Using subgraph worked :
This function should be used when you want to filter out of a graph either edges or vertices.
Here is the code I used for this particular problem :
val graph = Graph.apply(verticesTrain.map(vertex => (vertex,1.0)),edges.map{case(s,d)=>Edge(s,d,1.0)})
val filtered = graph.subgraph(vpred = (vid,vd)=>vd!=null.asInstanceOf[Double])
filtered.vertices.count()
Out: Long
44906
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