appealing theoretical properties, in principle allowing easier training convergence between distributions. In th…
Disentangled representation learning has undoubtedly benefited from objective function surgery. However, a delicate balancing act of tuning is still required in order to trade off reconstruction fidelity versus disentanglement. Building on previous successes of penalizing the total correlation in the latent variables, we propose TCWAE (Total Correlation Wasserstein Autoencoder). Working in the WAE paradigm naturally enables the separation of the total-correlation term, thus providing disentanglement control over the learned representation, while offering more flexibility in the choice of recon…
Gatsby Computational Neuroscience Unit, University College London（伦敦大学学院盖茨比计算神经科学单元）；Department of Mathematics and Center for Scientific Computation and Mathematical Modeling, University of Maryland College Park（马里兰大学帕克分校数学系与科学计算与数学建模中心）
While variational autoencoders have been successful in several tasks, the use of conventional priors are limited in their ability to encode the underlying structure of input data. We introduce an Encoded Prior Sliced Wasserstein AutoEncoder wherein an additional prior-encoder network learns an embedding of the data manifold which preserves topological and geometric properties of the data, thus improving the structure of latent space. The autoencoder and prior-encoder networks are iteratively trained using the Sliced Wasserstein distance. The effectiveness of the learned manifold encoding is ex…
University of Waterloo（滑铁卢大学）；ByteDance AI Lab（字节跳动人工智能实验室）
The variational autoencoder (VAE) imposes a probabilistic distribution (typically Gaussian) on the latent space and penalizes the Kullback--Leibler (KL) divergence between the posterior and prior. In NLP, VAEs are extremely difficult to train due to the problem of KL collapsing to zero. One has to implement various heuristics such as KL weight annealing and word dropout in a carefully engineered manner to successfully train a VAE for text. In this paper, we propose to use the Wasserstein autoencoder (WAE) for probabilistic sentence generation, where the encoder could be either stochastic or de…
The de novo design of drug molecules is recognized as a time-consuming and costly process, and computational approaches have been applied in each stage of the drug discovery pipeline. Variational autoencoder is one of the computer-aided design methods which explores the chemical space based on existing molecular dataset. Quantum machine learning has emerged as an atypical learning method that may speed up some classical learning tasks because of its strong expressive power. However, near-term quantum computers suffer from limited number of qubits which hinders the representation learning in hi…
Leveraging the framework of Optimal Transport, we introduce a new family of generative autoencoders with a learnable prior, called Symmetric Wasserstein Autoencoders (SWAEs). We propose to symmetrically match the joint distributions of the observed data and the latent representation induced by the encoder and the decoder. The resulting algorithm jointly optimizes the modelling losses in both the data and the latent spaces with the loss in the data space leading to the denoising effect. With the symmetric treatment of the data and the latent representation, the algorithm implicitly preserves th…
Variational Autoencoder (VAE)-based generative models offer flexible representation learning by incorporating meta-priors, general premises considered beneficial for downstream tasks. However, the incorporated meta-priors often involve ad-hoc model deviations from the original likelihood architecture, causing undesirable changes in their training. In this paper, we propose a novel representation learning method, Gromov-Wasserstein Autoencoders (GWAE), which directly matches the latent and data distributions using the variational autoencoding scheme. Instead of likelihood-based objectives, GWAE…
University of California, Berkeley（加州大学伯克利分校）；University of Chicago（芝加哥大学）；University of Notre Dame（圣母大学）
In the past several months, COVID-19 has spread over the globe and caused severe damage to the people and the society. In the context of this severe situation, an effective drug discovery method to generate potential drugs is extremely meaningful. In this paper, we provide a methodology of discovering potential drugs for the treatment of Severe Acute Respiratory Syndrome Corona-Virus 2 (commonly known as SARS-CoV-2). We proposed a new model called Genetic Constrained Graph Variational Autoencoder (GCGVAE) to solve this problem. We trained our model based on the data of various viruses' protein…
Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements and bonds respectively. Although existing deep learning models perform remarkably well at predicting physicochemical properties and binding affinities, the generation of new molecules with optimized properties remains challenging. Inherently, most GNNs perform poorly in whole-graph representation due to the limitations of the message-passing paradigm. Furthe…
Conditional Sampling via Wasserstein Autoencoders and Triangular Transport
Department of Aeronautics & Astronautics, University of Washington, Seattle（华盛顿大学西雅图分校航空与航天系）；Department of Applied Mathematics, University of Washington, Seattle（华盛顿大学西雅图分校应用数学系）；Department of Mathematics, University of Washington, Seattle（华盛顿大学西雅图分校数学系）
University of California, Santa Barbara（加州大学圣巴巴拉分校）
Recurrent Variational Autoencoder has been widely used for language modeling and text generation tasks. These models often face a difficult optimization problem, also known as the Kullback-Leibler (KL) term vanishing issue, where the posterior easily collapses to the prior, and the model will ignore latent codes in generative tasks. To address this problem, we introduce an improved Wasserstein Variational Autoencoder (WAE) with Riemannian Normalizing Flow (RNF) for text modeling. The RNF transforms a latent variable into a space that respects the geometric characteristics of input space, which…
Duke University（杜克大学）；Infinia ML Inc.（Infinia ML公司）
A new algorithmic framework is proposed for learning autoencoders of data distributions. We minimize the discrepancy between the model and target distributions, with a \emph{relational regularization} on the learnable latent prior. This regularization penalizes the fused Gromov-Wasserstein (FGW) distance between the latent prior and its corresponding posterior, allowing one to flexibly learn a structured prior distribution associated with the generative model. Moreover, it helps co-training of multiple autoencoders even if they have heterogeneous architectures and incomparable latent spaces. W…
Amazon（亚马逊）；Amazon Web Services（亚马逊云科技）；Compass Inc（Compass公司）
We propose a novel neural topic model in the Wasserstein autoencoders (WAE) framework. Unlike existing variational autoencoder based models, we directly enforce Dirichlet prior on the latent document-topic vectors. We exploit the structure of the latent space and apply a suitable kernel in minimizing the Maximum Mean Discrepancy (MMD) to perform distribution matching. We discover that MMD performs much better than the Generative Adversarial Network (GAN) in matching high dimensional Dirichlet distribution. We further discover that incorporating randomness in the encoder output during training …
Approximating distributions over complicated manifolds, such as natural images, are conceptually attractive. The deep latent variable model, trained using variational autoencoders and generative adversarial networks, is now a key technique for representation learning. However, it is difficult to unify these two models for exact latent-variable inference and parallelize both reconstruction and sampling, partly due to the regularization under the latent variables, to match a simple explicit prior distribution. These approaches are prone to be oversimplified, and can only characterize a few modes…
One of the key challenges in learning joint embeddings of multiple modalities, e.g. of images and text, is to ensure coherent cross-modal semantics that generalize across datasets. We propose to address this through joint Gaussian regularization of the latent representations. Building on Wasserstein autoencoders (WAEs) to encode the input in each domain, we enforce the latent embeddings to be similar to a Gaussian prior that is shared across the two domains, ensuring compatible continuity of the encoded semantic representations of images and texts. Semantic alignment is achieved through superv…
A Bayesian Non-parametric Approach to Generative Models: Integrating Variational Autoencoder and Generative Adversarial Networks using Wasserstein and Maximum Mean Discrepancy
Department of Statistics and Actuarial Science University of Hong Kong（统计与精算科学系香港大学）
Graduate Center, City University of New York（纽约城市大学研究生中心）；Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University（康奈尔大学威尔康奈尔医学院菲尔家族脑与心智研究所）；Hunter College, City University of New York（纽约城市大学亨特学院）
Accurate and robust prediction of patient's response to drug treatments is critical for developing precision medicine. However, it is often difficult to obtain a sufficient amount of coherent drug response data from patients directly for training a generalized machine learning model. Although the utilization of rich cell line data provides an alternative solution, it is challenging to transfer the knowledge obtained from cell lines to patients due to various confounding factors. Few existing transfer learning methods can reliably disentangle common intrinsic biological signals from confounding…
