Non-coding RNA (ncRNA) are RNA sequences which don't code for a gene but instead carry important biological functions. The task of ncRNA classification consists in classifying a given ncRNA sequence into its family. While it has been shown that the graph structure of an ncRNA sequence folding is of great importance for the prediction of its family, current methods make use of machine learning classifiers on hand-crafted graph features. We improve on the state-of-the-art for this task with a graph convolutional network model which achieves an accuracy of 85.73% and an F1-score of 85.61% over 13 classes. Moreover, our model learns in an end-to-end fashion from the raw RNA graphs and removes the need for expensive feature extraction. To the best of our knowledge, this also represents the first successful application of graph convolutional networks to RNA folding data.

Stochastic multi-armed bandits form a class of online learning problems that have important applications in online recommendation systems, adaptive medical treatment, and many others. Even though potential attacks against these learning algorithms may hijack their behavior, causing catastrophic loss in real-world applications, little is known about adversarial attacks on bandit algorithms. In this paper, we propose a framework of offline attacks on bandit algorithms and study convex optimization based attacks on several popular bandit algorithms. We show that the attacker can force the bandit algorithm to pull a target arm with high probability by a slight manipulation of the rewards in the data. Then we study a form of online attacks on bandit algorithms and propose an adaptive attack strategy against any bandit algorithm without the knowledge of the bandit algorithm. Our adaptive attack strategy can hijack the behavior of the bandit algorithm to suffer a linear regret with only a logarithmic cost to the attacker. Our results demonstrate a significant security threat to stochastic bandits.

Purpose: Arterial Spin Labeling (ASL) is a quantitative, non-invasive alternative to perfusion imaging with contrast agents. Fixing values of certain model parameters in traditional ASL, which actually vary from region to region, may introduce bias in perfusion estimates. Adopting Magnetic Resonance Fingerprinting (MRF) for ASL is an alternative where these parameters are estimated alongside perfusion, but multiparametric estimation can degrade precision. We aim to improve the sensitivity of ASL-MRF signals to underlying parameters to counter this problem, and provide precise estimates. We also propose a regression based estimation framework for MRF-ASL. Methods: To improve the sensitivity of MRF-ASL signals to underlying parameters, we optimize ASL labeling durations using the Cramer-Rao Lower Bound (CRLB). This paper also proposes a neural network regression based estimation framework trained using noisy synthetic signals generated from our ASL signal model. Results: We test our methods in silico and in vivo, and compare with multiple post labeling delay (multi-PLD) ASL and unoptimized MRF-ASL. We present comparisons of estimated maps for six parameters accounted for in our signal model. Conclusions: The scan design process facilitates precise estimates of multiple hemodynamic parameters and tissue properties from a single scan, in regions of gray and white matter, as well as regions with anomalous perfusion activity in the brain. The regression based estimation approach provides perfusion estimates rapidly, and bypasses problems with quantization error. Keywords: Arterial Spin Labeling, Magnetic Resonance Fingerprinting, Optimization, Cramer-Rao Bound, Scan Design, Regression, Neural Networks, Deep Learning, Precision, Estimation, Brain Hemodynamics.

Humans achieve efficient learning by relying on prior knowledge about the structure of naturally occurring tasks. There has been considerable interest in designing reinforcement learning algorithms with similar properties. This includes several proposals to learn the learning algorithm itself, an idea also referred to as meta learning. One formal interpretation of this idea is in terms of a partially observable multi-task reinforcement learning problem in which information about the task is hidden from the agent. Although agents that solve partially observable environments can be trained from rewards alone, shaping an agent's memory with additional supervision has been shown to boost learning efficiency. It is thus natural to ask what kind of supervision, if any, facilitates meta-learning. Here we explore several choices and develop an architecture that separates learning of the belief about the unknown task from learning of the policy, and that can be used effectively with privileged information about the task during training. We show that this approach can be very effective at solving standard meta-RL environments, as well as a complex continuous control environment in which a simulated robot has to execute various movement sequences.

Taxi demand prediction has recently attracted increasing research interest due to its huge potential application in large-scale intelligent transportation systems. However, most of the previous methods only considered the taxi demand prediction in origin regions, but neglected the modeling of the specific situation of the destination passengers. We believe it is suboptimal to preallocate the taxi into each region based solely on the taxi origin demand. In this paper, we present a challenging and worth-exploring task, called taxi origin-destination demand prediction, which aims at predicting the taxi demand between all region pairs in a future time interval. Its main challenges come from how to effectively capture the diverse contextual information to learn the demand patterns. We address this problem with a novel Contextualized Spatial-Temporal Network (CSTN), which consists of three components for the modeling of local spatial context (LSC), temporal evolution context (TEC) and global correlation context (GCC) respectively. Firstly, an LSC module utilizes two convolution neural networks to learn the local spatial dependencies of taxi demand respectively from the origin view and the destination view. Secondly, a TEC module incorporates both the local spatial features of taxi demand and the meteorological information to a Convolutional Long Short-term Memory Network (ConvLSTM) for the analysis of taxi demand evolution. Finally, a GCC module is applied to model the correlation between all regions by computing a global correlation feature as a weighted sum of all regional features, with the weights being calculated as the similarity between the corresponding region pairs. Extensive experiments and evaluations on a large-scale dataset well demonstrate the superiority of our CSTN over other compared methods for taxi origin-destination demand prediction.

