Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural information from it. Almost all of the existing approaches exploit MSAs in an indirect fashion, i.e., they transform MSAs into position-specific scoring matrices (PSSM) that represent the distribution of amino acid types at each column. PSSM could capture column-wise characteristics of MSA, however, the column-wise characteristics embedded in each individual component sequence were nearly totally neglected. The drawback of PSSM is rooted in the fact that an MSA is essentially an unordered sequence set rather than a matrix. Specifically, the interchange of any two sequences will not affect the whole MSA. In contrast, the pixels in an image essentially form a matrix since any two rows of pixels cannot be interchanged. Therefore, the traditional deep neural networks designed for image processing cannot be directly applied on sequence sets. Here, we proposed a novel deep neural network framework (called Seq-SetNet) for sequence set processing. By employing a {\it symmetric function} module to integrate features calculated from preceding layers, Seq-SetNet are immune to the order of sequences in the input MSA. This advantage enables us to directly and fully exploit MSAs by considering each component protein individually. We evaluated Seq-SetNet by using it to extract structural information from MSA for protein secondary structure prediction. Experimental results on popular benchmark sets suggests that Seq-SetNet outperforms the state-of-the-art approaches by 3.6% in precision. These results clearly suggest the advantages of Seq-SetNet in sequence set processing and it can be readily used in a wide range of fields, say natural language processing.

We show that the basic classification framework alone can be used to tackle some of the most challenging computer vision tasks. In contrast to other state-of-the-art approaches, the toolkit we develop is rather minimal: it uses a single, off-the-shelf classifier for all these tasks. The crux of our approach is that we train this classifier to be adversarially robust. It turns out that adversarial robustness is precisely what we need to directly manipulate salient features of the input. Overall, our findings demonstrate the utility of robustness in the broader machine learning context. Code and models for our experiments can be found at https://git.io/robust-apps.

Stochastic Volatility (SV) models are widely used in the financial sector while Long Short-Term Memory (LSTM) models have been successfully used in many large-scale industrial applications of Deep Learning. Our article combines these two methods non trivially and proposes a model for capturing the dynamics of financial volatility process, which we call the LSTM-SV model. The proposed model overcomes the short-term memory problem in conventional SV models, is able to capture non-linear dependence in the latent volatility process, and often has a better out-of-sample forecast performance than SV models. The conclusions are illustrated through simulation studies and applications to three financial time series datasets: US stock market weekly index SP500, Australian stock weekly index ASX200 and Australian-US dollar daily exchange rates. We argue that there are significant differences in the underlying dynamics between the volatility process of SP500 and ASX200 datasets and that of the exchange rate dataset. For the stock index data, there is strong evidence of long-term memory and non-linear dependence in the volatility process, while this is not the case for the exchange rates. An user-friendly software package together with the examples reported in the paper are available at https://github.com/vbayeslab.

Neural architecture search (NAS), or automated design of neural network models, remains a very challenging meta-learning problem. Several recent works (called "one-shot" approaches) have focused on dramatically reducing NAS running time by leveraging proxy models that still provide architectures with competitive performance. In our work, we propose a new meta-learning algorithm that we call CoNAS, or Compressive sensing-based Neural Architecture Search. Our approach merges ideas from one-shot approaches with iterative techniques for learning low-degree sparse Boolean polynomial functions. We validate our approach on several standard test datasets, discover novel architectures hitherto unreported, and achieve competitive (or better) results in both performance and search time compared to existing NAS approaches. Further, we support our algorithm with a theoretical analysis, providing upper bounds on the number of measurements needed to perform reliable meta-learning; to our knowledge, these analysis tools are novel to the NAS literature and may be of independent interest.

In this paper we first analyzed the inductive bias underlying the data scattered across complex free energy landscapes (FEL), and exploited it to train deep neural networks which yield reduced and clustered representation for the FEL. Our parametric method, called Information Distilling of Metastability (IDM), is end-to-end differentiable thus scalable to ultra-large dataset. IDM is also a clustering algorithm and is able to cluster the samples in the meantime of reducing the dimensions. Besides, as an unsupervised learning method, IDM differs from many existing dimensionality reduction and clustering methods in that it neither requires a cherry-picked distance metric nor the ground-true number of clusters, and that it can be used to unroll and zoom-in the hierarchical FEL with respect to different timescales. Through multiple experiments, we show that IDM can achieve physically meaningful representations which partition the FEL into well-defined metastable states hence are amenable for downstream tasks such as mechanism analysis and kinetic modeling.

