We propose Cormorant, a rotationally covariant neural network architecture for learning the behavior and properties of complex many-body physical systems. We apply these networks to molecular systems with two goals: learning atomic potential energy surfaces for use in Molecular Dynamics simulations, and learning ground state properties of molecules calculated by Density Functional Theory. Some of the key features of our network are that (a) each neuron explicitly corresponds to a subset of atoms; (b) the activation of each neuron is covariant to rotations, ensuring that overall the network is fully rotationally invariant. Furthermore, the non-linearity in our network is based upon tensor products and the Clebsch-Gordan decomposition, allowing the network to operate entirely in Fourier space. Cormorant significantly outperforms competing algorithms in learning molecular Potential Energy Surfaces from conformational geometries in the MD-17 dataset, and is competitive with other methods at learning geometric, energetic, electronic, and thermodynamic properties of molecules on the GDB-9 dataset.

Classical approaches for approximate inference depend on cleverly designed variational distributions and bounds. Modern approaches employ amortized variational inference, which uses a neural network to approximate any posterior without leveraging the structures of the generative models. In this paper, we propose Amortized Conjugate Posterior (ACP), a hybrid approach taking advantages of both types of approaches. Specifically, we use the classical methods to derive specific forms of posterior distributions and then learn the variational parameters using amortized inference. We study the effectiveness of the proposed approach on the Noisy-OR model and compare to both the classical and the modern approaches for approximate inference and parameter learning. Our results show that ACP outperforms other methods when there is a limited amount of training data.

Non-parallel many-to-many voice conversion, as well as zero-shot voice conversion, remain under-explored areas. Deep style transfer algorithms, such as generative adversarial networks (GAN) and conditional variational autoencoder (CVAE), are being applied as new solutions in this field. However, GAN training is sophisticated and difficult, and there is no strong evidence that its generated speech is of good perceptual quality. On the other hand, CVAE training is simple but does not come with the distribution-matching property of a GAN. In this paper, we propose a new style transfer scheme that involves only an autoencoder with a carefully designed bottleneck. We formally show that this scheme can achieve distribution-matching style transfer by training only on a self-reconstruction loss. Based on this scheme, we proposed AUTOVC, which achieves state-of-the-art results in many-to-many voice conversion with non-parallel data, and which is the first to perform zero-shot voice conversion.

Recently, there is a growing interest in the study of median-based algorithms for distributed non-convex optimization. Two prominent such algorithms include signSGD with majority vote, an effective approach for communication reduction via 1-bit compression on the local gradients, and medianSGD, an algorithm recently proposed to ensure robustness against Byzantine workers. The convergence analyses for these algorithms critically rely on the assumption that all the distributed data are drawn iid from the same distribution. However, in applications such as Federated Learning, the data across different nodes or machines can be inherently heterogeneous, which violates such an iid assumption. This work analyzes signSGD and medianSGD in distributed settings with heterogeneous data. We show that these algorithms are non-convergent whenever there is some disparity between the expected median and mean over the local gradients. To overcome this gap, we provide a novel gradient correction mechanism that perturbs the local gradients with noise, together with a series results that provable close the gap between mean and median of the gradients. The proposed methods largely preserve nice properties of these methods, such as the low per-iteration communication complexity of signSGD, and further enjoy global convergence to stationary solutions. Our perturbation technique can be of independent interest when one wishes to estimate mean through a median estimator.

We introduce a novel co-learning paradigm for manifolds naturally equipped with a group action, motivated by recent developments on learning a manifold from attached fibre bundle structures. We utilize a representation theoretic mechanism that canonically associates multiple independent vector bundles over a common base manifold, which provides multiple views for the geometry of the underlying manifold. The consistency across these fibre bundles provide a common base for performing unsupervised manifold co-learning through the redundancy created artificially across irreducible representations of the transformation group. We demonstrate the efficacy of the proposed algorithmic paradigm through drastically improved robust nearest neighbor search and community detection on rotation-invariant cryo-electron microscopy image analysis.

