Continuing to experiment. Identifying infections vs seeds might be

impossible :/. We may want to try a model where we just assume
infections — can get parameters for the benchmark test.

7 files changed, 564 insertions, 1111 deletions

diff --git a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o
index 5018cbc..cbe973b 100644
--- a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o
+++ b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o
diff --git a/experiments/ml.c b/experiments/ml.c
index 976accb..cdf4064 100644
--- a/experiments/ml.c
+++ b/experiments/ml.c
@@ -759,7 +759,7 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
  */
 typedef npy_cdouble __pyx_t_5numpy_complex_t;
 
-/* "ml.pyx":37
+/* "ml.pyx":38
  *     return result
  * 
  * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,             # <<<<<<<<<<<<<<
@@ -773,7 +773,7 @@ struct __pyx_obj_2ml___pyx_scope_struct__ml {
 };
 
 
-/* "ml.pyx":61
+/* "ml.pyx":62
  *                      for (dist, dt, w1, w2, w3) in parents]
  *         # find parent that maximizes log(p) - log(\tilde{p})
  *         probs[i] = max(s - failures[l] for l, s in enumerate(successes))             # <<<<<<<<<<<<<<
@@ -990,6 +990,8 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj);
  PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
 #endif
 
+static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
+
 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
 
 #if PY_MAJOR_VERSION >= 3
@@ -1070,8 +1072,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
 
 static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
 
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
-
 #if CYTHON_CCOMPLEX
   #ifdef __cplusplus
     #define __Pyx_CREAL(z) ((z).real())
@@ -1170,6 +1170,8 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
     #endif
 #endif
 
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
+
 static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
 
 static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
@@ -1266,7 +1268,6 @@ int __pyx_module_is_main_ml = 0;
 static PyObject *__pyx_builtin_enumerate;
 static PyObject *__pyx_builtin_sum;
 static PyObject *__pyx_builtin_max;
-static PyObject *__pyx_builtin_xrange;
 static PyObject *__pyx_builtin_ValueError;
 static PyObject *__pyx_builtin_range;
 static PyObject *__pyx_builtin_RuntimeError;
@@ -1287,7 +1288,7 @@ static char __pyx_k_d[] = "d";
 static char __pyx_k_f[] = "f";
 static char __pyx_k_g[] = "g";
 static char __pyx_k_h[] = "h";
-static char __pyx_k_i[] = "i:";
+static char __pyx_k_i[] = "i";
 static char __pyx_k_l[] = "l";
 static char __pyx_k_q[] = "q";
 static char __pyx_k_t[] = "t";
@@ -1298,14 +1299,11 @@ static char __pyx_k_dt[] = "dt";
 static char __pyx_k_ll[] = "ll";
 static char __pyx_k_ml[] = "ml";
 static char __pyx_k_np[] = "np";
-static char __pyx_k_st[] = "st";
 static char __pyx_k_w1[] = "w1";
 static char __pyx_k_w2[] = "w2";
 static char __pyx_k_w3[] = "w3";
-static char __pyx_k_add[] = "add:";
 static char __pyx_k_age[] = "age";
 static char __pyx_k_end[] = "end";
-static char __pyx_k_i_2[] = "i";
 static char __pyx_k_inf[] = "-inf";
 static char __pyx_k_max[] = "max";
 static char __pyx_k_sum[] = "sum";
@@ -1315,37 +1313,34 @@ static char __pyx_k_dist[] = "dist";
 static char __pyx_k_file[] = "file";
 static char __pyx_k_main[] = "__main__";
 static char __pyx_k_send[] = "send";
-static char __pyx_k_stnv[] = "stnv";
 static char __pyx_k_test[] = "__test__";
 static char __pyx_k_DTYPE[] = "DTYPE";
 static char __pyx_k_alpha[] = "alpha";
-static char __pyx_k_beta2[] = "beta2";
 static char __pyx_k_close[] = "close";
 static char __pyx_k_delta[] = "delta";
 static char __pyx_k_dtype[] = "dtype";
-static char __pyx_k_max_i[] = "max_i";
 static char __pyx_k_numpy[] = "numpy";
 static char __pyx_k_print[] = "print";
 static char __pyx_k_probs[] = "probs";
 static char __pyx_k_range[] = "range";
-static char __pyx_k_roots[] = "roots:";
+static char __pyx_k_roots[] = "roots";
 static char __pyx_k_throw[] = "throw";
 static char __pyx_k_zeros[] = "zeros";
+static char __pyx_k_arange[] = "arange";
 static char __pyx_k_import[] = "__import__";
-static char __pyx_k_thresh[] = "thresh:";
-static char __pyx_k_xrange[] = "xrange";
+static char __pyx_k_thresh[] = "thresh";
 static char __pyx_k_float64[] = "float64";
 static char __pyx_k_genexpr[] = "genexpr";
 static char __pyx_k_n_nodes[] = "n_nodes";
 static char __pyx_k_n_roots[] = "n_roots";
 static char __pyx_k_parents[] = "parents";
-static char __pyx_k_roots_2[] = "roots";
 static char __pyx_k_victims[] = "victims";
 static char __pyx_k_beta_add[] = "beta_add";
 static char __pyx_k_failures[] = "failures";
+static char __pyx_k_max_beta[] = "max_beta";
 static char __pyx_k_probs_nv[] = "probs_nv";
-static char __pyx_k_thresh_2[] = "thresh";
 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_successes[] = "successes";
 static char __pyx_k_ValueError[] = "ValueError";
@@ -1357,7 +1352,6 @@ static char __pyx_k_max_beta_add[] = "max_beta_add";
 static char __pyx_k_root_victims[] = "root_victims";
 static char __pyx_k_UNDERFLOW_ERROR[] = "UNDERFLOW ERROR";
 static char __pyx_k_ml_locals_genexpr[] = "ml.<locals>.genexpr";
-static char __pyx_k_len_probs_probs_thresh[] = "len(probs[probs>=thresh]):";
 static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
 static char __pyx_k_Users_ben_Documents_Cascade_Pro[] = "/Users/ben/Documents/Cascade Project/criminal_cascades/experiments/ml.pyx";
 static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
@@ -1373,12 +1367,11 @@ static PyObject *__pyx_n_s_RuntimeError;
 static PyObject *__pyx_kp_s_UNDERFLOW_ERROR;
 static PyObject *__pyx_kp_s_Users_ben_Documents_Cascade_Pro;
 static PyObject *__pyx_n_s_ValueError;
-static PyObject *__pyx_kp_s_add;
 static PyObject *__pyx_n_s_age;
 static PyObject *__pyx_n_s_alpha;
+static PyObject *__pyx_n_s_arange;
 static PyObject *__pyx_n_s_args;
 static PyObject *__pyx_n_s_beta;
-static PyObject *__pyx_n_s_beta2;
 static PyObject *__pyx_n_s_beta_add;
 static PyObject *__pyx_n_s_close;
 static PyObject *__pyx_n_s_delta;
@@ -1391,18 +1384,17 @@ static PyObject *__pyx_n_s_failures;
 static PyObject *__pyx_n_s_file;
 static PyObject *__pyx_n_s_float64;
 static PyObject *__pyx_n_s_genexpr;
-static PyObject *__pyx_kp_s_i;
-static PyObject *__pyx_n_s_i_2;
+static PyObject *__pyx_n_s_i;
 static PyObject *__pyx_n_s_import;
 static PyObject *__pyx_kp_s_inf;
 static PyObject *__pyx_n_s_itervalues;
 static PyObject *__pyx_n_s_l;
-static PyObject *__pyx_kp_s_len_probs_probs_thresh;
 static PyObject *__pyx_n_s_ll;
 static PyObject *__pyx_n_s_main;
 static PyObject *__pyx_n_s_max;
+static PyObject *__pyx_n_s_max_beta;
 static PyObject *__pyx_n_s_max_beta_add;
-static PyObject *__pyx_n_s_max_i;
+static PyObject *__pyx_n_s_max_roots;
 static PyObject *__pyx_n_s_ml;
 static PyObject *__pyx_n_s_ml_locals_genexpr;
 static PyObject *__pyx_n_s_n_nodes;
@@ -1420,26 +1412,23 @@ static PyObject *__pyx_n_s_probs_fail;
 static PyObject *__pyx_n_s_probs_nv;
 static PyObject *__pyx_n_s_range;
 static PyObject *__pyx_n_s_root_victims;
-static PyObject *__pyx_kp_s_roots;
-static PyObject *__pyx_n_s_roots_2;
+static PyObject *__pyx_n_s_roots;
 static PyObject *__pyx_n_s_send;
-static PyObject *__pyx_n_s_st;
-static PyObject *__pyx_n_s_stnv;
 static PyObject *__pyx_n_s_successes;
 static PyObject *__pyx_n_s_sum;
 static PyObject *__pyx_n_s_t;
 static PyObject *__pyx_n_s_test;
-static PyObject *__pyx_kp_s_thresh;
-static PyObject *__pyx_n_s_thresh_2;
+static PyObject *__pyx_n_s_thresh;
 static PyObject *__pyx_n_s_throw;
 static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd;
 static PyObject *__pyx_n_s_victims;
 static PyObject *__pyx_n_s_w1;
 static PyObject *__pyx_n_s_w2;
 static PyObject *__pyx_n_s_w3;
-static PyObject *__pyx_n_s_xrange;
 static PyObject *__pyx_n_s_zeros;
-static PyObject *__pyx_int_neg_1;
+static PyObject *__pyx_float__1;
+static PyObject *__pyx_float__001;
+static PyObject *__pyx_float_0_001;
 static PyObject *__pyx_tuple_;
 static PyObject *__pyx_tuple__2;
 static PyObject *__pyx_tuple__3;
@@ -1447,7 +1436,8 @@ static PyObject *__pyx_tuple__4;
 static PyObject *__pyx_tuple__5;
 static PyObject *__pyx_tuple__6;
 static PyObject *__pyx_tuple__7;
-static PyObject *__pyx_codeobj__8;
+static PyObject *__pyx_tuple__8;
+static PyObject *__pyx_codeobj__9;
 
