diff options
Diffstat (limited to 'experiments')
| -rw-r--r-- | experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o | bin | 256828 -> 264960 bytes | |||
| -rw-r--r-- | experiments/ml.pyx | 2 | ||||
| -rw-r--r-- | experiments/ml3.c | 801 | ||||
| -rw-r--r-- | experiments/ml3.pyx | 22 | ||||
| -rwxr-xr-x | experiments/ml3.so | bin | 97868 -> 101972 bytes | |||
| -rw-r--r-- | experiments/out.log | 1400 | ||||
| -rw-r--r-- | experiments/process.py | 8 |
7 files changed, 798 insertions, 1435 deletions
diff --git a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o Binary files differindex 445b01b..81dad16 100644 --- a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o +++ b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o diff --git a/experiments/ml.pyx b/experiments/ml.pyx index 785986c..c8c99cc 100644 --- a/experiments/ml.pyx +++ b/experiments/ml.pyx @@ -89,7 +89,7 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # add probability for realized edges and subtract probability these edges fail beta_add += (probs[probs>=thresh]).sum() # add probability for the seeds and non-seeds - beta_add += roots * log(beta) + (n_nodes-roots) * log(1. - beta) + beta_add += roots * log(beta/3012.) + (n_nodes-roots) * log(1. - beta) if beta_add > max_beta_add: max_beta = beta diff --git a/experiments/ml3.c b/experiments/ml3.c index 90842d8..1f271a8 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 plogis(DTYPE_t weight, DTYPE_t delta): + * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, */ typedef __pyx_t_5numpy_float_t __pyx_t_3ml3_DTYPE_t; #if CYTHON_CCOMPLEX @@ -913,6 +913,7 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { #define __Pyx_ListComp_Append(L,x) PyList_Append(L,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) \ @@ -925,7 +926,6 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj); PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) #endif -#define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0) #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) : \ @@ -1177,6 +1177,7 @@ int __pyx_module_is_main_ml3 = 0; /* Implementation of 'ml3' */ static PyObject *__pyx_builtin_enumerate; +static PyObject *__pyx_builtin_sum; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; @@ -1318,9 +1319,8 @@ static PyObject *__pyx_n_s_w1; static PyObject *__pyx_n_s_w2; static PyObject *__pyx_n_s_w3; static PyObject *__pyx_n_s_zeros; -static PyObject *__pyx_float__1; static PyObject *__pyx_float_1_; -static PyObject *__pyx_float_0_1; +static PyObject *__pyx_float_0_2; static PyObject *__pyx_tuple_; static PyObject *__pyx_tuple__2; static PyObject *__pyx_tuple__3; @@ -1334,43 +1334,6 @@ static PyObject *__pyx_codeobj__9; /* "ml3.pyx":9 * ctypedef np.float_t DTYPE_t * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<< - * return 1./(1. + exp(-weight/delta)) - * - */ - -static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_plogis(__pyx_t_3ml3_DTYPE_t __pyx_v_weight, __pyx_t_3ml3_DTYPE_t __pyx_v_delta) { - __pyx_t_3ml3_DTYPE_t __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("plogis", 0); - - /* "ml3.pyx":10 - * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): - * return 1./(1. + exp(-weight/delta)) # <<<<<<<<<<<<<< - * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, - */ - __pyx_r = (1. / (1. + exp(((-__pyx_v_weight) / __pyx_v_delta)))); - goto __pyx_L0; - - /* "ml3.pyx":9 - * ctypedef np.float_t DTYPE_t - * - * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<< - * return 1./(1. + exp(-weight/delta)) - * - */ - - /* function exit code */ - __pyx_L0:; - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -/* "ml3.pyx":12 - * return 1./(1. + exp(-weight/delta)) - * * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for successful infection, exponential time model""" @@ -1384,17 +1347,17 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __ __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_success", 0); - /* "ml3.pyx":16 + /* "ml3.pyx":13 * """weight for successful infection, exponential time model""" * cdef DTYPE_t structural, temporal, result - * structural = dist * log(delta) # <<<<<<<<<<<<<< + * structural = delta ** dist # <<<<<<<<<<<<<< * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = log(exp(alpha)-1.) - alpha*dt */ - __pyx_v_structural = (__pyx_v_dist * log(__pyx_v_delta)); + __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml3_DTYPE_t)__pyx_v_dist)); - /* "ml3.pyx":18 - * structural = dist * log(delta) + /* "ml3.pyx":15 + * structural = delta ** dist * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = log(exp(alpha)-1.) - alpha*dt # <<<<<<<<<<<<<< * # temporal = 1 - exp(-alpha*dt) @@ -1402,27 +1365,27 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __ */ __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt)); - /* "ml3.pyx":22 + /* "ml3.pyx":19 * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 - * result = structural + temporal # <<<<<<<<<<<<<< + * result = log(structural) + temporal # <<<<<<<<<<<<<< * # print 'st', structural, temporal * return result */ - __pyx_v_result = (__pyx_v_structural + __pyx_v_temporal); + __pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal); - /* "ml3.pyx":24 - * result = structural + temporal + /* "ml3.pyx":21 + * result = log(structural) + temporal * # print 'st', structural, temporal * return result # <<<<<<<<<<<<<< * - * + * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, */ __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml3.pyx":12 - * return 1./(1. + exp(-weight/delta)) + /* "ml3.pyx":9 + * ctypedef np.float_t DTYPE_t * * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): @@ -1435,8 +1398,8 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __ return __pyx_r; } -/* "ml3.pyx":27 - * +/* "ml3.pyx":23 + * return result * * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): @@ -1445,13 +1408,13 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __ 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) { __pyx_t_3ml3_DTYPE_t __pyx_v_structural; - CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_temporal; + __pyx_t_3ml3_DTYPE_t __pyx_v_temporal; __pyx_t_3ml3_DTYPE_t __pyx_v_result; __pyx_t_3ml3_DTYPE_t __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_failure", 0); - /* "ml3.pyx":31 + /* "ml3.pyx":27 * """weight for failed infection, exponential time model""" * cdef DTYPE_t structural, temporal, result * structural = delta ** dist # <<<<<<<<<<<<<< @@ -1460,26 +1423,26 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __ */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml3_DTYPE_t)__pyx_v_dist)); - /* "ml3.pyx":33 + /* "ml3.pyx":29 * structural = delta ** dist * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = exp(-alpha * dt) # <<<<<<<<<<<<<< * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 - * result = log(1. - structural) + * result = log(1. - structural + structural*temporal) */ __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt)); - /* "ml3.pyx":35 + /* "ml3.pyx":31 * temporal = exp(-alpha * dt) * # temporal = 1. - 1. / (1. + dt/alpha)**0.01 - * result = log(1. - structural) # <<<<<<<<<<<<<< + * result = log(1. - structural + structural*temporal) # <<<<<<<<<<<<<< * # print 'stnv', structural, temporal * return result */ - __pyx_v_result = log((1. - __pyx_v_structural)); + __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal))); - /* "ml3.pyx":37 - * result = log(1. - structural) + /* "ml3.pyx":33 + * result = log(1. - structural + structural*temporal) * # print 'stnv', structural, temporal * return result # <<<<<<<<<<<<<< * @@ -1488,8 +1451,8 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __ __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml3.pyx":27 - * + /* "ml3.pyx":23 + * return result * * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): @@ -1502,7 +1465,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __ return __pyx_r; } -/* "ml3.pyx":39 +/* "ml3.pyx":35 * return result * * def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< @@ -1550,31 +1513,31 @@ static PyObject *__pyx_pw_3ml3_1ml3(PyObject *__pyx_self, PyObject *__pyx_args, case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_victims)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_non_victims)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_age)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml3") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml3") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 6) { goto __pyx_L5_argtuple_error; @@ -1589,21 +1552,21 @@ static PyObject *__pyx_pw_3ml3_1ml3(PyObject *__pyx_self, PyObject *__pyx_args, __pyx_v_root_victims = ((PyObject*)values[0]); __pyx_v_victims = ((PyObject*)values[1]); __pyx_v_non_victims = ((PyObject*)values[2]); - __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_age = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_age == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_delta = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml3", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("ml3.ml3", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __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 = 39; __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 = 39; __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 = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_3ml3_ml3(__pyx_self, __pyx_v_root_victims, __pyx_v_victims, __pyx_v_non_victims, __pyx_v_age, __pyx_v_alpha, __pyx_v_delta); /* function exit code */ @@ -1679,8 +1642,8 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_t_3ml3_DTYPE_t __pyx_t_23; __pyx_t_3ml3_DTYPE_t __pyx_t_24; __pyx_t_3ml3_DTYPE_t __pyx_t_25; - double __pyx_t_26; - int __pyx_t_27; + int __pyx_t_26; + double __pyx_t_27; int __pyx_t_28; int __pyx_t_29; int __pyx_t_30; @@ -1708,7 +1671,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_pybuffernd_parent_dts.data = NULL; __pyx_pybuffernd_parent_dts.rcbuffer = &__pyx_pybuffer_parent_dts; - /* "ml3.pyx":45 + /* "ml3.pyx":41 * DTYPE_t beta, ll, beta_add, max_beta, max_beta_add * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<< @@ -1717,54 +1680,54 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject */ if (unlikely(__pyx_v_root_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 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 = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_n_roots = __pyx_t_1; __pyx_v_n_victims = __pyx_t_2; - /* "ml3.pyx":47 + /* "ml3.pyx":43 * n_roots, n_victims = len(root_victims), len(victims) * cdef: * np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<< * np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE) */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __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 = 47; __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 = 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__Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_3); 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); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_7 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs.rcbuffer->pybuffer, (PyObject*)__pyx_t_7, &__Pyx_TypeInfo_nn___pyx_t_3ml3_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| 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__pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_9 = ((PyArrayObject *)__pyx_t_3); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parent_dists.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__Pyx_TypeInfo_nn___pyx_t_3ml3_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_parent_dists = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_parent_dists.diminfo[0].strides = __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_parent_dists.diminfo[0].shape = __pyx_pybuffernd_parent_dists.rcbuffer->pybuffer.shape[0]; } } @@ -1860,43 +1823,43 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_parent_dists = ((PyArrayObject *)__pyx_t_3); __pyx_t_3 = 0; - /* "ml3.pyx":50 + /* "ml3.pyx":46 * np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<< * * # loop through victims */ - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __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 = 46; __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 = 50; __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 = 46; __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 = 50; __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 = 46; __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 = 50; __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 = 46; __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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyDict_New(); 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); - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __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 = 46; __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 = 50; __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __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 = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __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 = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + 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;} __pyx_t_10 = ((PyArrayObject *)__pyx_t_6); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_parent_dts.rcbuffer->pybuffer, (PyObject*)__pyx_t_10, &__Pyx_TypeInfo_nn___pyx_t_3ml3_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __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 = 50; __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_parent_dts.diminfo[0].strides = __pyx_pybuffernd_parent_dts.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_parent_dts.diminfo[0].shape = __pyx_pybuffernd_parent_dts.rcbuffer->pybuffer.shape[0]; } } @@ -1904,7 +1867,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __pyx_v_parent_dts = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "ml3.pyx":53 + /* "ml3.pyx":49 * * # loop through victims * for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<< @@ -1915,9 +1878,9 @@ static PyObject *__pyx_pf_3ml3_ml3(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 = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_3 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_12)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_12)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = __pyx_t_3; @@ -1925,42 +1888,42 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject while (1) { __pyx_t_13 = __Pyx_dict_iter_next(__pyx_t_6, __pyx_t_1, &__pyx_t_2, NULL, &__pyx_t_3, NULL, __pyx_t_12); if (unlikely(__pyx_t_13 == 0)) break; - if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (!(likely(PyList_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(PyList_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; __pyx_v_i = __pyx_t_11; __pyx_t_11 = (__pyx_t_11 + 1); - /* "ml3.pyx":57 + /* "ml3.pyx":53 * # fail to infect it, also computes the probability that its most * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] - * # probs_fail[i] = sum(failures) + * probs_fail[i] = sum(failures) */ - __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - /* "ml3.pyx":58 + /* "ml3.pyx":54 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< - * # probs_fail[i] = sum(failures) + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_5 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_5); __pyx_t_14 = 0; for (;;) { if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_5)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_4 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_4); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_4); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_4 = PySequence_ITEM(__pyx_t_5, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(__pyx_t_5, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) { PyObject* sequence = __pyx_t_4; @@ -1972,7 +1935,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __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))) { @@ -1998,7 +1961,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __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; } @@ -2008,7 +1971,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject } else { Py_ssize_t index = -1; PyObject** temps[5] = {&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18,&__pyx_t_19}; - __pyx_t_20 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_20 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_20); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_21 = Py_TYPE(__pyx_t_20)->tp_iternext; @@ -2017,7 +1980,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_21 = NULL; __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; goto __pyx_L8_unpacking_done; @@ -2025,12 +1988,12 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; __pyx_t_21 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L8_unpacking_done:; } - __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; - __pyx_t_22 = __Pyx_PyInt_As_int(__pyx_t_16); if (unlikely((__pyx_t_22 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __Pyx_PyInt_As_int(__pyx_t_16); if (unlikely((__pyx_t_22 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; __pyx_v_dist = __pyx_t_13; __pyx_v_dt = __pyx_t_22; @@ -2041,26 +2004,26 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_19); __pyx_t_19 = 0; - /* "ml3.pyx":57 + /* "ml3.pyx":53 * # fail to infect it, also computes the probability that its most * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] - * # probs_fail[i] = sum(failures) + * probs_fail[i] = sum(failures) */ - __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_4 = PyFloat_FromDouble(__pyx_f_3ml3_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_23, __pyx_t_24, __pyx_t_25)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyFloat_FromDouble(__pyx_f_3ml3_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_23, __pyx_t_24, __pyx_t_25)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "ml3.pyx":58 + /* "ml3.pyx":54 * # likely parent infects it * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< - * # probs_fail[i] = sum(failures) + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) */ } @@ -2068,18 +2031,39 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_XDECREF_SET(__pyx_v_failures, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "ml3.pyx":60 + /* "ml3.pyx":55 + * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] - * # probs_fail[i] = sum(failures) + * probs_fail[i] = sum(failures) # <<<<<<<<<<<<<< + * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) + * for (dist, dt, w1, w2, w3) in parents] + */ + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_INCREF(__pyx_v_failures); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_failures); + __Pyx_GIVEREF(__pyx_v_failures); + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_25 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_25 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + __pyx_t_22 = __pyx_v_i; + if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_pybuffernd_probs_fail.diminfo[0].shape; + *__Pyx_BufPtrStrided1d(__pyx_t_3ml3_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_22, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_25; + + /* "ml3.pyx":56 + * for (dist, dt, w1, w2, w3) in parents] + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * dists = [dist for (dist, dt, w1, w2, w3) in parents] */ - __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); - /* "ml3.pyx":61 - * # probs_fail[i] = sum(failures) + /* "ml3.pyx":57 + * probs_fail[i] = sum(failures) * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * dists = [dist for (dist, dt, w1, w2, w3) in parents] @@ 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__Pyx_INCREF(__pyx_t_4); __pyx_t_14++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_4 = PySequence_ITEM(__pyx_t_5, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(__pyx_t_3, __pyx_t_14); __pyx_t_14++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) { PyObject* sequence = __pyx_t_4; @@ -2107,7 +2091,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2133,7 +2117,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_19,&__pyx_t_18,&__pyx_t_17,&__pyx_t_16,&__pyx_t_15}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2143,7 +2127,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject } else { Py_ssize_t index = -1; PyObject** temps[5] = {&__pyx_t_19,&__pyx_t_18,&__pyx_t_17,&__pyx_t_16,&__pyx_t_15}; - __pyx_t_20 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_20 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_20); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_21 = Py_TYPE(__pyx_t_20)->tp_iternext; @@ -2152,7 +2136,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_21(__pyx_t_20), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_21 = NULL; __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; goto __pyx_L12_unpacking_done; @@ -2160,15 +2144,15 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; __pyx_t_21 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L12_unpacking_done:; } - __pyx_t_22 = __Pyx_PyInt_As_int(__pyx_t_19); if (unlikely((__pyx_t_22 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_19); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; - __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_18); if 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PyFloat_FromDouble(0.2); if (unlikely(!