A Formal Framework for Linguistic Annotation

`Linguistic annotation' covers any descriptive or analytic notations applied to raw language data. The basic data may be in the form of time functions -- audio, video and/or physiological recordings -- or it may be textual. The added notations may include transcriptions of all sorts (from phonetic features to discourse structures), part-of-speech and sense tagging, syntactic analysis, `named entity' identification, co-reference annotation, and so on. While there are several ongoing efforts to provide formats and tools for such annotations and to publish annotated linguistic databases, the lack of widely accepted standards is becoming a critical problem. Proposed standards, to the extent they exist, have focussed on file formats. This paper focuses instead on the logical structure of linguistic annotations. We survey a wide variety of existing annotation formats and demonstrate a common conceptual core, the annotation graph. This provides a formal framework for constructing, maintaining and searching linguistic annotations, while remaining consistent with many alternative data structures and file formats.Comment: 49 page

An information-driven framework for image mining

[Abstract]: Image mining systems that can automatically extract semantically meaningful information (knowledge) from image data are increasingly in demand. The fundamental challenge in image mining is to determine how low-level, pixel representation contained in a raw image or image sequence can be processed to identify high-level spatial objects and relationships. To meet this challenge, we propose an efficient information-driven framework for image mining. We distinguish four levels of information: the Pixel Level, the Object Level, the Semantic Concept Level, and the Pattern and Knowledge Level. High-dimensional indexing schemes and retrieval techniques are also included in the framework to support the flow of information among the levels. We believe this framework represents the first step towards capturing the different levels of information present in image data and addressing the issues and challenges of discovering useful patterns/knowledge from each level

Learning-based Analysis on the Exploitability of Security Vulnerabilities

The purpose of this thesis is to develop a tool that uses machine learning techniques to make predictions about whether or not a given vulnerability will be exploited. Such a tool could help organizations such as electric utilities to prioritize their security patching operations. Three different models, based on a deep neural network, a random forest, and a support vector machine respectively, are designed and implemented. Training data for these models is compiled from a variety of sources, including the National Vulnerability Database published by NIST and the Exploit Database published by Offensive Security. Extensive experiments are conducted, including testing the accuracy of each model, dynamically training the models on a rolling window of training data, and filtering the training data by various features. Of the chosen models, the deep neural network and the support vector machine show the highest accuracy (approximately 94% and 93%, respectively), and could be developed by future researchers into an effective tool for vulnerability analysis

Multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis

BACKGROUND. Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge. RESULTS. We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. CONCLUSION. Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.Dana-Farber Cancer Institute; National Human Genome Research Institute (P50HG004233); National Science Foundation Integrative Graduate Education and Research Traineeship grant (DGE-0654108

CamFlow: Managed Data-sharing for Cloud Services

A model of cloud services is emerging whereby a few trusted providers manage the underlying hardware and communications whereas many companies build on this infrastructure to offer higher level, cloud-hosted PaaS services and/or SaaS applications. From the start, strong isolation between cloud tenants was seen to be of paramount importance, provided first by virtual machines (VM) and later by containers, which share the operating system (OS) kernel. Increasingly it is the case that applications also require facilities to effect isolation and protection of data managed by those applications. They also require flexible data sharing with other applications, often across the traditional cloud-isolation boundaries; for example, when government provides many related services for its citizens on a common platform. Similar considerations apply to the end-users of applications. But in particular, the incorporation of cloud services within `Internet of Things' architectures is driving the requirements for both protection and cross-application data sharing. These concerns relate to the management of data. Traditional access control is application and principal/role specific, applied at policy enforcement points, after which there is no subsequent control over where data flows; a crucial issue once data has left its owner's control by cloud-hosted applications and within cloud-services. Information Flow Control (IFC), in addition, offers system-wide, end-to-end, flow control based on the properties of the data. We discuss the potential of cloud-deployed IFC for enforcing owners' dataflow policy with regard to protection and sharing, as well as safeguarding against malicious or buggy software. In addition, the audit log associated with IFC provides transparency, giving configurable system-wide visibility over data flows. [...]Comment: 14 pages, 8 figure