ICLR 2019 Papers

Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for understanding function. Existing approaches for detecting structural similarity between proteins from sequence are unable to recognize and exploit structural patterns when sequences have diverged too far, limiting our ability to transfer knowledge between structurally related proteins. We newly approach this problem through the lens of representation learning. We introduce a framework that maps any protein sequence to a sequence of vector embeddings --- one per amino acid position --- that encode structural information. We train bidirectional long short-term memory (LSTM) models on protein sequences with a two-part feedback mechanism that incorporates information from (i) global structural similarity between proteins and (ii) pairwise residue contact maps for individual proteins. To enable learning from structural similarity information, we define a novel similarity measure between arbitrary-length sequences of vector embeddings based on a soft symmetric alignment (SSA) between them. Our method is able to learn useful position-specific embeddings despite lacking direct observations of position-level correspondence between sequences. We show empirically that our multi-task framework outperforms other sequence-based methods and even a top-performing structure-based alignment method when predicting structural similarity, our goal. Finally, we demonstrate that our learned embeddings can be transferred to other protein sequence problems, improving the state-of-the-art in transmembrane domain prediction.

Most deep learning models rely on expressive high-dimensional representations to achieve good performance on tasks such as classification. However, the high dimensionality of these representations makes them difficult to interpret and prone to over-fitting. We propose a simple, intuitive and scalable dimension reduction framework that takes into account the soft probabilistic interpretation of standard deep models for classification. When applying our framework to visualization, our representations more accurately reflect inter-class distances than standard visualization techniques such as t-SNE. We show experimentally that our framework improves generalization performance to unseen categories in zero-shot learning. We also provide a finite sample error upper bound guarantee for the method.

By injecting adversarial examples into training data, adversarial training is promising for improving the robustness of deep learning models. However, most existing adversarial training approaches are based on a specific type of adversarial attack. It may not provide sufficiently representative samples from the adversarial domain, leading to a weak generalization ability on adversarial examples from other attacks. Moreover, during the adversarial training, adversarial perturbations on inputs are usually crafted by fast single-step adversaries so as to scale to large datasets. This work is mainly focused on the adversarial training yet efficient FGSM adversary. In this scenario, it is difficult to train a model with great generalization due to the lack of representative adversarial samples, aka the samples are unable to accurately reflect the adversarial domain. To alleviate this problem, we propose a novel Adversarial Training with Domain Adaptation (ATDA) method. Our intuition is to regard the adversarial training on FGSM adversary as a domain adaption task with limited number of target domain samples. The main idea is to learn a representation that is semantically meaningful and domain invariant on the clean domain as well as the adversarial domain. Empirical evaluations on Fashion-MNIST, SVHN, CIFAR-10 and CIFAR-100 demonstrate that ATDA can greatly improve the generalization of adversarial training and the smoothness of the learned models, and outperforms state-of-the-art methods on standard benchmark datasets. To show the transfer ability of our method, we also extend ATDA to the adversarial training on iterative attacks such as PGD-Adversial Training (PAT) and the defense performance is improved considerably.

The goal of few-shot learning is to learn a classifier that generalizes well even when trained with a limited number of training instances per class. The recently introduced meta-learning approaches tackle this problem by learning a generic classifier across a large number of multiclass classification tasks and generalizing the model to a new task. Yet, even with such meta-learning, the low-data problem in the novel classification task still remains. In this paper, we propose Transductive Propagation Network (TPN), a novel meta-learning framework for transductive inference that classifies the entire test set at once to alleviate the low-data problem. Specifically, we propose to learn to propagate labels from labeled instances to unlabeled test instances, by learning a graph construction module that exploits the manifold structure in the data. TPN jointly learns both the parameters of feature embedding and the graph construction in an end-to-end manner. We validate TPN on multiple benchmark datasets, on which it largely outperforms existing few-shot learning approaches and achieves the state-of-the-art results.

