A comparison of two methods to establish drug-reaction relationships in the ADRAC database
- Authors: Mammadov, Musa , Saunders, Gary
- Date: 2004
- Type: Text , Conference paper
- Relation: Paper presented at the Fourth International ICSC Symposium on Engineering of Intelligent Systems (EIS 2004), Island of Madeira, Portugal, Island of Madeira, Portugal : 29th February, 2004
- Full Text: false
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- Description: Adverse drug reactions (ADRs) are estimated to be one of the leading causes of death. Many national and international agencies have set up databases of ADR reports for the express purpose of determining the relationship between drugs and adverse reactions that they cause. We formulate the drug-reaction relationship problem as a continuous optimization problem and utilize C-GRASP, a new continuous global optimization heuristic, to approximately determine the relationship between drugs and adverse reactions. Our approach is compared against others in the literature and is shown to find better solutions. 1.
- Description: E1
- Description: 2003000897
A fuzzy derivative approach to classification of outcomes from the ADRAC database
- Authors: Mammadov, Musa , Saunders, Gary , Yearwood, John
- Date: 2004
- Type: Text , Journal article
- Relation: International Transactions in Operational Research Vol. 11, no. 2 (2004), p. 169-180
- Full Text: false
- Reviewed:
- Description: The Australian Adverse Drug Reaction Advisory Committee (ADRAC) database has been collected and maintained by the Therapeutic Goods Administration. In this paper we study a part of his database (Card2) which contains records having just reactions from the Cardiovascular group. Drug-reaction relationships are presented by a vector of degrees which shows the degree of association of a drug with each class of reactions. In this work we examine these relationships in the classification of reaction outcomes. A modified version of the fuzzy derivative method (FDM2) is used for classification.
- Description: C1
- Description: 2003000895
A study of drug-reaction relationships in Australian drug safety data
- Authors: Mammadov, Musa , Saunders, Gary , Dekker, Evan
- Date: 2003
- Type: Text , Conference paper
- Relation: Paper presented at the 2nd Australian Data Mining Workshop, Sydney, New South Wales : 8th December, 2003
- Full Text: false
- Reviewed:
- Description: The sparse nature of voluntarily reported drug safety data benefits from a system that consolidates the massive amount of data into a manageable format for analysis. This has been done for Australian drug safety data by the Australian Adverse Drug Reaction Advisory Committee (ADRAC) for reactions using the systems organ class (SOC) ontology. There has long been a need for a similar kind of grouping to apply to drugs in this type of data. In ADRAC, drugs are currently listed by trade-name, where only some of these trade-names were assigned anatomical-therapeutic-chemical classification (ATC) codes. We assigned an ATC code for each ADRAC trade-name and show that this ontology facilitates the detection of drug class / reaction class associations at various levels of specificity. This allows different views of these associations (even very rare ones) and their significance measured for the development of more sensitive signal detection methods. We report that this ATC classification enables both the grouping of association rule approach that is useful for studying rare associations, and the development of an adverse reaction signal detection method.
- Description: E1
- Description: 2003000340
Analysis of cardiovascular adverse drug reactions from the ADRAC database
- Authors: Mammadov, Musa , Saunders, Gary
- Date: 2003
- Type: Text , Conference paper
- Relation: Paper presented at the APAC Conference and Exhibition on Advanced Computing, Grid Applications and eResearch, Gold Coast, Queensland : 29th September, 2003
- Full Text: false
- Reviewed:
- Description: E1
- Description: 2003000342
Applying anatomical therapeutic chemical (ATC) and critical term ontologies to Australian drug safety data for association rules and adverse event signalling
- Authors: Saunders, Gary , Ivkovic, Sasha , Ghosh, Ranadhir , Yearwood, John
- Date: 2005
- Type: Text , Journal article
- Relation: Conferences in Research and Practice in Information Technology, Advances in Ontologies 2005: Proceedings of the Australasian Ontology Workshop AOW 2005 Vol. 58, no. (2005), p. 93-98
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- Description: C1
- Description: 2003001450
Fuzzy set analysis of Australian drug safety data
- Authors: Mammadov, Musa , Saunders, Gary
- Date: 2002
- Type: Text , Conference paper
- Relation: Paper presented at HIC 2002, Melbourne : 5th August, 2002
- Full Text: false
- Reviewed:
- Description: This report describes a preliminary analysis of the Australian Adverse Drug Reaction Database (ADRAC) using a new approach, which is being developed for the analysis of this drug safety data. This differs significantly from the statistical methods that have been used in that we utilize vectors of degrees to define drug-reaction relationships. A quasi-classification algorithm was developed to discover drugs associated with adverse reactions and possible drug-drug interactions. The machine learning algorithm FDM (Fuzzy Derivative Method) was used to predict good and bad outcomes based on observed reactions and potential vectors of degrees. This work extends existing methods for drug safety analysis and should also be of general interest in the field of data mining.