We introduce a novel stochastic contextual bandit model, where at each step the adversary chooses a distribution over a context set. The learner observes only the context distribution while the exact context realization remains hidden. This allows for a broader range of applications, for instance when the context itself is based on predictions. By leveraging the UCB algorithm to this setting, we propose an algorithm that achieves a $\tilde{\mathcal{O}}(d\sqrt{T})$ high-probability regret bound for linearly parametrized reward functions. Our results strictly generalize previous work in the sense that both our model and the algorithm reduce to the standard setting when the environment chooses only Dirac delta distributions and therefore provides the exact context to the learner. We further obtain similar results for a variant where the learner observes the realized context after choosing the action, and we extend the results to the kernelized setting. Finally, we demonstrate the proposed method on synthetic and real-world datasets.

Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural information from it. Almost all of the existing approaches exploit MSAs in an indirect fashion, i.e., they transform MSAs into position-specific scoring matrices (PSSM) that represent the distribution of amino acid types at each column. PSSM could capture column-wise characteristics of MSA, however, the column-wise characteristics embedded in each individual component sequence were nearly totally neglected. The drawback of PSSM is rooted in the fact that an MSA is essentially an unordered sequence set rather than a matrix. Specifically, the interchange of any two sequences will not affect the whole MSA. In contrast, the pixels in an image essentially form a matrix since any two rows of pixels cannot be interchanged. Therefore, the traditional deep neural networks designed for image processing cannot be directly applied on sequence sets. Here, we proposed a novel deep neural network framework (called Seq-SetNet) for sequence set processing. By employing a {\it symmetric function} module to integrate features calculated from preceding layers, Seq-SetNet are immune to the order of sequences in the input MSA. This advantage enables us to directly and fully exploit MSAs by considering each component protein individually. We evaluated Seq-SetNet by using it to extract structural information from MSA for protein secondary structure prediction. Experimental results on popular benchmark sets suggests that Seq-SetNet outperforms the state-of-the-art approaches by 3.6% in precision. These results clearly suggest the advantages of Seq-SetNet in sequence set processing and it can be readily used in a wide range of fields, say natural language processing.

Discontinuous Finite Element Methods (DFEM) have been widely used for solving $S_n$ radiation transport problems in participative and non-participative media. In the DFEM $S_n$ methodology, the transport equation is discretized into a set of algebraic equations that have to be solved for each spatial cell and angular direction, strictly preserving the following of radiation in the system. At the core of a DFEM solver a small matrix-vector system (of 8 independent equations for tri-linear DFEM in 3D hexehdral cells) has to be assembled and solved for each cell, angle, energy group, and time step. These systems are generally solved by direct Gaussian Elimination. The computational cost of the Gaussian Elimination, repeated for each phase-space cell, amounts to a large fraction to the total compute time. Here, we have designed a Machine Learning algorithm based in a shallow Artificial Neural Networks (ANNs) to replace that Gaussian Elimination step, enabling a sizeable speed up in the solution process. The key idea is to train an ANN with a large set of solutions of random one-cell transport problems and then to use the trained ANN to replace Gaussian Elimination large scale transport solvers. It has been observed that ANNs decrease the solution times by at least a factor of 4, while introducing mean absolute errors between 1-3 \% in large scale transport solutions.

We propose a new objective function for finite-horizon episodic Markov decision processes that better captures Bellman's principle of optimality, and provide an expression for the gradient of the objective.

This paper proposes a discrimination technique for vertices in a weighted network. We assume that the edge weights and adjacencies in the network are conditionally independent and that both sources of information encode class membership information. In particular, we introduce a edge weight distribution matrix to the standard K-Block Stochastic Block Model to model weighted networks. This allows us to develop simple yet powerful extensions of classification techniques using the spectral embedding of the unweighted adjacency matrix. We consider two assumptions on the edge weight distributions and propose classification procedures in both settings. We show the effectiveness of the proposed classifiers by comparing them to quadratic discriminant analysis following the spectral embedding of a transformed weighted network. Moreover, we discuss and show how the methods perform when the edge weights do not encode class membership information.