Finding Anchor Verbs for Biomedical IE
Using Predicate-Argument Structures
Akane YAKUSHIJI† Yuka TATEISI‡† Yusuke MIYAO†
†Department of Computer Science, University of Tokyo
Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 JAPAN
‡CREST, JST (Japan Science and Technology Agency)
Honcho 4-1-8, Kawaguchi-shi, Saitama 332-0012 JAPAN
{akane,yucca,yusuke,tsujii}@is.s.u-tokyo.ac.jp
Jun’ichi TSUJII†‡
Abstract
For biomedical information extraction, most sys-
tems use syntactic patterns on verbs (anchor verbs)
and their arguments. Anchor verbs can be se-
lected by focusing on their arguments. We propose
to use predicate-argument structures (PASs), which
are outputs of a full parser, to obtain verbs and their
arguments. In this paper, we evaluated PAS method
by comparing it to a method using part of speech
(POSs) pattern matching. POS patterns produced
larger results with incorrect arguments, and the re-
sults will cause adverse effects on a phase selecting
appropriate verbs.
1 Introduction
Research in molecular-biology ﬁeld is discovering
enormous amount of new facts, and thus there is
an increasing need for information extraction (IE)
technology to support database building and to ﬁnd
novel knowledge in online journals.
To implement IE systems, we need to construct
extraction rules, i.e., rules to extract desired infor-
mation from processed resource. One subtask of the
construction is deﬁning a set of anchor verbs, which
express realization of desired information in natural
language text.
In this paper, we propose a novel method of
ﬁnding anchor verbs: extracting anchor verbs from
predicate-argument structures (PASs) obtained by
full parsing. We here discuss only ﬁnding anchor
verbs, although our ﬁnal purpose is construction
of extraction rules. Most anchor verbs take topi-
cal nouns, i.e., nouns describing target entities for
IE, as their arguments. Thus verbs which take top-
ical nouns can be candidates for anchor verbs. Our
methodcollectsanchorverbcandidatesbychoosing
PASs whose arguments are topical nouns. Then, se-
mantically inappropriate verbs are ﬁltered out. We
leave this ﬁltering phase as a future work, and dis-
cuss the acquisition of candidates. We have also in-
vestigated difference in verbs and their arguments
extracted by naive POS patterns and PAS method.
When anchor verbs are found based on whether
their arguments are topical nouns, like in (Hatzivas-
siloglou and Weng, 2002), it is important to obtain
correct arguments. Thus, in this paper, we set our
goal to obtain anchor verb candidates and their cor-
rect arguments.
2 Background
There are some works on acquiring extraction rules
automatically. Sudo et al. (2003) acquired subtrees
derived from dependency trees as extraction rules
forIEingeneraldomains. Oneproblemoftheirsys-
tem is that dependency trees cannot treat non-local
dependencies, and thus rules acquired from the con-
structions are partial. Hatzivassiloglou and Weng
(2002) used frequency of collocation of verbs and
topical nouns and verb occurrence rates in several
domains to obtain anchor verbs for biological inter-
action. They used only POSs and word positions
to detect relations between verbs and topical nouns.
Their performance was 87.5% precision and 82.4%
recall. One of the reasons of errors they reported is
failures to detect verb-noun relations.
To avoid these problems, we decided to use PASs
obtained by full parsing to get precise relations be-
tween verbs and their arguments. The obtained pre-
cise relations will improve precision. In addition,
PASs obtained by full parsing can treat non-local
dependencies, thus recall will also be improved.
The sentence below is an example which sup-
ports advantage of full parsing. A gerund  activat-
ing takes a non-local semantic subject  IL-4 . In
full parsing based on Head-Driven Phrase Structure
Grammar (HPSG) (Sag and Wasow, 1999), the sub-
ject of the whole sentence and the semantic subject
of  activating are shared, and thus we can extract
the subject of  activating .
IL-4 may mediate its biological effects by activat-
ing a tyrosine-phosphorylated DNA binding pro-
tein.
interactsARG1 it1 withMODIFY
ARG1      regions21
ofMODIFY
ARG1 molecules2,
,
(a) (b) (c)
It interacts with non-polymorphic regions of major his-
tocompatibility complex class II molecules.
Figure 1: PAS examples
withMODIFYinteracts
ARG1 itARG1 regions
Core verb serves
ARG1      IL-51ARG2to
ARG1ARG2stimulate
ARG1ARG2 binding
1
Core verb
1
Figure 2: Core verbs of PASs
3 Anchor Verb Finding by PASs
By using PASs, we extract candidates for anchor
verbs from a sentence in the following steps:
1. Obtain all PASs of a sentence by a full
parser. ThePASscorrespondnotonlytoverbal
phrases but also other phrases such as preposi-
tional phrases.
2. Select PASs which take one or more topical
nouns as arguments.
3. From the selected PASs in Step 2, select PASs
which include one or more verbs.