 /* "ml.pyx":9
  * ctypedef np.float_t DTYPE_t
@@ -1501,9 +1491,6 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
   __pyx_t_2ml_DTYPE_t __pyx_r;
   __Pyx_RefNannyDeclarations
   int __pyx_t_1;
-  PyObject *__pyx_t_2 = NULL;
-  PyObject *__pyx_t_3 = NULL;
-  PyObject *__pyx_t_4 = NULL;
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
@@ -1514,70 +1501,45 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
  *     cdef DTYPE_t structural, temporal, result
  *     structural = delta ** dist             # <<<<<<<<<<<<<<
  *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
- *     temporal = exp(-alpha*dt) * (exp(alpha)-1)
+ *     # temporal = exp(-alpha*dt) * (exp(alpha)-1)
  */
   __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist));
 
-  /* "ml.pyx":18
- *     structural = delta ** dist
+  /* "ml.pyx":19
  *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
- *     temporal = exp(-alpha*dt) * (exp(alpha)-1)             # <<<<<<<<<<<<<<
+ *     # temporal = exp(-alpha*dt) * (exp(alpha)-1)
+ *     temporal = 1 - exp(-alpha*dt)             # <<<<<<<<<<<<<<
  *     if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
  *     # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
  */
-  __pyx_v_temporal = (exp(((-__pyx_v_alpha) * __pyx_v_dt)) * (exp(__pyx_v_alpha) - 1.0));
+  __pyx_v_temporal = (1.0 - exp(((-__pyx_v_alpha) * __pyx_v_dt)));
 
-  /* "ml.pyx":19
- *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
- *     temporal = exp(-alpha*dt) * (exp(alpha)-1)
+  /* "ml.pyx":20
+ *     # temporal = exp(-alpha*dt) * (exp(alpha)-1)
+ *     temporal = 1 - exp(-alpha*dt)
  *     if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'             # <<<<<<<<<<<<<<
  *     # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
  *     result = log(structural * temporal)
  */
   __pyx_t_1 = ((exp(((-__pyx_v_alpha) * __pyx_v_dt)) == 0.) != 0);
   if (__pyx_t_1) {
-    if (__Pyx_PrintOne(0, __pyx_kp_s_UNDERFLOW_ERROR) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (__Pyx_PrintOne(0, __pyx_kp_s_UNDERFLOW_ERROR) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     goto __pyx_L3;
   }
   __pyx_L3:;
 
-  /* "ml.pyx":21
+  /* "ml.pyx":22
  *     if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
  *     # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
  *     result = log(structural * temporal)             # <<<<<<<<<<<<<<
- *     print 'st', structural, temporal
+ *     # print 'st', structural, temporal
  *     return result
  */
   __pyx_v_result = log((__pyx_v_structural * __pyx_v_temporal));
 
