Isabelle/PIDE as Platform for Educational Tools

The Isabelle/PIDE platform addresses the question whether proof assistants of the LCF family are suitable as technological basis for educational tools. The traditionally strong logical foundations of systems like HOL, Coq, or Isabelle have so far been counter-balanced by somewhat inaccessible interaction via the TTY (or minor variations like the well-known Proof General / Emacs interface). Thus the fundamental question of math education tools with fully-formal background theories has often been answered negatively due to accidental weaknesses of existing proof engines. The idea of "PIDE" (which means "Prover IDE") is to integrate existing provers like Isabelle into a larger environment, that facilitates access by end-users and other tools. We use Scala to expose the proof engine in ML to the JVM world, where many user-interfaces, editor frameworks, and educational tools already exist. This shall ultimately lead to combined mathematical assistants, where the logical engine is in the background, without obstructing the view on applications of formal methods, formalized mathematics, and math education in particular.Comment: In Proceedings THedu'11, arXiv:1202.453

The Topology ToolKit

This system paper presents the Topology ToolKit (TTK), a software platform designed for topological data analysis in scientific visualization. TTK provides a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due to a tight integration with ParaView. It is also easily accessible to developers through a variety of bindings (Python, VTK/C++) for fast prototyping or through direct, dependence-free, C++, to ease integration into pre-existing complex systems. While developing TTK, we faced several algorithmic and software engineering challenges, which we document in this paper. In particular, we present an algorithm for the construction of a discrete gradient that complies to the critical points extracted in the piecewise-linear setting. This algorithm guarantees a combinatorial consistency across the topological abstractions supported by TTK, and importantly, a unified implementation of topological data simplification for multi-scale exploration and analysis. We also present a cached triangulation data structure, that supports time efficient and generic traversals, which self-adjusts its memory usage on demand for input simplicial meshes and which implicitly emulates a triangulation for regular grids with no memory overhead. Finally, we describe an original software architecture, which guarantees memory efficient and direct accesses to TTK features, while still allowing for researchers powerful and easy bindings and extensions. TTK is open source (BSD license) and its code, online documentation and video tutorials are available on TTK's website

Transit Performance Measures in California

This research is the result of a California Department of Transportation (Caltrans) request to assess the most commonly available transit performance measures in California. Caltrans wanted to understand performance measures and data used by Metropolitan Planning Organizations (MPOs) and transit agencies to help it develop statewide measures. This report serves as a summary reference guide to help Caltrans understand the numerous and diverse performance measures used by MPOs and transit agencies in California. First, investigators review the available literature to identify a complete transit performance framework for the purposes of organizing agency measures, metrics, and data sources. Next, they review the latest transit performance measures documented in planning reports for the four largest MPOs in California (San Francisco Bay Area, Los Angeles, San Diego, and Sacramento). Researchers pay special attention to the transit performance measures used by these MPOs, because these measures are available for the majority of California’s population. Finally, investigators summarize 231 performance measures used by a total 26 local transit agencies in the State of California, based on transit planning documents available on the internet

Enhancing Undergraduate AI Courses through Machine Learning Projects

It is generally recognized that an undergraduate introductory Artificial Intelligence course is challenging to teach. This is, in part, due to the diverse and seemingly disconnected core topics that are typically covered. The paper presents work funded by the National Science Foundation to address this problem and to enhance the student learning experience in the course. Our work involves the development of an adaptable framework for the presentation of core AI topics through a unifying theme of machine learning. A suite of hands-on semester-long projects are developed, each involving the design and implementation of a learning system that enhances a commonly-deployed application. The projects use machine learning as a unifying theme to tie together the core AI topics. In this paper, we will first provide an overview of our model and the projects being developed and will then present in some detail our experiences with one of the projects – Web User Profiling which we have used in our AI class

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

An evaluation framework to drive future evolution of a research prototype

The Open Source Component Artefact Repository (OSCAR) requires evaluation to confirm its suitability as a development environment for distributed software engineers. The evaluation will take note of several factors including usability of OSCAR as a stand-alone system, scalability and maintainability of the system and novel features not provided by existing artefact management systems. Additionally, the evaluation design attempts to address some of the omissions (due to time constraints) from the industrial partner evaluations. This evaluation is intended to be a prelude to the evaluation of the awareness support being added to OSCAR; thus establishing a baseline to which the effects of awareness support may be compared

Genetic Programming for Smart Phone Personalisation

Personalisation in smart phones requires adaptability to dynamic context based on user mobility, application usage and sensor inputs. Current personalisation approaches, which rely on static logic that is developed a priori, do not provide sufficient adaptability to dynamic and unexpected context. This paper proposes genetic programming (GP), which can evolve program logic in realtime, as an online learning method to deal with the highly dynamic context in smart phone personalisation. We introduce the concept of collaborative smart phone personalisation through the GP Island Model, in order to exploit shared context among co-located phone users and reduce convergence time. We implement these concepts on real smartphones to demonstrate the capability of personalisation through GP and to explore the benefits of the Island Model. Our empirical evaluations on two example applications confirm that the Island Model can reduce convergence time by up to two-thirds over standalone GP personalisation.Comment: 43 pages, 11 figure