Worked on process to generate cascades in R, recover them in ml2, and

compare true/recovered. Results look good: ml2 finds close-to-actual
parameters and gets ~60% of the infectors right. I will check how many
recovery gets in the top 2 or 3 infectors.

9 files changed, 2149 insertions, 1211 deletions

diff --git a/R Scripts/generate-network.R b/R Scripts/generate-network.R
new file mode 100644
index 0000000..dc4a4f8
--- /dev/null
+++ b/R Scripts/generate-network.R
@@ -0,0 +1,78 @@
+library(igraph)
+setwd("~/Documents/Cascade Project/")
+source('criminal_cascades/R Scripts/temporal.R')
+source('criminal_cascades/R Scripts/structural.R')
+
+alpha = 1/100
+beta = 0.02
+delta = 0.15
+# lmbda = 1/10
+t_max = 1000
+
+# g = watts.strogatz.game(1, 100, 3, 0.25)
+N = 5000
+g = forest.fire.game(nodes=N, fw.prob=0.3, ambs=1, directed=F)
+plot(g, vertex.size=5, vertex.label=NA)
+
+V(g)$seed = runif(vcount(g))<beta
+seeds = which(V(g)$seed)
+V(g)$vic = V(g)$seed
+V(g)$vic.day[V(g)$seed] = sample(1:t_max, sum(V(g)$seed))
+V(g)$spawn.date = 0
+V(g)$infector = NA
+
+for (day in 1:t_max){
+  day.vics = match(day,V(g)$vic.day)
+  if (is.na(day.vics)) next
+  for (vic in day.vics){
+    neighbors = (unlist(neighborhood(g,3,vic)))[-1]
+    dists = as.numeric(shortest.paths(g,vic,neighbors))
+    infected = neighbors[which(runif(length(neighbors))<structural(delta, dists))]
+    infected = setdiff(infected,seeds) # don't try to infect seeds
+    inf.days = day + ceiling(alpha*rexp(length(infected),alpha))
+    V(g)$vic[infected] = TRUE
+    infects = (inf.days < V(g)$vic.day[infected]) %in% c(NA,T)
+    V(g)$vic.day[infected[infects]] = inf.days[infects]
+    V(g)$infector[infected[infects]] = vic
+  }
+}
+
+vic_ids = which(V(g)$vic)
+cols = rep('lightblue',N); cols[V(g)$vic]='red'; cols[V(g)$seed]='darkred'
+plot(g, vertex.size=5, vertex.label=NA, vertex.color=cols)
+
+##### generate dag_dat
+dag_dat_test = data.frame(matrix(nrow=1,ncol=10))
+ei = 1
+for (u in vic_ids){
+  if ((which(vic_ids==u) %% 1000)==0)  print(which(vic_ids==u))
+  tu    = V(g)$vic.day[u]
+  u_spawn = V(g)$spawn.date[u]
+  nbhd  = (unlist(neighborhood(g,nodes=u,order=3)))[-1] # get nodes within neighborhood
+  tvs   = V(g)$vic.day[nbhd]
+  v_spawn = V(g)$spawn.date[nbhd]
+  nbhd  = nbhd[tu>v_spawn & (is.na(tvs) | tu<tvs)]
+  tvs   = V(g)$vic.day[nbhd]
+  dists = as.numeric(shortest.paths(g,u,nbhd))
+  
+  weights = matrix(1,nrow=length(nbhd),ncol=3)
+  
+  #will be faster to pre-allocate and fill in rather than rbind each time
+  dag_dat_test[ei:(ei+length(nbhd)-1),] = data.frame(rep(u,length(nbhd)), nbhd, 
+                                                    rep(tu,length(nbhd)), tvs, dists, 
+                                                    weights, rep(u_spawn,length(nbhd)),
+                                                    rep(0,length(nbhd)), row.names=NULL)
+  ei = ei + length(nbhd)
+}
+colnames(dag_dat_test) = c('from','to','t1','t2','dist','w1','w2','w3','spawn1','spawn2')
+rownames(dag_dat_test) = NULL
+
+write.csv(dag_dat_test, file='Results/dag_dat_test.csv')
+
+##### analyze performance of recovery algorithm
+recovered = read.csv('Results/infectors.csv',header=F,col.names=c('victim','infector'))
+recovered = recovered[order(recovered$victim),]
+infectors = cbind(setdiff(vic_ids,seeds),
+                  V(g)$infector[setdiff(vic_ids,seeds)],
+                  recovered$infector[recovered$victim %in% setdiff(vic_ids,seeds)])
+mean(infectors[,2]==infectors[,3])
diff --git a/R Scripts/structural.R b/R Scripts/structural.R
index 132aa6c..b68711c 100755
--- a/R Scripts/structural.R
+++ b/R Scripts/structural.R
@@ -1,5 +1,5 @@
-# structural = function(w1,w2,w3,gamma){
-#   return (plogis(w1,scale=gamma) * plogis(w2,scale=gamma) * plogis(w3,scale=gamma))
+# structural = function(delta,lmbda,w1,w2,w3){
+#   return (delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda)))
 # }
 
