The COVID-19 pandemic has highlighted the urgency for developing more efficient molecular discovery pathways. As exhaustive exploration of the vast chemical space is infeasible, discovering novel inhibitor molecules for emerging drug-target proteins is challenging, particularly for targets with unknown structure or ligands. We demonstrate the broad utility of a single deep generative framework toward discovering novel drug-like inhibitor molecules against two distinct SARS-CoV-2 targets -- the main protease (Mpro) and the receptor binding domain (RBD) of the spike protein. To perform target-aware design, the framework employs a target sequence-conditioned sampling of novel molecules from a generative model. Micromolar-level in vitro inhibition was observed for two candidates (out of four synthesized) for each target. The most potent spike RBD inhibitor also emerged as a rare non-covalent antiviral with broad-spectrum activity against several SARS-CoV-2 variants in live virus neutralization assays. These results show a broadly deployable machine intelligence framework can accelerate hit discovery across different emerging drug-targets.
Given a graph with partial observations of node features, how can we estimate the missing features accurately? Feature estimation is a crucial problem for analyzing real-world graphs whose features are commonly missing during the data collection process. Accurate estimation not only provides diverse information of nodes but also supports the inference of graph neural networks that require the full observation of node features. However, designing an effective approach for estimating high-dimensional features is challenging, since it requires an estimator to have large representation power, increasing the risk of overfitting. In this work, we propose SVGA (Structured Variational Graph Autoencoder), an accurate method for feature estimation. SVGA applies strong regularization to the distribution of latent variables by structured variational inference, which models the prior of variables as Gaussian Markov random field based on the graph structure. As a result, SVGA combines the advantages of probabilistic inference and graph neural networks, achieving state-of-the-art performance in real datasets.
Motivated by the recent empirical success of policy-based reinforcement learning (RL), there has been a research trend studying the performance of policy-based RL methods on standard control benchmark problems. In this paper, we examine the effectiveness of policy-based RL methods on an important robust control problem, namely $\mu$ synthesis. We build a connection between robust adversarial RL and $\mu$ synthesis, and develop a model-free version of the well-known $DK$-iteration for solving state-feedback $\mu$ synthesis with static $D$-scaling. In the proposed algorithm, the $K$ step mimics the classical central path algorithm via incorporating a recently-developed double-loop adversarial RL method as a subroutine, and the $D$ step is based on model-free finite difference approximation. Extensive numerical study is also presented to demonstrate the utility of our proposed model-free algorithm. Our study sheds new light on the connections between adversarial RL and robust control.
Score-based generative models (SGMs) have recently emerged as a promising class of generative models. The key idea is to produce high-quality images by recurrently adding Gaussian noises and gradients to a Gaussian sample until converging to the target distribution, a.k.a. the diffusion sampling. To ensure stability of convergence in sampling and generation quality, however, this sequential sampling process has to take a small step size and many sampling iterations (e.g., 2000). Several acceleration methods have been proposed with focus on low-resolution generation. In this work, we consider the acceleration of high-resolution generation with SGMs, a more challenging yet more important problem. We prove theoretically that this slow convergence drawback is primarily due to the ignorance of the target distribution. Further, we introduce a novel Target Distribution Aware Sampling (TDAS) method by leveraging the structural priors in space and frequency domains. Extensive experiments on CIFAR-10, CelebA, LSUN, and FFHQ datasets validate that TDAS can consistently accelerate state-of-the-art SGMs, particularly on more challenging high resolution (1024x1024) image generation tasks by up to 18.4x, whilst largely maintaining the synthesis quality. With fewer sampling iterations, TDAS can still generate good quality images. In contrast, the existing methods degrade drastically or even fails completely
Depth and ego-motion estimations are essential for the localization and navigation of autonomous robots and autonomous driving. Recent studies make it possible to learn the per-pixel depth and ego-motion from the unlabeled monocular video. A novel unsupervised training framework is proposed with 3D hierarchical refinement and augmentation using explicit 3D geometry. In this framework, the depth and pose estimations are hierarchically and mutually coupled to refine the estimated pose layer by layer. The intermediate view image is proposed and synthesized by warping the pixels in an image with the estimated depth and coarse pose. Then, the residual pose transformation can be estimated from the new view image and the image of the adjacent frame to refine the coarse pose. The iterative refinement is implemented in a differentiable manner in this paper, making the whole framework optimized uniformly. Meanwhile, a new image augmentation method is proposed for the pose estimation by synthesizing a new view image, which creatively augments the pose in 3D space but gets a new augmented 2D image. The experiments on KITTI demonstrate that our depth estimation achieves state-of-the-art performance and even surpasses recent approaches that utilize other auxiliary tasks. Our visual odometry outperforms all recent unsupervised monocular learning-based methods and achieves competitive performance to the geometry-based method, ORB-SLAM2 with back-end optimization.
