A unique challenge in predictive model building for omics data has been the small number of samples (n) versus the large amount of features (p). This "n p" property brings difficulties for disease outcome classification using deep learning techniques. Sparse learning by incorporating external gene network information such as the graph-embedded deep feedforward network (GEDFN) [19] model has been a solution to this issue. However, such methods require an existing feature graph, and potential mis-specification of the feature graph can be harmful on classification and feature selection. To address this limitation and develop a robust classification model without relying on external knowledge, we propose a forest graph-embedded deep feedforward network (forgeNet) model, to integrate the GEDFN architecture with a forest feature graph extractor, so that the feature graph can be learned in a supervised manner and specifically constructed for a given prediction task. To validate the method's capability, we experimented the forgeNet model with both synthetic and real datasets. The resulting high classification accuracy suggests that the method is a valuable addition to sparse deep learning models for omics data.

Optimising discrete data for a desired characteristic using gradient-based methods involves projecting the data into a continuous latent space and carrying out optimisation in this space. Carrying out global optimisation is difficult as optimisers are likely to follow gradients into regions of the latent space that the model has not been exposed to during training; samples generated from these regions are likely to be too dissimilar to the training data to be useful. We propose Constrained Optimisation with Latent Distributions (COLD), a constrained global optimisation procedure to find samples with high values of a desired property that are similar to yet distinct from the training data. We find that on MNIST, our procedure yields optima for each of three different objectives, and that enforcing tighter constraints improves the quality and increases the diversity of the generated images. On the ChEMBL molecular dataset, our method generates a diverse set of new molecules with drug-likeness scores similar to those of the highest-scoring molecules in the training data. We also demonstrate a computationally efficient way to approximate the constraint when evaluating it exactly is computationally expensive.

A fundamental problem in Bayesian inference and statistical machine learning is to efficiently sample from multimodal distributions. Due to metastability, multimodal distributions are difficult to sample using standard Markov chain Monte Carlo methods. We propose a new sampling algorithm based on a birth-death mechanism to accelerate the mixing of Langevin diffusion. Our algorithm is motivated by its mean field partial differential equation (PDE), which is a Fokker-Planck equation supplemented by a nonlocal birth-death term. This PDE can be viewed as a gradient flow of the Kullback-Leibler divergence with respect to the Wasserstein-Fisher-Rao metric. We prove that under some assumptions the asymptotic convergence rate of the nonlocal PDE is independent of the potential barrier, in contrast to the exponential dependence in the case of the Langevin diffusion. We illustrate the efficiency of the birth-death accelerated Langevin method through several analytical examples and numerical experiments.

The optimal predictor for a linear dynamical system (with hidden state and Gaussian noise) takes the form of an autoregressive linear filter, namely the Kalman filter. However, a fundamental problem in reinforcement learning and control theory is to make optimal predictions in an unknown dynamical system. To this end, we take the approach of directly learning an autoregressive filter for time-series prediction under unknown dynamics. Our analysis differs from previous statistical analyses in that we regress not only on the inputs to the dynamical system, but also the outputs, which is essential to dealing with process noise. The main challenge is to estimate the filter under worst case input (in $\mathcal H_\infty$ norm), for which we use an $L^\infty$-based objective rather than ordinary least-squares. For learning an autoregressive model, our algorithm has optimal sample complexity in terms of the rollout length, which does not seem to be attained by naive least-squares.

Recent works have shown that stochastic gradient descent (SGD) achieves the fast convergence rates of full-batch gradient descent for over-parameterized models satisfying certain interpolation conditions. However, the step-size used in these works depends on unknown quantities, and SGD's practical performance heavily relies on the choice of the step-size. We propose to use line-search methods to automatically set the step-size when training models that can interpolate the data. We prove that SGD with the classic Armijo line-search attains the fast convergence rates of full-batch gradient descent in convex and strongly-convex settings. We also show that under additional assumptions, SGD with a modified line-search can attain a fast rate of convergence for non-convex functions. Furthermore, we show that a stochastic extra-gradient method with a Lipschitz line-search attains a fast convergence rate for an important class of non-convex functions and saddle-point problems satisfying interpolation. We then give heuristics to use larger step-sizes and acceleration with our line-search techniques. We compare the proposed algorithms against numerous optimization methods for standard classification tasks using both kernel methods and deep networks. The proposed methods are robust and result in competitive performance across all models and datasets. Moreover, for the deep network models, SGD with our line-search results in both faster convergence and better generalization.

