updated calculation of structural component with edge weights, and to

penalize less for longer distances

1 files changed, 520 insertions, 786 deletions

diff --git a/experiments/ml3.c b/experiments/ml3.c
index 64796d7..90842d8 100644
--- a/experiments/ml3.c
+++ b/experiments/ml3.c
@@ -1177,11 +1177,10 @@ int __pyx_module_is_main_ml3 = 0;
 
 /* Implementation of 'ml3' */
 static PyObject *__pyx_builtin_enumerate;
-static PyObject *__pyx_builtin_sum;
 static PyObject *__pyx_builtin_ValueError;
 static PyObject *__pyx_builtin_range;
 static PyObject *__pyx_builtin_RuntimeError;
-static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_age, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta); /* proto */
+static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, CYTHON_UNUSED PyObject *__pyx_v_non_victims, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_age, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_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 char __pyx_k_B[] = "B";
@@ -1233,14 +1232,12 @@ 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_n_nodes[] = "n_nodes";
 static char __pyx_k_n_roots[] = "n_roots";
 static char __pyx_k_parents[] = "parents";
 static char __pyx_k_victims[] = "victims";
 static char __pyx_k_beta_add[] = "beta_add";
 static char __pyx_k_failures[] = "failures";
 static char __pyx_k_max_beta[] = "max_beta";
-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";
@@ -1293,7 +1290,6 @@ 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_ml3;
-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;
@@ -1307,7 +1303,6 @@ static PyObject *__pyx_n_s_parents;
 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;
@@ -1323,9 +1318,9 @@ static PyObject *__pyx_n_s_w1;
 static PyObject *__pyx_n_s_w2;
 static PyObject *__pyx_n_s_w3;
 static PyObject *__pyx_n_s_zeros;
+static PyObject *__pyx_float__1;
 static PyObject *__pyx_float_1_;
-static PyObject *__pyx_float__05;
-static PyObject *__pyx_float_0_09;
+static PyObject *__pyx_float_0_1;
 static PyObject *__pyx_tuple_;
 static PyObject *__pyx_tuple__2;
 static PyObject *__pyx_tuple__3;
@@ -1450,7 +1445,7 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_success(int __pyx_v_dist, int __
 
 static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_w3) {
   __pyx_t_3ml3_DTYPE_t __pyx_v_structural;
-  __pyx_t_3ml3_DTYPE_t __pyx_v_temporal;
+  CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_temporal;
   __pyx_t_3ml3_DTYPE_t __pyx_v_result;
   __pyx_t_3ml3_DTYPE_t __pyx_r;
   __Pyx_RefNannyDeclarations
@@ -1470,21 +1465,21 @@ static __pyx_t_3ml3_DTYPE_t __pyx_f_3ml3_weight_failure(int __pyx_v_dist, int __
  *     # structural = plogis(w1,delta) * plogis(w2,delta) * plogis(w3,delta)
  *     temporal = exp(-alpha * dt)             # <<<<<<<<<<<<<<
  *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
- *     result = log(1. - structural + structural * temporal)
+ *     result = log(1. - structural)
  */
   __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt));
 
   /* "ml3.pyx":35
  *     temporal = exp(-alpha * dt)
  *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
- *     result = log(1. - structural + structural * temporal)             # <<<<<<<<<<<<<<
+ *     result = log(1. - structural)             # <<<<<<<<<<<<<<
  *     # print 'stnv', structural, temporal
  *     return result
  */
-  __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
+  __pyx_v_result = log((1. - __pyx_v_structural));
 
   /* "ml3.pyx":37
- *     result = log(1. - structural + structural * temporal)
+ *     result = log(1. - structural)
  *     # print 'stnv', structural, temporal
  *     return result             # <<<<<<<<<<<<<<
  * 
@@ -1521,7 +1516,7 @@ static PyMethodDef __pyx_mdef_3ml3_1ml3 = {"ml3", (PyCFunction)__pyx_pw_3ml3_1ml
 static PyObject *__pyx_pw_3ml3_1ml3(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
   PyObject *__pyx_v_root_victims = 0;
   PyObject *__pyx_v_victims = 0;
-  PyObject *__pyx_v_non_victims = 0;
+  CYTHON_UNUSED PyObject *__pyx_v_non_victims = 0;
   CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_age;
   __pyx_t_3ml3_DTYPE_t __pyx_v_alpha;
   __pyx_t_3ml3_DTYPE_t __pyx_v_delta;
@@ -1620,10 +1615,9 @@ static PyObject *__pyx_pw_3ml3_1ml3(PyObject *__pyx_self, PyObject *__pyx_args,
   return __pyx_r;
 }
 