Many of the successes of machine learning are based on minimizing an averaged loss function. However, it is well-known that this paradigm suffers from robustness issues that hinder its applicability in safety-critical domains. These issues are often addressed by training against worst-case perturbations of data, a technique known as adversarial training. Although empirically effective, adversarial training can be overly conservative, leading to unfavorable trade-offs between nominal performance and robustness. To this end, in this paper we propose a framework called probabilistic robustness that bridges the gap between the accurate, yet brittle average case and the robust, yet conservative worst case by enforcing robustness to most rather than to all perturbations. From a theoretical point of view, this framework overcomes the trade-offs between the performance and the sample-complexity of worst-case and average-case learning. From a practical point of view, we propose a novel algorithm based on risk-aware optimization that effectively balances average- and worst-case performance at a considerably lower computational cost relative to adversarial training. Our results on MNIST, CIFAR-10, and SVHN illustrate the advantages of this framework on the spectrum from average- to worst-case robustness.
As a highly ill-posed issue, single image super-resolution (SISR) has been widely investigated in recent years. The main task of SISR is to recover the information loss caused by the degradation procedure. According to the Nyquist sampling theory, the degradation leads to aliasing effect and makes it hard to restore the correct textures from low-resolution (LR) images. In practice, there are correlations and self-similarities among the adjacent patches in the natural images. This paper considers the self-similarity and proposes a hierarchical image super-resolution network (HSRNet) to suppress the influence of aliasing. We consider the SISR issue in the optimization perspective, and propose an iterative solution pattern based on the half-quadratic splitting (HQS) method. To explore the texture with local image prior, we design a hierarchical exploration block (HEB) and progressive increase the receptive field. Furthermore, multi-level spatial attention (MSA) is devised to obtain the relations of adjacent feature and enhance the high-frequency information, which acts as a crucial role for visual experience. Experimental result shows HSRNet achieves better quantitative and visual performance than other works, and remits the aliasing more effectively.
We consider a linear stochastic bandit problem involving $M$ agents that can collaborate via a central server to minimize regret. A fraction $\alpha$ of these agents are adversarial and can act arbitrarily, leading to the following tension: while collaboration can potentially reduce regret, it can also disrupt the process of learning due to adversaries. In this work, we provide a fundamental understanding of this tension by designing new algorithms that balance the exploration-exploitation trade-off via carefully constructed robust confidence intervals. We also complement our algorithms with tight analyses. First, we develop a robust collaborative phased elimination algorithm that achieves $\tilde{O}\left(\alpha+ 1/\sqrt{M}\right) \sqrt{dT}$ regret for each good agent; here, $d$ is the model-dimension and $T$ is the horizon. For small $\alpha$, our result thus reveals a clear benefit of collaboration despite adversaries. Using an information-theoretic argument, we then prove a matching lower bound, thereby providing the first set of tight, near-optimal regret bounds for collaborative linear bandits with adversaries. Furthermore, by leveraging recent advances in high-dimensional robust statistics, we significantly extend our algorithmic ideas and results to (i) the generalized linear bandit model that allows for non-linear observation maps; and (ii) the contextual bandit setting that allows for time-varying feature vectors.
It is important to detect anomalous inputs when deploying machine learning systems. The use of larger and more complex inputs in deep learning magnifies the difficulty of distinguishing between anomalous and in-distribution examples. At the same time, diverse image and text data are available in enormous quantities. We propose leveraging these data to improve deep anomaly detection by training anomaly detectors against an auxiliary dataset of outliers, an approach we call Outlier Exposure (OE). This enables anomaly detectors to generalize and detect unseen anomalies. In extensive experiments on natural language processing and small- and large-scale vision tasks, we find that Outlier Exposure significantly improves detection performance. We also observe that cutting-edge generative models trained on CIFAR-10 may assign higher likelihoods to SVHN images than to CIFAR-10 images; we use OE to mitigate this issue. We also analyze the flexibility and robustness of Outlier Exposure, and identify characteristics of the auxiliary dataset that improve performance.
In structure learning, the output is generally a structure that is used as supervision information to achieve good performance. Considering the interpretation of deep learning models has raised extended attention these years, it will be beneficial if we can learn an interpretable structure from deep learning models. In this paper, we focus on Recurrent Neural Networks (RNNs) whose inner mechanism is still not clearly understood. We find that Finite State Automaton (FSA) that processes sequential data has more interpretable inner mechanism and can be learned from RNNs as the interpretable structure. We propose two methods to learn FSA from RNN based on two different clustering methods. We first give the graphical illustration of FSA for human beings to follow, which shows the interpretability. From the FSA's point of view, we then analyze how the performance of RNNs are affected by the number of gates, as well as the semantic meaning behind the transition of numerical hidden states. Our results suggest that RNNs with simple gated structure such as Minimal Gated Unit (MGU) is more desirable and the transitions in FSA leading to specific classification result are associated with corresponding words which are understandable by human beings.
We propose a new method for event extraction (EE) task based on an imitation learning framework, specifically, inverse reinforcement learning (IRL) via generative adversarial network (GAN). The GAN estimates proper rewards according to the difference between the actions committed by the expert (or ground truth) and the agent among complicated states in the environment. EE task benefits from these dynamic rewards because instances and labels yield to various extents of difficulty and the gains are expected to be diverse -- e.g., an ambiguous but correctly detected trigger or argument should receive high gains -- while the traditional RL models usually neglect such differences and pay equal attention on all instances. Moreover, our experiments also demonstrate that the proposed framework outperforms state-of-the-art methods, without explicit feature engineering.