 structural = function(delta,dist){
diff --git a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml2.o b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml2.o
index d3704b1..285f8be 100644
--- a/experiments/build/temp.macosx-10.6-x86_64-2.7/ml2.o
+++ b/experiments/build/temp.macosx-10.6-x86_64-2.7/ml2.o
diff --git a/experiments/build_network.py b/experiments/build_network.py
index 6cb994c..0e912b0 100644
--- a/experiments/build_network.py
+++ b/experiments/build_network.py
@@ -14,12 +14,12 @@ def build_network(filename):
             from_, to = int(float(row["from"])), int(float(row["to"]))
             dist = int(row["dist"])
             w1, w2, w3 = float(row["w1"]), float(row["w2"]), float(row["w3"])
-            if int(float(row["dist"])) > 1:
-                continue
+            # if int(float(row["dist"])) > 1:
+            #     continue
             # 'to' is a victim
             if row["t2"] != "NA":
                 dt = int(row["t2"]) - int(row["t1"])
-                parent = (dist, dt, w1, w2, w3)
+                parent = (from_, dist, dt, w1, w2, w3)
                 if to not in victims:
                     age += int(row["t2"]) - int(row["spawn2"])
                     victims[to] = []
@@ -29,8 +29,8 @@ def build_network(filename):
                     victims[from_] = []
             # 'to' is not a victim
             else:
-                dt = 3012 - int(row["t1"])
-                parent = (dist, dt, w1, w2, w3)
+                dt = 1000 - int(row["t1"])
+                parent = (from_, dist, dt, w1, w2, w3)
                 if to not in non_victims:
                     # age += 3012 - int(row["spawn2"])
                     non_victims[to] = []
@@ -39,13 +39,14 @@ def build_network(filename):
                     age += int(row["t1"]) - int(row["spawn1"])
                     victims[from_] = []
     root_victims = {}
-    # print victims.keys()
+    print sorted(victims.keys())
+    # print victims
     for victim in victims.keys():
         if not victims[victim]:
             del victims[victim]
             root_victims[victim] = []
-    # print root_victims.keys()
-    # print len(root_victims), len(victims), len(non_victims)
+    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/ml2.c b/experiments/ml2.c
index 572a8c5..a61a0d3 100644
--- a/experiments/ml2.c
+++ b/experiments/ml2.c
@@ -947,10 +947,39 @@ 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_PyObject_GetSlice(
-        PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
-        PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
-        int has_cstart, int has_cstop, int wraparound);
+#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000
+static CYTHON_INLINE PyObject* __Pyx_PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name) {
+    PyObject *res;
+    PyTypeObject *tp = Py_TYPE(obj);
+#if PY_MAJOR_VERSION < 3
+    if (unlikely(PyInstance_Check(obj)))
+        return __Pyx_PyObject_GetAttrStr(obj, attr_name);
+#endif
+    res = _PyType_Lookup(tp, attr_name);
+    if (likely(res)) {
+        descrgetfunc f = Py_TYPE(res)->tp_descr_get;
+        if (!f) {
+            Py_INCREF(res);
+        } else {
+            res = f(res, obj, (PyObject *)tp);
+        }
+    } else {
+        PyErr_SetObject(PyExc_AttributeError, attr_name);
+    }
+    return res;
+}
+#else
+#define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n)
+#endif
+
+static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg);
+
+static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d);
+
+static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb);
+static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb);
+
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
 
 static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb);
 static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb);
@@ -1025,14 +1054,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
 
 static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
 
-static int __Pyx_Print(PyObject*, PyObject *, int);
-#if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3
-static PyObject* __pyx_print = 0;
-static PyObject* __pyx_print_kwargs = 0;
-#endif
-
-static int __Pyx_PrintOne(PyObject* stream, PyObject *o);
-
 #if CYTHON_CCOMPLEX
   #ifdef __cplusplus
     #define __Pyx_CREAL(z) ((z).real())
@@ -1191,6 +1212,7 @@ int __pyx_module_is_main_ml2 = 0;
 /* Implementation of 'ml2' */
 static PyObject *__pyx_builtin_enumerate;
 static PyObject *__pyx_builtin_sum;
+static PyObject *__pyx_builtin_open;
 static PyObject *__pyx_builtin_ValueError;
 static PyObject *__pyx_builtin_range;
 static PyObject *__pyx_builtin_RuntimeError;
@@ -1213,6 +1235,7 @@ 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_w[] = "w";
 static char __pyx_k_Zd[] = "Zd";
 static char __pyx_k_Zf[] = "Zf";
 static char __pyx_k_Zg[] = "Zg";
@@ -1223,14 +1246,16 @@ static char __pyx_k_w1[] = "w1";
 static char __pyx_k_w2[] = "w2";
 static char __pyx_k_w3[] = "w3";
 static char __pyx_k_dts[] = "dts";
-static char __pyx_k_end[] = "end";
 static char __pyx_k_inf[] = "-inf";
 static char __pyx_k_ml2[] = "ml2";
+static char __pyx_k_s_s[] = "%s, %s\n";
 static char __pyx_k_sum[] = "sum";
 static char __pyx_k_dist[] = "dist";
-static char __pyx_k_file[] = "file";
+static char __pyx_k_exit[] = "__exit__";
+static char __pyx_k_keys[] = "keys";
 static char __pyx_k_main[] = "__main__";
-static char __pyx_k_mean[] = "mean";
+static char __pyx_k_open[] = "open";
+static char __pyx_k_prnt[] = "prnt";
 static char __pyx_k_prob[] = "prob";
 static char __pyx_k_test[] = "__test__";
 static char __pyx_k_DTYPE[] = "DTYPE";
@@ -1238,12 +1263,14 @@ static char __pyx_k_alpha[] = "alpha";
 static char __pyx_k_delta[] = "delta";
 static char __pyx_k_dists[] = "dists";
 static char __pyx_k_dtype[] = "dtype";
+static char __pyx_k_enter[] = "__enter__";
 static char __pyx_k_lmbda[] = "lmbda";
 static char __pyx_k_numpy[] = "numpy";
-static char __pyx_k_print[] = "print";
+static char __pyx_k_prnts[] = "prnts";
 static char __pyx_k_probs[] = "probs";
 static char __pyx_k_range[] = "range";
 static char __pyx_k_roots[] = "roots";
+static char __pyx_k_write[] = "write";
 static char __pyx_k_zeros[] = "zeros";
 static char __pyx_k_import[] = "__import__";
 static char __pyx_k_float64[] = "float64";
@@ -1251,8 +1278,10 @@ static char __pyx_k_n_roots[] = "n_roots";
 static char __pyx_k_parents[] = "parents";
 static char __pyx_k_victims[] = "victims";
 static char __pyx_k_failures[] = "failures";
+static char __pyx_k_infector[] = "infector";
 static char __pyx_k_probs_nv[] = "probs_nv";
 static char __pyx_k_enumerate[] = "enumerate";
+static char __pyx_k_infectors[] = "infectors";
 static char __pyx_k_n_victims[] = "n_victims";
 static char __pyx_k_successes[] = "successes";
 static char __pyx_k_ValueError[] = "ValueError";
@@ -1263,6 +1292,8 @@ static char __pyx_k_non_victims[] = "non_victims";
 static char __pyx_k_RuntimeError[] = "RuntimeError";
 static char __pyx_k_parent_dists[] = "parent_dists";
 static char __pyx_k_root_victims[] = "root_victims";
+static char __pyx_k_infectors_file[] = "infectors_file";
+static char __pyx_k_Results_infectors_csv[] = "../../Results/infectors.csv";
 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/ml2.pyx";
 static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
@@ -1274,6 +1305,7 @@ static PyObject *__pyx_n_s_DTYPE;
 static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
 static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
 static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor;
+static PyObject *__pyx_kp_s_Results_infectors_csv;
 static PyObject *__pyx_n_s_RuntimeError;
 static PyObject *__pyx_kp_s_Users_ben_Documents_Cascade_Pro;
 static PyObject *__pyx_n_s_ValueError;
@@ -1284,20 +1316,23 @@ 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_end;
+static PyObject *__pyx_n_s_enter;
 static PyObject *__pyx_n_s_enumerate;
+static PyObject *__pyx_n_s_exit;
 static PyObject *__pyx_n_s_failures;
-static PyObject *__pyx_n_s_file;
 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_infector;
+static PyObject *__pyx_n_s_infectors;
+static PyObject *__pyx_n_s_infectors_file;
 static PyObject *__pyx_n_s_itervalues;
+static PyObject *__pyx_n_s_keys;
 static PyObject *__pyx_n_s_l;
 static PyObject *__pyx_n_s_ll;
 static PyObject *__pyx_n_s_lmbda;
 static PyObject *__pyx_n_s_main;
-static PyObject *__pyx_n_s_mean;
 static PyObject *__pyx_n_s_ml2;
 static PyObject *__pyx_n_s_n_roots;
 static PyObject *__pyx_n_s_n_victims;
@@ -1306,10 +1341,12 @@ static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
 static PyObject *__pyx_n_s_non_victims;
 static PyObject *__pyx_n_s_np;
 static PyObject *__pyx_n_s_numpy;
+static PyObject *__pyx_n_s_open;
 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_print;
+static PyObject *__pyx_n_s_prnt;
+static PyObject *__pyx_n_s_prnts;
 static PyObject *__pyx_n_s_prob;
 static PyObject *__pyx_n_s_probs;
 static PyObject *__pyx_n_s_probs_fail;
@@ -1318,20 +1355,21 @@ static PyObject *__pyx_n_s_range;
 static PyObject *__pyx_n_s_root_victims;
 static PyObject *__pyx_n_s_roots;
 static PyObject *__pyx_n_s_s;
+static PyObject *__pyx_kp_s_s_s;
 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_kp_u_unknown_dtype_code_in_numpy_pxd;
 static PyObject *__pyx_n_s_victims;
+static PyObject *__pyx_n_s_w;
 static PyObject *__pyx_n_s_w1;
 static PyObject *__pyx_n_s_w2;
 static PyObject *__pyx_n_s_w3;
+static PyObject *__pyx_n_s_write;
 static PyObject *__pyx_n_s_zeros;
-static PyObject *__pyx_int_1;
-static PyObject *__pyx_int_100;
-static PyObject *__pyx_slice_;
-static PyObject *__pyx_slice__2;
+static PyObject *__pyx_tuple_;
+static PyObject *__pyx_tuple__2;
 static PyObject *__pyx_tuple__3;
 static PyObject *__pyx_tuple__4;
 static PyObject *__pyx_tuple__5;
@@ -1349,7 +1387,7 @@ static PyObject *__pyx_codeobj__10;
  *     """weight for successful infection, exponential time model"""
  */
 
