Automatically selecting patients for clinical trials with justifications

Clinical trials are human research studies that are used to evaluate the effectiveness of a surgical, medical, or behavioral intervention. They have been widely used by researchers to determine whether a new treatment, such as a new medication, is safe and effective in humans. A clinical trial is frequently performed to determine whether a new treatment is more successful than the current treatment or has less harmful side effects. However, clinical trials have a high failure rate. One method applied is to find patients based on patient records. Unfortunately, this is a difficult process. This is because this process is typically performed manually, making it time-consuming and error-prone. Consequently, clinical trial deadlines are often missed, and studies do not move forward. Time can be a determining factor for success. Therefore, it would be advantageous to have automatic support in this process. Since it is also important to be able to validate whether the patients were selected correctly for the trial, avoiding eventual health problems, it would be important to have a mechanism to present justifications for the selected patients. In this dissertation, we present one possible solution to solve the problem of patient selection for clinical trials. We developed the necessary algorithms and created a simple and intuitive web application that features the selection of patients for clinical trials automatically. This was achieved by combining knowledge expressed in different formalisms. We integrated medical knowledge using ontologies, with criteria that were expressed using nonmonotonic rules. To address the validation procedure automatically, we developed a mechanism that generates the justifications for each selection together with the results of the patients who were selected. In the end, it is expected that a user can easily enter a set of trial criteria, and the application will generate the results of the selected patients and their respective justifications, based on the criteria inserted, medical information and a database of patient information.Os ensaios clínicos são estudos de pesquisa em humanos, utilizados para avaliar a eficácia de uma intervenção cirúrgica, médica ou comportamental. Estes estudos, têm sido amplamente utilizados pelos investigadores para determinar se um novo tratamento, como é o caso de um novo medicamento, é seguro e eficaz em humanos. Um ensaio clínico é realizado frequentemente, para determinar se um novo tratamento tem mais sucesso do que o tratamento atual ou se tem menos efeitos colaterais prejudiciais. No entanto, os ensaios clínicos têm uma taxa de insucesso alta. Um método aplicado é encontrar pacientes com base em registos. Infelizmente, este é um processo difícil. Isto deve-se ao facto deste processo ser normalmente realizado à mão, o que o torna demorado e propenso a erros. Consequentemente, o prazo dos ensaios clínicos é muitas vezes ultrapassado e os estudos acabam por não avançar. O tempo pode ser por vezes um fator determinante para o sucesso. Seria então vantajoso ter algum apoio automático neste processo. Visto que também seria importante validar se os pacientes foram selecionados corretamente para o ensaio, evitando até eventuais problemas de saúde, seria importante ter um mecanismo que apresente justificações para os pacientes selecionados. Nesta dissertação, apresentamos uma possível solução para resolver o problema da seleção de pacientes para ensaios clínicos, através da criação de uma aplicação web, intuitiva e fácil de utilizar, que apresenta a seleção de pacientes para ensaios clínicos de forma automática. Isto foi alcançado através da combinação de conhecimento expresso em diferentes formalismos. Integrámos o conhecimento médico usando ontologias, com os critérios que serão expressos usando regras não monotónicas. Para tratar do processo de validação, desenvolvemos um mecanismo que gera justificações para cada seleção juntamente com os resultados dos pacientes selecionados. No final, é esperado que o utilizador consiga inserir facilmente um conjunto de critérios de seleção, e a aplicação irá gerar os resultados dos pacientes selecionados e as respetivas justificações, com base nos critérios inseridos, informações médicas e uma base de dados com informações dos pacientes

Integración de patrones en el proceso de diseño de sistemas hipermedia mediante el uso de ontologías

