What is a sequence?
A sequence is a group of vertices that is repeated multiple times in the network. The vertices in one group can (optionally) depend on vertices in the previous group. They typically represent a concept larger than a vertex like an agent in an ABM, a time series or some observations that are associated.
How do you build them?
Let’s say you have a class MyData that looks like this:
public static class MyData {
public double x;
public double y;
public MyData(String x, String y) {
this.x = Double.parseDouble(x);
this.y = Double.parseDouble(y);
}
}
This is an example of how you could pull in data from a csv file and run linear regression, using a sequence to build identical sections of the graph for each line of the csv.
/**
* Each sequence item contains a linear regression model:
* VertexY = VertexX * VertexM + VertexB
*
* @param dataFileName The input data file defines, for each sequence item:
* - the value of the input, VertexX
* - the value of the observed output, VertexY
*/
public Sequence buildSequence(String dataFileName) {
//Parse the csv data to MyData objects
List<MyData> allMyData = ReadCsv.fromFile(dataFileName)
.asRowsDefinedBy(MyData.class)
.load();
DoubleVertex m = new GaussianVertex(0, 1);
DoubleVertex b = new GaussianVertex(0, 1);
VertexLabel xLabel = new VertexLabel("x");
VertexLabel yLabel = new VertexLabel("y");
//Build sequence from each line in the csv
Sequence sequence = new SequenceBuilder<MyData>()
.fromIterator(allMyData.iterator())
.withFactory((item, csvMyData) -> {
ConstantDoubleVertex x = new ConstantDoubleVertex(csvMyData.x).setLabel(xLabel);
DoubleVertex y = m.multiply(x).plus(b).setLabel(yLabel);
DoubleVertex yObserved = new GaussianVertex(y, 1);
yObserved.observe(csvMyData.y);
// this labels the x and y vertex for later use
item.add(x);
item.add(y);
})
.build();
//now you have access to the "x" from any one of the sequence
DoubleTensor valueForXAtCSVLine1 = sequence.asList()
.get(1) // get sequence item 1 which is built from csv line 1
.<DoubleVertex>get(xLabel) //get the vertex that we labelled "x" in that item
.getValue(); //get the value from that vertex
//Now run an inference algorithm on vertex m and vertex b and you have linear regression
return sequence;
}