BACKGROUND: Finding highly relevant articles from biomedical databases is challenging not only because it is often difficult to accurately express a user's underlying intention through keywords but also because a keyword-based query normally returns a long list of hits with many citations being unwanted by the user. This paper proposes a novel biomedical literature search system, called BiomedSearch, which supports complex queries and relevance feedback. METHODS: The system employed association mining techniques to build a k-profile representing a user's relevance feedback. More specifically, we developed a weighted interest measure and an association mining algorithm to find the strength of association between a query and each concept in the article(s) selected by the user as feedback. The top concepts were utilized to form a k-profile used for the next-round search. BiomedSearch relies on Unified Medical Language System (UMLS) knowledge sources to map text files to standard biomedical concepts. It was designed to support queries with any levels of complexity. RESULTS: A prototype of BiomedSearch software was made and it was preliminarily evaluated using the Genomics data from TREC (Text Retrieval Conference) 2006 Genomics Track. Initial experiment results indicated that BiomedSearch increased the mean average precision (MAP) for a set of queries. CONCLUSIONS: With UMLS and association mining techniques, BiomedSearch can effectively utilize users' relevance feedback to improve the performance of biomedical literature search.

Finding highly relevant articles from biomedical databases is challenging because it is often very difficult to accurately express a user's underlying intention through keywords, and a keyword-based query normally returns a long list of hits. This paper proposes a novel biomedical literature search system, called BiomedSearch, which supports complex queries and relevance feedback. In this system, we developed a weighted interest measure and an association mining algorithm to find the strength of association between the query and each concept in the article(s) selected by the user as feedback. The top ?? concepts were utilized to form a k-profile used for the next-round search. BiomedSearch relies on Unified Medical Language System (UMLS) knowledge sources to map text files to standard biomedical concepts. It was designed to support queries with any levels of complexity. The prototype system was preliminarily evaluated using three topics and related Genomics data from TREC (Text Retrieval Conference) 2006 Genomics Track. Initial results indicated that BiomedSearch could effectively utilize users' relevance feedback to improve search performance.

In many real-world applications, it is important to mine causal relationships where an event or event pattern causes certain outcomes with low probability. Discovering this kind of causal relationships can help us prevent or correct negative outcomes caused by their antecedents. In this paper, we propose an innovative data mining framework and apply it to mine potential causal associations in electronic patient data sets where the drug-related events of interest occur infrequently. Specifically, we created a novel interestingness measure, exclusive causal-leverage, based on a computational, fuzzy recognition-primed decision (RPD) model that we previously developed. On the basis of this new measure, a data mining algorithm was developed to mine the causal relationship between drugs and their associated adverse drug reactions (ADRs). The algorithm was tested on real patient data retrieved from the Veterans Affairs Medical Center in Detroit, Michigan. The retrieved data included 16,206 patients (15,605 male, 601 female). The exclusive causal-leverage was employed to rank the potential causal associations between each of the three selected drugs (i.e., enalapril, pravastatin, and rosuvastatin) and 3,954 recorded symptoms, each of which corresponded to a potential ADR. The top 10 drug-symptom pairs for each drug were evaluated by the physicians on our project team. The numbers of symptoms considered as likely real ADRs for enalapril, pravastatin, and rosuvastatin were 8, 7, and 6, respectively. These preliminary results indicate the usefulness of our method in finding potential ADR signal pairs for further analysis (e.g., epidemiology study) and investigation (e.g., case review) by drug safety professionals.

Early detection of unknown adverse drug reactions (ADRs) in postmarketing surveillance saves lives and prevents harmful consequences. We propose a novel data mining approach to signaling potential ADRs from electronic health databases. More specifically, we introduce potential causal association rules (PCARs) to represent the potential causal relationship between a drug and ICD-9 (CDC. (2010). International Classification of Diseases, Ninth Revision (ICD-9). [Online]. Available: http://www.cdc.gov/nchs/icd/icd9.html) coded signs or symptoms representing potential ADRs. Due to the infrequent nature of ADRs, the existing frequency-based data mining methods cannot effectively discover PCARs. We introduce a new interestingness measure, potential causal leverage, to quantify the degree of association of a PCAR. This measure is based on the computational, experience-based fuzzy recognition-primed decision (RPD) model that we developed previously (Y. Ji, R. M. Massanari, J. Ager, J. Yen, R. E. Miller, and H. Ying, "A fuzzy logic-based computational recognition-primed decision model," Inf. Sci., vol. 177, pp. 4338-4353, 2007) on the basis of the well-known, psychology-originated qualitative RPD model (G. A. Klein, "A recognition-primed decision making model of rapid decision making," in Decision Making in Action: Models and Methods, 1993, pp. 138-147). The potential causal leverage assesses the strength of the association of a drug-symptom pair given a collection of patient cases. To test our data mining approach, we retrieved electronic medical data for 16,206 patients treated by one or more than eight drugs of our interest at the Veterans Affairs Medical Center in Detroit between 2007 and 2009. We selected enalapril as the target drug for this ADR signal generation study. We used our algorithm to preliminarily evaluate the associations between enalapril and all the ICD-9 codes associated with it. The experimental results indicate that our approach has a potential to better signal potential ADRs than risk ratio and leverage, two traditional frequency-based measures. Among the top 50 signal pairs (i.e., enalapril versus symptoms) ranked by the potential causal-leverage measure, the physicians on the project determined that eight of them probably represent true causal associations.