- Description: E1
- Description: 2003000055
New algorithms for multi-class cancer diagnosis using tumor gene expression signatures
- Authors: Bagirov, Adil , Ferguson, Brent , Ivkovic, Sasha , Saunders, Gary , Yearwood, John
- Date: 2003
- Type: Text , Journal article
- Relation: Bioinformatics Vol. 19, no. 14 (2003), p. 1800-1807
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- Description: Motivation: The increasing use of DNA microarray-based tumor gene expression profiles for cancer diagnosis requires mathematical methods with high accuracy for solving clustering, feature selection and classification problems of gene expression data. Results: New algorithms are developed for solving clustering, feature selection and classification problems of gene expression data. The clustering algorithm is based on optimization techniques and allows the calculation of clusters step-by-step. This approach allows us to find as many clusters as a data set contains with respect to some tolerance. Feature selection is crucial for a gene expression database. Our feature selection algorithm is based on calculating overlaps of different genes. The database used, contains over 16 000 genes and this number is considerably reduced by feature selection. We propose a classification algorithm where each tissue sample is considered as the center of a cluster which is a ball. The results of numerical experiments confirm that the classification algorithm in combination with the feature selection algorithm perform slightly better than the published results for multi-class classifiers based on support vector machines for this data set.
- Description: C1
- Description: 2003000439
Pharmacovigilance Decision Support : The value of Disproportionality Analysis Signal Detection Methods, the development and testing of Covariability Techniques, and the importance of Ontology
- Authors: Saunders, Gary
- Date: 2006
- Type: Text , Thesis , PhD
- Full Text:
- Description: The cost of adverse drug reactions to society in the form of deaths, chronic illness, foetal malformation, and many other effects is quite significant. For example, in the United States of America, adverse reactions to prescribed drugs is around the fourth leading cause of death. The reporting of adverse drug reactions is spontaneous and voluntary in Australia. Many methods that have been used for the analysis of adverse drug reaction data, mostly using a statistical approach as a basis for clinical analysis in drug safety surveillance decision support. This thesis examines new approaches that may be used in the analysis of drug safety data. These methods differ significantly from the statistical methods in that they utilize co variability methods of association to define drug-reaction relationships. Co variability algorithms were developed in collaboration with Musa Mammadov to discover drugs associated with adverse reactions and possible drug-drug interactions. This method uses the system organ class (SOC) classification in the Australian Adverse Drug Reaction Advisory Committee (ADRAC) data to stratify reactions. The text categorization algorithm BoosTexter was found to work with the same drug safety data and its performance and modus operandi was compared to our algorithms. These alternative methods were compared to a standard disproportionality analysis methods for signal detection in drug safety data including the Bayesean mulit-item gamma Poisson shrinker (MGPS), which was found to have a problem with similar reaction terms in a report and innocent by-stander drugs. A classification of drug terms was made using the anatomical-therapeutic-chemical classification (ATC) codes. This reduced the number of drug variables from 5081 drug terms to 14 main drug classes. The ATC classification is structured into a hierarchy of five levels. Exploitation of the ATC hierarchy allows the drug safety data to be stratified in such a way as to make them accessible to powerful existing tools. A data mining method that uses association rules, which groups them on the basis of content, was used as a basis for applying the ATC and SOC ontologies to ADRAC data. This allows different views of these associations (even very rare ones). A signal detection method was developed using these association rules, which also incorporates critical reaction terms.
- Description: Doctor of Philosophy
Using anatomical therapeutic chemical (ATC) classification to reduce combinatorial complexity for Australian drug safety data analysis
- Authors: Saunders, Gary , Mammadov, Musa , Ivkovic, Sasha
- Date: 2005
- Type: Text , Conference paper
- Relation: Paper presented at the Sixteenth Australasian Workshop on Combinatorial Algorithms, Ballarat, Victoria : 18th - 21st September, 2005
- Full Text: false
- Reviewed:
- Description: E1
- Description: 2003001449
Using association and overlapping time window approach to detect drug reaction signals
- Authors: Ivkovic, Sasha , Saunders, Gary , Ghosh, Ranadhir , Yearwood, John
- Date: 2006
- Type: Text , Conference paper
- Relation: Paper presented at CIMCA 2005 International Conference on Computational Intelligence for Modelling Control & Automation jointly with IAWTIC 2005 International Conference on Intelligent Agents, Web Technologies & Internet Commerce, Vienna, Austria : 28th November, 2005 p. 1045-1053
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- Description: The problem with detecting adverse drug reactions (ADRs) from drugs is that they may not be obvious until long after they are widely prescribed. Part of the problem is these events are rare. This work describes an approach to signal detection of ADRs based on association rules (AR) in Australian drug safety data. This work was carried out using the Australian Adverse Drug Reactions Advisory Committee (ADRAC) database, which contains a hundred and thirty seven thousand records collected in 1972-2001 period. Many signal detection methods have been developed for drug safety data, most of which use a classical statistical approach. Some of these stratify the data using an ontology for reactions, but the application of drug ontologies to ADR signal detection methods has not been reported. We propose a novel approach for detecting various signal levels by using an overlapped windowing approach. The overlapping windows help to detect smooth transition of signal. We use association rules for measuring significant change over time for different hierarchical levels of drugs (using the Anatomical-Therapeutic-Chemical (ATC) system of drug classification ontology) and their reactions based on the System Organ Classes (SOC) ontology. Using association rules and their strength for different levels in the drug and reaction hierarchy, helps in the detection of signals at particular levels in higher order using a bottom up approach. The results of a preliminary investigation of ADRAC data using our method demonstrate that this approach could produce a powerful and robust ADR signal detection method.
- Description: E1
- Description: 2003001838