Yuval Shahar

A framework for knowledge-based temporal abstraction

A new domain-independent knowledge-based inference structure is presented, specific to the task of abstracting higher-level concepts from time-stamped data. The framework includes a model of time, parameters, events and contexts. A formal specification of a domains temporal abstraction knowledge supports acquisition, maintenance, reuse and sharing of that knowledge. The knowledge-based temporal abstraction method decomposes the temporal abstraction task into five subtasks. These subtasks are solved by five domain-independent temporal abstraction mechanisms. The temporal abstraction mechanisms depend on four domain-specific knowledge types: structural, classification (functional), temporal semantic (logical) and temporal dynamic (probabilistic) knowledge. Domain values for all knowledge types are specified when a temporal abstraction system is developed. The knowledge-based temporal abstraction method has been implemented in the RESUME system and has been evaluated in several clinical domains (protocol-based care, monitoring of childrens growth and therapy of diabetes) and in an engineering domain (monitoring of traffic control), with encouraging results.

EON: A Component-Based Approach to Automation of Protocol-Directed Therapy

Provision of automated support for planning protocol-directed therapy requires a computer program to take as input clinical data stored in an electronic patient-record system and to generate as output recommendations for therapeutic interventions and laboratory testing that are defined by applicable protocols. This paper presents a synthesis of research carried out at Stanford University to model the therapy-planning task and to demonstrate a component-based architecture for building protocol-based decision-support systems. We have constructed general-purpose software components that (1) interpret abstract protocol specifications to construct appropriate patient-specific treatment plans; (2) infer from time-stamped patient data higher-level, interval-based, abstract concepts; (3) perform time-oriented queries on a time-oriented patient database; and (4) allow acquisition and maintenance of protocol knowledge in a manner that facilitates efficient processing both by humans and by computers. We have implemented these components in a computer system known as EON. Each of the components has been developed, evaluated, and reported independently. We have evaluated the integration of the components as a composite architecture by implementing T-HELPER, a computer-based patient-record system that uses EON to offer advice regarding the management of patients who are following clinical trial protocols for AIDS or HIV infection. A test of the reuse of the software components in a different clinical domain demonstrated rapid development of a prototype application to support protocol-based care of patients who have breast cancer.

Task modeling with reusable problem-solving methods

Problem-solving methods for knowledge-based systems establish the behavior of such systems by defining the roles in which domain knowledge is used and the ordering of inferences. Developers can compose problem-solving methods that accomplish complex application tasks from primitive, reusable methods. The key steps in this development approach are task analysis, method selection (from a library), and method configuration. Protege-ii is a knowledge-engineering environment that allows developers to select and configure problem-solving methods. In addition, Protege-ii generates domain-specific knowledge-acquisition tools that domain specialists can use to create knowledge bases on which the methods may operate. The board-game method is a problem-solving method that defines control knowledge for a class of tasks that developers can model in a highly specific way. The method adopts a conceptual model of problem solving in which the solution space is construed as a “game board” on which the problem solver moves “playing pieces” according to prespecified rules. This familiar conceptual model simplifies the developers cognitive demands when configuring the board-game method to support new application tasks. We compare configuration of the board-game method to that of a chronological-backtracking problem-solving method for the same application tasks (for example, towers of Hanoi and the Sisyphus room-assignment problem). We also examine how method designers can specialize problem-solving methods by making ontological commitments to certain classes of tasks. We exemplify this technique by specializing the chronological-backtracking method to the board-game method.

Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTÉGÉ-II to protocol-based decision support

PROTEGE-II is a suite of tools and a methodology for building knowledge-based systems and domain-specific knowledge-acquisition tools. In this paper, we show how PROTEGE-II can be applied to the task of providing protocol-based decision support in the domain of treating HIV-infected patients. To apply PROTEGE-II, (1) we construct a decomposable problem-solving method called episodic skeletal-plan refinement, (2) we build an application ontology that consists of the terms and relations in the domain, and of method-specific distinctions not already captured in the domain terms, and (3) we specify mapping relations that link terms from the application ontology to the domain-independent terms used in the problem-solving method. From the application ontology, we automatically generate a domain-specific knowledge-acquisition tool that is custom-tailored for the application. The knowledge-acquisition tool is used for the creation and maintenance of domain knowledge used by the problem-solving method. The general goal of the PROTEGE-II approach is to produce systems and components that are reusable and easily maintained. This is the rationale for constructing ontologies and problem-solving methods that can be composed from a set of smaller-grained methods and mechanisms. This is also why we tightly couple the knowledge-acquisition tools to the application ontology that specifies the domain terms used in the problem-solving systems. Although our evaluation is still preliminary, for the application task of providing protocol-based decision support, we show that these goals of reusability and easy maintenance can be achieved. We discuss design decisions and the tradeoffs that have to be made in the development of the system.

A framework for a distributed, hybrid, multiple-ontology clinical-guideline library, and automated guideline-support tools

Clinical guidelines are a major tool in improving the quality of medical care. However, most guidelines are in free text, not in a formal, executable format, and are not easily accessible to clinicians at the point of care. We introduce a Web-based, modular, distributed architecture, the Digital Electronic Guideline Library (DeGeL), which facilitates gradual conversion of clinical guidelines from text to a formal representation in chosen target guideline ontology. The architecture supports guideline classification, semantic markup, context-sensitive search, browsing, run-time application, and retrospective quality assessment. The DeGeL hybrid meta-ontology includes elements common to all guideline ontologies, such as semantic classification and domain knowledge; it also includes four content-representation formats: free text, semi-structured text, semi-formal representation, and a formal representation. These formats support increasingly sophisticated computational tasks. The DeGeL tools for support of guideline-based care operate, at some level, on all guideline ontologies. We have demonstrated the feasibility of the architecture and the tools for several guideline ontologies, including Asbru and GEM.

