Multi-Objective Latent Space Optimization of Generative Molecular Design Models
Texas A&M University（德克萨斯农工大学）；Brookhaven National Laboratory（布鲁克海文国家实验室）；Frederick National Laboratory（弗雷德里克国家实验室）；Argonne National Laboratory（阿贡国家实验室）
A N M Nafiz Abeer, Nathan Urban, M Ryan Weil, Francis J. Alexander, Byung-Jun Yoon
Molecular design based on generative models, such as variational autoencoders (VAEs), has become increasingly popular in recent years due to its efficiency for exploring high-dimensional molecular space to identify molecules with desired properties. While the efficacy of the initial model strongly depends on the training data, the sampling efficiency of the model for suggesting novel molecules with enhanced properties can be further enhanced via latent space optimization. In this paper, we propose a multi-objective latent space optimization (LSO) method that can significantly enhance the performance of generative molecular design (GMD). The proposed method adopts an iterative weighted retraining approach, where the respective weights of the molecules in the training data are determined by their Pareto efficiency. We demonstrate that our multi-objective GMD LSO method can significantly improve the performance of GMD for jointly optimizing multiple molecular properties.
Deep generative models are increasingly becoming integral parts of the in silico molecule design pipeline and have dual goals of learning the chemical and structural features that render candidate molecules viable while also being flexible enough to generate novel designs. Specifically, Variational Auto Encoders (VAEs) are generative models in which encoder-decoder network pairs are trained to reconstruct training data distributions in such a way that the latent space of the encoder network is smooth. Therefore, novel candidates can be found by sampling from this latent space. However, the sco…
Latent representations are the essence of deep generative models and determine their usefulness and power. For latent representations to be useful as generative concept representations, their latent space must support latent space interpolation, attribute vectors and concept vectors, among other things. We investigate and discuss latent variable modeling, including latent variable models, latent representations and latent spaces, particularly hierarchical latent representations and latent space vectors and geometry. Our focus is on that used in variational autoencoders and generative adversari…
The Generator of a Generative Adversarial Network (GAN) is trained to transform latent vectors drawn from a prior distribution into realistic looking photos. These latent vectors have been shown to encode information about the content of their corresponding images. Projecting input images onto the latent space of a GAN is non-trivial, but previous work has successfully performed this task for latent spaces with a uniform prior. We extend these techniques to latent spaces with a Gaussian prior, and demonstrate our technique's effectiveness.
In this paper, we present a general method that can improve the sample quality of pre-trained likelihood based generative models. Our method constructs an energy function on the latent variable space that yields an energy function on samples produced by the pre-trained generative model. The energy based model is efficiently trained by maximizing the data likelihood, and after training, new samples in the latent space are generated from the energy based model and passed through the generator to producing samples in observation space. We show that using our proposed method, we can greatly improv…
In this work, we propose the Generative Latent Flow (GLF), an algorithm for generative modeling of the data distribution. GLF uses an Auto-encoder (AE) to learn latent representations of the data, and a normalizing flow to map the distribution of the latent variables to that of simple i.i.d noise. In contrast to some other Auto-encoder based generative models, which use various regularizers that encourage the encoded latent distribution to match the prior distribution, our model explicitly constructs a mapping between these two distributions, leading to better density matching while avoiding o…
Generative adversarial networks (GANs) transform latent vectors into visually plausible images. It is generally thought that the original GAN formulation gives no out-of-the-box method to reverse the mapping, projecting images back into latent space. We introduce a simple, gradient-based technique called stochastic clipping. In experiments, for images generated by the GAN, we precisely recover their latent vector pre-images 100% of the time. Additional experiments demonstrate that this method is robust to noise. Finally, we show that even for unseen images, our method appears to recover unique…
3M-Diffusion: Latent Multi-Modal Diffusion for Language-Guided Molecular Structure Generation
Artificial Intelligence Research Laboratory（人工智能研究实验室）；College of Information Sciences and Technology（信息科学与技术学院）；Center for Artificial Intelligence Foundations and Scientific Applications（人工智能基础与科学应用中心）；Institute for Computational and Data Sciences（计算与数据科学研究所）；The Pennsylvania State University（宾夕法尼亚州立大学）
In this work, we propose a new family of generative flows on an augmented data space, with an aim to improve expressivity without drastically increasing the computational cost of sampling and evaluation of a lower bound on the likelihood. Theoretically, we prove the proposed flow can approximate a Hamiltonian ODE as a universal transport map. Empirically, we demonstrate state-of-the-art performance on standard benchmarks of flow-based generative modeling.
