Image segmentation is widely used in a variety of computer vision tasks, such as object localization and recognition, boundary detection, and medical imaging. This thesis proposes deep learning architectures to improve automatic object localization and boundary delineation for salient object segmentation in natural images and for 2D medical image segmentation. First, we propose and evaluate a novel dilated dense encoder-decoder architecture with a custom dilated spatial pyramid pooling block to accurately localize and delineate boundaries for salient object segmentation. The dilation offers better spatial understanding and the dense connectivity preserves features learned at shallower levels of the network for better localization. Tested on three publicly available datasets, our architecture outperforms the state-of-the-art for one and is very competitive on the other two. Second, we propose and evaluate a custom 2D dilated dense UNet architecture for accurate lesion localization and segmentation in medical images. This architecture can be utilized as a stand-alone segmentation framework or used as a rich feature extracting backbone to aid other models in medical image segmentation. Our architecture outperforms all baseline models for accurate lesion localization and segmentation on a new dataset. We furthermore explore the main considerations that should be taken into account for 3D medical image segmentation, among them preprocessing techniques and specialized loss functions.

Reducing traffic accidents is an important public safety challenge, therefore, accident analysis and prediction has been a topic of much research over the past few decades. Using small-scale datasets with limited coverage, being dependent on extensive set of data, and being not applicable for real-time purposes are the important shortcomings of the existing studies. To address these challenges, we propose a new solution for real-time traffic accident prediction using easy-to-obtain, but sparse data. Our solution relies on a deep-neural-network model (which we have named DAP, for Deep Accident Prediction); which utilizes a variety of data attributes such as traffic events, weather data, points-of-interest, and time. DAP incorporates multiple components including a recurrent (for time-sensitive data), a fully connected (for time-insensitive data), and a trainable embedding component (to capture spatial heterogeneity). To fill the data gap, we have - through a comprehensive process of data collection, integration, and augmentation - created a large-scale publicly available database of accident information named US-Accidents. By employing the US-Accidents dataset and through an extensive set of experiments across several large cities, we have evaluated our proposal against several baselines. Our analysis and results show significant improvements to predict rare accident events. Further, we have shown the impact of traffic information, time, and points-of-interest data for real-time accident prediction.

Multimodal datasets contain an enormous amount of relational information, which grows exponentially with the introduction of new modalities. Learning representations in such a scenario is inherently complex due to the presence of multiple heterogeneous information channels. These channels can encode both (a) inter-relations between the items of different modalities and (b) intra-relations between the items of the same modality. Encoding multimedia items into a continuous low-dimensional semantic space such that both types of relations are captured and preserved is extremely challenging, especially if the goal is a unified end-to-end learning framework. The two key challenges that need to be addressed are: 1) the framework must be able to merge complex intra and inter relations without losing any valuable information and 2) the learning model should be invariant to the addition of new and potentially very different modalities. In this paper, we propose a flexible framework which can scale to data streams from many modalities. To that end we introduce a hypergraph-based model for data representation and deploy Graph Convolutional Networks to fuse relational information within and across modalities. Our approach provides an efficient solution for distributing otherwise extremely computationally expensive or even unfeasible training processes across multiple-GPUs, without any sacrifices in accuracy. Moreover, adding new modalities to our model requires only an additional GPU unit keeping the computational time unchanged, which brings representation learning to truly multimodal datasets. We demonstrate the feasibility of our approach in the experiments on multimedia datasets featuring second, third and fourth order relations.

Question semantic similarity is a challenging and active research problem that is very useful in many NLP applications, such as detecting duplicate questions in community question answering platforms such as Quora. Arabic is considered to be an under-resourced language, has many dialects, and rich in morphology. Combined together, these challenges make identifying semantically similar questions in Arabic even more difficult. In this paper, we introduce a novel approach to tackle this problem, and test it on two benchmarks; one for Modern Standard Arabic (MSA), and another for the 24 major Arabic dialects. We are able to show that our new system outperforms state-of-the-art approaches by achieving 93% F1-score on the MSA benchmark and 82% on the dialectical one. This is achieved by utilizing contextualized word representations (ELMo embeddings) trained on a text corpus containing MSA and dialectic sentences. This in combination with a pairwise fine-grained similarity layer, helps our question-to-question similarity model to generalize predictions on different dialects while being trained only on question-to-question MSA data.