4. Extractacoreverb, whichistheinnermostver-
bal predicate, from each of the chosen PASs.
In Step 1, we use a probabilistic HPSG parser
developed by Miyao et al. (2003), (2004). PASs
obtained by the parser are illustrated in Figure 1.1
Boldwords are predicates. Arguments of the predi-
cates are described in ARGn (n = 1,2,...). MOD-
IFY denotes the modiﬁed PAS. Numbers in squares
denote shared structures. Examples of core verbs
are illustrated in Figure 2. We regard all arguments
in a PAS are arguments of the core verb.
Extraction of candidates for anchor verbs from
the sentence in Figure 1 is as follows. Here,  re-
gions and  molecules are topical nouns.
In Step 1, we obtain all the PASs, (a), (b) and (c),
in Figure 1.
1Here, named entities are regarded as chunked, and thus
internal structures of noun phrases are not illustrated.
Next, in Step 2, we check each argument of (a),
(b) and (c). (a) is discarded because it does not have
a topical noun argument.2 (b) is selected because
ARG1  regions is a topical noun. Similarly, (c) is
selected because of ARG1  molecules .
And then, in Step 3, we check each POS of a
predicate included in (b) and (c). (b) is selected be-
cause it has the verb  interacts in 1 which shares
the structure with (a). (c) is discarded because it
includes no verbs.
Finally, inStep 4, weextracta coreverbfrom (b).
(b) includes 1 asMODIFY, and the predicate of 1
is the verb,  interacts . So we extract it.
4 Experiments
We investigated the verbs and their arguments ex-
tracted by PAS method and POS pattern matching,
whichislessexpressiveinanalyzingsentencestruc-
tures but would be more robust.
For topical nouns and POSs, we used the GENIA
corpus (Kim et al., 2003), a corpus of annotated ab-
stracts taken from National Library of Medicine’s
MEDLINE database. We deﬁned topical nouns as
the names tagged as protein, peptide, amino acid,
DNA, RNA, or nucleic acid. We chose PASs which
take one or more topical nouns as an argument or
arguments, and substrings matched by POS patterns
which include topical nouns. All names tagged in
the corpus were replaced by their head nouns in
order to reduce complexity of sentences and thus
reduce the task of the parser and the POS pattern
matcher.
4.1 Implementation of PAS method
We implemented PAS method on LiLFeS, a
uniﬁcation-based programming system for typed
feature structures (Makino et al., 1998; Miyao et al.,
2000).
The selection in Step 2 described in Section 3
is realized by matching PASs with nine PAS tem-
plates. Four of the templates are illustrated in Fig-
ure 3.
4.2 POS Pattern Method
We constructed a POS pattern matcher with a par-
tial verb chunking function according to (Hatzivas-
siloglou and Weng, 2002). Because the original
matcher has problems in recall (its verb group de-
tector has low coverage) and precision (it does not
consider other words to detect relations between
verb groups and topical nouns), we implemented
2(a) may be selected if the anaphora ( it ) is resolved. But
we regard anaphora resolving is too hard task as a subprocess
of ﬁnding anchor verbs.
*any*ARG1 N1 N1= topicalnoun
*any*ARG1 N1
ARG2 N2 N1= topical nounor N2 = topical noun
… …
*any*MODIFY *any*
ARG1 N1 N1= topicalnoun
*any*MODIFY *any*
ARG1 N1ARG2N2 N1= topical nounor N2 = topical noun
Figure 3: PAS templates
N ω VG ω N
N ω VG
VG ω N
N: is a topical noun
VG: is a verb group which is accepted by a ﬁnite state
machinedescribedin(HatzivassiloglouandWeng, 2002)
or one of {VB, VBD, VBG, VBN, VBP, VBZ}
ω: is 0 4 tokens which do not include {FW, NN, NNS,
NNP, NNPS, PRP, VBG, WP, *}
(Parts in Bold letters are added to the patterns of Hatzi-
vassiloglou and Weng (2002).)
Figure 4: POS patterns
our POS pattern matcher as a modiﬁed version of
one in (Hatzivassiloglou and Weng, 2002).
Figure 4 shows patterns in our experiment. The
last verb of VG is extracted if all of Ns are topical
nouns. Non-topical nouns are disregarded. Adding
candidates for verb groups raises recall of obtained
relations of verbs and their arguments. Restriction
on intervening tokens to non-nouns raises the preci-
sion, although it decreases the recall.
4.3 Experiment 1
We extracted last verbs of POS patterns and core
verbs of PASs with their arguments from 100 ab-
stracts (976 sentences) of the GENIA corpus. We
took up not the verbs only but tuples of the verbs
and their arguments (VAs), in order to estimate ef-
fect of the arguments on semantical ﬁltering.
