With the goal of designing novel inhibitors for SARS-CoV-1 and SARS-CoV-2, we propose the general molecule optimization framework, Molecular Neural Assay Search (MONAS), consisting of three components: a property predictor which identifies molecules with specific desirable properties, an energy model which approximates the statistical similarity of a given molecule to known training molecules, and a molecule search method. In this work, these components are instantiated with graph neural networks (GNNs), Deep Energy Estimator Networks (DEEN) and Monte Carlo tree search (MCTS), respectively. This implementation is used to identify 120K molecules (out of 40-million explored) which the GNN determined to be likely SARS-CoV-1 inhibitors, and, at the same time, are statistically close to the dataset used to train the GNN.

Convolutional neural networks have achieved extraordinary results in many computer vision and pattern recognition applications; however, their adoption in the computer graphics and geometry processing communities is limited due to the non-Euclidean structure of their data. In this paper, we propose Anisotropic Convolutional Neural Network (ACNN), a generalization of classical CNNs to non-Euclidean domains, where classical convolutions are replaced by projections over a set of oriented anisotropic diffusion kernels. We use ACNNs to effectively learn intrinsic dense correspondences between deformable shapes, a fundamental problem in geometry processing, arising in a wide variety of applications. We tested ACNNs performance in very challenging settings, achieving state-of-the-art results on some of the most difficult recent correspondence benchmarks. Papers published at the Neural Information Processing Systems Conference.

We extend Neural Processes (NPs) to sequential data through Recurrent NPs or RNPs, a family of conditional state space models. RNPs can learn dynamical patterns from sequential data and deal with non-stationarity. Given time series observed on fast real-world time scales but containing slow long-term variabilities, RNPs may derive appropriate slow latent time scales. They do so in an efficient manner by establishing conditional independence among subsequences of the time series. Our theoretically grounded framework for stochastic processes expands the applicability of NPs while retaining their benefits of flexibility, uncertainty estimation and favourable runtime with respect to Gaussian Processes. We demonstrate that state spaces learned by RNPs benefit predictive performance on real-world time-series data and nonlinear system identification, even in the case of limited data availability.

This paper introduces Non-Autonomous Input-Output Stable Network (NAIS-Net), a very deep architecture where each stacked processing block is derived from a time-invariant non-autonomous dynamical system. Non-autonomy is implemented by skip connections from the block input to each of the unrolled processing stages and allows stability to be enforced so that blocks can be unrolled adaptively to a pattern-dependent processing depth. NAIS-Net induces non-trivial, Lipschitz input-output maps, even for an infinite unroll length. We prove that the network is globally asymptotically stable so that for every initial condition there is exactly one input-dependent equilibrium assuming tanh units, and multiple stable equilibria for ReL units. An efficient implementation that enforces the stability under derived conditions for both fully-connected and convolutional layers is also presented. Experimental results show how NAIS-Net exhibits stability in practice, yielding a significant reduction in generalization gap compared to ResNets.

This paper introduces Non-Autonomous Input-Output Stable Network (NAIS-Net), a very deep architecture where each stacked processing block is derived from a time-invariant non-autonomous dynamical system. Non-autonomy is implemented by skip connections from the block input to each of the unrolled processing stages and allows stability to be enforced so that blocks can be unrolled adaptively to a pattern-dependent processing depth. NAIS-Net induces non-trivial, Lipschitz input-output maps, even for an infinite unroll length. We prove that the network is globally asymptotically stable so that for every initial condition there is exactly one input-dependent equilibrium assuming tanh units, and multiple stable equilibria for ReL units. An efficient implementation that enforces the stability under derived conditions for both fully-connected and convolutional layers is also presented. Experimental results show how NAIS-Net exhibits stability in practice, yielding a significant reduction in generalization gap compared to ResNets.

Deep learning systems have become ubiquitous in many aspects of our lives. Unfortunately, it has been shown that such systems are vulnerable to adversarial attacks, making them prone to potential unlawful uses. Designing deep neural networks that are robust to adversarial attacks is a fundamental step in making such systems safer and deployable in a broader variety of applications (e.g. autonomous driving), but more importantly is a necessary step to design novel and more advanced architectures built on new computational paradigms rather than marginally building on the existing ones. In this paper we introduce PeerNets, a novel family of convolutional networks alternating classical Euclidean convolutions with graph convolutions to harness information from a graph of peer samples. This results in a form of non-local forward propagation in the model, where latent features are conditioned on the global structure induced by the graph, that is up to 3 times more robust to a variety of white- and black-box adversarial attacks compared to conventional architectures with almost no drop in accuracy.

This paper introduces "Non-Autonomous Input-Output Stable Network" (NAIS-Net), a very deep architecture where each stacked processing block is derived from a time-invariant non-autonomous dynamical system. Non-autonomy is implemented by skip connections from the block input to each of the unrolled processing stages and allows stability to be enforced so that blocks can be unrolled adaptively to a pattern-dependent processing depth. We prove that the network is globally asymptotically stable so that for every initial condition there is exactly one input-dependent equilibrium assuming tanh units, and multiple stable equilibria for ReLU units. An efficient implementation that enforces the stability under derived conditions for both fully-connected and convolutional layers is also presented. Experimental results show how NAIS-Net exhibits stability in practice, yielding a significant reduction in generalization gap compared to ResNets.

Convolutional neural networks have achieved extraordinary results in many computer vision and pattern recognition applications; however, their adoption in the computer graphics and geometry processing communities is limited due to the non-Euclidean structure of their data. In this paper, we propose Anisotropic Convolutional Neural Network (ACNN), a generalization of classical CNNs to non-Euclidean domains, where classical convolutions are replaced by projections over a set of oriented anisotropic diffusion kernels. We use ACNNs to effectively learn intrinsic dense correspondences between deformable shapes, a fundamental problem in geometry processing, arising in a wide variety of applications. We tested ACNNs performance in very challenging settings, achieving state-of-the-art results on some of the most difficult recent correspondence benchmarks.

Traditional convolutional neural networks (CNN) are stationary and feedforward. They neither change their parameters during evaluation nor use feedback from higher to lower layers. Real brains, however, do. So does our Deep Attention Selective Network (dasNet) architecture. DasNet's feedback structure can dynamically alter its convolutional filter sensitivities during classification. It harnesses the power of sequential processing to improve classification performance, by allowing the network to iteratively focus its internal attention on some of its convolutional filters. Feedback is trained through direct policy search in a huge million-dimensional parameter space, through scalable natural evolution strategies (SNES). On the CIFAR-10 and CIFAR-100 datasets, dasNet outperforms the previous state-of-the-art model on unaugmented datasets.

Local competition among neighboring neurons is common in biological neural networks(NNs). In this paper, we apply the concept to gradient-based, backprop-trained artificial multilayer NNs. NNs with competing linear units tend to outperform those with non-competing nonlinear units, and avoid catastrophic forgetting when training sets change over time.