The current approach to postmarketing surveillance primarily relies on spontaneous reporting. It is a passive surveillance system and limited by gross underreporting (<;;10% reporting rate), latency, and inconsistent reporting. We propose a new interestingness measure, causal-leverage, to signal potential adverse drug reactions (ADRs) from electronic health databases which are readily available in most modern hospitals. This measure is based on an experience-based fuzzy recognition-primed decision (RPD) model that we developed previously which assesses the strength of association of a drug-ADR pair within each individual patient case. Using the causal-leverage measure, we develop a data mining algorithm to evaluate the associations between a given drug enalapril and all potential ADRs in a real-world electronic health database. The experimental results have shown that our approach can effectively shortlist some known ADRs. For example, the known ADR hyperkalemia caused by enalapril was ranked as top 1% among all the 3954 potential ADRs in our database.

Discovering unknown adverse drug reactions (ADRs) in postmarketing surveillance as early as possible is of great importance. The current approach to postmarketing surveillance primarily relies on spontaneous reporting. It is a passive surveillance system and limited by gross underreporting (<10% reporting rate), latency, and inconsistent reporting. We propose a novel team-based intelligent agent software system approach for proactively monitoring and detecting potential ADRs of interest using electronic patient records. We designed such a system and named it ADRMonitor. The intelligent agents, operating on computers located in different places, are capable of continuously and autonomously collaborating with each other and assisting the human users (e.g., the food and drug administration (FDA), drug safety professionals, and physicians). The agents should enhance current systems and accelerate early ADR identification. To evaluate the performance of the ADRMonitor with respect to the current spontaneous reporting approach, we conducted simulation experiments on identification of ADR signal pairs (i.e., potential links between drugs and apparent adverse reactions) under various conditions. The experiments involved over 275,000 simulated patients created on the basis of more than 1000 real patients treated by the drug cisapride that was on the market for seven years until its withdrawal by the FDA in 2000 due to serious ADRs. Healthcare professionals utilizing the spontaneous reporting approach and the ADRMonitor were separately simulated by decision-making models derived from a general cognitive decision model called fuzzy recognition-primed decision (RPD) model that we recently developed. The quantitative simulation results show that 1) the number of true ADR signal pairs detected by the ADRMonitor is 6.6 times higher than that by the spontaneous reporting strategy; 2) the ADR detection rate of the ADRMonitor agents with even moderate decision-making skills is five times higher than that of spontaneous reporting; and 3) as the number of patient cases increases, ADRs could be detected significantly earlier by the ADRMonitor.

Discovering unknown adverse drug reactions (ADRs) in postmarketing surveillance as early as possible is highly desirable. Nevertheless, current postmarketing surveillance methods largely rely on spontaneous reports that suffer from serious underreporting, latency, and inconsistent reporting. Thus these methods are not ideal for rapidly identifying rare ADRs. The multiagent systems paradigm is an emerging and effective approach to tackling distributed problems, especially when data sources and knowledge are geographically located in different places and coordination and collaboration are necessary for decision making. In this article, we propose an active, multiagent framework for early detection of ADRs by utilizing electronic patient data distributed across many different sources and locations. In this framework, intelligent agents assist a team of experts based on the well-known human decision-making model called Recognition-Primed Decision (RPD). We generalize the RPD model to a fuzzy RPD model and utilize fuzzy logic technology to not only represent, interpret, and compute imprecise and subjective cues that are commonly encountered in the ADR problem but also to retrieve prior experiences by evaluating the extent of matching between the current situation and a past experience. We describe our preliminary multiagent system design and illustrate its potential benefits for assisting expert teams in early detection of previously unknown ADRs. © 2007 Wiley Periodicals, Inc. Int J Int Syst 22: 827–845, 2007.