Automatic understanding of domain specific texts in order to extract useful relationships for later use is a non-trivial task. One such relationship would be between railroad accidents' causes and their correspondent descriptions in reports. From 2001 to 2016 rail accidents in the U.S. cost more than $4.6B. Railroads involved in accidents are required to submit an accident report to the Federal Railroad Administration (FRA). These reports contain a variety of fixed field entries including primary cause of the accidents (a coded variable with 389 values) as well as a narrative field which is a short text description of the accident. Although these narratives provide more information than a fixed field entry, the terminologies used in these reports are not easy to understand by a non-expert reader. Therefore, providing an assisting method to fill in the primary cause from such domain specific texts(narratives) would help to label the accidents with more accuracy. Another important question for transportation safety is whether the reported accident cause is consistent with narrative description. To address these questions, we applied deep learning methods together with powerful word embeddings such as Word2Vec and GloVe to classify accident cause values for the primary cause field using the text in the narratives. The results show that such approaches can both accurately classify accident causes based on report narratives and find important inconsistencies in accident reporting.

The UCR Time Series Archive - introduced in 2002, has become an important resource in the time series data mining community, with at least one thousand published papers making use of at least one dataset from the archive. The original incarnation of the archive had sixteen datasets but since that time, it has gone through periodic expansions. The last expansion took place in the summer of 2015 when the archive grew from 45 datasets to 85 datasets. This paper introduces and will focus on the new data expansion from 85 to 128 datasets. Beyond expanding this valuable resource, this paper offers pragmatic advice to anyone who may wish to evaluate a new algorithm on the archive. Finally, this paper makes a novel and yet actionable claim: of the hundreds of papers that show an improvement over the standard baseline (1-Nearest Neighbor classification), a large fraction may be misattributing the reasons for their improvement. Moreover, they may have been able to achieve the same improvement with a much simpler modification, requiring just a single line of code.

This research tested the following well known strategies to deal with binary imbalanced data on 82 different real life data sets (sampled to imbalance rates of 5%, 3%, 1%, and 0.1%): class weight, SMOTE, Underbagging, and a baseline (just the base classifier). As base classifiers we used SVM with RBF kernel, random forests, and gradient boosting machines and we measured the quality of the resulting classifier using 6 different metrics (Area under the curve, Accuracy, F-measure, G-mean, Matthew's correlation coefficient and Balanced accuracy). The best strategy strongly depends on the metric used to measure the quality of the classifier. For AUC and accuracy class weight and the baseline perform better; for F-measure and MCC, SMOTE performs better; and for G-mean and balanced accuracy, underbagging.

Advances in supervised learning have enabled accurate prediction in biological systems governed by complex interactions among biomolecules. However, state-of-the-art predictive algorithms are typically black-boxes, learning statistical interactions that are difficult to translate into testable hypotheses. The iterative Random Forest algorithm took a step towards bridging this gap by providing a computationally tractable procedure to identify the stable, high-order feature interactions that drive the predictive accuracy of Random Forests (RF). Here we refine the interactions identified by iRF to explicitly map responses as a function of interacting features. Our method, signed iRF, describes subsets of rules that frequently occur on RF decision paths. We refer to these rule subsets as signed interactions. Signed interactions share not only the same set of interacting features but also exhibit similar thresholding behavior, and thus describe a consistent functional relationship between interacting features and responses. We describe stable and predictive importance metrics to rank signed interactions. For each SPIM, we define null importance metrics that characterize its expected behavior under known structure. We evaluate our proposed approach in biologically inspired simulations and two case studies: predicting enhancer activity and spatial gene expression patterns. In the case of enhancer activity, s-iRF recovers one of the few experimentally validated high-order interactions and suggests novel enhancer elements where this interaction may be active. In the case of spatial gene expression patterns, s-iRF recovers all 11 reported links in the gap gene network. By refining the process of interaction recovery, our approach has the potential to guide mechanistic inquiry into systems whose scale and complexity is beyond human comprehension.

This paper studies the problem of domain division problem which aims to segment instances drawn from different probabilistic distributions. Such a problem exists in many previous recognition tasks, such as Open Set Learning (OSL) and Generalized Zero-Shot Learning (G-ZSL), where the testing instances come from either seen or novel/unseen classes with different probabilistic distributions. Previous works only calibrate the confident prediction of classifiers of seen classes (W-SVM Scheirer et al. (2014)), or taking unseen classes as outliers Socher et al. (2013). In contrast, this paper proposes a probabilistic way of directly estimating and fine-tuning the decision boundary between seen and novel/unseen classes. In particular, we propose a domain division algorithm of learning to split the testing instances into known, unknown and uncertain domains, and then conduct recognition tasks in each domain. Two statistical tools, namely, bootstrapping and Kolmogorov-Smirnov (KS) Test, for the first time, are introduced to uncover and fine-tune the decision boundary of each domain. Critically, the uncertain domain is newly introduced in our framework to adopt those instances whose domain labels cannot be predicted confidently. Extensive experiments demonstrate that our approach achieved the state-of-the-art performance on OSL and G-ZSL benchmarks.