-static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, __pyx_t_3ml2_DTYPE_t __pyx_v_w1, __pyx_t_3ml2_DTYPE_t __pyx_v_w2, __pyx_t_3ml2_DTYPE_t __pyx_v_w3) {
+static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w3) {
   __pyx_t_3ml2_DTYPE_t __pyx_v_structural;
   __pyx_t_3ml2_DTYPE_t __pyx_v_temporal;
   __pyx_t_3ml2_DTYPE_t __pyx_v_result;
@@ -1357,26 +1395,26 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("weight_success", 0);
 
-  /* "ml2.pyx":14
+  /* "ml2.pyx":13
+ *     """weight for successful infection, exponential time model"""
  *     cdef DTYPE_t structural, temporal, result
- *     # structural = delta ** dist
- *     structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))             # <<<<<<<<<<<<<<
+ *     structural = delta ** dist             # <<<<<<<<<<<<<<
+ *     # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
  *     temporal = log(exp(alpha)-1.) - alpha*dt
- *     # temporal = 1 - exp(-alpha*dt)
  */
-  __pyx_v_structural = (__pyx_v_delta / (((1. + (1. / (__pyx_v_w1 * __pyx_v_lmbda))) + (1. / (__pyx_v_w2 * __pyx_v_lmbda))) + (1. / (__pyx_v_w3 * __pyx_v_lmbda))));
+  __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml2_DTYPE_t)__pyx_v_dist));
 
   /* "ml2.pyx":15
- *     # structural = delta ** dist
- *     structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+ *     structural = delta ** dist
+ *     # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
  *     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 = log(structural) + temporal
  */
   __pyx_v_temporal = (log((exp(__pyx_v_alpha) - 1.)) - (__pyx_v_alpha * __pyx_v_dt));
 
-  /* "ml2.pyx":19
- *     # if exp(-alpha*dt)==0.: print 'UNDERFLOW ERROR'
+  /* "ml2.pyx":17
+ *     temporal = log(exp(alpha)-1.) - alpha*dt
  *     # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
  *     result = log(structural) + temporal             # <<<<<<<<<<<<<<
  *     # print 'st', structural, temporal
@@ -1384,7 +1422,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_
  */
   __pyx_v_result = (log(__pyx_v_structural) + __pyx_v_temporal);
 
-  /* "ml2.pyx":21
+  /* "ml2.pyx":19
  *     result = log(structural) + temporal
  *     # print 'st', structural, temporal
  *     return result             # <<<<<<<<<<<<<<
@@ -1408,7 +1446,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_
   return __pyx_r;
 }
 
-/* "ml2.pyx":23
+/* "ml2.pyx":21
  *     return result
  * 
  * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda,             # <<<<<<<<<<<<<<
@@ -1416,7 +1454,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_success(CYTHON_UNUSED int __pyx_
  *     """weight for failed infection, exponential time model"""
  */
 
-static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, __pyx_t_3ml2_DTYPE_t __pyx_v_w1, __pyx_t_3ml2_DTYPE_t __pyx_v_w2, __pyx_t_3ml2_DTYPE_t __pyx_v_w3) {
+static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(int __pyx_v_dist, int __pyx_v_dt, __pyx_t_3ml2_DTYPE_t __pyx_v_alpha, __pyx_t_3ml2_DTYPE_t __pyx_v_delta, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_lmbda, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w1, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w2, CYTHON_UNUSED __pyx_t_3ml2_DTYPE_t __pyx_v_w3) {
   __pyx_t_3ml2_DTYPE_t __pyx_v_structural;
   __pyx_t_3ml2_DTYPE_t __pyx_v_temporal;
   __pyx_t_3ml2_DTYPE_t __pyx_v_result;
@@ -1424,25 +1462,25 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_
   __Pyx_RefNannyDeclarations
   __Pyx_RefNannySetupContext("weight_failure", 0);
 