Temporal reasoning and temporal data maintenance in medicine: issues and challenges.

We present a brief, nonexhaustive overview of research efforts in designing and developing time-oriented systems in medicine. The growing volume of research on time-oriented systems in medicine can be viewed from either an application point of view, focusing on different generic tasks (e.g. diagnosis) and clinical areas (e.g. cardiology), or from a methodological point of view, distinguishing between different theoretical approaches. In this overview, we focus on highlighting methodological and theoretical choices, and conclude with suggestions for new research directions. Two main research directions can be noted: temporal reasoning, which supports various temporal inference tasks (e.g. temporal abstraction, time-oriented decision support, forecasting, data validation), and temporal data maintenance, which deals with storage and retrieval of data that have heterogeneous temporal dimensions. Efforts common to both research areas include the modeling of time, of temporal entities, and of temporal queries. We suggest that tasks such as abstraction of time-oriented data and the handling of different temporal-granularity levels should provide common ground for collaboration between the two research directions and fruitful areas for future research.

Distributed, intelligent, interactive visualization and exploration of time-oriented clinical data and their abstractions

OBJECTIVES We present KNAVE-II, an intelligent interface to a distributed architecture specific to the tasks of query, knowledge-based interpretation, summarization, visualization, interactive exploration of large numbers of distributed time-oriented clinical data, and dynamic sensitivity analysis of these data. KNAVE-II main contributions to the fields of temporal reasoning and intelligent user interfaces are: (1) the capability for interactive computation and visualization of domain specific temporal abstractions, supported by ALMA--a computational engine that applies the domain knowledge base to the clinical time-oriented database. (2) Semantic (ontology-based) navigation and exploration of the data, knowledge, and temporal abstractions, supported by the IDAN mediator, a distributed architecture that enables runtime access to domain-specific knowledge bases that are maintained by expert physicians. METHODS AND MATERIALS KNAVE-II was designed according to 12 requirements that were defined through iterative cycles of design and user-centered evaluation. The complete architecture has been implemented and evaluated in a cross-over study design that compared the KNAVE-II module versus two existing methods: paper charts and an Excel electronic spreadsheet. A small group of clinicians answered the same queries, using the domain of oncology and a set of 1000 patients followed after bone-marrow transplantation. RESULTS The results show that users are able to perform medium to hard difficulty level queries faster and more accurately by using KNAVE-II than paper charts and Excel. Moreover, KNAVE-II was ranked first in preference by all users, along all usability dimensions. CONCLUSIONS Initial evaluation of KNAVE-II and its supporting knowledge based temporal-mediation architecture, by applying it to a large data base of patients monitored several years after bone marrow transplantation (BMT), has produced highly encouraging results.

Representation of change in controlled medical terminologies.

Computer-based systems that support health care require large controlled terminologies to manage names and meanings of data elements. These terminologies are not static, because change in health care is inevitable. To share data and applications in health care, we need standards not only for terminologies and concept representation, but also for representing change. To develop a principled approach to managing change, we analyze the requirements of controlled medical terminologies and consider features that frame knowledge-representation systems have to offer. Based on our analysis, we present a concept model, a set of change operations, and a change-documentation model that may be appropriate for controlled terminologies in health care. We are currently implementing our modeling approach within a computational architecture.

DEGEL: A Hybrid, Multiple-Ontology Framework for Specification and Retrieval of Clinical Guidelines

Clinical Guidelines are a major tool in improving the quality of medical care. However, most guidelines are in free text, not machine comprehensible, and are not easily accessible to clinicians at the point of care. We introduce a Web-based, modular, distributed architecture, the Digital Electronic Guideline Library (DeGeL), which facilitates gradual conversion of clinical guidelines from text to a formal representation in a chosen guideline ontology. The architecture supports guideline classification, semantic markup, context-sensitive search, browsing, run-time application, and retrospective quality assessment. The DeGeL hybrid meta-ontology includes elements common to all guideline ontologies, such as semantic classification, and domain knowledge. The hybrid meta-ontology also includes three guideline-content representation formats: free text, semi-structured text; and a formal representation. These formats support increasingly sophisticated computational tasks. All tools are designed to operate on all representations. We demonstrated the feasibility of the architecture and the tools for the Asbru and GEM guideline ontologies.

Intelligent visualization and exploration of time-oriented clinical data

We describe a conceptual architecture and software implementation specific to the task of interpretation, summarization, visualization, explanation, and interactive exploration of time oriented clinical data and the multiple levels of meaningful concepts that can be abstracted from these data. We build on our work on abstraction of time oriented clinical data using a knowledge base, acquired from clinical experts, of temporal properties of the data. We call the new framework KNAVE (Knowledge-based Navigation of Abstractions for Visualization and Explanation). The visualization and exploration operators whose semantics are domain independent, access the domain specific knowledge base. Exploration exploits key relations (e.g., the abstraction hierarchy) in each clinical domain. Preliminary assessment of the prototype with several clinical users has been encouraging. The KNAVE methodology has broad ramifications for reducing the load that large numbers of time oriented clinical data put on practising physicians.