Deep learning models designed for visual classification tasks on natural images have become prevalent in medical image analysis. However, medical images differ from typical natural images in many ways, such as significantly higher resolutions and smaller regions of interest. Moreover, both the global structure and local details play important roles in medical image analysis tasks. To address these unique properties of medical images, we propose a neural network that is able to classify breast cancer lesions utilizing information from both a global saliency map and multiple local patches. The proposed model outperforms the ResNet-based baseline and achieves radiologist-level performance in the interpretation of screening mammography. Although our model is trained only with image-level labels, it is able to generate pixel-level saliency maps that provide localization of possible malignant findings.

Discriminative neural networks offer little or no performance guarantees when deployed on data not generated by the same process as the training distribution. On such out-of-distribution (OOD) inputs, the prediction may not only be erroneous, but confidently so, limiting the safe deployment of classifiers in real-world applications. One such challenging application is bacteria identification based on genomic sequences, which holds the promise of early detection of diseases, but requires a model that can output low confidence predictions on OOD genomic sequences from new bacteria that were not present in the training data. We introduce a genomics dataset for OOD detection that allows other researchers to benchmark progress on this important problem. We investigate deep generative model based approaches for OOD detection and observe that the likelihood score is heavily affected by population level background statistics. We propose a likelihood ratio method for deep generative models which effectively corrects for these confounding background statistics. We benchmark the OOD detection performance of the proposed method against existing approaches on the genomics dataset and show that our method achieves state-of-the-art performance. We demonstrate the generality of the proposed method by showing that it significantly improves OOD detection when applied to deep generative models of images.

Nonstationary, anisotropic spatial processes are often used when modelling, analysing and predicting complex environmental phenomena. One such class of processes considers a stationary, isotropic process on a warped spatial domain. The warping function is generally difficult to fit and not constrained to be bijective, often resulting in 'space-folding.' Here, we propose modelling a bijective warping function through a composition of multiple elemental bijective functions in a deep-learning framework. We consider two cases; first, when these functions are known up to some weights that need to be estimated, and, second, when the weights in each layer are random. Inspired by recent methodological and technological advances in deep learning and deep Gaussian processes, we employ approximate Bayesian methods to make inference with these models using graphical processing units. Through simulation studies in one and two dimensions we show that the deep compositional spatial models are quick to fit, and are able to provide better predictions and uncertainty quantification than other deep stochastic models of similar complexity. We also show their remarkable capacity to model highly nonstationary, anisotropic spatial data using radiances from the MODIS instrument aboard the Aqua satellite.

Many important classification problems, such as object classification, speech recognition, and machine translation, have been tackled by the supervised learning paradigm in the past, where training corpora of parallel input-output pairs are required with high cost. To remove the need for the parallel training corpora has practical significance for real-world applications, and it is one of the main goals of unsupervised learning. Recently, encouraging progress in unsupervised learning for solving such classification problems has been made and the nature of the challenges has been clarified. In this article, we review this progress and disseminate a class of promising new methods to facilitate understanding the methods for machine learning researchers. In particular, we emphasize the key information that enables the success of unsupervised learning - the sequential statistics as the distributional prior in the labels. Exploitation of such sequential statistics makes it possible to estimate parameters of classifiers without the need of paired input-output data. In this paper, we first introduce the concept of Caesar Cipher and its decryption, which motivated the construction of the novel loss function for unsupervised learning we use throughout the paper. Then we use a simple but representative binary classification task as an example to derive and describe the unsupervised learning algorithm in a step-by-step, easy-to-understand fashion. We include two cases, one with Bigram language model as the sequential statistics for use in unsupervised parameter estimation, and another with a simpler Unigram language model. For both cases, detailed derivation steps for the learning algorithm are included. Further, a summary table compares computational steps of the two cases in executing the unsupervised learning algorithm for learning binary classifiers.

We address the challenge of designing optimal adversarial noise algorithms for settings where a learner has access to multiple classifiers. We demonstrate how this problem can be framed as finding strategies at equilibrium in a two-player, zero-sum game between a learner and an adversary. In doing so, we illustrate the need for randomization in adversarial attacks. In order to compute Nash equilibrium, our main technical focus is on the design of best response oracles that can then be implemented within a Multiplicative Weights Update framework to boost deterministic perturbations against a set of models into optimal mixed strategies. We demonstrate the practical effectiveness of our approach on a series of image classification tasks using both linear classifiers and deep neural networks.