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Integrating Discovery, Development, and Commercial Data into
Data Mining
Jennifer Sloan
Data Mining Consultant
GlaxoSmithKline: US Pharma IT
15 September 2004
Data Mining Definition
Data Mining is a process that uses a variety of data analysis tools to discover patterns and relationships in data that
may be used to make valid and accurate predictions.
Data Mining is a tool that allows us to
Identify problematic areas Control process variability Make concrete decisions on business needs Develop a model which can aid in future
business decisions
Multivariate Data Sets
Data are multivariate in nature
Large data sets containing multiple criteria within each observation
Comparing multiple vectors is nearly impossible without reducing to a single point
Here we view 5-dimensional information on one observation. Each point represents a prescriber and the color represents a Market Share increase or decrease. Overlapping distributions make this difficult to interpret and further analysis is required. Over 200K observations are represented in this graph.
The same observations are observed but now two-way interactions between the variables help us determine which variables are affecting market shifts and lead to constructing models which will predict prescriber behavior.
Drug Development Issues
Adverse Event Reporting System (AERS) Over 2 million AE reports and approximately 2000
drugs and biologics submitted to the FDA since 1968
Creates Extremely Complicated Matrix of Data Recently, Data Mining methods have helped
address this issue with the development of a method used to examine large databases for associations between drugs and AEs
Data Mining Algorithm
Multi-Item Gamma Poisson Shrinker (MGPS) Developed by William DuMochel (AT&T)
Through statistical modeling, this Empirical Bayesian method identifies higher-than-expected reporting relationships of drug-event combinations
Automated, web-based system with rapid drill-down capability
MGPS runs using all event terms and drugs in the AERS database and produces results for all drug-event combinations
MGPS: Significance
Handles Complex Stratification
(age, gender, year of report > 945 categories) Performs complex computations in minimal
amount of time: Much MORE EFFICIENT Real World Example:
Membership: PhRMA-FDAWorking Group
Chair: June Almenoff (GSK)
FDA Involvement
Involved PhRMA companies: Abbott, Allergan, AstraZeneca, Bristol-Myers Squibb, GlaxoSmithKline, Johnson & Johnson, Lilly, Merck, Novartis, Schering-Plough, Pfizer, Roche, Wyeth
SCAM—Statistical Classification of Activities of Molecules
Recursive partitioning customized for chemistry
Creates a structure activity relationship (SAR) mode7l
Handles large numbers of descriptors (> 1 million)
SCAM : Data Structure
1 0 1 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 11 0 1 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1
1 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 11 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 11 0 1 0 1 1 1 1 1 0 0 0 0 1 0 0 0 1 0 0 0 11 0 1 0 1 1 1 1 1 0 0 0 0 1 0 0 0 1 0 0 0 1
1 0 1 0 0 1 1 0 1 0 0 0 0 0 1 0 0 1 0 0 0 11 0 1 0 0 1 1 0 1 0 0 0 0 0 1 0 0 1 0 0 0 1
1 0 0 0 1 1 1 1 0 1 0 1 0 0 0 1 0 0 0 0 0 11 0 0 0 1 1 1 1 0 1 0 1 0 0 0 1 0 0 0 0 0 1
......
YY11
YY22
YY33
YY44
YYnn
ON S
HN
NO
ONH
......
BiologicalBiologicalActivitiesActivities
>100K>100K > 2 million> 2 million
SCAM’s Recursive Partitioning
n = 1614ave = 0.29sd = 0.73
n = 36ave = 2.60sd = 0.9
Signal 2.60 - 0.29t = = = 18.68
Noise 0.734 1 1 36 1614
+
FeaturerP = 2.03E-70aP = 1.30E-66
n = 1650Ave = 0.34SD = 0.81
Advantages of SCAM
Works for complex situations, mixtures and interactions.
Output is easy to understand and explain
High statistical power
Produces a valid answer
SCAM Drawbacks
Data greedy Only one view of the data Binary descriptors may be too “crude” Disposition of outliers is difficult Highly correlated variables may be obscured Higher order interactions may be masked
Concluding Remarks
Data Mining enables us to efficiently handle LARGE amounts of data
Data Mining allows us to perform analyses IN REAL TIME
Data Mining covers a wide array of topics in
drug industry and its benefits are plentiful
References
Almenoff, June S, et al. “Disproportionality Analysis Using Empirical Bayes Data Mining: A tool for the Evaluation of Drug Interactions in the Post-Marketing Setting.” Pharmacoepidemiology and Drug Safety,12, 517-521 (2003).
Donahue, Rafe. “An Overview of Data Mining in Drug Development and Marketing.” http://home.earthlink.net/~rafedonahue. May 2003.
Hawkins, D.M. and G.V. Kass, “Automatic Interaction Detection.” Topics in Applied Multivariate Analysis, ed. Hawkins, (1982).
Hawkins, D.M., S.S. Young and A. Rusinko. “Analysis of a Large Structure-Activity Data Set Using Recursive Partitioning.” QSAR, 16, 296-302 (1997).