-  /* "ml2.pyx":28
+  /* "ml2.pyx":25
+ *     """weight for failed infection, exponential time model"""
  *     cdef DTYPE_t structural, temporal, result
- *     # structural = delta ** dist
- *     structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))             # <<<<<<<<<<<<<<
+ *     structural = delta ** dist             # <<<<<<<<<<<<<<
+ *     # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
  *     temporal = exp(-alpha * dt)
- *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
  */
-  __pyx_v_structural = (__pyx_v_delta / (((1. + (1. / (__pyx_v_w1 * __pyx_v_lmbda))) + (1. / (__pyx_v_w2 * __pyx_v_lmbda))) + (1. / (__pyx_v_w3 * __pyx_v_lmbda))));
+  __pyx_v_structural = pow(__pyx_v_delta, ((__pyx_t_3ml2_DTYPE_t)__pyx_v_dist));
 
-  /* "ml2.pyx":29
- *     # structural = delta ** dist
- *     structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+  /* "ml2.pyx":27
+ *     structural = delta ** dist
+ *     # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
  *     temporal = exp(-alpha * dt)             # <<<<<<<<<<<<<<
  *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
  *     result = log(1. - structural + structural * temporal)
  */
   __pyx_v_temporal = exp(((-__pyx_v_alpha) * __pyx_v_dt));
 
-  /* "ml2.pyx":31
+  /* "ml2.pyx":29
  *     temporal = exp(-alpha * dt)
  *     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
  *     result = log(1. - structural + structural * temporal)             # <<<<<<<<<<<<<<
@@ -1451,7 +1489,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_
  */
   __pyx_v_result = log(((1. - __pyx_v_structural) + (__pyx_v_structural * __pyx_v_temporal)));
 
-  /* "ml2.pyx":33
+  /* "ml2.pyx":31
  *     result = log(1. - structural + structural * temporal)
  *     # print 'stnv', structural, temporal
  *     return result             # <<<<<<<<<<<<<<
@@ -1461,7 +1499,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_
   __pyx_r = __pyx_v_result;
   goto __pyx_L0;
 
-  /* "ml2.pyx":23
+  /* "ml2.pyx":21
  *     return result
  * 
  * cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda,             # <<<<<<<<<<<<<<
@@ -1475,7 +1513,7 @@ static __pyx_t_3ml2_DTYPE_t __pyx_f_3ml2_weight_failure(CYTHON_UNUSED int __pyx_
   return __pyx_r;
 }
 
-/* "ml2.pyx":35
+/* "ml2.pyx":33
  *     return result
  * 
  * def ml2(dict root_victims, dict victims, dict non_victims,             # <<<<<<<<<<<<<<
@@ -1523,31 +1561,31 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args,
         case  1:
         if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_victims)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  2:
         if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_non_victims)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  3:
         if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_alpha)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  4:
         if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_delta)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
         case  5:
         if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lmbda)) != 0)) kw_args--;
         else {
-          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+          __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
         }
       }
       if (unlikely(kw_args > 0)) {
-        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml2") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+        if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ml2") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
       }
     } else if (PyTuple_GET_SIZE(__pyx_args) != 6) {
       goto __pyx_L5_argtuple_error;
@@ -1562,21 +1600,21 @@ static PyObject *__pyx_pw_3ml2_1ml2(PyObject *__pyx_self, PyObject *__pyx_args,
     __pyx_v_root_victims = ((PyObject*)values[0]);
     __pyx_v_victims = ((PyObject*)values[1]);
     __pyx_v_non_victims = ((PyObject*)values[2]);
-    __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-    __pyx_v_delta = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
-    __pyx_v_lmbda = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_lmbda == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_alpha = __pyx_PyFloat_AsDouble(values[3]); if (unlikely((__pyx_v_alpha == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_delta = __pyx_PyFloat_AsDouble(values[4]); if (unlikely((__pyx_v_delta == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+    __pyx_v_lmbda = __pyx_PyFloat_AsDouble(values[5]); if (unlikely((__pyx_v_lmbda == (npy_double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
   }
   goto __pyx_L4_argument_unpacking_done;
   __pyx_L5_argtuple_error:;
-  __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+  __Pyx_RaiseArgtupleInvalid("ml2", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
   __pyx_L3_error:;
   __Pyx_AddTraceback("ml2.ml2", __pyx_clineno, __pyx_lineno, __pyx_filename);
   __Pyx_RefNannyFinishContext();
   return NULL;
   __pyx_L4_argument_unpacking_done:;
-  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_root_victims), (&PyDict_Type), 1, "root_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_victims), (&PyDict_Type), 1, "victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_non_victims), (&PyDict_Type), 1, "non_victims", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_r = __pyx_pf_3ml2_ml2(__pyx_self, __pyx_v_root_victims, __pyx_v_victims, __pyx_v_non_victims, __pyx_v_alpha, __pyx_v_delta, __pyx_v_lmbda);
 
