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1. Attention-based generative models for de novo molecular design

   https://doi.org/10.1039/D1SC01050F  

   Dollar, Orion; Joshi, Nisarg; Beck, David A.; Pfaendtner, Jim (June 2021, Chemical Science)

   null (Ed.)

   Attention mechanisms have led to many breakthroughs in sequential data modeling but have yet to be incorporated into any generative algorithms for molecular design. Here we explore the impact of adding self-attention layers to generative β -VAE models and show that those with attention are able to learn a complex “molecular grammar” while improving performance on downstream tasks such as accurately sampling from the latent space (“model memory”) or exploring novel chemistries not present in the training data. There is a notable relationship between a model's architecture, the structure of its latent memory and its performance during inference. We demonstrate that there is an unavoidable tradeoff between model exploration and validity that is a function of the complexity of the latent memory. However, novel sampling schemes may be used that optimize this tradeoff. We anticipate that attention will play an important role in future molecular design algorithms that can make efficient use of the detailed molecular substructures learned by the transformer. 

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2. Learning multi-layer latent variable model with short run MCMC inference dynamics

   Nijkamp, E.; Pang, B.; Han, T.; Zhou, L.; Zhu, S. C.; Wu, Y. N. (January 2021, European Conference on Computer Vision)

   This paper studies the fundamental problem of learning deep generative models that consist of multiple layers of latent variables organized in top-down architectures. Such models have high expressivity and allow for learning hierarchical representations. Learning such a generative model requires inferring the latent variables for each training example based on the posterior distribution of these latent variables. The inference typically requires Markov chain Monte Caro (MCMC) that can be time consuming. In this paper, we propose to use noise initialized non-persistent short run MCMC, such as nite step Langevin dynamics initialized from the prior distribution of the latent variables, as an approximate inference engine, where the step size of the Langevin dynamics is variationally optimized by minimizing the Kullback-Leibler divergence between the distribution produced by the short run MCMC and the posterior distribution. Our experiments show that the proposed method outperforms variational auto-encoder (VAE) in terms of reconstruction error and synthesis quality. The advantage of the proposed method is that it is simple and automatic without the need to design an inference model. 

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3. A Generative Reinforcement Learning Framework for Predictive Analytics

   Skordilis, Erotokritos; Moghaddass, Ramin.; Farhat, Tazin. (January 2023, Proceedings annual Reliability and Maintainability Symposium)

   In this work, we present a new approach for latent system dynamics and remaining useful life (RUL) estimation of complex degrading systems using generative modeling and reinforcement learning. The main contributions of the proposed method are two-fold. First, we show how a deep generative model can approximate the functionality of high-fidelity simulators and, thus, is able to substitute expensive and complex physics-based models with data-driven surrogate ones. In other words, we can use the generative model in lieu of the actual system as a surrogate model of the system. Furthermore, we show how to use such surrogate models for predictive analytics. Our method follows two main steps. First, we use a deep variational autoencoder (VAE) to learn the distribution over the latent state-space that characterizes the dynamics of the system under monitoring. After model training, the probabilistic VAE decoder becomes the surrogate system model. Then, we develop a scalable reinforcement learning framework using the decoder as the environment, to train an agent for identifying adequate approximate values of the latent dynamics, as well as the RUL.To our knowledge, the method presented in this paper is the first in industrial prognostics that utilizes generative models and reinforcement learning in that capacity. While the process requires extensive data preprocessing and environment tailored design, which is not always possible, it demonstrates the ability of generative models working in conjunction with reinforcement learning to provide proper value estimations for system dynamics and their RUL. To validate the quality of the proposed method, we conducted numerical experiments using the train_FD002 dataset provided by the NASA CMAPSS data repository. Different subsets were used to train the VAE and the RL agent, and a leftover set was then used for model validation. The results shown prove the merit of our method and will further assist us in developing a data-driven RL environment that incorporates more complex latent dynamic layers, such as normal/faulty operating conditions and hazard processes. 

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4. Using deep LSD to build operators in GANs latent space with meaning in real space

   https://doi.org/10.1371/journal.pone.0287736  

   Toledo-Marín, J. Quetzalcóatl; Glazier, James A. (June 2023, PLOS ONE)

   Liu, Jin (Ed.)

   Generative models rely on the idea that data can be represented in terms of latent variables which are uncorrelated by definition. Lack of correlation among the latent variable support is important because it suggests that the latent-space manifold is simpler to understand and manipulate than the real-space representation. Many types of generative model are used in deep learning,e.g., variational autoencoders (VAEs) and generative adversarial networks (GANs). Based on the idea that the latent space behaves like a vector space Radford et al. (2015), we ask whether we can expand the latent space representation of our data elements in terms of an orthonormal basis set. Here we propose a method to build a set of linearly independent vectors in the latent space of a trained GAN, which we call quasi-eigenvectors. These quasi-eigenvectors have two key properties: i) They span the latent space, ii) A set of these quasi-eigenvectors map to each of the labeled features one-to-one. We show that in the case of the MNIST image data set, while the number of dimensions in latent space is large by design, 98% of the data in real space map to a sub-domain of latent space of dimensionality equal to the number of labels. We then show how the quasi-eigenvectors can be used for Latent Spectral Decomposition (LSD). We apply LSD to denoise MNIST images. Finally, using the quasi-eigenvectors, we construct rotation matrices in latent space which map to feature transformations in real space. Overall, from quasi-eigenvectors we gain insight regarding the latent space topology. 

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5. A Generative Reinforcement Learning Framework for Predictive Analytics

   https://doi.org/10.1109/RAMS51473.2023.10088246  

   Skordilis, Erotokritos; Moghaddass, Ramin; Farhat, Md Tanzin (January 2023, A Generative reinforcement learning framework for predictive analytics)

   In this work, we present a new approach for latent system dynamics and remaining useful life (RUL) estimation of complex degrading systems using generative modeling and reinforcement learning. The main contributions of the proposed method are two-fold. First, we show how a deep generative model can approximate the functionality of high-fidelity simulators and, thus, is able to substitute expensive and complex physics-based models with data-driven surrogate ones. In other words, we can use the generative model in lieu of the actual system as a surrogate model of the system. Furthermore, we show how to use such surrogate models for predictive analytics. Our method follows two main steps. First, we use a deep variational autoencoder (VAE) to learn the distribution over the latent state-space that characterizes the dynamics of the system under monitoring. After model training, the probabilistic VAE decoder becomes the surrogate system model. Then, we develop a scalable reinforcement learning framework using the decoder as the environment, to train an agent for identifying adequate approximate values of the latent dynamics, as well as the RUL. 

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