Humans have a remarkable capacity to understand the physical dynamics of objects in their environment, flexibly capturing complex structures and interactions at multiple levels of detail. Inspired by this ability, we propose a hierarchical particle-based object representation that covers a wide variety of types of three-dimensional objects, including both arbitrary rigid geometrical shapes and deformable materials. We then describe the Hierarchical Relation Network (HRN), an end-to-end differentiable neural network based on hierarchical graph convolution, that learns to predict physical dynamics in this representation. Compared to other neural network baselines, the HRN accurately handles complex collisions and nonrigid deformations, generating plausible dynamics predictions at long time scales in novel settings, and scaling to large scene configurations. These results demonstrate an architecture with the potential to form the basis of next-generation physics predictors for use in computer vision, robotics, and quantitative cognitive science.

We consider the optimization of an uncertain objective over continuous and multi-dimensional decision spaces in problems in which we are only provided with observational data. We propose a novel algorithmic framework that is tractable, asymptotically consistent, and superior to comparable methods on example problems. Our approach leverages predictive machine learning methods and incorporates information on the uncertainty of the predicted outcomes for the purpose of prescribing decisions. We demonstrate the efficacy of our method on examples involving both synthetic and real data sets.

We analyze stochastic gradient algorithms for optimizing nonconvex, nonsmooth finite-sum problems. In particular, the objective function is given by the summation of a differentiable (possibly nonconvex) component, together with a possibly non-differentiable but convex component. We propose a proximal stochastic gradient algorithm based on variance reduction, called ProxSVRG+. Our main contribution lies in the analysis of ProxSVRG+. It recovers several existing convergence results and improves/generalizes them (in terms of the number of stochastic gradient oracle calls and proximal oracle calls). In particular, ProxSVRG+ generalizes the best results given by the SCSG algorithm, recently proposed by [Lei et al., NIPS'17] for the smooth nonconvex case. ProxSVRG+ is also more straightforward than SCSG and yields simpler analysis. Moreover, ProxSVRG+ outperforms the deterministic proximal gradient descent (ProxGD) for a wide range of minibatch sizes, which partially solves an open problem proposed in [Reddi et al., NIPS'16].

Variational inference is increasingly being addressed with stochastic optimization. In this setting, the gradient's variance plays a crucial role in the optimization procedure, since high variance gradients lead to poor convergence. A popular approach used to reduce gradient's variance involves the use of control variates. Despite the good results obtained, control variates developed for variational inference are typically looked at in isolation. In this paper we clarify the large number of control variates that are available by giving a systematic view of how they are derived. We also present a Bayesian risk minimization framework in which the quality of a procedure for combining control variates is quantified by its effect on optimization convergence rates, which leads to a very simple combination rule. Results show that combining a large number of control variates this way significantly improves the convergence of inference over using the typical gradient estimators or a reduced number of control variates.

The evolution of biological sequences, such as proteins or DNAs, is driven by the three basic edit operations: substitution, insertion, and deletion. Motivated by the recent progress of neural network models for biological tasks, we implement two neural network architectures that can treat such edit operations. The first proposal is the edit invariant neural networks, based on differentiable Needleman-Wunsch algorithms. The second is the use of deep CNNs with concatenations. Our analysis shows that CNNs can recognize star-free regular expressions, and that deeper CNNs can recognize more complex regular expressions including the insertion/deletion of characters. The experimental results for the protein secondary structure prediction task suggest the importance of insertion/deletion. The test accuracy on the widely-used CB513 dataset is 71.5%, which is 1.2-points better than the current best result on non-ensemble models.

Beyond local convolution networks, we explore how to harness various external human knowledge for endowing the networks with the capability of semantic global reasoning.

We propose a new type of generative model for high-dimensional data that learns a manifold geometry of the data, rather than density, and can generate points evenly along this manifold. This is in contrast to existing generative models that represent data density, and are strongly affected by noise and other artifacts of data collection. We demonstrate how this approach corrects sampling biases and artifacts, thus improves several downstream data analysis tasks, such as clustering and classification. Finally, we demonstrate that this approach is especially useful in biology where, despite the advent of single-cell technologies, rare subpopulations and gene-interaction relationships are affected by biased sampling. We show that SUGAR can generate hypothetical populations, and it is able to reveal intrinsic patterns and mutual-information relationships between genes on a single-cell RNA sequencing dataset of hematopoiesis.

We consider a multi-armed bandit game where N players compete for K arms for T turns. Each player has different expected rewards for the arms, and the instantaneous rewards are independent and identically distributed. Performance is measured using the expected sum of regrets, compared to the optimal assignment of arms to players. We assume that each player only knows her actions and the reward she received each turn. Players cannot observe the actions of other players, and no communication between players is possible. We present a distributed algorithm and prove that it achieves an expected sum of regrets of near-O\left(\log^{2}T\right). This is the first algorithm to achieve a poly-logarithmic regret in this fully distributed scenario. All other works have assumed that either all players have the same vector of expected rewards or that communication between players is possible.

Recurrent networks of spiking neurons (RSNNs) underlie the astounding computing and learning capabilities of the brain. But computing and learning capabilities of RSNN models have remained poor, at least in comparison with ANNs. We address two possible reasons for that. One is that RSNNs in the brain are not randomly connected or designed according to simple rules, and they do not start learning as a tabula rasa network. Rather, RSNNs in the brain were optimized for their tasks through evolution, development, and prior experience. Details of these optimization processes are largely unknown. But their functional contribution can be approximated through powerful optimization methods, such as backpropagation through time (BPTT). A second major mismatch between RSNNs in the brain and models is that the latter only show a small fraction of the dynamics of neurons and synapses in the brain. We include neurons in our RSNN model that reproduce one prominent dynamical process of biological neurons that takes place at the behaviourally relevant time scale of seconds: neuronal adaptation.

Gaussian processes provide a flexible framework for forecasting, removing noise, and interpreting long temporal datasets. State space modelling (Kalman filtering) enables these non-parametric models to be deployed on long datasets by reducing the complexity to linear in the number of data points. The complexity is still cubic in the state dimension m which is an impediment to practical application. In certain special cases (Gaussian likelihood, regular spacing) the GP posterior will reach a steady posterior state when the data are very long. We leverage this and formulate an inference scheme for GPs with general likelihoods, where inference is based on single-sweep EP (assumed density filtering). The infinite-horizon model tackles the cubic cost in the state dimensionality and reduces the cost in the state dimension m to O(m^2) per data point. The model is extended to online-learning of hyperparameters. We show examples for large finite-length modelling problems, and present how the method runs in real-time on a smartphone on a continuous data stream updated at 100 Hz.