Many machine learning problems can be framed in the context of estimating functions, and often these are time-dependent functions that are estimated in real-time as observations arrive. Gaussian processes (GPs) are an attractive choice for modeling real-valued nonlinear functions due to their flexibility and uncertainty quantification. However, the typical GP regression model suffers from several drawbacks: i) Conventional GP inference scales $O(N^{3})$ with respect to the number of observations; ii) updating a GP model sequentially is not trivial; and iii) covariance kernels often enforce stationarity constraints on the function, while GPs with non-stationary covariance kernels are often intractable to use in practice. To overcome these issues, we propose an online sequential Monte Carlo algorithm to fit mixtures of GPs that capture non-stationary behavior while allowing for fast, distributed inference. By formulating hyperparameter optimization as a multi-armed bandit problem, we accelerate mixing for real time inference. Our approach empirically improves performance over state-of-the-art methods for online GP estimation in the context of prediction for simulated non-stationary data and hospital time series data.

Generative neural network models, including Generative Adversarial Network (GAN) and Auto-Encoders (AE), are among the most popular neural network models to generate adversarial data. The GAN model is composed of a generator that produces synthetic data and of a discriminator that discriminates between the generator's output and the true data. AE consist of an encoder which maps the model distribution to a latent manifold and of a decoder which maps the latent manifold to a reconstructed distribution. However, generative models are known to provoke chaotically scattered reconstructed distribution during their training, and consequently, incomplete generated adversarial distributions. Current distance measures fail to address this problem because they are not able to acknowledge the shape of the data manifold, i.e. its topological features, and the scale at which the manifold should be analyzed. We propose Persistent Homology for Generative Models, PHom-GeM, a new methodology to assess and measure the distribution of a generative model. PHom-GeM minimizes an objective function between the true and the reconstructed distributions and uses persistent homology, the study of the topological features of a space at different spatial resolutions, to compare the nature of the true and the generated distributions. Our experiments underline the potential of persistent homology for Wasserstein GAN in comparison to Wasserstein AE and Variational AE. The experiments are conducted on a real-world data set particularly challenging for traditional distance measures and generative neural network models. PHom-GeM is the first methodology to propose a topological distance measure, the bottleneck distance, for generative models used to compare adversarial samples in the context of credit card transactions.

Power iteration has been generalized to solve many interesting problems in machine learning and statistics. Despite its striking success, theoretical understanding of when and how such an algorithm enjoys good convergence property is limited. In this work, we introduce a new class of optimization problems called scale invariant problems and prove that they can be efficiently solved by scale invariant power iteration (SCI-PI) with a generalized convergence guarantee of power iteration. By deriving that a stationary point is an eigenvector of the Hessian evaluated at the point, we show that scale invariant problems indeed resemble the leading eigenvector problem near a local optimum. Also, based on a novel reformulation, we geometrically derive SCI-PI which has a general form of power iteration. The convergence analysis shows that SCI-PI attains local linear convergence with a rate being proportional to the top two eigenvalues of the Hessian at the optimum. Moreover, we discuss some extended settings of scale invariant problems and provide similar convergence results for them. In numerical experiments, we introduce applications to independent component analysis, Gaussian mixtures, and non-negative matrix factorization. Experimental results demonstrate that SCI-PI is competitive to state-of-the-art benchmark algorithms and often yield better solutions.

Continuous queries over data streams may suffer from blocking operations and/or unbound wait, which may delay answers until some relevant input arrives through the data stream. These delays may turn answers, when they arrive, obsolete to users who sometimes have to make decisions with no help whatsoever. Therefore, it can be useful to provide hypothetical answers - "given the current information, it is possible that X will become true at time t" - instead of no information at all. In this paper we present a semantics for queries and corresponding answers that covers such hypothetical answers, together with an online algorithm for updating the set of facts that are consistent with the currently available information.

We identify a fundamental problem in policy gradient-based methods in continuous control. As policy gradient methods require the agent's underlying probability distribution, they limit policy representation to parametric distribution classes. We show that optimizing over such sets results in local movement in the action space and thus convergence to sub-optimal solutions. We suggest a novel distributional framework, able to represent arbitrary distribution functions over the continuous action space. Using this framework, we construct a generative scheme, trained using an off-policy actor-critic paradigm, which we call the Generative Actor Critic (GAC). Compared to policy gradient methods, GAC does not require knowledge of the underlying probability distribution, thereby overcoming these limitations. Empirical evaluation shows that our approach is comparable and often surpasses current state-of-the-art baselines in continuous domains.