def test_TP_scores_better_than_FP(self):
"""FPs must score lower than TPs"""
# make a new reference set with different (lower) priors
priors2 = self.priors.copy()
priors2["Y:002"] = 0.55
priors2["Y:007"] = 0.15
rs2 = ReferenceSet(dict(null=0.4, refA=0.3, refB=0.3),
ids=Yobo.ids(),
row_priors=priors2)
rs2.add(self.refnull).add(self.refA).add(self.refB)
rs2.learn_obo(Yobo)
# compare with refA, which has Y:002 equal to 1
FP = Representation(name="FP").set("Y:007", 1)
chain_FP = rs2.inference_chain(FP, "refA", verbose=True, fp_penalty=2)
chain_FP.evaluate_inference()
TP = Representation(name="TP").set("Y:002", 1)
chain_TP = rs2.inference_chain(TP, "refA", verbose=True)
chain_TP.evaluate_inference()
self.assertGreaterEqual(chain_TP.posterior, chain_FP.posterior)
def test_FP_with_fp_penalty(self):
"""FP increases more with lower fp_penalty"""
# make a new reference set with different priors
priors2 = self.priors.copy()
priors2["Y:003"] = 0.4
priors2["Y:002"] = 0.15
priors2["Y:007"] = 0.1
rs2 = ReferenceSet(dict(null=0.4, ref=0.3),
ids=Yobo.ids(),
row_priors=priors2)
ref = Representation(name="ref")
ref.set("Y:001", 1).impute(Yobo, priors2)
ref.set("Y:007", priors2["Y:007"] / 2)
rs2.add(self.refnull).add(ref)
rs2.learn_obo(Yobo)
FP = Representation(name="model").set("Y:007", 0.35)
chain1 = rs2.inference_chain(FP, "ref", verbose=True, fp_penalty=0.1)
chain1.evaluate_inference()
self.assertGreater(chain1.posterior, chain1.prior)
chain2 = rs2.inference_chain(FP, "ref", verbose=True, fp_penalty=1)
chain2.evaluate_inference()
self.assertLess(chain2.posterior, chain1.posterior)
def test_FP_can_increase(self):
"""FP can in principle yield greater score"""
# make a new reference set with different priors
priors2 = self.priors.copy()
priors2["Y:002"] = 0.1
rs2 = ReferenceSet(dict(null=0.4, refA=0.3, refB=0.3),
ids=Yobo.ids(),
row_priors=priors2)
rs2.add(self.refnull).add(self.refA).add(self.refB)
rs2.learn_obo(Yobo)
FP = Representation(name="model").set("Y:002", 0.2)
chain = rs2.inference_chain(FP, "refB", verbose=True, fp_penalty=1)
chain.evaluate_inference()
self.assertGreater(chain.posterior, chain.prior)
def test_inference_chain(self):
"""compute an inference chain."""
# create a reference set
refA = Representation(name="refA")
refA.set("Y:002", 1).impute(Yobo, Ydefaults)
refB = Representation(name="refB")
refB.set("Y:001", 1).impute(Yobo, Ydefaults)
rs = ReferenceSet(dict(refA=0.5, refB=0.5),
ids=Yobo.ids(),
row_priors=Ydefaults)
rs.add(refA).add(refB)
rs.learn_obo(Yobo)
# compute a chain object explaining scoring steps
chain = rs.inference_chain(refA, "refB", verbose=True)
self.assertEqual(chain.__dict__["model"], "refA")
self.assertEqual(chain.__dict__["reference"], "refB")
self.assertGreater(len(chain.data), 2,
"data chain should describe multiple features")
self.assertTrue("background" in chain.data[0].__dict__,
"chain data have comparison information")
self.assertTrue("result" in chain.data[0].__dict__,
"chain data have TP/FP/etc codes")
