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

Mining semantics for culturomics: towards a knowledge-based approach

The massive amounts of text data made available through the Google Books digitization project have inspired a new field of big-data textual research. Named culturomics, this field has attracted the attention of a growing number of scholars over recent years. However, initial studies based on these data have been criticized for not referring to relevant work in linguistics and language technology. This paper provides some ideas, thoughts and first steps towards a new culturomics initiative, based this time on Swedish data, which pursues a more knowledge-based approach than previous work in this emerging field. The amount of new Swedish text produced daily and older texts being digitized in cultural heritage projects grows at an accelerating rate. These volumes of text being available in digital form have grown far beyond the capacity of human readers, leaving automated semantic processing of the texts as the only realistic option for accessing and using the information contained in them. The aim of our recently initiated research program is to advance the state of the art in language technology resources and methods for semantic processing of Big Swedish text and focus on the theoretical and methodological advancement of the state of the art in extracting and correlating information from large volumes of Swedish text using a combination of knowledge-based and statistical methods

BioInfer: a corpus for information extraction in the biomedical domain

BACKGROUND: Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scientific publications. The development and evaluation of such methods requires annotated domain corpora. RESULTS: We present BioInfer (Bio Information Extraction Resource), a new public resource providing an annotated corpus of biomedical English. We describe an annotation scheme capturing named entities and their relationships along with a dependency analysis of sentence syntax. We further present ontologies defining the types of entities and relationships annotated in the corpus. Currently, the corpus contains 1100 sentences from abstracts of biomedical research articles annotated for relationships, named entities, as well as syntactic dependencies. Supporting software is provided with the corpus. The corpus is unique in the domain in combining these annotation types for a single set of sentences, and in the level of detail of the relationship annotation. CONCLUSION: We introduce a corpus targeted at protein, gene, and RNA relationships which serves as a resource for the development of information extraction systems and their components such as parsers and domain analyzers. The corpus will be maintained and further developed with a current version being available at

Task-based parser output combination : workflow and infrastructure

This dissertation introduces the method of task-based parser output combination as a device to enhance the reliability of automatically generated syntactic information for further processing tasks. Parsers, i.e. tools generating syntactic analyses, are usually based on reference data. Typically these are modern news texts. However, the data relevant for applications or tasks beyond parsing often differs from this standard domain, or only specific phenomena from the syntactic analysis are actually relevant for further processing. In these cases, the reliability of the parsing output might deviate essentially from the expected outcome on standard news text. Studies for several levels of analysis in natural language processing have shown that combining systems from the same analysis level outperforms the best involved single system. This is due to different error distributions of the involved systems which can be exploited, e.g. in a majority voting approach. In other words: for an effective combination, the involved systems have to be sufficiently different. In these combination studies, usually the complete analyses are combined and evaluated. However, to be able to combine the analyses completely, a full mapping of their structures and tagsets has to be found. The need for a full mapping either restricts the degree to which the participating systems are allowed to differ or it results in information loss. Moreover, the evaluation of the combined complete analyses does not reflect the reliability achieved in the analysis of the specific aspects needed to resolve a given task. This work presents an abstract workflow which can be instantiated based on the respective task and the available parsers. The approach focusses on the task-relevant aspects and aims at increasing the reliability of their analysis. Moreover, this focus allows a combination of more diverging systems, since no full mapping of the structures and tagsets from the single systems is needed. The usability of this method is also increased by focussing on the output of the parsers: It is not necessary for the users to reengineer the tools. Instead, off-the-shelf parsers and parsers for which no configuration options or sources are available to the users can be included. Based on this, the method is applicable to a broad range of applications. For instance, it can be applied to tasks from the growing field of Digital Humanities, where the focus is often on tasks different from syntactic analysis