Citances: Citation Sentences for Semantic Analysis of Bioscience Text

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Citances Citation Sentences for Semantic
Analysis ofBioscience Text

• Preslav I. Nakov, Ariel S. Schwartz, and Marti
  A. HearstComputer Science Division and
  SIMSUniversity of California, Berkeley
  http//biotext.berkeley.edu

Supported by NSF DBI-0317510 and a gift from
Genentech
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Overview

• We propose the use of the text of the sentences
  surrounding citations as an important tool for
  semantic interpretation of bioscience text.
• We hypothesize several different uses of citation
  sentences (which we call citances), including
• the creation of training and testing data for
  semantic analysis (especially for entity and
  relation recognition),
• synonym set creation,
• database curation,
• document summarization,
• and information retrieval generally.
• We illustrate some of these ideas, showing that
  citations to one document in particular align
  well with what a hand-built curator extracted.
• We also show preliminary results on the problem
  of normalizing the different ways that the same
  concepts are expressed within a set of citances,
  using and improving on existing techniques in
  automatic paraphrase generation.

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Motivation for using Citances in Bioscience Text

• We are interested in utilizing the large volume
  of available bioscience text when designing
  information extraction and retrieval tools.
• While the size of available text is growing
  rapidly, only few small annotated corpora for the
  bioscience domain exist.
• Full text (as opposed to abstracts) is becoming
  more available, providing new opportunities for
  automatic text processing.
• Citances provide an opportunity for coping with
  this limitation. They essentially contain a
  semi-annotated corpora for free.

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The Nature of Citances in Bioscience Literature

• Citations are particularly abundant in
  biosciences.
• Nearly every statement is backed up with at least
  one citation.
• It is quite common for papers in the bioscience
  domain to be cited by 30-100 other papers.
• The citances tend to state known biological facts
  with reference to the original papers that
  discovered them.
• The cited facts are typically stated in a more
  concise way in the citing papers than in the
  original papers.
• As the same facts are repeatedly stated in
  different ways in different papers, statistical
  models can be trained on existing citances to
  identify similar facts in unseen text.

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Examples of Citances
The genetic data presented here clearly show
that the Eiger-induced small eye phenotype
depends strongly on the JNK signaling pathway. In
mammals, it has been demonstrated that the JNK
pathway is essential for the execution of
stress-induced cell death. JNK3, a JNK isoform
that is selectively expressed in the nervous
system, is required for neuronal cell death
caused by excitotoxic stress (Yang et al., 1997).
Embryonic fibroblasts from mouse deficient for
both JNK1 and JNK2 are resistant to UV-stimulated
apoptosis (Tournier et al., 2000). Whitfield et
al. (2001) have shown that Bim acts downstream of
the JNK pathway in NGF-deprivation-induced
neuronal cell death. One possible downstream
mechanism of the JNK pathway to induce cell death
may be transcriptional upregulation of Bim.
However, our results suggest the possibility that
Eiger-induced cell death signaling may be
independent of downstream jun expression, similar
to the observation that the effect of UV to cause
cell death does not require new gene expression
(Tournier et al., 2000). The JNK signaling also
mediates heat shock-induced cell death, the
execution of which is caspase independent (Gabai
et al., 2000). Furthermore, overexpression of the
EDA receptor or TAJ/TROY, a member of the TNF
receptor superfamily that exhibits extensive
homology to the EDA receptor, results in the
activation of the JNK pathway and
caspase-independent cell death (Eby et al., 2000
Kumar et al., 2001). In some cases, JNK-induced
cell death is mediated by the release of
mitochondrial apoptogenic factors (Tournier et
al., 2000). Recently, it has been shown that
cancer cell death induced by TRAIL, a mammalian
TNF superfamily ligand, requires mitochondrial
release of Smac (Deng et al., 2002). One possible
mechanism of Eiger-induced cell death may be
JNK-mediated release of mitochondrial
caspase-independent cell death factors. In fact,
the Drosophila genome also encodes homologs of
such molecules AIF, endo G and HtrA2. (Igaki
et al., EMBO J. 2002 June 21 (12) 30093018)
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Illustrating Diagram
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Fact 1
Fact 2

Fact n
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A Source for Unannotated Comparable Corpora

• Comparable corpora are a useful resource for the
  development of NLP tools for question answering
  and summarization.
• Most domains outside of news do not contain many
  articles discussing the same events, but
  bioscience citances have some of the requisite
  characteristics in that they include redundancies
  that allow identification of comparable
  sentences.
• We later demonstrate the use of citances as
  comparable corpora for automatic paraphrase
  extraction.

