allow missing information in deps and heads annotations

spacy/pipeline/_parser_internals/arc_eager.pyx

@@ -195,8 +195,7 @@ cdef class ArcEagerGold:
     def __init__(self, ArcEager moves, StateClass stcls, Example example):
         self.mem = Pool()
         heads, labels = example.get_aligned_parse(projectivize=True)
-        labels = [label if label is not None else "" for label in labels]
-        labels = [example.x.vocab.strings.add(label) for label in labels]
+        labels = [example.x.vocab.strings.add(label) if label is not None else 0 for label in labels]
         sent_starts = example.get_aligned_sent_starts()
         assert len(heads) == len(labels) == len(sent_starts), (len(heads), len(labels), len(sent_starts))
         self.c = create_gold_state(self.mem, stcls.c, heads, labels, sent_starts)
@@ -783,7 +782,7 @@ cdef class ArcEager(TransitionSystem):
             for i in range(self.n_moves):
                 print(self.get_class_name(i), is_valid[i], costs[i])
             print("Gold sent starts?", is_sent_start(&gold_state, state.B(0)), is_sent_start(&gold_state, state.B(1)))
-            raise ValueError
+            raise ValueError("Could not find gold transition - see logs above.")
 
     def get_oracle_sequence_from_state(self, StateClass state, ArcEagerGold gold, _debug=None):
         cdef int i

spacy/symbols.pxd

@@ -467,3 +467,4 @@ cdef enum symbol_t:
 
     IDX
     _
+    MISSING_LABEL

spacy/symbols.pyx

@@ -466,6 +466,7 @@ IDS = {
     "LAW": LAW,
     "MORPH": MORPH,
     "_": _,
+    "MISSING_LABEL": MISSING_LABEL,
 }
 
 

spacy/tests/doc/test_array.py

@@ -98,10 +98,16 @@ def test_doc_from_array_heads_in_bounds(en_vocab):
     doc_from_array = Doc(en_vocab, words=words)
     doc_from_array.from_array(["HEAD"], arr)
 
-    # head before start
+    # head before start is used to denote a missing value
     arr = doc.to_array(["HEAD"])
     arr[0] = -1
     doc_from_array = Doc(en_vocab, words=words)
+    doc_from_array.from_array(["HEAD"], arr)
+
+    # other negative values are invalid
+    arr = doc.to_array(["HEAD"])
+    arr[0] = -2
+    doc_from_array = Doc(en_vocab, words=words)
     with pytest.raises(ValueError):
         doc_from_array.from_array(["HEAD"], arr)
 

spacy/tests/parser/test_parse.py

@@ -45,7 +45,17 @@ CONFLICTING_DATA = [
     ),
 ]
 
-eps = 0.01
+PARTIAL_DATA = [
+    (
+        "I like London.",
+        {
+            "heads": [1, 1, 1, None],
+            "deps": ["nsubj", "ROOT", "dobj", None],
+        },
+    ),
+]
+
+eps = 0.1
 
 
 def test_parser_root(en_vocab):
@@ -205,6 +215,32 @@ def test_parser_set_sent_starts(en_vocab):
             assert token.head in sent
 
 
+@pytest.mark.parametrize("pipe_name", ["parser", "beam_parser"])
+def test_incomplete_data(pipe_name):
+    # Test that the parser works with incomplete information
+    nlp = English()
+    parser = nlp.add_pipe(pipe_name)
+    train_examples = []
+    for text, annotations in PARTIAL_DATA:
+        train_examples.append(Example.from_dict(nlp.make_doc(text), annotations))
+        for dep in annotations.get("deps", []):
+            if dep is not None:
+                parser.add_label(dep)
+    optimizer = nlp.initialize(get_examples=lambda: train_examples)
+    for i in range(150):
+        losses = {}
+        nlp.update(train_examples, sgd=optimizer, losses=losses)
+    assert losses[pipe_name] < 0.0001
+
+    # test the trained model
+    test_text = "I like securities."
+    doc = nlp(test_text)
+    assert doc[0].dep_ == "nsubj"
+    assert doc[2].dep_ == "dobj"
+    assert doc[0].head.i == 1
+    assert doc[2].head.i == 1
+
+
 @pytest.mark.parametrize("pipe_name", ["parser", "beam_parser"])
 def test_overfitting_IO(pipe_name):
     # Simple test to try and quickly overfit the dependency parser (normal or beam)

