[core] tweak defaults

Author: terhorst

smcpp/defaults.py

@@ -1,9 +1,9 @@
 additional_knots = [2]
-regularization_penalty = 6
+regularization_penalty = 7
 xtol = .1
 ftol = 1e-4
 pieces = 100
-knots = 32
+knots = 10
 minimum = 1e-4
 maximum = 1e4
 M = 40

smcpp/model.py

@@ -41,7 +41,7 @@ def regularizer(self):
         y = ad.admath.log(a)
         rd = smcpp.defaults.regularization_degree
         cs = np.cumsum(self.s)[:-rd]
-        d1 = np.diff(y, rd) * np.exp(-cs)
+        d1 = np.diff(y, rd)
         r1 = abs(d1 ** rd).sum() ** (1. / rd)
         return r1
 

smcpp/optimize/optimizers.py

@@ -203,7 +203,7 @@ def __init__(self, analysis, algorithm, xtol, ftol):
     def _coordinates(self):
         model = self._analysis.model
         K = model.K - 1
-        return [[k] for k in range(K)][::-1] + [list(range(K // 3))]
+        return [[k] for k in range(K)][::-1]  # + [list(range(K // 3))]
 
 class TwoPopulationOptimizer(SMCPPOptimizer):
     'Model fitting for two populations.'

smcpp/optimize/plugins/scale_optimizer.py

@@ -7,7 +7,7 @@
 logger = getLogger(__name__)
 
 class ScaleOptimizer(OptimizerPlugin):
-    DISABLED = True
+    DISABLED = False
     def _f(self, alpha, x0, analysis):
         analysis.model[:] = x0 + alpha
         ret = float(analysis.Q())