Dietrich Rebholz Schuhmann

Also published as: Dietrich Rebholz-Schuhmann


2014

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Collaboratively Annotating Multilingual Parallel Corpora in the Biomedical Domain—some MANTRAs
Johannes Hellrich | Simon Clematide | Udo Hahn | Dietrich Rebholz-Schuhmann
Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14)

The coverage of multilingual biomedical resources is high for the English language, yet sparse for non-English languages―an observation which holds for seemingly well-resourced, yet still dramatically low-resourced ones such as Spanish, French or German but even more so for really under-resourced ones such as Dutch. We here present experimental results for automatically annotating parallel corpora and simultaneously acquiring new biomedical terminology for these under-resourced non-English languages on the basis of two types of language resources, namely parallel corpora (i.e. full translation equivalents at the document unit level) and (admittedly deficient) multilingual biomedical terminologies, with English as their anchor language. We automatically annotate these parallel corpora with biomedical named entities by an ensemble of named entity taggers and harmonize non-identical annotations the outcome of which is a so-called silver standard corpus. We conclude with an empirical assessment of this approach to automatically identify both known and new terms in multilingual corpora.

2013

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A Discourse-Driven Content Model for Summarising Scientific Articles Evaluated in a Complex Question Answering Task
Maria Liakata | Simon Dobnik | Shyamasree Saha | Colin Batchelor | Dietrich Rebholz-Schuhmann
Proceedings of the 2013 Conference on Empirical Methods in Natural Language Processing

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GRO Task: Populating the Gene Regulation Ontology with events and relations
Jung-jae Kim | Xu Han | Vivian Lee | Dietrich Rebholz-Schuhmann
Proceedings of the BioNLP Shared Task 2013 Workshop

2012

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Centroids: Gold standards with distributional variation
Ian Lewin | Şenay Kafkas | Dietrich Rebholz-Schuhmann
Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC'12)

Motivation: Gold Standards for named entities are, ironically, not standard themselves. Some specify the “one perfect annotation”. Others specify “perfectly good alternatives”. The concept of Silver standard is relatively new. The objective is consensus rather than perfection. How should the two concepts be best represented and related? Approach: We examine several Biomedical Gold Standards and motivate a new representational format, centroids, which simply and effectively represents name distributions. We define an algorithm for finding centroids, given a set of alternative input annotations and we test the outputs quantitatively and qualitatively. We also define a metric of relatively acceptability on top of the centroid standard. Results: Precision, recall and F-scores of over 0.99 are achieved for the simple sanity check of giving the algorithm Gold Standard inputs. Qualitative analysis of the differences very often reveals errors and incompleteness in the original Gold Standard. Given automatically generated annotations, the centroids effectively represent the range of those contributions and the quality of the centroid annotations is highly competitive with the best of the contributors. Conclusion: Centroids cleanly represent alternative name variations for Silver and Gold Standards. A centroid Silver Standard is derived just like a Gold Standard, only from imperfect inputs.

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CALBC: Releasing the Final Corpora
Şenay Kafkas | Ian Lewin | David Milward | Erik van Mulligen | Jan Kors | Udo Hahn | Dietrich Rebholz-Schuhmann
Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC'12)

A number of gold standard corpora for named entity recognition are available to the public. However, the existing gold standard corpora are limited in size and semantic entity types. These usually lead to implementation of trained solutions (1) for a limited number of semantic entity types and (2) lacking in generalization capability. In order to overcome these problems, the CALBC project has aimed to automatically generate large scale corpora annotated with multiple semantic entity types in a community-wide manner based on the consensus of different named entity solutions. The generated corpus is called the silver standard corpus since the corpus generation process does not involve any manual curation. In this publication, we announce the release of the final CALBC corpora which include the silver standard corpus in different versions and several gold standard corpora for the further usage of the biomedical text mining community. The gold standard corpora are utilised to benchmark the methods used in the silver standard corpora generation process and released in a shared format. All the corpora are released in a shared format and accessible at www.calbc.eu.

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Finding small molecule and protein pairs in scientific literature using a bootstrapping method
Ying Yan | Jee-Hyub Kim | Samuel Croset | Dietrich Rebholz-Schuhmann
BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing

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A Hybrid Approach to Finding Phenotype Candidates in Genetic Texts
Nigel Collier | Mai-Vu Tran | Hoang-Quynh Le | Anika Oellrich | Ai Kawazoe | Martin Hall-May | Dietrich Rebholz-Schuhmann
Proceedings of COLING 2012

2010

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The CALBC Silver Standard Corpus for Biomedical Named Entities — A Study in Harmonizing the Contributions from Four Independent Named Entity Taggers
Dietrich Rebholz-Schuhmann | Antonio José Jimeno Yepes | Erik M. van Mulligen | Ning Kang | Jan Kors | David Milward | Peter Corbett | Ekaterina Buyko | Katrin Tomanek | Elena Beisswanger | Udo Hahn
Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC'10)

The production of gold standard corpora is time-consuming and costly. We propose an alternative: the ‚silver standard corpus‘ (SSC), a corpus that has been generated by the harmonisation of the annotations that have been delivered from a selection of annotation systems. The systems have to share the type system for the annotations and the harmonisation solution has use a suitable similarity measure for the pair-wise comparison of the annotations. The annotation systems have been evaluated against the harmonised set (630.324 sentences, 15,956,841 tokens). We can demonstrate that the annotation of proteins and genes shows higher diversity across all used annotation solutions leading to a lower agreement against the harmonised set in comparison to the annotations of diseases and species. An analysis of the most frequent annotations from all systems shows that a high agreement amongst systems leads to the selection of terms that are suitable to be kept in the harmonised set. This is the first large-scale approach to generate an annotated corpus from automated annotation systems. Further research is required to understand, how the annotations from different systems have to be combined to produce the best annotation result for a harmonised corpus.

2009

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How Feasible and Robust is the Automatic Extraction of Gene Regulation Events? A Cross-Method Evaluation under Lab and Real-Life Conditions
Udo Hahn | Katrin Tomanek | Ekaterina Buyko | Jung-jae Kim | Dietrich Rebholz-Schuhmann
Proceedings of the BioNLP 2009 Workshop

2006

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Annotation and Disambiguation of Semantic Types in Biomedical Text: A Cascaded Approach to Named Entity Recognition
Dietrich Rebholz-Schuhmann | Harald Kirsch | Sylvain Gaudan | Miguel Arregui | Goran Nenadic
Proceedings of the 5th Workshop on NLP and XML (NLPXML-2006): Multi-Dimensional Markup in Natural Language Processing

2004

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Distributed Modules for Text Annotation and IE Applied to the Biomedical Domain
Harald Kirsch | Dietrich Rebholz-Schuhmann
Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP)