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-rw-r--r--experiments/build/temp.macosx-10.6-x86_64-2.7/ml.obin299264 -> 306196 bytes
-rw-r--r--experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.obin285944 -> 275440 bytes
-rw-r--r--experiments/build_network.py5
-rw-r--r--experiments/ml.c3039
-rw-r--r--experiments/ml.pyx56
-rwxr-xr-xexperiments/ml.sobin108744 -> 119284 bytes
-rw-r--r--experiments/ml3.c964
-rw-r--r--experiments/ml3.pyx27
-rwxr-xr-xexperiments/ml3.sobin110884 -> 106596 bytes
-rw-r--r--experiments/out.log130
-rw-r--r--experiments/process.py38
11 files changed, 1865 insertions, 2394 deletions
diff --git a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o
index 5861fce..8667998 100644
--- a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o
+++ b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml.o
Binary files differ
diff --git a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o
index 8ac85ca..9a4f66b 100644
--- a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o
+++ b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml3.o
Binary files differ
diff --git a/experiments/build_network.py b/experiments/build_network.py
index 2226070..a481a90 100644
--- a/experiments/build_network.py
+++ b/experiments/build_network.py
@@ -8,7 +8,7 @@ def build_network(filename):
victims = {}
non_victims = {}
age = 0
- t_max = 1000
+ t_max = 3012
with open(filename) as fh:
reader = DictReader(fh)
for row in reader:
@@ -40,13 +40,10 @@ def build_network(filename):
age += int(row["t1"]) - int(row["spawn1"])
victims[from_] = []
root_victims = {}
- print sorted(victims.keys())
- # print victims
for victim in victims.keys():
if not victims[victim]:
del victims[victim]
root_victims[victim] = []
- print sorted(root_victims.keys())
print len(root_victims), len(victims), len(non_victims)
return root_victims, victims, non_victims, age
diff --git a/experiments/ml.c b/experiments/ml.c
index eb67db6..92e313f 100644
--- a/experiments/ml.c
+++ b/experiments/ml.c
@@ -720,8 +720,6 @@ typedef __pyx_t_5numpy_float_t __pyx_t_2ml_DTYPE_t;
/*--- Type declarations ---*/
-struct __pyx_obj_2ml___pyx_scope_struct__ml;
-struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr;
/* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765
* ctypedef npy_longdouble longdouble_t
@@ -759,38 +757,6 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "ml.pyx":35
- * return result
- *
- * def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
- * DTYPE_t alpha, DTYPE_t delta):
- * cdef:
- */
-struct __pyx_obj_2ml___pyx_scope_struct__ml {
- PyObject_HEAD
- PyObject *__pyx_v_failures;
- PyObject *__pyx_v_successes;
-};
-
-
-/* "ml.pyx":59
- * for (dist, dt, w1, w2, w3) in parents]
- * # 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
- */
-struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr {
- PyObject_HEAD
- struct __pyx_obj_2ml___pyx_scope_struct__ml *__pyx_outer_scope;
- Py_ssize_t __pyx_v_l;
- PyObject *__pyx_v_s;
- Py_ssize_t __pyx_t_0;
- PyObject *__pyx_t_1;
- Py_ssize_t __pyx_t_2;
-};
-
-
/* --- Runtime support code (head) --- */
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
@@ -883,29 +849,6 @@ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact);
-static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname);
-
-#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i))))
-#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck);
-#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck);
-
static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);
#if CYTHON_COMPILING_IN_CPYTHON
@@ -983,6 +926,27 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj);
PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
#endif
+#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
+ __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
+ (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i))))
+#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
+ __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
+ (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck);
+#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
+ __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
+ (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck);
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
+ int is_list, int wraparound, int boundscheck);
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb);
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb);
@@ -1008,8 +972,6 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif
-#include <string.h>
-
typedef struct {
int code_line;
PyCodeObject* code_object;
@@ -1160,41 +1122,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
-static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
-
-static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb);
-
-static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg);
-
-#define __Pyx_Generator_USED
-#include <structmember.h>
-#include <frameobject.h>
-typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
-typedef struct {
- PyObject_HEAD
- __pyx_generator_body_t body;
- PyObject *closure;
- PyObject *exc_type;
- PyObject *exc_value;
- PyObject *exc_traceback;
- PyObject *gi_weakreflist;
- PyObject *classobj;
- PyObject *yieldfrom;
- PyObject *gi_name;
- PyObject *gi_qualname;
- int resume_label;
- char is_running;
-} __pyx_GeneratorObject;
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure, PyObject *name, PyObject *qualname);
-static int __pyx_Generator_init(void);
-static int __Pyx_Generator_clear(PyObject* self);
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
-#else
-#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
-#endif
-
static int __Pyx_check_binary_version(void);
#if !defined(__Pyx_PyIdentifier_FromString)
@@ -1242,8 +1169,6 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha
/* Module declarations from 'libc.math' */
/* 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, __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 };
@@ -1253,16 +1178,12 @@ int __pyx_module_is_main_ml = 0;
/* Implementation of 'ml' */
static PyObject *__pyx_builtin_enumerate;
static PyObject *__pyx_builtin_sum;
-static PyObject *__pyx_builtin_max;
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, CYTHON_UNUSED __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*/
-static PyObject *__pyx_tp_new_2ml___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static char __pyx_k_B[] = "B";
static char __pyx_k_H[] = "H";
static char __pyx_k_I[] = "I";
@@ -1277,6 +1198,7 @@ static char __pyx_k_h[] = "h";
static char __pyx_k_i[] = "i";
static char __pyx_k_l[] = "l";
static char __pyx_k_q[] = "q";
+static char __pyx_k_s[] = "s";
static char __pyx_k_t[] = "t";
static char __pyx_k_Zd[] = "Zd";
static char __pyx_k_Zf[] = "Zf";
@@ -1289,31 +1211,30 @@ static char __pyx_k_w1[] = "w1";
static char __pyx_k_w2[] = "w2";
static char __pyx_k_w3[] = "w3";
static char __pyx_k_age[] = "age";
+static char __pyx_k_dts[] = "dts";
static char __pyx_k_inf[] = "-inf";
-static char __pyx_k_max[] = "max";
static char __pyx_k_sum[] = "sum";
-static char __pyx_k_args[] = "args";
static char __pyx_k_beta[] = "beta";
static char __pyx_k_dist[] = "dist";
static char __pyx_k_main[] = "__main__";
-static char __pyx_k_send[] = "send";
+static char __pyx_k_prnt[] = "prnt";
+static char __pyx_k_prob[] = "prob";
