ran some experiments with ml3, still no good results

1 files changed, 385 insertions, 416 deletions

diff --git a/experiments/ml3.c b/experiments/ml3.c
index 90842d8..1f271a8 100644
--- a/experiments/ml3.c
+++ b/experiments/ml3.c
@@ -695,7 +695,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
  * DTYPE = np.float64
  * ctypedef np.float_t DTYPE_t             # <<<<<<<<<<<<<<
  * 
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta):
+ * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
  */
 typedef __pyx_t_5numpy_float_t __pyx_t_3ml3_DTYPE_t;
 #if CYTHON_CCOMPLEX
@@ -913,6 +913,7 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
 #define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
 #endif
 
+#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
 static double __Pyx__PyObject_AsDouble(PyObject* obj);
 #if CYTHON_COMPILING_IN_PYPY
 #define __Pyx_PyObject_AsDouble(obj) \
@@ -925,7 +926,6 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj);
  PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
 #endif
 
-#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
 #define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
     (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
     __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
@@ -1177,6 +1177,7 @@ int __pyx_module_is_main_ml3 = 0;
 
 /* Implementation of 'ml3' */
 static PyObject *__pyx_builtin_enumerate;
+static PyObject *__pyx_builtin_sum;
 static PyObject *__pyx_builtin_ValueError;
 static PyObject *__pyx_builtin_range;
 static PyObject *__pyx_builtin_RuntimeError;
@@ -1318,9 +1319,8 @@ static PyObject *__pyx_n_s_w1;
 static PyObject *__pyx_n_s_w2;
 static PyObject *__pyx_n_s_w3;
 static PyObject *__pyx_n_s_zeros;
-static PyObject *__pyx_float__1;
 static PyObject *__pyx_float_1_;
-static PyObject *__pyx_float_0_1;
+static PyObject *__pyx_float_0_2;
 static PyObject *__pyx_tuple_;
 static PyObject *__pyx_tuple__2;
 static PyObject *__pyx_tuple__3;
@@ -1334,43 +1334,6 @@ static PyObject *__pyx_codeobj__9;
 /* "ml3.pyx":9
  * ctypedef np.float_t DTYPE_t
  * 
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta):             # <<<<<<<<<<<<<<
- *     return 1./(1. + exp(-weight/delta))
- * 
- */
-
-static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_plogis(__pyx_t_3ml3_DTYPE_t __pyx_v_weight, __pyx_t_3ml3_DTYPE_t __pyx_v_delta) {
-  __pyx_t_3ml3_DTYPE_t __pyx_r;
-  __Pyx_RefNannyDeclarations
-  __Pyx_RefNannySetupContext("plogis", 0);
-
-  /* "ml3.pyx":10
- * 
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta):
- *     return 1./(1. + exp(-weight/delta))             # <<<<<<<<<<<<<<
- * 
- * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
- */
-  __pyx_r = (1. / (1. + exp(((-__pyx_v_weight) / __pyx_v_delta))));
-  goto __pyx_L0;
-
-  /* "ml3.pyx":9
- * ctypedef np.float_t DTYPE_t
- * 
- * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta):             # <<<<<<<<<<<<<<
- *     return 1./(1. + exp(-weight/delta))
- * 
- */
-
-  /* function exit code */
-  __pyx_L0:;
-  __Pyx_RefNannyFinishContext();
-  return __pyx_r;
-}
-
-/* "ml3.pyx":12
- *     return 1./(1. + exp(-weight/delta))
- * 
  * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
  *                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
  *     """weight for successful infection, exponential time model"""
@@ -1384,17 +1347,17 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("weight_success", 0);
 
-  /* "ml3.pyx":16
+  /* "ml3.pyx":13
  *     """weight for successful infection, exponential time model"""
  *     cdef DTYPE_t structural, temporal, result
- *     structural = dist * log(delta)             # <<<<<<<<<<<<<<
+ *     structural = delta ** dist             # <<<<<<<<<<<<<<
  *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
  *     temporal = log(exp(alpha)-1.) - alpha*dt
  */
-  __pyx_v_structural = (__pyx_v_dist * log(__pyx_v_delta));
+  __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml3_DTYPE_t)__pyx_v_dist));
 