Learning disentangled representations leads to interpretable models and facilitates data generation with style transfer, which has been extensively studied on static data such as images in an unsupervised learning framework. However, only a few works have explored unsupervised disentangled sequential representation learning due to challenges of generating sequential data. In this paper, we propose recurrent Wasserstein Autoencoder (R-WAE), a new framework for generative modeling of sequential data. R-WAE disentangles the representation of an input sequence into static and dynamic factors (i.e.…
Harbin Institute of Technology, Shenzhen（哈尔滨工业大学（深圳））
The recommender systems have long been investigated in the literature. Recently, users' implicit feedback like `click' or `browse' are considered to be able to enhance the recommendation performance. Therefore, a number of attempts have been made to resolve this issue. Among them, the variational autoencoders (VAE) approach already achieves a superior performance. However, the distributions of the encoded latent variables overlap a lot which may restrict its recommendation ability. To cope with this challenge, this paper tries to extend the Wasserstein autoencoders (WAE) for collaborative filt…
The ultimate goal of various fields is to directly generate molecules with desired properties, such as finding water-soluble molecules in drug development and finding molecules suitable for organic light-emitting diode (OLED) or photosensitizers in the field of development of new organic materials. In this respect, this study proposes a molecular graph generative model based on the autoencoder for de novo design. The performance of molecular graph conditional variational autoencoder (MGCVAE) for generating molecules having specific desired properties is investigated by comparing it to molecula…
Predicting gene essentiality and drug response from perturbation screens in preclinical cancer models with LEAP: Layered Ensemble of Autoencoders and Predictors
Washington University School of Medicine, Washington University in St. Louis（圣路易斯华盛顿大学医学院）；Dalian University of Technology（大连理工大学）
Drug resistance is still a major challenge in cancer therapy. Drug combination is expected to overcome drug resistance. However, the number of possible drug combinations is enormous, and thus it is infeasible to experimentally screen all effective drug combinations considering the limited resources. Therefore, computational models to predict and prioritize effective drug combinations is important for combinatory therapy discovery in cancer. In this study, we proposed a novel deep learning model, AuDNNsynergy, to prediction drug combinations by integrating multi-omics data and chemical structur…
University of Applied Sciences Darmstadt（达姆施塔特应用科学大学）
The need for reliable systems to determine fingerprint presentation attacks grows with the rising use of the fingerprint for authentication. This work presents a new approach to single-class classification for software-based fingerprint presentation attach detection. The described method utilizes a Wasserstein GAN to apply transfer learning to a deep convolutional autoencoder. By doing so, the autoencoder could be pretrained and finetuned on the LivDet2021 Dermalog sensor dataset with only 1122 bona fide training samples. Without making use of any presentation attack samples, the model could a…
Recent emergence of high-throughput drug screening assays sparkled an intensive development of machine learning methods, including models for prediction of sensitivity of cancer cell lines to anti-cancer drugs, as well as methods for generation of potential drug candidates. However, a concept of generation of compounds with specific properties and simultaneous modeling of their efficacy against cancer cell lines has not been comprehensively explored. To address this need, we present VADEERS, a Variational Autoencoder-based Drug Efficacy Estimation Recommender System. The generation of compound…
FPT AI Center（FPT人工智能中心）；University of California San Diego（加州大学圣迭戈分校）；University of Chicago（芝加哥大学）
Latent representations of drugs and their targets produced by contemporary graph autoencoder-based models have proved useful in predicting many types of node-pair interactions on large networks, including drug-drug, drug-target, and target-target interactions. However, most existing approaches model the node's latent spaces in which node distributions are rigid and disjoint; these limitations hinder the methods from generating new links among pairs of nodes. In this paper, we present the effectiveness of variational graph autoencoders (VGAE) in modeling latent node representations on multimoda…