static char __pyx_k_test[] = "__test__";
static char __pyx_k_DTYPE[] = "DTYPE";
static char __pyx_k_alpha[] = "alpha";
-static char __pyx_k_close[] = "close";
static char __pyx_k_delta[] = "delta";
+static char __pyx_k_dists[] = "dists";
static char __pyx_k_dtype[] = "dtype";
static char __pyx_k_numpy[] = "numpy";
static char __pyx_k_probs[] = "probs";
static char __pyx_k_range[] = "range";
static char __pyx_k_roots[] = "roots";
-static char __pyx_k_throw[] = "throw";
+static char __pyx_k_seeds[] = "seeds";
static char __pyx_k_zeros[] = "zeros";
static char __pyx_k_arange[] = "arange";
static char __pyx_k_import[] = "__import__";
static char __pyx_k_thresh[] = "thresh";
static char __pyx_k_float64[] = "float64";
-static char __pyx_k_genexpr[] = "genexpr";
static char __pyx_k_n_nodes[] = "n_nodes";
static char __pyx_k_n_roots[] = "n_roots";
static char __pyx_k_parents[] = "parents";
@@ -1325,15 +1246,17 @@ static char __pyx_k_probs_nv[] = "probs_nv";
static char __pyx_k_enumerate[] = "enumerate";
static char __pyx_k_max_roots[] = "max_roots";
static char __pyx_k_n_victims[] = "n_victims";
+static char __pyx_k_non_seeds[] = "non_seeds";
static char __pyx_k_successes[] = "successes";
static char __pyx_k_ValueError[] = "ValueError";
static char __pyx_k_itervalues[] = "itervalues";
+static char __pyx_k_parent_dts[] = "parent_dts";
static char __pyx_k_probs_fail[] = "probs_fail";
static char __pyx_k_non_victims[] = "non_victims";
static char __pyx_k_RuntimeError[] = "RuntimeError";
static char __pyx_k_max_beta_add[] = "max_beta_add";
+static char __pyx_k_parent_dists[] = "parent_dists";
static char __pyx_k_root_victims[] = "root_victims";
-static char __pyx_k_ml_locals_genexpr[] = "ml.<locals>.genexpr";
static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
static char __pyx_k_Users_ben_Documents_Cascade_Pro[] = "/Users/ben/Documents/Cascade Project/criminal_cascades/experiments/ml.pyx";
static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
@@ -1351,18 +1274,17 @@ static PyObject *__pyx_n_s_ValueError;
static PyObject *__pyx_n_s_age;
static PyObject *__pyx_n_s_alpha;
static PyObject *__pyx_n_s_arange;
-static PyObject *__pyx_n_s_args;
static PyObject *__pyx_n_s_beta;
static PyObject *__pyx_n_s_beta_add;
-static PyObject *__pyx_n_s_close;
static PyObject *__pyx_n_s_delta;
static PyObject *__pyx_n_s_dist;
+static PyObject *__pyx_n_s_dists;
static PyObject *__pyx_n_s_dt;
+static PyObject *__pyx_n_s_dts;
static PyObject *__pyx_n_s_dtype;
static PyObject *__pyx_n_s_enumerate;
static PyObject *__pyx_n_s_failures;
static PyObject *__pyx_n_s_float64;
-static PyObject *__pyx_n_s_genexpr;
static PyObject *__pyx_n_s_i;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_kp_s_inf;
@@ -1370,43 +1292,47 @@ static PyObject *__pyx_n_s_itervalues;
static PyObject *__pyx_n_s_l;
static PyObject *__pyx_n_s_ll;
static PyObject *__pyx_n_s_main;
-static PyObject *__pyx_n_s_max;
static PyObject *__pyx_n_s_max_beta;
static PyObject *__pyx_n_s_max_beta_add;
static PyObject *__pyx_n_s_max_roots;
static PyObject *__pyx_n_s_ml;
-static PyObject *__pyx_n_s_ml_locals_genexpr;
static PyObject *__pyx_n_s_n_nodes;
static PyObject *__pyx_n_s_n_roots;
static PyObject *__pyx_n_s_n_victims;
static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous;
static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
+static PyObject *__pyx_n_s_non_seeds;
static PyObject *__pyx_n_s_non_victims;
static PyObject *__pyx_n_s_np;
static PyObject *__pyx_n_s_numpy;
+static PyObject *__pyx_n_s_parent_dists;
+static PyObject *__pyx_n_s_parent_dts;
static PyObject *__pyx_n_s_parents;
+static PyObject *__pyx_n_s_prnt;
+static PyObject *__pyx_n_s_prob;
static PyObject *__pyx_n_s_probs;
static PyObject *__pyx_n_s_probs_fail;
static PyObject *__pyx_n_s_probs_nv;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_root_victims;
static PyObject *__pyx_n_s_roots;
-static PyObject *__pyx_n_s_send;
+static PyObject *__pyx_n_s_s;
+static PyObject *__pyx_n_s_seeds;
static PyObject *__pyx_n_s_successes;
static PyObject *__pyx_n_s_sum;
static PyObject *__pyx_n_s_t;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_thresh;
-static PyObject *__pyx_n_s_throw;
static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd;
static PyObject *__pyx_n_s_victims;
static PyObject *__pyx_n_s_w1;
static PyObject *__pyx_n_s_w2;
static PyObject *__pyx_n_s_w3;
static PyObject *__pyx_n_s_zeros;
-static PyObject *__pyx_float__2;
-static PyObject *__pyx_float__002;
-static PyObject *__pyx_float_0_001;
+static PyObject *__pyx_float_1_;
+static PyObject *__pyx_float__01;
+static PyObject *__pyx_float_0_01;
+static PyObject *__pyx_int_148152;
static PyObject *__pyx_tuple_;
static PyObject *__pyx_tuple__2;
static PyObject *__pyx_tuple__3;
@@ -1436,33 +1362,33 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
/* "ml.pyx":13
* """weight for successful infection, exponential time model"""
* cdef DTYPE_t structural, temporal, result
- * structural = dist * log(delta) # <<<<<<<<<<<<<<
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
- * temporal = log(exp(alpha)-1.) - alpha*dt
+ * structural = delta ** dist # <<<<<<<<<<<<<<
+ * temporal = log(exp(alpha)-1.) - alpha*dt/7.
+ * result = log(structural) + temporal
*/
- __pyx_v_structural = (__pyx_v_dist * log(__pyx_v_delta));
+ __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist));
- /* "ml.pyx":15
- * structural = dist * log(delta)
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
- * temporal = log(exp(alpha)-1.) - alpha*dt # <<<<<<<<<<<<<<
- * # temporal = 1 - exp(-alpha*dt)
- * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
+ /* "ml.pyx":14
+ * cdef DTYPE_t structural, temporal, result
+ * structural = delta ** dist
+ * temporal = log(exp(alpha)-1.) - alpha*dt/7. # <<<<<<<<<<<<<<
+ * result = log(structural) + temporal
+ * return result
*/
- __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt));
+ __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - ((__pyx_v_alpha * __pyx_v_dt) / 7.));
- /* "ml.pyx":19
- * # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
- * # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
- * result = structural + temporal # <<<<<<<<<<<<<<
- * # print 'st', structural, temporal
+ /* "ml.pyx":15
+ * structural = delta ** dist
+ * temporal = log(exp(alpha)-1.) - alpha*dt/7.
+ * result = log(structural) + temporal # <<<<<<<<<<<<<<
* return result
+ *
*/
- __pyx_v_result = (__pyx_v_structural + __pyx_v_temporal);
+ __pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal);
- /* "ml.pyx":21
- * result = structural + temporal
- * # print 'st', structural, temporal
+ /* "ml.pyx":16
+ * temporal = log(exp(alpha)-1.) - alpha*dt/7.
+ * result = log(structural) + temporal
* return result # <<<<<<<<<<<<<<
*
* cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
@@ -1484,7 +1410,7 @@ static __pyx_t_2ml_DTYPE_t __pyx_f_2ml_weight_success(int __pyx_v_dist, int __py
return __pyx_r;
}
-/* "ml.pyx":23
+/* "ml.pyx":18
* return result
*
* cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
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__Pyx_RefNannySetupContext("weight_failure", 0);
- /* "ml.pyx":27
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- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
- * temporal = exp(-alpha * dt)
+ * temporal = exp(-alpha * dt/7.)
