Cheng Thao

GoldMiner: A Radiology Image Search Engine

OBJECTIVE We sought to create an Internet-based search engine to retrieve images from a large collection of figures published in peer-reviewed journals. CONCLUSION The GoldMiner search engine provides easy, rapid access to a large library of images and their associated text, and it is freely available for use on the Internet.

An infrastructure for development of object-oriented, multi-level configuration management services

In an integrated development environment, the ability to manage the evolution of a software system in terms of logical abstractions, compositions, and their interrelations is crucial to successful software development. This paper presents a novel framework and infrastructure, Molhado, upon which to build object-oriented software configuration management (SCM) services in a SCM-centered integrated development environment. Key contributions of this paper include a product versioning model, an extensible, logical, and object-oriented system model, and a reusable product versioning SCM infrastructure, that allow new types of objects to be implemented as extensions of the system models basic entities. Versions and configurations of objects are managed at different levels of abstraction and granularity. A new SCM-centered editing environment or development environment for a specific development paradigm can be rapidly realized by re-using Molhados infrastructure and implementing new object types and their associated tools. This paper also demonstrates our approach in creating prototypes of SCM-centered development environments for different paradigms.

Software Configuration Management for Product Derivation in Software Product Families

A key process in software product line (SPL) engineering is product derivation, which is the process of building software products from a base set of core assets. During product derivation, the components in both core assets and derived software products are modified to meet needs for different functionality, platforms, quality attributes, etc. However, existing software configuration management (SCM) systems do not sufficiently support the derivation process in SPL. In this paper, we introduce a novel SCM system that is well-suited for product derivation in SPL. Our tool, MoSPL handles version management at the component level via its product versioning and data models. It explicitly manages logical constraints and derivation relations among components in both core assets and derived products, thus enabling the automatic propagation of changes in the core assets to their copies in derived products and vice versa. The system can also detect conflicting changes to different copies of components in software product lines.

Enhancing electronic medical record retrieval through semantic query expansion

There are currently many active movements towards computerizing patient healthcare information. As Electronic Medical Record (EMR) systems are being increasingly adopted in healthcare facilities, however, there is a big challenge in effectively utilizing this massive information source. It is very time-consuming for healthcare providers to dig into the voluminous medical records of a patient to find the few that are indeed relevant to the patient’s current problem. Due to the complex semantic relationships among medical concepts and use of many synonyms, antonyms, and hypernym/hyponym, simple word-based information retrieval does not produce satisfactory results. In this paper, we propose an EMR retrieval system that leverages semantic query expansion to retrieve medical records that are relevant to the patient’s current symptom/problem. The proposed framework integrates various technologies, including information retrieval, domain ontologies, automatic semantic relationship learning, as well as a body of domain knowledge elicited from healthcare experts. Knowledge of semantic relationships among medical concepts, such as symptoms, exams and tests, diagnoses, and treatments, as well as knowledge of synonyms and hypernym/hyponyms, is used to expand and enhance initial queries posed by a user. We have implemented a preliminary prototype and conducted a pilot testing using sample nursing notes drawn from the EMR system of a community health center.

Using versioned tree data structure, change detection and node identity for three-way XML merging

XML has become the standard document representation for many popular tools in various domains. When multiple authors collaborate to produce a document, they must be able to work in parallel and periodically merge their efforts into a single work. While there exist a small number of three-way XML merging tools, their performance could be improved in several areas and they lack any form of user interface for resolving conflicts. In this paper, we present an implementation of a three-way XML merge algorithm that is faster, uses less memory and is more precise than existing tools. It uses a specialized versioning tree data structure that supports node identity and change detection. The algorithm applies the traditional three-way merge found in GNU diff3 to the children of changed nodes. The editing operations it supports are addition, deletion, update, and move. A graphical interface for visualizing and resolving conflicts is also provided. An evaluation experiment was conducted comparing the proposed algorithm with three other tools on randomly generated XML data.

A Presentation System for Just-in-time Learning in Radiology

There is growing interest in bringing medical educational materials to the point of care. We sought to develop a system for just-in-time learning in radiology. A database of 34 learning modules was derived from previously published journal articles. Learning objectives were specified for each module, and multiple-choice test items were created. A web-based system—called TEMPO—was developed to allow radiologists to select and view the learning modules. Web services were used to exchange clinical context information between TEMPO and the simulated radiology work station. Preliminary evaluation was conducted using the System Usability Scale (SUS) questionnaire. TEMPO identified learning modules that were relevant to the age, sex, imaging modality, and body part or organ system of the patient being viewed by the radiologist on the simulated clinical work station. Users expressed a high degree of satisfaction with the system’s design and user interface. TEMPO enables just-in-time learning in radiology, and can be extended to create a fully functional learning management system for point-of-care learning in radiology.

Fine-grained, structured configuration management for web projects

Researchers in Web engineering have regularly noted that existing Web application development environments provide little support for managing the evolution of Web applications. Key limitations of Web development environments include line-oriented change models that inadequately represent Web document semantics and in ability to model changes to link structure or the set of objects making up the Webapplication. Developers may find it difficult to grasp how theoverall structure of the Web application has changed over time and may respond by using ad hoc solutions that lead to problems of maintain ability, quality and reliability. Web applications are software artifacts, and as such, can benefit from advanced version control and software configuration management (SCM)technologies from software engineering. We have modified an integrated development environment to manage the evolution and maintenance of Web applications. The resulting environment is distinguished by itsfine-grained version control framework, fine-grained Web contentchange management, and product versioning configuration management, in which a Web project can be organized at the logical level and itsstructure and components are versioned in a fine-grained manner aswell. This paper describes the motivation for this environment as well as its user interfaces, features, and implementation.

Flexible fine-grained version control for software documents

Internal structures of software artifacts, especially program source code, are very important to software engineers in developing and maintaining a high-quality software. However, existing version control and configuration management systems often treat a software system as a set of files in directories on a file system. They usually disregard the logical structures of documentations and program source code and treat them as a set of lines for version control. Therefore, it creates burdensome for ordinary developers because the implementation domain (logical level) and the version control domain (file level) require different mental models. This paper describes the fine-grained version control tool of the software concordance environment that is flexible to manage the evolution of many different structural levels in a software document.

Object-oriented configuration management technology can improve software architectural traceability

Software development is a dynamic process where engineers constantly modify and refine their systems. As a consequence, everything evolves including designs, systems architectural structure, and implementation source code. Software evolution can easily make architectural traceability relationships between software architectural entities and corresponding source code become out of date. This paper suggests the use of object-oriented software configuration (SCM) and version management technology to manage versions of architectural structure/entities, source code, and the traceability relationships among them. The resulting architectural SCM system, MolhadoArch, always keeps architectural entities version-consistent with source code. Consistent configurations are maintained not only among source code but also with the high-level software architecture. MolhadoArch supports the management of both planned and unplanned evolution of software architecture.

Architectural software configuration management in Molhado

Software development is a dynamic process where engineers constantly modify and refine their systems. As a consequence, everything evolves including designs, systems architectural structure, and implementation source code. This paper contributes a novel approach to manage architectural evolution of software systems at the logical level. Key to Molhado architectural software configuration management (SCM) system is its architectural system model in which the architectural concepts are integrated into the system model to enable the management of unplanned evolution of software architecture. Via our product versioning SCM approach, consistent configurations are maintained not only among source code but also with the high-level software architecture. Molhados architectural system model can also be extended to support different architectural description languages and architectural styles.