Learning a deep neural network requires solving a challenging optimization problem: it is a high-dimensional, non-convex and non-smooth minimization problem with a large number of terms. The current practice in neural network optimization is to rely on the stochastic gradient descent (SGD) algorithm or its adaptive variants. However, SGD requires a hand-designed schedule for the learning rate. In addition, its adaptive variants tend to produce solutions that generalize less well on unseen data than SGD with a hand-designed schedule. We present an optimization method that offers empirically the best of both worlds: our algorithm yields good generalization performance while requiring only one hyper-parameter. Our approach is based on a composite proximal framework, which exploits the compositional nature of deep neural networks and can leverage powerful convex optimization algorithms by design. Specifically, we employ the Frank-Wolfe (FW) algorithm for SVM, which computes an optimal step-size in closed-form at each time-step. We further show that the descent direction is given by a simple backward pass in the network, yielding the same computational cost per iteration as SGD. We present experiments on the CIFAR and SNLI data sets, where we demonstrate the significant superiority of our method over Adam, Adagrad, as well as the recently proposed BPGrad and AMSGrad. Furthermore, we compare our algorithm to SGD with a hand-designed learning rate schedule, and show that it provides similar generalization while often converging faster. The code is publicly available at https://github.com/oval-group/dfw.

As people learn to navigate the world, autonomic nervous system (e.g., ``fight or flight) responses provide intrinsic feedback about the potential consequence of action choices (e.g., becoming nervous when close to a cliff edge or driving fast around a bend.) Physiological changes are correlated with these biological preparations to protect one-self from danger. We present a novel approach to reinforcement learning that leverages a task-independent intrinsic reward function trained on peripheral pulse measurements that are correlated with human autonomic nervous system responses. Our hypothesis is that such reward functions can circumvent the challenges associated with sparse and skewed rewards in reinforcement learning settings and can help improve sample efficiency. We test this in a simulated driving environment and show that it can increase the speed of learning and reduce the number of collisions during the learning stage.

Human scene perception goes beyond recognizing a collection of objects and their pairwise relations. We understand higher-level, abstract regularities within the scene such as symmetry and repetition. Current vision recognition modules and scene representations fall short in this dimension. In this paper, we present scene programs, representing a scene via a symbolic program for its objects, attributes, and their relations. We also propose a model that infers such scene programs by exploiting a hierarchical, object-based scene representation. Experiments demonstrate that our model works well on synthetic data and transfers to real images with such compositional structure. The use of scene programs has enabled a number of applications, such as complex visual analogy-making and scene extrapolation.

We investigate the properties of multidimensional probability distributions in the context of latent space prior distributions of implicit generative models. Our work revolves around the phenomena arising while decoding linear interpolations between two random latent vectors -- regions of latent space in close proximity to the origin of the space are oversampled, which restricts the usability of linear interpolations as a tool to analyse the latent space. We show that the distribution mismatch can be eliminated completely by a proper choice of the latent probability distribution or using non-linear interpolations. We prove that there is a trade off between the interpolation being linear, and the latent distribution having even the most basic properties required for stable training, such as finite mean. We use the multidimensional Cauchy distribution as an example of the prior distribution, and also provide a general method of creating non-linear interpolations, that is easily applicable to a large family of commonly used latent distributions.

Numerous past works have tackled the problem of task-driven navigation. But, how to effectively explore a new environment to enable a variety of down-stream tasks has received much less attention. In this work, we study how agents can autonomously explore realistic and complex 3D environments without the context of task-rewards. We propose a learning-based approach and investigate different policy architectures, reward functions, and training paradigms. We find that use of policies with spatial memory that are bootstrapped with imitation learning and finally finetuned with coverage rewards derived purely from on-board sensors can be effective at exploring novel environments. We show that our learned exploration policies can explore better than classical approaches based on geometry alone and generic learning-based exploration techniques. Finally, we also show how such task-agnostic exploration can be used for down-stream tasks. Videos are available at https://sites.google.com/view/exploration-for-nav/.