-  /* "ml3.pyx":18
- *     structural = dist * log(delta)
+  /* "ml3.pyx":15
+ *     structural = delta ** dist
  *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
  *     temporal = log(exp(alpha)-1.) - alpha*dt             # <<<<<<<<<<<<<<
  *     # temporal = 1 - exp(-alpha*dt)
@@ -1402,27 +1365,27 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
  */
   __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt));
 
-  /* "ml3.pyx":22
+  /* "ml3.pyx":19
  *     # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
  *     # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
- *     result = structural + temporal             # <<<<<<<<<<<<<<
+ *     result = log(structural) + temporal             # <<<<<<<<<<<<<<
  *     # print 'st', structural, temporal
  *     return result
  */
-  __pyx_v_result = (__pyx_v_structural + __pyx_v_temporal);
+  __pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal);
 
-  /* "ml3.pyx":24
- *     result = structural + temporal
+  /* "ml3.pyx":21
+ *     result = log(structural) + temporal
  *     # print 'st', structural, temporal
  *     return result             # <<<<<<<<<<<<<<
  * 
- * 
+ * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
  */
   __pyx_r = __pyx_v_result;
   goto __pyx_L0;
 
-  /* "ml3.pyx":12
- *     return 1./(1. + exp(-weight/delta))
+  /* "ml3.pyx":9
+ * ctypedef np.float_t DTYPE_t
  * 
  * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
  *                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
@@ -1435,8 +1398,8 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
   return __pyx_r;
 }
 
-/* "ml3.pyx":27
- * 
+/* "ml3.pyx":23
+ *     return result
  * 
  * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
  *                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
@@ -1445,13 +1408,13 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
 
 static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
   __pyx_t_3ml3_DTYPE_t __pyx_v_structural;
-  CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_temporal;
+  __pyx_t_3ml3_DTYPE_t __pyx_v_temporal;
   __pyx_t_3ml3_DTYPE_t __pyx_v_result;
   __pyx_t_3ml3_DTYPE_t __pyx_r;
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("weight_failure", 0);
 
-  /* "ml3.pyx":31
+  /* "ml3.pyx":27
  *     """weight for failed infection, exponential time model"""
  *     cdef DTYPE_t structural, temporal, result
  *     structural = delta ** dist             # <<<<<<<<<<<<<<
@@ -1460,26 +1423,26 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
  */
   __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml3_DTYPE_t)__pyx_v_dist));
 
-  /* "ml3.pyx":33
+  /* "ml3.pyx":29
  *     structural = delta ** dist
  *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
  *     temporal = exp(-alpha * dt)             # <<<<<<<<<<<<<<
  *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
- *     result = log(1. - structural)
+ *     result = log(1. - structural + structural*temporal)
  */
   __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt));
 
-  /* "ml3.pyx":35
+  /* "ml3.pyx":31
  *     temporal = exp(-alpha * dt)
  *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
- *     result = log(1. - structural)             # <<<<<<<<<<<<<<
+ *     result = log(1. - structural + structural*temporal)             # <<<<<<<<<<<<<<
  *     # print 'stnv', structural, temporal
  *     return result
  */
-  __pyx_v_result = log((1. - __pyx_v_structural));
+  __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
 
-  /* "ml3.pyx":37
- *     result = log(1. - structural)
+  /* "ml3.pyx":33
+ *     result = log(1. - structural + structural*temporal)
  *     # print 'stnv', structural, temporal
  *     return result             # <<<<<<<<<<<<<<
  * 
@@ -1488,8 +1451,8 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
   __pyx_r = __pyx_v_result;
   goto __pyx_L0;
 
-  /* "ml3.pyx":27
- * 
+  /* "ml3.pyx":23
+ *     return result
  * 
  * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
  *                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
@@ -1502,7 +1465,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
   return __pyx_r;
 }
 