   /* function exit code */
@@ -1605,13 +1643,20 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   PyArrayObject *__pyx_v_probs_nv = 0;
   PyArrayObject *__pyx_v_parent_dists = 0;
   PyArrayObject *__pyx_v_parent_dts = 0;
+  PyArrayObject *__pyx_v_infectors = 0;
   PyObject *__pyx_v_dists = NULL;
   PyObject *__pyx_v_dts = NULL;
+  PyObject *__pyx_v_prnts = NULL;
   PyObject *__pyx_v_s = NULL;
   PyObject *__pyx_v_prob = NULL;
+  PyObject *__pyx_v_infectors_file = NULL;
+  PyObject *__pyx_v_infector = NULL;
+  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_infectors;
+  __Pyx_Buffer __pyx_pybuffer_infectors;
   __Pyx_LocalBuf_ND __pyx_pybuffernd_parent_dists;
   __Pyx_Buffer __pyx_pybuffer_parent_dists;
   __Pyx_LocalBuf_ND __pyx_pybuffernd_parent_dts;
@@ -1635,29 +1680,39 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
   PyArrayObject *__pyx_t_9 = NULL;
   PyArrayObject *__pyx_t_10 = NULL;
   PyArrayObject *__pyx_t_11 = NULL;
-  int __pyx_t_12;
+  PyArrayObject *__pyx_t_12 = NULL;
   int __pyx_t_13;
   int __pyx_t_14;
-  Py_ssize_t __pyx_t_15;
-  PyObject *__pyx_t_16 = NULL;
+  int __pyx_t_15;
+  Py_ssize_t __pyx_t_16;
   PyObject *__pyx_t_17 = NULL;
   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;
-  __pyx_t_3ml2_DTYPE_t __pyx_t_24;
-  __pyx_t_3ml2_DTYPE_t __pyx_t_25;
+  PyObject *__pyx_t_22 = NULL;
+  PyObject *__pyx_t_23 = NULL;
+  PyObject *(*__pyx_t_24)(PyObject *);
+  int __pyx_t_25;
   __pyx_t_3ml2_DTYPE_t __pyx_t_26;
-  int __pyx_t_27;
-  double __pyx_t_28;
+  __pyx_t_3ml2_DTYPE_t __pyx_t_27;
+  __pyx_t_3ml2_DTYPE_t __pyx_t_28;
   int __pyx_t_29;
-  int __pyx_t_30;
+  double __pyx_t_30;
   int __pyx_t_31;
   int __pyx_t_32;
   int __pyx_t_33;
   int __pyx_t_34;
+  int __pyx_t_35;
+  int __pyx_t_36;
+  int __pyx_t_37;
+  PyObject *__pyx_t_38 = NULL;
+  PyObject *__pyx_t_39 = NULL;
+  PyObject *__pyx_t_40 = NULL;
+  PyObject *__pyx_t_41 = NULL;
+  PyObject *(*__pyx_t_42)(PyObject *);
+  PyObject *__pyx_t_43 = NULL;
+  int __pyx_t_44;
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
@@ -1682,8 +1737,12 @@ static PyObject *__pyx_pf_3ml2_ml2(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_infectors.pybuffer.buf = NULL;
+  __pyx_pybuffer_infectors.refcount = 0;
+  __pyx_pybuffernd_infectors.data = NULL;
+  __pyx_pybuffernd_infectors.rcbuffer = &__pyx_pybuffer_infectors;
 
-  /* "ml2.pyx":41
+  /* "ml2.pyx":39
  *         DTYPE_t ll
  *         list parents, failures, successes
  *     n_roots, n_victims = len(root_victims), len(victims)             # <<<<<<<<<<<<<<
@@ -1692,54 +1751,54 @@ static PyObject *__pyx_pf_3ml2_ml2(CYTHON_UNUSED PyObject *__pyx_self, PyObject
  */
   if (unlikely(__pyx_v_root_victims == Py_None)) {
     PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
-  __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_1 = PyDict_Size(__pyx_v_root_victims); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (unlikely(__pyx_v_victims == Py_None)) {
     PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
-    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   }
-  __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = PyDict_Size(__pyx_v_victims); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_v_n_roots = __pyx_t_1;
   __pyx_v_n_victims = __pyx_t_2;
 
-  /* "ml2.pyx":43
+  /* "ml2.pyx":41
  *     n_roots, n_victims = len(root_victims), len(victims)
  *     cdef:
  *         np.ndarray[DTYPE_t] probs = np.zeros(n_victims, dtype=DTYPE)             # <<<<<<<<<<<<<<
  *         np.ndarray[DTYPE_t] probs_fail = np.zeros(n_victims, dtype=DTYPE)
  *         np.ndarray[DTYPE_t] probs_nv = np.zeros(len(non_victims), dtype=DTYPE)
  */
-  __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_4);
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
-  __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n_victims); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_5);
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- *     print parent_dts[1:100]
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+  /* "ml2.pyx":94
+ *     # print np.mean(parent_dts)
+ * 
+ *     with open('../../Results/infectors.csv', 'w') as infectors_file:             # <<<<<<<<<<<<<<
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- *     print np.mean(parent_dists)
- *     print np.mean(parent_dts)
+          /* "ml2.pyx":95
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- *     print parent_dts[1:100]
- *     print np.mean(parent_dists)             # <<<<<<<<<<<<<<
- *     print np.mean(parent_dts)
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+ *         for i, infector in enumerate(infectors):
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   __Pyx_XDECREF((PyObject *)__pyx_v_parent_dists);
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- *     print np.mean(parent_dists)
- */
-  __pyx_slice_ = PySlice_New(__pyx_int_1, __pyx_int_100, Py_None); if (unlikely(!__pyx_slice_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_slice_);
-  __Pyx_GIVEREF(__pyx_slice_);
-
-  /* "ml2.pyx":87
- *     # print n_nodes, n_roots, n_victims, max_i, roots
- *     print parent_dists[1:100]
- *     print parent_dts[1:100]             # <<<<<<<<<<<<<<
- *     print np.mean(parent_dists)
- *     print np.mean(parent_dts)
+  /* "ml2.pyx":94
+ *     # print np.mean(parent_dts)
+ * 
+ *     with open('../../Results/infectors.csv', 'w') as infectors_file:             # <<<<<<<<<<<<<<
+ *         for i, infector in enumerate(infectors):
+ *             infectors_file.write("%s, %s\n" % ((victims.keys())[i], infector))
  */
-  __pyx_slice__2 = PySlice_New(__pyx_int_1, __pyx_int_100, Py_None); if (unlikely(!__pyx_slice__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __Pyx_GOTREF(__pyx_slice__2);
-  __Pyx_GIVEREF(__pyx_slice__2);
+  __pyx_tuple_ = PyTuple_Pack(2, __pyx_kp_s_Results_infectors_csv, __pyx_n_s_w); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple_);
+  __Pyx_GIVEREF(__pyx_tuple_);
+  __pyx_tuple__2 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __Pyx_GOTREF(__pyx_tuple__2);
+  __Pyx_GIVEREF(__pyx_tuple__2);
 
   /* "../../../../Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218
  *             if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
@@ -5263,17 +5672,17 @@ static int __Pyx_InitCachedConstants(void) {
   __Pyx_GOTREF(__pyx_tuple__8);
   __Pyx_GIVEREF(__pyx_tuple__8);
 