-  /* "ml.pyx":22
- *     # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
+  /* "ml.pyx":24
  *     result = log(structural * temporal)
- *     print 'st', structural, temporal             # <<<<<<<<<<<<<<
- *     return result
- * 
- */
-  __pyx_t_2 = PyFloat_FromDouble(__pyx_v_structural); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_2);
-  __pyx_t_3 = PyFloat_FromDouble(__pyx_v_temporal); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_3);
-  __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_4);
-  __Pyx_INCREF(__pyx_n_s_st);
-  PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_n_s_st);
-  __Pyx_GIVEREF(__pyx_n_s_st);
-  PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_2);
-  __Pyx_GIVEREF(__pyx_t_2);
-  PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_t_3);
-  __Pyx_GIVEREF(__pyx_t_3);
-  __pyx_t_2 = 0;
-  __pyx_t_3 = 0;
-  if (__Pyx_Print(0, __pyx_t_4, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 22; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-
-  /* "ml.pyx":23
- *     result = log(structural * temporal)
- *     print 'st', structural, temporal
+ *     # print 'st', structural, temporal
  *     return result             # <<<<<<<<<<<<<<
  * 
  * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
@@ -1595,9 +1557,6 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
 
   /* function exit code */
   __pyx_L1_error:;
-  __Pyx_XDECREF(__pyx_t_2);
-  __Pyx_XDECREF(__pyx_t_3);
-  __Pyx_XDECREF(__pyx_t_4);
   __Pyx_WriteUnraisable("ml.weight_success", __pyx_clineno, __pyx_lineno, __pyx_filename, 0);
   __pyx_r = 0;
   __pyx_L0:;
@@ -1605,7 +1564,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
   return __pyx_r;
 }
 
-/* "ml.pyx":25
+/* "ml.pyx":26
  *     return result
  * 
  * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
@@ -1619,15 +1578,9 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
   __pyx_t_2ml_DTYPE_t __pyx_v_result;
   __pyx_t_2ml_DTYPE_t __pyx_r;
   __Pyx_RefNannyDeclarations
-  PyObject *__pyx_t_1 = NULL;
-  PyObject *__pyx_t_2 = NULL;
-  PyObject *__pyx_t_3 = NULL;
-  int __pyx_lineno = 0;
-  const char *__pyx_filename = NULL;
-  int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("weight_failure", 0);
 
-  /* "ml.pyx":29
+  /* "ml.pyx":30
  *     """weight for failed infection, exponential time model"""
  *     cdef DTYPE_t structural, temporal, result
  *     structural = delta ** dist             # <<<<<<<<<<<<<<
@@ -1636,7 +1589,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
  */
   __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist));
 
-  /* "ml.pyx":31
+  /* "ml.pyx":32
  *     structural = delta ** dist
  *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
  *     temporal = exp(-alpha * dt)             # <<<<<<<<<<<<<<
@@ -1645,43 +1598,18 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
  */
   __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt));
 
-  /* "ml.pyx":33
+  /* "ml.pyx":34
  *     temporal = exp(-alpha * dt)
  *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
  *     result = log(1. - structural + structural * temporal)             # <<<<<<<<<<<<<<
- *     print 'stnv', structural, temporal
+ *     # print 'stnv', structural, temporal
  *     return result
  */
   __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
 
-  /* "ml.pyx":34
- *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
- *     result = log(1. - structural + structural * temporal)
- *     print 'stnv', structural, temporal             # <<<<<<<<<<<<<<
- *     return result
- * 
- */
-  __pyx_t_1 = PyFloat_FromDouble(__pyx_v_structural); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_1);
-  __pyx_t_2 = PyFloat_FromDouble(__pyx_v_temporal); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_2);
-  __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_3);
-  __Pyx_INCREF(__pyx_n_s_stnv);
-  PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_n_s_stnv);
-  __Pyx_GIVEREF(__pyx_n_s_stnv);
-  PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
-  __Pyx_GIVEREF(__pyx_t_1);
-  PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_t_2);
-  __Pyx_GIVEREF(__pyx_t_2);
-  __pyx_t_1 = 0;
-  __pyx_t_2 = 0;
-  if (__Pyx_Print(0, __pyx_t_3, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-
-  /* "ml.pyx":35
+  /* "ml.pyx":36
  *     result = log(1. - structural + structural * temporal)
- *     print 'stnv', structural, temporal
+ *     # print 'stnv', structural, temporal
  *     return result             # <<<<<<<<<<<<<<
  * 
  * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
@@ -1689,7 +1617,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
   __pyx_r = __pyx_v_result;
   goto __pyx_L0;
 
-  /* "ml.pyx":25
+  /* "ml.pyx":26
  *     return result
  * 
  * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
@@ -1698,18 +1626,12 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
  */
 
   /* function exit code */
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-  __Pyx_XDECREF(__pyx_t_1);
-  __Pyx_XDECREF(__pyx_t_2);
-  __Pyx_XDECREF(__pyx_t_3);
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-/* "ml.pyx":37
+/* "ml.pyx":38
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@@ -1757,31 +1679,31 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py
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-          __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-          __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-          __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+          __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+          __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -1796,21 +1718,21 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py
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-    __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 = 38; __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 = 38; __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 = 39; __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 = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-  __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __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 = 37; __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 = 38; __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 = 38; __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 = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   /* function exit code */
@@ -1823,7 +1745,7 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py
 }
 static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
 
-/* "ml.pyx":61
+/* "ml.pyx":62
  *                      for (dist, dt, w1, w2, w3) in parents]
  *         # find parent that maximizes log(p) - log(\tilde{p})
  *         probs[i] = max(s - failures[l] for l, s in enumerate(successes))             # <<<<<<<<<<<<<<
@@ -1849,7 +1771,7 @@ static PyObject *__pyx_pf_2ml_2ml_genexpr(PyObject *__pyx_self) {
   __Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_outer_scope));
   __Pyx_GIVEREF(__pyx_cur_scope->__pyx_outer_scope);
   {
-    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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     __Pyx_RefNannyFinishContext();
     return (PyObject *) gen;
@@ -1887,16 +1809,16 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera
     return NULL;
   }
   __pyx_L3_first_run:;
-  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_t_1 = 0;
-  if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+  if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
   __pyx_t_2 = __pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
   for (;;) {
     if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
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-    __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; 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_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; 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_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -1904,14 +1826,14 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera
     __pyx_t_4 = 0;
     __pyx_cur_scope->__pyx_v_l = __pyx_t_1;
     __pyx_t_1 = (__pyx_t_1 + 1);
-    if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures)) { __Pyx_RaiseClosureNameError("failures"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+    if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures)) { __Pyx_RaiseClosureNameError("failures"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
     if (unlikely(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures == Py_None)) {
       PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures, __pyx_cur_scope->__pyx_v_l, Py_ssize_t, 1, PyInt_FromSsize_t, 1, 1, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+    __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures, __pyx_cur_scope->__pyx_v_l, Py_ssize_t, 1, PyInt_FromSsize_t, 1, 1, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
     __Pyx_GOTREF(__pyx_t_4);
-    __pyx_t_5 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -1931,7 +1853,7 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera
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-    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -1951,7 +1873,7 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera
   return NULL;
 }
 
