playing around with ml3

1 files changed, 362 insertions, 301 deletions

diff --git a/experiments/ml3.c b/experiments/ml3.c
index 1f271a8..08730d3 100644
--- a/experiments/ml3.c
+++ b/experiments/ml3.c
@@ -1228,6 +1228,7 @@ static char __pyx_k_numpy[] = "numpy";
 static char __pyx_k_probs[] = "probs";
 static char __pyx_k_range[] = "range";
 static char __pyx_k_roots[] = "roots";
+static char __pyx_k_seeds[] = "seeds";
 static char __pyx_k_zeros[] = "zeros";
 static char __pyx_k_arange[] = "arange";
 static char __pyx_k_import[] = "__import__";
@@ -1242,6 +1243,7 @@ static char __pyx_k_max_beta[] = "max_beta";
 static char __pyx_k_enumerate[] = "enumerate";
 static char __pyx_k_max_roots[] = "max_roots";
 static char __pyx_k_n_victims[] = "n_victims";
+static char __pyx_k_non_seeds[] = "non_seeds";
 static char __pyx_k_successes[] = "successes";
 static char __pyx_k_ValueError[] = "ValueError";
 static char __pyx_k_itervalues[] = "itervalues";
@@ -1295,6 +1297,7 @@ static PyObject *__pyx_n_s_n_roots;
 static PyObject *__pyx_n_s_n_victims;
 static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous;
 static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
+static PyObject *__pyx_n_s_non_seeds;
 static PyObject *__pyx_n_s_non_victims;
 static PyObject *__pyx_n_s_np;
 static PyObject *__pyx_n_s_numpy;
@@ -1308,6 +1311,7 @@ static PyObject *__pyx_n_s_range;
 static PyObject *__pyx_n_s_root_victims;
 static PyObject *__pyx_n_s_roots;
 static PyObject *__pyx_n_s_s;
+static PyObject *__pyx_n_s_seeds;
 static PyObject *__pyx_n_s_successes;
 static PyObject *__pyx_n_s_sum;
 static PyObject *__pyx_n_s_t;
@@ -1319,6 +1323,7 @@ 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_2;
 static PyObject *__pyx_tuple_;
@@ -1351,32 +1356,32 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
  *     """weight for successful infection, exponential time model"""
  *     cdef DTYPE_t structural, temporal, result
  *     structural = delta ** dist             # <<<<<<<<<<<<<<
- *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
  *     temporal = log(exp(alpha)-1.) - alpha*dt
+ *     result = log(structural) + temporal
  */
   __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml3_DTYPE_t)__pyx_v_dist));
 
-  /* "ml3.pyx":15
+  /* "ml3.pyx":14
+ *     cdef DTYPE_t structural, temporal, result
  *     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)
- *     # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
+ *     result = log(structural) + temporal
+ *     return result
  */
   __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt));
 
-  /* "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
+  /* "ml3.pyx":15
+ *     structural = delta ** dist
+ *     temporal = log(exp(alpha)-1.) - alpha*dt
  *     result = log(structural) + temporal             # <<<<<<<<<<<<<<
- *     # print 'st', structural, temporal
  *     return result
+ * 
  */
   __pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal);
 
-  /* "ml3.pyx":21
+  /* "ml3.pyx":16
+ *     temporal = log(exp(alpha)-1.) - alpha*dt
  *     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,
@@ -1398,7 +1403,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
   return __pyx_r;
 }
 
-/* "ml3.pyx":23
+/* "ml3.pyx":18
  *     return result
  * 
  * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
@@ -1414,36 +1419,36 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("weight_failure", 0);
 
-  /* "ml3.pyx":27
+  /* "ml3.pyx":22
  *     """weight for failed infection, exponential time model"""
  *     cdef DTYPE_t structural, temporal, result
  *     structural = delta ** dist             # <<<<<<<<<<<<<<
- *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
  *     temporal = exp(-alpha * dt)
+ *     result = log(1. - structural + structural * temporal)
  */
   __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml3_DTYPE_t)__pyx_v_dist));
 
-  /* "ml3.pyx":29
+  /* "ml3.pyx":23
+ *     cdef DTYPE_t structural, temporal, result
  *     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 + structural*temporal)
+ *     result = log(1. - structural + structural * temporal)
+ *     return result
  */
   __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt));
 
-  /* "ml3.pyx":31
+  /* "ml3.pyx":24
+ *     structural = delta ** dist
  *     temporal = exp(-alpha * dt)
- *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
- *     result = log(1. - structural + structural*temporal)             # <<<<<<<<<<<<<<
- *     # print 'stnv', structural, temporal
+ *     result = log(1. - structural + structural * temporal)             # <<<<<<<<<<<<<<
  *     return result
+ * 
  */
   __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
 
-  /* "ml3.pyx":33
- *     result = log(1. - structural + structural*temporal)
- *     # print 'stnv', structural, temporal
+  /* "ml3.pyx":25
+ *     temporal = exp(-alpha * dt)
+ *     result = log(1. - structural + structural * temporal)
  *     return result             # <<<<<<<<<<<<<<
  * 
  * def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
@@ -1451,7 +1456,7 @@ 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":23
+  /* "ml3.pyx":18
  *     return result
  * 
  * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
@@ -1465,7 +1470,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
   return __pyx_r;
 }
 
-/* "ml3.pyx":35
+/* "ml3.pyx":27
  *     return result
  * 
  * def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,             # <<<<<<<<<<<<<<
@@ -1513,31 +1518,31 @@ 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 = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __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 = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __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 = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __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 = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __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 = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __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 = 35; __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 = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
       }
     } else if (PyTuple_GET_SIZE(__pyx_args) != 6) {
       goto __pyx_L5_argtuple_error;
@@ -1552,21 +1557,21 @@ 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 = 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;}
+    __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 = 27; __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 = 28; __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 = 28; __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 = 35; __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 = 27; __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 = 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;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __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 = 27; __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 = 27; __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 */
@@ -1603,6 +1608,8 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   PyObject *__pyx_v_s = NULL;
   PyObject *__pyx_v_prob = NULL;
   double __pyx_v_thresh;
+  PyObject *__pyx_v_seeds = NULL;
+  PyObject *__pyx_v_non_seeds = NULL;
   int __pyx_v_max_roots;
   PyObject *__pyx_v_w1 = NULL;
   PyObject *__pyx_v_w2 = NULL;
@@ -1671,7 +1678,7 @@ 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":41
+  /* "ml3.pyx":33
  *         DTYPE_t beta, ll, beta_add, max_beta, max_beta_add
  *         list parents, failures, successes
  *     n_roots, n_victims = len(root_victims), len(victims)             # <<<<<<<<<<<<<<
@@ -1680,54 +1687,54 @@ 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 = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __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;}
+  __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __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 = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
-  __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_n_roots = __pyx_t_1;
   __pyx_v_n_victims = __pyx_t_2;
 
-  /* "ml3.pyx":43
+  /* "ml3.pyx":35
  *     n_roots, n_victims = len(root_victims), len(victims)
  *     cdef:
  *         np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE)             # <<<<<<<<<<<<<<
  *         np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
  *         np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
  */
-  __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_4);
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-  __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_5);
   PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3);
   __Pyx_GIVEREF(__pyx_t_3);
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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 = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "ml3.pyx":49
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-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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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+  __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 = 41; __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 = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __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_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "ml3.pyx":54
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  *         # likely parent infects it
  *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
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-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -1971,7 +1978,7 @@ 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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      /* "ml3.pyx":53
+      /* "ml3.pyx":45
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+    __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __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_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 = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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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 = 57; __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 = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __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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+            PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2127,7 +2134,7 @@ 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 = 57; __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 = 49; __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 = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        {__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 = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_26 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_26 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2160,22 +2167,22 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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       __pyx_t_15 = 0;
 
-      /* "ml3.pyx":56
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-      __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;}
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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 = 48; __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 = 48; __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 = 48; __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 = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      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;}
+      if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
 
-      /* "ml3.pyx":57
+      /* "ml3.pyx":49
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     __pyx_t_5 = 0;
 
-    /* "ml3.pyx":58
+    /* "ml3.pyx":50
  *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
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-    __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_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __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 = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __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 = 58; __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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2218,7 +2225,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2254,7 +2261,7 @@ 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 = 58; __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 = 50; __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 = 50; __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_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        /* "ml3.pyx":68
+        /* "ml3.pyx":60
  *                 probs[i] = prob
  *                 parent_dists[i] = dists[l]
  *                 parent_dts[i] = dts[l]             # <<<<<<<<<<<<<<
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  * 
  */
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+        __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_dts, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+        __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_t_3); 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;}
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@@ -2513,7 +2520,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
       }
       __pyx_L23:;
 
-      /* "ml3.pyx":63
+      /* "ml3.pyx":55
  *         # probs[i] = max(s - failures[l] for l, s in enumerate(successes))
  *         probs[i] = float("-inf")
  *         for l, s in enumerate(successes):             # <<<<<<<<<<<<<<
@@ -2525,14 +2532,14 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   }
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-  /* "ml3.pyx":72
+  /* "ml3.pyx":64
  * 
  *     # calculate log likelihood
  *     ll =  probs_fail.sum() # add probability that all edges to all victims fail             # <<<<<<<<<<<<<<
  * 
  *     # print 'probs', probs
  */
-  __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_fail), __pyx_n_s_sum); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_fail), __pyx_n_s_sum); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2545,49 +2552,49 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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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 = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_v_ll = __pyx_t_23;
 
-  /* "ml3.pyx":75
+  /* "ml3.pyx":67
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  *     # print 'probs', probs
  *     max_beta_add = float('-inf')             # <<<<<<<<<<<<<<
  *     # iterate over all victim nodes to find the optimal threshold
- *     for beta in np.arange(0.2, 1., 1.):
+ *     for beta in np.arange(0.2, 1., .1):
  */
-  __pyx_t_27 = __Pyx_PyObject_AsDouble(__pyx_kp_s_inf); if (unlikely(__pyx_t_27 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_27 = __Pyx_PyObject_AsDouble(__pyx_kp_s_inf); if (unlikely(__pyx_t_27 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_max_beta_add = __pyx_t_27;
 
-  /* "ml3.pyx":77
+  /* "ml3.pyx":69
  *     max_beta_add = float('-inf')
  *     # iterate over all victim nodes to find the optimal threshold
- *     for beta in np.arange(0.2, 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])
+ *         seeds = probs<thresh
  */
-  __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_1 = -1; __pyx_t_5 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_33 = Py_TYPE(__pyx_t_5)->tp_iternext; if (unlikely(!__pyx_t_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_33 = Py_TYPE(__pyx_t_5)->tp_iternext; if (unlikely(!__pyx_t_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2595,16 +2602,16 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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         #if CYTHON_COMPILING_IN_CPYTHON
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+        __pyx_t_6 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_1); __Pyx_INCREF(__pyx_t_6); __pyx_t_1++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         #else
-        __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-        __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_1); __Pyx_INCREF(__pyx_t_6); __pyx_t_1++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_1); __Pyx_INCREF(__pyx_t_6); __pyx_t_1++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         #else
-        __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_1); __pyx_t_1++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2613,117 +2620,166 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
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         if (exc_type) {
           if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
-          else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __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;}
+    __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 = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
     __pyx_v_beta = __pyx_t_23;
 
-    /* "ml3.pyx":78
+    /* "ml3.pyx":70
  *     # iterate over all victim nodes to find the optimal threshold
- *     for beta in np.arange(0.2, 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])
+ *         seeds = probs<thresh
+ *         non_seeds = probs>=thresh
  */
     __pyx_v_thresh = log((__pyx_v_beta / (3012. * (1. - __pyx_v_beta))));
 
-    /* "ml3.pyx":80
+    /* "ml3.pyx":71
+ *     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])             # <<<<<<<<<<<<<<
- * 
- *         beta_add = 0.
+ *         seeds = probs<thresh             # <<<<<<<<<<<<<<
+ *         non_seeds = probs>=thresh
+ *         roots = n_roots + sum(seeds)
  */
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+    __pyx_t_6 = PyFloat_FromDouble(__pyx_v_thresh); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __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;}
+    __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 = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_3 = 0;
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+    /* "ml3.pyx":72
+ *         thresh = log(beta/(3012.*(1.-beta)))
+ *         seeds = probs<thresh
+ *         non_seeds = probs>=thresh             # <<<<<<<<<<<<<<
+ *         roots = n_roots + sum(seeds)
+ * 
+ */
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+    __pyx_t_6 = 0;
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+    /* "ml3.pyx":73
+ *         seeds = probs<thresh
+ *         non_seeds = probs>=thresh
+ *         roots = n_roots + sum(seeds)             # <<<<<<<<<<<<<<
+ * 
+ *         beta_add = 0.
+ */
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+    PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_seeds);
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+    __Pyx_GOTREF(__pyx_t_3);
     __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-    __pyx_v_roots = (__pyx_v_n_roots + __pyx_t_2);
+    __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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-    /* "ml3.pyx":82
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+    /* "ml3.pyx":75
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  * 
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- *         beta_add += (probs[probs>=thresh]).sum()
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  */
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-    /* "ml3.pyx":84
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+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+    __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_t_16); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
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-    /* "ml3.pyx":88
- *         beta_add += roots * log(beta/3012.) + len(probs[probs>=thresh]) * log(1. - beta)
+    /* "ml3.pyx":83
+ *         beta_add += roots * log(beta/3012.) + sum(non_seeds) * log(1. - beta)
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-      /* "ml3.pyx":91
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-    /* "ml3.pyx":77
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+ *         seeds = probs<thresh
  */
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-  /* "ml3.pyx":94
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-  /* "ml3.pyx":95
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-  /* "ml3.pyx":98
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-  /* "ml3.pyx":35
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   __Pyx_XDECREF(__pyx_v_s);
   __Pyx_XDECREF(__pyx_v_prob);
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   {&__pyx_n_s_non_victims, __pyx_k_non_victims, sizeof(__pyx_k_non_victims), 0, 0, 1, 1},
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   {&__pyx_n_s_s, __pyx_k_s, sizeof(__pyx_k_s), 0, 0, 1, 1},
+  {&__pyx_n_s_seeds, __pyx_k_seeds, sizeof(__pyx_k_seeds), 0, 0, 1, 1},
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+  __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "ml3.pyx":77
+  /* "ml3.pyx":69
  *     max_beta_add = float('-inf')
  *     # iterate over all victim nodes to find the optimal threshold
- *     for beta in np.arange(0.2, 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])
+ *         seeds = probs<thresh
  */
-  __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_2, __pyx_float_1_, __pyx_float_1_); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_2, __pyx_float_1_, __pyx_float__1); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -5060,17 +5120,17 @@ static int __Pyx_InitCachedConstants(void) {
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-  /* "ml3.pyx":35
+  /* "ml3.pyx":27
  *     return result
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  *        DTYPE_t alpha, DTYPE_t delta):
  *     cdef:
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@@ -5080,6 +5140,7 @@ static int __Pyx_InitCachedConstants(void) {
 
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+  __pyx_float__1 = PyFloat_FromDouble(.1); if (unlikely(!__pyx_float__1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_float_1_ = PyFloat_FromDouble(1.); if (unlikely(!__pyx_float_1_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-  /* "ml3.pyx":35
+  /* "ml3.pyx":27
  *     return result
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  * def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,             # <<<<<<<<<<<<<<
  *        DTYPE_t alpha, DTYPE_t delta):
  *     cdef:
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+  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_3ml3_1ml3, NULL, __pyx_n_s_ml3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml3, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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