-/* "ml3.pyx":39
+/* "ml3.pyx":35
  *     return result
  * 
  * def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,             # <<<<<<<<<<<<<<
@@ -1550,31 +1513,31 @@ static PyObject *__pyx_pw_3ml3_1ml3(PyObject *__pyx_self, PyObject *__pyx_args,
         case  1:
         if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_victims)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  2:
         if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_non_victims)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  3:
         if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_age)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  4:
         if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  5:
         if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
       }
       if (unlikely(kw_args > 0)) {
-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml3") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml3") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
       }
     } else if (PyTuple_GET_SIZE(__pyx_args) != 6) {
       goto __pyx_L5_argtuple_error;
@@ -1589,21 +1552,21 @@ static PyObject *__pyx_pw_3ml3_1ml3(PyObject *__pyx_self, PyObject *__pyx_args,
     __pyx_v_root_victims = ((PyObject*)values[0]);
     __pyx_v_victims = ((PyObject*)values[1]);
     __pyx_v_non_victims = ((PyObject*)values[2]);
-    __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-    __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-    __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
   }
   goto __pyx_L4_argument_unpacking_done;
   __pyx_L5_argtuple_error:;
-  __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
   __pyx_L3_error:;
   __Pyx_AddTraceback("ml3.ml3", __pyx_clineno, __pyx_lineno, __pyx_filename);
   __Pyx_RefNannyFinishContext();
   return NULL;
   __pyx_L4_argument_unpacking_done:;
-  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_r = __pyx_pf_3ml3_ml3(__pyx_self, __pyx_v_root_victims, __pyx_v_victims, __pyx_v_non_victims, __pyx_v_age, __pyx_v_alpha, __pyx_v_delta);
 
   /* function exit code */
@@ -1679,8 +1642,8 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   __pyx_t_3ml3_DTYPE_t __pyx_t_23;
   __pyx_t_3ml3_DTYPE_t __pyx_t_24;
   __pyx_t_3ml3_DTYPE_t __pyx_t_25;
-  double __pyx_t_26;
-  int __pyx_t_27;
+  int __pyx_t_26;
+  double __pyx_t_27;
   int __pyx_t_28;
   int __pyx_t_29;
   int __pyx_t_30;
@@ -1708,7 +1671,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   __pyx_pybuffernd_parent_dts.data = NULL;
   __pyx_pybuffernd_parent_dts.rcbuffer = &__pyx_pybuffer_parent_dts;
 
-  /* "ml3.pyx":45
+  /* "ml3.pyx":41
  *         DTYPE_t beta, ll, beta_add, max_beta, max_beta_add
  *         list parents, failures, successes
  *     n_roots, n_victims = len(root_victims), len(victims)             # <<<<<<<<<<<<<<
@@ -1717,54 +1680,54 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
   if (unlikely(__pyx_v_root_victims == Py_None)) {
     PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
-  __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (unlikely(__pyx_v_victims == Py_None)) {
     PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
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  * 
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+  __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "ml3.pyx":53
+  /* "ml3.pyx":49
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-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_3 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_12)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_12)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_XDECREF(__pyx_t_6);
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+    if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    if (!(likely(PyList_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "ml3.pyx":57
+    /* "ml3.pyx":53
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  *         # likely parent infects it
  *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
  *                     for (dist, dt, w1, w2, w3) in parents]
- *         # probs_fail[i] = sum(failures)
+ *         probs_fail[i] = sum(failures)
  */
-    __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_3);
 
-    /* "ml3.pyx":58
+    /* "ml3.pyx":54
  *         # likely parent infects it
  *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
  *                     for (dist, dt, w1, w2, w3) in parents]             # <<<<<<<<<<<<<<
- *         # probs_fail[i] = sum(failures)
+ *         probs_fail[i] = sum(failures)
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     if (unlikely(__pyx_v_parents == Py_None)) {
       PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_4); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_4 = PySequence_ITEM(__pyx_t_5, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = PySequence_ITEM(__pyx_t_5, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+            PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "ml3.pyx":57
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+      if (unlikely(__Pyx_ListComp_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-      /* "ml3.pyx":58
+      /* "ml3.pyx":54
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  *                     for (dist, dt, w1, w2, w3) in parents]             # <<<<<<<<<<<<<<
- *         # probs_fail[i] = sum(failures)
+ *         probs_fail[i] = sum(failures)
  *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
  */
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@@ -2068,18 +2031,39 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
     __Pyx_XDECREF_SET(__pyx_v_failures, ((PyObject*)__pyx_t_3));
     __pyx_t_3 = 0;
 