We develop a mean field theory for batch normalization in fully-connected feedforward neural networks. In so doing, we provide a precise characterization of signal propagation and gradient backpropagation in wide batch-normalized networks at initialization. Our theory shows that gradient signals grow exponentially in depth and that these exploding gradients cannot be eliminated by tuning the initial weight variances or by adjusting the nonlinear activation function. Indeed, batch normalization itself is the cause of gradient explosion. As a result, vanilla batch-normalized networks without skip connections are not trainable at large depths for common initialization schemes, a prediction that we verify with a variety of empirical simulations. While gradient explosion cannot be eliminated, it can be reduced by tuning the network close to the linear regime, which improves the trainability of deep batch-normalized networks without residual connections. Finally, we investigate the learning dynamics of batch-normalized networks and observe that after a single step of optimization the networks achieve a relatively stable equilibrium in which gradients have dramatically smaller dynamic range. Our theory leverages Laplace, Fourier, and Gegenbauer transforms and we derive new identities that may be of independent interest.

A growing number of learning methods are actually differentiable games whose players optimise multiple, interdependent objectives in parallel – from GANs and intrinsic curiosity to multi-agent RL. Opponent shaping is a powerful approach to improve learning dynamics in these games, accounting for player influence on others’ updates. Learning with Opponent-Learning Awareness (LOLA) is a recent algorithm that exploits this response and leads to cooperation in settings like the Iterated Prisoner’s Dilemma. Although experimentally successful, we show that LOLA agents can exhibit ‘arrogant’ behaviour directly at odds with convergence. In fact, remarkably few algorithms have theoretical guarantees applying across all (n-player, non-convex) games. In this paper we present Stable Opponent Shaping (SOS), a new method that interpolates between LOLA and a stable variant named LookAhead. We prove that LookAhead converges locally to equilibria and avoids strict saddles in all differentiable games. SOS inherits these essential guarantees, while also shaping the learning of opponents and consistently either matching or outperforming LOLA experimentally.

Recent literature suggests that averaged word vectors followed by simple post-processing outperform many deep learning methods on semantic textual similarity tasks. Furthermore, when averaged word vectors are trained supervised on large corpora of paraphrases, they achieve state-of-the-art results on standard STS benchmarks. Inspired by these insights, we push the limits of word embeddings even further. We propose a novel fuzzy bag-of-words (FBoW) representation for text that contains all the words in the vocabulary simultaneously but with different degrees of membership, which are derived from similarities between word vectors. We show that max-pooled word vectors are only a special case of fuzzy BoW and should be compared via fuzzy Jaccard index rather than cosine similarity. Finally, we propose DynaMax, a completely unsupervised and non-parametric similarity measure that dynamically extracts and max-pools good features depending on the sentence pair. This method is both efficient and easy to implement, yet outperforms current baselines on STS tasks by a large margin and is even competitive with supervised word vectors trained to directly optimise cosine similarity.

Credit assignment in Meta-reinforcement learning (Meta-RL) is still poorly understood. Existing methods either neglect credit assignment to pre-adaptation behavior or implement it naively. This leads to poor sample-efficiency during meta-training as well as ineffective task identification strategies. This paper provides a theoretical analysis of credit assignment in gradient-based Meta-RL. Building on the gained insights we develop a novel meta-learning algorithm that overcomes both the issue of poor credit assignment and previous difficulties in estimating meta-policy gradients. By controlling the statistical distance of both pre-adaptation and adapted policies during meta-policy search, the proposed algorithm endows efficient and stable meta-learning. Our approach leads to superior pre-adaptation policy behavior and consistently outperforms previous Meta-RL algorithms in sample-efficiency, wall-clock time, and asymptotic performance.

Multi-domain learning (MDL) aims at obtaining a model with minimal average risk across multiple domains. Our empirical motivation is automated microscopy data, where cultured cells are imaged after being exposed to known and unknown chemical perturbations, and each dataset displays significant experimental bias. This paper presents a multi-domain adversarial learning approach, MuLANN, to leverage multiple datasets with overlapping but distinct class sets, in a semi-supervised setting. Our contributions include: i) a bound on the average- and worst-domain risk in MDL, obtained using the H-divergence; ii) a new loss to accommodate semi-supervised multi-domain learning and domain adaptation; iii) the experimental validation of the approach, improving on the state of the art on two standard image benchmarks, and a novel bioimage dataset, Cell.