-/* "ml.pyx":37
+/* "ml.pyx":38
  *     return result
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@@ -1974,10 +1896,11 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
   PyArrayObject *__pyx_v_probs = 0;
   PyArrayObject *__pyx_v_probs_fail = 0;
   PyArrayObject *__pyx_v_probs_nv = 0;
-  PyObject *__pyx_v_max_i = NULL;
   PyObject *__pyx_v_max_beta_add = NULL;
   double __pyx_v_thresh;
   PyObject *__pyx_v_beta_add = NULL;
+  PyObject *__pyx_v_max_beta = NULL;
+  int __pyx_v_max_roots;
   PyObject *__pyx_v_w1 = NULL;
   PyObject *__pyx_v_w2 = NULL;
   PyObject *__pyx_v_w3 = NULL;
@@ -2014,10 +1937,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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   __pyx_t_2ml_DTYPE_t __pyx_t_24;
   int __pyx_t_25;
-  int __pyx_t_26;
-  double __pyx_t_27;
-  long __pyx_t_28;
-  int __pyx_t_29;
+  double __pyx_t_26;
+  PyObject *(*__pyx_t_27)(PyObject *);
+  int __pyx_t_28;
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
@@ -2041,72 +1963,72 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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   __pyx_pybuffernd_probs_nv.rcbuffer = &__pyx_pybuffer_probs_nv;
 
-  /* "ml.pyx":43
- *         DTYPE_t beta, ll, beta2
+  /* "ml.pyx":44
+ *         DTYPE_t beta, ll
  *         list parents, failures, successes
  *     n_roots, n_victims = len(root_victims), len(victims)             # <<<<<<<<<<<<<<
- *     n_nodes = 4#148152
+ *     n_nodes = 11270
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-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __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 = 43; __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 = 44; __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 = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __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 = 43; __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 = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_n_roots = __pyx_t_1;
   __pyx_v_n_victims = __pyx_t_2;
 
-  /* "ml.pyx":44
+  /* "ml.pyx":45
  *         list parents, failures, successes
  *     n_roots, n_victims = len(root_victims), len(victims)
- *     n_nodes = 4#148152             # <<<<<<<<<<<<<<
+ *     n_nodes = 11270             # <<<<<<<<<<<<<<
  *     cdef:
  *         np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE)
  */
-  __pyx_v_n_nodes = 4;
+  __pyx_v_n_nodes = 11270;
 
-  /* "ml.pyx":46
- *     n_nodes = 4#148152
+  /* "ml.pyx":47
+ *     n_nodes = 11270
  *     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] probs_nv = np.zeros(len(non_victims), dtype=DTYPE)
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@@ -2218,9 +2140,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
   __pyx_t_2 = 0;
   if (unlikely(__pyx_v_victims == Py_None)) {
     PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues");
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
-  __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_4);
   __Pyx_XDECREF(__pyx_t_3);
   __pyx_t_3 = __pyx_t_4;
@@ -2228,25 +2150,25 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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     __pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_3, __pyx_t_1, &__pyx_t_2, NULL, &__pyx_t_4, NULL, __pyx_t_11);
     if (unlikely(__pyx_t_12 == 0)) break;
-    if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
-    if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_4));
     __pyx_t_4 = 0;
     __pyx_v_i = __pyx_t_10;
     __pyx_t_10 = (__pyx_t_10 + 1);
 
-    /* "ml.pyx":55
+    /* "ml.pyx":56
  *         # fail to infect it, also computes the probability that its most
  *         # 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)
  */
-    __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
 
-    /* "ml.pyx":56
+    /* "ml.pyx":57
  *         # likely parent infects it
  *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
  *                     for (dist, dt, w1, w2, w3) in parents]             # <<<<<<<<<<<<<<
@@ -2255,15 +2177,15 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
  */
     if (unlikely(__pyx_v_parents == Py_None)) {
       PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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_13 = 0;
     for (;;) {
       if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_5)) break;
       #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_6 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       #else
-      __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       #endif
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         PyObject* sequence = __pyx_t_6;
@@ -2275,7 +2197,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
         if (unlikely(size != 5)) {
           if (size > 5) __Pyx_RaiseTooManyValuesError(5);
           else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
-          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         }
         #if CYTHON_COMPILING_IN_CPYTHON
         if (likely(PyTuple_CheckExact(sequence))) {
@@ -2301,7 +2223,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
           Py_ssize_t i;
           PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18};
           for (i=0; i < 5; i++) {
-            PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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;}
             __Pyx_GOTREF(item);
             *(temps[i]) = item;
           }
@@ -2311,7 +2233,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
       } else {
         Py_ssize_t index = -1;
         PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18};
-        __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __Pyx_GOTREF(__pyx_t_19);
         __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
         __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext;
@@ -2320,7 +2242,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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           *(temps[index]) = item;
         }
-        if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __pyx_t_20 = NULL;
         __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
         goto __pyx_L8_unpacking_done;
@@ -2328,12 +2250,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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         __pyx_t_20 = NULL;
         if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
-        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
         __pyx_L8_unpacking_done:;
       }
-      __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
-      __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
       __pyx_v_dist = __pyx_t_12;
       __pyx_v_dt = __pyx_t_21;
@@ -2344,22 +2266,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
       __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_18);
       __pyx_t_18 = 0;
 
-      /* "ml.pyx":55
+      /* "ml.pyx":56
  *         # fail to infect it, also computes the probability that its most
  *         # 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)
  */
-      __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_22, __pyx_t_23, __pyx_t_24)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_22 == (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_w2); 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_24 = __pyx_PyFloat_AsDouble(__pyx_v_w3); 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_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_22, __pyx_t_23, __pyx_t_24)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_6);
-      if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
 