Results
The numbers of VAs extracted from the 100 ab-
stracts using POS patterns and PASs are shown in
Table 1. (Total ¡ VAs of verbs not extracted by the
other method) are not the same, because more than
one VA can be extracted on a verb in a sentence.
POS patterns method extracted more VAs, although
POS patterns PASs
Total 1127 766
VAs of verbs
not extracted 478 105
by the other
Table 1: Numbers of VAs extracted from the 100
abstracts
Appropriate Inappropriate Total
Correct 43 12 55
Incorrect 20 23 43
Total 63 35 98
Table 2: Numbers of VAs extracted by POS patterns
(in detail)
their correctness is not considered.
4.4 Experiment 2
For the ﬁrst 10 abstracts (92 sentences), we man-
ually investigated whether extracted VAs are syn-
tactically or semantically correct. The investigation
was based on two criteria:  appropriateness based
on whether the extracted verb can be used for an an-
chor verb and  correctness based on whether the
syntactical analysis is correct, i.e., whether the ar-
guments were extracted correctly.
Based on human judgment, the verbs that rep-
resent interactions, events, and properties were se-
lected as semantically appropriate for anchor verbs,
and the others were treated as inappropriate. For ex-
ample,  identiﬁed in  We identiﬁed ZEBRA pro-
tein. is not appropriate and discarded.
We did not consider non-topical noun arguments
for POS pattern method, whereas we considered
them for PAS method. Thus decision on correctness
is stricter for PAS method.
Results
The manual investigation results on extracted
VAs from the 10 abstracts using POS patterns and
PASs are shown in Table 2 and 3 respectively.
POS patterns extracted more (98) VAs than PASs
(75), but many of the increment were from incor-
rect POS pattern matching. By POS patterns, 43
VAs (44%) were extracted based on incorrect anal-
ysis. On the other hand, by PASs, 20 VAs (27%)
were extracted incorrectly. Thus the ratio of VAs
extracted by syntactically correct analysis is larger
on PAS method.
POS pattern method extracted 38 VAs of verbs
not extracted by PAS method and 7 of them are cor-
rect. For PAS method, correspondent numbers are
Appropriate Inappropriate Total
Correct 44 11 55
Incorrect 14 6 20
Total 58 17 75
Table 3: Numbers of VAs extracted by PASs (in de-
tail)
11 and 4 respectively. Thus the increments tend to
be caused by incorrect analysis, and the tendency is
greater in POS pattern method.
Since not all of verbs that take topical nouns are
appropriate for anchor verbs, automatic ﬁltering is
required. In the ﬁltering phase that we leave as a
future work, we can use semantical classes and fre-
quenciesofargumentsoftheverbs. Theresultswith
syntacticallyincorrectargumentswillcauseadverse
effect on ﬁltering because they express incorrect re-
lationship between verbs and arguments. Since the
numbers of extracted VAs after excluding the ones
with incorrect arguments are the same (55) between
PAS and POS pattern methods, it can be concluded
that the precision of PAS method is higher. Al-
though there are few (7) correct VAs which were
extracted by POS pattern method but not by PAS
method, we expect the number of such verbs can be
reduced using a larger corpus.
Examples of appropriate VAs extracted by only
one method are as follows: (A) is correct and (B)
incorrect, extracted by only POS pattern method,
and (C) is correct and (D) incorrect, extracted by
only PAS method. Bold words are extracted verbs
or predicates and italic words their extracted argu-
ments.
(A) This delay is associated with down-regulation
of many erythroid cell-speciﬁc genes, including
alpha- and beta-globin, band 3, band 4.1, and ....
(B) ... show that several elements in the ... region of
the IL-2R alpha gene contribute to IL-1 respon-
siveness, ....
(C) The CD4 coreceptor interacts with non-
polymorphic regions of ... molecules on
non-polymorphic cells and contributes to T cell
activation.
(D) Whereas activation of the HIV-1 enhancer follow-
ing T-cell stimulation is mediated largely through
binding of the ... factor NF-kappa B to two adja-
cent kappa B sites in ....
5 Conclusions
We have proposed a method of extracting anchor
verbs as elements of extraction rules for IE by us-
ing PASs obtained by full parsing. To compare
our method with more naive and robust methods,
we have extracted verbs and their arguments using
POS patterns and PASs. POS pattern method could
obtain more candidate verbs for anchor verbs, but
many of them were extracted with incorrect argu-
ments by incorrect matching. A later ﬁltering pro-
cess beneﬁts by precise relations between verbs and
their arguments which PASs obtained. The short-
coming of PAS method is expected to be reduced by
using a larger corpus, because verbs to extract will
appearmanytimesinmanyforms. Oneofthefuture
works is to extend PAS method to handle events in
nominalized forms.
Acknowledgements
This work was partially supported by Grant-in-
Aid for Scientiﬁc Research on Priority Areas (C)
 Genome Information Science from the Ministry
of Education, Culture, Sports, Science and Technol-
ogy of Japan.
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