Worked on synthetic data recovery so we can tell how high the actual

infector is ranked among all potential parents. Cleaned up code for the
predicting victims benchmarking test.

1 files changed, 234 insertions, 229 deletions

diff --git a/experiments/ml3.c b/experiments/ml3.c
index 12d0e1d..59de174 100644
--- a/experiments/ml3.c
+++ b/experiments/ml3.c
@@ -695,7 +695,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
  * DTYPE = np.float64
  * ctypedef np.float_t DTYPE_t             # <<<<<<<<<<<<<<
  * 
- * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
+ * cdef DTYPE_t weight_success(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,
  */
 typedef __pyx_t_5numpy_float_t __pyx_t_3ml3_DTYPE_t;
 #if CYTHON_CCOMPLEX
@@ -914,6 +914,18 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
 #endif
 
 #define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0)
+static double __Pyx__PyObject_AsDouble(PyObject* obj);
+#if CYTHON_COMPILING_IN_PYPY
+#define __Pyx_PyObject_AsDouble(obj) \
+(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \
+ likely(PyInt_CheckExact(obj)) ? \
+ PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
+#else
+#define __Pyx_PyObject_AsDouble(obj) \
+((likely(PyFloat_CheckExact(obj))) ? \
+ PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
+#endif
+
 #define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
     (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
     __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
@@ -935,18 +947,6 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
                                                      int is_list, int wraparound, int boundscheck);
 
-static double __Pyx__PyObject_AsDouble(PyObject* obj);
-#if CYTHON_COMPILING_IN_PYPY
-#define __Pyx_PyObject_AsDouble(obj) \
-(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \
- likely(PyInt_CheckExact(obj)) ? \
- PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
-#else
-#define __Pyx_PyObject_AsDouble(obj) \
-((likely(PyFloat_CheckExact(obj))) ? \
- PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
-#endif
-
 static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb);
 static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb);
 
@@ -1169,8 +1169,8 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha
 /* Module declarations from 'libc.math' */
 
 /* Module declarations from 'ml3' */
-static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int, int, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t); /*proto*/
-static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int, int, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t); /*proto*/
+static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t); /*proto*/
+static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t); /*proto*/
 static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_3ml3_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_3ml3_DTYPE_t), { 0 }, 0, 'R', 0, 0 };
 #define __Pyx_MODULE_NAME "ml3"
 int __pyx_module_is_main_ml3 = 0;
@@ -1329,7 +1329,6 @@ static PyObject *__pyx_n_s_w3;
 static PyObject *__pyx_n_s_zeros;
 static PyObject *__pyx_float_1_;
 static PyObject *__pyx_float_0_00001;
-static PyObject *__pyx_float_neg_19_523275053840013;
 static PyObject *__pyx_int_0;
 static PyObject *__pyx_int_1;
 static PyObject *__pyx_tuple_;
@@ -1345,12 +1344,12 @@ static PyObject *__pyx_codeobj__9;
 /* "ml3.pyx":9
  * ctypedef np.float_t DTYPE_t
  * 
- * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
+ * cdef DTYPE_t weight_success(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
  *                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
  *     """weight for successful infection, exponential time model"""
  */
 
-static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
+static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, __pyx_t_3ml3_DTYPE_t __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
   __pyx_t_3ml3_DTYPE_t __pyx_v_structural;
   __pyx_t_3ml3_DTYPE_t __pyx_v_temporal;
   __pyx_t_3ml3_DTYPE_t __pyx_v_result;
@@ -1390,7 +1389,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
  *     result = log(structural) + temporal
  *     return result             # <<<<<<<<<<<<<<
  * 
- * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
+ * cdef DTYPE_t weight_failure(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,
  */
   __pyx_r = __pyx_v_result;
   goto __pyx_L0;
@@ -1398,7 +1397,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
   /* "ml3.pyx":9
  * ctypedef np.float_t DTYPE_t
  * 
- * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
+ * cdef DTYPE_t weight_success(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
  *                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
  *     """weight for successful infection, exponential time model"""
  */
@@ -1412,12 +1411,12 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
 /* "ml3.pyx":18
  *     return result
  * 
- * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
+ * cdef DTYPE_t weight_failure(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
  *                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
  *     """weight for failed infection, exponential time model"""
  */
 
