added a greedy algorithm, a pruning procedure to remove 1-1-pairs

README.md

@@ -8,10 +8,40 @@ First things first, install the required libraries:
 pip install -r requirements.txt
 ```
 
-Now, try:
+To warm up, try:
 ```python
-python is_simplicial.py -k degs.txt -s sizes.txt
+python is_simplicial.py -k datasets/00_degs.txt -s datasets/00_sizes.txt
 ```
+By running the snippet several times, you may notice that the algorithm is not deterministic. 
+Indeed, we are building the state space tree with the backtracking algorithm, 
+and therefore sampling the ensemble that satisfies the joint degree sequence
+(defined by `00_degs.txt` & `00_sizes.txt`). In other words, the joint sequence is simplicial!
 
-It should tell you that the joint degree sequence defined by `degs.txt` & `sizes.txt` is simplicial! 
-However, currently, the code only works for very small systems.   
+The backtracking algorithm is an exhaustive search; 
+that is, all feasible solutions are considered and it will always find the optimal solution. 
+This means that, unfortunately, our sampling algorithm only works for very small systems.  
+
+We still lack a proper existence test to check whether a joint sequence is simplicial. 
+Luckily, when the sequence is simplicial, 
+we do find a greedy deterministic algorithm that picks up an simplicial instance! 
+This can work in fairly large inputs.
+
+For example,   
+```python
+python is_simplicial.py -k datasets/01_degs.txt -s datasets/01_sizes.txt --greedy
+```
+The dataset is the [crime network dataset](https://github.com/jg-you/scm/blob/master/datasets/crime_facet_list.txt)
+from the [Phys. Rev. E paper](https://doi.org/10.1103/PhysRevE.96.032312), having 551 nodes and 194 facets. 
+
+Moreover, we find that the greedy algorithm can go with two directions,
+and sometimes only the "backward direction" work.
+
+For example,
+```python
+python is_simplicial.py -k datasets/02_degs.txt -s datasets/02_sizes.txt --greedy --no-forward
+``` 
+
+Interesting? I think it is!
+
+## MISC notes (to clean up later)
+* The graphical [Erdős–Gallai theorem](https://en.wikipedia.org/wiki/Erd%C5%91s%E2%80%93Gallai_theorem). 

SimplicialTest.py

@@ -35,6 +35,25 @@ def log_forbidden(self, name, reason_id):
         }
 
 
+def prune_ones(size_list, degree_list):
+    _1 = count_summary(size_list)[1]
+    _2 = count_summary(degree_list)[1]
+    if _1 > _2:
+        print("Too many 0-simplices. We cannot satisfy the inclusive constraint.")
+    else:
+        for _ in range(_1):
+            size_list.remove(1)
+            degree_list.remove(1)
+    return size_list, degree_list
+
+
+def count_summary(seq):
+    d = defaultdict(int)
+    for s in seq:
+        d[s] += 1
+    return d
+
+
 class SimplicialTest(SimplexRegistrar):
     """Base class for SimplicialCheck.
 
@@ -80,12 +99,15 @@ def update_deg_seq(self, facet, value):
     def checkpoint_1(self):
         return np.all(np.sort(self.degree_list) - np.sort(self.deg_seq) >= 0)
 
-    def _break_symmetry(self):
+    def _break_symmetry(self, greedy=False, forward=True):
         m = self.sorted_s.pop(0)
-        picked_facet, picked_facet_id = self.register(random.sample(range(self.n), k=m))
+        if greedy:
+            picked_facet, picked_facet_id = self.sample_simplex_greedy([], m, forward=forward)
+        else:
+            picked_facet, picked_facet_id = self.register(random.sample(range(self.n), k=m))
         self.update_deg_seq(picked_facet, +1)
         identifier = [picked_facet_id]
-        self.symmetry_breaker = picked_facet_id  # Actually, `picked_facet_id` is always 0 here.
