diff options
| -rw-r--r-- | R Scripts/find-cascades.R | 10 | ||||
| -rw-r--r-- | experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o | bin | 308424 -> 311532 bytes | |||
| -rw-r--r-- | experiments/build_network.py | 7 | ||||
| -rw-r--r-- | experiments/ml.c | 733 | ||||
| -rw-r--r-- | experiments/ml.pyx | 32 | ||||
| -rwxr-xr-x | experiments/ml.so | bin | 109500 -> 109364 bytes | |||
| -rw-r--r-- | experiments/out.log | 580 | ||||
| -rw-r--r-- | experiments/plot3d.py | 2 | ||||
| -rw-r--r-- | experiments/process.py | 4 |
9 files changed, 493 insertions, 875 deletions
diff --git a/R Scripts/find-cascades.R b/R Scripts/find-cascades.R index ecd5c83..0a69c5c 100644 --- a/R Scripts/find-cascades.R +++ b/R Scripts/find-cascades.R @@ -2,17 +2,17 @@ library(igraph) setwd("~/Documents/Cascade Project/") load('Results/hyper-lcc.RData') load('Results/dag_dat_vics.RData') -source('Scripts/temporal.R') +source('criminal_cascades/R Scripts/temporal.R') # source('Scripts/homophily.R') -source('Scripts/structural.R') +source('criminal_cascades/R Scripts/structural.R') vic_ids = which(V(hyp_lcc)$vic==TRUE) #### Initialize model parameters -alpha = 1/5 +alpha = 1/21 # gamma = 0.3 -delta = 0.1 -beta = 9.955713e-6 +delta = 0.001 +beta = 0.00796964464237 ##### Get weights # find max n days where infection possible given alpha 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 Binary files differindex 51e37b0..42c7292 100644 --- a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o +++ b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o diff --git a/experiments/build_network.py b/experiments/build_network.py index 47f657b..fd7179f 100644 --- a/experiments/build_network.py +++ b/experiments/build_network.py @@ -14,8 +14,8 @@ def build_network(filename): from_, to = int(float(row["from"])), int(float(row["to"])) dist = int(row["dist"]) w1, w2, w3 = float(row["w1"]), float(row["w2"]), float(row["w3"]) - if int(float(row["dist"])) > 2: - continue + # if int(float(row["dist"])) > 1: + # continue # 'to' is a victim if row["t2"] != "NA": dt = int(row["t2"]) - int(row["t1"]) @@ -32,7 +32,7 @@ def build_network(filename): dt = 3012 - int(row["t1"]) parent = (dist, dt, w1, w2, w3) if to not in non_victims: - age += 3012 - int(row["spawn2"]) + # age += 3012 - int(row["spawn2"]) non_victims[to] = [] non_victims[to].append(parent) if from_ not in victims: @@ -53,4 +53,5 @@ if __name__ == "__main__": filename = sys.argv[1] root, _ = splitext(filename) root_victims, victims, non_victims, age = build_network(filename) + print age dump((root_victims, victims, non_victims, age), open(root + ".pickle", "w")) diff --git a/experiments/ml.c b/experiments/ml.c index d8318de..1bc0ddb 100644 --- a/experiments/ml.c +++ b/experiments/ml.c @@ -759,11 +759,11 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; */ typedef npy_cdouble __pyx_t_5numpy_complex_t; -/* "ml.pyx":52 +/* "ml.pyx":56 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta, DTYPE_t gamma=10): + * DTYPE_t alpha, DTYPE_t delta): * cdef: */ struct __pyx_obj_2ml___pyx_scope_struct__ml { @@ -773,9 +773,9 @@ struct __pyx_obj_2ml___pyx_scope_struct__ml { }; -/* "ml.pyx":76 +/* "ml.pyx":80 * for (dist, dt, w1, w2, w3) in parents] - * # find parent that maximizes p/\tilde{p} + * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< * * # loop through non-victims @@ -1242,8 +1242,8 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha /* Module declarations from 'ml' */ static PyTypeObject *__pyx_ptype_2ml___pyx_scope_struct__ml = 0; static PyTypeObject *__pyx_ptype_2ml___pyx_scope_struct_1_genexpr = 0; -static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int, int, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t); /*proto*/ -static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int, int, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t); /*proto*/ +static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int, int, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t); /*proto*/ +static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int, int, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t, __pyx_t_2ml_DTYPE_t); /*proto*/ static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_2ml_DTYPE_t), { 0 }, 0, 'R', 0, 0 }; #define __Pyx_MODULE_NAME "ml" int __pyx_module_is_main_ml = 0; @@ -1257,7 +1257,7 @@ static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; static PyObject *__pyx_pf_2ml_2ml_genexpr(PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_2ml_DTYPE_t __pyx_v_age, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, __pyx_t_2ml_DTYPE_t __pyx_v_gamma); /* proto */ +static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_2ml_DTYPE_t __pyx_v_age, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static PyObject *__pyx_tp_new_2ml___pyx_scope_struct__ml(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ @@ -1306,7 +1306,6 @@ static char __pyx_k_beta2[] = "beta2"; static char __pyx_k_close[] = "close"; static char __pyx_k_delta[] = "delta"; static char __pyx_k_dtype[] = "dtype"; -static char __pyx_k_gamma[] = "gamma"; static char __pyx_k_numpy[] = "numpy"; static char __pyx_k_print[] = "print"; static char __pyx_k_probs[] = "probs"; @@ -1370,7 +1369,6 @@ static PyObject *__pyx_n_s_failures; static PyObject *__pyx_n_s_file; static PyObject *__pyx_n_s_float64; static PyObject *__pyx_n_s_format; -static PyObject *__pyx_n_s_gamma; static PyObject *__pyx_n_s_genexpr; static PyObject *__pyx_n_s_i; static PyObject *__pyx_n_s_import; @@ -1426,7 +1424,7 @@ static PyObject *__pyx_codeobj__9; * ctypedef np.float_t DTYPE_t * * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<< - * return 1/(1 + exp(-weight/delta)) + * return 1./(1. + exp(-weight/delta)) * */ @@ -1438,18 +1436,18 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_plogis(__pyx_t_2ml_DTYPE_t __pyx_v_weight /* "ml.pyx":10 * * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): - * return 1/(1 + exp(-weight/delta)) # <<<<<<<<<<<<<< + * return 1./(1. + exp(-weight/delta)) # <<<<<<<<<<<<<< * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, + * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, */ - __pyx_r = (1.0 / (1.0 + exp(((-__pyx_v_weight) / __pyx_v_delta)))); + __pyx_r = (1. / (1. + exp(((-__pyx_v_weight) / __pyx_v_delta)))); goto __pyx_L0; /* "ml.pyx":9 * ctypedef np.float_t DTYPE_t * * cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): # <<<<<<<<<<<<<< - * return 1/(1 + exp(-weight/delta)) + * return 1./(1. + exp(-weight/delta)) * */ @@ -1460,14 +1458,14 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_plogis(__pyx_t_2ml_DTYPE_t __pyx_v_weight } /* "ml.pyx":12 - * return 1/(1 + exp(-weight/delta)) + * return 1./(1. + exp(-weight/delta)) * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, # <<<<<<<<<<<<<< - * DTYPE_t delta, DTYPE_t gamma): + * 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""" */ -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_gamma) { +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_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; @@ -1479,22 +1477,22 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py * """weight for successful infection, exponential time model""" * cdef DTYPE_t structural, temporal, result * structural = delta ** (dist) # <<<<<<<<<<<<<< + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = exp(-alpha * dt) * (1 - exp(-alpha)) - * result = log(structural * temporal) */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist)); - /* "ml.pyx":17 - * cdef DTYPE_t structural, temporal, result + /* "ml.pyx":18 * structural = delta ** (dist) + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = exp(-alpha * dt) * (1 - exp(-alpha)) # <<<<<<<<<<<<<< * result = log(structural * temporal) * return result */ __pyx_v_temporal = (exp(((-__pyx_v_alpha) * __pyx_v_dt)) * (1.0 - exp((-__pyx_v_alpha)))); - /* "ml.pyx":18 - * structural = delta ** (dist) + /* "ml.pyx":19 + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = exp(-alpha * dt) * (1 - exp(-alpha)) * result = log(structural * temporal) # <<<<<<<<<<<<<< * return result @@ -1502,7 +1500,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py */ __pyx_v_result = log((__pyx_v_structural * __pyx_v_temporal)); - /* "ml.pyx":19 + /* "ml.pyx":20 * temporal = exp(-alpha * dt) * (1 - exp(-alpha)) * result = log(structural * temporal) * return result # <<<<<<<<<<<<<< @@ -1513,10 +1511,10 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py goto __pyx_L0; /* "ml.pyx":12 - * return 1/(1 + exp(-weight/delta)) + * return 1./(1. + exp(-weight/delta)) * - * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, # <<<<<<<<<<<<<< - * DTYPE_t delta, DTYPE_t gamma): + * 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""" */ @@ -1526,15 +1524,15 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py return __pyx_r; } -/* "ml.pyx":22 +/* "ml.pyx":23 * * - * cdef DTYPE_t weight_success_power(int dist, int dt, DTYPE_t alpha, # <<<<<<<<<<<<<< - * DTYPE_t delta, DTYPE_t gamma): + * cdef DTYPE_t weight_success_power(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< + * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for successful infection, power-law time model""" */ -static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success_power(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_gamma) { +static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success_power(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_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; @@ -1542,26 +1540,26 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success_power(int __pyx_v_dist, in __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_success_power", 0); - /* "ml.pyx":26 + /* "ml.pyx":27 * """weight for successful infection, power-law time model""" * cdef DTYPE_t structural, temporal, result * structural = delta ** (dist) # <<<<<<<<<<<<<< + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 - * result = log(structural * temporal) */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist)); - /* "ml.pyx":27 - * cdef DTYPE_t structural, temporal, result + /* "ml.pyx":29 * structural = delta ** (dist) + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 # <<<<<<<<<<<<<< * result = log(structural * temporal) * return result */ __pyx_v_temporal = ((1. / pow(((double)(1. + ((__pyx_v_dt - 1.) / __pyx_v_alpha))), 0.01)) - (1. / pow(((double)(1. + (__pyx_v_dt / __pyx_v_alpha))), 0.01))); - /* "ml.pyx":28 - * structural = delta ** (dist) + /* "ml.pyx":30 + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 * result = log(structural * temporal) # <<<<<<<<<<<<<< * return result @@ -1569,7 +1567,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success_power(int __pyx_v_dist, in */ __pyx_v_result = log((__pyx_v_structural * __pyx_v_temporal)); - /* "ml.pyx":29 + /* "ml.pyx":31 * temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 * result = log(structural * temporal) * return result # <<<<<<<<<<<<<< @@ -1579,11 +1577,11 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success_power(int __pyx_v_dist, in __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml.pyx":22 + /* "ml.pyx":23 * * - * cdef DTYPE_t weight_success_power(int dist, int dt, DTYPE_t alpha, # <<<<<<<<<<<<<< - * DTYPE_t delta, DTYPE_t gamma): + * cdef DTYPE_t weight_success_power(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< + * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for successful infection, power-law time model""" */ @@ -1593,15 +1591,15 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success_power(int __pyx_v_dist, in return __pyx_r; } -/* "ml.pyx":32 +/* "ml.pyx":34 * * - * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, # <<<<<<<<<<<<<< - * DTYPE_t delta, DTYPE_t gamma): + * 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""" */ -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_gamma) { +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_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; @@ -1609,25 +1607,25 @@ 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":36 + /* "ml.pyx":38 * """weight for failed infection, exponential time model""" * cdef DTYPE_t structural, temporal, result * structural = delta ** (dist) # <<<<<<<<<<<<<< + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = 1. - exp(-alpha * dt) - * #result = log(1. - structural) */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist)); - /* "ml.pyx":37 - * cdef DTYPE_t structural, temporal, result + /* "ml.pyx":40 * structural = delta ** (dist) + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = 1. - exp(-alpha * dt) # <<<<<<<<<<<<<< * #result = log(1. - structural) * result = log(1. - structural * temporal) */ __pyx_v_temporal = (1. - exp(((-__pyx_v_alpha) * __pyx_v_dt))); - /* "ml.pyx":39 + /* "ml.pyx":42 * temporal = 1. - exp(-alpha * dt) * #result = log(1. - structural) * result = log(1. - structural * temporal) # <<<<<<<<<<<<<< @@ -1636,7 +1634,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py */ __pyx_v_result = log((1. - (__pyx_v_structural * __pyx_v_temporal))); - /* "ml.pyx":40 + /* "ml.pyx":43 * #result = log(1. - structural) * result = log(1. - structural * temporal) * return result # <<<<<<<<<<<<<< @@ -1646,11 +1644,11 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml.pyx":32 + /* "ml.pyx":34 * * - * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, # <<<<<<<<<<<<<< - * DTYPE_t delta, DTYPE_t gamma): + * 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""" */ @@ -1660,15 +1658,15 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure(int __pyx_v_dist, int __py return __pyx_r; } -/* "ml.pyx":43 +/* "ml.pyx":46 * * - * cdef DTYPE_t weight_failure_power(int dist, int dt, DTYPE_t alpha, # <<<<<<<<<<<<<< - * DTYPE_t delta, DTYPE_t gamma): + * cdef DTYPE_t weight_failure_power(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< + * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for failed infection, power-law time model""" */ -static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure_power(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_gamma) { +static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure_power(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_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; @@ -1676,26 +1674,26 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure_power(int __pyx_v_dist, in __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("weight_failure_power", 0); - /* "ml.pyx":47 + /* "ml.pyx":50 * """weight for failed infection, power-law time model""" * cdef DTYPE_t structural, temporal, result * structural = delta ** (dist) # <<<<<<<<<<<<<< + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = 1. - 1. / (1. + dt/alpha)**0.01 - * result = log(1. - structural * temporal) */ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist)); - /* "ml.pyx":48 - * cdef DTYPE_t structural, temporal, result + /* "ml.pyx":52 * structural = delta ** (dist) + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = 1. - 1. / (1. + dt/alpha)**0.01 # <<<<<<<<<<<<<< * result = log(1. - structural * temporal) * return result */ __pyx_v_temporal = (1. - (1. / pow(((double)(1. + (__pyx_v_dt / __pyx_v_alpha))), 0.01))); - /* "ml.pyx":49 - * structural = delta ** (dist) + /* "ml.pyx":53 + * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) * temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural * temporal) # <<<<<<<<<<<<<< * return result @@ -1703,7 +1701,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure_power(int __pyx_v_dist, in */ __pyx_v_result = log((1. - (__pyx_v_structural * __pyx_v_temporal))); - /* "ml.pyx":50 + /* "ml.pyx":54 * temporal = 1. - 1. / (1. + dt/alpha)**0.01 * result = log(1. - structural * temporal) * return result # <<<<<<<<<<<<<< @@ -1713,11 +1711,11 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure_power(int __pyx_v_dist, in __pyx_r = __pyx_v_result; goto __pyx_L0; - /* "ml.pyx":43 + /* "ml.pyx":46 * * - * cdef DTYPE_t weight_failure_power(int dist, int dt, DTYPE_t alpha, # <<<<<<<<<<<<<< - * DTYPE_t delta, DTYPE_t gamma): + * cdef DTYPE_t weight_failure_power(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<< + * DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): * """weight for failed infection, power-law time model""" */ @@ -1727,11 +1725,11 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_failure_power(int __pyx_v_dist, in return __pyx_r; } -/* "ml.pyx":52 +/* "ml.pyx":56 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta, DTYPE_t gamma=10): + * DTYPE_t alpha, DTYPE_t delta): * cdef: */ @@ -1745,7 +1743,6 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py __pyx_t_2ml_DTYPE_t __pyx_v_age; __pyx_t_2ml_DTYPE_t __pyx_v_alpha; __pyx_t_2ml_DTYPE_t __pyx_v_delta; - __pyx_t_2ml_DTYPE_t __pyx_v_gamma; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -1753,13 +1750,12 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ml (wrapper)", 0); { - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_root_victims,&__pyx_n_s_victims,&__pyx_n_s_non_victims,&__pyx_n_s_age,&__pyx_n_s_alpha,&__pyx_n_s_delta,&__pyx_n_s_gamma,0}; - PyObject* values[7] = {0,0,0,0,0,0,0}; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_root_victims,&__pyx_n_s_victims,&__pyx_n_s_non_victims,&__pyx_n_s_age,&__pyx_n_s_alpha,&__pyx_n_s_delta,0}; + PyObject* values[6] = {0,0,0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { - case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6); case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); @@ -1777,74 +1773,61 @@ 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", 0, 6, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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", 0, 6, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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("ml", 0, 6, 7, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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("ml", 0, 6, 7, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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("ml", 0, 6, 7, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - } - case 6: - if (kw_args > 0) { - PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s_gamma); - if (value) { values[6] = value; kw_args--; } + __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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 = 52; __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 = 56; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } + } else if (PyTuple_GET_SIZE(__pyx_args) != 6) { + goto __pyx_L5_argtuple_error; } else { - switch (PyTuple_GET_SIZE(__pyx_args)) { - case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6); - case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); - values[4] = PyTuple_GET_ITEM(__pyx_args, 4); - values[3] = PyTuple_GET_ITEM(__pyx_args, 3); - values[2] = PyTuple_GET_ITEM(__pyx_args, 2); - values[1] = PyTuple_GET_ITEM(__pyx_args, 1); - values[0] = PyTuple_GET_ITEM(__pyx_args, 0); - break; - default: goto __pyx_L5_argtuple_error; - } + values[0] = PyTuple_GET_ITEM(__pyx_args, 0); + values[1] = PyTuple_GET_ITEM(__pyx_args, 1); + values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + values[3] = PyTuple_GET_ITEM(__pyx_args, 3); + values[4] = PyTuple_GET_ITEM(__pyx_args, 4); + values[5] = PyTuple_GET_ITEM(__pyx_args, 5); } __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 = 52; __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 = 53; __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 = 53; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - if (values[6]) { - __pyx_v_gamma = __pyx_PyFloat_AsDouble(values[6]); if (unlikely((__pyx_v_gamma == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - } else { - __pyx_v_gamma = ((__pyx_t_2ml_DTYPE_t)10.0); - } + __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 = 56; __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 = 57; __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 = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("ml", 0, 6, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __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 = 56; __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 = 52; __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 = 52; __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 = 52; __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_age, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __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 = 56; __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 = 56; __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_age, __pyx_v_alpha, __pyx_v_delta); /* function exit code */ goto __pyx_L0; @@ -1856,9 +1839,9 @@ static PyObject *__pyx_pw_2ml_1ml(PyObject *__pyx_self, PyObject *__pyx_args, Py } static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */ -/* "ml.pyx":76 +/* "ml.pyx":80 * for (dist, dt, w1, w2, w3) in parents] - * # find parent that maximizes p/\tilde{p} + * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< * * # loop through non-victims @@ -1882,7 +1865,7 @@ static PyObject *__pyx_pf_2ml_2ml_genexpr(PyObject *__pyx_self) { __Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_outer_scope)); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_outer_scope); { - __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_2ml_2ml_2generator, (PyObject *) __pyx_cur_scope, __pyx_n_s_genexpr, __pyx_n_s_ml_locals_genexpr); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_cur_scope); __Pyx_RefNannyFinishContext(); return (PyObject *) gen; @@ -1920,16 +1903,16 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera return NULL; } __pyx_L3_first_run:; - if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = 0; - if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes)) { __Pyx_RaiseClosureNameError("successes"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_2 = __pyx_cur_scope->__pyx_outer_scope->__pyx_v_successes; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0; for (;;) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_4); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif __Pyx_XGOTREF(__pyx_cur_scope->__pyx_v_s); __Pyx_XDECREF_SET(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); @@ -1937,14 +1920,14 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera __pyx_t_4 = 0; __pyx_cur_scope->__pyx_v_l = __pyx_t_1; __pyx_t_1 = (__pyx_t_1 + 1); - if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures)) { __Pyx_RaiseClosureNameError("failures"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures)) { __Pyx_RaiseClosureNameError("failures"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } if (unlikely(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures, __pyx_cur_scope->__pyx_v_l, Py_ssize_t, 1, PyInt_FromSsize_t, 1, 1, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + __pyx_t_4 = __Pyx_GetItemInt_List(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_failures, __pyx_cur_scope->__pyx_v_l, Py_ssize_t, 1, PyInt_FromSsize_t, 1, 1, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_Subtract(__pyx_cur_scope->__pyx_v_s, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_r = __pyx_t_5; @@ -1964,7 +1947,7 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera __pyx_cur_scope->__pyx_t_1 = 0; __Pyx_XGOTREF(__pyx_t_2); __pyx_t_3 = __pyx_cur_scope->__pyx_t_2; - if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -1984,15 +1967,15 @@ static PyObject *__pyx_gb_2ml_2ml_2generator(__pyx_GeneratorObject *__pyx_genera return NULL; } -/* "ml.pyx":52 +/* "ml.pyx":56 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta, DTYPE_t gamma=10): + * DTYPE_t alpha, DTYPE_t delta): * cdef: */ -static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_2ml_DTYPE_t __pyx_v_age, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta, __pyx_t_2ml_DTYPE_t __pyx_v_gamma) { +static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, __pyx_t_2ml_DTYPE_t __pyx_v_age, __pyx_t_2ml_DTYPE_t __pyx_v_alpha, __pyx_t_2ml_DTYPE_t __pyx_v_delta) { struct __pyx_obj_2ml___pyx_scope_struct__ml *__pyx_cur_scope; int __pyx_v_n_roots; int __pyx_v_n_victims; @@ -2008,9 +1991,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ PyArrayObject *__pyx_v_probs_fail = 0; PyArrayObject *__pyx_v_probs_nv = 0; PyArrayObject *__pyx_v_cums = 0; - CYTHON_UNUSED PyObject *__pyx_v_w1 = NULL; - CYTHON_UNUSED PyObject *__pyx_v_w2 = NULL; - CYTHON_UNUSED PyObject *__pyx_v_w3 = NULL; + PyObject *__pyx_v_w1 = NULL; + PyObject *__pyx_v_w2 = NULL; + PyObject *__pyx_v_w3 = NULL; __Pyx_LocalBuf_ND __pyx_pybuffernd_cums; __Pyx_Buffer __pyx_pybuffer_cums; __Pyx_LocalBuf_ND __pyx_pybuffernd_probs; @@ -2043,13 +2026,15 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ PyObject *(*__pyx_t_20)(PyObject *); int __pyx_t_21; __pyx_t_2ml_DTYPE_t __pyx_t_22; - int __pyx_t_23; - int __pyx_t_24; - PyObject *__pyx_t_25 = NULL; - PyObject *__pyx_t_26 = NULL; + __pyx_t_2ml_DTYPE_t __pyx_t_23; + __pyx_t_2ml_DTYPE_t __pyx_t_24; + int __pyx_t_25; + int __pyx_t_26; PyObject *__pyx_t_27 = NULL; - PyArrayObject *__pyx_t_28 = NULL; - int __pyx_t_29; + PyObject *__pyx_t_28 = NULL; + PyObject *__pyx_t_29 = NULL; + PyArrayObject *__pyx_t_30 = NULL; + int __pyx_t_31; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -2077,7 +2062,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_pybuffernd_cums.data = NULL; __pyx_pybuffernd_cums.rcbuffer = &__pyx_pybuffer_cums; - /* "ml.pyx":58 + /* "ml.pyx":62 * DTYPE_t beta, ll, beta2 * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) # <<<<<<<<<<<<<< @@ -2086,18 +2071,18 @@ 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 = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __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 = 58; __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 = 62; __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 = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __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 = 58; __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 = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_n_roots = __pyx_t_1; __pyx_v_n_victims = __pyx_t_2; - /* "ml.pyx":59 + /* "ml.pyx":63 * list parents, failures, successes * n_roots, n_victims = len(root_victims), len(victims) * n_nodes = n_roots + n_victims + len(non_victims) # <<<<<<<<<<<<<< @@ -2106,48 +2091,48 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ if (unlikely(__pyx_v_non_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_2 = PyDict_Size(__pyx_v_non_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_Size(__pyx_v_non_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; 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if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs.rcbuffer->pybuffer, (PyObject*)__pyx_t_7, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_probs = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_probs.diminfo[0].strides = __pyx_pybuffernd_probs.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_probs.diminfo[0].shape = __pyx_pybuffernd_probs.rcbuffer->pybuffer.shape[0]; } } @@ -2155,43 +2140,43 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_probs = ((PyArrayObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":62 + /* "ml.pyx":66 * cdef: * np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<< * np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE) * */ - __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); 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__pyx_lineno = 62; __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 = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __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 = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __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 = 66; __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; - if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_8 = ((PyArrayObject *)__pyx_t_4); { __Pyx_BufFmt_StackElem __pyx_stack[1]; if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_probs_fail.rcbuffer->pybuffer, (PyObject*)__pyx_t_8, &__Pyx_TypeInfo_nn___pyx_t_2ml_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) { __pyx_v_probs_fail = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf = NULL; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else {__pyx_pybuffernd_probs_fail.diminfo[0].strides = __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_probs_fail.diminfo[0].shape = __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.shape[0]; } } @@ -2199,48 +2184,48 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_probs_fail = ((PyArrayObject *)__pyx_t_4); __pyx_t_4 = 0; - /* "ml.pyx":63 + /* "ml.pyx":67 * np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE) * np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE) # <<<<<<<<<<<<<< * * # loop through victims */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_zeros); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_zeros); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (unlikely(__pyx_v_non_victims == Py_None)) { PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_2 = PyDict_Size(__pyx_v_non_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_4 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyDict_Size(__pyx_v_non_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyInt_FromSsize_t(__pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __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 = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __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 = 63; __pyx_clineno = __LINE__; goto __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 = 67; __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 = 63; __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 = 67; __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_probs_nv.rcbuffer->pybuffer, (PyObject*)__pyx_t_9, &__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 = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __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]; } } @@ -2248,7 +2233,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_v_probs_nv = ((PyArrayObject *)__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":66 + /* "ml.pyx":70 * * # loop through victims * for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<< @@ -2259,9 +2244,9 @@ 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 = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_11)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = __pyx_t_4; @@ -2269,42 +2254,42 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ while (1) { __pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_3, __pyx_t_1, &__pyx_t_2, NULL, &__pyx_t_4, NULL, __pyx_t_11); if (unlikely(__pyx_t_12 == 0)) break; - if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(PyList_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_i = __pyx_t_10; __pyx_t_10 = (__pyx_t_10 + 1); - /* "ml.pyx":70 + /* "ml.pyx":74 * # fail to infect it, also computes the probability that its most * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< + * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) */ - __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - /* "ml.pyx":71 + /* "ml.pyx":75 * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, gamma) + * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, gamma) + * 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 = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_5 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_5); __pyx_t_13 = 0; for (;;) { if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_5)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_6 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_ITEM(__pyx_t_5, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) { PyObject* sequence = __pyx_t_6; @@ -2316,7 +2301,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2342,7 +2327,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2352,7 +2337,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; - __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_19); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext; @@ -2361,7 +2346,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_20 = NULL; __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; goto __pyx_L8_unpacking_done; @@ -2369,12 +2354,12 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; __pyx_t_20 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L8_unpacking_done:; } - __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; - __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; __pyx_v_dist = __pyx_t_12; __pyx_v_dt = __pyx_t_21; @@ -2385,24 +2370,27 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_18); __pyx_t_18 = 0; - /* "ml.pyx":70 + /* "ml.pyx":74 * # fail to infect it, also computes the probability that its most * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< + * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) */ - __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_22, __pyx_t_23, __pyx_t_24)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_4, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":71 + /* "ml.pyx":75 * # likely parent infects it - * failures = [weight_failure(dist, dt, alpha, delta, gamma) + * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, gamma) + * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) */ } __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; @@ -2411,55 +2399,55 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = 0; - /* "ml.pyx":72 - * failures = [weight_failure(dist, dt, alpha, delta, gamma) + /* "ml.pyx":76 + * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) # <<<<<<<<<<<<<< - * successes = [weight_success(dist, dt, alpha, delta, gamma) + * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] */ - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_cur_scope->__pyx_v_failures); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_cur_scope->__pyx_v_failures); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_failures); - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_21 = __pyx_v_i; if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_pybuffernd_probs_fail.diminfo[0].shape; - *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_22; + *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs_fail.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_probs_fail.diminfo[0].strides) = __pyx_t_24; - /* "ml.pyx":73 + /* "ml.pyx":77 * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< + * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] - * # find parent that maximizes p/\tilde{p} + * # find parent that maximizes log(p) - log(\tilde{p}) */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml.pyx":74 + /* "ml.pyx":78 * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, gamma) + * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< - * # find parent that maximizes p/\tilde{p} + * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_4 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_4); __pyx_t_13 = 0; for (;;) { if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_4)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) { PyObject* sequence = __pyx_t_6; @@ -2471,7 +2459,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2497,7 +2485,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_18,&__pyx_t_17,&__pyx_t_16,&__pyx_t_15,&__pyx_t_14}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2507,7 +2495,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[5] = {&__pyx_t_18,&__pyx_t_17,&__pyx_t_16,&__pyx_t_15,&__pyx_t_14}; - __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_19); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext; @@ -2516,7 +2504,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_20 = NULL; __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; goto __pyx_L12_unpacking_done; @@ -2524,15 +2512,15 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; __pyx_t_20 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L12_unpacking_done:; } - __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_18); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; - __pyx_t_23 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_23 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_25 = __Pyx_PyInt_As_int(__pyx_t_17); if (unlikely((__pyx_t_25 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; __pyx_v_dist = __pyx_t_12; - __pyx_v_dt = __pyx_t_23; + __pyx_v_dt = __pyx_t_25; __Pyx_XDECREF_SET(__pyx_v_w1, __pyx_t_16); __pyx_t_16 = 0; __Pyx_XDECREF_SET(__pyx_v_w2, __pyx_t_15); @@ -2540,23 +2528,26 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_14); __pyx_t_14 = 0; - /* "ml.pyx":73 + /* "ml.pyx":77 * for (dist, dt, w1, w2, w3) in parents] * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< + * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] - * # find parent that maximizes p/\tilde{p} + * # find parent that maximizes log(p) - log(\tilde{p}) */ - __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_v_w1); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_23 = __pyx_PyFloat_AsDouble(__pyx_v_w2); if (unlikely((__pyx_t_23 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_v_w3); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_success(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_t_24, __pyx_t_23, __pyx_t_22)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_ListComp_Append(__pyx_t_5, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "ml.pyx":74 + /* "ml.pyx":78 * probs_fail[i] = sum(failures) - * successes = [weight_success(dist, dt, alpha, delta, gamma) + * successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< - * # find parent that maximizes p/\tilde{p} + * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) */ } @@ -2566,32 +2557,32 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - /* "ml.pyx":76 + /* "ml.pyx":80 * for (dist, dt, w1, w2, w3) in parents] - * # find parent that maximizes p/\tilde{p} + * # find parent that maximizes log(p) - log(\tilde{p}) * probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # <<<<<<<<<<<<<< * * # loop through non-victims */ - __pyx_t_5 = __pyx_pf_2ml_2ml_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __pyx_pf_2ml_2ml_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_max, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_max, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_23 = __pyx_v_i; - if (__pyx_t_23 < 0) __pyx_t_23 += __pyx_pybuffernd_probs.diminfo[0].shape; - *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_23, __pyx_pybuffernd_probs.diminfo[0].strides) = __pyx_t_22; + __pyx_t_25 = __pyx_v_i; + if (__pyx_t_25 < 0) __pyx_t_25 += __pyx_pybuffernd_probs.diminfo[0].shape; + *__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_probs.diminfo[0].strides) = __pyx_t_22; } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "ml.pyx":79 + /* "ml.pyx":83 * * # loop through non-victims * for i, parents in enumerate(non_victims.itervalues()): # <<<<<<<<<<<<<< @@ -2602,9 +2593,9 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_1 = 0; if (unlikely(__pyx_v_non_victims == Py_None)) { PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_5 = __Pyx_dict_iterator(__pyx_v_non_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_2), (&__pyx_t_11)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_dict_iterator(__pyx_v_non_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_2), (&__pyx_t_11)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = __pyx_t_5; @@ -2612,42 +2603,42 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ while (1) { __pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_3, __pyx_t_2, &__pyx_t_1, NULL, &__pyx_t_5, NULL, __pyx_t_11); if (unlikely(__pyx_t_12 == 0)) break; - if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - 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 = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + 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 = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF_SET(__pyx_v_parents, ((PyObject*)__pyx_t_5)); __pyx_t_5 = 0; __pyx_v_i = __pyx_t_10; __pyx_t_10 = (__pyx_t_10 + 1); - /* "ml.pyx":82 + /* "ml.pyx":86 * # for each non victim node, compute the probability that all its * # parents fail to infect it - * failures = [weight_failure(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< + * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_nv[i] = sum(failures) */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - /* "ml.pyx":83 + /* "ml.pyx":87 * # parents fail to infect it - * failures = [weight_failure(dist, dt, alpha, delta, gamma) + * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) * for (dist, dt, w1, w2, w3) in parents] # <<<<<<<<<<<<<< * probs_nv[i] = sum(failures) * */ if (unlikely(__pyx_v_parents == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_4 = __pyx_v_parents; __Pyx_INCREF(__pyx_t_4); __pyx_t_13 = 0; for (;;) { if (__pyx_t_13 >= PyList_GET_SIZE(__pyx_t_4)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_13); __Pyx_INCREF(__pyx_t_6); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PySequence_ITEM(__pyx_t_4, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) { PyObject* sequence = __pyx_t_6; @@ -2659,7 +2650,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (unlikely(size != 5)) { if (size > 5) __Pyx_RaiseTooManyValuesError(5); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -2685,7 +2676,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ Py_ssize_t i; PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; for (i=0; i < 5; i++) { - PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(item); *(temps[i]) = item; } @@ -2695,7 +2686,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } else { Py_ssize_t index = -1; PyObject** temps[5] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_16,&__pyx_t_17,&__pyx_t_18}; - __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_19 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_19); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_20 = Py_TYPE(__pyx_t_19)->tp_iternext; @@ -2704,7 +2695,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GOTREF(item); *(temps[index]) = item; } - if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_20(__pyx_t_19), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_20 = NULL; __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; goto __pyx_L18_unpacking_done; @@ -2712,15 +2703,15 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0; __pyx_t_20 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L18_unpacking_done:; } - __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; - __pyx_t_24 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_24 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_26 = __Pyx_PyInt_As_int(__pyx_t_15); if (unlikely((__pyx_t_26 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; __pyx_v_dist = __pyx_t_12; - __pyx_v_dt = __pyx_t_24; + __pyx_v_dt = __pyx_t_26; __Pyx_XDECREF_SET(__pyx_v_w1, __pyx_t_16); __pyx_t_16 = 0; __Pyx_XDECREF_SET(__pyx_v_w2, __pyx_t_17); @@ -2728,21 +2719,24 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_XDECREF_SET(__pyx_v_w3, __pyx_t_18); __pyx_t_18 = 0; - /* "ml.pyx":82 + /* "ml.pyx":86 * # for each non victim node, compute the probability that all its * # parents fail to infect it - * failures = [weight_failure(dist, dt, alpha, delta, gamma) # <<<<<<<<<<<<<< + * failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) # <<<<<<<<<<<<<< * for (dist, dt, w1, w2, w3) in parents] * probs_nv[i] = sum(failures) */ - __pyx_t_6 = PyFloat_FromDouble(__pyx_f_2ml_weight_failure(__pyx_v_dist, __pyx_v_dt, __pyx_v_alpha, __pyx_v_delta, __pyx_v_gamma)); 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__pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_nv), __pyx_n_s_sum); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_probs_nv), __pyx_n_s_sum); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_6 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) { @@ -2923,22 +2917,22 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } } if (__pyx_t_6) { - __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; } else { - __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_22 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_22 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_24 = __pyx_PyFloat_AsDouble(__pyx_t_5); if (unlikely((__pyx_t_24 == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_v_ll = __pyx_t_22; + __pyx_v_ll = __pyx_t_24; - /* "ml.pyx":93 + /* "ml.pyx":97 * ll += probs_nv.sum() * * for i in xrange(n_victims - 1, 0, -1): # <<<<<<<<<<<<<< @@ -2948,7 +2942,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ for (__pyx_t_10 = (__pyx_v_n_victims - 1); __pyx_t_10 > 0; __pyx_t_10-=1) { __pyx_v_i = __pyx_t_10; - /* "ml.pyx":95 + /* "ml.pyx":99 * for i in xrange(n_victims - 1, 0, -1): * # iterate over all victim nodes to find the optimal threshold * roots = n_roots + n_victims - 1 - i # <<<<<<<<<<<<<< @@ -2957,7 +2951,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ __pyx_v_roots = (((__pyx_v_n_roots + __pyx_v_n_victims) - 1) - __pyx_v_i); - /* "ml.pyx":96 + /* "ml.pyx":100 * # iterate over all victim nodes to find the optimal threshold * roots = n_roots + n_victims - 1 - i * beta = 1. / (1. + exp(-probs[i]))#exp(probs[i])# # <<<<<<<<<<<<<< @@ -2968,17 +2962,17 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_probs.diminfo[0].shape; __pyx_v_beta = (1. / (1. + exp((-(*__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_probs.diminfo[0].strides)))))); - /* "ml.pyx":97 + /* "ml.pyx":101 * roots = n_roots + n_victims - 1 - i * beta = 1. / (1. + exp(-probs[i]))#exp(probs[i])# * if beta > float(roots) / age: # <<<<<<<<<<<<<< * break * else: */ - __pyx_t_29 = ((__pyx_v_beta > (((double)__pyx_v_roots) / __pyx_v_age)) != 0); - if (__pyx_t_29) { + __pyx_t_31 = ((__pyx_v_beta > (((double)__pyx_v_roots) / __pyx_v_age)) != 0); + if (__pyx_t_31) { - /* "ml.pyx":98 + /* "ml.pyx":102 * beta = 1. / (1. + exp(-probs[i]))#exp(probs[i])# * if beta > float(roots) / age: * break # <<<<<<<<<<<<<< @@ -2990,18 +2984,18 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } /*else*/ { - /* "ml.pyx":100 + /* "ml.pyx":104 * break * else: * print "alpha: {0}, delta: {1}. Everyone is a root".format(alpha, delta) # <<<<<<<<<<<<<< * roots = n_victims + n_roots * i = -1 */ - __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_alpha_0_delta_1_Everyone_is_a_ro, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_alpha_0_delta_1_Everyone_is_a_ro, __pyx_n_s_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = PyFloat_FromDouble(__pyx_v_alpha); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyFloat_FromDouble(__pyx_v_alpha); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_6 = PyFloat_FromDouble(__pyx_v_delta); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyFloat_FromDouble(__pyx_v_delta); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_18 = NULL; __pyx_t_2 = 0; @@ -3015,7 +3009,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_2 = 1; } } - __pyx_t_17 = PyTuple_New(2+__pyx_t_2); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_17 = PyTuple_New(2+__pyx_t_2); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_17); if (__pyx_t_18) { PyTuple_SET_ITEM(__pyx_t_17, 0, __pyx_t_18); __Pyx_GIVEREF(__pyx_t_18); __pyx_t_18 = NULL; @@ -3026,14 +3020,14 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __Pyx_GIVEREF(__pyx_t_6); __pyx_t_3 = 0; __pyx_t_6 = 0; - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_17, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_17, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - if (__Pyx_PrintOne(0, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_PrintOne(0, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "ml.pyx":101 + /* "ml.pyx":105 * else: * print "alpha: {0}, delta: {1}. 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-3081,10 +3075,10 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ __pyx_t_12 = __pyx_v_i; if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_probs.diminfo[0].shape; - __pyx_t_29 = (((*__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_probs.diminfo[0].strides)) >= log((__pyx_v_beta / (1. - __pyx_v_beta)))) != 0); - if (__pyx_t_29) { + __pyx_t_31 = (((*__Pyx_BufPtrStrided1d(__pyx_t_2ml_DTYPE_t *, __pyx_pybuffernd_probs.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_probs.diminfo[0].strides)) >= log((__pyx_v_beta / (1. - __pyx_v_beta)))) != 0); + if (__pyx_t_31) { - /* "ml.pyx":106 + /* "ml.pyx":110 * for i in xrange(n_victims - 1, 0, -1): * if probs[i] >= log(beta/(1.- beta)): * break # <<<<<<<<<<<<<< @@ -3096,7 +3090,7 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L23_break:; - /* "ml.pyx":107 + /* "ml.pyx":111 * if probs[i] >= log(beta/(1.- beta)): * break * ll += age * log(1 - beta) # <<<<<<<<<<<<<< @@ -3105,17 +3099,17 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ */ __pyx_v_ll = (__pyx_v_ll + (__pyx_v_age * log((1.0 - __pyx_v_beta)))); - /* "ml.pyx":108 + /* "ml.pyx":112 * break * ll += age * log(1 - beta) * if i >= 0: # <<<<<<<<<<<<<< * ll += cums[i] * if roots > 0: */ - __pyx_t_29 = ((__pyx_v_i >= 0) != 0); - if (__pyx_t_29) { + __pyx_t_31 = ((__pyx_v_i >= 0) != 0); + if (__pyx_t_31) { - /* "ml.pyx":109 + /* "ml.pyx":113 * ll += age * log(1 - beta) * if i >= 0: * ll += cums[i] # <<<<<<<<<<<<<< @@ -3129,17 +3123,17 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L25:; - /* "ml.pyx":110 + /* "ml.pyx":114 * if i >= 0: * ll += cums[i] * if roots > 0: # <<<<<<<<<<<<<< * ll += roots * log(beta) - roots * log(1 - beta) * return (beta, roots, ll) */ - __pyx_t_29 = ((__pyx_v_roots > 0) != 0); - if (__pyx_t_29) { + __pyx_t_31 = ((__pyx_v_roots > 0) != 0); + if (__pyx_t_31) { - /* "ml.pyx":111 + /* "ml.pyx":115 * ll += cums[i] * if roots > 0: * ll += roots * log(beta) - roots * log(1 - beta) # <<<<<<<<<<<<<< @@ -3150,19 +3144,19 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ } __pyx_L26:; - /* "ml.pyx":112 + /* "ml.pyx":116 * if roots > 0: * ll += roots * log(beta) - roots * log(1 - beta) * return (beta, roots, ll) # <<<<<<<<<<<<<< */ __Pyx_XDECREF(__pyx_r); - __pyx_t_5 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyFloat_FromDouble(__pyx_v_beta); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_roots); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_roots); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_17 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_17 = PyFloat_FromDouble(__pyx_v_ll); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_17); - __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); @@ -3177,11 +3171,11 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_ __pyx_t_6 = 0; goto __pyx_L0; - /* "ml.pyx":52 + /* "ml.pyx":56 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta, DTYPE_t gamma=10): + * DTYPE_t alpha, DTYPE_t delta): * cdef: */ @@ -5505,7 +5499,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_file, __pyx_k_file, sizeof(__pyx_k_file), 0, 0, 1, 1}, {&__pyx_n_s_float64, __pyx_k_float64, sizeof(__pyx_k_float64), 0, 0, 1, 1}, {&__pyx_n_s_format, __pyx_k_format, sizeof(__pyx_k_format), 0, 0, 1, 1}, - {&__pyx_n_s_gamma, __pyx_k_gamma, sizeof(__pyx_k_gamma), 0, 0, 1, 1}, {&__pyx_n_s_genexpr, __pyx_k_genexpr, sizeof(__pyx_k_genexpr), 0, 0, 1, 1}, {&__pyx_n_s_i, __pyx_k_i, sizeof(__pyx_k_i), 0, 0, 1, 1}, {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, @@ -5549,13 +5542,13 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {0, 0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { - __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_max = __Pyx_GetBuiltinName(__pyx_n_s_max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if PY_MAJOR_VERSION >= 3 - __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_xrange); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 93; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_xrange); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -5569,14 +5562,14 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "ml.pyx":87 + /* "ml.pyx":91 * * # calculate log likelihood * probs.sort(); probs = probs[::-1] # sort probs in descending order # <<<<<<<<<<<<<< * cdef: * np.ndarray[DTYPE_t] cums = probs.cumsum() */ - __pyx_slice_ = PySlice_New(Py_None, Py_None, __pyx_int_neg_1); if (unlikely(!__pyx_slice_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_slice_ = PySlice_New(Py_None, Py_None, __pyx_int_neg_1); if (unlikely(!__pyx_slice_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_slice_); __Pyx_GIVEREF(__pyx_slice_); @@ -5646,17 +5639,17 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "ml.pyx":52 + /* "ml.pyx":56 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta, DTYPE_t gamma=10): + * DTYPE_t alpha, DTYPE_t delta): * cdef: */ - __pyx_tuple__8 = PyTuple_Pack(31, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_gamma, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_beta2, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_cums, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__8 = PyTuple_Pack(30, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_age, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_n_roots, __pyx_n_s_n_victims, __pyx_n_s_n_nodes, __pyx_n_s_roots, __pyx_n_s_i, __pyx_n_s_dist, __pyx_n_s_dt, __pyx_n_s_t, __pyx_n_s_l, __pyx_n_s_beta, __pyx_n_s_ll, __pyx_n_s_beta2, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_probs_nv, __pyx_n_s_cums, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3, __pyx_n_s_genexpr, __pyx_n_s_genexpr); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(7, 0, 31, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__8, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 52, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 30, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__8, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml, 56, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -5753,10 +5746,10 @@ PyMODINIT_FUNC PyInit_ml(void) /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ - if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct__ml) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_2ml___pyx_scope_struct__ml.tp_print = 0; __pyx_ptype_2ml___pyx_scope_struct__ml = &__pyx_type_2ml___pyx_scope_struct__ml; - if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_2ml___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type_2ml___pyx_scope_struct_1_genexpr.tp_print = 0; __pyx_ptype_2ml___pyx_scope_struct_1_genexpr = &__pyx_type_2ml___pyx_scope_struct_1_genexpr; /*--- Type import code ---*/ @@ -5802,16 +5795,16 @@ PyMODINIT_FUNC PyInit_ml(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; - /* "ml.pyx":52 + /* "ml.pyx":56 * return result * * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<< - * DTYPE_t alpha, DTYPE_t delta, DTYPE_t gamma=10): + * DTYPE_t alpha, DTYPE_t delta): * cdef: */ - __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; /* "ml.pyx":1 diff --git a/experiments/ml.pyx b/experiments/ml.pyx index 9c570e9..9a786db 100644 --- a/experiments/ml.pyx +++ b/experiments/ml.pyx @@ -7,50 +7,54 @@ DTYPE = np.float64 ctypedef np.float_t DTYPE_t cdef DTYPE_t plogis(DTYPE_t weight, DTYPE_t delta): - return 1/(1 + exp(-weight/delta)) + return 1./(1. + exp(-weight/delta)) -cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, - DTYPE_t delta, DTYPE_t gamma): +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 = delta ** (dist) + # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) temporal = exp(-alpha * dt) * (1 - exp(-alpha)) result = log(structural * temporal) return result -cdef DTYPE_t weight_success_power(int dist, int dt, DTYPE_t alpha, - DTYPE_t delta, DTYPE_t gamma): +cdef DTYPE_t weight_success_power(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, + DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): """weight for successful infection, power-law time model""" cdef DTYPE_t structural, temporal, result structural = delta ** (dist) + # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01 result = log(structural * temporal) return result -cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, - DTYPE_t delta, DTYPE_t gamma): +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""" cdef DTYPE_t structural, temporal, result structural = delta ** (dist) + # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) temporal = 1. - exp(-alpha * dt) #result = log(1. - structural) result = log(1. - structural * temporal) return result -cdef DTYPE_t weight_failure_power(int dist, int dt, DTYPE_t alpha, - DTYPE_t delta, DTYPE_t gamma): +cdef DTYPE_t weight_failure_power(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, + DTYPE_t w1, DTYPE_t w2, DTYPE_t w3): """weight for failed infection, power-law time model""" cdef DTYPE_t structural, temporal, result structural = delta ** (dist) + # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta) temporal = 1. - 1. / (1. + dt/alpha)**0.01 result = log(1. - structural * temporal) return result def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, - DTYPE_t alpha, DTYPE_t delta, DTYPE_t gamma=10): + DTYPE_t alpha, DTYPE_t delta): cdef: int n_roots, n_victims, n_nodes, roots, i, dist, dt, t, l DTYPE_t beta, ll, beta2 @@ -67,19 +71,19 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # for each victim node i, compute the probability that all its parents # fail to infect it, also computes the probability that its most # likely parent infects it - failures = [weight_failure(dist, dt, alpha, delta, gamma) + failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) for (dist, dt, w1, w2, w3) in parents] probs_fail[i] = sum(failures) - successes = [weight_success(dist, dt, alpha, delta, gamma) + successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3) for (dist, dt, w1, w2, w3) in parents] - # find parent that maximizes p/\tilde{p} + # find parent that maximizes log(p) - log(\tilde{p}) probs[i] = max(s - failures[l] for l, s in enumerate(successes)) # loop through non-victims for i, parents in enumerate(non_victims.itervalues()): # for each non victim node, compute the probability that all its # parents fail to infect it - failures = [weight_failure(dist, dt, alpha, delta, gamma) + failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3) for (dist, dt, w1, w2, w3) in parents] probs_nv[i] = sum(failures) diff --git a/experiments/ml.so b/experiments/ml.so Binary files differindex c681095..6708b62 100755 --- a/experiments/ml.so +++ b/experiments/ml.so diff --git a/experiments/out.log b/experiments/out.log index 3d1c011..21d7647 100644 --- a/experiments/out.log +++ b/experiments/out.log @@ -1,480 +1,100 @@ -1.0 0.01 3.82496925296e-05 10927 -123894.745252 -1.0 0.06 3.72415556715e-05 10639 -132428.544958 -1.0 0.11 3.69615176554e-05 10559 -146433.341002 -1.0 0.16 3.66569763128e-05 10472 -165973.170107 -1.0 0.21 3.66569763128e-05 10472 -191235.823611 -1.0 0.26 3.64469478007e-05 10412 -222581.705257 -0.0196078431373 0.01 3.51272686497e-05 10035 -123198.774923 -0.0196078431373 0.06 2.65441034549e-05 7583 -129019.702528 -0.0196078431373 0.11 2.16819433997e-05 6194 -139106.948457 -0.0196078431373 0.16 1.98161901172e-05 5661 -155427.756691 -0.0196078431373 0.21 1.87135404286e-05 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+0.00105152471083 0.01 0.000701217976547 11179 -93179.8329341 +0.00105152471083 0.11 0.000701217976547 11179 -114561.733755 +0.00105152471083 0.21 0.000701217976547 11179 -180134.424545 +0.00105152471083 0.31 0.000701217976547 11179 -319513.784174 +0.00105152471083 0.41 0.000701217976547 11179 -566356.987655 diff --git a/experiments/plot3d.py b/experiments/plot3d.py index 2158588..64c144d 100644 --- a/experiments/plot3d.py +++ b/experiments/plot3d.py @@ -7,7 +7,7 @@ with open("out.log") as fh: values = [map(float, line.strip().split()) for line in fh] #values = [(b, a, l) for (b, a, l) in values if b >= 0.04] am = max(values, key=lambda x: x[4]) - # am[0] = 1./am[0] + am[0] = 1./am[0] print am alpha, delta, beta, _ , l = zip(*values) alpha = 1./np.array(alpha) diff --git a/experiments/process.py b/experiments/process.py index 98406d6..8ebe953 100644 --- a/experiments/process.py +++ b/experiments/process.py @@ -11,8 +11,8 @@ if __name__ == "__main__": sys.exit("usage: {0} <file>".format(sys.argv[0])) root_victims, victims, non_victims, age = load(open(sys.argv[1])) - alphas = 1. / np.arange(1., 4000., 50.) # parameter of the time component - deltas = np.arange(0.01, 0.3, 0.05) # parameter of the structural component + alphas = 1. / np.arange(1., 1000., 50.) # parameter of the time component + deltas = np.arange(0.01, 0.5, 0.1) # parameter of the structural component with open("out.log", "w") as fh: for alpha, delta in product(alphas, deltas): beta, roots, ll = ml(root_victims, victims, non_victims, age, alpha, delta) |