FPT Software AI Center（FPT软件人工智能中心）；Halıcıoğlu Data Science Institute（哈利哲奥卢数据科学研究所）；University of California San Diego（加州大学圣地亚哥分校）；University of Chicago（芝加哥大学）
Latent representations of drugs and their targets produced by contemporary graph autoencoder models have proved useful in predicting many types of node-pair interactions on large networks, including drug-drug, drug-target, and target-target interactions. However, most existing approaches model either the node's latent spaces in which node distributions are rigid or do not effectively capture the interrelations between drugs; these limitations hinder the methods from accurately predicting drug-pair interactions. In this paper, we present the effectiveness of variational graph autoencoders (VGAE…
Missing data is one of the most common preprocessing problems. In this paper, we experimentally research the use of generative and non-generative models for feature reconstruction. Variational Autoencoder with Arbitrary Conditioning (VAEAC) and Generative Adversarial Imputation Network (GAIN) were researched as representatives of generative models, while the denoising autoencoder (DAE) represented non-generative models. Performance of the models is compared to traditional methods k-nearest neighbors (k-NN) and Multiple Imputation by Chained Equations (MICE). Moreover, we introduce WGAIN as the…
Australian National University（澳大利亚国立大学）；Data61；University of Sydney（悉尼大学）
Since the introduction of Generative Adversarial Networks (GANs) and Variational Autoencoders (VAE), the literature on generative modelling has witnessed an overwhelming resurgence. The impressive, yet elusive empirical performance of GANs has lead to the rise of many GAN-VAE hybrids, with the hopes of GAN level performance and additional benefits of VAE, such as an encoder for feature reduction, which is not offered by GANs. Recently, the Wasserstein Autoencoder (WAE) was proposed, achieving performance similar to that of GANs, yet it is still unclear whether the two are fundamentally differe…
University of Amsterdam（阿姆斯特丹大学）；Deeptrace；Google Brain（谷歌大脑）；DeepMind（深度思考）；École Polytechnique（巴黎综合理工学院）；Sony CSL（索尼计算机科学实验室）
Optimal transport offers an alternative to maximum likelihood for learning generative autoencoding models. We show that minimizing the p-Wasserstein distance between the generator and the true data distribution is equivalent to the unconstrained min-min optimization of the p-Wasserstein distance between the encoder aggregated posterior and the prior in latent space, plus a reconstruction error. We also identify the role of its trade-off hyperparameter as the capacity of the generator: its Lipschitz constant. Moreover, we prove that optimizing the encoder over any class of universal approximato…
Hong Kong University of Science and Technology（香港科技大学）；Clova AI Research, NAVER（NAVER Clova AI研究）；CIFAR Azrieli Global Scholar（CIFAR Azrieli全球学者）
Variational autoencoders~(VAEs) have shown a promise in data-driven conversation modeling. However, most VAE conversation models match the approximate posterior distribution over the latent variables to a simple prior such as standard normal distribution, thereby restricting the generated responses to a relatively simple (e.g., unimodal) scope. In this paper, we propose DialogWAE, a conditional Wasserstein autoencoder~(WAE) specially designed for dialogue modeling. Unlike VAEs that impose a simple distribution over the latent variables, DialogWAE models the distribution of data by training a G…
Helsinki Institute for Information Technology HIIT（赫尔辛基信息技术研究所（HIIT））；Aalto University（阿尔托大学）；University of Helsinki（赫尔辛基大学）
Motivation: Human genomic datasets often contain sensitive information that limits use and sharing of the data. In particular, simple anonymisation strategies fail to provide sufficient level of protection for genomic data, because the data are inherently identifiable. Differentially private machine learning can help by guaranteeing that the published results do not leak too much information about any individual data point. Recent research has reached promising results on differentially private drug sensitivity prediction using gene expression data. Differentially private learning with genomic…
