DEVELOPING A CLINICAL LINGUISTIC FRAMEWORK FOR PROBLEM LIST GENERATION FROM CLINICAL TEXT

Regulatory institutions such as the Institute of Medicine and Joint Commission endorse problem lists as an effective method to facilitate transitions of care for patients. In practice, the problem list is a common model for documenting a care provider's medical reasoning with respect to a problem and its status during patient care. Although natural language processing (NLP) systems have been developed to support problem list generation, encoding many information layers - morphological, syntactic, semantic, discourse, and pragmatic - can prove computationally expensive. The contribution of each information layer for accurate problem list generation has not been formally assessed. We would expect a problem list generator that relies on natural language processing would improve its performance with the addition of rich semantic features We hypothesize that problem list generation can be approached as a two-step classification problem - problem mention status (Aim One) and patient problem status (Aim Two) classification. In Aim One, we will automatically classify the status of each problem mention using semantic features about problems described in the clinical narrative. In Aim Two, we will classify active patient problems from individual problem mentions and their statuses. We believe our proposal is significant in two ways. First, our experiments will develop and evaluate semantic features, some commonly modeled and others not in the clinical text. The annotations we use will be made openly available to other NLP researchers to encourage future research on this task and other related problems including foundational NLP algorithms (assertion classification and coreference resolution) and applied clinical applications (patient timeline and record visualization). Second, by generating and evaluating existing NLP systems, we are building an open-source problem list generator and demonstrating the performance for problem list generation using these features

MaMaDroid: Detecting Android malware by building markov chains of behavioral models (extended version)

As Android has become increasingly popular, so has malware targeting it, thus motivating the research community to propose different detection techniques. However, the constant evolution of the Android ecosystem, and of malware itself, makes it hard to design robust tools that can operate for long periods of time without the need for modifications or costly re-training. Aiming to address this issue, we set to detect malware from a behavioral point of view, modeled as the sequence of abstracted API calls. We introduce MaMaDroid, a static-analysis based system that abstracts app’s API calls to their class, package, or family, and builds a model from their sequences obtained from the call graph of an app as Markov chains. This ensures that the model is more resilient to API changes and the features set is of manageable size. We evaluate MaMaDroid using a dataset of 8.5K benign and 35.5K malicious apps collected over a period of six years, showing that it effectively detects malware (with up to 0.99 F-measure) and keeps its detection capabilities for long periods of time (up to 0.87 F-measure two years after training). We also show that MaMaDroid remarkably overperforms DroidAPIMiner, a state-of-the-art detection system that relies on the frequency of (raw) API calls. Aiming to assess whether MaMaDroid’s effectiveness mainly stems from the API abstraction or from the sequencing modeling, we also evaluate a variant of it that uses frequency (instead of sequences), of abstracted API calls. We find that it is not as accurate, failing to capture maliciousness when trained on malware samples that include API calls that are equally or more frequently used by benign apps

Online failure prediction in air traffic control systems

This thesis introduces a novel approach to online failure prediction for mission critical distributed systems that has the distinctive features to be black-box, non-intrusive and online. The approach combines Complex Event Processing (CEP) and Hidden Markov Models (HMM) so as to analyze symptoms of failures that might occur in the form of anomalous conditions of performance metrics identified for such purpose. The thesis presents an architecture named CASPER, based on CEP and HMM, that relies on sniffed information from the communication network of a mission critical system, only, for predicting anomalies that can lead to software failures. An instance of Casper has been implemented, trained and tuned to monitor a real Air Traffic Control (ATC) system developed by Selex ES, a Finmeccanica Company. An extensive experimental evaluation of CASPER is presented. The obtained results show (i) a very low percentage of false positives over both normal and under stress conditions, and (ii) a sufficiently high failure prediction time that allows the system to apply appropriate recovery procedures

Personalized data analytics for internet-of-things-based health monitoring

The Internet-of-Things (IoT) has great potential to fundamentally alter the delivery of modern healthcare, enabling healthcare solutions outside the limits of conventional clinical settings. It can offer ubiquitous monitoring to at-risk population groups and allow diagnostic care, preventive care, and early intervention in everyday life. These services can have profound impacts on many aspects of health and well-being. However, this field is still at an infancy stage, and the use of IoT-based systems in real-world healthcare applications introduces new challenges. Healthcare applications necessitate satisfactory quality attributes such as reliability and accuracy due to their mission-critical nature, while at the same time, IoT-based systems mostly operate over constrained shared sensing, communication, and computing resources. There is a need to investigate this synergy between the IoT technologies and healthcare applications from a user-centered perspective. Such a study should examine the role and requirements of IoT-based systems in real-world health monitoring applications. Moreover, conventional computing architecture and data analytic approaches introduced for IoT systems are insufficient when used to target health and well-being purposes, as they are unable to overcome the limitations of IoT systems while fulfilling the needs of healthcare applications. This thesis aims to address these issues by proposing an intelligent use of data and computing resources in IoT-based systems, which can lead to a high-level performance and satisfy the stringent requirements. For this purpose, this thesis first delves into the state-of-the-art IoT-enabled healthcare systems proposed for in-home and in-hospital monitoring. The findings are analyzed and categorized into different domains from a user-centered perspective. The selection of home-based applications is focused on the monitoring of the elderly who require more remote care and support compared to other groups of people. In contrast, the hospital-based applications include the role of existing IoT in patient monitoring and hospital management systems. Then, the objectives and requirements of each domain are investigated and discussed. This thesis proposes personalized data analytic approaches to fulfill the requirements and meet the objectives of IoT-based healthcare systems. In this regard, a new computing architecture is introduced, using computing resources in different layers of IoT to provide a high level of availability and accuracy for healthcare services. This architecture allows the hierarchical partitioning of machine learning algorithms in these systems and enables an adaptive system behavior with respect to the user's condition. In addition, personalized data fusion and modeling techniques are presented, exploiting multivariate and longitudinal data in IoT systems to improve the quality attributes of healthcare applications. First, a real-time missing data resilient decision-making technique is proposed for health monitoring systems. The technique tailors various data resources in IoT systems to accurately estimate health decisions despite missing data in the monitoring. Second, a personalized model is presented, enabling variations and event detection in long-term monitoring systems. The model evaluates the sleep quality of users according to their own historical data. Finally, the performance of the computing architecture and the techniques are evaluated in this thesis using two case studies. The first case study consists of real-time arrhythmia detection in electrocardiography signals collected from patients suffering from cardiovascular diseases. The second case study is continuous maternal health monitoring during pregnancy and postpartum. It includes a real human subject trial carried out with twenty pregnant women for seven months