A multi-level methodology for the automated translation of a coreference resolution dataset: an application to the Italian language

In the last decade, the demand for readily accessible corpora has touched all areas of natural language processing, including coreference resolution. However, it is one of the least considered sub-fields in recent developments. Moreover, almost all existing resources are only available for the English language. To overcome this lack, this work proposes a methodology to create a corpus for coreference resolution in Italian exploiting knowledge of annotated resources in other languages. Starting from OntonNotes, the methodology translates and refines English utterances to obtain utterances respecting Italian grammar, dealing with language-specific phenomena and preserving coreference and mentions. A quantitative and qualitative evaluation is performed to assess the well-formedness of generated utterances, considering readability, grammaticality, and acceptability indexes. The results have confirmed the effectiveness of the methodology in generating a good dataset for coreference resolution starting from an existing one. The goodness of the dataset is also assessed by training a coreference resolution model based on BERT language model, achieving the promising results. Even if the methodology has been tailored for English and Italian languages, it has a general basis easily extendable to other languages, adapting a small number of language-dependent rules to generalize most of the linguistic phenomena of the language under examination

Exploring subdomain variation in biomedical language.

BACKGROUND: Applications of Natural Language Processing (NLP) technology to biomedical texts have generated significant interest in recent years. In this paper we identify and investigate the phenomenon of linguistic subdomain variation within the biomedical domain, i.e., the extent to which different subject areas of biomedicine are characterised by different linguistic behaviour. While variation at a coarser domain level such as between newswire and biomedical text is well-studied and known to affect the portability of NLP systems, we are the first to conduct an extensive investigation into more fine-grained levels of variation. RESULTS: Using the large OpenPMC text corpus, which spans the many subdomains of biomedicine, we investigate variation across a number of lexical, syntactic, semantic and discourse-related dimensions. These dimensions are chosen for their relevance to the performance of NLP systems. We use clustering techniques to analyse commonalities and distinctions among the subdomains. CONCLUSIONS: We find that while patterns of inter-subdomain variation differ somewhat from one feature set to another, robust clusters can be identified that correspond to intuitive distinctions such as that between clinical and laboratory subjects. In particular, subdomains relating to genetics and molecular biology, which are the most common sources of material for training and evaluating biomedical NLP tools, are not representative of all biomedical subdomains. We conclude that an awareness of subdomain variation is important when considering the practical use of language processing applications by biomedical researchers

Semantic text mining support for lignocellulose research

Biofuels produced from biomass are considered to be promising sustainable alternatives to fossil fuels. The conversion of lignocellulose into fermentable sugars for biofuels production requires the use of enzyme cocktails that can efficiently and economically hydrolyze lignocellulosic biomass. As many fungi naturally break down lignocellulose, the identification and characterization of the enzymes involved is a key challenge in the research and development of biomass-derived products and fuels. One approach to meeting this challenge is to mine the rapidly-expanding repertoire of microbial genomes for enzymes with the appropriate catalytic properties. Semantic technologies, including natural language processing, ontologies, semantic Web services and Web-based collaboration tools, promise to support users in handling complex data, thereby facilitating knowledge-intensive tasks. An ongoing challenge is to select the appropriate technologies and combine them in a coherent system that brings measurable improvements to the users. We present our ongoing development of a semantic infrastructure in support of genomics-based lignocellulose research. Part of this effort is the automated curation of knowledge from information on fungal enzymes that is available in the literature and genome resources. Working closely with fungal biology researchers who manually curate the existing literature, we developed ontological natural language processing pipelines integrated in a Web-based interface to assist them in two main tasks: mining the literature for relevant knowledge, and at the same time providing rich and semantically linked information

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.Siirretty Doriast

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein--protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence ``Protein A causes protein B to bind protein C&#39;&#39; can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP&#39;09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing.&nbsp; Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP&#39;09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP&#39;11 and BioNLP&#39;13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.</p

Structured Named Entities

The names of people, locations, and organisations play a central role in language, and named entity recognition (NER) has been widely studied, and successfully incorporated, into natural language processing (NLP) applications. The most common variant of NER involves identifying and classifying proper noun mentions of these and miscellaneous entities as linear spans in text. Unfortunately, this version of NER is no closer to a detailed treatment of named entities than chunking is to a full syntactic analysis. NER, so construed, reflects neither the syntactic nor semantic structure of NE mentions, and provides insufficient categorical distinctions to represent that structure. Representing this nested structure, where a mention may contain mention(s) of other entities, is critical for applications such as coreference resolution. The lack of this structure creates spurious ambiguity in the linear approximation. Research in NER has been shaped by the size and detail of the available annotated corpora. The existing structured named entity corpora are either small, in specialist domains, or in languages other than English. This thesis presents our Nested Named Entity (NNE) corpus of named entities and numerical and temporal expressions, taken from the WSJ portion of the Penn Treebank (PTB, Marcus et al., 1993). We use the BBN Pronoun Coreference and Entity Type Corpus (Weischedel and Brunstein, 2005a) as our basis, manually annotating it with a principled, fine-grained, nested annotation scheme and detailed annotation guidelines. The corpus comprises over 279,000 entities over 49,211 sentences (1,173,000 words), including 118,495 top-level entities. Our annotations were designed using twelve high-level principles that guided the development of the annotation scheme and difficult decisions for annotators. We also monitored the semantic grammar that was being induced during annotation, seeking to identify and reinforce common patterns to maintain consistent, parsimonious annotations. The result is a scheme of 118 hierarchical fine-grained entity types and nesting rules, covering all capitalised mentions of entities, and numerical and temporal expressions. Unlike many corpora, we have developed detailed guidelines, including extensive discussion of the edge cases, in an ongoing dialogue with our annotators which is critical for consistency and reproducibility. We annotated independently from the PTB bracketing, allowing annotators to choose spans which were inconsistent with the PTB conventions and errors, and only refer back to it to resolve genuine ambiguity consistently. We merged our NNE with the PTB, requiring some systematic and one-off changes to both annotations. This allows the NNE corpus to complement other PTB resources, such as PropBank, and inform PTB-derived corpora for other formalisms, such as CCG and HPSG. We compare this corpus against BBN. We consider several approaches to integrating the PTB and NNE annotations, which affect the sparsity of grammar rules and visibility of syntactic and NE structure. We explore their impact on parsing the NNE and merged variants using the Berkeley parser (Petrov et al., 2006), which performs surprisingly well without specialised NER features. We experiment with flattening the NNE annotations into linear NER variants with stacked categories, and explore the ability of a maximum entropy and a CRF NER system to reproduce them. The CRF performs substantially better, but is infeasible to train on the enormous stacked category sets. The flattened output of the Berkeley parser are almost competitive with the CRF. Our results demonstrate that the NNE corpus is feasible for statistical models to reproduce. We invite researchers to explore new, richer models of (joint) parsing and NER on this complex and challenging task. Our nested named entity corpus will improve a wide range of NLP tasks, such as coreference resolution and question answering, allowing automated systems to understand and exploit the true structure of named entities