University of Electronic Science and Technology of China（电子科技大学）
We study the problem of multimodal generative modelling of images based on generative adversarial networks (GANs). Despite the success of existing methods, they often ignore the underlying structure of vision data or its multimodal generation characteristics. To address this problem, we introduce the Dirichlet prior for multimodal image generation, which leads to a new Latent Dirichlet Allocation based GAN (LDAGAN). In detail, for the generative process modelling, LDAGAN defines a generative mode for each sample, determining which generative sub-process it belongs to. For the adversarial train…
IIT Delhi（德里印度理工学院）；Flipkart Internet Pvt. Ltd.（Flipkart互联网私人有限公司）；TIFR（塔塔基础研究院）
The field of neural generative models is dominated by the highly successful Generative Adversarial Networks (GANs) despite their challenges, such as training instability and mode collapse. Auto-Encoders (AE) with regularized latent space provide an alternative framework for generative models, albeit their performance levels have not reached that of GANs. In this work, we hypothesise that the dimensionality of the AE model's latent space has a critical effect on the quality of generated data. Under the assumption that nature generates data by sampling from a "true" generative latent space follo…
Generative Adversarial networks (GANs) have obtained remarkable success in many unsupervised learning tasks and unarguably, clustering is an important unsupervised learning problem. While one can potentially exploit the latent-space back-projection in GANs to cluster, we demonstrate that the cluster structure is not retained in the GAN latent space. In this paper, we propose ClusterGAN as a new mechanism for clustering using GANs. By sampling latent variables from a mixture of one-hot encoded variables and continuous latent variables, coupled with an inverse network (which projects the data to…
Heidelberg University（海德堡大学）；Université catholique de Louvain（鲁汶天主教大学）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）；University of California, Berkeley（加州大学伯克利分校）
Deep generative models are becoming widely used across science and industry for a variety of purposes. A common challenge is achieving a precise implicit or explicit representation of the data probability density. Recent proposals have suggested using classifier weights to refine the learned density of deep generative models. We extend this idea to all types of generative models and show how latent space refinement via iterated generative modeling can circumvent topological obstructions and improve precision. This methodology also applies to cases were the target model is non-differentiable an…
OCL-PDE: A Generative Framework for PDE Inverse Problems with Observation-Complementary Latents
The Hong Kong University of Science and Technology（香港科技大学）；University of Michigan（密歇根大学）；HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute（香港科技大学深圳-香港协同创新研究院）
Generative adversarial networks (GANs) with clustered latent spaces can perform conditional generation in a completely unsupervised manner. In the real world, the salient attributes of unlabeled data can be imbalanced. However, most of existing unsupervised conditional GANs cannot cluster attributes of these data in their latent spaces properly because they assume uniform distributions of the attributes. To address this problem, we theoretically derive Stein latent optimization that provides reparameterizable gradient estimations of the latent distribution parameters assuming a Gaussian mixtur…
Training generative adversarial networks requires balancing of delicate adversarial dynamics. Even with careful tuning, training may diverge or end up in a bad equilibrium with dropped modes. In this work, we improve CS-GAN with natural gradient-based latent optimisation and show that it improves adversarial dynamics by enhancing interactions between the discriminator and the generator. Our experiments demonstrate that latent optimisation can significantly improve GAN training, obtaining state-of-the-art performance for the ImageNet ($128 \times 128$) dataset. Our model achieves an Inception S…
Columbia University（哥伦比亚大学）；Harvard University（哈佛大学）
Variational autoencoders learn distributions of high-dimensional data. They model data with a deep latent-variable model and then fit the model by maximizing a lower bound of the log marginal likelihood. VAEs can capture complex distributions, but they can also suffer from an issue known as "latent variable collapse," especially if the likelihood model is powerful. Specifically, the lower bound involves an approximate posterior of the latent variables; this posterior "collapses" when it is set equal to the prior, i.e., when the approximate posterior is independent of the data. While VAEs learn…