+ * result = log(1. - structural + structural * temporal)
*/
__pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_2ml_DTYPE_t)__pyx_v_dist));
- /* "ml.pyx":29
+ /* "ml.pyx":23
+ * cdef DTYPE_t structural, temporal, result
* structural = delta ** dist
- * # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
- * temporal = exp(-alpha * dt) # <<<<<<<<<<<<<<
- * # temporal = 1. - 1. / (1. + dt/alpha)**0.01
+ * temporal = exp(-alpha * dt/7.) # <<<<<<<<<<<<<<
* result = log(1. - structural + structural * temporal)
+ * return result
*/
- __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt));
+ __pyx_v_temporal = exp((((-__pyx_v_alpha) * __pyx_v_dt) / 7.));
- /* "ml.pyx":31
- * temporal = exp(-alpha * dt)
- * # temporal = 1. - 1. / (1. + dt/alpha)**0.01
+ /* "ml.pyx":24
+ * structural = delta ** dist
+ * temporal = exp(-alpha * dt/7.)
* result = log(1. - structural + structural * temporal) # <<<<<<<<<<<<<<
- * # print 'stnv', structural, temporal
* return result
+ *
*/
__pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
- /* "ml.pyx":33
+ /* "ml.pyx":25
+ * temporal = exp(-alpha * dt/7.)
* result = log(1. - structural + structural * temporal)
- * # print 'stnv', structural, temporal
* return result # <<<<<<<<<<<<<<
*
* def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
@@ -1537,7 +1463,7 @@ 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":23
+ /* "ml.pyx":18
* return result
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return __pyx_r;
}
-/* "ml.pyx":35
+/* "ml.pyx":27
* return result
*
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case 1:
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+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ __Pyx_RaiseArgtupleInvalid("ml", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ PyObject *__pyx_v_prob = NULL;
double __pyx_v_thresh;
+ PyObject *__pyx_v_seeds = NULL;
+ PyObject *__pyx_v_non_seeds = NULL;
int __pyx_v_max_roots;
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PyArrayObject *__pyx_t_8 = NULL;
PyArrayObject *__pyx_t_9 = NULL;
- int __pyx_t_10;
- int __pyx_t_11;
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int __pyx_t_12;
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- int __pyx_t_26;
- double __pyx_t_27;
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- int __pyx_t_29;
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+ PyObject *(*__pyx_t_23)(PyObject *);
+ int __pyx_t_24;
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+ __pyx_t_2ml_DTYPE_t __pyx_t_27;
+ int __pyx_t_28;
+ double __pyx_t_29;
+ int __pyx_t_30;
+ int __pyx_t_31;
+ int __pyx_t_32;
+ int __pyx_t_33;
+ int __pyx_t_34;
+ int __pyx_t_35;
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__pyx_pybuffernd_probs_fail.data = NULL;
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+ __pyx_pybuffer_parent_dts.refcount = 0;
+ __pyx_pybuffernd_parent_dts.data = NULL;
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*/
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- * np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE)
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*/
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- PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
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+ __pyx_t_20 = 0;
__pyx_t_4 = 0;
- __pyx_t_18 = 0;
- __pyx_t_3 = 0;
- __pyx_r = __pyx_t_5;
- __pyx_t_5 = 0;
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+ __pyx_t_21 = 0;
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- /* "ml.pyx":35
+ /* "ml.pyx":27
* return result
*
* def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
@@ -2931,14 +3220,17 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
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- __Pyx_XDECREF(__pyx_t_15);
__Pyx_XDECREF(__pyx_t_16);
__Pyx_XDECREF(__pyx_t_17);
__Pyx_XDECREF(__pyx_t_18);
__Pyx_XDECREF(__pyx_t_19);
+ __Pyx_XDECREF(__pyx_t_20);
+ __Pyx_XDECREF(__pyx_t_21);
+ __Pyx_XDECREF(__pyx_t_22);
{ PyObject *__pyx_type, *__pyx_value, *__pyx_tb;
__Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb);
+ __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_parent_dists.rcbuffer->pybuffer);
+ __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_parent_dts.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_probs.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_probs_fail.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_probs_nv.rcbuffer->pybuffer);
@@ -2947,18 +3239,31 @@ static PyObject *__pyx_pf_2ml_ml(CYTHON_UNUSED PyObject *__pyx_self, PyObject *_
__pyx_r = NULL;
goto __pyx_L2;
__pyx_L0:;
+ __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_parent_dists.rcbuffer->pybuffer);
+ __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_parent_dts.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_probs.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_probs_fail.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_probs_nv.rcbuffer->pybuffer);
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__Pyx_XDECREF(__pyx_v_parents);
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+ __Pyx_XDECREF(__pyx_v_successes);
+ __Pyx_XDECREF(__pyx_v_n_nodes);
__Pyx_XDECREF((PyObject *)__pyx_v_probs);
__Pyx_XDECREF((PyObject *)__pyx_v_probs_fail);
+ __Pyx_XDECREF((PyObject *)__pyx_v_parent_dists);
+ __Pyx_XDECREF((PyObject *)__pyx_v_parent_dts);
__Pyx_XDECREF((PyObject *)__pyx_v_probs_nv);
+ __Pyx_XDECREF(__pyx_v_dists);
+ __Pyx_XDECREF(__pyx_v_dts);
+ __Pyx_XDECREF(__pyx_v_s);
+ __Pyx_XDECREF(__pyx_v_prob);
+ __Pyx_XDECREF(__pyx_v_seeds);
+ __Pyx_XDECREF(__pyx_v_non_seeds);
+ __Pyx_XDECREF(__pyx_v_prnt);
__Pyx_XDECREF(__pyx_v_w1);
__Pyx_XDECREF(__pyx_v_w2);
__Pyx_XDECREF(__pyx_v_w3);
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return __pyx_r;
@@ -4966,233 +5271,6 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
return __pyx_r;
}
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-static int __pyx_freecount_2ml___pyx_scope_struct__ml = 0;
-
-static PyObject *__pyx_tp_new_2ml___pyx_scope_struct__ml(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- PyObject *o;
- if (CYTHON_COMPILING_IN_CPYTHON && likely((__pyx_freecount_2ml___pyx_scope_struct__ml > 0) & (t->tp_basicsize == sizeof(struct __pyx_obj_2ml___pyx_scope_struct__ml)))) {
- o = (PyObject*)__pyx_freelist_2ml___pyx_scope_struct__ml[--__pyx_freecount_2ml___pyx_scope_struct__ml];
- memset(o, 0, sizeof(struct __pyx_obj_2ml___pyx_scope_struct__ml));
- (void) PyObject_INIT(o, t);
- PyObject_GC_Track(o);
- } else {
- o = (*t->tp_alloc)(t, 0);
- if (unlikely(!o)) return 0;
- }
- return o;
-}
-
-static void __pyx_tp_dealloc_2ml___pyx_scope_struct__ml(PyObject *o) {
- struct __pyx_obj_2ml___pyx_scope_struct__ml *p = (struct __pyx_obj_2ml___pyx_scope_struct__ml *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->__pyx_v_failures);
- Py_CLEAR(p->__pyx_v_successes);
- if (CYTHON_COMPILING_IN_CPYTHON && ((__pyx_freecount_2ml___pyx_scope_struct__ml < 8) & (Py_TYPE(o)->tp_basicsize == sizeof(struct __pyx_obj_2ml___pyx_scope_struct__ml)))) {
- __pyx_freelist_2ml___pyx_scope_struct__ml[__pyx_freecount_2ml___pyx_scope_struct__ml++] = ((struct __pyx_obj_2ml___pyx_scope_struct__ml *)o);
- } else {
- (*Py_TYPE(o)->tp_free)(o);
- }
-}
-
-static int __pyx_tp_traverse_2ml___pyx_scope_struct__ml(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_2ml___pyx_scope_struct__ml *p = (struct __pyx_obj_2ml___pyx_scope_struct__ml *)o;
- if (p->__pyx_v_failures) {
- e = (*v)(p->__pyx_v_failures, a); if (e) return e;
- }
- if (p->__pyx_v_successes) {
- e = (*v)(p->__pyx_v_successes, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_2ml___pyx_scope_struct__ml(PyObject *o) {
- PyObject* tmp;
- struct __pyx_obj_2ml___pyx_scope_struct__ml *p = (struct __pyx_obj_2ml___pyx_scope_struct__ml *)o;
- tmp = ((PyObject*)p->__pyx_v_failures);
- p->__pyx_v_failures = ((PyObject*)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->__pyx_v_successes);
- p->__pyx_v_successes = ((PyObject*)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyTypeObject __pyx_type_2ml___pyx_scope_struct__ml = {
- PyVarObject_HEAD_INIT(0, 0)