Chinese word segmentation (CWS) is a fundamental task for Chinese language understanding. Recently, neural network-based models have attained superior performance in solving the in-domain CWS task. Last year, Bidirectional Encoder Representation from Transformers (BERT), a new language representation model, has been proposed as a backbone model for many natural language tasks and redefined the corresponding performance. The excellent performance of BERT motivates us to apply it to solve the CWS task. By conducting intensive experiments in the benchmark datasets from the second International Chinese Word Segmentation Bake-off, we obtain several keen observations. BERT can slightly improve the performance even when the datasets contain the issue of labeling inconsistency. When applying sufficiently learned features, Softmax, a simpler classifier, can attain the same performance as that of a more complicated classifier, e.g., Conditional Random Field (CRF). The performance of BERT usually increases as the model size increases. The features extracted by BERT can be also applied as good candidates for other neural network models.

Supporting model interpretability for complex phenomena where annotators can legitimately disagree, such as emotion recognition, is a challenging machine learning task. In this work, we show that explicitly quantifying the uncertainty in such settings has interpretability benefits. We use a simple modification of a classical network inference using Monte Carlo dropout to give measures of epistemic and aleatoric uncertainty. We identify a significant correlation between aleatoric uncertainty and human annotator disagreement ($r\approx.3$). Additionally, we demonstrate how difficult and subjective training samples can be identified using aleatoric uncertainty and how epistemic uncertainty can reveal data bias that could result in unfair predictions. We identify the total uncertainty as a suitable surrogate for model calibration, i.e. the degree we can trust model's predicted confidence. In addition to explainability benefits, we observe modest performance boosts from incorporating model uncertainty.

Are two sets of observations drawn from the same distribution? This problem is a two-sample test. Kernel methods lead to many appealing properties. Indeed state-of-the-art approaches use the $L^2$ distance between kernel-based distribution representatives to derive their test statistics. Here, we show that $L^p$ distances (with $p\geq 1$) between these distribution representatives give metrics on the space of distributions that are well-behaved to detect differences between distributions as they metrize the weak convergence. Moreover, for analytic kernels, we show that the $L^1$ geometry gives improved testing power for scalable computational procedures. Specifically, we derive a finite dimensional approximation of the metric given as the $\ell_1$ norm of a vector which captures differences of expectations of analytic functions evaluated at spatial locations or frequencies (i.e, features). The features can be chosen to maximize the differences of the distributions and give interpretable indications of how they differs. Using an $\ell_1$ norm gives better detection because differences between representatives are dense as we use analytic kernels (non-zero almost everywhere). The tests are consistent, while much faster than state-of-the-art quadratic-time kernel-based tests. Experiments on artificial and real-world problems demonstrate improved power/time tradeoff than the state of the art, based on $\ell_2$ norms, and in some cases, better outright power than even the most expensive quadratic-time tests.

Information in electronic health records (EHR), such as clinical narratives, examination reports, lab measurements, demographics, and other patient encounter entries, can be transformed into appropriate data representations that can be used for downstream clinical machine learning tasks using representation learning. Learning better representations is critical to improve the performance of downstream tasks. Due to the advances in machine learning, we now can learn better and meaningful representations from EHR through disentangling the underlying factors inside data and distilling large amounts of information and knowledge from heterogeneous EHR sources. In this chapter, we first introduce the background of learning representations and reasons why we need good EHR representations in machine learning for medicine and healthcare in Section 1. Next, we explain the commonly-used machine learning and evaluation methods for representation learning using a deep learning approach in Section 2. Following that, we review recent related studies of learning patient state representation from EHR for clinical machine learning tasks in Section 3. Finally, in Section 4 we discuss more techniques, studies, and challenges for learning natural language representations when free texts, such as clinical notes, examination reports, or biomedical literature are used. W e also discuss challenges and opportunities in these rapidly growing research fields.

In this chapter, we provide a brief overview of applying machine learning techniques for clinical prediction tasks. We begin with a quick introduction to the concepts of machine learning and outline some of the most common machine learning algorithms. Next, we demonstrate how to apply the algorithms with appropriate toolkits to conduct machine learning experiments for clinical prediction tasks. The objectives of this chapter are to (1) understand the basics of machine learning techniques and the reasons behind why they are useful for solving clinical prediction problems, (2) understand the intuition behind some machine learning models, including regression, decision trees, and support vector machines, and (3) understand how to apply these models to clinical prediction problems using publicly available datasets via case studies.

InterpretML is an open-source Python package which exposes machine learning interpretability algorithms to practitioners and researchers. InterpretML exposes two types of interpretability - glassbox models, which are machine learning models designed for interpretability (ex: linear models, rule lists, generalized additive models), and blackbox explainability techniques for explaining existing systems (ex: Partial Dependence, LIME). The package enables practitioners to easily compare interpretability algorithms by exposing multiple methods under a unified API, and by having a built-in, extensible visualization platform. InterpretML also includes the first implementation of the Explainable Boosting Machine, a powerful, interpretable, glassbox model that can be as accurate as many blackbox models. The MIT licensed source code can be downloaded from github.com/microsoft/interpret.