-      /* "ml.pyx":56
+      /* "ml.pyx":57
  *         # likely parent infects it
  *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
  *                     for (dist, dt, w1, w2, w3) in parents]             # <<<<<<<<<<<<<<
@@ -2373,38 +2295,38 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
     __Pyx_GIVEREF(__pyx_t_4);
     __pyx_t_4 = 0;
 
-    /* "ml.pyx":57
+    /* "ml.pyx":58
  *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
  *                     for (dist, dt, w1, w2, w3) in parents]
  *         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_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_4);
     __Pyx_INCREF(__pyx_cur_scope->__pyx_v_failures);
     PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_cur_scope->__pyx_v_failures);
     __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_failures);
-    __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_4, NULL); 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);
     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
-    __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
     __pyx_t_21 = __pyx_v_i;
     if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_pybuffernd_probs_fail.diminfo[0].shape;
     *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_24;
 
-    /* "ml.pyx":58
+    /* "ml.pyx":59
  *                     for (dist, dt, w1, w2, w3) in parents]
  *         probs_fail[i] = sum(failures)
  *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
  *                      for (dist, dt, w1, w2, w3) in parents]
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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 = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_5);
 
-    /* "ml.pyx":59
+    /* "ml.pyx":60
  *         probs_fail[i] = sum(failures)
  *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
  *                      for (dist, dt, w1, w2, w3) in parents]             # <<<<<<<<<<<<<<
@@ -2413,15 +2335,15 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
  */
     if (unlikely(__pyx_v_parents == Py_None)) {
       PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     }
     __pyx_t_4 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_4); __pyx_t_13 = 0;
     for (;;) {
       if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_4)) break;
       #if CYTHON_COMPILING_IN_CPYTHON
-      __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       #else
-      __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       #endif
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@@ -2433,7 +2355,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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-          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+          {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+        __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __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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+          else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        }
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+      }
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     /* "ml.pyx":83
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-
-    /* "ml.pyx":84
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- *         beta = 1. / (1. + exp(-probs[i]))
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- */
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-    /* "ml.pyx":85
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- *         beta = 1. / (1. + exp(-probs[i]))             # <<<<<<<<<<<<<<
- *         thresh = log(beta/(1.-beta))
- *         print 'thresh:', thresh
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-
-    /* "ml.pyx":86
- *         roots = n_roots + n_victims - i
- *         beta = 1. / (1. + exp(-probs[i]))
+ *     for beta in np.arange(0.001, .1, .001):
  *         thresh = log(beta/(1.-beta))             # <<<<<<<<<<<<<<
- *         print 'thresh:', thresh
- * 
+ *         # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
+ *         roots = n_roots + len(probs[probs<thresh])
  */
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-    /* "ml.pyx":87
- *         beta = 1. / (1. + exp(-probs[i]))
+    /* "ml.pyx":85
  *         thresh = log(beta/(1.-beta))
- *         print 'thresh:', thresh             # <<<<<<<<<<<<<<
+ *         # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
+ *         roots = n_roots + len(probs[probs<thresh])             # <<<<<<<<<<<<<<
  * 
  *         # add probability for realized edges and subtract probability these edges fail
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     __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+    /* "ml.pyx":88
  * 
  *         # add probability for realized edges and subtract probability these edges fail
  *         beta_add = (probs[probs>=thresh]).sum()             # <<<<<<<<<<<<<<
- *         print 'len(probs[probs>=thresh]):', len(probs[probs>=thresh])
  *         # add probability for the seeds and non-seeds
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-    __Pyx_GOTREF(__pyx_t_5);
+    __pyx_t_3 = PyFloat_FromDouble(__pyx_v_thresh); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_3 = PyObject_GetItem(((PyObject *)__pyx_v_probs), __pyx_t_6); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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+    __Pyx_GOTREF(__pyx_t_6);
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-      __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+    if (__pyx_t_3) {
+      __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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- *         # add probability for realized edges and subtract probability these edges fail
+    /* "ml.pyx":90
  *         beta_add = (probs[probs>=thresh]).sum()
- *         print 'len(probs[probs>=thresh]):', len(probs[probs>=thresh])             # <<<<<<<<<<<<<<
- *         # add probability for the seeds and non-seeds
- *         beta_add += roots * log(beta) + (n_nodes-roots) * log(1 - beta)
- */
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+    /* "ml.pyx":92
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-      /* "ml.pyx":96
+      /* "ml.pyx":93
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+ *             max_beta = beta             # <<<<<<<<<<<<<<
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+      /* "ml.pyx":94
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+ *             max_beta = beta
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+ */
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+      /* "ml.pyx":95
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- *             print 'i:', max_i, 'add:', max_beta_add, 'roots:', roots
- *         else:
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+ * 
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-      goto __pyx_L21;
+      goto __pyx_L15;
     }
-    /*else*/ {
+    __pyx_L15:;
 
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- *         else:
- *             print i             # <<<<<<<<<<<<<<
- * 
- *     ll += max_beta_add
+    /* "ml.pyx":82
+ *     max_beta_add = float('-inf')
+ *     # iterate over all victim nodes to find the optimal threshold
+ *     for beta in np.arange(0.001, .1, .001):             # <<<<<<<<<<<<<<
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-    __pyx_L21:;
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+  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
 
-  /* "ml.pyx":102
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+  /* "ml.pyx":98
+ *             # print 'beta:', max_beta, 'add:', max_beta_add, 'roots:', max_roots
  * 
  *     ll += max_beta_add             # <<<<<<<<<<<<<<
- *     roots = n_roots + n_victims - max_i
- *     beta = float(roots)/float(n_nodes)
+ *     roots = max_roots
+ *     beta = max_beta
  */
-  __pyx_t_3 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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+  __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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-  /* "ml.pyx":103
+  /* "ml.pyx":99
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  *     ll += max_beta_add
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- *     beta = float(roots)/float(n_nodes)
+ *     roots = max_roots             # <<<<<<<<<<<<<<
+ *     beta = max_beta
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-  __pyx_v_roots = __pyx_t_10;
+  __pyx_v_roots = __pyx_v_max_roots;
 
