MicroRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs) which play key roles in post-transcriptional gene regulation. Direct identification of mature miRNAs is infeasible due to their short lengths, and researchers instead aim at identifying precursor miRNAs (pre-miRNAs). Many of the known pre-miRNAs have distinctive stem-loop secondary structure, and structure-based filtering is usually the first step to predict the possibility of a given sequence being a pre-miRNA. To identify new pre-miRNAs that often have non-canonical structure, however, we need to consider additional features other than structure. To obtain such additional characteristics, existing computational methods rely on manual feature extraction, which inevitably limits the efficiency, robustness, and generalization of computational identification. To address the limitations of existing approaches, we propose a pre-miRNA identification method that incorporates (1) a deep recurrent neural network (RNN) for automated feature learning and classification, (2) multimodal architecture for seamless integration of prior knowledge (secondary structure), (3) an attention mechanism for improving long-term dependence modeling, and (4) an RNN-based class activation mapping for highlighting the learned representations that can contrast pre-miRNAs and non-pre-miRNAs. In our experiments with recent benchmarks, the proposed approach outperformed the compared state-of-the-art alternatives in terms of various performance metrics.

Policy-gradient approaches to reinforcement learning have two common and undesirable overhead procedures, namely warm-start training and sample variance reduction. In this paper, we describe a reinforcement learning method based on a softmax value function that requires neither of these procedures. Our method combines the advantages of policy-gradient methods with the efficiency and simplicity of maximum-likelihood approaches. We apply this new cold-start reinforcement learning method in training sequence generation models for structured output prediction problems. Empirical evidence validates this method on automatic summarization and image captioning tasks.

This study deals with neural networks in the sense of geometric transformations acting on the coordinate representation of the underlying data manifold which the data is sampled from. It forms part of an attempt to construct a formalized general theory of neural networks in the setting of Riemannian geometry. From this perspective, the following theoretical results are developed and proven for feedforward networks. First it is shown that residual neural networks are finite difference approximations to dynamical systems of first order differential equations, as opposed to ordinary networks that are static. This implies that the network is learning systems of differential equations governing the coordinate transformations that represent the data. Second it is shown that a closed form solution of the metric tensor on the underlying data manifold can be found by backpropagating the coordinate representations learned by the neural network itself. This is formulated in a formal abstract sense as a sequence of Lie group actions on the metric fibre space in the principal and associated bundles on the data manifold. Toy experiments were run to confirm parts of the proposed theory, as well as to provide intuitions as to how neural networks operate on data.

Data augmentation is an essential part of the training process applied to deep learning models. The motivation is that a robust training process for deep learning models depends on large annotated datasets, which are expensive to be acquired, stored and processed. Therefore a reasonable alternative is to be able to automatically generate new annotated training samples using a process known as data augmentation. The dominant data augmentation approach in the field assumes that new training samples can be obtained via random geometric or appearance transformations applied to annotated training samples, but this is a strong assumption because it is unclear if this is a reliable generative model for producing new training samples. In this paper, we provide a novel Bayesian formulation to data augmentation, where new annotated training points are treated as missing variables and generated based on the distribution learned from the training set. For learning, we introduce a theoretically sound algorithm --- generalised Monte Carlo expectation maximisation, and demonstrate one possible implementation via an extension of the Generative Adversarial Network (GAN). Classification results on MNIST, CIFAR-10 and CIFAR-100 show the better performance of our proposed method compared to the current dominant data augmentation approach mentioned above --- the results also show that our approach produces better classification results than similar GAN models.

We propose a deep learning-based approach to the problem of premise selection: selecting mathematical statements relevant for proving a given conjecture. We represent a higher-order logic formula as a graph that is invariant to variable renaming but still fully preserves syntactic and semantic information. We then embed the graph into a vector via a novel embedding method that preserves the information of edge ordering. Our approach achieves state-of-the-art results on the HolStep dataset, improving the classification accuracy from 83% to 90.3%.

Kernel machines as well as neural networks possess universal function approximation properties. Nevertheless in practice their ways of choosing the appropriate function class differ. Specifically neural networks learn a representation by adapting their basis functions to the data and the task at hand, while kernel methods typically use a basis that is not adapted during training. In this work, we contrast random features of approximated kernel machines with learned features of neural networks. Our analysis reveals how these random and adaptive basis functions affect the quality of learning. Furthermore, we present basis adaptation schemes that allow for a more compact representation, while retaining the generalization properties of kernel machines.

