Your GraphML files are not well-formed.
E.g in CCR4-dependent immune cell chemotaxis in asthma and atopic dermatitis.graphml there is a <node> element with id="extracellular::membrane" and a <graph> element with id="extracellular::membrane".
This is not allowed in XML - the values of id attributes have to be unique.
Moreover, the aforementioned "extracellular::membrane" node is a group node with a <graph> child element and a <node> child element.
This is not allowed in GraphML. A <node> element may not have other <node> elements as (direct) children. (Instead there has to be exactly one <graph> child element holding all the required <node> descendants.)
See the Structural View in the GraphML Specification for information on valid GraphML structure.