- "ml.__pyx_scope_struct__ml", /*tp_name*/
- sizeof(struct __pyx_obj_2ml___pyx_scope_struct__ml), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2ml___pyx_scope_struct__ml, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- 0, /*tp_doc*/
- __pyx_tp_traverse_2ml___pyx_scope_struct__ml, /*tp_traverse*/
- __pyx_tp_clear_2ml___pyx_scope_struct__ml, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- 0, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_2ml___pyx_scope_struct__ml, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- 0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
- #endif
-};
-
-static struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr *__pyx_freelist_2ml___pyx_scope_struct_1_genexpr[8];
-static int __pyx_freecount_2ml___pyx_scope_struct_1_genexpr = 0;
-
-static PyObject *__pyx_tp_new_2ml___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- PyObject *o;
- if (CYTHON_COMPILING_IN_CPYTHON && likely((__pyx_freecount_2ml___pyx_scope_struct_1_genexpr > 0) & (t->tp_basicsize == sizeof(struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr)))) {
- o = (PyObject*)__pyx_freelist_2ml___pyx_scope_struct_1_genexpr[--__pyx_freecount_2ml___pyx_scope_struct_1_genexpr];
- memset(o, 0, sizeof(struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr));
- (void) PyObject_INIT(o, t);
- PyObject_GC_Track(o);
- } else {
- o = (*t->tp_alloc)(t, 0);
- if (unlikely(!o)) return 0;
- }
- return o;
-}
-
-static void __pyx_tp_dealloc_2ml___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->__pyx_outer_scope);
- Py_CLEAR(p->__pyx_v_s);
- Py_CLEAR(p->__pyx_t_1);
- if (CYTHON_COMPILING_IN_CPYTHON && ((__pyx_freecount_2ml___pyx_scope_struct_1_genexpr < 8) & (Py_TYPE(o)->tp_basicsize == sizeof(struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr)))) {
- __pyx_freelist_2ml___pyx_scope_struct_1_genexpr[__pyx_freecount_2ml___pyx_scope_struct_1_genexpr++] = ((struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr *)o);
- } else {
- (*Py_TYPE(o)->tp_free)(o);
- }
-}
-
-static int __pyx_tp_traverse_2ml___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr *)o;
- if (p->__pyx_outer_scope) {
- e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
- }
- if (p->__pyx_v_s) {
- e = (*v)(p->__pyx_v_s, a); if (e) return e;
- }
- if (p->__pyx_t_1) {
- e = (*v)(p->__pyx_t_1, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_2ml___pyx_scope_struct_1_genexpr(PyObject *o) {
- PyObject* tmp;
- struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr *)o;
- tmp = ((PyObject*)p->__pyx_outer_scope);
- p->__pyx_outer_scope = ((struct __pyx_obj_2ml___pyx_scope_struct__ml *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->__pyx_v_s);
- p->__pyx_v_s = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->__pyx_t_1);
- p->__pyx_t_1 = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyTypeObject __pyx_type_2ml___pyx_scope_struct_1_genexpr = {
- PyVarObject_HEAD_INIT(0, 0)
- "ml.__pyx_scope_struct_1_genexpr", /*tp_name*/
- sizeof(struct __pyx_obj_2ml___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2ml___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
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- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- 0, /*tp_doc*/
- __pyx_tp_traverse_2ml___pyx_scope_struct_1_genexpr, /*tp_traverse*/
- __pyx_tp_clear_2ml___pyx_scope_struct_1_genexpr, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- 0, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
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- 0, /*tp_alloc*/
- __pyx_tp_new_2ml___pyx_scope_struct_1_genexpr, /*tp_new*/
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- 0, /*tp_is_gc*/
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- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
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- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
- #endif
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static PyMethodDef __pyx_methods[] = {
{0, 0, 0, 0}
};
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{&__pyx_n_s_age, __pyx_k_age, sizeof(__pyx_k_age), 0, 0, 1, 1},
{&__pyx_n_s_alpha, __pyx_k_alpha, sizeof(__pyx_k_alpha), 0, 0, 1, 1},
{&__pyx_n_s_arange, __pyx_k_arange, sizeof(__pyx_k_arange), 0, 0, 1, 1},
- {&__pyx_n_s_args, __pyx_k_args, sizeof(__pyx_k_args), 0, 0, 1, 1},
{&__pyx_n_s_beta, __pyx_k_beta, sizeof(__pyx_k_beta), 0, 0, 1, 1},
{&__pyx_n_s_beta_add, __pyx_k_beta_add, sizeof(__pyx_k_beta_add), 0, 0, 1, 1},
- {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1},
{&__pyx_n_s_delta, __pyx_k_delta, sizeof(__pyx_k_delta), 0, 0, 1, 1},
{&__pyx_n_s_dist, __pyx_k_dist, sizeof(__pyx_k_dist), 0, 0, 1, 1},
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{&__pyx_n_s_dt, __pyx_k_dt, sizeof(__pyx_k_dt), 0, 0, 1, 1},
+ {&__pyx_n_s_dts, __pyx_k_dts, sizeof(__pyx_k_dts), 0, 0, 1, 1},
{&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1},
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{&__pyx_n_s_float64, __pyx_k_float64, sizeof(__pyx_k_float64), 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},
{&__pyx_kp_s_inf, __pyx_k_inf, sizeof(__pyx_k_inf), 0, 0, 1, 0},
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{&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
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{&__pyx_n_s_ml, __pyx_k_ml, sizeof(__pyx_k_ml), 0, 0, 1, 1},
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{&__pyx_n_s_n_nodes, __pyx_k_n_nodes, sizeof(__pyx_k_n_nodes), 0, 0, 1, 1},
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{&__pyx_n_s_n_victims, __pyx_k_n_victims, sizeof(__pyx_k_n_victims), 0, 0, 1, 1},
{&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0},
{&__pyx_kp_u_ndarray_is_not_Fortran_contiguou, __pyx_k_ndarray_is_not_Fortran_contiguou, sizeof(__pyx_k_ndarray_is_not_Fortran_contiguou), 0, 1, 0, 0},
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{&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1},
+ {&__pyx_n_s_parent_dists, __pyx_k_parent_dists, sizeof(__pyx_k_parent_dists), 0, 0, 1, 1},
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{&__pyx_n_s_parents, __pyx_k_parents, sizeof(__pyx_k_parents), 0, 0, 1, 1},
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{&__pyx_n_s_probs, __pyx_k_probs, sizeof(__pyx_k_probs), 0, 0, 1, 1},
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- {&__pyx_n_s_send, __pyx_k_send, sizeof(__pyx_k_send), 0, 0, 1, 1},
+ {&__pyx_n_s_s, __pyx_k_s, sizeof(__pyx_k_s), 0, 0, 1, 1},
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{&__pyx_n_s_successes, __pyx_k_successes, sizeof(__pyx_k_successes), 0, 0, 1, 1},
{&__pyx_n_s_sum, __pyx_k_sum, sizeof(__pyx_k_sum), 0, 0, 1, 1},
{&__pyx_n_s_t, __pyx_k_t, sizeof(__pyx_k_t), 0, 0, 1, 1},
{&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
{&__pyx_n_s_thresh, __pyx_k_thresh, sizeof(__pyx_k_thresh), 0, 0, 1, 1},
- {&__pyx_n_s_throw, __pyx_k_throw, sizeof(__pyx_k_throw), 0, 0, 1, 1},
{&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0},
{&__pyx_n_s_victims, __pyx_k_victims, sizeof(__pyx_k_victims), 0, 0, 1, 1},
{&__pyx_n_s_w1, __pyx_k_w1, sizeof(__pyx_k_w1), 0, 0, 1, 1},
@@ -5282,9 +5362,8 @@ 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 = 49; __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 = 55; __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 = 59; __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 = 43; __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 = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__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;}
__pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -5297,14 +5376,14 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
- /* "ml.pyx":83
+ /* "ml.pyx":80
* max_beta_add = float('-inf')
* # iterate over all victim nodes to find the optimal threshold
- * for beta in np.arange(0.001, .2, .002): # <<<<<<<<<<<<<<
+ * for beta in np.arange(0.01, 1., .01): # <<<<<<<<<<<<<<
* thresh = log(beta/(3012.*(1.-beta)))
- * # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
+ * seeds = probs<thresh
*/
- __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_001, __pyx_float__2, __pyx_float__002); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple_ = PyTuple_Pack(3, __pyx_float_0_01, __pyx_float_1_, __pyx_float__01); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple_);
__Pyx_GIVEREF(__pyx_tuple_);
@@ -5374,17 +5453,17 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GOTREF(__pyx_tuple__7);
__Pyx_GIVEREF(__pyx_tuple__7);
- /* "ml.pyx":35
+ /* "ml.pyx":27
* return result
*
* def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
* DTYPE_t alpha, DTYPE_t delta):
* cdef:
*/
- __pyx_tuple__8 = PyTuple_Pack(33, __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_beta_add, __pyx_n_s_max_beta, __pyx_n_s_max_beta_add, __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_thresh, __pyx_n_s_max_roots, __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 = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__8 = PyTuple_Pack(40, __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_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_beta_add, __pyx_n_s_max_beta, __pyx_n_s_max_beta_add, __pyx_n_s_parents, __pyx_n_s_failures, __pyx_n_s_successes, __pyx_n_s_n_nodes, __pyx_n_s_probs, __pyx_n_s_probs_fail, __pyx_n_s_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_probs_nv, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_thresh, __pyx_n_s_seeds, __pyx_n_s_non_seeds, __pyx_n_s_max_roots, __pyx_n_s_prnt, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__8);
__Pyx_GIVEREF(__pyx_tuple__8);
- __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 33, 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, 35, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__9 = (PyObject*)__Pyx_PyCode_New(6, 0, 40, 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, 27, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -5394,9 +5473,10 @@ static int __Pyx_InitCachedConstants(void) {
static int __Pyx_InitGlobals(void) {
if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __pyx_float__2 = PyFloat_FromDouble(.2); if (unlikely(!__pyx_float__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_float__002 = PyFloat_FromDouble(.002); if (unlikely(!__pyx_float__002)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_float_0_001 = PyFloat_FromDouble(0.001); if (unlikely(!__pyx_float_0_001)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_float_1_ = PyFloat_FromDouble(1.); if (unlikely(!__pyx_float_1_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_float__01 = PyFloat_FromDouble(.01); if (unlikely(!__pyx_float__01)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_float_0_01 = PyFloat_FromDouble(0.01); if (unlikely(!__pyx_float_0_01)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_int_148152 = PyInt_FromLong(148152L); if (unlikely(!__pyx_int_148152)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -5483,12 +5563,6 @@ 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 = 35; __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 = 59; __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 ---*/
__pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
#if CYTHON_COMPILING_IN_PYPY
@@ -5532,16 +5606,16 @@ 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":35
+ /* "ml.pyx":27
* return result
*
* def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age, # <<<<<<<<<<<<<<
* DTYPE_t alpha, DTYPE_t delta):
* cdef:
*/
- __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_2ml_1ml, NULL, __pyx_n_s_ml); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __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 = 27; __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 = 35; __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 = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "ml.pyx":1
@@ -5780,88 +5854,6 @@ static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, in
return 0;
}
-static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) {
- PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname);
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return NULL;
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-}
-
static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
PyObject *result;
#if CYTHON_COMPILING_IN_CPYTHON
@@ -6793,6 +6785,84 @@ bad:
return (double)-1;
}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
+ PyObject *r;
+ if (!j) return NULL;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ return r;
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
+ if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
+ if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
+ int is_list, int wraparound, int boundscheck) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (is_list || PyList_CheckExact(o)) {
+ Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ else if (PyTuple_CheckExact(o)) {
+ Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ } else {
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (likely(l >= 0)) {
+ i += l;
+ } else {
+ if (PyErr_ExceptionMatches(PyExc_OverflowError))
+ PyErr_Clear();
+ else
+ return NULL;
+ }
+ }
+ return m->sq_item(o, i);
+ }
+ }
+#else
+ if (is_list || PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
+#endif
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
@@ -7737,639 +7807,6 @@ raise_neg_overflow:
return (long) -1;
}
-static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) {
- PyObject* fake_module;
- PyTypeObject* cached_type = NULL;
- fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI);
- if (!fake_module) return NULL;
- Py_INCREF(fake_module);
- cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name);
- if (cached_type) {
- if (!PyType_Check((PyObject*)cached_type)) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s is not a type object",
- type->tp_name);
- goto bad;
- }
- if (cached_type->tp_basicsize != type->tp_basicsize) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s has the wrong size, try recompiling",
- type->tp_name);
- goto bad;
- }
- } else {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
- PyErr_Clear();
- if (PyType_Ready(type) < 0) goto bad;
- if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0)
- goto bad;
- Py_INCREF(type);
- cached_type = type;
- }
-done:
- Py_DECREF(fake_module);
- return cached_type;
-bad:
- Py_XDECREF(cached_type);
- cached_type = NULL;
- goto done;
-}
-
-static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = *type;
- tstate->exc_value = *value;
- tstate->exc_traceback = *tb;
-#else
- PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
- PyErr_SetExcInfo(*type, *value, *tb);
-#endif
- *type = tmp_type;
- *value = tmp_value;
- *tb = tmp_tb;
-}
-
-static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) {
- PyObject *method, *result = NULL;
- method = __Pyx_PyObject_GetAttrStr(obj, method_name);
- if (unlikely(!method)) goto bad;
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely(PyMethod_Check(method))) {
- PyObject *self = PyMethod_GET_SELF(method);
- if (likely(self)) {
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- Py_INCREF(arg);
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- Py_INCREF(function);
- Py_DECREF(method); method = NULL;
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- else
- ret = __Pyx_PyObject_CallMethod1(yf, __pyx_n_s_send, value);
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- return -1;
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diff --git a/experiments/ml.pyx b/experiments/ml.pyx
index c8c99cc..858207f 100644
--- a/experiments/ml.pyx
+++ b/experiments/ml.pyx
@@ -10,14 +10,9 @@ cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
"""weight for successful infection, exponential time model"""
cdef DTYPE_t structural, temporal, result
- structural = dist * log(delta)
- # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
- temporal = log(exp(alpha)-1.) - alpha*dt
- # temporal = 1 - exp(-alpha*dt)
- # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
- # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
- result = structural + temporal
- # print 'st', structural, temporal
+ structural = delta ** dist
+ temporal = log(exp(alpha)-1.) - alpha*dt/7.
