Ensemble models refer to methods that combine a typically large number of classifiers into a compound prediction. The output of an ensemble method is the result of fitting a base-learning algorithm to a given data set, and obtaining diverse answers by reweighting the observations or by resampling them using a given probabilistic selection. A key challenge of using ensembles in large-scale multidimensional data lies in the complexity and the computational burden associated with them. The models created by ensembles are often difficult, if not impossible, to interpret and their implementation requires more computational power than single classifiers. Recent research effort in the field has concentrated in reducing ensemble size, while maintaining their predictive accuracy. We propose a method to prune an ensemble solution by optimizing its margin distribution, while increasing its diversity. The proposed algorithm results in an ensemble that uses only a fraction of the original classifiers, with improved or similar generalization performance. We analyze and test our method on both synthetic and real data sets. The simulations show that the proposed method compares favorably to the original ensemble solutions and to other existing ensemble pruning methodologies.

Substring kernels are classical tools for representing biological sequences or text. However, when large amounts of annotated data is available, models that allow end-to-end training such as neural networks are often prefered. Links between recurrent neural networks (RNNs) and substring kernels have recently been drawn, by formally showing that RNNs with specific activation functions were points in a reproducing kernel Hilbert space (RKHS). In this paper, we revisit this link by generalizing convolutional kernel networks---originally related to a relaxation of the mismatch kernel---to model gaps in sequences. It results in a new type of recurrent neural network which can be trained end-to-end with backpropagation, or without supervision by using kernel approximation techniques. We experimentally show that our approach is well suited to biological sequences, where it outperforms existing methods for protein classification tasks.

Probabilistic programming has emerged as a powerful paradigm in statistics, applied science, and machine learning: by decoupling modelling from inference, it promises to allow modellers to directly reason about the processes generating data. However, the performance of inference algorithms can be dramatically affected by the parameterisation used to express a model, requiring users to transform their programs in non-intuitive ways. We argue for automating these transformations, and demonstrate that mechanisms available in recent modeling frameworks can implement non-centring and related reparameterisations. This enables new inference algorithms, and we propose two: a simple approach using interleaved sampling and a novel variational formulation that searches over a continuous space of parameterisations. We show that these approaches enable robust inference across a range of models, and can yield more efficient samplers than the best fixed parameterisation.

Recent work has shown that deep generative models can assign higher likelihood to out-of-distribution data sets than to their training data. We posit that this phenomenon is caused by a mismatch between the model's typical set and its areas of high probability density. In-distribution inputs should reside in the former but not necessarily in the latter, as previous work has presumed. To determine whether or not inputs reside in the typical set, we propose a statistically principled, easy-to-implement test using the empirical distribution of model likelihoods. The test is model agnostic and widely applicable, only requiring that the likelihood can be computed or closely approximated. We report experiments showing that our procedure can successfully detect the out-of-distribution sets in several of the challenging cases reported by Nalisnick et al. (2019).

This paper introduces Task 2 of the DCASE2019 Challenge, titled "Audio tagging with noisy labels and minimal supervision". This task was hosted on the Kaggle platform as "Freesound Audio Tagging 2019". The task evaluates systems for multi-label audio tagging using a large set of noisy-labeled data, and a much smaller set of manually-labeled data, under a large vocabulary setting of 80 everyday sound classes. In addition, the proposed dataset poses an acoustic mismatch problem between the noisy train set and the test set due to the fact that they come from different web audio sources. This can correspond to a realistic scenario given by the difficulty of gathering large amounts of manually labeled data. We present the task setup, the FSDKaggle2019 dataset prepared for this scientific evaluation, and a baseline system consisting of a convolutional neural network. All these resources are freely available.

Segmentation maps of medical images annotated by medical experts contain rich spatial information. In this paper, we propose to decompose annotation maps to learn disentangled and richer feature transforms for segmentation problems in medical images. Our new scheme consists of two main stages: decompose and integrate. Decompose: by annotation map decomposition, the original segmentation problem is decomposed into multiple segmentation sub-problems; these new segmentation sub-problems are modeled by training multiple deep learning modules, each with its own set of feature transforms. Integrate: a procedure summarizes the solutions of the modules in the previous stage; a final solution is then formed for the original segmentation problem. Multiple ways of annotation map decomposition are presented and a new end-to-end trainable K-to-1 deep network framework is developed for implementing our proposed "decompose-and-integrate" learning scheme. In experiments, we demonstrate that our decompose-and-integrate segmentation scheme, utilizing state-of-the-art fully convolutional networks (e.g., DenseVoxNet in 3D and CUMedNet in 2D), improves segmentation performance on multiple 3D and 2D datasets. Ablation study confirms the effectiveness of our proposed learning scheme for medical images.

