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-rw-r--r--experiments/build/temp.macosx-10.6-x86_64-2.7/ml.obin326236 -> 326092 bytes
-rw-r--r--experiments/ml.c666
-rw-r--r--experiments/ml.pyx6
-rwxr-xr-xexperiments/ml.sobin125128 -> 125136 bytes
-rw-r--r--experiments/out.log228
-rw-r--r--experiments/out2.log125
-rw-r--r--experiments/process.py26
7 files changed, 688 insertions, 363 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 80ba2ba..e82f8b2 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
Binary files differ
diff --git a/experiments/ml.c b/experiments/ml.c
index 0dfbb02..f0a7125 100644
--- a/experiments/ml.c
+++ b/experiments/ml.c
@@ -1018,6 +1018,8 @@ static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1};
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
+static CYTHON_INLINE long __Pyx_pow_long(long, long); /* proto */
+
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
@@ -1276,7 +1278,7 @@ static char __pyx_k_max_beta_add[] = "max_beta_add";
static char __pyx_k_parent_dists[] = "parent_dists";
static char __pyx_k_root_victims[] = "root_victims";
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_Users_ben_Documents_Violence_Ca[] = "/Users/ben/Documents/Violence Cascades/criminal_cascades/experiments/ml.pyx";
static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd";
static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported";
@@ -1287,7 +1289,7 @@ static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor;
static PyObject *__pyx_n_s_RuntimeError;
-static PyObject *__pyx_kp_s_Users_ben_Documents_Cascade_Pro;
+static PyObject *__pyx_kp_s_Users_ben_Documents_Violence_Ca;
static PyObject *__pyx_n_s_ValueError;
static PyObject *__pyx_n_s_alpha;
static PyObject *__pyx_n_s_arange;
@@ -1389,14 +1391,14 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
/* "ml.pyx":13
* """weight for successful infection, exponential time model"""
* cdef DTYPE_t structural, temporal, result
- * structural = delta ** dist # <<<<<<<<<<<<<<
+ * structural = delta ** (dist**1) # <<<<<<<<<<<<<<
* # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
* temporal = log(exp(alpha/t_scale)-1.) - alpha*dt/t_scale
*/
- __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist));
+ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__Pyx_pow_long(((long)__pyx_v_dist), 1)));
/* "ml.pyx":15
- * structural = delta ** dist
+ * structural = delta ** (dist**1)
* # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
* temporal = log(exp(alpha/t_scale)-1.) - alpha*dt/t_scale # <<<<<<<<<<<<<<
* # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
@@ -1456,14 +1458,14 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
/* "ml.pyx":24
* """weight for failed infection, exponential time model"""
* cdef DTYPE_t structural, temporal, result
- * structural = delta ** dist # <<<<<<<<<<<<<<
+ * structural = delta ** (dist**1) # <<<<<<<<<<<<<<
* # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
* temporal = exp(-alpha * dt/t_scale)
*/
- __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist));
+ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__Pyx_pow_long(((long)__pyx_v_dist), 1)));
/* "ml.pyx":26
- * structural = delta ** dist
+ * structural = delta ** (dist**1)
* # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
* temporal = exp(-alpha * dt/t_scale) # <<<<<<<<<<<<<<
* # temporal = 1. - 1. / (1. + dt/alpha)**0.01
@@ -1475,14 +1477,14 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
* temporal = exp(-alpha * dt/t_scale)
* # temporal = 1. - 1. / (1. + dt/alpha)**0.01
* result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<<
+ * # if dt>100: result=0
* return result
- *
*/
__pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
- /* "ml.pyx":29
- * # temporal = 1. - 1. / (1. + dt/alpha)**0.01
+ /* "ml.pyx":30
* result = log(1. - structural + structural * temporal)
+ * # if dt>100: result=0
* return result # <<<<<<<<<<<<<<
*
* def ml(dict root_victims, dict victims, dict non_victims,
@@ -1504,7 +1506,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
return __pyx_r;
}
-/* "ml.pyx":31
+/* "ml.pyx":32
* return result
*
* def ml(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<<
@@ -1552,31 +1554,31 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_victims)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_non_victims)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 5:
if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lmbda)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 6) {
goto __pyx_L5_argtuple_error;
@@ -1591,21 +1593,21 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py
__pyx_v_root_victims = ((PyObject*)values[0]);
__pyx_v_victims = ((PyObject*)values[1]);
__pyx_v_non_victims = ((PyObject*)values[2]);
- __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_delta = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_lmbda = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_lmbda == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_delta = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_lmbda = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_lmbda == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("ml.ml", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 31; __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 = 31; __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 = 32; __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 = 32; __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 = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_2ml_ml(__pyx_self, __pyx_v_root_victims, __pyx_v_victims, __pyx_v_non_victims, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda);
/* function exit code */
@@ -1728,7 +1730,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__pyx_pybuffernd_probs_nv.data = NULL;
__pyx_pybuffernd_probs_nv.rcbuffer = &__pyx_pybuffer_probs_nv;
- /* "ml.pyx":37
+ /* "ml.pyx":38
* DTYPE_t beta, ll, beta_add, max_beta, max_beta_add
* list parents, failures, successes
* n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<<
@@ -1737,18 +1739,18 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
*/