Multi-agent predictive modeling is an essential step for understanding physical, social and team-play systems. Recently, Interaction Networks (INs) were proposed for the task of modeling multi-agent physical systems. One of the drawbacks of INs is scaling with the number of interactions in the system (typically quadratic or higher order in the number of agents). In this paper we introduce VAIN, a novel attentional architecture for multi-agent predictive modeling that scales linearly with the number of agents. We show that VAIN is effective for multi-agent predictive modeling. Our method is evaluated on tasks from challenging multi-agent prediction domains: chess and soccer, and outperforms competing multi-agent approaches.

In this paper, we propose ELF, an Extensive, Lightweight and Flexible platform for fundamental reinforcement learning research. Using ELF, we implement a highly customizable real-time strategy (RTS) engine with three game environments (Mini-RTS, Capture the Flag and Tower Defense). Mini-RTS, as a miniature version of StarCraft, captures key game dynamics and runs at 165K frame-per-second (FPS) on a laptop. When coupled with modern reinforcement learning methods, the system can train a full-game bot against built-in AIs end-to-end in one day with 6 CPUs and 1 GPU. In addition, our platform is flexible in terms of environment-agent communication topologies, choices of RL methods, changes in game parameters, and can host existing C/C++-based game environments like ALE. Using ELF, we thoroughly explore training parameters and show that a network with Leaky ReLU and Batch Normalization coupled with long-horizon training and progressive curriculum beats the rule-based built-in AI more than 70% of the time in the full game of Mini-RTS. Strong performance is also achieved on the other two games. In game replays, we show our agents learn interesting strategies. ELF, along with its RL platform, is open-sourced at https://github.com/facebookresearch/ELF.

Neural network configurations with random weights play an important role in the analysis of deep learning. They define the initial loss landscape and are closely related to kernel and random feature methods. Despite the fact that these networks are built out of random matrices, the vast and powerful machinery of random matrix theory has so far found limited success in studying them. A main obstacle in this direction is that neural networks are nonlinear, which prevents the straightforward utilization of many of the existing mathematical results. In this work, we open the door for direct applications of random matrix theory to deep learning by demonstrating that the pointwise nonlinearities typically applied in neural networks can be incorporated into a standard method of proof in random matrix theory known as the moments method. The test case for our study is the Gram matrix $Y^TY$, $Y=f(WX)$, where $W$ is a random weight matrix, $X$ is a random data matrix, and $f$ is a pointwise nonlinear activation function. We derive an explicit representation for the trace of the resolvent of this matrix, which defines its limiting spectral distribution. We apply these results to the computation of the asymptotic performance of single-layer random feature methods on a memorization task and to the analysis of the eigenvalues of the data covariance matrix as it propagates through a neural network. As a byproduct of our analysis, we identify an intriguing new class of activation functions with favorable properties.

In large part, rodents “see” the world through their whiskers, a powerful tactile sense enabled by a series of brain areas that form the whisker-trigeminal system. Raw sensory data arrives in the form of mechanical input to the exquisitely sensitive, actively-controllable whisker array, and is processed through a sequence of neural circuits, eventually arriving in cortical regions that communicate with decision making and memory areas. Although a long history of experimental studies has characterized many aspects of these processing stages, the computational operations of the whisker-trigeminal system remain largely unknown. In the present work, we take a goal-driven deep neural network (DNN) approach to modeling these computations. First, we construct a biophysically-realistic model of the rat whisker array. We then generate a large dataset of whisker sweeps across a wide variety of 3D objects in highly-varying poses, angles, and speeds. Next, we train DNNs from several distinct architectural families to solve a shape recognition task in this dataset. Each architectural family represents a structurally-distinct hypothesis for processing in the whisker-trigeminal system, corresponding to different ways in which spatial and temporal information can be integrated. We find that most networks perform poorly on the challenging shape recognition task, but that specific architectures from several families can achieve reasonable performance levels. Finally, we show that Representational Dissimilarity Matrices (RDMs), a tool for comparing population codes between neural systems, can separate these higher performing networks with data of a type that could plausibly be collected in a neurophysiological or imaging experiment. Our results are a proof-of-concept that DNN models of the whisker-trigeminal system are potentially within reach.