Assessing how individuals perform different activities is key information for modeling health states of individuals and populations. Descriptions of activity performance in clinical free text are complex, including syntactic negation and similarities to textual entailment tasks. We explore a variety of methods for the novel task of classifying four types of assertions about activity performance: Able, Unable, Unclear, and None (no information). We find that ensembling an SVM trained with lexical features and a CNN achieves 77.9% macro F1 score on our task, and yields nearly 80% recall on the rare Unclear and Unable samples. Finally, we highlight several challenges in classifying performance assertions, including capturing information about sources of assistance, incorporating syntactic structure and negation scope, and handling new modalities at test time. Our findings establish a strong baseline for this novel task, and identify intriguing areas for further research.

The concept of neuromuscular activity recognition using instantaneous high-density surface electromyography (HD-sEMG) images opens up new avenues for the development of more fluid and natural muscle-computer interfaces. However, the existing approaches employed a very large deep convolutional neural network (ConvNet) architecture and complex training schemes for HD-sEMG image recognition, which requires the network architecture to be pre-trained on a very large-scale labeled training dataset, as a result, it makes computationally very expensive. To overcome this problem, we propose S-ConvNet and All-ConvNet models, a simple yet efficient framework for learning instantaneous HD-sEMG images from scratch for neuromuscular activity recognition. Without using any pre-trained models, our proposed S-ConvNet and All-ConvNet demonstrate very competitive recognition accuracy to the more complex state of the art for neuromuscular activity recognition based on instantaneous HD-sEMG images, while using a ~ 12 x smaller dataset and reducing learning parameters to a large extent. The experimental results proved that the S-ConvNet and All-ConvNet are highly effective for learning discriminative features for instantaneous HD-sEMG image recognition especially in the data and high-end resource constrained scenarios.

Deep neural networks (DNNs) have achieved state-of-the-art performances in many important domains, including medical diagnosis, security, and autonomous driving. In these domains where safety is highly critical, an erroneous decision can result in serious consequences. While a perfect prediction accuracy is not always achievable, recent work on Bayesian deep networks shows that it is possible to know when DNNs are more likely to make mistakes. Knowing what DNNs do not know is desirable to increase the safety of deep learning technology in sensitive applications. Bayesian neural networks attempt to address this challenge. However, traditional approaches are computationally intractable and do not scale well to large, complex neural network architectures. In this paper, we develop a theoretical framework to approximate Bayesian inference for DNNs by imposing a Bernoulli distribution on the model weights. This method, called MC-DropConnect, gives us a tool to represent the model uncertainty with little change in the overall model structure or computational cost. We extensively validate the proposed algorithm on multiple network architectures and datasets for classification and semantic segmentation tasks. We also propose new metrics to quantify the uncertainty estimates. This enables an objective comparison between MC-DropConnect and prior approaches. Our empirical results demonstrate that the proposed framework yields significant improvement in both prediction accuracy and uncertainty estimation quality compared to the state of the art.

Parametric spatial transformation models have been successfully applied to image registration tasks. In such models, the transformation of interest is parameterized by a fixed set of basis functions as for example B-splines. Each basis function is located on a fixed regular grid position among the image domain, because the transformation of interest is not known in advance. As a consequence, not all basis functions will necessarily contribute to the final transformation which results in a non-compact representation of the transformation. We reformulate the pairwise registration problem as a recursive sequence of successive alignments. For each element in the sequence, a local deformation defined by its position, shape, and weight is computed by our recurrent registration neural network. The sum of all local deformations yield the final spatial alignment of both images. Formulating the registration problem in this way allows the network to detect non-aligned regions in the images and to learn how to locally refine the registration properly. In contrast to current non-sequence-based registration methods, our approach iteratively applies local spatial deformations to the images until the desired registration accuracy is achieved. We trained our network on 2D magnetic resonance images of the lung and compared our method to a standard parametric B-spline registration. The experiments show, that our method performs on par for the accuracy but yields a more compact representation of the transformation. Furthermore, we achieve a speedup of around 15 compared to the B-spline registration.