Barbara Oliboni

Temporal similarity measures for querying clinical workflows

OBJECTIVE In this paper, we extend a preliminary proposal and discuss in a deeper and more formal way an approach to evaluate temporal similarity between clinical workflow cases (i.e., executions of clinical processes). More precisely, we focus on (i) the representation of clinical processes by using a temporal conceptual workflow model; (ii) the definition of ad hoc temporal constraint networks to formally represent clinical workflow cases; (iii) the definition of temporal similarity for clinical workflow cases based on the comparison of temporal constraint networks; (iv) the management of the similarity of clinical processes related to the Italian guideline for stroke prevention and management (SPREAD). BACKGROUND Clinical processes are composed by clinical activities to be done by given actors in a given order satisfying given temporal constraints. This description means that clinical processes can be seen as organizational processes, and modeled by workflow schemata. When a workflow schema represents a clinical process, its cases represent different instances derived from dealing with different patients in different situations. With respect to all the cases related to a workflow schema, each clinical case can be different with respect to its structure and to its temporal aspects. Clinical cases can be stored in clinical databases and information retrieval can be done evaluating the similarity between workflow cases. METHODOLOGY We first describe a possible approach to the conceptual modeling of a clinical process, by using a temporally extended workflow model. Then, we define how a workflow case can be represented as a set of activities, and show how to express them through temporal constraint networks. Once we have built temporal constraint networks related to the cases to compare, we propose a similarity function able to evaluate the differences between the considered cases with respect to the order and duration of corresponding activities, and with respect to the presence/absence of some activities. RESULTS In this work, we propose an approach to evaluate temporal similarity between workflow cases. The proposed approach can be used (i) to query clinical databases storing clinical cases representing activities related to the management of different patients in different situations; (ii) to evaluate the quality of the service comparing the similarity between a (possibly synthetic) case, perceived as the good one with respect to a given clinical situation, and the other clinical cases; and (iii) to retrieve a particular class of cases similar to an interesting one.

Expression microarray classification using topic models

Classification of samples in expression microarray experiments represents a crucial task in bioinformatics and biomedicine. In this paper this scenario is addressed by employing a particular class of statistical approaches, called Topic Models. These models, firstly introduced in the text mining community, permit to extract from a set of objects (typically documents) an interpretable and rich description, based on an intermediate representation called topics (or processes). In this paper the expression microarray classification task is cast into this probabilistic context, providing a parallelism with the text mining domain and an interpretation. Two different topic models are investigated, namely the Probabilistic Latent Semantic Analysis (PLSA) and the Latent Dirichlet Allocation (LDA). An experimental evaluation of the proposed methodologies on three standard datasets confirms their effectiveness, also in comparison with other classification methodologies.

Representing Fuzzy Information by Using XML Schema

Issues related to fuzzy data have been investigated in the classical database research field, and in the last years are becoming interesting topics also in the XML data context. In this work we propose a general XML schema definition for representing fuzzy information.

Temporal aspects of semistructured data

In many applications information about the history of data and their dynamic aspects are just as important as static information. The increasing amount of information accessible through the Web has presented new challenges to academic and industrial research on databases. In this context, data are either structured, when coming from relational or object-oriented databases, or partially or completely unstructured, when they consist of simple collections of text or image files. In the context of semistructured data, models and query languages must be extended in order to consider dynamic aspects. We present a model based on labeled graphs for representing changes in semistructured data and a SQL-like query language for querying it.

Conceptual modeling of XML data

In this paper, we propose a conceptual model for building schemata for XML documents. In particular, we define the conceptual model UXS (UML & XML Schema), which is based on UML and provides several graphical constructs to help the programmer to define complex XML schemata. The model is completed by the support of several translation approaches for building the XML Schema code, corresponding to the defined conceptual schema. A prototype has been developed, and allows the conceptual definition of XML schemata by using the introduced approach.