Los métodos de diseño hipermedia asisten al diseñador a través de una serie de fases y productos. Sin embargo, un diseñador, tanto si es experto como no, puede llegar a tomar una solución inadecuada a un determinado problema de diseño que puede ser perjudicial para el usuario. Los patrones de diseño son ese mecanismo que puede ayudar a aliviar tanto el acometido de nuevos desarrollos como la dificultad en la toma de decisiones para la mejora de sistemas ya existentes, en tanto en cuanto puedan integrarse de forma eficiente con los métodos de diseño y sean accesibles de manera efectiva a los diferentes integrantes del equipo de desarrollo. Para resolver estas carencias, el primer objetivo de esta tesis ha sido organizar el conocimiento de los pdh, proporcionando unos criterios de clasificación, un catálogo de patrones, un lenguaje de patrones y un marco de integración con los métodos de diseño, en el cual un conjunto de pasos guían una aproximación basada en patrones que permite transformar la especificación de requisitos en entidades de diseño en el modelado conceptual, gracias a las soluciones capturadas por los patrones. Además para poder automatizar este conjunto de herramientas se ha propuesto un modelo de representación semántico basado en ontologías que permite mantener enlazada la representación textual del patrón mediante anotaciones, haciendo a los patrones mutuamente comprensibles a diseñadores y a programas.______________________________________________ The development of large-scale hypermedia and web systems must be carried out following a well defined systematic process, that is, applying hypermedia and web engineering methods and techniques. In addition, considering that the development process of web systems is characterized by obtaining an operative product in a short period of time, designers can alleviate decision making resorting to design patterns. A design pattern records the knowledge and the experience of domain experts on how to make a software system more reusable and flexible as a result of many efforts on the design and codification of systems. Currently, if a designer or a developer of hypermedia applications wants to solve or to communicate a specific design problem by means of hypermedia design patterns (hdp), as starting point, she would have to search across multiple existing publications or some of web repositories available in order to identify the pattern or patterns that best fit her needs. To date, the necessary mechanisms to help the designer to find the appropriate pattern or patterns and to integrate them into hypermedia design methods do not exist. Therefore, the success of this activity will depend only on the designer knowledge about the existing resources and her experience in the use of patterns. In order to solve these lacks, the first aim of this thesis has been to organize the knowledge of hdp, providing a set of classification criteria which takes into account as much hypermedia application modeling needs as the different levels of abstraction used in the pdh literature. From these criteria, a pattern catalogue has been elaborated to facilitate the search of patterns during the resolution of particular design problems as well as a pattern language as a step-by-step guide that advises designers how to accomplish the design process from different levels of abstraction, whereas it proposes alternative problems to resolve. Finally, from the pattern language, an integration framework with design methods has been specified, in which a set of steps guides a pattern based approach to transform requirements specifications to design entities into the conceptual modeling, thanks to the solutions captured by patterns. This process has been evaluated in an empirical way to verify its validity and utility. Once the space and the knowledge of patterns are organized, new challenges and realities should be faced up to. In particular, the great amount of patterns and its different sources, even counting on the mechanisms before mentioned, lead a non-experienced des- igner in the use of patterns to the necessity to explore most of them, in addition to the effort to understand when and how the pattern must be applied. At this stage, it is worth counting on software tools that allow for the organization, recovery and exploration of patterns with searches dedicated to finding appropiate patterns to generic design problems as well as their application in other software systems, such as CASE tools. However, firstly it is necessary to share a formal specification of patterns in order to preserve compatibility among software tools. To date, the hypermedia engineering field does not have its own formalization that allows the development of software tools for patterns, and the formalizations proposed in the software engineering field only take into account the pattern solution and leave aside the textual pattern description, so important to understand the foundation that underlies pattern’s problem and solution. All elements of a pattern are required to develop effective tools for patterns organization, recovery and exploration. For example, to include the intention of pattern would allow for indexing patterns according to the problem that solve, helping users to find the appropiate pattern for a design problem. For that reason, a semantic representation model based on ontologies that combines the domain knowledge about hypermedia used for the pattern description with the pattern format has been proposed. Afterwards, this representation provides the underlying framework to complement the textual pattern representation by means of semantic annotations, which is supported by a tool that helps both users and authors of patterns to formalize their own repositories. This combination of the formal representation linked to the textual pattern representation by means of annotations allows to patterns to be mutually comprehensible by designers and programs. An example of this is the development of a semantic web repository and the automatization of the integration process of hdp in a tool support for the design of hypermedia applications, using both developments the pattern language formalized by means of the annotation tool proposed. The development of these tools have proven the technical feasibility of the solution here proposed