Wide-coverage deep statistical parsing using automatic dependency structure annotation

A number of researchers (Lin 1995; Carroll, Briscoe, and Sanfilippo 1998; Carroll et al. 2002; Clark and Hockenmaier 2002; King et al. 2003; Preiss 2003; Kaplan et al. 2004;Miyao and Tsujii 2004) have convincingly argued for the use of dependency (rather than CFG-tree) representations for parser evaluation. Preiss (2003) and Kaplan et al. (2004) conducted a number of experiments comparing “deep” hand-crafted wide-coverage with “shallow” treebank- and machine-learning based parsers at the level of dependencies, using simple and automatic methods to convert tree output generated by the shallow parsers into dependencies. In this article, we revisit the experiments in Preiss (2003) and Kaplan et al. (2004), this time using the sophisticated automatic LFG f-structure annotation methodologies of Cahill et al. (2002b, 2004) and Burke (2006), with surprising results. We compare various PCFG and history-based parsers (based on Collins, 1999; Charniak, 2000; Bikel, 2002) to find a baseline parsing system that fits best into our automatic dependency structure annotation technique. This combined system of syntactic parser and dependency structure annotation is compared to two hand-crafted, deep constraint-based parsers (Carroll and Briscoe 2002; Riezler et al. 2002). We evaluate using dependency-based gold standards (DCU 105, PARC 700, CBS 500 and dependencies for WSJ Section 22) and use the Approximate Randomization Test (Noreen 1989) to test the statistical significance of the results. Our experiments show that machine-learning-based shallow grammars augmented with sophisticated automatic dependency annotation technology outperform hand-crafted, deep, widecoverage constraint grammars. Currently our best system achieves an f-score of 82.73% against the PARC 700 Dependency Bank (King et al. 2003), a statistically significant improvement of 2.18%over the most recent results of 80.55%for the hand-crafted LFG grammar and XLE parsing system of Riezler et al. (2002), and an f-score of 80.23% against the CBS 500 Dependency Bank (Carroll, Briscoe, and Sanfilippo 1998), a statistically significant 3.66% improvement over the 76.57% achieved by the hand-crafted RASP grammar and parsing system of Carroll and Briscoe (2002)

The multilingual entity task (MET) overview

Conference-6 (MUC-6) evaluation of named entity identification demonstrated that systems are approach-ing human performance onEnglish language t xts [10]. Informal and anonymous, the MET provided a new opportunity to assess progress on the same task in Span-ish, Japanese, and Chinese. Preliminary results indicate that MET systems in all three languages performed comparably to those of the MUC-6 evaluatien in English. Based upon the Named Entity Task Guidelines [ 11], the task was to locate and tag with SGML named entity expressions (people, organizations, and locations), time expressions (time and date), and numeric expressions (percentage and money) in Spanish texts from Agence France Presse, in Japanese texts from Kyodo newswire, or in Chinese texts from Xinhua newswkel. Across lan-guages the keywords "press conference " retrieved a rich subcorpus of texts, covering awide spectrum of topics. Frequency and types of expressions vary in the three language sets [2] [8] [9]. The original task guidelines were modified so that he core guidelines were language independent with language specific rules appended. The schedule was quite abbreviated. In the fall, Government language teams retrieved training and test texts with multilingual software for the Fast Data Finder (FDF), refined the MUC-6 guidelines, and manually tagged 100 training texts using the SRA Named Entity Tool. In January, the training texts were released along with 200 sample unannotated training texts to the partic-ipating sites. A dry run was held in late March and early April and in late April the official test on 100 texts was. The language t xts were supplied by the Linguistic Data Consortium (LDC) at the University of Pennsylvania. performed anonymously. SAIC created language ver-sions of the scoring program and provided technical support throughout. Both commercial and academic groups partici-pated. Two groups, New Mexico State University/Com

Datasets for generic relation extraction

A vast amount of usable electronic data is in the form of unstructured text. The relation extraction task aims to identify useful information in text (e.g. PersonW works for OrganisationX, GeneY encodes ProteinZ) and recode it in a format such as a relational database or RDF triplestore that can be more effectively used for querying and automated reasoning. A number of resources have been developed for training and evaluating automatic systems for relation extraction in different domains. However, comparative evaluation is impeded by the fact that these corpora use different markup formats and notions of what constitutes a relation. We describe the preparation of corpora for comparative evaluation of relation extraction across domains based on the publicly available ACE 2004, ACE 2005 and BioInfer data sets. We present a common document type using token standoff and including detailed linguistic markup, while maintaining all information in the original annotation. The subsequent reannotation process normalises the two data sets so that they comply with a notion of relation that is intuitive, simple and informed by the semantic web. For the ACE data, we describe an automatic process that automatically converts many relations involving nested, nominal entity mentions to relations involving non-nested, named or pronominal entity mentions. For example, the first entity is mapped from 'one' to 'Amidu Berry' in the membership relation described in 'Amidu Berry, one half of PBS'. Moreover, we describe a comparably reannotated version of the BioInfer corpus that flattens nested relations, maps part-whole to part-part relations and maps n-ary to binary relations. Finally, we summarise experiments that compare approaches to generic relation extraction, a knowledge discovery task that uses minimally supervised techniques to achieve maximally portable extractors. These experiments illustrate the utility of the corpora.39 page(s