+ result = log(structural) + temporal
return result
cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
@@ -25,17 +20,14 @@ cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
"""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 = exp(-alpha * dt)
- # temporal = 1. - 1. / (1. + dt/alpha)**0.01
+ temporal = exp(-alpha * dt/7.)
result = log(1. - structural + structural * temporal)
- # print 'stnv', structural, temporal
return result
def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
DTYPE_t alpha, DTYPE_t delta):
cdef:
- int n_roots, n_victims, n_nodes, roots, i, dist, dt, t, l
+ int n_roots, n_victims, roots, i, dist, dt, t, l
DTYPE_t beta, ll, beta_add, max_beta, max_beta_add
list parents, failures, successes
n_roots, n_victims = len(root_victims), len(victims)
@@ -43,6 +35,8 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
cdef:
np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE)
np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
+ np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
+ np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE)
np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE)
# loop through victims
@@ -51,43 +45,47 @@ def ml(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
# fail to infect it, also computes the probability that its most
# likely parent infects it
failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
- for (dist, dt, w1, w2, w3) in parents]
+ for (prnt, dist, dt, w1, w2, w3) in parents]
probs_fail[i] = sum(failures)
successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
- for (dist, dt, w1, w2, w3) in parents]
+ for (prnt, dist, dt, w1, w2, w3) in parents]
+ dists = [dist for (prnt, dist, dt, w1, w2, w3) in parents]
+ dts = [dt for (prnt, dist, dt, w1, w2, w3) in parents]
# find parent that maximizes log(p) - log(\tilde{p})
- probs[i] = max(s - failures[l] for l, s in enumerate(successes))
+ # probs[i] = max(s - failures[l] for l, s in enumerate(successes))
+ probs[i] = float("-inf")
+ for l, s in enumerate(successes):
+ prob = s - failures[l]
+ if prob > probs[i]:
+ probs[i] = prob
+ parent_dists[i] = dists[l]
+ parent_dts[i] = dts[l]
+ # probs_fail[i] = failures[l]
# loop through non-victims
for i, parents in enumerate(non_victims.itervalues()):
# for each non victim node, compute the probability that all its
# parents fail to infect it
failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
- for (dist, dt, w1, w2, w3) in parents]
+ for (prnt, dist, dt, w1, w2, w3) in parents]
probs_nv[i] = sum(failures)
- # print successes
- # print failures
- # print probs
-
# calculate log likelihood
- # probs.sort(); probs = probs[::-1] # sort probs in descending order
- # cdef:
- # np.ndarray[DTYPE_t] cums = probs.cumsum()
- ll = probs_fail.sum() # add probability that all edges to victims fail
+ ll = probs_fail.sum() # add probability that all edges to all victims fail
ll += probs_nv.sum() # add probability that all edges to non_victims fail
# print 'probs', probs
max_beta_add = float('-inf')
# iterate over all victim nodes to find the optimal threshold
- for beta in np.arange(0.001, .2, .002):
+ for beta in np.arange(0.01, 1., .01):
thresh = log(beta/(3012.*(1.-beta)))
- # print 'beta:', beta, 'thresh:', thresh, 'infected:', len(probs[probs>=thresh])
- roots = n_roots + len(probs[probs<thresh])
+ seeds = probs<thresh
+ non_seeds = probs>=thresh
+ roots = n_roots + sum(seeds)
beta_add = 0.
# add probability for realized edges and subtract probability these edges fail
- beta_add += (probs[probs>=thresh]).sum()
+ beta_add += (probs[non_seeds]).sum()
# add probability for the seeds and non-seeds
beta_add += roots * log(beta/3012.) + (n_nodes-roots) * log(1. - beta)
diff --git a/experiments/ml.so b/experiments/ml.so
index 7832e67..a08d635 100755
--- a/experiments/ml.so
+++ b/experiments/ml.so
Binary files differ
diff --git a/experiments/ml3.c b/experiments/ml3.c
index 59de174..7ad3edb 100644
--- a/experiments/ml3.c
+++ b/experiments/ml3.c
@@ -695,7 +695,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
* DTYPE = np.float64
* ctypedef np.float_t DTYPE_t # <<<<<<<<<<<<<<
*
- * cdef DTYPE_t weight_success(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,
+ * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
*/
typedef __pyx_t_5numpy_float_t __pyx_t_3ml3_DTYPE_t;
#if CYTHON_CCOMPLEX
@@ -1169,8 +1169,8 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha
/* Module declarations from 'libc.math' */
/* Module declarations from 'ml3' */
-static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t); /*proto*/
-static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t); /*proto*/
+static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int, int, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t); /*proto*/
+static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int, int, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t, __pyx_t_3ml3_DTYPE_t); /*proto*/
static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_3ml3_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_3ml3_DTYPE_t), { 0 }, 0, 'R', 0, 0 };
#define __Pyx_MODULE_NAME "ml3"
int __pyx_module_is_main_ml3 = 0;
@@ -1217,7 +1217,7 @@ static char __pyx_k_sum[] = "sum";
static char __pyx_k_beta[] = "beta";
static char __pyx_k_dist[] = "dist";
static char __pyx_k_main[] = "__main__";
-static char __pyx_k_ones[] = "ones";
+static char __pyx_k_prnt[] = "prnt";
static char __pyx_k_prob[] = "prob";
static char __pyx_k_test[] = "__test__";
static char __pyx_k_DTYPE[] = "DTYPE";
@@ -1233,7 +1233,6 @@ static char __pyx_k_seeds[] = "seeds";
static char __pyx_k_zeros[] = "zeros";
static char __pyx_k_arange[] = "arange";
static char __pyx_k_import[] = "__import__";
-static char __pyx_k_isSeed[] = "isSeed";
static char __pyx_k_thresh[] = "thresh";
static char __pyx_k_float64[] = "float64";
static char __pyx_k_n_roots[] = "n_roots";
@@ -1287,7 +1286,6 @@ static PyObject *__pyx_n_s_float64;
static PyObject *__pyx_n_s_i;
static PyObject *__pyx_n_s_import;
static PyObject *__pyx_kp_s_inf;
-static PyObject *__pyx_n_s_isSeed;
static PyObject *__pyx_n_s_itervalues;
static PyObject *__pyx_n_s_l;
static PyObject *__pyx_n_s_ll;
@@ -1304,10 +1302,10 @@ static PyObject *__pyx_n_s_non_seeds;
static PyObject *__pyx_n_s_non_victims;
static PyObject *__pyx_n_s_np;
static PyObject *__pyx_n_s_numpy;
-static PyObject *__pyx_n_s_ones;
static PyObject *__pyx_n_s_parent_dists;
static PyObject *__pyx_n_s_parent_dts;
static PyObject *__pyx_n_s_parents;
+static PyObject *__pyx_n_s_prnt;
static PyObject *__pyx_n_s_prob;
static PyObject *__pyx_n_s_probs;
static PyObject *__pyx_n_s_probs_fail;
@@ -1327,9 +1325,8 @@ static PyObject *__pyx_n_s_w1;
static PyObject *__pyx_n_s_w2;
static PyObject *__pyx_n_s_w3;