-static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
+static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, __pyx_t_3ml3_DTYPE_t __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
   __pyx_t_3ml3_DTYPE_t __pyx_v_structural;
   __pyx_t_3ml3_DTYPE_t __pyx_v_temporal;
   __pyx_t_3ml3_DTYPE_t __pyx_v_result;
@@ -1465,7 +1464,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
   /* "ml3.pyx":18
  *     return result
  * 
- * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
+ * cdef DTYPE_t weight_failure(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,             # <<<<<<<<<<<<<<
  *                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
  *     """weight for failed infection, exponential time model"""
  */
@@ -1660,12 +1659,13 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   __pyx_t_3ml3_DTYPE_t __pyx_t_25;
   __pyx_t_3ml3_DTYPE_t __pyx_t_26;
   int __pyx_t_27;
-  int __pyx_t_28;
+  double __pyx_t_28;
   int __pyx_t_29;
   int __pyx_t_30;
   int __pyx_t_31;
-  double __pyx_t_32;
-  PyObject *(*__pyx_t_33)(PyObject *);
+  int __pyx_t_32;
+  int __pyx_t_33;
+  PyObject *(*__pyx_t_34)(PyObject *);
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
@@ -1921,7 +1921,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   __pyx_t_11 = ((PyArrayObject *)__pyx_t_4);
   {
     __Pyx_BufFmt_StackElem __pyx_stack[1];
-    if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_isSeed.rcbuffer->pybuffer, (PyObject*)__pyx_t_11, &__Pyx_TypeInfo_nn___pyx_t_3ml3_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
+    if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_isSeed.rcbuffer->pybuffer, (PyObject*)__pyx_t_11, &__Pyx_TypeInfo_nn___pyx_t_3ml3_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {
       __pyx_v_isSeed = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_isSeed.rcbuffer->pybuffer.buf = NULL;
       {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     } else {__pyx_pybuffernd_isSeed.diminfo[0].strides = __pyx_pybuffernd_isSeed.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_isSeed.diminfo[0].shape = __pyx_pybuffernd_isSeed.rcbuffer->pybuffer.shape[0];
@@ -1963,7 +1963,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
     /* "ml3.pyx":46
  *         # 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)             # <<<<<<<<<<<<<<
+ *         failures = [weight_failure(dist, dt/100., alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
  *                     for (dist, dt, w1, w2, w3) in parents]
  *         probs_fail[i] = sum(failures)
  */
@@ -1972,10 +1972,10 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
 
     /* "ml3.pyx":47
  *         # likely parent infects it
- *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
+ *         failures = [weight_failure(dist, dt/100., 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)
+ *         successes = [weight_success(dist, dt/100., alpha, delta, w1, w2, w3)
  */
     if (unlikely(__pyx_v_parents == Py_None)) {
       PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
@@ -2071,24 +2071,24 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
       /* "ml3.pyx":46
  *         # 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)             # <<<<<<<<<<<<<<
+ *         failures = [weight_failure(dist, dt/100., alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
  *                     for (dist, dt, w1, w2, w3) in parents]
  *         probs_fail[i] = sum(failures)
  */
       __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_3 = PyFloat_FromDouble(__pyx_f_3ml3_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_24, __pyx_t_25, __pyx_t_26)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_3 = PyFloat_FromDouble(__pyx_f_3ml3_weight_failure(__pyx_v_dist, (__pyx_v_dt / 100.), __pyx_v_alpha, __pyx_v_delta, __pyx_t_24, __pyx_t_25, __pyx_t_26)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_3);
       if (unlikely(__Pyx_ListComp_Append(__pyx_t_6, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
       /* "ml3.pyx":47
  *         # likely parent infects it
- *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
+ *         failures = [weight_failure(dist, dt/100., 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)
+ *         successes = [weight_success(dist, dt/100., alpha, delta, w1, w2, w3)
  */
     }
     __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -2096,10 +2096,10 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
     __pyx_t_6 = 0;
 
     /* "ml3.pyx":48
- *         failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
+ *         failures = [weight_failure(dist, dt/100., 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)
+ *         successes = [weight_success(dist, dt/100., alpha, delta, w1, w2, w3)
  *                      for (dist, dt, w1, w2, w3) in parents]
  */
     __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -2119,7 +2119,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
     /* "ml3.pyx":49
  *                     for (dist, dt, w1, w2, w3) in parents]
  *         probs_fail[i] = sum(failures)
- *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
+ *         successes = [weight_success(dist, dt/100., alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
  *                      for (dist, dt, w1, w2, w3) in parents]
  *         dists = [dist for (dist, dt, w1, w2, w3) in parents]
  */
@@ -2128,7 +2128,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
 
     /* "ml3.pyx":50
  *         probs_fail[i] = sum(failures)
- *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
+ *         successes = [weight_success(dist, dt/100., alpha, delta, w1, w2, w3)
  *                      for (dist, dt, w1, w2, w3) in parents]             # <<<<<<<<<<<<<<
  *         dists = [dist for (dist, dt, w1, w2, w3) in parents]
  *         dts = [dt for (dist, dt, w1, w2, w3) in parents]
@@ -2227,21 +2227,21 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
       /* "ml3.pyx":49
  *                     for (dist, dt, w1, w2, w3) in parents]
  *         probs_fail[i] = sum(failures)
- *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
+ *         successes = [weight_success(dist, dt/100., alpha, delta, w1, w2, w3)             # <<<<<<<<<<<<<<
  *                      for (dist, dt, w1, w2, w3) in parents]
  *         dists = [dist for (dist, dt, w1, w2, w3) in parents]
  */
       __pyx_t_26 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_26 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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 = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-      __pyx_t_3 = PyFloat_FromDouble(__pyx_f_3ml3_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_26, __pyx_t_25, __pyx_t_24)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      __pyx_t_3 = PyFloat_FromDouble(__pyx_f_3ml3_weight_success(__pyx_v_dist, (__pyx_v_dt / 100.), __pyx_v_alpha, __pyx_v_delta, __pyx_t_26, __pyx_t_25, __pyx_t_24)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_GOTREF(__pyx_t_3);
       if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
       /* "ml3.pyx":50
  *         probs_fail[i] = sum(failures)
- *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
+ *         successes = [weight_success(dist, dt/100., alpha, delta, w1, w2, w3)
  *                      for (dist, dt, w1, w2, w3) in parents]             # <<<<<<<<<<<<<<
  *         dists = [dist for (dist, dt, w1, w2, w3) in parents]
  *         dts = [dt for (dist, dt, w1, w2, w3) in parents]
@@ -2252,7 +2252,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
     __pyx_t_5 = 0;
 
     /* "ml3.pyx":51
- *         successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
+ *         successes = [weight_success(dist, dt/100., alpha, delta, w1, w2, w3)
  *                      for (dist, dt, w1, w2, w3) in parents]
  *         dists = [dist for (dist, dt, w1, w2, w3) in parents]             # <<<<<<<<<<<<<<
  *         dts = [dt for (dist, dt, w1, w2, w3) in parents]
@@ -2467,14 +2467,26 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
     __Pyx_XDECREF_SET(__pyx_v_dts, ((PyObject*)__pyx_t_5));
     __pyx_t_5 = 0;
 
+    /* "ml3.pyx":55
+ *         # find parent that maximizes log(p) - log(\tilde{p})
+ *         # probs[i] = max(s - failures[l] for l, s in enumerate(successes))
+ *         probs[i] = float("-inf")             # <<<<<<<<<<<<<<
+ *         for l, s in enumerate(successes):
+ *             prob = s - failures[l]
+ */
+    __pyx_t_28 = __Pyx_PyObject_AsDouble(__pyx_kp_s_inf); if (unlikely(__pyx_t_28 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_27 = __pyx_v_i;
+    if (__pyx_t_27 < 0) __pyx_t_27 += __pyx_pybuffernd_probs.diminfo[0].shape;
+    *__Pyx_BufPtrStrided1d(__pyx_t_3ml3_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_27, __pyx_pybuffernd_probs.diminfo[0].strides) = __pyx_t_28;
+
     /* "ml3.pyx":56
  *         # probs[i] = max(s - failures[l] for l, s in enumerate(successes))
- *         # probs[i] = 0.
+ *         probs[i] = float("-inf")
  *         for l, s in enumerate(successes):             # <<<<<<<<<<<<<<
  *             prob = s - failures[l]
- *             if prob > -19.523275053840013:
+ *             if prob > probs[i]:
  */
-    __pyx_t_27 = 0;
+    __pyx_t_14 = 0;
     __pyx_t_5 = __pyx_v_successes; __Pyx_INCREF(__pyx_t_5); __pyx_t_15 = 0;
     for (;;) {
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@@ -2485,15 +2497,15 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
       #endif
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       __pyx_t_6 = 0;
-      __pyx_v_l = __pyx_t_27;
-      __pyx_t_27 = (__pyx_t_27 + 1);
+      __pyx_v_l = __pyx_t_14;
+      __pyx_t_14 = (__pyx_t_14 + 1);
 
       /* "ml3.pyx":57
- *         # probs[i] = 0.
+ *         probs[i] = float("-inf")
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  *             prob = s - failures[l]             # <<<<<<<<<<<<<<
- *             if prob > -19.523275053840013:
- *                 isSeed[i] = 0
+ *             if prob > probs[i]:
+ *                 probs[i] = prob
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@@ -2506,182 +2518,176 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
       /* "ml3.pyx":58
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- *             if prob > -19.523275053840013:             # <<<<<<<<<<<<<<
- *                 isSeed[i] = 0
- *                 probs[i] += prob
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-      if (__pyx_t_28) {
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-        /* "ml3.pyx":60
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+        __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_prob); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        __pyx_t_31 = __pyx_v_i;
+        if (__pyx_t_31 < 0) __pyx_t_31 += __pyx_pybuffernd_probs.diminfo[0].shape;
+        *__Pyx_BufPtrStrided1d(__pyx_t_3ml3_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_31, __pyx_pybuffernd_probs.diminfo[0].strides) = __pyx_t_24;
 
-        /* "ml3.pyx":61
- *                 isSeed[i] = 0
- *                 probs[i] += prob
+        /* "ml3.pyx":60
+ *             if prob > probs[i]:
+ *                 probs[i] = prob
  *                 parent_dists[i] = dists[l]             # <<<<<<<<<<<<<<
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+        __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_dists, __pyx_v_l, int, 1, __Pyx_PyInt_From_int, 1, 1, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+        __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+        __pyx_t_32 = __pyx_v_i;
+        if (__pyx_t_32 < 0) __pyx_t_32 += __pyx_pybuffernd_parent_dists.diminfo[0].shape;
+        *__Pyx_BufPtrStrided1d(__pyx_t_3ml3_DTYPE_t *, __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.buf, __pyx_t_32, __pyx_pybuffernd_parent_dists.diminfo[0].strides) = __pyx_t_24;
 
-        /* "ml3.pyx":62
- *                 probs[i] += prob
+        /* "ml3.pyx":61
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  *                 parent_dists[i] = dists[l]
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       /* "ml3.pyx":56
  *         # probs[i] = max(s - failures[l] for l, s in enumerate(successes))
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  *         for l, s in enumerate(successes):             # <<<<<<<<<<<<<<
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-  /* "ml3.pyx":66
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+    __pyx_t_6 = PyNumber_Add(__pyx_t_3, __pyx_t_17); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_GOTREF(__pyx_t_6);
+    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
     __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
-    __pyx_t_17 = PyNumber_InPlaceAdd(__pyx_t_16, __pyx_t_3); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_17 = PyNumber_InPlaceAdd(__pyx_t_16, __pyx_t_6); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_GOTREF(__pyx_t_17);
     __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
-    __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-    __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_17); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+    __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_17); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
     __pyx_v_beta_add = __pyx_t_24;
 
-    /* "ml3.pyx":83
+    /* "ml3.pyx":82
  *         beta_add += roots * log(beta/3012.) + sum(non_seeds) * log(1. - beta)
  * 
  *         if beta_add > max_beta_add:             # <<<<<<<<<<<<<<
  *             max_beta = beta
  *             max_roots = roots
  */
-    __pyx_t_28 = ((__pyx_v_beta_add > __pyx_v_max_beta_add) != 0);
-    if (__pyx_t_28) {
+    __pyx_t_30 = ((__pyx_v_beta_add > __pyx_v_max_beta_add) != 0);
+    if (__pyx_t_30) {
 
-      /* "ml3.pyx":84
+      /* "ml3.pyx":83
  * 
  *         if beta_add > max_beta_add:
  *             max_beta = beta             # <<<<<<<<<<<<<<
@@ -2842,7 +2848,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
       __pyx_v_max_beta = __pyx_v_beta;
 
-      /* "ml3.pyx":85
+      /* "ml3.pyx":84
  *         if beta_add > max_beta_add:
  *             max_beta = beta
  *             max_roots = roots             # <<<<<<<<<<<<<<
@@ -2851,7 +2857,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
       __pyx_v_max_roots = __pyx_v_roots;
 
-      /* "ml3.pyx":86
+      /* "ml3.pyx":85
  *             max_beta = beta
  *             max_roots = roots
  *             max_beta_add = beta_add             # <<<<<<<<<<<<<<
@@ -2863,7 +2869,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
     }
     __pyx_L26:;
 
-    /* "ml3.pyx":71
+    /* "ml3.pyx":70
  *     max_beta_add = float('-inf')
  *     # iterate over all victim nodes to find the optimal threshold
  *     for beta in np.arange(0.00001, 1., 1.):             # <<<<<<<<<<<<<<
@@ -2873,7 +2879,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   }
   __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
 
-  /* "ml3.pyx":89
+  /* "ml3.pyx":88
  *             # print 'beta:', max_beta, 'add:', max_beta_add, 'roots:', max_roots
  * 
  *     ll += max_beta_add             # <<<<<<<<<<<<<<
@@ -2882,7 +2888,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
   __pyx_v_ll = (__pyx_v_ll + __pyx_v_max_beta_add);
 
-  /* "ml3.pyx":90
+  /* "ml3.pyx":89
  * 
  *     ll += max_beta_add
  *     roots = max_roots             # <<<<<<<<<<<<<<
@@ -2891,7 +2897,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
   __pyx_v_roots = __pyx_v_max_roots;
 
-  /* "ml3.pyx":91
+  /* "ml3.pyx":90
  *     ll += max_beta_add
  *     roots = max_roots
  *     beta = max_beta             # <<<<<<<<<<<<<<
@@ -2900,29 +2906,29 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
   __pyx_v_beta = __pyx_v_max_beta;
 
-  /* "ml3.pyx":93
+  /* "ml3.pyx":92
  *     beta = max_beta
  *     # print n_nodes, n_roots, n_victims, max_i, roots
  *     return (beta, roots, ll)             # <<<<<<<<<<<<<<
  */
   __Pyx_XDECREF(__pyx_r);
-  __pyx_t_5 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_5 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_5);
-  __pyx_t_17 = __Pyx_PyInt_From_int(__pyx_v_roots); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_17 = __Pyx_PyInt_From_int(__pyx_v_roots); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_17);
-  __pyx_t_3 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_t_3);
-  __pyx_t_16 = PyTuple_New(3); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_6 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_t_6);
+  __pyx_t_16 = PyTuple_New(3); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_16);
   PyTuple_SET_ITEM(__pyx_t_16, 0, __pyx_t_5);
   __Pyx_GIVEREF(__pyx_t_5);
   PyTuple_SET_ITEM(__pyx_t_16, 1, __pyx_t_17);
   __Pyx_GIVEREF(__pyx_t_17);
-  PyTuple_SET_ITEM(__pyx_t_16, 2, __pyx_t_3);
-  __Pyx_GIVEREF(__pyx_t_3);
+  PyTuple_SET_ITEM(__pyx_t_16, 2, __pyx_t_6);
+  __Pyx_GIVEREF(__pyx_t_6);
   __pyx_t_5 = 0;
   __pyx_t_17 = 0;
-  __pyx_t_3 = 0;
+  __pyx_t_6 = 0;
   __pyx_r = __pyx_t_16;
   __pyx_t_16 = 0;
   goto __pyx_L0;
@@ -5093,14 +5099,14 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
 