-  /* "ml.pyx":104
+  /* "ml.pyx":100
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- *     beta = float(roots)/float(n_nodes)             # <<<<<<<<<<<<<<
+ *     roots = max_roots
+ *     beta = max_beta             # <<<<<<<<<<<<<<
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  *     return (beta, roots, ll)
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+  if (unlikely(!__pyx_v_max_beta)) { __Pyx_RaiseUnboundLocalError("max_beta"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
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-  /* "ml.pyx":106
- *     beta = float(roots)/float(n_nodes)
+  /* "ml.pyx":102
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-  __Pyx_GIVEREF(__pyx_t_4);
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+  __Pyx_GIVEREF(__pyx_t_4);
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+  __pyx_t_5 = 0;
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+  __pyx_t_3 = 0;
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-  /* "ml.pyx":37
+  /* "ml.pyx":38
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   __Pyx_XDECREF(__pyx_v_max_beta_add);
   __Pyx_XDECREF(__pyx_v_beta_add);
+  __Pyx_XDECREF(__pyx_v_max_beta);
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   {&__pyx_n_s_ml, __pyx_k_ml, sizeof(__pyx_k_ml), 0, 0, 1, 1},
   {&__pyx_n_s_ml_locals_genexpr, __pyx_k_ml_locals_genexpr, sizeof(__pyx_k_ml_locals_genexpr), 0, 0, 1, 1},
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-  {&__pyx_kp_s_roots, __pyx_k_roots, sizeof(__pyx_k_roots), 0, 0, 1, 0},
-  {&__pyx_n_s_roots_2, __pyx_k_roots_2, sizeof(__pyx_k_roots_2), 0, 0, 1, 1},
+  {&__pyx_n_s_roots, __pyx_k_roots, sizeof(__pyx_k_roots), 0, 0, 1, 1},
   {&__pyx_n_s_send, __pyx_k_send, sizeof(__pyx_k_send), 0, 0, 1, 1},
-  {&__pyx_n_s_st, __pyx_k_st, sizeof(__pyx_k_st), 0, 0, 1, 1},
-  {&__pyx_n_s_stnv, __pyx_k_stnv, sizeof(__pyx_k_stnv), 0, 0, 1, 1},
   {&__pyx_n_s_successes, __pyx_k_successes, sizeof(__pyx_k_successes), 0, 0, 1, 1},
   {&__pyx_n_s_sum, __pyx_k_sum, sizeof(__pyx_k_sum), 0, 0, 1, 1},
   {&__pyx_n_s_t, __pyx_k_t, sizeof(__pyx_k_t), 0, 0, 1, 1},
   {&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
-  {&__pyx_kp_s_thresh, __pyx_k_thresh, sizeof(__pyx_k_thresh), 0, 0, 1, 0},
-  {&__pyx_n_s_thresh_2, __pyx_k_thresh_2, sizeof(__pyx_k_thresh_2), 0, 0, 1, 1},
+  {&__pyx_n_s_thresh, __pyx_k_thresh, sizeof(__pyx_k_thresh), 0, 0, 1, 1},
   {&__pyx_n_s_throw, __pyx_k_throw, sizeof(__pyx_k_throw), 0, 0, 1, 1},
   {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0},
   {&__pyx_n_s_victims, __pyx_k_victims, sizeof(__pyx_k_victims), 0, 0, 1, 1},
   {&__pyx_n_s_w1, __pyx_k_w1, sizeof(__pyx_k_w1), 0, 0, 1, 1},
   {&__pyx_n_s_w2, __pyx_k_w2, sizeof(__pyx_k_w2), 0, 0, 1, 1},
   {&__pyx_n_s_w3, __pyx_k_w3, sizeof(__pyx_k_w3), 0, 0, 1, 1},
-  {&__pyx_n_s_xrange, __pyx_k_xrange, sizeof(__pyx_k_xrange), 0, 0, 1, 1},
   {&__pyx_n_s_zeros, __pyx_k_zeros, sizeof(__pyx_k_zeros), 0, 0, 1, 1},
   {0, 0, 0, 0, 0, 0, 0}
 };
 static int __Pyx_InitCachedBuiltins(void) {
-  __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __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 = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  #if PY_MAJOR_VERSION >= 3
-  __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  #else
-  __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_xrange); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  #endif
+  __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __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 = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -5556,6 +5202,17 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
 
+  /* "ml.pyx":82
+ *     max_beta_add = float('-inf')
+ *     # iterate over all victim nodes to find the optimal threshold
+ *     for beta in np.arange(0.001, .1, .001):             # <<<<<<<<<<<<<<
+ *         thresh = log(beta/(1.-beta))
+ *         # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
+ */
+  __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_001, __pyx_float__1, __pyx_float__001); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple_);
+  __Pyx_GIVEREF(__pyx_tuple_);
+
   /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218
  *             if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
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@@ -5563,9 +5220,9 @@ static int __Pyx_InitCachedConstants(void) {
  * 
  *             if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
  */
-  __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_tuple_);
-  __Pyx_GIVEREF(__pyx_tuple_);
+  __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple__2);
+  __Pyx_GIVEREF(__pyx_tuple__2);
 
   /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222
  *             if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
@@ -5574,9 +5231,9 @@ static int __Pyx_InitCachedConstants(void) {
  * 
  *             info.buf = PyArray_DATA(self)
  */
-  __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_tuple__2);
-  __Pyx_GIVEREF(__pyx_tuple__2);
+  __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple__3);
+  __Pyx_GIVEREF(__pyx_tuple__3);
 
   /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260
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@@ -5585,9 +5242,9 @@ static int __Pyx_InitCachedConstants(void) {
  *                 if   t == NPY_BYTE:        f = "b"
  *                 elif t == NPY_UBYTE:       f = "B"
  */
-  __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_tuple__3);
-  __Pyx_GIVEREF(__pyx_tuple__3);
+  __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple__4);
+  __Pyx_GIVEREF(__pyx_tuple__4);
 
   /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802
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@@ -5596,9 +5253,9 @@ static int __Pyx_InitCachedConstants(void) {
  * 
  *         if ((child.byteorder == c'>' and little_endian) or
  */
-  __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_tuple__4);
-  __Pyx_GIVEREF(__pyx_tuple__4);
+  __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple__5);
+  __Pyx_GIVEREF(__pyx_tuple__5);
 
   /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806
  *         if ((child.byteorder == c'>' and little_endian) or
@@ -5607,9 +5264,9 @@ static int __Pyx_InitCachedConstants(void) {
  *             # One could encode it in the format string and have Cython
  *             # complain instead, BUT: < and > in format strings also imply
  */
-  __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_tuple__5);
-  __Pyx_GIVEREF(__pyx_tuple__5);
+  __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple__6);
+  __Pyx_GIVEREF(__pyx_tuple__6);
 
