def LF_relative(span):
"""Context includes any familial mention (e.g., mother father)"""
left = get_left_span(span, span.sentence, window=6)
right = get_right_span(span, span.sentence, window=6)
left_trigger = match_regex(rgx_relatives, left)
right_trigger = match_regex(rgx_relatives, right)
return OTHER if left_trigger or right_trigger else PATIENT
def LF_definite_right_expanded(span):
right = get_right_span(span, span.sentence, window=6)
rgx = r'''\b(not present|no evidence|is (absent|not seen)|ruled out|were negative)\b'''
trigger = match_regex(rgx, right)
if trigger and token_distance(trigger, span) <= 1:
return NEGATED
return ABSTAIN
def LF_header(span):
rgx = re.compile(
r'^(admitting diagnosis|chief complaint|discharge diagnosis|past medical history|history of present illness|indication)[:]*',
re.I)
v = rgx.search(span.sentence.text.strip()) is not None
right = get_right_span(span, window=1).text
v |= right == ':'
return NON_NEGATED if v else ABSTAIN
def LF_social(span):
rgx_social = re.compile(r'''\b(friend(s)*|roomate(s)*|passenger(s)*)\b''',
re.I)
left = get_left_span(span, span.sentence, window=6)
right = get_right_span(span, span.sentence, window=6)
left_trigger = match_regex(rgx_social, left)
right_trigger = match_regex(rgx_social, right)
return OTHER if left_trigger or right_trigger else ABSTAIN
def LF_probable_left_4_6(span, negex):
left = get_left_span(span, span.sentence, window=6)
trigger = match_regex(negex.rgxs['probable']['left'], left)
if not trigger:
return ABSTAIN
dist = token_distance(trigger, span)
right = get_right_span(trigger, window=2)
if pseudo_negation.search(right.text):
return ABSTAIN
return NEGATED if (dist >= 4 and dist <= 6) else ABSTAIN
def LF_right_context(span):
text = get_right_span(span, span.sentence, window=6).text
regxes = [
r'''((?<!no )(mild|minimal|severe|moderate|extensive|coarse|marked|extreme|significant|trivial|progressive|slight)(ly)*)''',
# LF_severity_right
r'''(was (found to have|impaired|relieved|stable)|is present|withdrawal|of the)''' # LF_present_now_right
]
regxes = [re.compile(rgx, re.I) for rgx in regxes]
for rgx in regxes:
if rgx.search(text):
return NON_NEGATED
return ABSTAIN
def LF_definite_left_7_10(span, negex):
left = get_left_span(span, span.sentence)
trigger = match_regex(negex.rgxs['definite']['left'], left)
if not trigger:
return ABSTAIN
dist = token_distance(trigger, span)
right = get_right_span(trigger, window=2)
if pseudo_negation.search(right.text):
return ABSTAIN
return NEGATED if (dist >= 7 and dist <= 10) else ABSTAIN
def LF_definite_left_list(span, negex):
left = get_left_span(span, span.sentence, window=100)
trigger = match_regex(negex.rgxs['definite']['left'], left)
if not trigger:
return ABSTAIN
dist = token_distance(trigger, span)
btw = get_between_span(trigger, span)
right = get_right_span(trigger, window=2)
if pseudo_negation_rgx.search(right.text):
return ABSTAIN
return NEGATED if dist <= 10 and btw and len(re.findall(r'''[,;]''', btw.text)) > 1 else ABSTAIN
def LF_pseudo_negation_exclusion(span):
left_rgx = r'''(inadequate\s+to|does\s+not|cannot|can't)\s+exclude'''
right_rgx = r'''(cannot\s+be|not\s+be|doesn't|not|to)\s+exclude[d]*'''
left = get_left_span(span)
trigger = match_regex(left_rgx, left)
if trigger and token_distance(trigger, span) <= 3:
return NON_NEGATED
right = get_right_span(span)
trigger = match_regex(right_rgx, right)
if trigger and token_distance(trigger, span) <= 3:
return NON_NEGATED
return ABSTAIN
def _apply_lfs(self, span, sentence, ngrams):
"""
Apply NegEx labeling functions.
TODO: Window size is fixed here, choices of 5-8 perform well
"""
left = get_left_span(span, sentence, window=ngrams)
right = get_right_span(span, sentence, window=ngrams)
L = []
for name in sorted(self.negex.rgxs):
for cxt in sorted(self.negex.rgxs[name]):
v = 0
text = left.text if cxt == 'left' else right.text
if self.negex.rgxs[name][cxt].search(text):
v = self.class_map[name]
L.append(v)
return np.array(L)
def negation(self, span, category, direction, window=3):
"""
Return any matched negex phrases
:param span:
:param category:
:param direction:
:param window:
:return:
"""
rgx = self.rgxs[category][direction]
if not rgx.pattern:
return None
cxt = get_left_span(span, window=window) if direction == 'left' \
else get_right_span(span, window=window)
m = rgx.findall(cxt.text)
return m if m else None
def LF_none(span):
right_rgx = r'''\bnone\b'''
right = get_right_span(span)
trigger = match_regex(right_rgx, right)
return NEGATED if trigger and token_distance(trigger, span) <= 2 else ABSTAIN
def LF_probable_right(span, negex):
text = get_right_span(span, span.sentence, window=6).text
rgx = negex.rgxs['probable']['right']
if pseudo_negation(span):
return ABSTAIN
return NEGATED if rgx.search(text) else ABSTAIN