static PyObject *__pyx_n_s_zeros;
-static PyObject *__pyx_float_1_;
-static PyObject *__pyx_float_0_00001;
-static PyObject *__pyx_int_0;
+static PyObject *__pyx_float__01;
+static PyObject *__pyx_float_0_01;
static PyObject *__pyx_int_1;
static PyObject *__pyx_tuple_;
static PyObject *__pyx_tuple__2;
@@ -1344,12 +1341,12 @@ static PyObject *__pyx_codeobj__9;
/* "ml3.pyx":9
* ctypedef np.float_t DTYPE_t
*
- * cdef DTYPE_t weight_success(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
+ * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
* DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
* """weight for successful infection, exponential time model"""
*/
-static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, __pyx_t_3ml3_DTYPE_t __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
+static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
__pyx_t_3ml3_DTYPE_t __pyx_v_structural;
__pyx_t_3ml3_DTYPE_t __pyx_v_temporal;
__pyx_t_3ml3_DTYPE_t __pyx_v_result;
@@ -1389,7 +1386,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, __pyx_
* result = log(structural) + temporal
* return result # <<<<<<<<<<<<<<
*
- * cdef DTYPE_t weight_failure(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,
+ * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
*/
__pyx_r = __pyx_v_result;
goto __pyx_L0;
@@ -1397,7 +1394,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, __pyx_
/* "ml3.pyx":9
* ctypedef np.float_t DTYPE_t
*
- * cdef DTYPE_t weight_success(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
+ * cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
* DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
* """weight for successful infection, exponential time model"""
*/
@@ -1411,12 +1408,12 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, __pyx_
/* "ml3.pyx":18
* return result
*
- * cdef DTYPE_t weight_failure(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
+ * 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_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, __pyx_t_3ml3_DTYPE_t __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
+static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
__pyx_t_3ml3_DTYPE_t __pyx_v_structural;
__pyx_t_3ml3_DTYPE_t __pyx_v_temporal;
__pyx_t_3ml3_DTYPE_t __pyx_v_result;
@@ -1464,7 +1461,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, __pyx_
/* "ml3.pyx":18
* return result
*
- * cdef DTYPE_t weight_failure(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta, # <<<<<<<<<<<<<<
+ * 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"""
*/
@@ -1608,20 +1605,18 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
PyArrayObject *__pyx_v_probs_fail = 0;
PyArrayObject *__pyx_v_parent_dists = 0;
PyArrayObject *__pyx_v_parent_dts = 0;
- PyArrayObject *__pyx_v_isSeed = 0;
PyObject *__pyx_v_dists = NULL;
PyObject *__pyx_v_dts = NULL;
PyObject *__pyx_v_s = NULL;
PyObject *__pyx_v_prob = NULL;
- CYTHON_UNUSED double __pyx_v_thresh;
+ double __pyx_v_thresh;
PyObject *__pyx_v_seeds = NULL;
PyObject *__pyx_v_non_seeds = NULL;
int __pyx_v_max_roots;
+ CYTHON_UNUSED PyObject *__pyx_v_prnt = NULL;
PyObject *__pyx_v_w1 = NULL;
PyObject *__pyx_v_w2 = NULL;
PyObject *__pyx_v_w3 = NULL;
- __Pyx_LocalBuf_ND __pyx_pybuffernd_isSeed;
- __Pyx_Buffer __pyx_pybuffer_isSeed;
__Pyx_LocalBuf_ND __pyx_pybuffernd_parent_dists;
__Pyx_Buffer __pyx_pybuffer_parent_dists;
__Pyx_LocalBuf_ND __pyx_pybuffernd_parent_dts;
@@ -1642,11 +1637,11 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
PyArrayObject *__pyx_t_8 = NULL;
PyArrayObject *__pyx_t_9 = NULL;
PyArrayObject *__pyx_t_10 = NULL;
- PyArrayObject *__pyx_t_11 = NULL;
+ int __pyx_t_11;
int __pyx_t_12;
int __pyx_t_13;
- int __pyx_t_14;
- Py_ssize_t __pyx_t_15;
+ Py_ssize_t __pyx_t_14;
+ PyObject *__pyx_t_15 = NULL;
PyObject *__pyx_t_16 = NULL;
PyObject *__pyx_t_17 = NULL;
PyObject *__pyx_t_18 = NULL;
@@ -1686,10 +1681,6 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
__pyx_pybuffer_parent_dts.refcount = 0;
__pyx_pybuffernd_parent_dts.data = NULL;
__pyx_pybuffernd_parent_dts.rcbuffer = &__pyx_pybuffer_parent_dts;
- __pyx_pybuffer_isSeed.pybuffer.buf = NULL;
- __pyx_pybuffer_isSeed.refcount = 0;
- __pyx_pybuffernd_isSeed.data = NULL;
- __pyx_pybuffernd_isSeed.rcbuffer = &__pyx_pybuffer_isSeed;
/* "ml3.pyx":33
* DTYPE_t beta, ll, beta_add, max_beta, max_beta_add
@@ -1804,7 +1795,7 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
* np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
* np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<<
* np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE)
- * np.ndarray[DTYPE_t] isSeed = np.ones(n_victims, dtype=DTYPE)
+ *
*/
__pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
@@ -1847,8 +1838,8 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
* np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
* np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
* np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<<
- * np.ndarray[DTYPE_t] isSeed = np.ones(n_victims, dtype=DTYPE)
*
+ * # loop through victims
*/
__pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
@@ -1887,134 +1878,93 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
__pyx_v_parent_dts = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
- /* "ml3.pyx":39
- * np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
- * np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE)
- * np.ndarray[DTYPE_t] isSeed = np.ones(n_victims, dtype=DTYPE) # <<<<<<<<<<<<<<
- *
- * # loop through victims
- */
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_ones); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_DTYPE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __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 = 39; __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 = 39; __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 = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = ((PyArrayObject *)__pyx_t_4);
- {
- __Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_isSeed.rcbuffer->pybuffer, (PyObject*)__pyx_t_11, &__Pyx_TypeInfo_nn___pyx_t_3ml3_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {
- __pyx_v_isSeed = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_isSeed.rcbuffer->pybuffer.buf = NULL;
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- } else {__pyx_pybuffernd_isSeed.diminfo[0].strides = __pyx_pybuffernd_isSeed.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_isSeed.diminfo[0].shape = __pyx_pybuffernd_isSeed.rcbuffer->pybuffer.shape[0];
- }
- }
- __pyx_t_11 = 0;
- __pyx_v_isSeed = ((PyArrayObject *)__pyx_t_4);
- __pyx_t_4 = 0;
-
- /* "ml3.pyx":42
+ /* "ml3.pyx":41
*
* # loop through victims
* for i, parents in enumerate(victims.itervalues()): # <<<<<<<<<<<<<<
