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-rw-r--r--experiments/build/temp.macosx-10.6-x86_64-2.7/ml.obin326092 -> 326540 bytes
-rw-r--r--experiments/ml.c676
-rw-r--r--experiments/ml.pyx9
-rwxr-xr-xexperiments/ml.sobin125136 -> 125136 bytes
-rw-r--r--experiments/out.log317
-rw-r--r--experiments/process.py10
6 files changed, 460 insertions, 552 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 e82f8b2..20d0673 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 f0a7125..25c10ac 100644
--- a/experiments/ml.c
+++ b/experiments/ml.c
@@ -1018,8 +1018,6 @@ 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 *);
@@ -1380,7 +1378,7 @@ static PyObject *__pyx_codeobj__9;
* """weight for successful infection, exponential time model"""
*/
-static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_lmbda, __pyx_t_2ml_DTYPE_t __pyx_v_t_scale, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w3) {
+static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, __pyx_t_2ml_DTYPE_t __pyx_v_lmbda, __pyx_t_2ml_DTYPE_t __pyx_v_t_scale, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w3) {
__pyx_t_2ml_DTYPE_t __pyx_v_structural;
__pyx_t_2ml_DTYPE_t __pyx_v_temporal;
__pyx_t_2ml_DTYPE_t __pyx_v_result;
@@ -1388,18 +1386,18 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("weight_success", 0);
- /* "ml.pyx":13
- * """weight for successful infection, exponential time model"""
+ /* "ml.pyx":14
* cdef DTYPE_t structural, temporal, result
- * structural = delta ** (dist**1) # <<<<<<<<<<<<<<
- * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+ * # structural = delta ** (dist**1)
+ * structural = delta * lmbda**(dist-1) # <<<<<<<<<<<<<<
* 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
*/
- __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__Pyx_pow_long(((long)__pyx_v_dist), 1)));
+ __pyx_v_structural = (__pyx_v_delta * pow(__pyx_v_lmbda, ((__pyx_t_2ml_DTYPE_t)(__pyx_v_dist - 1))));
/* "ml.pyx":15
- * structural = delta ** (dist**1)
- * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+ * # structural = delta ** (dist**1)
+ * structural = delta * lmbda**(dist-1)
* 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
* result = log(structural) + temporal
@@ -1447,7 +1445,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
* """weight for failed infection, exponential time model"""
*/
-static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_lmbda, __pyx_t_2ml_DTYPE_t __pyx_v_t_scale, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w3) {
+static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, __pyx_t_2ml_DTYPE_t __pyx_v_lmbda, __pyx_t_2ml_DTYPE_t __pyx_v_t_scale, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_2ml_DTYPE_t __pyx_v_w3) {
__pyx_t_2ml_DTYPE_t __pyx_v_structural;
__pyx_t_2ml_DTYPE_t __pyx_v_temporal;
__pyx_t_2ml_DTYPE_t __pyx_v_result;
@@ -1455,18 +1453,18 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("weight_failure", 0);
- /* "ml.pyx":24
- * """weight for failed infection, exponential time model"""
+ /* "ml.pyx":25
* cdef DTYPE_t structural, temporal, result
- * structural = delta ** (dist**1) # <<<<<<<<<<<<<<
- * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+ * # structural = delta ** (dist**1)
+ * structural = delta * lmbda**(dist-1) # <<<<<<<<<<<<<<
* temporal = exp(-alpha * dt/t_scale)
+ * # temporal = 1. - 1. / (1. + dt/alpha)**0.01
*/
- __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__Pyx_pow_long(((long)__pyx_v_dist), 1)));
+ __pyx_v_structural = (__pyx_v_delta * pow(__pyx_v_lmbda, ((__pyx_t_2ml_DTYPE_t)(__pyx_v_dist - 1))));
/* "ml.pyx":26
- * structural = delta ** (dist**1)
- * # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+ * # structural = delta ** (dist**1)
+ * structural = delta * lmbda**(dist-1)
* temporal = exp(-alpha * dt/t_scale) # <<<<<<<<<<<<<<
* # temporal = 1. - 1. / (1. + dt/alpha)**0.01
* result = log(1. - structural + structural * temporal)
@@ -1477,14 +1475,14 @@ 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":30
+ /* "ml.pyx":29
+ * # 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,
@@ -1506,7 +1504,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py
return __pyx_r;
}
-/* "ml.pyx":32
+/* "ml.pyx":31
* return result
*
* def ml(dict root_victims, dict victims, dict non_victims, # <<<<<<<<<<<<<<
@@ -1554,31 +1552,31 @@ 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 = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 32; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 31; __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 = 32; __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 = 31; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 6) {
goto __pyx_L5_argtuple_error;
@@ -1593,21 +1591,21 @@ 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 = 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;}
+ __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;}
}
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 = 32; __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 = 31; __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 = 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;}
+ 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;}
__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 */
@@ -1730,7 +1728,7 @@ 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":38
+ /* "ml.pyx":37
* DTYPE_t beta, ll, beta_add, max_beta, max_beta_add
* list parents, failures, successes
* n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<<