+        self.symmetry_breaker = picked_facet_id
         return identifier
 
     def ensure_valid_draw(self, identifier, size):
@@ -105,25 +127,70 @@ def ensure_valid_draw(self, identifier, size):
 
         pass
 
-    @staticmethod
-    def count_summary(seq):
-        d = defaultdict(int)
-        for s in seq:
-            d[s] += 1
-        return d
+    def sample_simplex_greedy(self, identifier, size, forward=True):
+        deg = self.compute_joint_seq_from_identifier(identifier, sorted_deg=False)[1]
+        larger_selected_simplex_ids = self.get_selected_facet_ids(identifier, size)
+
+        candidate_facet = []
+
+        if forward:
+            shift = 0
+            while len(candidate_facet) < size:
+                if shift >= self.n:
+                    print("This sequence may not be simplicial.")
+                    raise NotImplementedError
+
+                # print(candidate_facet, shift)
+                if len(candidate_facet) == size - 1:  # the last vertex to choose
+                    for _id in larger_selected_simplex_ids:
+                        while set(candidate_facet + [shift]).issubset(set(self.id2name[_id])):
+                            shift += 1
+                            continue
+                # print(deg, self._sorted_d, shift, candidate_facet)
+                if deg[shift] + 1 <= self._sorted_d[shift]:
+                    candidate_facet += [shift]
+                shift += 1
+        else:
+            shift = self.n - 1
+            while len(candidate_facet) < size:
+                if shift < 0:
+                    print("This sequence may not be simplicial.")
+                    raise NotImplementedError
+
+                # print(candidate_facet, shift)
+                if len(candidate_facet) == size - 1:  # the last vertex to choose
+                    for _id in larger_selected_simplex_ids:
+                        while set(candidate_facet + [shift]).issubset(set(self.id2name[_id])):
+                            shift -= 1
+                            continue
+                # print(deg, self._sorted_d, shift, candidate_facet)
+                if deg[shift] + 1 <= self._sorted_d[shift]:
+                    candidate_facet += [shift]
+                shift -= 1
+        picked_facet, picked_facet_id = self.register(candidate_facet)
+        # print(picked_facet, picked_facet_id)
+        return picked_facet, picked_facet_id
 
-    def sample_simplex(self, identifier, size):
+    def get_selected_facet_ids(self, identifier, size):
+        return [index for index, i in enumerate(self.facet_size_per_id) if (index in identifier and i >= size)]
+
+    def sample_simplex(self, identifier, size, greedy=False, forward=True):
         """
 
         Parameters
         ----------
         identifier
         size
+        greedy
+        forward
 
         Returns
         -------
 
         """
+        if greedy:
+            return self.sample_simplex_greedy(identifier, size, forward=forward)
+
         # Here, we have a good criterion! We may not need to explore further if...
         deg_sequence = np.array(self.compute_joint_seq_from_identifier(identifier)[1])
         deg_sequence_goal = self._sorted_d
@@ -136,8 +203,7 @@ def sample_simplex(self, identifier, size):
             self._backtrack_steps = 1
             return list(), -1
 
-        larger_selected_simplex_ids = [index for index, i in enumerate(self.facet_size_per_id) if
-                                       (index in identifier and i >= size)]
+        larger_selected_simplex_ids = self.get_selected_facet_ids(identifier, size)
 
         set_of_vertices = set(range(self.n))
         picked_facet, picked_facet_id = self.register(random.sample(list(set_of_vertices), k=size))
@@ -168,7 +234,7 @@ def sample_simplex(self, identifier, size):
 
         return picked_facet, picked_facet_id
 
-    def is_simplicial(self):
+    def is_simplicial(self, greedy=False, forward=True):
         if max(self.degree_list) > self.m:
             print("1. This can never be simplicial.")  # TODO.... why??
             return False
@@ -180,7 +246,7 @@ def is_simplicial(self):