* # for each victim node i, compute the probability that all its parents
* # fail to infect it, also computes the probability that its most
*/
- __pyx_t_12 = 0;
+ __pyx_t_11 = 0;
__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 = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_6 = __Pyx_dict_iterator(__pyx_v_victims, 1, __pyx_n_s_itervalues, (&__pyx_t_1), (&__pyx_t_13)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_4);
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- __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_float__01 = PyFloat_FromDouble(.01); if (unlikely(!__pyx_float__01)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_float_0_01 = PyFloat_FromDouble(0.01); if (unlikely(!__pyx_float_0_01)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
diff --git a/experiments/ml3.pyx b/experiments/ml3.pyx
index da993bc..6e031ef 100644
--- a/experiments/ml3.pyx
+++ b/experiments/ml3.pyx
@@ -6,7 +6,7 @@ from libc.math cimport log, exp
DTYPE = np.float64
ctypedef np.float_t DTYPE_t
-cdef DTYPE_t weight_success(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,
+cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta,
DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
"""weight for successful infection, exponential time model"""
cdef DTYPE_t structural, temporal, result
@@ -15,7 +15,7 @@ cdef DTYPE_t weight_success(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,
result = log(structural) + temporal
return result
-cdef DTYPE_t weight_failure(int dist, DTYPE_t dt, DTYPE_t alpha, DTYPE_t delta,
+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
@@ -36,20 +36,19 @@ def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE)
- np.ndarray[DTYPE_t] isSeed = np.ones(n_victims, dtype=DTYPE)
# loop through victims
for i, parents in enumerate(victims.itervalues()):
# 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/100., alpha, delta, w1, w2, w3)
- for (dist, dt, w1, w2, w3) in parents]
+ failures = [weight_failure(dist, dt, alpha, delta, w1, w2, w3)
+ for (prnt, dist, dt, w1, w2, w3) in parents]
probs_fail[i] = sum(failures)
- successes = [weight_success(dist, dt/100., alpha, delta, w1, w2, w3)
- for (dist, dt, w1, w2, w3) in parents]
- dists = [dist for (dist, dt, w1, w2, w3) in parents]
- dts = [dt for (dist, dt, w1, w2, w3) in parents]
+ successes = [weight_success(dist, dt, alpha, delta, w1, w2, w3)
+ for (prnt, dist, dt, w1, w2, w3) in parents]
+ dists = [dist for (prnt, dist, dt, w1, w2, w3) in parents]
+ dts = [dt for (prnt, dist, dt, w1, w2, w3) in parents]
# find parent that maximizes log(p) - log(\tilde{p})
# probs[i] = max(s - failures[l] for l, s in enumerate(successes))
probs[i] = float("-inf")
@@ -62,15 +61,15 @@ def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
# probs_fail[i] = failures[l]
# calculate log likelihood
- ll = probs_fail.sum() # add probability that all edges to all victims fail
+ ll = probs_fail.sum() # add probability that all edges to all victims fail
# print 'probs', probs
max_beta_add = float('-inf')
# iterate over all victim nodes to find the optimal threshold
- for beta in np.arange(0.00001, 1., 1.):
+ for beta in np.arange(0.01, 1, .01):
thresh = log(beta/(3012.*(1.-beta)))
- seeds = isSeed==1
- non_seeds = isSeed==0
+ seeds = probs<thresh
+ non_seeds = probs>=thresh
roots = n_roots + sum(seeds)
beta_add = 0.
@@ -89,4 +88,4 @@ def ml3(dict root_victims, dict victims, dict non_victims, DTYPE_t age,
roots = max_roots
beta = max_beta
# print n_nodes, n_roots, n_victims, max_i, roots
- return (beta, roots, ll)
+ return (beta, roots, ll) \ No newline at end of file
diff --git a/experiments/ml3.so b/experiments/ml3.so
index d2b6898..fb8afc9 100755
--- a/experiments/ml3.so
+++ b/experiments/ml3.so
Binary files differ
diff --git a/experiments/out.log b/experiments/out.log
index 98ddbb1..a718511 100644
--- a/experiments/out.log
+++ b/experiments/out.log
@@ -1,30 +1,100 @@
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-0.24 0.1 0.1 47 -9284.2416322
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diff --git a/experiments/process.py b/experiments/process.py
index 0115bd4..a0c9b98 100644
--- a/experiments/process.py
+++ b/experiments/process.py
@@ -15,29 +15,29 @@ if __name__ == "__main__":
sys.exit("usage: {0} <file>".format(sys.argv[0]))
root_victims, victims, non_victims, age = load(open(sys.argv[1]))
- # # alphas = np.arange(1e-3, 1e-2, 8e-4) # parameter of the time component
- # alphas = np.logspace(-4,-1,num=15)
- # # deltas = np.arange(0.001, 0.3, 0.008) # parameter of the structural component
- # deltas = np.logspace(-4,-1.7,num=15)
- # with open("out.log", "w") as fh:
- # for alpha, delta in product(alphas, deltas):
- # beta, roots, ll = ml3(root_victims, victims, non_victims, age, alpha, delta)
- # print "\t".join(map(str, [alpha, delta, beta, roots, ll]))
- # fh.write("\t".join(map(str, [alpha, delta, beta, roots, ll])) + "\n")
- # fh.flush()
-
- alphas = np.arange(.15, .25, .01) # parameter of the time component
- # alphas = np.logspace(-4,-.5,num=15)
- deltas = np.arange(.08, .1, .01) # parameter of the structural component
- # deltas = np.logspace(-2,-.1,num=15)
- lmbda = 0.10#np.logspace(-12,-3,num=10)
+ # alphas = np.arange(.02, .1, .01) # parameter of the time component
+ alphas = np.logspace(-3,-1,num=10)
+ # deltas = np.arange(.02, .1, .01) # parameter of the structural component
+ deltas = np.logspace(-3,-1,num=10)
with open("out.log", "w") as fh:
for alpha, delta in product(alphas, deltas):
- lmbda, roots, ll = ml2(root_victims, victims, non_victims, alpha, delta, lmbda)
- print "\t".join(map(str, [alpha, delta, lmbda, roots, ll]))
- fh.write("\t".join(map(str, [alpha, delta, lmbda, roots, ll])) + "\n")
+ beta, roots, ll = ml(root_victims, victims, non_victims, age, alpha, delta)
+ print "\t".join(map(str, [alpha, delta, beta, roots, ll]))
+ fh.write("\t".join(map(str, [alpha, delta, beta, roots, ll])) + "\n")
fh.flush()
+ # alphas = np.arange(.15, .25, .01) # parameter of the time component
+ # # alphas = np.logspace(-4,-.5,num=15)
+ # deltas = np.arange(.08, .1, .01) # parameter of the structural component
+ # # deltas = np.logspace(-2,-.1,num=15)
+ # lmbda = 0.10#np.logspace(-12,-3,num=10)
+ # with open("out.log", "w") as fh:
+ # for alpha, delta in product(alphas, deltas):
+ # lmbda, roots, ll = ml2(root_victims, victims, non_victims, alpha, delta, lmbda)
+ # print "\t".join(map(str, [alpha, delta, lmbda, roots, ll]))
+ # fh.write("\t".join(map(str, [alpha, delta, lmbda, roots, ll])) + "\n")
+ # fh.flush()
+
# alpha = .016
# delta = 0.077
# beta, roots, ll = ml2(root_victims, victims, non_victims, alpha, delta, 1.)
generated by cgit v1.2.3-70-g09d2 (git 2.52.0) at 2025-12-21 14:57:29 +0000