-    /* "ml3.pyx":60
+    /* "ml3.pyx":55
+ *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
  *                     for (dist, dt, w1, w2, w3) in parents]
- *         # probs_fail[i] = sum(failures)
+ *         probs_fail[i] = sum(failures)             # <<<<<<<<<<<<<<
+ *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
+ *                      for (dist, dt, w1, w2, w3) in parents]
+ */
+    __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_3);
+    __Pyx_INCREF(__pyx_v_failures);
+    PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_failures);
+    __Pyx_GIVEREF(__pyx_v_failures);
+    __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_5);
+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+    __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+    __pyx_t_22 = __pyx_v_i;
+    if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_pybuffernd_probs_fail.diminfo[0].shape;
+    *__Pyx_BufPtrStrided1d(__pyx_t_3ml3_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_22, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_25;
+
+    /* "ml3.pyx":56
+ *                     for (dist, dt, w1, w2, w3) in parents]
+ *         probs_fail[i] = sum(failures)
  *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
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-    __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(__pyx_t_3);
+    __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_5);
 
-    /* "ml3.pyx":61
- *         # probs_fail[i] = sum(failures)
+    /* "ml3.pyx":57
+ *         probs_fail[i] = sum(failures)
  *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
  *                      for (dist, dt, w1, w2, w3) in parents]             # <<<<<<<<<<<<<<
  *         dists = [dist for (dist, dt, w1, w2, w3) in parents]
@@ -2087,15 +2071,15 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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       PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     }
-    __pyx_t_5 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_5); __pyx_t_14 = 0;
+    __pyx_t_3 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_3); __pyx_t_14 = 0;
     for (;;) {
-      if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_5)) break;
+      if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_3)) break;
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-      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_4); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_14); __Pyx_INCREF(__pyx_t_4); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_4 = PySequence_ITEM(__pyx_t_5, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = PySequence_ITEM(__pyx_t_3, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2107,7 +2091,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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-          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2133,7 +2117,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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-            PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+            PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2143,7 +2127,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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-        __pyx_t_20 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_20 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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         __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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@@ -2152,7 +2136,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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-        if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_19); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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       __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
-      __pyx_v_dist = __pyx_t_22;
-      __pyx_v_dt = __pyx_t_13;
+      __pyx_v_dist = __pyx_t_13;
+      __pyx_v_dt = __pyx_t_26;
       __Pyx_XDECREF_SET(__pyx_v_w1, __pyx_t_17);
       __pyx_t_17 = 0;
       __Pyx_XDECREF_SET(__pyx_v_w2, __pyx_t_16);
@@ -2176,53 +2160,53 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
       __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_15);
       __pyx_t_15 = 0;
 
-      /* "ml3.pyx":60
+      /* "ml3.pyx":56
  *                     for (dist, dt, w1, w2, w3) in parents]
- *         # probs_fail[i] = sum(failures)
+ *         probs_fail[i] = sum(failures)
  *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
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  *         dists = [dist for (dist, dt, w1, w2, w3) in parents]
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-      __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_4 = PyFloat_FromDouble(__pyx_f_3ml3_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_25, __pyx_t_24, __pyx_t_23)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = PyFloat_FromDouble(__pyx_f_3ml3_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_25, __pyx_t_24, __pyx_t_23)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      if (unlikely(__Pyx_ListComp_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-      /* "ml3.pyx":61
- *         # probs_fail[i] = sum(failures)
+      /* "ml3.pyx":57
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  *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
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  *         dists = [dist for (dist, dt, w1, w2, w3) in parents]
  *         dts = [dt for (dist, dt, w1, w2, w3) in parents]
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-    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
-    __Pyx_XDECREF_SET(__pyx_v_successes, ((PyObject*)__pyx_t_3));
-    __pyx_t_3 = 0;
+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+    __Pyx_XDECREF_SET(__pyx_v_successes, ((PyObject*)__pyx_t_5));
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-    /* "ml3.pyx":62
+    /* "ml3.pyx":58
  *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
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-    __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-    __Pyx_GOTREF(__pyx_t_3);
+    __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_5);
     if (unlikely(__pyx_v_parents == Py_None)) {
       PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     }
-    __pyx_t_5 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_5); __pyx_t_14 = 0;
+    __pyx_t_3 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_3); __pyx_t_14 = 0;
     for (;;) {
-      if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_5)) break;
+      if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_3)) break;
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+      __pyx_t_4 = PySequence_ITEM(__pyx_t_3, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "ml3.pyx":67
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-      __pyx_t_6 = __pyx_t_33(__pyx_t_3);
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-          else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_t_6); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __pyx_v_beta = __pyx_t_23;
 