@@ -1739,18 +1737,18 @@ 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 = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__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;}
+ __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;}
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 = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__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_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_v_n_roots = __pyx_t_1;
__pyx_v_n_victims = __pyx_t_2;
- /* "ml.pyx":39
+ /* "ml.pyx":38
* list parents, failures, successes
* n_roots, n_victims = len(root_victims), len(victims)
* n_nodes = 148152 # <<<<<<<<<<<<<<
@@ -1760,7 +1758,7 @@ 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":40
+ /* "ml.pyx":39
* n_roots, n_victims = len(root_victims), len(victims)
* n_nodes = 148152
* n_days = 3012 # <<<<<<<<<<<<<<
@@ -1769,7 +1767,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
*/
__pyx_v_n_days = 3012;
- /* "ml.pyx":41
+ /* "ml.pyx":40
* n_nodes = 148152
* n_days = 3012
* t_scale = 1. # <<<<<<<<<<<<<<
@@ -1778,43 +1776,43 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
*/
__pyx_v_t_scale = 1.;
- /* "ml.pyx":43
+ /* "ml.pyx":42
* 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 = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 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 = 45; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -1954,48 +1952,48 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__pyx_v_parent_dts = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
- /* "ml.pyx":47
+ /* "ml.pyx":46
* 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 = 46; __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;}
+ __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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+ __pyx_t_2 = PyDict_Size(__pyx_v_non_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
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+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __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;}
+ __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
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+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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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 = 46; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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{
__Pyx_BufFmt_StackElem __pyx_stack[1];
if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs_nv.rcbuffer->pybuffer, (PyObject*)__pyx_t_11, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) {
__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 = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
} else {__pyx_pybuffernd_probs_nv.diminfo[0].strides = __pyx_pybuffernd_probs_nv.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_probs_nv.diminfo[0].shape = __pyx_pybuffernd_probs_nv.rcbuffer->pybuffer.shape[0];
}
}
@@ -2003,7 +2001,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__pyx_v_probs_nv = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "ml.pyx":50
+ /* "ml.pyx":49
*
* # loop through victims
* for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<<
@@ -2014,9 +2012,9 @@ 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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__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_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_GOTREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_4);
__pyx_t_4 = __pyx_t_6;
@@ -2024,25 +2022,25 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
while (1) {
__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;
- if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __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 = 50; __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 = 49; __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":54
+ /* "ml.pyx":53
* # fail to infect it, also computes the probability that its most
* # likely parent infects it
* failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3) # <<<<<<<<<<<<<<
* for (prnt, dist, dt, w1, w2, w3) in parents]
* probs_fail[i] = sum(failures)
*/
- __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_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_GOTREF(__pyx_t_6);
- /* "ml.pyx":55
+ /* "ml.pyx":54
* # likely parent infects it
* failures = [weight_failure(dist, dt, alpha, delta, lmbda, t_scale, w1, w2, w3)
* for (prnt, dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<<
@@ -2051,15 +2049,15 @@ 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 = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __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;
#if CYTHON_COMPILING_IN_CPYTHON
- __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;}
+ __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 = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __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;}
+ __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 = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
PyObject* sequence = __pyx_t_3;
@@ -2071,7 +2069,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
if (unlikely(size != 6)) {
if (size > 6) __Pyx_RaiseTooManyValuesError(6);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -2100,7 +2098,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
Py_ssize_t i;
PyObject** temps[6] = {&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19,&__pyx_t_20,&__pyx_t_21};