spacy/tokens/doc.pyx

@@ -266,7 +266,7 @@ cdef class Doc:
             self.push_back(lexeme, has_space)
 
         if heads is not None:
-            heads = [head - i for i, head in enumerate(heads)]
+            heads = [head - i if head is not None else None for i, head in enumerate(heads)]
         if deps and not heads:
             heads = [0] * len(deps)
         if sent_starts is not None:
@@ -328,7 +328,8 @@ cdef class Doc:
                 if annot is not heads and annot is not sent_starts and annot is not ent_iobs:
                     values.extend(annot)
         for value in values:
-            self.vocab.strings.add(value)
+            if value is not None:
+                self.vocab.strings.add(value)
 
         # if there are any other annotations, set them
         if headings:
@@ -1039,7 +1040,8 @@ cdef class Doc:
                 # cast index to signed int
                 abs_head_index = <int32_t>values[col * stride + i]
                 abs_head_index += i
-                if abs_head_index < 0 or abs_head_index >= length:
+                # abs_head_index -1 refers to missing value
+                if abs_head_index < -1 or abs_head_index >= length:
                     raise ValueError(
                         Errors.E190.format(
                             index=i,

spacy/tokens/token.pyx

@@ -639,13 +639,16 @@ cdef class Token:
         return any(ancestor.i == self.i for ancestor in descendant.ancestors)
 
     property head:
-        """The syntactic parent, or "governor", of this token.
+        """The syntactic parent, or "governor", of this token. 
 
         RETURNS (Token): The token predicted by the parser to be the head of
-            the current token.
+            the current token. Returns None if unknown.
         """
         def __get__(self):
-            return self.doc[self.i + self.c.head]
+            head_i = self.i + self.c.head
+            if head_i == -1:
+                return None
+            return self.doc[head_i]
 
         def __set__(self, Token new_head):
             # This function sets the head of self to new_head and updates the

spacy/training/example.pyx

@@ -11,6 +11,7 @@ from .alignment import Alignment
 from .iob_utils import biluo_to_iob, offsets_to_biluo_tags, doc_to_biluo_tags
 from .iob_utils import biluo_tags_to_spans
 from ..errors import Errors, Warnings
+from ..symbols import MISSING_LABEL
 from ..pipeline._parser_internals import nonproj
 from ..util import logger
 
@@ -179,14 +180,18 @@ cdef class Example:
         gold_to_cand = self.alignment.y2x
         aligned_heads = [None] * self.x.length
         aligned_deps = [None] * self.x.length
-        heads = [token.head.i for token in self.y]
+        heads = [token.head.i if token.head is not None else -1 for token in self.y]
         deps = [token.dep_ for token in self.y]
         if projectivize:
-            heads, deps = nonproj.projectivize(heads, deps)
+            proj_heads, proj_deps = nonproj.projectivize(heads, deps)
+            # don't touch the missing data
+            heads = [h if heads[i] != -1 else -1 for i, h in enumerate(proj_heads)]
+            MISSING = self.x.vocab.strings[MISSING_LABEL]
+            deps = [d if deps[i] != MISSING else MISSING for i, d in enumerate(proj_deps)]
         for cand_i in range(self.x.length):
             if cand_to_gold.lengths[cand_i] == 1:
                 gold_i = cand_to_gold[cand_i].dataXd[0, 0]
-                if gold_to_cand.lengths[heads[gold_i]] == 1:
+                if heads[gold_i] != -1 and gold_to_cand.lengths[heads[gold_i]] == 1:
                     aligned_heads[cand_i] = int(gold_to_cand[heads[gold_i]].dataXd[0, 0])
                     aligned_deps[cand_i] = deps[gold_i]
         return aligned_heads, aligned_deps
@@ -329,7 +334,10 @@ def _annot2array(vocab, tok_annot, doc_annot):
             pass
         elif key == "HEAD":
             attrs.append(key)
-            values.append([h-i for i, h in enumerate(value)])
+            values.append([h-i if h is not None else -(i+1) for i, h in enumerate(value)])
+        elif key == "DEP":
+            attrs.append(key)
+            values.append([vocab.strings.add(h) if h is not None else MISSING_LABEL for h in value])
         elif key == "SENT_START":
             attrs.append(key)
             values.append(value)