   /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826
  *             t = child.type_num
@@ -5618,21 +5275,21 @@ static int __Pyx_InitCachedConstants(void) {
  * 
  *             # Until ticket #99 is fixed, use integers to avoid warnings
  */
-  __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_tuple__6);
-  __Pyx_GIVEREF(__pyx_tuple__6);
+  __pyx_tuple__7 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple__7);
+  __Pyx_GIVEREF(__pyx_tuple__7);
 
-  /* "ml.pyx":37
+  /* "ml.pyx":38
  *     return result
  * 
  * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,             # <<<<<<<<<<<<<<
  *        DTYPE_t alpha, DTYPE_t delta):
  *     cdef:
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-  __pyx_tuple__7 = PyTuple_Pack(33, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __pyx_n_s_roots_2, __pyx_n_s_i_2, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_beta2, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_max_i, __pyx_n_s_max_beta_add, __pyx_n_s_thresh_2, __pyx_n_s_beta_add, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_tuple__7);
-  __Pyx_GIVEREF(__pyx_tuple__7);
-  __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(6, 0, 33, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 37, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__8 = PyTuple_Pack(33, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_max_beta_add, __pyx_n_s_thresh, __pyx_n_s_beta_add, __pyx_n_s_max_beta, __pyx_n_s_max_roots, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple__8);
+  __Pyx_GIVEREF(__pyx_tuple__8);
+  __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 33, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__8, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 38, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_RefNannyFinishContext();
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@@ -5642,7 +5299,9 @@ static int __Pyx_InitCachedConstants(void) {
 
 static int __Pyx_InitGlobals(void) {
   if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
-  __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_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;}
+  __pyx_float__001 = PyFloat_FromDouble(.001); if (unlikely(!__pyx_float__001)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_float_0_001 = PyFloat_FromDouble(0.001); if (unlikely(!__pyx_float_0_001)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -5729,10 +5388,10 @@ PyMODINIT_FUNC PyInit_ml(void)
   /*--- Variable export code ---*/
   /*--- Function export code ---*/
   /*--- Type init code ---*/
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+  if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_ptype_2ml___pyx_scope_struct__ml = &__pyx_type_2ml___pyx_scope_struct__ml;
-  if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -5778,16 +5437,16 @@ PyMODINIT_FUNC PyInit_ml(void)
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   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
-  /* "ml.pyx":37
+  /* "ml.pyx":38
  *     return result
  * 
  * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,             # <<<<<<<<<<<<<<
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+  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
   /* "ml.pyx":1
@@ -7097,6 +6756,10 @@ bad:
     return (double)-1;
 }
 
+static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
+    PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
+}
+
 #if PY_MAJOR_VERSION < 3
 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
                         CYTHON_UNUSED PyObject *cause) {
@@ -7790,32 +7453,6 @@ raise_neg_overflow:
     return (int) -1;
 }
 
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
-    const long neg_one = (long) -1, const_zero = 0;
-    const int is_unsigned = neg_one > const_zero;
-    if (is_unsigned) {
-        if (sizeof(long) < sizeof(long)) {
-            return PyInt_FromLong((long) value);
-        } else if (sizeof(long) <= sizeof(unsigned long)) {
-            return PyLong_FromUnsignedLong((unsigned long) value);
-        } else if (sizeof(long) <= sizeof(unsigned long long)) {
-            return PyLong_FromUnsignedLongLong((unsigned long long) value);
-        }
-    } else {
-        if (sizeof(long) <= sizeof(long)) {
-            return PyInt_FromLong((long) value);
-        } else if (sizeof(long) <= sizeof(long long)) {
-            return PyLong_FromLongLong((long long) value);
-        }
-    }
-    {
-        int one = 1; int little = (int)*(unsigned char *)&one;
-        unsigned char *bytes = (unsigned char *)&value;
-        return _PyLong_FromByteArray(bytes, sizeof(long),
-                                     little, !is_unsigned);
-    }
-}
-
 #if CYTHON_CCOMPLEX
   #ifdef __cplusplus
     static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
@@ -8056,6 +7693,32 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
     #endif
 #endif
 
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
+    const long neg_one = (long) -1, const_zero = 0;
+    const int is_unsigned = neg_one > const_zero;
+    if (is_unsigned) {
+        if (sizeof(long) < sizeof(long)) {
+            return PyInt_FromLong((long) value);
+        } else if (sizeof(long) <= sizeof(unsigned long)) {
+            return PyLong_FromUnsignedLong((unsigned long) value);
+        } else if (sizeof(long) <= sizeof(unsigned long long)) {
+            return PyLong_FromUnsignedLongLong((unsigned long long) value);
+        }
+    } else {
+        if (sizeof(long) <= sizeof(long)) {
+            return PyInt_FromLong((long) value);
+        } else if (sizeof(long) <= sizeof(long long)) {
+            return PyLong_FromLongLong((long long) value);
+        }
+    }
+    {
+        int one = 1; int little = (int)*(unsigned char *)&one;
+        unsigned char *bytes = (unsigned char *)&value;
+        return _PyLong_FromByteArray(bytes, sizeof(long),
+                                     little, !is_unsigned);
+    }
+}
+
 static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
     const long neg_one = (long) -1, const_zero = 0;
     const int is_unsigned = neg_one > const_zero;
diff --git a/experiments/ml.pyx b/experiments/ml.pyx
index 853c934..67b561c 100644
--- a/experiments/ml.pyx
+++ b/experiments/ml.pyx
@@ -15,11 +15,12 @@ cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
     cdef DTYPE_t structural, temporal, result
     structural = delta ** dist
     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
-    temporal = exp(-alpha*dt) * (exp(alpha)-1)
+    # temporal = exp(-alpha*dt) * (exp(alpha)-1)
+    temporal = 1 - exp(-alpha*dt)
     if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
     # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
     result = log(structural * temporal)
-    print 'st', structural, temporal
+    # print 'st', structural, temporal
     return result
 
 cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
@@ -31,17 +32,17 @@ cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
     temporal = exp(-alpha * dt)
     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
     result = log(1. - structural + structural * temporal)
-    print 'stnv', structural, temporal
+    # print 'stnv', structural, temporal
     return result
 
 def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
        DTYPE_t alpha, DTYPE_t delta):
     cdef:
         int n_roots, n_victims, n_nodes, roots, i, dist, dt, t, l
-        DTYPE_t beta, ll, beta2
+        DTYPE_t beta, ll
         list parents, failures, successes
     n_roots, n_victims = len(root_victims), len(victims)
-    n_nodes = 4#148152
+    n_nodes = 11270
     cdef:
         np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE)
         np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
@@ -61,12 +62,12 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
         probs[i] = max(s - failures[l] for l, s in enumerate(successes)) 
 
