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_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_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 LF_definite_left_0(span, negex):
left = get_left_span(span, span.sentence, window=6)
trigger = match_regex(negex.rgxs['definite']['left'], left)
if not trigger:
return ABSTAIN
dist = token_distance(trigger, span)
return NEGATED if dist == 0 else ABSTAIN
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_left_context(span):
left = get_left_span(span, span.sentence, window=6)
# negated mentions
neg_rgxes = [
r'''\b(no|did not have|neg(ative)* for) (mild|slight|minimal|severe|moderate|extensive|marked|extreme|significant|progressive)\b''',
r'''\b(no|did not have|neg(ative)* for) (known|evidence of|evidence)\b'''
]
neg_rgxes = [re.compile(rgx, re.I) for rgx in neg_rgxes]
for rgx in neg_rgxes:
trigger = match_regex(rgx, left)
if trigger and token_distance(trigger, span) <= 2:
return NEGATED
# positive mentions
pos_regxes = [
r'''(cannot exclude|does not become|may not|possible|evaluate for|suggests)''', # hedged
r'''(mild|minimal|severe|moderate|extensive|coarse|marked|extreme|significant|trivial|progressive|slight)(ly)*''',
# severity
r'''(diagnosed with|known to have|known|non-specific|presented|secondary to|treated for|acute onset|improving|improved|improvement|involvement|resolved|consistent with|showed|presumed|suspicious for|check for|revealed|new onset|were noted|found to be|demonstrate(d)*)''',
# present now
r'''\b((in|de)creas(e|ed|ing)|up|down)\b''', # LF_change_words_left
r'''(s/p|status[- ]post)''',
]
pos_regxes = [re.compile(rgx, re.I) for rgx in pos_regxes]
for rgx in pos_regxes:
if rgx.search(span.text):
return NON_NEGATED
return ABSTAIN
def LF_pseudo_negation_rule_out(span):
left_rgx = r'''(cannot|does not|doesn't) rule[s]* out'''
left = get_left_span(span)
trigger = match_regex(left_rgx, left)
if not trigger or token_distance(trigger, span) > 5:
return ABSTAIN
return NON_NEGATED if re.search(r'''(cannot|does not|doesn't)''',
trigger.text, re.I) else NEGATED
def LF_header(span, negex):
"""All spans under Family History are assumed to refer to family"""
rgx = re.compile(r'''(family history[:]*|family hx)\b''', re.I)
left = get_left_span(span, span.sentence, window=6)
trigger = match_regex(rgx, left)
if trigger:
# check for negation ("no family history")
neg = match_regex(negex.rgxs['definite']['left'],
get_left_span(trigger, window=2))
return ABSTAIN if neg else OTHER
if 'section' in span.props:
header = span.props['section']
if header and rgx.search(header.text):
return OTHER
return ABSTAIN
def LF_positive_left(span):
left = get_left_span(span, window=10)
rgx = r'''\b(positive for|suggestive of|due to|shows)\b'''
trigger = match_regex(rgx, left)
if not trigger:
return ABSTAIN
left = get_left_span(trigger, window=50)
m = re.search(r'''\b(no|not)\b''', left.text, re.I)
return NON_NEGATED if not re.search(r'''\b(no|not)\b''', left.text, re.I) else ABSTAIN
def LF_header_break_negation(span, negex):
left = get_left_span(span)
trigger = match_regex(negex.rgxs['definite']['left'], left)
if not trigger:
return ABSTAIN
btw = get_between_span(trigger, span)
if not btw:
return ABSTAIN
rgx = r'''\s{2,}((?:(?:[A-Z][A-Za-z]+\s){1,4}(?:[A-Za-z]+))[:])'''
return NON_NEGATED if re.search(rgx, btw.text) 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_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_denies_list(span):
""" Patient denies X,Y,Z. """
rgx = re.compile(r'''\b(den(ying|y|ies|ied))\b''', re.I)
left = get_left_span(span, window=100)
trigger = match_regex(rgx, left)
if not trigger:
return ABSTAIN
btw = get_between_span(trigger, span)
if not btw:
return ABSTAIN
n = len(re.findall(r'''[,;/]''', btw.text))
return NEGATED if n >= 1 else ABSTAIN
def LF_pseudo_left_expanded(span, negex):
pseudo_rgxs = [
r'''\b((significant )*(change[s]* in|improvement))\b''',
r'''\b((in|de)creas(e|ed|ing)|up|down)\b'''
]
left = get_left_span(span)
trigger = match_regex(negex.rgxs['definite']['left'], left)
if not trigger or token_distance(trigger, span) > 20:
return ABSTAIN
btw = get_between_span(span, trigger)
if not btw:
return ABSTAIN
for rgx in pseudo_rgxs:
if re.search(rgx, btw.text, re.I):
return NON_NEGATED
return ABSTAIN
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