__pyx_float_0_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; return -1; @@ -5242,16 +5211,16 @@ PyMODINIT_FUNC PyInit_ml3(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_DTYPE, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "ml3.pyx":39 + /* "ml3.pyx":35 * return result * * def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< * DTYPE_t alpha, DTYPE_t delta): * cdef: */ - __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_3ml3_1ml3, NULL, __pyx_n_s_ml3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_3ml3_1ml3, NULL, __pyx_n_s_ml3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml3, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml3, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; /* "ml3.pyx":1 diff --git a/experiments/ml3.pyx b/experiments/ml3.pyx index 1f46ef5..5cbe3ba 100644 --- a/experiments/ml3.pyx +++ b/experiments/ml3.pyx @@ -10,17 +10,16 @@ cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): """weight for successful infection, exponential time model""" cdef DTYPE_t structural, temporal, result - structural = dist * log(delta) + structural = delta ** dist # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) temporal = log(exp(alpha)-1.) - alpha*dt # temporal = 1 - exp(-alpha*dt) # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR' # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 - result = structural + temporal + result = log(structural) + temporal # print 'st', structural, temporal return result - cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): """weight for failed infection, exponential time model""" @@ -29,7 +28,7 @@ cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) temporal = exp(-alpha * dt) # temporal = 1. - 1. / (1. + dt/alpha)**0.01 - result = log(1. - structural) + result = log(1. - structural + structural*temporal) # print 'stnv', structural, temporal return result @@ -53,7 +52,7 @@ def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # likely parent infects it failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) for (dist, dt, w1, w2, w3) in parents] - # probs_fail[i] = sum(failures) + probs_fail[i] = sum(failures) successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) for (dist, dt, w1, w2, w3) in parents] dists = [dist for (dist, dt, w1, w2, w3) in parents] @@ -67,20 +66,15 @@ def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age, probs[i] = prob parent_dists[i] = dists[l] parent_dts[i] = dts[l] - probs_fail[i] = failures[l] - - # print successes - # print failures - # print probs + # probs_fail[i] = failures[l] # calculate log likelihood - ll = probs_fail.sum() # add probability that all edges to victims fail - # ll += probs_nv.sum() # add probability that all edges to non_victims fail + ll = probs_fail.sum() # add probability that all edges to all victims fail # print 'probs', probs max_beta_add = float('-inf') # iterate over all victim nodes to find the optimal threshold - for beta in np.arange(0.1, 1., .1): + for beta in np.arange(0.2, 1., 1.): thresh = log(beta/(3012.*(1.-beta))) # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh]) roots = n_roots + len(probs[probs<thresh]) @@ -89,7 +83,7 @@ def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # add probability for realized edges and subtract probability these edges fail beta_add += (probs[probs>=thresh]).sum() # add probability for the seeds and non-seeds - beta_add += roots * log(beta) + len(probs[probs>=thresh]) * log(1. - beta) + beta_add += roots * log(beta/3012.) + len(probs[probs>=thresh]) * log(1. - beta) if beta_add > max_beta_add: max_beta = beta diff --git a/experiments/ml3.so b/experiments/ml3.so Binary files differindex 3f515d5..a1f5718 100755 --- a/experiments/ml3.so +++ b/experiments/ml3.so diff --git a/experiments/out.log b/experiments/out.log index 77e6ca1..a9e77a5 100644 --- a/experiments/out.log +++ b/experiments/out.log @@ -1,1000 +1,400 @@ -0.001 0.01 0.9 11270 -1235.94455231 -0.001 0.06 0.9 11270 -1497.58353681 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a/experiments/process.py +++ b/experiments/process.py @@ -13,10 +13,10 @@ 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(1e-3, 5e-1, 1e-2) # parameter of the time component - # alphas = np.logspace(-4,0,num=20) - deltas = np.arange(0.01, 0.99, 0.05) # parameter of the structural component - # deltas = np.logspace(-3,-0.001,num=20) + # alphas = np.arange(1e-3, 1e-2, 8e-4) # parameter of the time component + alphas = np.logspace(-4,-.8,num=20) + # deltas = np.arange(0.001, 0.3, 0.008) # parameter of the structural component + deltas = np.logspace(-2,-.0001,num=20) with open("out.log", "w") as fh: for alpha, delta in product(alphas, deltas): beta, roots, ll = ml3(root_victims, victims, non_victims, age, alpha, delta) |