HypWeb Tutorial: LA2K Explorer

HypWeb Tutorial: LA2K Explorer



HypWeb is an interface for developing hypotheses in the LA2K database. HypWeb currently allows specification of hypotheses involving this database, with the LA2K Explorer system.

If a user describes a rough hypothesis about several groups of subjects (such as Female Hispanics and Female non-Hispanics) and LA2K data about these subjects, LA2K Explorer generates visual presentations of this data and produces a browsable web site with information about "effects" (hypothesized associations) between the groups. This hypothesis web can then be a hub for collaborative hypothesis development.

Click here to use LA2K Explorer


A Quick Walkthrough of LA2K Explorer


LA2K Explorer is a program that acts as a front-end to tools that analyze LA2K data. The initial LA2K Explorer query form looks like this:
figures/LA2K_Explorer_Start_Page.png
As this page indicates, an input query to LA2K Explorer is a hypothesis space -- a rough hypothesis that includes three things: From these three things, LA2K Explorer generates a hypothesis web -- a web site that integrates relevant information about the space of hypotheses. LA2K Explorer generates automated data visualizations and links the results with relevant literature and published findings; the resulting web site is a kind of review or report, but it can be developed over time.

LA2K Explorer interaction is made with selections from a large number of options. The group definition interface is particularly powerful.

For example, can define two groups based primarily on gender:

figures/MFGroupChoices.jpg
The two columns with selections indicate the features of the two groups; one is Male and the other is Female. The other features selected restrict consideration to Healthy Control subjects, and to subjects whose data is Complete.

Similarly, can define six groups with choices like these:

figures/MenuChoicesMFAge.jpg
Each of the six columns defines the features of one group. Beyond having Control and Complete features, the six groups here correspond to the pairs
{Male, Female} x {Age up to 30, Age 31-40, Age 41 and above}.
Group 6 subjects are Female, with Age 41 and above.

The first two rows of checkboxes define subjects to be EITHER Control OR Patient subjects that have complete data.

A Sample Session



Suppose we want to study the effect of alcohol abuse on response time and accuracy of LA2K subjects. With HypWeb we can define a hypothesis space for these subjects that we can then explore.

For this space of hypotheses, we might want to focus on female subjects, and also limit our attention to differences between Hispanic and non-Hispanic subjects. The SCID diagnoses in LA2K provide 3 classifications regarding Alcohol (`Normal' (No Alcohol Diagnosis), Alcohol Abuse, Alcohol Dependence), so altogether we are considering 6 different groups of subjects: We can specify these groups with the LA2K GROUP DEFINITIONS menu:
figures/SixGroupsFemaleHispanicAlcohol.jpg


Notice that the checked boxes specify the six groups we want: the first column specifies Group 1 (Female, Hispanic, No Diagnosis) and the last column specifies Group 6 (Female, not Hispanic, Alcohol Dependent). This interface is extremely flexible, and permits very general definition of groups.
With these group definitions, we then specify which effect variables we are interested in. These variables are indicators (field names) in the LA2K database, and they can be chosen from the HYPOTHESIZED EFFECTS OVER THESE GROUPS menu:
figures/MedianAndSDRTFeatureSelections.png

Finally we can select exploratory data analysis schemes of interest from the HYPOTHESIS EXPLORATION METHODS menu:
figures/FiveHypothesisExplorationMethods.png

The four selections (Histograms, Correlation Ellipses, Parallel Coordinates Plots, and Principal Components Analysis) are used in generating results.
The page generated by compiling this information starts with a summary of our specification of the space of hypotheses here.
figures/HypwebSampleResultSpecification.png

Things are pretty self-explanatory after this.

By clicking on any image you can get PDF for it, and for related images that are not shown. For example, result sizes for each of the six groups can be obtained by clicking on the result image:
figures/ResultingGroupSizes.jpg

All results are color-coded by group, and the interface allows you to select these colors if you want to. With a little experience you will discover HypWeb options give many useful ways to explore LA2K data:
figures/LA2K_Explorer_Session_Results.jpg



Click here to use LA2K Explorer


HypWeb Performance



HypWeb first extracts the relevant information from the LA2K database, based on the specifications for groups and effect variables. It then executes a script in R that performs all the requested tests.

Some caveats: Be thoughtful.

Acknowledgements




Output information here is provided "as is", and with no representation or warranty expressed or implied by any parties.



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