Deep learning has achieved remarkable successes in solving challenging reinforcement learning (RL) problems when dense reward function is provided. However, in sparse reward environment it still often suffers from the need to carefully shape reward function to guide policy optimization. This limits the applicability of RL in the real world since both reinforcement learning and domain-specific knowledge are required. It is therefore of great practical importance to develop algorithms which can learn from a binary signal indicating successful task completion or other unshaped, sparse reward signals. We propose a novel method called competitive experience replay, which efficiently supplements a sparse reward by placing learning in the context of an exploration competition between a pair of agents. Our method complements the recently proposed hindsight experience replay (HER) by inducing an automatic exploratory curriculum. We evaluate our approach on the tasks of reaching various goal locations in an ant maze and manipulating objects with a robotic arm. Each task provides only binary rewards indicating whether or not the goal is achieved. Our method asymmetrically augments these sparse rewards for a pair of agents each learning the same task, creating a competitive game designed to drive exploration. Extensive experiments demonstrate that this method leads to faster converge and improved task performance.

Neuronal assemblies, loosely defined as subsets of neurons with reoccurring spatio-temporally coordinated activation patterns, or "motifs", are thought to be building blocks of neural representations and information processing. We here propose LeMoNADe, a new exploratory data analysis method that facilitates hunting for motifs in calcium imaging videos, the dominant microscopic functional imaging modality in neurophysiology. Our nonparametric method extracts motifs directly from videos, bypassing the difficult intermediate step of spike extraction. Our technique augments variational autoencoders with a discrete stochastic node, and we show in detail how a differentiable reparametrization and relaxation can be used. An evaluation on simulated data, with available ground truth, reveals excellent quantitative performance. In real video data acquired from brain slices, with no ground truth available, LeMoNADe uncovers nontrivial candidate motifs that can help generate hypotheses for more focused biological investigations.

We propose Distributional Concavity (DC) regularization for Generative Adversarial Networks (GANs), a functional gradient-based method that promotes the entropy of the generator distribution and works against mode collapse. Our DC regularization is an easy-to-implement method that can be used in combination with the current state of the art methods like Spectral Normalization and Wasserstein GAN with gradient penalty to further improve the performance. We will not only show that our DC regularization can achieve highly competitive results on ILSVRC2012 and CIFAR datasets in terms of Inception score and Fr\'echet inception distance, but also provide a mathematical guarantee that our method can always increase the entropy of the generator distribution. We will also show an intimate theoretical connection between our method and the theory of optimal transport.

Training activation quantized neural networks involves minimizing a piecewise constant training loss whose gradient vanishes almost everywhere, which is undesirable for the standard back-propagation or chain rule. An empirical way around this issue is to use a straight-through estimator (STE) (Bengio et al., 2013) in the backward pass only, so that the "gradient" through the modified chain rule becomes non-trivial. Since this unusual "gradient" is certainly not the gradient of loss function, the following question arises: why searching in its negative direction minimizes the training loss? In this paper, we provide the theoretical justification of the concept of STE by answering this question. We consider the problem of learning a two-linear-layer network with binarized ReLU activation and Gaussian input data. We shall refer to the unusual "gradient" given by the STE-modifed chain rule as coarse gradient. The choice of STE is not unique. We prove that if the STE is properly chosen, the expected coarse gradient correlates positively with the population gradient (not available for the training), and its negation is a descent direction for minimizing the population loss. We further show the associated coarse gradient descent algorithm converges to a critical point of the population loss minimization problem. Moreover, we show that a poor choice of STE leads to instability of the training algorithm near certain local minima, which is verified with CIFAR-10 experiments.

In model-based reinforcement learning, the agent interleaves between model learning and planning. These two components are inextricably intertwined. If the model is not able to provide sensible long-term prediction, the executed planer would exploit model flaws, which can yield catastrophic failures. This paper focuses on building a model that reasons about the long-term future and demonstrates how to use this for efficient planning and exploration. To this end, we build a latent-variable autoregressive model by leveraging recent ideas in variational inference. We argue that forcing latent variables to carry future information through an auxiliary task substantially improves long-term predictions. Moreover, by planning in the latent space, the planner's solution is ensured to be within regions where the model is valid. An exploration strategy can be devised by searching for unlikely trajectories under the model. Our methods achieves higher reward faster compared to baselines on a variety of tasks and environments in both the imitation learning and model-based reinforcement learning settings.