University of Calgary（卡尔加里大学）；MILA, Université de Montréal（蒙特利尔大学MILA）；Wuhan University（武汉大学）
Modern generative models are usually designed to match target distributions directly in the data space, where the intrinsic dimension of data can be much lower than the ambient dimension. We argue that this discrepancy may contribute to the difficulties in training generative models. We therefore propose to map both the generated and target distributions to a latent space using the encoder of a standard autoencoder, and train the generator (or decoder) to match the target distribution in the latent space. Specifically, we enforce the consistency in both the data space and the latent space with…
Neural Networks and Deep Learning Lab（神经网络与深度学习实验室）；Moscow Institute of Physics and Technology（莫斯科物理技术学院）
Conventional prior for Variational Auto-Encoder (VAE) is a Gaussian distribution. Recent works demonstrated that choice of prior distribution affects learning capacity of VAE models. We propose a general technique (embedding-reparameterization procedure, or ER) for introducing arbitrary manifold-valued variables in VAE model. We compare our technique with a conventional VAE on a toy benchmark problem. This is work in progress.
We propose a molecular generative model based on the conditional variational autoencoder for de novo molecular design. It is specialized to control multiple molecular properties simultaneously by imposing them on a latent space. As a proof of concept, we demonstrate that it can be used to generate drug-like molecules with five target properties. We were also able to adjust a single property without changing the others and to manipulate it beyond the range of the dataset.
University of Toronto（多伦多大学）；Vector Institute for AI（矢量人工智能研究院）；Samsung AI Center Toronto（多伦多三星人工智能中心）；Samsung Research America, Inc.（美国三星研究公司）
Representing 3D shape is a fundamental problem in artificial intelligence, which has numerous applications within computer vision and graphics. One avenue that has recently begun to be explored is the use of latent representations of generative models. However, it remains an open problem to learn a generative model of shape that is interpretable and easily manipulated, particularly in the absence of supervised labels. In this paper, we propose an unsupervised approach to partitioning the latent space of a variational autoencoder for 3D point clouds in a natural way, using only geometric inform…
University of Copenhagen（哥本哈根大学）；Rigshospitalet（哥本哈根大学国立医院）
Generative models such as Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs) play an increasingly important role in medical image analysis. The latent spaces of these models often show semantically meaningful directions corresponding to human-interpretable image transformations. However, until now, their exploration for medical images has been limited due to the requirement of supervised data. Several methods for unsupervised discovery of interpretable directions in GAN latent spaces have shown interesting results on natural images. This work explores the potential of a…
Score-based generative models (SGMs) have recently demonstrated impressive results in terms of both sample quality and distribution coverage. However, they are usually applied directly in data space and often require thousands of network evaluations for sampling. Here, we propose the Latent Score-based Generative Model (LSGM), a novel approach that trains SGMs in a latent space, relying on the variational autoencoder framework. Moving from data to latent space allows us to train more expressive generative models, apply SGMs to non-continuous data, and learn smoother SGMs in a smaller space, re…
Generative Adversarial Networks (GANs) have achieved remarkable results in the task of generating realistic natural images. In most successful applications, GAN models share two common aspects: solving a challenging saddle point optimization problem, interpreted as an adversarial game between a generator and a discriminator functions; and parameterizing the generator and the discriminator as deep convolutional neural networks. The goal of this paper is to disentangle the contribution of these two factors to the success of GANs. In particular, we introduce Generative Latent Optimization (GLO), …
Uncovering Physical Drivers of Dark Matter Halo Structures with Auxiliary-Variable-Guided Generative Models
Mathematics and Computer Science Division Argonne National Laboratory（阿贡国家实验室数学与计算机科学部）；High Energy Physics Division Argonne National Laboratory（阿贡国家实验室高能物理部）；Computational Science Division Argonne National Laboratory（阿贡国家实验室计算科学部）；Computational Science Center Data, Analysis and Visualization Group National Renewable Energy Laboratory（国家可再生能源实验室计算科学中心数据、分析与可视化组）