-  /* "ml2.pyx":35
+  /* "ml2.pyx":33
  *     return result
  * 
  * def ml2(dict root_victims, dict victims, dict non_victims,             # <<<<<<<<<<<<<<
  *        DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda):
  *     cdef:
  */
-  __pyx_tuple__9 = PyTuple_Pack(30, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_lmbda, __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_ll, __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_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_tuple__9 = PyTuple_Pack(35, __pyx_n_s_root_victims, __pyx_n_s_victims, __pyx_n_s_non_victims, __pyx_n_s_alpha, __pyx_n_s_delta, __pyx_n_s_lmbda, __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_ll, __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_parent_dists, __pyx_n_s_parent_dts, __pyx_n_s_infectors, __pyx_n_s_dists, __pyx_n_s_dts, __pyx_n_s_prnts, __pyx_n_s_s, __pyx_n_s_prob, __pyx_n_s_infectors_file, __pyx_n_s_infector, __pyx_n_s_prnt, __pyx_n_s_w1, __pyx_n_s_w2, __pyx_n_s_w3); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_tuple__9);
   __Pyx_GIVEREF(__pyx_tuple__9);
-  __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(6, 0, 30, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml2, 35, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(6, 0, 35, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_ben_Documents_Cascade_Pro, __pyx_n_s_ml2, 33, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_RefNannyFinishContext();
   return 0;
   __pyx_L1_error:;
@@ -5283,8 +5692,6 @@ 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_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;}
-  __pyx_int_100 = PyInt_FromLong(100); if (unlikely(!__pyx_int_100)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   return 0;
   __pyx_L1_error:;
   return -1;
@@ -5414,16 +5821,16 @@ PyMODINIT_FUNC PyInit_ml2(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;
 
-  /* "ml2.pyx":35
+  /* "ml2.pyx":33
  *     return result
  * 
  * def ml2(dict root_victims, dict victims, dict non_victims,             # <<<<<<<<<<<<<<
  *        DTYPE_t alpha, DTYPE_t delta, DTYPE_t lmbda):
  *     cdef:
  */
-  __pyx_t_2 = PyCFunction_NewEx(&__pyx_mdef_3ml2_1ml2, NULL, __pyx_n_s_ml2); 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_3ml2_1ml2, NULL, __pyx_n_s_ml2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_2);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s_ml2, __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_ml2, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
 
   /* "ml2.pyx":1
@@ -6671,101 +7078,130 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
     return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
 }
 
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
-        PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
-        PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
-        int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
+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
-    PyMappingMethods* mp;
-#if PY_MAJOR_VERSION < 3
-    PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
-    if (likely(ms && ms->sq_slice)) {
-        if (!has_cstart) {
-            if (_py_start && (*_py_start != Py_None)) {
-                cstart = __Pyx_PyIndex_AsSsize_t(*_py_start);
-                if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
-            } else
-                cstart = 0;
-        }
-        if (!has_cstop) {
-            if (_py_stop && (*_py_stop != Py_None)) {
-                cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop);
-                if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
-            } else
-                cstop = PY_SSIZE_T_MAX;
-        }
-        if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
-            Py_ssize_t l = ms->sq_length(obj);
-            if (likely(l >= 0)) {
-                if (cstop < 0) {
-                    cstop += l;
-                    if (cstop < 0) cstop = 0;
-                }
-                if (cstart < 0) {
-                    cstart += l;
-                    if (cstart < 0) cstart = 0;
-                }
-            } else {
-                if (PyErr_ExceptionMatches(PyExc_OverflowError))
-                    PyErr_Clear();
-                else
-                    goto bad;
-            }
+    if (likely(PyMethod_Check(method))) {
+        PyObject *self = PyMethod_GET_SELF(method);
+        if (likely(self)) {
+            PyObject *args;
+            PyObject *function = PyMethod_GET_FUNCTION(method);
+            args = PyTuple_New(2);
+            if (unlikely(!args)) goto bad;
+            Py_INCREF(self);
+            PyTuple_SET_ITEM(args, 0, self);
+            Py_INCREF(arg);
+            PyTuple_SET_ITEM(args, 1, arg);
+            Py_INCREF(function);
+            Py_DECREF(method); method = NULL;
+            result = __Pyx_PyObject_Call(function, args, NULL);
+            Py_DECREF(args);
+            Py_DECREF(function);
+            return result;
         }
-        return ms->sq_slice(obj, cstart, cstop);
     }
 #endif
-    mp = Py_TYPE(obj)->tp_as_mapping;
-    if (likely(mp && mp->mp_subscript))
+    result = __Pyx_PyObject_CallOneArg(method, arg);
+bad:
+    Py_XDECREF(method);
+    return result;
+}
+
+static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d) {
+    if (PY_MAJOR_VERSION >= 3)
+        return __Pyx_PyObject_CallMethod1((PyObject*)&PyDict_Type, __pyx_n_s_keys, d);
+    else
+        return PyDict_Keys(d);
+}
+
+static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
+    PyThreadState *tstate = PyThreadState_GET();
+    *type = tstate->exc_type;
+    *value = tstate->exc_value;
+    *tb = tstate->exc_traceback;
+    Py_XINCREF(*type);
+    Py_XINCREF(*value);
+    Py_XINCREF(*tb);
+#else
+    PyErr_GetExcInfo(type, value, tb);
 #endif
-    {
-        PyObject* result;
-        PyObject *py_slice, *py_start, *py_stop;
-        if (_py_slice) {
-            py_slice = *_py_slice;
-        } else {
-            PyObject* owned_start = NULL;
-            PyObject* owned_stop = NULL;
-            if (_py_start) {
-                py_start = *_py_start;
-            } else {
-                if (has_cstart) {
-                    owned_start = py_start = PyInt_FromSsize_t(cstart);
-                    if (unlikely(!py_start)) goto bad;
-                } else
-                    py_start = Py_None;
-            }
-            if (_py_stop) {
-                py_stop = *_py_stop;
-            } else {
-                if (has_cstop) {
-                    owned_stop = py_stop = PyInt_FromSsize_t(cstop);
-                    if (unlikely(!py_stop)) {
-                        Py_XDECREF(owned_start);
-                        goto bad;
-                    }
-                } else
-                    py_stop = Py_None;
-            }
-            py_slice = PySlice_New(py_start, py_stop, Py_None);
-            Py_XDECREF(owned_start);
-            Py_XDECREF(owned_stop);
-            if (unlikely(!py_slice)) goto bad;
-        }
+}
+static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
 #if CYTHON_COMPILING_IN_CPYTHON
-        result = mp->mp_subscript(obj, py_slice);
+    PyObject *tmp_type, *tmp_value, *tmp_tb;
+    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;
+    Py_XDECREF(tmp_type);
+    Py_XDECREF(tmp_value);
+    Py_XDECREF(tmp_tb);
 #else
-        result = PyObject_GetItem(obj, py_slice);
+    PyErr_SetExcInfo(type, value, tb);
 #endif
-        if (!_py_slice) {
-            Py_DECREF(py_slice);
-        }
-        return result;
+}
+
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
+    PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
+    PyObject *tmp_type, *tmp_value, *tmp_tb;
+    PyThreadState *tstate = PyThreadState_GET();
+    local_type = tstate->curexc_type;
+    local_value = tstate->curexc_value;
+    local_tb = tstate->curexc_traceback;
+    tstate->curexc_type = 0;
+    tstate->curexc_value = 0;
+    tstate->curexc_traceback = 0;
+#else
+    PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
+    PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
+    if (unlikely(tstate->curexc_type))
+#else
+    if (unlikely(PyErr_Occurred()))
+#endif
+        goto bad;
+    #if PY_MAJOR_VERSION >= 3
+    if (local_tb) {
+        if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+            goto bad;
     }
-    PyErr_Format(PyExc_TypeError,
-        "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
+    #endif
+    Py_XINCREF(local_tb);
+    Py_XINCREF(local_type);
+    Py_XINCREF(local_value);
+    *type = local_type;
+    *value = local_value;
+    *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
+    tmp_type = tstate->exc_type;
+    tmp_value = tstate->exc_value;
+    tmp_tb = tstate->exc_traceback;
+    tstate->exc_type = local_type;
+    tstate->exc_value = local_value;
+    tstate->exc_traceback = local_tb;
+    Py_XDECREF(tmp_type);
+    Py_XDECREF(tmp_value);
+    Py_XDECREF(tmp_tb);
+#else
+    PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
+    return 0;
 bad:
-    return NULL;
+    *type = 0;
+    *value = 0;
+    *tb = 0;
+    Py_XDECREF(local_type);
+    Py_XDECREF(local_value);
+    Py_XDECREF(local_tb);
+    return -1;
 }
 