for (i=0; i < 6; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
*(temps[i]) = item;
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@@ -2110,7 +2108,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
} else {
Py_ssize_t index = -1;
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+ __pyx_t_22 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_23 = Py_TYPE(__pyx_t_22)->tp_iternext;
@@ -2119,7 +2117,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__Pyx_GOTREF(item);
*(temps[index]) = item;
}
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+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_23(__pyx_t_22), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_23 = NULL;
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
goto __pyx_L8_unpacking_done;
@@ -2127,12 +2125,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
__pyx_t_23 = NULL;
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* # likely parent infects it
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* probs_fail[i] = sum(failures)
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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 = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_5);
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+ /* "ml.pyx":75
* # parents fail to infect it
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@@ -2778,7 +2776,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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* for beta in np.arange(0.01, 1., 0.01):
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@@ -3017,60 +3015,60 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
*/
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- /* "ml.pyx":87
+ /* "ml.pyx":86
* for beta in np.arange(0.01, 1., 0.01):
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* non_seeds = probs>=thresh
* roots = n_roots + sum(seeds)
*/
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+ /* "ml.pyx":87
* thresh = log(beta/(n_days*(1.-beta)))
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* non_seeds = probs>=thresh # <<<<<<<<<<<<<<
* roots = n_roots + sum(seeds)
*
*/
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+ /* "ml.pyx":88
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* beta_add = 0.
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- /* "ml.pyx":91
+ /* "ml.pyx":90
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@@ -3079,18 +3077,18 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
*/
__pyx_v_beta_add = 0.;
- /* "ml.pyx":93
+ /* "ml.pyx":92
* beta_add = 0.
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* # add probability for the seeds and non-seeds
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*/
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+ __pyx_t_5 = PyObject_GetItem(((PyObject *)__pyx_v_probs), __pyx_v_non_seeds); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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}
}
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+ /* "ml.pyx":94
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if (__pyx_t_31) {
- /* "ml.pyx":98
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*/
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*/
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* max_roots = roots
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@@ -3213,26 +3211,26 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
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+ __pyx_t_20 = __Pyx_PyObject_CallNoArg(__pyx_t_21); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-}
-
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 91536b5..e1bf26b 100644
--- a/experiments/ml.pyx
+++ b/experiments/ml.pyx
@@ -10,8 +10,8 @@ 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**1)
- # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+ # structural = delta ** (dist**1)
+ structural = delta * lmbda**(dist-1)
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
result = log(structural) + temporal
@@ -21,12 +21,11 @@ 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**1)
- # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+ # structural = delta ** (dist**1)
+ structural = delta * lmbda**(dist-1)
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,
diff --git a/experiments/ml.so b/experiments/ml.so
index c6e5623..73b6dbd 100755
--- a/experiments/ml.so
+++ b/experiments/ml.so
Binary files differ
diff --git a/experiments/out.log b/experiments/out.log
index 3ef6b13..55df723 100644
--- a/experiments/out.log
+++ b/experiments/out.log
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diff --git a/experiments/process.py b/experiments/process.py
index ffa3162..f339fd1 100644
--- a/experiments/process.py
+++ b/experiments/process.py
@@ -16,12 +16,14 @@ if __name__ == "__main__":
root_victims, victims, non_victims, age = load(open(sys.argv[1]))
# alphas = np.arange(1, 200, 10) # parameter of the time component
- alphas = np.logspace(-3,1,num=16)
+ alphas = np.logspace(-6,1,num=5)
# deltas = np.arange(.00003, .0003, .00002) # parameter of the structural component
- deltas = np.logspace(-4,-1,num=12)
- lmbda = 1.
+ deltas = np.logspace(-6,-1,num=5)
+ lmbdas = np.logspace(-8,-3,num=5)
+ # lmbda = 1
with open("out.log", "w") as fh:
- for alpha, delta in product(alphas, deltas):
+ for alpha, delta, lmbda in product(alphas, deltas, lmbdas):
+ # 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")
generated by cgit v1.2.3-70-g09d2 (git 2.52.0) at 2025-12-24 05:43:24 +0000