if (unlikely(__pyx_v_root_victims == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __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 = 37; __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 = 38; __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 = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __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 = 37; __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 = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_n_roots = __pyx_t_1;
__pyx_v_n_victims = __pyx_t_2;
- /* "ml.pyx":38
+ /* "ml.pyx":39
* list parents, failures, successes
* n_roots, n_victims = len(root_victims), len(victims)
* n_nodes = 148152 # <<<<<<<<<<<<<<
@@ -1758,7 +1760,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__Pyx_INCREF(__pyx_int_148152);
__pyx_v_n_nodes = __pyx_int_148152;
- /* "ml.pyx":39
+ /* "ml.pyx":40
* n_roots, n_victims = len(root_victims), len(victims)
* n_nodes = 148152
* n_days = 3012 # <<<<<<<<<<<<<<
@@ -1767,7 +1769,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
*/
__pyx_v_n_days = 3012;
- /* "ml.pyx":40
+ /* "ml.pyx":41
* n_nodes = 148152
* n_days = 3012
* t_scale = 1. # <<<<<<<<<<<<<<
@@ -1776,43 +1778,43 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
*/
__pyx_v_t_scale = 1.;
- /* "ml.pyx":42
+ /* "ml.pyx":43
* t_scale = 1.
* cdef:
* np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<<
* np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
* np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
*/
- __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_parent_dts = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_parent_dts.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -1952,48 +1954,48 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__pyx_v_parent_dts = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
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+ /* "ml.pyx":47
* np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
* np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE)
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*
* # loop through victims
*/
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+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
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__Pyx_GOTREF(__pyx_t_6);
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+ __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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{
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__pyx_v_probs_nv = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs_nv.rcbuffer->pybuffer.buf = NULL;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
}
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__pyx_v_probs_nv = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
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+ /* "ml.pyx":50
*
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__pyx_t_2 = 0;
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PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_13)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_13)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_4);
__pyx_t_4 = __pyx_t_6;
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__pyx_t_14 = __Pyx_dict_iter_next(__pyx_t_4, __pyx_t_1, &__pyx_t_2, NULL, &__pyx_t_6, NULL, __pyx_t_13);
if (unlikely(__pyx_t_14 == 0)) break;
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+ if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (!(likely(PyList_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyList_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_6));
__pyx_t_6 = 0;
__pyx_v_i = __pyx_t_12;
__pyx_t_12 = (__pyx_t_12 + 1);
- /* "ml.pyx":53
+ /* "ml.pyx":54
* # fail to infect it, also computes the probability that its most
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* for (prnt, dist, dt, w1, w2, w3) in parents]
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*/
- __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- /* "ml.pyx":54
+ /* "ml.pyx":55
* # likely parent infects it
* failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3)
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@@ -2049,15 +2051,15 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_5); __pyx_t_15 = 0;
for (;;) {
if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_5)) break;
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+ __pyx_t_3 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_15); __Pyx_INCREF(__pyx_t_3); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
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+ __pyx_t_3 = PySequence_ITEM(__pyx_t_5, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyObject* sequence = __pyx_t_3;
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if (size > 6) __Pyx_RaiseTooManyValuesError(6);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (likely(PyTuple_CheckExact(sequence))) {
@@ -2098,7 +2100,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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for (i=0; i < 6; i++) {
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_14 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_14 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_XDECREF_SET(__pyx_v_prnt, __pyx_t_16);
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@@ -2143,22 +2145,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_21);
__pyx_t_21 = 0;
- /* "ml.pyx":53
+ /* "ml.pyx":54
* # fail to infect it, also computes the probability that its most
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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* failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3)
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PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_failures);
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* for (prnt, dist, dt, w1, w2, w3) in parents]
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__Pyx_GOTREF(__pyx_t_5);
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* probs_fail[i] = sum(failures)
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__Pyx_GOTREF(__pyx_t_22);
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* for (prnt, dist, dt, w1, w2, w3) in parents]
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* for (prnt, dist, dt, w1, w2, w3) in parents]
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* successes = [weight_success(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3)
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2391,7 +2393,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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__Pyx_XDECREF_SET(__pyx_v_dists, ((PyObject*)__pyx_t_5));
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __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;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2504,7 +2506,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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for (i=0; i < 6; i++) {
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__Pyx_GOTREF(item);
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- __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
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@@ -2523,7 +2525,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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+ if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_3))) {__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_XDECREF_SET(__pyx_v_dts, ((PyObject*)__pyx_t_5));
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* dts = [dt for (prnt, dist, dt, w1, w2, w3) in parents]
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+ /* "ml.pyx":63
* # find parent that maximizes log(p) - log(\tilde{p})
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}
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+ if (!(likely(PyList_CheckExact(__pyx_t_5))||((__pyx_t_5) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_5)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_5);
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+ /* "ml.pyx":76
* # parents fail to infect it
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@@ -2776,7 +2778,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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+ __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__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;}
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+ t = 1;
+ while (likely(e)) {
+ t *= (b * (e&1)) | ((~e)&1); /* 1 or b */
+ b *= b;
+ e >>= 1;
+ }
+ return t;
+}
+
static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
const int neg_one = (int) -1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
diff --git a/experiments/ml.pyx b/experiments/ml.pyx
index 7eca30a..91536b5 100644
--- a/experiments/ml.pyx
+++ b/experiments/ml.pyx
@@ -10,7 +10,7 @@ cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYP
DTYPE_t t_scale, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
"""weight for successful infection, exponential time model"""
cdef DTYPE_t structural, temporal, result
- structural = delta ** dist
+ structural = delta ** (dist**1)
# structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
temporal = log(exp(alpha/t_scale)-1.) - alpha*dt/t_scale
# temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
@@ -21,11 +21,12 @@ cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYP
DTYPE_t t_scale, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
"""weight for failed infection, exponential time model"""
cdef DTYPE_t structural, temporal, result
- structural = delta ** dist
+ structural = delta ** (dist**1)
# structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
temporal = exp(-alpha * dt/t_scale)
# temporal = 1. - 1. / (1. + dt/alpha)**0.01
result = log(1. - structural + structural * temporal)
+ # if dt>100: result=0
return result
def ml(dict root_victims, dict victims, dict non_victims,
@@ -65,6 +66,7 @@ def ml(dict root_victims, dict victims, dict non_victims,
probs[i] = prob
parent_dists[i] = dists[l]
parent_dts[i] = dts[l]
+ # probs_fail[i] = failures[l]
# loop through non-victims
for i, parents in enumerate(non_victims.itervalues()):
diff --git a/experiments/ml.so b/experiments/ml.so
index 87d16ae..c6e5623 100755
--- a/experiments/ml.so
+++ b/experiments/ml.so
Binary files differ
diff --git a/experiments/out.log b/experiments/out.log
index b83b746..3ef6b13 100644
--- a/experiments/out.log
+++ b/experiments/out.log
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diff --git a/experiments/out2.log b/experiments/out2.log
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diff --git a/experiments/process.py b/experiments/process.py
index 33c83b6..ffa3162 100644
--- a/experiments/process.py
+++ b/experiments/process.py
@@ -15,10 +15,10 @@ if __name__ == "__main__":
sys.exit("usage: {0} <file>".format(sys.argv[0]))
root_victims, victims, non_victims, age = load(open(sys.argv[1]))
- # alphas = np.arange(.02, .1, .01) # parameter of the time component
- alphas = np.logspace(-2.5,-1,num=6)
- # deltas = np.arange(.02, .1, .01) # parameter of the structural component
- deltas = np.logspace(-3,-2,num=6)
+ # alphas = np.arange(1, 200, 10) # parameter of the time component
+ alphas = np.logspace(-3,1,num=16)
+ # deltas = np.arange(.00003, .0003, .00002) # parameter of the structural component
+ deltas = np.logspace(-4,-1,num=12)
lmbda = 1.
with open("out.log", "w") as fh:
for alpha, delta in product(alphas, deltas):
@@ -42,4 +42,20 @@ if __name__ == "__main__":
# alpha = 0.0373
# delta = 0.00518
# beta, roots, ll = ml(root_victims, victims, non_victims, alpha, delta, 1.)
- # print "\t".join(map(str, [alpha, delta, beta, roots, ll])) \ No newline at end of file
+ # print "\t".join(map(str, [alpha, delta, beta, roots, ll]))
+
+# from ml import ml
+# alphas = np.arange(.01, .05, .01) # parameter of the time component
+# # alphas = np.logspace(-4,1,num=5)
+# deltas = np.arange(.001, .02, .003) # parameter of the structural component
+# # deltas = np.logspace(-10,-1,num=8)
+# lmbda = 1.
+# with open("out.log", "w") as fh:
+# for alpha, delta in product(alphas, deltas):
+# beta, roots, ll = ml(root_victims, victims, non_victims, alpha, delta, lmbda)
+# print "\t".join(map(str, [alpha, delta, beta, roots, ll]))
+# fh.write("\t".join(map(str, [alpha, delta, beta, roots, ll])) + "\n")
+# fh.flush()
+
+
+
generated by cgit v1.2.3-70-g09d2 (git 2.52.0) at 2025-12-21 17:22:17 +0000