     # loop through non-victims
-    for i, parents in enumerate(non_victims.itervalues()):
-        # for each non victim node, compute the probability that all its
-        # parents fail to infect it
-        failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
-                    for (dist, dt, w1, w2, w3) in parents]
-        probs_nv[i] = sum(failures)
+    # for i, parents in enumerate(non_victims.itervalues()):
+    #     # for each non victim node, compute the probability that all its
+    #     # parents fail to infect it
+    #     failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
+    #                 for (dist, dt, w1, w2, w3) in parents]
+    #     probs_nv[i] = sum(failures)
 
     # calculate log likelihood
     # probs.sort(); probs = probs[::-1] # sort probs in descending order
@@ -75,32 +76,27 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
     ll =  probs_fail.sum() # add probability that all edges to victims fail
     ll += probs_nv.sum() # add probability that all edges to non_victims fail
 
-    print 'probs', probs
-    max_i = -1
+    # print 'probs', probs
     max_beta_add = float('-inf')
     # iterate over all victim nodes to find the optimal threshold
-    for i in xrange(0, n_victims+1, 1):
-        print
-        roots = n_roots + n_victims - i
-        beta = 1. / (1. + exp(-probs[i]))
-        # beta = float(roots)/float(n_nodes)
+    for beta in np.arange(0.001, .1, .001):
         thresh = log(beta/(1.-beta))
-        print 'thresh:', thresh
+        # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
+        roots = n_roots + len(probs[probs<thresh])
 
         # add probability for realized edges and subtract probability these edges fail
         beta_add = (probs[probs>=thresh]).sum()
-        print 'len(probs[probs>=thresh]):', len(probs[probs>=thresh])
         # add probability for the seeds and non-seeds
         beta_add += roots * log(beta) + (n_nodes-roots) * log(1 - beta)
 
         if beta_add > max_beta_add:
-            max_i = i
+            max_beta = beta
+            max_roots = roots
             max_beta_add = beta_add
-            print 'i:', max_i, 'add:', max_beta_add, 'roots:', roots
-        else:
-            print i
+            # print 'beta:', max_beta, 'add:', max_beta_add, 'roots:', max_roots
 
     ll += max_beta_add
-    roots = n_roots + n_victims - max_i
+    roots = max_roots
+    beta = max_beta
     # print n_nodes, n_roots, n_victims, max_i, roots
     return (beta, roots, ll)
diff --git a/experiments/ml.so b/experiments/ml.so
index a42cc37..df7f087 100755
--- a/experiments/ml.so
+++ b/experiments/ml.so
diff --git a/experiments/out.log b/experiments/out.log
index 69fb56d..7a1f0ab 100644
--- a/experiments/out.log
+++ b/experiments/out.log
@@ -1,257 +1,50 @@
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+10.0	1e-10	0.099	11270	-26063.4012843
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+10.0	1e-06	0.099	11270	-26063.4136042
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+100.0	1e-07	0.099	11270	-26063.4025152
+100.0	1e-06	0.099	11270	-26063.4136042
+100.0	1e-05	0.099	11270	-26063.5245019
+100.0	0.0001	0.099	11270	-26064.6342627
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diff --git a/experiments/plot3d.py b/experiments/plot3d.py
index b99ef61..b1b337f 100644
--- a/experiments/plot3d.py
+++ b/experiments/plot3d.py
@@ -7,10 +7,10 @@ with open("out.log") as fh:
     values = [map(float, line.strip().split()) for line in fh]
     #values = [(b, a, l) for (b, a, l) in values if b >= 0.04]
     am = max(values, key=lambda x: x[4])
-    am[0] = 1./am[0]
+    # am[0] = 1./am[0]
     print am
     alpha, delta, beta, r , l = zip(*values)
-    alpha = 1./np.array(alpha)
+    # alpha = 1./np.array(alpha)
 
     fig = plt.figure(figsize=(12, 8))
     ax = fig.gca(projection='3d')
diff --git a/experiments/process.py b/experiments/process.py
index 1b84d35..b5e0d6d 100644
--- a/experiments/process.py
+++ b/experiments/process.py
@@ -12,15 +12,16 @@ if __name__ == "__main__":
     root_victims, victims, non_victims, age = load(open(sys.argv[1]))
     
     # alphas = 1. / np.arange(1000., 10000., 50.)  # parameter of the time component
-    # deltas = np.arange(0.01, 0.5, 0.03)  # parameter of the structural component
-    # with open("out.log", "w") as fh:
-    #     for alpha, delta in product(alphas, deltas):
-    #         beta, roots, ll = ml(root_victims, victims, non_victims, age, alpha, delta)
-    #         print "\t".join(map(str, [1/alpha, delta, beta, roots, ll]))
-    #         fh.write("\t".join(map(str, [alpha, delta, beta, roots, ll])) + "\n")
-    #         fh.flush()
+    alphas = np.logspace(-2,2,num=5)
+    deltas = np.logspace(-10,-1,num=10)#np.arange(0.000001, 0.005, 0.001)  # parameter of the structural component
+    with open("out.log", "w") as fh:
+        for alpha, delta in product(alphas, deltas):
+            beta, roots, ll = ml(root_victims, victims, non_victims, age, alpha, delta)
+            print "\t".join(map(str, [alpha, delta, beta, roots, ll]))
+            fh.write("\t".join(map(str, [alpha, delta, beta, roots, ll])) + "\n")
+            fh.flush()
 
-    alpha = 1/10.
-    delta = 0.2
-    beta, roots, ll = ml(root_victims, victims, non_victims, age, alpha, delta)
-    print "\t".join(map(str, [1./alpha, delta, beta, roots, ll]))
\ No newline at end of file
+    # alpha = 20000.
+    # delta = .5
+    # beta, roots, ll = ml(root_victims, victims, non_victims, age, alpha, delta)
+    # print "\t".join(map(str, [1./alpha, delta, beta, roots, ll]))
\ No newline at end of file