Fuzzy Techniques for XML Data Smushing

The recently proposed notion of a Semantic Web requires XML/RDF processing techniques able to locate, extract and organise heterogeneous information contained in XML documents coming from different sites, dealing flexibly with differences in structure and tag vocabulary. Such techniques should operate even when tagging is done in accordance with non-informative schemata, and even when no schema is available at all. In this paper, we review the main problems related to the processing and restructuring of large amounts of XML-based data, and propose some solutions in the framework of a flexible query and processing model for well-formed XML documents.

Visually defining and querying consistent multi-granular clinical temporal abstractions

OBJECTIVE The main goal of this work is to propose a framework for the visual specification and query of consistent multi-granular clinical temporal abstractions. We focus on the issue of querying patient clinical information by visually defining and composing temporal abstractions, i.e., high level patterns derived from several time-stamped raw data. In particular, we focus on the visual specification of consistent temporal abstractions with different granularities and on the visual composition of different temporal abstractions for querying clinical databases. BACKGROUND Temporal abstractions on clinical data provide a concise and high-level description of temporal raw data, and a suitable way to support decision making. Granularities define partitions on the time line and allow one to represent time and, thus, temporal clinical information at different levels of detail, according to the requirements coming from the represented clinical domain. The visual representation of temporal information has been considered since several years in clinical domains. Proposed visualization techniques must be easy and quick to understand, and could benefit from visual metaphors that do not lead to ambiguous interpretations. Recently, physical metaphors such as strips, springs, weights, and wires have been proposed and evaluated on clinical users for the specification of temporal clinical abstractions. Visual approaches to boolean queries have been considered in the last years and confirmed that the visual support to the specification of complex boolean queries is both an important and difficult research topic. METHODOLOGY We propose and describe a visual language for the definition of temporal abstractions based on a set of intuitive metaphors (striped wall, plastered wall, brick wall), allowing the clinician to use different granularities. A new algorithm, underlying the visual language, allows the physician to specify only consistent abstractions, i.e., abstractions not containing contradictory conditions on the component abstractions. Moreover, we propose a visual query language where different temporal abstractions can be composed to build complex queries: temporal abstractions are visually connected through the usual logical connectives AND, OR, and NOT. RESULTS The proposed visual language allows one to simply define temporal abstractions by using intuitive metaphors, and to specify temporal intervals related to abstractions by using different temporal granularities. The physician can interact with the designed and implemented tool by point-and-click selections, and can visually compose queries involving several temporal abstractions. The evaluation of the proposed granularity-related metaphors consisted in two parts: (i) solving 30 interpretation exercises by choosing the correct interpretation of a given screenshot representing a possible scenario, and (ii) solving a complex exercise, by visually specifying through the interface a scenario described only in natural language. The exercises were done by 13 subjects. The percentage of correct answers to the interpretation exercises were slightly different with respect to the considered metaphors (54.4--striped wall, 73.3--plastered wall, 61--brick wall, and 61--no wall), but post hoc statistical analysis on means confirmed that differences were not statistically significant. The result of the users satisfaction questionnaire related to the evaluation of the proposed granularity-related metaphors ratified that there are no preferences for one of them. The evaluation of the proposed logical notation consisted in two parts: (i) solving five interpretation exercises provided by a screenshot representing a possible scenario and by three different possible interpretations, of which only one was correct, and (ii) solving five exercises, by visually defining through the interface a scenario described only in natural language. Exercises had an increasing difficulty. The evaluation involved a total of 31 subjects. Results related to this evaluation phase confirmed us about the soundness of the proposed solution even in comparison with a well known proposal based on a tabular query form (the only significant difference is that our proposal requires more time for the training phase: 21 min versus 14 min). DISCUSSION AND CONCLUSIONS In this work we have considered the issue of visually composing and querying temporal clinical patient data. In this context we have proposed a visual framework for the specification of consistent temporal abstractions with different granularities and for the visual composition of different temporal abstractions to build (possibly) complex queries on clinical databases. A new algorithm has been proposed to check the consistency of the specified granular abstraction. From the evaluation of the proposed metaphors and interfaces and from the comparison of the visual query language with a well known visual method for boolean queries, the soundness of the overall system has been confirmed; moreover, pros and cons and possible improvements emerged from the comparison of different visual metaphors and solutions.

