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Clinicians are often very sceptical about applying automatic image processing approaches, especially deep learning based methods, in practice. One main reason for this is the black-box nature of these approaches and the inherent problem of missing insights of the automatically derived decisions. In order to increase trust in these methods, this paper presents approaches that help to interpret and explain the results of deep learning algorithms by depicting the anatomical areas which influence the decision of the algorithm most. Moreover, this research presents a unified framework, TorchEsegeta, for applying various interpretability and explainability techniques for deep learning models and generate visual interpretations and explanations for clinicians to corroborate their clinical findings. In addition, this will aid in gaining confidence in such methods. The framework builds on existing interpretability and explainability techniques that are currently focusing on classification models, extending them to segmentation tasks. In addition, these methods have been adapted to 3D models for volumetric analysis. The proposed framework provides methods to quantitatively compare visual explanations using infidelity and sensitivity metrics. This framework can be used by data scientists to perform post-hoc interpretations and explanations of their models, develop more explainable tools and present the findings to clinicians to increase their faith in such models. The proposed framework was evaluated based on a use case scenario of vessel segmentation models trained on Time-of-fight (TOF) Magnetic Resonance Angiogram (MRA) images of the human brain. Quantitative and qualitative results of a comparative study of different models and interpretability methods are presented. Furthermore, this paper provides an extensive overview of several existing interpretability and explainability methods.

Modern neural network training relies heavily on data augmentation for improved generalization. After the initial success of label-preserving augmentations, there has been a recent surge of interest in label-perturbing approaches, which combine features and labels across training samples to smooth the learned decision surface. In this paper, we propose a new augmentation method that leverages the first and second moments extracted and re-injected by feature normalization. We replace the moments of the learned features of one training image by those of another, and also interpolate the target labels. As our approach is fast, operates entirely in feature space, and mixes different signals than prior methods, one can effectively combine it with existing augmentation methods. We demonstrate its efficacy across benchmark data sets in computer vision, speech, and natural language processing, where it consistently improves the generalization performance of highly competitive baseline networks.

This review paper discusses how context has been used in neural machine translation (NMT) in the past two years (2017-2018). Starting with a brief retrospect on the rapid evolution of NMT models, the paper then reviews studies that evaluate NMT output from various perspectives, with emphasis on those analyzing limitations of the translation of contextual phenomena. In a subsequent version, the paper will then present the main methods that were proposed to leverage context for improving translation quality, and distinguishes methods that aim to improve the translation of specific phenomena from those that consider a wider unstructured context.

We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to these existing approaches, while also supporting weaker supervision scenarios. Importantly, it can be trained purely from 2D images, without ground-truth pose annotations, and with a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach on synthetic data in various settings, showing that (i) it learns to disentangle shape from pose; (ii) using shading in the loss improves performance; (iii) our model is comparable or superior to state-of-the-art voxel-based approaches on quantitative metrics, while producing results that are visually more pleasing; (iv) it still performs well when given supervision weaker than in prior works.

Matter evolved under influence of gravity from minuscule density fluctuations. Non-perturbative structure formed hierarchically over all scales, and developed non-Gaussian features in the Universe, known as the Cosmic Web. To fully understand the structure formation of the Universe is one of the holy grails of modern astrophysics. Astrophysicists survey large volumes of the Universe and employ a large ensemble of computer simulations to compare with the observed data in order to extract the full information of our own Universe. However, to evolve trillions of galaxies over billions of years even with the simplest physics is a daunting task. We build a deep neural network, the Deep Density Displacement Model (hereafter D$^3$M), to predict the non-linear structure formation of the Universe from simple linear perturbation theory. Our extensive analysis, demonstrates that D$^3$M outperforms the second order perturbation theory (hereafter 2LPT), the commonly used fast approximate simulation method, in point-wise comparison, 2-point correlation, and 3-point correlation. We also show that D$^3$M is able to accurately extrapolate far beyond its training data, and predict structure formation for significantly different cosmological parameters. Our study proves, for the first time, that deep learning is a practical and accurate alternative to approximate simulations of the gravitational structure formation of the Universe.

In multi-label text classification, each textual document can be assigned with one or more labels. Due to this nature, the multi-label text classification task is often considered to be more challenging compared to the binary or multi-class text classification problems. As an important task with broad applications in biomedicine such as assigning diagnosis codes, a number of different computational methods (e.g. training and combining binary classifiers for each label) have been proposed in recent years. However, many suffered from modest accuracy and efficiency, with only limited success in practical use. We propose ML-Net, a novel deep learning framework, for multi-label classification of biomedical texts. As an end-to-end system, ML-Net combines a label prediction network with an automated label count prediction mechanism to output an optimal set of labels by leveraging both predicted confidence score of each label and the contextual information in the target document. We evaluate ML-Net on three independent, publicly-available corpora in two kinds of text genres: biomedical literature and clinical notes. For evaluation, example-based measures such as precision, recall and f-measure are used. ML-Net is compared with several competitive machine learning baseline models. Our benchmarking results show that ML-Net compares favorably to the state-of-the-art methods in multi-label classification of biomedical texts. ML-NET is also shown to be robust when evaluated on different text genres in biomedicine. Unlike traditional machine learning methods, ML-Net does not require human efforts in feature engineering and is highly efficient and scalable approach to tasks with a large set of labels (no need to build individual classifiers for each separate label). Finally, ML-NET is able to dynamically estimate the label count based on the document context in a more systematic and accurate manner.

Deep structured models are widely used for tasks like semantic segmentation, where explicit correlations between variables provide important prior information which generally helps to reduce the data needs of deep nets. However, current deep structured models are restricted by oftentimes very local neighborhood structure, which cannot be increased for computational complexity reasons, and by the fact that the output configuration, or a representation thereof, cannot be transformed further. Very recent approaches which address those issues include graphical model inference inside deep nets so as to permit subsequent non-linear output space transformations. However, optimization of those formulations is challenging and not well understood. Here, we develop a novel model which generalizes existing approaches, such as structured prediction energy networks, and discuss a formulation which maintains applicability of existing inference techniques.

Many deep learning architectures for semantic segmentation involve a Fully Convolutional Neural Network (FCN) followed by a Conditional Random Field (CRF) to carry out inference over an image. These models typically involve unary potentials based on local appearance features computed by FCNs, and binary potentials based on the displacement between pixels. We show that while current methods succeed in segmenting whole objects, they perform poorly in situations involving a large number of object parts. We therefore suggest incorporating into the inference algorithm additional higher-order potentials inspired by the way humans identify and localize parts. We incorporate two relations that were shown to be useful to human object identification - containment and attachment - into the energy term of the CRF and evaluate their performance on the Pascal VOC Parts dataset. Our experimental results show that the segmentation of fine parts is positively affected by the addition of these two relations, and that the segmentation of fine parts can be further influenced by complex structural features.

In this paper, we propose a novel method called AlignedReID that extracts a global feature which is jointly learned with local features. Global feature learning benefits greatly from local feature learning, which performs an alignment/matching by calculating the shortest path between two sets of local features, without requiring extra supervision. After the joint learning, we only keep the global feature to compute the similarities between images. Our method achieves rank-1 accuracy of 94.4% on Market1501 and 97.8% on CUHK03, outperforming state-of-the-art methods by a large margin. We also evaluate human-level performance and demonstrate that our method is the first to surpass human-level performance on Market1501 and CUHK03, two widely used Person ReID datasets.