Combination therapy has shown to improve therapeutic efficacy while reducing side effects. Importantly, it has become an indispensable strategy to overcome resistance in antibiotics, anti-microbials, and anti-cancer drugs. Facing enormous chemical space and unclear design principles for small-molecule combinations, the computational drug-combination design has not seen generative models to meet its potential to accelerate resistance-overcoming drug combination discovery. We have developed the first deep generative model for drug combination design, by jointly embedding graph-structured domain …
Generative Adversarial Networks (GANs) have been impactful on many problems and applications but suffer from unstable training. The Wasserstein GAN (WGAN) leverages the Wasserstein distance to avoid the caveats in the minmax two-player training of GANs but has other defects such as mode collapse and lack of metric to detect the convergence. We introduce a novel inferential Wasserstein GAN (iWGAN) model, which is a principled framework to fuse auto-encoders and WGANs. The iWGAN model jointly learns an encoder network and a generator network motivated by the iterative primal dual optimization pr…
In order to continuously represent molecules, we propose a generative model in the form of a VAE which is operating on the 2D-graph structure of molecules. A side predictor is employed to prune the latent space and help the decoder in generating meaningful adjacency tensor of molecules. Other than the potential applicability in drug design and property prediction, we show the superior performance of this technique in comparison to other similar methods based on the SMILES representation of the molecules with RNN based encoder and decoder.
Generative AutoEncoders require a chosen probability distribution in latent space, usually multivariate Gaussian. The original Variational AutoEncoder (VAE) uses randomness in encoder - causing problematic distortion, and overlaps in latent space for distinct inputs. It turned out unnecessary: we can instead use deterministic encoder with additional regularizer to ensure that sample distribution in latent space is close to the required. The original approach (WAE) uses Wasserstein metric, what required comparing with random sample and using an arbitrarily chosen kernel. Later CWAE finally deri…
University of Maryland College Park（马里兰大学帕克分校）；IBM Research（IBM研究院）
Detecting out of distribution (OOD) samples is of paramount importance in all Machine Learning applications. Deep generative modeling has emerged as a dominant paradigm to model complex data distributions without labels. However, prior work has shown that generative models tend to assign higher likelihoods to OOD samples compared to the data distribution on which they were trained. First, we propose Adversarial Mirrored Autoencoder (AMA), a variant of Adversarial Autoencoder, which uses a mirrored Wasserstein loss in the discriminator to enforce better semantic-level reconstruction. We also pr…
Aligned latent spaces, where meaningful semantic shifts in the input space correspond to a translation in the embedding space, play an important role in the success of downstream tasks such as unsupervised clustering and data imputation. In this work, we prove that linear and nonlinear autoencoders produce aligned latent spaces by stretching along the left singular vectors of the data. We fully characterize the amount of stretching in linear autoencoders and provide an initialization scheme to arbitrarily stretch along the top directions using these networks. We also quantify the amount of str…
Argonne National Laboratory（阿贡国家实验室）；Pacific Northwest National Laboratory（太平洋西北国家实验室）
Design of new drug compounds with target properties is a key area of research in generative modeling. We present a small drug molecule design pipeline based on graph-generative models and a comparison study of two state-of-the-art graph generative models for designing COVID-19 targeted drug candidates: 1) a variational autoencoder-based approach (VAE) that uses prior knowledge of molecules that have been shown to be effective for earlier coronavirus treatments and 2) a deep Q-learning method (DQN) that generates optimized molecules without any proximity constraints. We evaluate the novelty of …
Virginia Tech（弗吉尼亚理工大学）；University of Minnesota（明尼苏达大学）；Purdue University（普渡大学）
Image hashing is one of the fundamental problems that demand both efficient and effective solutions for various practical scenarios. Adversarial autoencoders are shown to be able to implicitly learn a robust, locality-preserving hash function that generates balanced and high-quality hash codes. However, the existing adversarial hashing methods are inefficient to be employed for large-scale image retrieval applications. Specifically, they require an exponential number of samples to be able to generate optimal hash codes and a significantly high computational cost to train. In this paper, we sho…