We observe a rapid increase in machine learning models for learning data representations that remove the semantics of protected characteristics, and are therefore able to mitigate unfair prediction outcomes. This is indeed a positive proliferation. All available models however learn latent embeddings, therefore the produced representations do not have the semantic meaning of the input. Our aim here is to learn fair representations that are directly interpretable in the original input domain. We cast this problem as a data-to-data translation; to learn a mapping from data in a source domain to a target domain such that data in the target domain enforces fairness definitions, such as statistical parity or equality of opportunity. Unavailability of fair data in the target domain is the crux of the problem. This paper provides the first approach to learn a highly unconstrained mapping from source to target by maximizing (conditional) dependence of residuals - the difference between data and its translated version - and protected characteristics. The usage of residual statistics ensures that our generated fair data should only be an adjustment of the input data, and this adjustment should reveal the main difference between protected characteristic groups. When applied to CelebA face image dataset with gender as protected characteristic, our model enforces equality of opportunity by adjusting eyes and lips regions. In Adult income dataset, also with gender as protected characteristic, our model achieves equality of opportunity by, among others, obfuscating wife and husband relationship. Visualizing those systematic changes will allow us to scrutinize the interplay of fairness criterion, chosen protected characteristics, and the prediction performance.

Unsupervised ensemble learning has long been an interesting yet challenging problem that comes to prominence in recent years with the increasing demand of crowdsourcing in various applications. In this paper, we propose a novel method-- unsupervised ensemble learning via Ising model approximation (unElisa) that combines a pruning step with a predicting step. We focus on the binary case and use an Ising model to characterize interactions between the ensemble and the underlying true classifier. The presence of an edge between an observed classifier and the true classifier indicates a direct dependence whereas the absence indicates the corresponding one provides no additional information and shall be eliminated. This observation leads to the pruning step where the key is to recover the neighborhood of the true classifier. We show that it can be recovered successfully with exponentially decaying error in the high-dimensional setting by performing nodewise $\ell_1$-regularized logistic regression. The pruned ensemble allows us to get a consistent estimate of the Bayes classifier for predicting. We also propose an augmented version of majority voting by reversing all labels given by a subgroup of the pruned ensemble. We demonstrate the efficacy of our method through extensive numerical experiments and through the application to EHR-based phenotyping prediction on Rheumatoid Arthritis (RA) using data from Partners Healthcare System.

Use of medical data, also known as electronic health records, in research helps develop and advance medical science. However, protecting patient confidentiality and identity while using medical data for analysis is crucial. Medical data can be in the form of tabular structures (i.e. tables), free-form narratives, and images. This study focuses on medical data in the free form longitudinal text. De-identification of electronic health records provides the opportunity to use such data for research without it affecting patient privacy, and avoids the need for individual patient consent. In recent years there is increasing interest in developing an accurate, robust and adaptable automatic de-identification system for electronic health records. This is mainly due to the dilemma between the availability of an abundance of health data, and the inability to use such data in research due to legal and ethical restrictions. De-identification tracks in competitions such as the 2014 i2b2 UTHealth and the 2016 CEGS N-GRID shared tasks have provided a great platform to advance this area. The primary reasons for this include the open source nature of the dataset and the fact that raw psychiatric data were used for 2016 competitions. This study focuses on noticeable trend changes in the techniques used in the development of automatic de-identification for longitudinal clinical narratives. More specifically, the shift from using conditional random fields (CRF) based systems only or rules (regular expressions, dictionary or combinations) based systems only, to hybrid models (combining CRF and rules), and more recently to deep learning based systems. We review the literature and results that arose from the 2014 and the 2016 competitions and discuss the outcomes of these systems. We also provide a list of research questions that emerged from this survey.

A 2009 study of 102 breast cancer patients at two Boston health centers found that one in four were affected by the "process of care" failures such as inadequate physical examinations and incomplete diagnostic tests. That's one of the reasons that of the half a million deaths worldwide caused by breast cancer, an estimated 90 percent are the result of metastasis. But researchers at the Naval Medical Center San Diego and Google AI, a division within Google dedicated to artificial intelligence (AI) research, have developed a promising solution employing cancer-detecting algorithms that autonomously evaluate lymph node biopsies. Their AI system -- dubbed Lymph Node Assistant, or LYNA -- is described in a paper titled "Artificial Intelligence-Based Breast Cancer Nodal Metastasis Detection," published in The American Journal of Surgical Pathology. In tests, it achieved an area under the receiver operating characteristic (AUC) -- a measure of detection accuracy -- of 99 percent.

In this paper, a novel circular and structural operator tracker (CSOT) is proposed for high performance visual tracking, it not only possesses the powerful discriminative capability of SOSVM but also efficiently inherits the superior computational efficiency of DCF. Based on the proposed circular and structural operators, a set of primal confidence score maps can be obtained by circular correlating feature maps with their corresponding structural correlation filters. Furthermore, an implicit interpolation is applied to convert the multi-resolution feature maps to the continuous domain and make all primal confidence score maps have the same spatial resolution. Then, we exploit an efficient ensemble post-processor based on relative entropy, which can coalesce primal confidence score maps and create an optimal confidence score map for more accurate localization. The target is localized on the peak of the optimal confidence score map. Besides, we introduce a collaborative optimization strategy to update circular and structural operators by iteratively training structural correlation filters, which significantly reduces computational complexity and improves robustness. Experimental results demonstrate that our approach achieves state-of-the-art performance in mean AUC scores of 71.5% and 69.4% on the OTB-2013 and OTB-2015 benchmarks respectively, and obtains a third-best expected average overlap (EAO) score of 29.8% on the VOT-2017 benchmark.