You can get your define function to return an object defining a number of functions and you can call one of those functions from the PHP code to pass in values.
e.g.
define(['jquery'], function($) {
// Some functions / variables here.
return {
init: function(param1, param2) {
// Do something with param1 and param2.
}
};
});(stored in myplugin/amd/src/myjavascriptfile.js, for example, then run through grunt to generate the amd/build/* files).Then, in the PHP code:
$PAGE->requires->js_call_amd('myplugin/myjavascriptfile', 'init', ['param1_value', 'param2_value']);
Where 'init' is the name of the function you want to call in the object you returned from the define function and 'param1_value' and 'param2_value' are the values you want to pass in to param1 and param2, respectively.