Research papers and code for "Stephanie Ger":
We introduce synthetic oversampling in anomaly detection for multi-feature sequence datasets based on autoencoders and generative adversarial networks. The first approach considers the use of an autoencoder in conjunction with standard oversampling methods to generate synthetic data that captures the sequential nature of the data. A different model uses generative adversarial networks to generate structure preserving synthetic data for the minority class. We also use generative adversarial networks on the majority class as an outlier detection method for novelty detection. We show that the use of generative adversarial network based synthetic data improves classification model performance on a variety of sequence data sets.

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The ability to predict the progression of biomarkers, notably in NDD, is limited by the size of the longitudinal data sets, in terms of number of patients, number of visits per patients and total follow-up time. To this end, we introduce a data augmentation technique that is able to reproduce the variability seen in a longitudinal training data set and simulate continuous biomarkers trajectories for any number of virtual patients. Thanks to this simulation framework, we propose to transform the training set into a simulated data set with more patients, more time-points per patient and longer follow-up duration. We illustrate this approach on the prediction of the MMSE of MCI subjects of the ADNI data set. We show that it allows to reach predictions with errors comparable to the noise in the data, estimated in test/retest studies, achieving a improvement of 37% of the mean absolute error compared to the same non-augmented model.

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Identifying relationships between concepts is a key aspect of scientific knowledge synthesis. Finding these links often requires a researcher to laboriously search through scien- tific papers and databases, as the size of these resources grows ever larger. In this paper we describe how distributional semantics can be used to unify structured knowledge graphs with unstructured text to predict new relationships between medical concepts, using a probabilistic generative model. Our approach is also designed to ameliorate data sparsity and scarcity issues in the medical domain, which make language modelling more challenging. Specifically, we integrate the medical relational database (SemMedDB) with text from electronic health records (EHRs) to perform knowledge graph completion. We further demonstrate the ability of our model to predict relationships between tokens not appearing in the relational database.

* 6 pages, 2 figures, to appear at SDM-DMMH 2016
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The language used in online forums differs in many ways from that of traditional language resources such as news. One difference is the use and frequency of nonliteral, subjective dialogue acts such as sarcasm. Whether the aim is to develop a theory of sarcasm in dialogue, or engineer automatic methods for reliably detecting sarcasm, a major challenge is simply the difficulty of getting enough reliably labelled examples. In this paper we describe our work on methods for achieving highly reliable sarcasm annotations from untrained annotators on Mechanical Turk. We explore the use of a number of common statistical reliability measures, such as Kappa, Karger's, Majority Class, and EM. We show that more sophisticated measures do not appear to yield better results for our data than simple measures such as assuming that the correct label is the one that a majority of Turkers apply.

* International Conference on Language Resources and Evaluation (LREC 2014)
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The predictive power of neural networks often costs model interpretability. Several techniques have been developed for explaining model outputs in terms of input features; however, it is difficult to translate such interpretations into actionable insight. Here, we propose a framework to analyze predictions in terms of the model's internal features by inspecting information flow through the network. Given a trained network and a test image, we select neurons by two metrics, both measured over a set of images created by perturbations to the input image: (1) magnitude of the correlation between the neuron activation and the network output and (2) precision of the neuron activation. We show that the former metric selects neurons that exert large influence over the network output while the latter metric selects neurons that activate on generalizable features. By comparing the sets of neurons selected by these two metrics, our framework suggests a way to investigate the internal attention mechanisms of convolutional neural networks.

* Presented at ICML 2017 Workshop on Visualization for Deep Learning
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A spoof attack, a subset of presentation attacks, is the use of an artificial replica of a biometric in an attempt to circumvent a biometric sensor. Liveness detection, or presentation attack detection, distinguishes between live and fake biometric traits and is based on the principle that additional information can be garnered above and beyond the data procured by a standard authentication system to determine if a biometric measure is authentic. The goals for the Liveness Detection (LivDet) competitions are to compare software-based fingerprint liveness detection and artifact detection algorithms (Part 1), as well as fingerprint systems which incorporate liveness detection or artifact detection capabilities (Part 2), using a standardized testing protocol and large quantities of spoof and live tests. The competitions are open to all academic and industrial institutions which have a solution for either softwarebased or system-based fingerprint liveness detection. The LivDet competitions have been hosted in 2009, 2011, 2013 and 2015 and have shown themselves to provide a crucial look at the current state of the art in liveness detection schemes. There has been a noticeable increase in the number of participants in LivDet competitions as well as a noticeable decrease in error rates across competitions. Participants have grown from four to the most recent thirteen submissions for Fingerprint Part 1. Fingerprints Part 2 has held steady at two submissions each competition in 2011 and 2013 and only one for the 2015 edition. The continuous increase of competitors demonstrates a growing interest in the topic.

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High-resolution three-dimensional (3D) cardiovascular magnetic resonance (CMR) is a valuable medical imaging technique, but its widespread application in clinical practice is hampered by long acquisition times. Here we present a novel compressed sensing (CS) reconstruction approach using shearlets as a sparsifying transform allowing for fast 3D CMR (3DShearCS). Shearlets are mathematically optimal for a simplified model of natural images and have been proven to be more efficient than classical systems such as wavelets. Data is acquired with a 3D Radial Phase Encoding (RPE) trajectory and an iterative reweighting scheme is used during image reconstruction to ensure fast convergence and high image quality. In our in-vivo cardiac MRI experiments we show that the proposed method 3DShearCS has lower relative errors and higher structural similarity compared to the other reconstruction techniques especially for high undersampling factors, i.e. short scan times. In this paper, we further show that 3DShearCS provides improved depiction of cardiac anatomy (measured by assessing the sharpness of coronary arteries) and two clinical experts qualitatively analyzed the image quality.