-    /* "ml3.pyx":87
+    /* "ml3.pyx":78
  *     # iterate over all victim nodes to find the optimal threshold
- *     for beta in np.arange(0.1, 1., .1):
+ *     for beta in np.arange(0.2, 1., 1.):
  *         thresh = log(beta/(3012.*(1.-beta)))             # <<<<<<<<<<<<<<
  *         # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
  *         roots = n_roots + len(probs[probs<thresh])
  */
     __pyx_v_thresh = log((__pyx_v_beta / (3012. * (1. - __pyx_v_beta))));
 
-    /* "ml3.pyx":89
+    /* "ml3.pyx":80
  *         thresh = log(beta/(3012.*(1.-beta)))
  *         # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
  *         roots = n_roots + len(probs[probs<thresh])             # <<<<<<<<<<<<<<
  * 
  *         beta_add = 0.
  */
-    __pyx_t_6 = PyFloat_FromDouble(__pyx_v_thresh); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = PyFloat_FromDouble(__pyx_v_thresh); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_3 = PyObject_RichCompare(((PyObject *)__pyx_v_probs), __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_6 = PyObject_GetItem(((PyObject *)__pyx_v_probs), __pyx_t_3); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
     __Pyx_GOTREF(__pyx_t_6);
-    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
-    __pyx_t_2 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+    __pyx_t_2 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
     __pyx_v_roots = (__pyx_v_n_roots + __pyx_t_2);
 
-    /* "ml3.pyx":91
+    /* "ml3.pyx":82
  *         roots = n_roots + len(probs[probs<thresh])
  * 
  *         beta_add = 0.             # <<<<<<<<<<<<<<
@@ -2690,23 +2659,23 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
     __pyx_v_beta_add = 0.;
 
-    /* "ml3.pyx":93
+    /* "ml3.pyx":84
  *         beta_add = 0.
  *         # add probability for realized edges and subtract probability these edges fail
  *         beta_add += (probs[probs>=thresh]).sum()             # <<<<<<<<<<<<<<
  *         # add probability for the seeds and non-seeds
- *         beta_add += roots * log(beta) + len(probs[probs>=thresh]) * log(1. - beta)
+ *         beta_add += roots * log(beta/3012.) + len(probs[probs>=thresh]) * log(1. - beta)
  */
-    __pyx_t_6 = PyFloat_FromDouble(__pyx_v_beta_add); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_6 = PyFloat_FromDouble(__pyx_v_beta_add); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PyFloat_FromDouble(__pyx_v_thresh); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyFloat_FromDouble(__pyx_v_thresh); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_15 = PyObject_RichCompare(((PyObject *)__pyx_v_probs), __pyx_t_4, Py_GE); __Pyx_XGOTREF(__pyx_t_15); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_15 = PyObject_RichCompare(((PyObject *)__pyx_v_probs), __pyx_t_4, Py_GE); __Pyx_XGOTREF(__pyx_t_15); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_4 = PyObject_GetItem(((PyObject *)__pyx_v_probs), __pyx_t_15); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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-    __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_sum); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_sum); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2720,50 +2689,50 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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-    __Pyx_GOTREF(__pyx_t_5);
+    __Pyx_GOTREF(__pyx_t_3);
     __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
-    __pyx_t_15 = PyNumber_InPlaceAdd(__pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_15 = PyNumber_InPlaceAdd(__pyx_t_6, __pyx_t_3); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+    __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_t_15); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
     __pyx_v_beta_add = __pyx_t_23;
 
