Organization with a struct
You could input a struct that has these parameters as it's fields. 
For example a structure with fields
setts.TrainNeg
     .TrainPos
     .nf
     .nT
     .factors
     .removeEachStage
     .applyEstEachStage
     .removeFeatures
That way when you set the fields it is clear what the field is, unlike a function call where you have to remember the order of the parameters. 
Then your function call becomes 
[Model threshold] = detect(setts);
and your function definition would be something like
function [model, threshold] = detect(setts)
Then simply replace the occurrences of e.g. param with setts.param. 
Mixed approach
You can also mix this approach with your current one if you prefer, e.g.
[Model threshold] = detect(in1, in2, setts);
if you wanted to still explicitly include in1 and in2, and bundle the rest into setts.
OOP approach
Another option is to turn detect into a class. The benefit to this is that a detect object would then have member variables with fixed names, as opposed to structs where if you make a typo when setting a field you just create a new field with the misspelled name. 
For example
classdef detect()
properties
  TrainNeg = [];
  TrainPos  = [];
  nf = [];
  nT = [];
  factors = [];
  removeEachStage = [];
  applyEstEachStage = [];
  removeFeatures =[];
end
methods
  function run(self)
    % Put the old detect code in here, use e.g. self.TrainNeg to access member variables (aka properties)
  end
end