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.

Finding minimum distortion of adversarial examples and thus certifying robustness in neural networks classifiers is known to be a challenging problem. Nevertheless, recently it has been shown to be possible to give a non-trivial certified lower bound of minimum distortion, and some recent progress has been made towards this direction by exploiting the piece-wise linear nature of ReLU activations. However, a generic robustness certification for \textit{general} activation functions still remains largely unexplored. To address this issue, in this paper we introduce CROWN, a general framework to certify robustness of neural networks with general activation functions. The novelty in our algorithm consists of bounding a given activation function with linear and quadratic functions, hence allowing it to tackle general activation functions including but not limited to the four popular choices: ReLU, tanh, sigmoid and arctan. In addition, we facilitate the search for a tighter certified lower bound by \textit{adaptively} selecting appropriate surrogates for each neuron activation. Experimental results show that CROWN on ReLU networks can notably improve the certified lower bounds compared to the current state-of-the-art algorithm Fast-Lin, while having comparable computational efficiency. Furthermore, CROWN also demonstrates its effectiveness and flexibility on networks with general activation functions, including tanh, sigmoid and arctan.

We propose DecaProp (Densely Connected Attention Propagation), a new densely connected neural architecture for reading comprehension (RC). There are two distinct characteristics of our model. Firstly, our model densely connects all pairwise layers of the network, modeling relationships between passage and query across all hierarchical levels. Secondly, the dense connectors in our network are learned via attention instead of standard residual skip-connectors. To this end, we propose novel Bidirectional Attention Connectors (BAC) for efficiently forging connections throughout the network. We conduct extensive experiments on four challenging RC benchmarks. Our proposed approach achieves state-of-the-art results on all four, outperforming existing baselines by up to 2.6% to 14.2% in absolute F1 score.

The variational autoencoder (VAE) is a popular model for density estimation and representation learning. Canonically, the variational principle suggests to prefer an expressive inference model so that the variational approximation is accurate. However, it is often overlooked that an overly-expressive inference model can be detrimental to the test set performance of both the amortized posterior approximator and, more importantly, the generative density estimator. In this paper, we leverage the fact that VAEs rely on amortized inference and propose techniques for amortized inference regularization (AIR) that control the smoothness of the inference model. We demonstrate that, by applying AIR, it is possible to improve VAE generalization on both inference and generative performance. Our paper challenges the belief that amortized inference is simply a mechanism for approximating maximum likelihood training and illustrates that regularization of the amortization family provides a new direction for understanding and improving generalization in VAEs.

A theoretical performance analysis of the graph neural network (GNN) is presented. For classification tasks, the neural network approach has the advantage in terms of flexibility that it can be employed in a data-driven manner, whereas Bayesian inference requires the assumption of a specific model. A fundamental question is then whether GNN has a high accuracy in addition to this flexibility. Moreover, whether the achieved performance is predominately a result of the backpropagation or the architecture itself is a matter of considerable interest. To gain a better insight into these questions, a mean-field theory of a minimal GNN architecture is developed for the graph partitioning problem. This demonstrates a good agreement with numerical experiments.

Compressing neural networks by pruning weights with small magnitudes can significantly reduce the computation and storage cost. Although pruning makes the model smaller, it is difficult to get practical speedup in modern computing platforms such as CPU and GPU due to the irregularity. Structural pruning has attract a lot of research interest to make sparsity hardware-friendly. Increasing the sparsity granularity can lead to better hardware utilization, but it will compromise the sparsity for maintaining accuracy. In this work, we propose a novel method, TETRIS, to achieve both better hardware utilization and higher sparsity. Just like a tile-matching game, we cluster the irregularly distributed weights with small value into structured groups by reordering the input/output dimension and structurally prune them. Results show that it can achieve comparable sparsity with the irregular element-wise pruning and demonstrate negligible accuracy loss. The experiments also shows ideal speedup, which is proportional to the sparsity, on GPU platforms. Our proposed method provides a new solution toward algorithm and architecture co-optimization for accuracy-efficiency trade-off.

Boltzmann machines (BMs) are appealing candidates for powerful priors in variational autoencoders (VAEs), as they are capable of capturing nontrivial and multi-modal distributions over discrete variables. However, non-differentiability of the discrete units prohibits using the reparameterization trick, essential for low-noise back propagation. The Gumbel trick resolves this problem in a consistent way by relaxing the variables and distributions, but it is incompatible with BM priors. Here, we propose the GumBolt, a model that extends the Gumbel trick to BM priors in VAEs. GumBolt is significantly simpler than the recently proposed methods with BM prior and outperforms them by a considerable margin. It achieves state-of-the-art performance on permutation invariant MNIST and OMNIGLOT datasets in the scope of models with only discrete latent variables. Moreover, the performance can be further improved by allowing multi-sampled (importance-weighted) estimation of log-likelihood in training, which was not possible with previous models.

Deep neural networks, and in particular recurrent networks, are promising candidates to control autonomous agents that interact in real-time with the physical world. However, this requires a seamless integration of temporal features into the network’s architecture. For the training of and inference with recurrent neural networks, they are usually rolled out over time, and different rollouts exist. Conventionally during inference, the layers of a network are computed in a sequential manner resulting in sparse temporal integration of information and long response times. In this study, we present a theoretical framework to describe rollouts, the level of model-parallelization they induce, and demonstrate differences in solving specific tasks. We prove that certain rollouts, also for networks with only skip and no recurrent connections, enable earlier and more frequent responses, and show empirically that these early responses have better performance. The streaming rollout maximizes these properties and enables a fully parallel execution of the network reducing runtime on massively parallel devices. Finally, we provide an open-source toolbox to design, train, evaluate, and interact with streaming rollouts.

We propose a method for learning landmark detectors for visual objects (such as the eyes and the nose in a face) without any manual supervision. We cast this as the problem of generating images that combine the appearance of the object as seen in a first example image with the geometry of the object as seen in a second example image, where the two examples differ by a viewpoint change and/or an object deformation. In order to factorize appearance and geometry, we introduce a tight bottleneck in the geometry-extraction process that selects and distils geometry-related features. Compared to standard image generation problems, which often use generative adversarial networks, our generation task is conditioned on both appearance and geometry and thus is significantly less ambiguous, to the point that adopting a simple perceptual loss formulation is sufficient. We demonstrate that our approach can learn object landmarks from synthetic image deformations or videos, all without manual supervision, while outperforming state-of-the-art unsupervised landmark detectors. We further show that our method is applicable to a large variety of datasets - faces, people, 3D objects, and digits - without any modifications.

Machine learning models are vulnerable to adversarial examples: small changes to images can cause computer vision models to make mistakes such as identifying a school bus as an ostrich. However, it is still an open question whether humans are prone to similar mistakes. Here, we address this question by leveraging recent techniques that transfer adversarial examples from computer vision models with known parameters and architecture to other models with unknown parameters and architecture, and by matching the initial processing of the human visual system. We find that adversarial examples that strongly transfer across computer vision models influence the classifications made by time-limited human observers.