 static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
@@ -7351,147 +7787,6 @@ raise_neg_overflow:
     return (int) -1;
 }
 
-#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3
-static PyObject *__Pyx_GetStdout(void) {
-    PyObject *f = PySys_GetObject((char *)"stdout");
-    if (!f) {
-        PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout");
-    }
-    return f;
-}
-static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) {
-    int i;
-    if (!f) {
-        if (!(f = __Pyx_GetStdout()))
-            return -1;
-    }
-    Py_INCREF(f);
-    for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) {
-        PyObject* v;
-        if (PyFile_SoftSpace(f, 1)) {
-            if (PyFile_WriteString(" ", f) < 0)
-                goto error;
-        }
-        v = PyTuple_GET_ITEM(arg_tuple, i);
-        if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0)
-            goto error;
-        if (PyString_Check(v)) {
-            char *s = PyString_AsString(v);
-            Py_ssize_t len = PyString_Size(v);
-            if (len > 0) {
-                switch (s[len-1]) {
-                    case ' ': break;
-                    case '\f': case '\r': case '\n': case '\t': case '\v':
-                        PyFile_SoftSpace(f, 0);
-                        break;
-                    default:  break;
-                }
-            }
-        }
-    }
-    if (newline) {
-        if (PyFile_WriteString("\n", f) < 0)
-            goto error;
-        PyFile_SoftSpace(f, 0);
-    }
-    Py_DECREF(f);
-    return 0;
-error:
-    Py_DECREF(f);
-    return -1;
-}
-#else
-static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) {
-    PyObject* kwargs = 0;
-    PyObject* result = 0;
-    PyObject* end_string;
-    if (unlikely(!__pyx_print)) {
-        __pyx_print = PyObject_GetAttr(__pyx_b, __pyx_n_s_print);
-        if (!__pyx_print)
-            return -1;
-    }
-    if (stream) {
-        kwargs = PyDict_New();
-        if (unlikely(!kwargs))
-            return -1;
-        if (unlikely(PyDict_SetItem(kwargs, __pyx_n_s_file, stream) < 0))
-            goto bad;
-        if (!newline) {
-            end_string = PyUnicode_FromStringAndSize(" ", 1);
-            if (unlikely(!end_string))
-                goto bad;
-            if (PyDict_SetItem(kwargs, __pyx_n_s_end, end_string) < 0) {
-                Py_DECREF(end_string);
-                goto bad;
-            }
-            Py_DECREF(end_string);
-        }
-    } else if (!newline) {
-        if (unlikely(!__pyx_print_kwargs)) {
-            __pyx_print_kwargs = PyDict_New();
-            if (unlikely(!__pyx_print_kwargs))
-                return -1;
-            end_string = PyUnicode_FromStringAndSize(" ", 1);
-            if (unlikely(!end_string))
-                return -1;
-            if (PyDict_SetItem(__pyx_print_kwargs, __pyx_n_s_end, end_string) < 0) {
-                Py_DECREF(end_string);
-                return -1;
-            }
-            Py_DECREF(end_string);
-        }
-        kwargs = __pyx_print_kwargs;
-    }
-    result = PyObject_Call(__pyx_print, arg_tuple, kwargs);
-    if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs))
-        Py_DECREF(kwargs);
-    if (!result)
-        return -1;
-    Py_DECREF(result);
-    return 0;
-bad:
-    if (kwargs != __pyx_print_kwargs)
-        Py_XDECREF(kwargs);
-    return -1;
-}
-#endif
-
-#if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION < 3
-static int __Pyx_PrintOne(PyObject* f, PyObject *o) {
-    if (!f) {
-        if (!(f = __Pyx_GetStdout()))
-            return -1;
-    }
-    Py_INCREF(f);
-    if (PyFile_SoftSpace(f, 0)) {
-        if (PyFile_WriteString(" ", f) < 0)
-            goto error;
-    }
-    if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0)
-        goto error;
-    if (PyFile_WriteString("\n", f) < 0)
-        goto error;
-    Py_DECREF(f);
-    return 0;
-error:
-    Py_DECREF(f);
-    return -1;
-    /* the line below is just to avoid C compiler
-     * warnings about unused functions */
-    return __Pyx_Print(f, NULL, 0);
-}
-#else
-static int __Pyx_PrintOne(PyObject* stream, PyObject *o) {
-    int res;
-    PyObject* arg_tuple = PyTuple_Pack(1, o);
-    if (unlikely(!arg_tuple))
-        return -1;
-    res = __Pyx_Print(stream, arg_tuple, 1);
-    Py_DECREF(arg_tuple);
-    return res;
-}
-#endif
-
 #if CYTHON_CCOMPLEX
   #ifdef __cplusplus
     static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
diff --git a/experiments/ml2.pyx b/experiments/ml2.pyx
index 99c9784..dd0e7a8 100644
--- a/experiments/ml2.pyx
+++ b/experiments/ml2.pyx
@@ -10,8 +10,8 @@ cdef DTYPE_t weight_success(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYP
                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
     """weight for successful infection, exponential time model"""
     cdef DTYPE_t structural, temporal, result
-    # structural = delta ** dist
-    structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+    structural = delta ** dist
+    # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
     temporal = log(exp(alpha)-1.) - alpha*dt
     # temporal = 1. / (1. + (dt - 1.)/alpha)**0.01 - 1. / (1. + dt/alpha)**0.01
     result = log(structural) + temporal
@@ -22,8 +22,8 @@ cdef DTYPE_t weight_failure(int dist, int dt, DTYPE_t alpha, DTYPE_t delta, DTYP
                             DTYPE_t w1, DTYPE_t w2, DTYPE_t w3):
     """weight for failed infection, exponential time model"""
     cdef DTYPE_t structural, temporal, result
-    # structural = delta ** dist
-    structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
+    structural = delta ** dist
+    # structural = delta/(1. + 1./(w1*lmbda) + 1./(w2*lmbda) + 1./(w3*lmbda))
     temporal = exp(-alpha * dt)
     # temporal = 1.  - 1. / (1. + dt/alpha)**0.01
     result = log(1. - structural + structural * temporal)
@@ -43,6 +43,7 @@ def ml2(dict root_victims, dict victims, dict non_victims,
         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)
+        np.ndarray[DTYPE_t] infectors = np.zeros(n_victims, dtype=DTYPE)
 