-  /* "ml3.pyx":71
+  /* "ml3.pyx":70
  *     max_beta_add = float('-inf')
  *     # iterate over all victim nodes to find the optimal threshold
  *     for beta in np.arange(0.00001, 1., 1.):             # <<<<<<<<<<<<<<
  *         thresh = log(beta/(3012.*(1.-beta)))
  *         seeds = isSeed==1
  */
-  __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_00001, __pyx_float_1_, __pyx_float_1_); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_00001, __pyx_float_1_, __pyx_float_1_); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple_);
   __Pyx_GIVEREF(__pyx_tuple_);
 
@@ -5192,7 +5198,6 @@ 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_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_0_00001 = PyFloat_FromDouble(0.00001); if (unlikely(!__pyx_float_0_00001)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_float_neg_19_523275053840013 = PyFloat_FromDouble(-19.523275053840013); if (unlikely(!__pyx_float_neg_19_523275053840013)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   return 0;
@@ -6464,6 +6469,45 @@ static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t ori
     return 1;
 }
 
+static double __Pyx__PyObject_AsDouble(PyObject* obj) {
+    PyObject* float_value;
+#if CYTHON_COMPILING_IN_PYPY
+    float_value = PyNumber_Float(obj);
+#else
+    PyNumberMethods *nb = Py_TYPE(obj)->tp_as_number;
+    if (likely(nb) && likely(nb->nb_float)) {
+        float_value = nb->nb_float(obj);
+        if (likely(float_value) && unlikely(!PyFloat_Check(float_value))) {
+            PyErr_Format(PyExc_TypeError,
+                "__float__ returned non-float (type %.200s)",
+                Py_TYPE(float_value)->tp_name);
+            Py_DECREF(float_value);
+            goto bad;
+        }
+    } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
+#if PY_MAJOR_VERSION >= 3
+        float_value = PyFloat_FromString(obj);
+#else
+        float_value = PyFloat_FromString(obj, 0);
+#endif
+    } else {
+        PyObject* args = PyTuple_New(1);
+        if (unlikely(!args)) goto bad;
+        PyTuple_SET_ITEM(args, 0, obj);
+        float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0);
+        PyTuple_SET_ITEM(args, 0, 0);
+        Py_DECREF(args);
+    }
+#endif
+    if (likely(float_value)) {
+        double value = PyFloat_AS_DOUBLE(float_value);
+        Py_DECREF(float_value);
+        return value;
+    }
+bad:
+    return (double)-1;
+}
+
 static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
     PyObject *r;
     if (!j) return NULL;
@@ -6542,45 +6586,6 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
     return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
 }
 
-static double __Pyx__PyObject_AsDouble(PyObject* obj) {
-    PyObject* float_value;
-#if CYTHON_COMPILING_IN_PYPY
-    float_value = PyNumber_Float(obj);
-#else
-    PyNumberMethods *nb = Py_TYPE(obj)->tp_as_number;
-    if (likely(nb) && likely(nb->nb_float)) {
-        float_value = nb->nb_float(obj);
-        if (likely(float_value) && unlikely(!PyFloat_Check(float_value))) {
-            PyErr_Format(PyExc_TypeError,
-                "__float__ returned non-float (type %.200s)",
-                Py_TYPE(float_value)->tp_name);
-            Py_DECREF(float_value);
-            goto bad;
-        }
-    } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
-#if PY_MAJOR_VERSION >= 3
-        float_value = PyFloat_FromString(obj);
-#else
-        float_value = PyFloat_FromString(obj, 0);
-#endif
-    } else {
-        PyObject* args = PyTuple_New(1);
-        if (unlikely(!args)) goto bad;
-        PyTuple_SET_ITEM(args, 0, obj);
-        float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0);
-        PyTuple_SET_ITEM(args, 0, 0);
-        Py_DECREF(args);
-    }
-#endif
-    if (likely(float_value)) {
-        double value = PyFloat_AS_DOUBLE(float_value);
-        Py_DECREF(float_value);
-        return value;
-    }
-bad:
-    return (double)-1;
-}
-
 static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
 #if CYTHON_COMPILING_IN_CPYTHON
     PyObject *tmp_type, *tmp_value, *tmp_tb;