Merging multimedia presentations and semistructured temporal data: a graph-based model and its application to clinical information

OBJECTIVE In this paper, we focus on the issue of providing physicians with the capability of representing in a seamless way both temporal aspects of multimedia semistructured data and their temporal presentation requirements. BACKGROUND Semistructured data are data having some structure, that may be irregular or incomplete and does not necessarily conform to a fixed schema. Semistructured data often contain the description of histories of the considered real world. The eXtensible Markup Language (XML) is becoming a cross compatible and standardized means for representing semistructured clinical data. In the field of medical informatics, there are many ongoing activities concerning XML. In the field of multimedia database systems, the topic related to the integration of several media objects (with their temporal aspects) have been considered both for data modeling and querying issues and for modeling multimedia presentations. METHODOLOGY We first propose the Multimedia Temporal Graphical Model (MTGM), by representing a clinical database for cardiology patients undergoing cardiac angiographies and then describe it in a formal way. We deal with the problem of expressing MTGM data by XML and of managing MTGM clinical data through an XML-based system. We provide both a technique for translating (a part of) an MTGM database into an XML document and some techniques allowing us to obtain presentations defined by means of the Synchronized Multimedia Integration Language (SMIL) from MTGM presentations. RESULTS MTGM allows one to represent and store clinical information in a semistructured, temporal, and multimedia database. The physician can define multimedia presentations based on the stored data. Multimedia presentations are then stored in the same MTGM database together with temporal clinical information and are thus represented according to the same data model. A prototype based on an XML native database system has been designed and implemented. DISCUSSION AND CONCLUSIONS In this work we have considered the theoretical and methodological issues concerning the definition of a general data model for describing temporal and multimedia features of semistructured clinical information. Other research and application oriented features, which have not been considered in MTGM, could be investigated for completing MTGM with regard to its applicability to clinical domains: MTGM does not allow one to express times at different levels of granularities, i.e. with different time units, or with indeterminacy; besides the considered valid time, it could be interesting to manage also other temporal dimensions such as the transaction and availability times. Besides being useful for managing multimedia data stored according to widely accepted standards as MPEG and DICOM, nowadays semistructured data, and XML in particular, are becoming the most important way for expressing and exchanging medical knowledge and data: MTGM can be considered as a data model allowing the seamless representation of both (multimedia and temporal) clinical data and knowledge.

Modeling Semistructured Data by Using Graph-Based Constraints

The widespread adoption of semistructured and more in particular XML data has opened a new venue for the application of formal methods to the speci.cation of models for de.ning classes of semistructured or XML documents [1,3]. Most current models for semistructured data are too speci.c to allow immediate comparison with each other, and do not easily support incremental model design. For this reason, we introduce the General Semistructured Meta-Model (GSMM), a simple meta-model for semistructured information which can be applied for the translation to a common formalism of the various abstract models proposed in literature; this approach fosters easy a priori comparison and discussion of concrete models’ features, such as allowed sets of values, handling of object identi .ers, relationships representation; moreover, it supports e.ective inter-model translation and design. Unlike other proposals [2], our meta-model does not rely on an extension of the concept of schema; rather, GSMM is based on a generic graph that can be instantiated into a number of concrete models by providing a) values for a restricted set of parameters (labels) and b) some high-level constraints, themselves represented as graphs. Here, constraints take the role of the schema, imposing constraints directly on the structure of semistructured data provides the designer with a powerful tool for controlling the degree of precision of the structure and introducing .exibility at the data representation level.

Schema versioning in τXSchema-based multitemporal XML repositories

τXSchema [7] is a framework (a language and a suite of tools) for the creation and validation of time-varying XML documents. A τXSchema schema is composed of a conventional XML Schema document annotated with physical and logical annotations. All components of a τXSchema schema (i.e., conventional schema, logical annotations, and physical annotations) can change over time to reflect changes in user requirements or in reference world of the database. Since many applications need to keep track of both data and schema evolution, schema versioning has been long advocated to be the best solution to do this. In this paper, we deal with schema versioning in the τXSchema framework. More precisely, we propose a set of schema change primitives for the maintenance of logical and physical annotations and define their operational semantics.