     # loop through victims
     for i, parents in enumerate(victims.itervalues()):
@@ -50,12 +51,13 @@ def ml2(dict root_victims, dict victims, dict non_victims,
         # fail to infect it, also computes the probability that its most
         # likely parent infects it
         failures = [weight_failure(dist, dt, alpha, delta, lmbda, 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, lmbda, 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]
+                     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]
+        prnts = [prnt 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")
@@ -63,6 +65,7 @@ def ml2(dict root_victims, dict victims, dict non_victims,
             prob = s - failures[l]
             if prob > probs[i]:
                 probs[i] = prob
+                infectors[i] = prnts[l]
                 parent_dists[i] = dists[l]
                 parent_dts[i] = dts[l]
 
@@ -71,7 +74,7 @@ def ml2(dict root_victims, dict victims, dict non_victims,
         # for each non victim node, compute the probability that all its
         # parents fail to infect it
         failures = [weight_failure(dist, dt, alpha, delta, lmbda, 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)
 
     # calculate log likelihood
@@ -81,8 +84,14 @@ def ml2(dict root_victims, dict victims, dict non_victims,
 
     roots = n_roots
     # print n_nodes, n_roots, n_victims, max_i, roots
-    print parent_dists[1:100]
-    print parent_dts[1:100]
-    print np.mean(parent_dists)
-    print np.mean(parent_dts)
+    # print parent_dists[1:100]
+    # print parent_dts[1:100]
+    # print victims.keys()
+    # print infectors
+    # print np.mean(parent_dists)
+    # print np.mean(parent_dts)
+    
+    with open('../../Results/infectors.csv', 'w') as infectors_file:
+        for i, infector in enumerate(infectors):
+            infectors_file.write("%s, %s\n" % ((victims.keys())[i], infector))
     return (lmbda, roots, ll)
diff --git a/experiments/ml2.so b/experiments/ml2.so
index b8c850b..162e007 100755
--- a/experiments/ml2.so
+++ b/experiments/ml2.so
diff --git a/experiments/out.log b/experiments/out.log
index dbc6e69..b6cddf7 100644
--- a/experiments/out.log
+++ b/experiments/out.log
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+0.061	0.108	0.1	8	-2531.65938685
+0.061	0.109	0.1	8	-2532.39176436
+0.061	0.11	0.1	8	-2533.20369902
+0.062	0.09	0.1	8	-2534.71548033
+0.062	0.091	0.1	8	-2533.91116631
+0.062	0.092	0.1	8	-2533.19906476
+0.062	0.093	0.1	8	-2532.57821314
+0.062	0.094	0.1	8	-2532.04768661
+0.062	0.095	0.1	8	-2531.60659646
+0.062	0.096	0.1	8	-2531.25408859
+0.062	0.097	0.1	8	-2530.98934213
+0.062	0.098	0.1	8	-2530.81156803
+0.062	0.099	0.1	8	-2530.72000778
+0.062	0.1	0.1	8	-2530.71393224
+0.062	0.101	0.1	8	-2530.79264044
+0.062	0.102	0.1	8	-2530.95545849
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diff --git a/experiments/process.py b/experiments/process.py
index 9ea2e81..5f3cff4 100644
--- a/experiments/process.py
+++ b/experiments/process.py
@@ -15,22 +15,22 @@ 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(-3,0,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(1e-3, 1e-2, 8e-4)  # parameter of the time component
-    # alphas = np.logspace(-4,-1.5,num=20)
+    # alphas = np.logspace(-3,0,num=15)
     # # deltas = np.arange(0.001, 0.3, 0.008)  # parameter of the structural component
-    # deltas = np.logspace(-4,-2,num=20)
-    # lmbda = 1.#np.logspace(-12,-3,num=10)
+    # 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(.03, .065, .001)  # parameter of the time component
+    # # alphas = np.logspace(-4,-1,num=20)
+    # deltas = np.arange(.09, .11, .001)  # parameter of the structural component
+    # # deltas = np.logspace(-2,-.5,num=20)
+    # 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)
@@ -38,7 +38,7 @@ if __name__ == "__main__":
     #         fh.write("\t".join(map(str, [alpha, delta, lmbda, roots, ll])) + "\n")
     #         fh.flush()
 
-    # alpha = 0.0094
-    # delta = 0.0048
-    # beta, roots, ll = ml2(root_victims, victims, non_victims, alpha, delta, 1.)
-    # print "\t".join(map(str, [alpha, delta, beta, roots, ll]))
\ No newline at end of file
+    alpha = 0.041
+    delta = 0.01
+    beta, roots, ll = ml2(root_victims, victims, non_victims, alpha, delta, 1.)
+    print "\t".join(map(str, [alpha, delta, beta, roots, ll]))
\ No newline at end of file