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In this paper, a graph-based nonlocal total variation method (NLTV) is proposed for unsupervised classification of hyperspectral images (HSI). The variational problem is solved by the primal-dual hybrid gradient (PDHG) algorithm. By squaring the labeling function and using a stable simplex clustering routine, an unsupervised clustering method with random initialization can be implemented. The effectiveness of this proposed algorithm is illustrated on both synthetic and real-world HSI, and numerical results show that the proposed algorithm outperforms other standard unsupervised clustering methods such as spherical K-means, nonnegative matrix factorization (NMF), and the graph-based Merriman-Bence-Osher (MBO) scheme.

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ScoutBot is a dialogue interface to physical and simulated robots that supports collaborative exploration of environments. The demonstration will allow users to issue unconstrained spoken language commands to ScoutBot. ScoutBot will prompt for clarification if the user's instruction needs additional input. It is trained on human-robot dialogue collected from Wizard-of-Oz experiments, where robot responses were initiated by a human wizard in previous interactions. The demonstration will show a simulated ground robot (Clearpath Jackal) in a simulated environment supported by ROS (Robot Operating System).

* Originally published in the Proceedings of the Association for Computational Linguistics (ACL) 2018, System Demonstrations, 93-98
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We describe a multi-phased Wizard-of-Oz approach to collecting human-robot dialogue in a collaborative search and navigation task. The data is being used to train an initial automated robot dialogue system to support collaborative exploration tasks. In the first phase, a wizard freely typed robot utterances to human participants. For the second phase, this data was used to design a GUI that includes buttons for the most common communications, and templates for communications with varying parameters. Comparison of the data gathered in these phases show that the GUI enabled a faster pace of dialogue while still maintaining high coverage of suitable responses, enabling more efficient targeted data collection, and improvements in natural language understanding using GUI-collected data. As a promising first step towards interactive learning, this work shows that our approach enables the collection of useful training data for navigation-based HRI tasks.

* Presented at AI-HRI AAAI-FSS, 2018 (arXiv:1809.06606)
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We describe the adaptation and refinement of a graphical user interface designed to facilitate a Wizard-of-Oz (WoZ) approach to collecting human-robot dialogue data. The data collected will be used to develop a dialogue system for robot navigation. Building on an interface previously used in the development of dialogue systems for virtual agents and video playback, we add templates with open parameters which allow the wizard to quickly produce a wide variety of utterances. Our research demonstrates that this approach to data collection is viable as an intermediate step in developing a dialogue system for physical robots in remote locations from their users - a domain in which the human and robot need to regularly verify and update a shared understanding of the physical environment. We show that our WoZ interface and the fixed set of utterances and templates therein provide for a natural pace of dialogue with good coverage of the navigation domain.

* 7 pages, 2 figures, accepted for oral presentation at the Symposium on Natural Communication for Human-Robot Collaboration, AAAI Fall Symposium Series, November 9-11, 2017, https://www.aaai.org/ocs/index.php/FSS/FSS17
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Fairness is an increasingly important concern as machine learning models are used to support decision making in high-stakes applications such as mortgage lending, hiring, and prison sentencing. This paper introduces a new open source Python toolkit for algorithmic fairness, AI Fairness 360 (AIF360), released under an Apache v2.0 license {https://github.com/ibm/aif360). The main objectives of this toolkit are to help facilitate the transition of fairness research algorithms to use in an industrial setting and to provide a common framework for fairness researchers to share and evaluate algorithms. The package includes a comprehensive set of fairness metrics for datasets and models, explanations for these metrics, and algorithms to mitigate bias in datasets and models. It also includes an interactive Web experience (https://aif360.mybluemix.net) that provides a gentle introduction to the concepts and capabilities for line-of-business users, as well as extensive documentation, usage guidance, and industry-specific tutorials to enable data scientists and practitioners to incorporate the most appropriate tool for their problem into their work products. The architecture of the package has been engineered to conform to a standard paradigm used in data science, thereby further improving usability for practitioners. Such architectural design and abstractions enable researchers and developers to extend the toolkit with their new algorithms and improvements, and to use it for performance benchmarking. A built-in testing infrastructure maintains code quality.

* 20 pages
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We present a deep convolutional neural network for breast cancer screening exam classification, trained and evaluated on over 200,000 exams (over 1,000,000 images). Our network achieves an AUC of 0.895 in predicting whether there is a cancer in the breast, when tested on the screening population. We attribute the high accuracy of our model to a two-stage training procedure, which allows us to use a very high-capacity patch-level network to learn from pixel-level labels alongside a network learning from macroscopic breast-level labels. To validate our model, we conducted a reader study with 14 readers, each reading 720 screening mammogram exams, and find our model to be as accurate as experienced radiologists when presented with the same data. Finally, we show that a hybrid model, averaging probability of malignancy predicted by a radiologist with a prediction of our neural network, is more accurate than either of the two separately. To better understand our results, we conduct a thorough analysis of our network's performance on different subpopulations of the screening population, model design, training procedure, errors, and properties of its internal representations.

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