Generalisation in named entity recognition: A quantitative analysis

Named Entity Recognition (NER) is a key NLP task, which is all the more challenging on Web and user-generated content with their diverse and continuously changing language. This paper aims to quantify how this diversity impacts state-of-the-art NER methods, by measuring named entity (NE) and context variability, feature sparsity, and their effects on precision and recall. In particular, our findings indicate that NER approaches struggle to generalise in diverse genres with limited training data. Unseen NEs, in particular, play an important role, which have a higher incidence in diverse genres such as social media than in more regular genres such as newswire. Coupled with a higher incidence of unseen features more generally and the lack of large training corpora, this leads to significantly lower F1 scores for diverse genres as compared to more regular ones. We also find that leading systems rely heavily on surface forms found in training data, having problems generalising beyond these, and offer explanations for this observation

Mining clinical relationships from patient narratives

Background The Clinical E-Science Framework (CLEF) project has built a system to extract clinically significant information from the textual component of medical records in order to support clinical research, evidence-based healthcare and genotype-meets-phenotype informatics. One part of this system is the identification of relationships between clinically important entities in the text. Typical approaches to relationship extraction in this domain have used full parses, domain-specific grammars, and large knowledge bases encoding domain knowledge. In other areas of biomedical NLP, statistical machine learning (ML) approaches are now routinely applied to relationship extraction. We report on the novel application of these statistical techniques to the extraction of clinical relationships. Results We have designed and implemented an ML-based system for relation extraction, using support vector machines, and trained and tested it on a corpus of oncology narratives hand-annotated with clinically important relationships. Over a class of seven relation types, the system achieves an average F1 score of 72%, only slightly behind an indicative measure of human inter annotator agreement on the same task. We investigate the effectiveness of different features for this task, how extraction performance varies between inter- and intra-sentential relationships, and examine the amount of training data needed to learn various relationships. Conclusion We have shown that it is possible to extract important clinical relationships from text, using supervised statistical ML techniques, at levels of accuracy approaching those of human annotators. Given the importance of relation extraction as an enabling technology for text mining and given also the ready adaptability of systems based on our supervised learning approach to other clinical relationship extraction tasks, this result has significance for clinical text mining more generally, though further work to confirm our encouraging results should be carried out on a larger sample of narratives and relationship types

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011

We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI), and the supporting task on Entity Relations (REL). The two main tasks represent extensions of the event extraction model introduced in the BioNLP Shared Task 2009 (ST'09) to two new areas of biomedical scientific literature, each motivated by the needs of specific biocuration tasks. The ID task concerns the molecular mechanisms of infection, virulence and resistance, focusing in particular on the functions of a class of signaling systems that are ubiquitous in bacteria. The EPI task is dedicated to the extraction of statements regarding chemical modifications of DNA and proteins, with particular emphasis on changes relating to the epigenetic control of gene expression. By contrast to these two application-oriented main tasks, the REL task seeks to support extraction in general by separating challenges relating to part-of relations into a subproblem that can be addressed by independent systems. Seven groups participated in each of the two main tasks and four groups in the supporting task. The participating systems indicated advances in the capability of event extraction methods and demonstrated generalization in many aspects: from abstracts to full texts, from previously considered subdomains to new ones, and from the ST'09 extraction targets to other entities and events. The highest performance achieved in the supporting task REL, 58% F-score, is broadly comparable with levels reported for other relation extraction tasks. For the ID task, the highest-performing system achieved 56% F-score, comparable to the state-of-the-art performance at the established ST'09 task. In the EPI task, the best result was 53% F-score for the full set of extraction targets and 69% F-score for a reduced set of core extraction targets, approaching a level of performance sufficient for user-facing applications. In this study, we extend on previously reported results and perform further analyses of the outputs of the participating systems. We place specific emphasis on aspects of system performance relating to real-world applicability, considering alternate evaluation metrics and performing additional manual analysis of system outputs. We further demonstrate that the strengths of extraction systems can be combined to improve on the performance achieved by any system in isolation. The manually annotated corpora, supporting resources, and evaluation tools for all tasks are available from http://www.bionlp-st.org and the tasks continue as open challenges for all interested parties

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

The role of syllables in sign language production

The aim of the present study was to investigate the functional role of syllables in sign language and how the different phonological combinations influence sign production. Moreover, the influence of age of acquisition was evaluated. Deaf signers (native and non-native) of Catalan Signed Language (LSC) were asked in a picture-sign interference task to sign picture names while ignoring distractor-signs with which they shared two phonological parameters (out of three of the main sign parameters: Location, Movement, and Handshape). The results revealed a different impact of the three phonological combinations. While no effect was observed for the phonological combination Handshape-Location, the combination Handshape-Movement slowed down signing latencies, but only in the non-native group. A facilitatory effect was observed for both groups when pictures and distractors shared Location-Movement. Importantly, linguistic models have considered this phonological combination to be a privileged unit in the composition of signs, as syllables are in spoken languages. Thus, our results support the functional role of syllable units during phonological articulation in sign language production