Bayesian neural network (BNN) priors are defined in parameter space, making it hard to encode prior knowledge expressed in function space. We formulate a prior that incorporates functional constraints about what the output can or cannot be in regions of the input space. Output-Constrained BNNs (OC-BNN) represent an interpretable approach of enforcing a range of constraints, fully consistent with the Bayesian framework and amenable to black-box inference. We demonstrate how OC-BNNs improve model robustness and prevent the prediction of infeasible outputs in two real-world applications of healthcare and robotics.

Model-free reinforcement learning based methods such as Proximal Policy Optimization, or Q-learning typically require thousands of interactions with the environment to approximate the optimum controller which may not always be feasible in robotics due to safety and time consumption. Model-based methods such as PILCO or BlackDrops, while data-efficient, provide solutions with limited robustness and complexity. To address this tradeoff, we introduce active uncertainty reduction-based virtual environments, which are formed through limited trials conducted in the original environment. We provide an efficient method for uncertainty management, which is used as a metric for self-improvement by identification of the points with maximum expected improvement through adaptive sampling. Capturing the uncertainty also allows for better mimicking of the reward responses of the original system. Our approach enables the use of complex policy structures and reward functions through a unique combination of model-based and model-free methods, while still retaining the data efficiency. We demonstrate the validity of our method on several classic reinforcement learning problems in OpenAI gym. We prove that our approach offers a better modeling capacity for complex system dynamics as compared to established methods.

Motivated by the study of $Q$-learning algorithms in reinforcement learning, we study a class of stochastic approximation procedures based on operators that satisfy monotonicity and quasi-contractivity conditions with respect to an underlying cone. We prove a general sandwich relation on the iterate error at each time, and use it to derive non-asymptotic bounds on the error in terms of a cone-induced gauge norm. These results are derived within a deterministic framework, requiring no assumptions on the noise. We illustrate these general bounds in application to synchronous $Q$-learning for discounted Markov decision processes with discrete state-action spaces, in particular by deriving non-asymptotic bounds on the $\ell_\infty$-norm for a range of stepsizes. These results are the sharpest known to date, and we show via simulation that the dependence of our bounds cannot be improved in a worst-case sense. These results show that relative to a model-based $Q$-iteration, the $\ell_\infty$-based sample complexity of $Q$-learning is suboptimal in terms of the discount factor $\gamma$.

Signed graphs encode positive (attractive) and negative (repulsive) relations between nodes. We extend spectral clustering to signed graphs via the one-parameter family of Signed Power Mean Laplacians, defined as the matrix power mean of normalized standard and signless Laplacians of positive and negative edges. We provide a thorough analysis of the proposed approach in the setting of a general Stochastic Block Model that includes models such as the Labeled Stochastic Block Model and the Censored Block Model. We show that in expectation the signed power mean Laplacian captures the ground truth clusters under reasonable settings where state-of-the-art approaches fail. Moreover, we prove that the eigenvalues and eigenvector of the signed power mean Laplacian concentrate around their expectation under reasonable conditions in the general Stochastic Block Model. Extensive experiments on random graphs and real world datasets confirm the theoretically predicted behaviour of the signed power mean Laplacian and show that it compares favourably with state-of-the-art methods.

This paper studies semi-supervised object classification in relational data, which is a fundamental problem in relational data modeling. The problem has been extensively studied in the literature of both statistical relational learning (e.g. relational Markov networks) and graph neural networks (e.g. graph convolutional networks). Statistical relational learning methods can effectively model the dependency of object labels through conditional random fields for collective classification, whereas graph neural networks learn effective object representations for classification through end-to-end training. In this paper, we propose the Graph Markov Neural Network (GMNN) that combines the advantages of both worlds. A GMNN models the joint distribution of object labels with a conditional random field, which can be effectively trained with the variational EM algorithm. In the E-step, one graph neural network learns effective object representations for approximating the posterior distributions of object labels. In the M-step, another graph neural network is used to model the local label dependency. Experiments on object classification, link classification, and unsupervised node representation learning show that GMNN achieves state-of-the-art results.