End-to-end optimization has achieved state-of-the-art performance on many specific problems, but there is no straight-forward way to combine pretrained models for new problems. Here, we explore improving modularity by learning a post-hoc interface between two existing models to solve a new task. Specifically, we take inspiration from neural machine translation, and cast the challenging problem of cross-modal domain transfer as unsupervised translation between the latent spaces of pretrained deep generative models. By abstracting away the data representation, we demonstrate that it is possible …
Integrating Predictive and Generative Capabilities by Latent Space Design via the DKL-VAE Model
Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen（杜伊斯堡-埃森大学纳米集成中心）；Department of Materials Science and Engineering, University of Tennessee（田纳西大学材料科学与工程系）；Pacific Northwest National Laboratory（太平洋西北国家实验室）
Deep generative neural networks have proven effective at both conditional and unconditional modeling of complex data distributions. Conditional generation enables interactive control, but creating new controls often requires expensive retraining. In this paper, we develop a method to condition generation without retraining the model. By post-hoc learning latent constraints, value functions that identify regions in latent space that generate outputs with desired attributes, we can conditionally sample from these regions with gradient-based optimization or amortized actor functions. Combining at…
Generative Modeling of Discrete Data Using Geometric Latent Subspaces
Institute for Mathematics, Heidelberg University（海德堡大学数学研究所）；Mannheim Institute for Intelligent Systems in Medicine, Heidelberg University（海德堡大学曼海姆智能医学系统研究所）；IWR, Heidelberg University（海德堡大学IWR研究所）；Research Station Geometry and Dynamics, Heidelberg University（海德堡大学几何与动力学研究站）
University of Science and Technology Beijing（北京科技大学）；Technical University of Denmark（丹麦技术大学）
Deep generative models are tremendously successful in learning low-dimensional latent representations that well-describe the data. These representations, however, tend to much distort relationships between points, i.e. pairwise distances tend to not reflect semantic similarities well. This renders unsupervised tasks, such as clustering, difficult when working with the latent representations. We demonstrate that taking the geometry of the generative model into account is sufficient to make simple clustering algorithms work well over latent representations. Leaning on the recent finding that dee…
Corti（Corti公司）；Unumed（Unumed公司）；Technical University of Denmark（丹麦技术大学）
With the introduction of the variational autoencoder (VAE), probabilistic latent variable models have received renewed attention as powerful generative models. However, their performance in terms of test likelihood and quality of generated samples has been surpassed by autoregressive models without stochastic units. Furthermore, flow-based models have recently been shown to be an attractive alternative that scales well to high-dimensional data. In this paper we close the performance gap by constructing VAE models that can effectively utilize a deep hierarchy of stochastic variables and model c…
Generative adversarial networks (GANs) learn to synthesise new samples from a high-dimensional distribution by passing samples drawn from a latent space through a generative network. When the high-dimensional distribution describes images of a particular data set, the network should learn to generate visually similar image samples for latent variables that are close to each other in the latent space. For tasks such as image retrieval and image classification, it may be useful to exploit the arrangement of the latent space by projecting images into it, and using this as a representation for dis…
Word alignments identify translational correspondences between words in a parallel sentence pair and are used, for instance, to learn bilingual dictionaries, to train statistical machine translation systems or to perform quality estimation. Variational autoencoders have been recently used in various of natural language processing to learn in an unsupervised way latent representations that are useful for language generation tasks. In this paper, we study these models for the task of word alignment and propose and assess several evolutions of a vanilla variational autoencoders. We demonstrate th…
A large number of objectives have been proposed to train latent variable generative models. We show that many of them are Lagrangian dual functions of the same primal optimization problem. The primal problem optimizes the mutual information between latent and visible variables, subject to the constraints of accurately modeling the data distribution and performing correct amortized inference. By choosing to maximize or minimize mutual information, and choosing different Lagrange multipliers, we obtain different objectives including InfoGAN, ALI/BiGAN, ALICE, CycleGAN, beta-VAE, adversarial auto…