-static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, PyObject *__pyx_v_non_victims, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_age, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta) {
+static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_root_victims, PyObject *__pyx_v_victims, CYTHON_UNUSED PyObject *__pyx_v_non_victims, CYTHON_UNUSED __pyx_t_3ml3_DTYPE_t __pyx_v_age, __pyx_t_3ml3_DTYPE_t __pyx_v_alpha, __pyx_t_3ml3_DTYPE_t __pyx_v_delta) {
   int __pyx_v_n_roots;
   int __pyx_v_n_victims;
-  CYTHON_UNUSED int __pyx_v_n_nodes;
   int __pyx_v_roots;
   int __pyx_v_i;
   int __pyx_v_dist;
@@ -1639,7 +1633,6 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   PyObject *__pyx_v_successes = 0;
   PyArrayObject *__pyx_v_probs = 0;
   PyArrayObject *__pyx_v_probs_fail = 0;
-  PyArrayObject *__pyx_v_probs_nv = 0;
   PyArrayObject *__pyx_v_parent_dists = 0;
   PyArrayObject *__pyx_v_parent_dts = 0;
   PyObject *__pyx_v_dists = NULL;
@@ -1659,8 +1652,6 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   __Pyx_Buffer __pyx_pybuffer_probs;
   __Pyx_LocalBuf_ND __pyx_pybuffernd_probs_fail;
   __Pyx_Buffer __pyx_pybuffer_probs_fail;
-  __Pyx_LocalBuf_ND __pyx_pybuffernd_probs_nv;
-  __Pyx_Buffer __pyx_pybuffer_probs_nv;
   PyObject *__pyx_r = NULL;
   __Pyx_RefNannyDeclarations
   Py_ssize_t __pyx_t_1;
@@ -1673,31 +1664,29 @@ 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;
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   PyObject *__pyx_t_18 = NULL;
   PyObject *__pyx_t_19 = NULL;
   PyObject *__pyx_t_20 = NULL;
-  PyObject *__pyx_t_21 = NULL;
-  PyObject *(*__pyx_t_22)(PyObject *);
-  int __pyx_t_23;
+  PyObject *(*__pyx_t_21)(PyObject *);
+  int __pyx_t_22;
+  __pyx_t_3ml3_DTYPE_t __pyx_t_23;
   __pyx_t_3ml3_DTYPE_t __pyx_t_24;
   __pyx_t_3ml3_DTYPE_t __pyx_t_25;
-  __pyx_t_3ml3_DTYPE_t __pyx_t_26;
-  double __pyx_t_27;
+  double __pyx_t_26;
+  int __pyx_t_27;
   int __pyx_t_28;
   int __pyx_t_29;
   int __pyx_t_30;
   int __pyx_t_31;
   int __pyx_t_32;
-  int __pyx_t_33;
-  int __pyx_t_34;
-  PyObject *(*__pyx_t_35)(PyObject *);
+  PyObject *(*__pyx_t_33)(PyObject *);
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
@@ -1710,10 +1699,6 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   __pyx_pybuffer_probs_fail.refcount = 0;
   __pyx_pybuffernd_probs_fail.data = NULL;
   __pyx_pybuffernd_probs_fail.rcbuffer = &__pyx_pybuffer_probs_fail;
-  __pyx_pybuffer_probs_nv.pybuffer.buf = NULL;
-  __pyx_pybuffer_probs_nv.refcount = 0;
-  __pyx_pybuffernd_probs_nv.data = NULL;
-  __pyx_pybuffernd_probs_nv.rcbuffer = &__pyx_pybuffer_probs_nv;
   __pyx_pybuffer_parent_dists.pybuffer.buf = NULL;
   __pyx_pybuffer_parent_dists.refcount = 0;
   __pyx_pybuffernd_parent_dists.data = NULL;
@@ -1727,8 +1712,8 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  *         DTYPE_t beta, ll, beta_add, max_beta, max_beta_add
  *         list parents, failures, successes
  *     n_roots, n_victims = len(root_victims), len(victims)             # <<<<<<<<<<<<<<
- *     n_nodes = 148152
  *     cdef:
+ *         np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE)
  */
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     PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
@@ -1743,52 +1728,43 @@ static PyObject *__pyx_pf_3ml3_ml3(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   __pyx_v_n_roots = __pyx_t_1;
   __pyx_v_n_victims = __pyx_t_2;
 
-  /* "ml3.pyx":46
- *         list parents, failures, successes
+  /* "ml3.pyx":47
  *     n_roots, n_victims = len(root_victims), len(victims)
- *     n_nodes = 148152             # <<<<<<<<<<<<<<
- *     cdef:
- *         np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE)
- */
-  __pyx_v_n_nodes = 148152;
-
-  /* "ml3.pyx":48
- *     n_nodes = 148152
  *     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)
+ *         np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
  */
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-      {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __pyx_t_6 = 0;
 
-  /* "ml3.pyx":49
+  /* "ml3.pyx":48
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  *         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)
  *         np.ndarray[DTYPE_t] parent_dists = np.zeros(n_victims, dtype=DTYPE)
+ *         np.ndarray[DTYPE_t] parent_dts = np.zeros(n_victims, dtype=DTYPE)
  */
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