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Summarization of the Target Papers

• The set of citances that refer to a specific
  paper can be viewed as an indication of the
  important facts in the paper as seen by the
  scientific community in that field.
• This is an excellent resource for summarization.
  In fact, we believe that a paper that is cited
  enough times can be summarized using only the
  citances pointing to it.
• Instead of showing the user all the citances
  pointing to a paper (as is done in CiteSeer and
  in Nanba et al. (2000)), we propose to first
  cluster related citances, and then display to the
  user only a summary of each cluster.
• The facts expressed by each cluster can be
  extracted and stored in a database.
• This could facilitate answering advanced queries
  on facts, such as retrieve all documents that
  describe which genes upregulate gene G.

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Synonym Identification and Disambiguation

• Bioscience literature is rife with abbreviations
  and synonyms.
• Citances referring to the same article may allow
  synonyms to be identified and recorded.
• A collection of related citances can help
  disambiguate terms with multiple meanings, since
  in some of the citances an unambiguous form of
  the term might be present.

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Entity Recognition and Relation Extraction

• Citances provide us a way to build a model of
  many of the different ways to express a
  relationship type R between entities of type A
  and B.
• We can seed learning algorithms with several
  examples using concepts that are semantically
  similar to A and similar to B, for which relation
  R is known to hold.
• Then we can train a model to recognize this kind
  of relation for situations for which the relation
  is not known.
• Since the results may extend to sentences that
  are not citances as well, citances-based corpora
  should provide a good collection for building NLP
  tools for recognizing entities and relations in
  unseen text.

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Targets for Curation

• We hypothesize that citances contain the most
  important information expressed in the cited
  document, and therefore contain the information
  that curators would want to make use of.
• We have found support for this hypothesis with
  two sample papers being used by a cancer
  researcher who is recording information about the
  process of apoptosis.

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Improved Citation Indexes for Information
Retrieval

• Citation indexes can be improved
• by combining methods that use citances context
  (e.g., Mercer and Di Marco (2004)) with methods
  that use citances content (e.g., Bradshaw
  (2003)).
• For example, indexing terms can be taken from
  citances referring to a target paper, weighting
  them both by their relative frequency and the
  type of citations they appear in.

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Related Work

• Traditional citation analysis dates back to the
  1960s (Garfield). Includes
• Citation categorization,
• Context analysis,
• Citer motivation.
• Citation indexing systems, such as ISIs SCI, and
  CiteSeer.
• Mercer and Di Marco (2004) propose to improve
  citation indexing using citation types.
• Bradshaw (2003) introduces Reference Directed
  Indexing (RDI), which indexes documents using the
  terms in the citances citing them.

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Related Work (cont.)

• Teufel and Moens (2002) identify citances to
  improve summarization of the citing paper. They
  give lower weight to citances as candidate
  sentences for summarization.
• Nanba et. al. (2000) use citances as features for
  classifying papers into topics.
• Related field to citation indexing is the use of
  link structure and anchor text of Web pages.
• Applications include IR, classification, Web
  crawlers, and summarization.
• See the full paper for references.

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Issues for Processing Citances

• Text span
• Identification of the appropriate phrase, clause,
  or sentence that constructs a citance.
• Correct mapping of citations when shown as lists
  or groups (e.g., 22-25).
• Grouping citances by topic
• Citances that cite the same document should be
  group by the facts they state.
• Normalizing or paraphrasing citances
• For IR, summarization, learning synonyms,
  relation extraction, question answering, and
  machine translation.

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Paraphrasing Citances
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Conclusions

• We have motivated and discussed the potentially
  enormous role that the use of sentences
  surrounding citations, or citances, can have for
  automated analysis of bioscience literature.
• In work not yet reported, we have found that
  citances align very well with rich information
  being curated by hand by a molecular biologist,
  and suspect they will be equally useful for other
  curation tasks.
• We also hypothesize that it will be a gold mine
  of data for training algorithms to perform
  semantic analysis of bioscience text, and will
  improve the results of querying the bioscience
  literature.
• Much work must be done before citances can be put
  to full use.
• We have demonstrated some initial results in
  paraphrasing citances that discuss the same
  topic, but more work remains to be done to
  improve results, and to group similar citances
  together.
• In future work, we plan to thoroughly explore the
  possibilities surrounding the analysis and use of
  citances for bioscience text analysis.