-    /* "ml3.pyx":95
+    /* "ml3.pyx":86
  *         beta_add += (probs[probs>=thresh]).sum()
  *         # add probability for the seeds and non-seeds
- *         beta_add += roots * log(beta) + len(probs[probs>=thresh]) * log(1. - beta)             # <<<<<<<<<<<<<<
+ *         beta_add += roots * log(beta/3012.) + len(probs[probs>=thresh]) * log(1. - beta)             # <<<<<<<<<<<<<<
  * 
  *         if beta_add > max_beta_add:
  */
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+    __pyx_t_15 = PyFloat_FromDouble(__pyx_v_thresh); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_15);
-    __pyx_t_5 = PyObject_RichCompare(((PyObject *)__pyx_v_probs), __pyx_t_15, Py_GE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_3 = PyObject_RichCompare(((PyObject *)__pyx_v_probs), __pyx_t_15, Py_GE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_15 = PyObject_GetItem(((PyObject *)__pyx_v_probs), __pyx_t_5); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+    __pyx_t_15 = PyObject_GetItem(((PyObject *)__pyx_v_probs), __pyx_t_3); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
     __Pyx_GOTREF(__pyx_t_15);
-    __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
-    __pyx_t_2 = PyObject_Length(__pyx_t_15); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+    __pyx_t_2 = PyObject_Length(__pyx_t_15); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_v_beta_add = (__pyx_v_beta_add + ((__pyx_v_roots * log(__pyx_v_beta)) + (__pyx_t_2 * log((1. - __pyx_v_beta)))));
+    __pyx_v_beta_add = (__pyx_v_beta_add + ((__pyx_v_roots * log((__pyx_v_beta / 3012.))) + (__pyx_t_2 * log((1. - __pyx_v_beta)))));
 
-    /* "ml3.pyx":97
- *         beta_add += roots * log(beta) + len(probs[probs>=thresh]) * log(1. - beta)
+    /* "ml3.pyx":88
+ *         beta_add += roots * log(beta/3012.) + len(probs[probs>=thresh]) * log(1. - beta)
  * 
  *         if beta_add > max_beta_add:             # <<<<<<<<<<<<<<
  *             max_beta = beta
  *             max_roots = roots
  */
-    __pyx_t_28 = ((__pyx_v_beta_add > __pyx_v_max_beta_add) != 0);
-    if (__pyx_t_28) {
+    __pyx_t_29 = ((__pyx_v_beta_add > __pyx_v_max_beta_add) != 0);
+    if (__pyx_t_29) {
 
-      /* "ml3.pyx":98
+      /* "ml3.pyx":89
  * 
  *         if beta_add > max_beta_add:
  *             max_beta = beta             # <<<<<<<<<<<<<<
@@ -2772,7 +2741,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
       __pyx_v_max_beta = __pyx_v_beta;
 
-      /* "ml3.pyx":99
+      /* "ml3.pyx":90
  *         if beta_add > max_beta_add:
  *             max_beta = beta
  *             max_roots = roots             # <<<<<<<<<<<<<<
@@ -2781,7 +2750,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
       __pyx_v_max_roots = __pyx_v_roots;
 
-      /* "ml3.pyx":100
+      /* "ml3.pyx":91
  *             max_beta = beta
  *             max_roots = roots
  *             max_beta_add = beta_add             # <<<<<<<<<<<<<<
@@ -2793,17 +2762,17 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
     }
     __pyx_L26:;
 
-    /* "ml3.pyx":86
+    /* "ml3.pyx":77
  *     max_beta_add = float('-inf')
  *     # iterate over all victim nodes to find the optimal threshold
- *     for beta in np.arange(0.1, 1., .1):             # <<<<<<<<<<<<<<
+ *     for beta in np.arange(0.2, 1., 1.):             # <<<<<<<<<<<<<<
  *         thresh = log(beta/(3012.*(1.-beta)))
  *         # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
  */
   }
-  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
 
-  /* "ml3.pyx":103
+  /* "ml3.pyx":94
  *             # print 'beta:', max_beta, 'add:', max_beta_add, 'roots:', max_roots
  * 
  *     ll += max_beta_add             # <<<<<<<<<<<<<<
@@ -2812,7 +2781,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
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-  /* "ml3.pyx":104
+  /* "ml3.pyx":95
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@@ -2821,7 +2790,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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-  /* "ml3.pyx":105
+  /* "ml3.pyx":96
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  *     roots = max_roots
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-  /* "ml3.pyx":107
+  /* "ml3.pyx":98
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-  /* "ml3.pyx":39
+  /* "ml3.pyx":35
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-  /* "ml3.pyx":86
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- *     for beta in np.arange(0.1, 1., .1):             # <<<<<<<<<<<<<<
+ *     for beta in np.arange(0.2, 1., 1.):             # <<<<<<<<<<<<<<
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@@ -5090,17 +5060,17 @@ static int __Pyx_InitCachedConstants(void) {
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-  /* "ml3.pyx":39
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-  /* "ml3.pyx":39
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