             return False
         # TODO: there is a second part of the GR criterion, which is not coded yet.
 
-        identifier = self._break_symmetry()
+        identifier = self._break_symmetry(greedy=greedy, forward=forward)
         if len(self.sorted_s) == 0:
             if sorted(self.deg_seq, reverse=True) == self._sorted_d:  # TODO: start from identifier
                 self.identifier = identifier
@@ -192,7 +258,7 @@ def is_simplicial(self):
             if len(self.logbook) == self._len_logbook:
                 self._counter += 1
             s = self.sorted_s.pop(0)
-            picked_facet, picked_facet_id = self.sample_simplex(identifier, s)
+            picked_facet, picked_facet_id = self.sample_simplex(identifier, s, greedy=greedy, forward=forward)
             if len(picked_facet) == 0:
                 self.sorted_s = [s] + self.sorted_s
                 self._pull_the_plug(identifier, self._backtrack_steps)

datasets/01_degs.txt

@@ -0,0 +1 @@
+1 1 1 2 1 1 1 1 1 1 1 1 1 5 1 1 1 1 1 1 2 1 4 2 1 1 1 1 1 1 1 2 1 2 1 1 1 1 8 3 1 1 2 1 2 6 5 2 2 1 1 3 2 1 2 1 1 2 3 1 1 1 1 1 1 1 1 2 1 2 2 4 1 1 4 1 3 1 1 1 4 2 1 1 1 1 1 1 1 3 2 1 1 3 7 2 1 2 1 1 2 2 1 2 1 1 2 2 2 14 1 3 1 1 2 1 4 1 3 1 1 1 1 2 2 2 1 1 2 2 2 2 2 2 2 1 1 1 1 3 1 1 1 1 1 3 1 2 1 1 2 1 2 1 2 2 1 2 1 3 1 1 1 1 1 1 2 1 3 1 1 1 3 2 1 1 2 1 1 1 1 1 2 1 3 1 1 2 5 1 1 1 2 2 2 3 2 2 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 2 1 2 2 1 1 1 1 1 1 1 1 2 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 2 2 1 2 1 1 2 1 2 1 1 2 1 1 2 4 2 1 3 2 1 1 1 1 1 1 3 1 1 3 2 1 2 1 2 1 3 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 2 2 4 2 1 1 2 2 1 2 1 1 1 2 1 3 1 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 2 2 1 1 2 3 3 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 1 1 1 1 1 1 1 2 1 1 1 1 1 1 2 2 1 1 2 2 1 1 1 1 1 1 1 2 1 1 1 1 2 2 1 2 2 1 1 1 1 2 1 1 2 1 2 3 4 2 4 1 1 1 1 2 1 1 1 1 1 1 1 5 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 3 1 1 1 1 1 3 1 2 1 1 1 1 2 1 1 1 1 2 3 2 1 1 1 1 1 1 1 2 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 2 2 1 2 1 2 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

datasets/01_sizes.txt

@@ -0,0 +1 @@
+25 22 18 17 14 12 11 11 11 10 10 9 9 9 9 9 9 9 8 8 8 8 8 7 7 7 7 7 7 7 7 7 7 6 6 6 6 6 6 6 6 6 6 6 6 5 5 5 5 5 5 5 5 5 5 5 5 5 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1

datasets/02_degs.txt

@@ -0,0 +1 @@
+2 2 2 3 2

datasets/02_sizes.txt

@@ -0,0 +1 @@
+2 3 4 2

is_simplicial.py

@@ -1,15 +1,19 @@
 import click
-from SimplicialTest import SimplicialTest
+from SimplicialTest import *
 
 
 @click.command()
 @click.option('-k', '--degree_seq_file', 'degree_sequence', type=click.File('r'), help='Path to degree sequence file.')
 @click.option('-s', '--size_seq_file', 'size_sequence', type=click.File('r'), help='Path to size sequence file.')
-def is_simplicial(degree_sequence, size_sequence):
+@click.option('--greedy/--no-greedy', default=False, help='Enable the Havel–Hakimi-type recursive algorithm.')
+@click.option('--forward/--no-forward', default=True,
+              help='[works only when greedy is on] Direction of the recursive algorithm.')
+def is_simplicial(degree_sequence, size_sequence, greedy, forward):
     degree_sequence = list(map(int, degree_sequence.read().replace("\n", "").split(" ")))
     size_sequence = list(map(int, size_sequence.read().replace("\n", "").split(" ")))
+    size_sequence, degree_sequence = prune_ones(size_sequence, degree_sequence)
     st = SimplicialTest(degree_sequence, size_sequence)
-    result = st.is_simplicial()
+    result = st.is_simplicial(greedy=greedy, forward=forward)
     if result is True:
         print(f"Yes, the joint sequence is simplicial. \nThe complex is: {st.identifier2facets(st.identifier)}")
     else: