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

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

Amorphous procedure extraction

The procedure extraction problem is concerned with the meaning preserving formation of a procedure from a (not necessarily contiguous) selected set of statements. Previous approaches to the problem have used dependence analysis to identify the non-selected statements which must be 'promoted' (also selected) in order to preserve semantics. All previous approaches to the problem have been syntax preserving. This work shows that by allowing transformation of the program's syntax it is possible to extract both procedures and functions in an amorphous manner. That is, although the amorphous extraction process is meaning preserving it is not necessarily syntax preserving. The amorphous approach is advantageous in a variety of situations. These include when it is desirable to avoid promotion, when a value-returning function is to be extracted from a scattered set of assignments to a variable, and when side effects are present in the program from which the procedure is to be extracted

Amorphous procedure extraction

The procedure extraction problem is concerned with the meaning preserving formation of a procedure from a (not necessarily contiguous) selected set of statements. Previous approaches to the problem have used dependence analysis to identify the non-selected statements which must be 'promoted' (also selected) in order to preserve semantics. All previous approaches to the problem have been syntax preserving. This work shows that by allowing transformation of the program's syntax it is possible to extract both procedures and functions in an amorphous manner. That is, although the amorphous extraction process is meaning preserving it is not necessarily syntax preserving. The amorphous approach is advantageous in a variety of situations. These include when it is desirable to avoid promotion, when a value-returning function is to be extracted from a scattered set of assignments to a variable, and when side effects are present in the program from which the procedure is to be extracted

The Parma Polyhedra Library: Toward a Complete Set of Numerical Abstractions for the Analysis and Verification of Hardware and Software Systems

Since its inception as a student project in 2001, initially just for the handling (as the name implies) of convex polyhedra, the Parma Polyhedra Library has been continuously improved and extended by joining scrupulous research on the theoretical foundations of (possibly non-convex) numerical abstractions to a total adherence to the best available practices in software development. Even though it is still not fully mature and functionally complete, the Parma Polyhedra Library already offers a combination of functionality, reliability, usability and performance that is not matched by similar, freely available libraries. In this paper, we present the main features of the current version of the library, emphasizing those that distinguish it from other similar libraries and those that are important for applications in the field of analysis and verification of hardware and software systems.Comment: 38 pages, 2 figures, 3 listings, 3 table

Discourse Structure in Machine Translation Evaluation

In this article, we explore the potential of using sentence-level discourse structure for machine translation evaluation. We first design discourse-aware similarity measures, which use all-subtree kernels to compare discourse parse trees in accordance with the Rhetorical Structure Theory (RST). Then, we show that a simple linear combination with these measures can help improve various existing machine translation evaluation metrics regarding correlation with human judgments both at the segment- and at the system-level. This suggests that discourse information is complementary to the information used by many of the existing evaluation metrics, and thus it could be taken into account when developing richer evaluation metrics, such as the WMT-14 winning combined metric DiscoTKparty. We also provide a detailed analysis of the relevance of various discourse elements and relations from the RST parse trees for machine translation evaluation. In particular we show that: (i) all aspects of the RST tree are relevant, (ii) nuclearity is more useful than relation type, and (iii) the similarity of the translation RST tree to the reference tree is positively correlated with translation quality.Comment: machine translation, machine translation evaluation, discourse analysis. Computational Linguistics, 201

Participatory Sustainability Approach to Value Capture-Based Urban Rail Financing in India through Deliberated Stakeholder Engagement

Increasingly, cities around the world are seeking innovative financial mechanisms to build rail transit projects. Land value capture (VC) is a financing mechanism to fund urban rail transit. Often VC mechanisms are viewed only as a financing tool applied in relation to increased land values from the administration and legislation perspectives, without actively involving the community in the process. The lack of such participation has resulted in the under collection of the true value established. The transit beneficiary community and city tax payers are especially important stakeholders in this process as their willingness to participate is really critical to the overall VC success and transport outcome. This paper introduces a participatory sustainability approach to enable a more deliberated stakeholder engagement intervention across the VC life cycle. A four-step “Participatory Strategic Value Capture (PSVC)” framework is proposed offering step-by-step guidance toward facilitating a meaningful stakeholder dialogue, deliberation, and collaboration around the stated engagement interests. The PSVC framework, applied to the proposed Bangalore sub-urban rail project in India, has demonstrated the importance of stakeholder engagement using deliberated participatory approaches from a win-win perspective

Argumentation Mining in User-Generated Web Discourse

The goal of argumentation mining, an evolving research field in computational linguistics, is to design methods capable of analyzing people's argumentation. In this article, we go beyond the state of the art in several ways. (i) We deal with actual Web data and take up the challenges given by the variety of registers, multiple domains, and unrestricted noisy user-generated Web discourse. (ii) We bridge the gap between normative argumentation theories and argumentation phenomena encountered in actual data by adapting an argumentation model tested in an extensive annotation study. (iii) We create a new gold standard corpus (90k tokens in 340 documents) and experiment with several machine learning methods to identify argument components. We offer the data, source codes, and annotation guidelines to the community under free licenses. Our findings show that argumentation mining in user-generated Web discourse is a feasible but challenging task.Comment: Cite as: Habernal, I. & Gurevych, I. (2017). Argumentation Mining in User-Generated Web Discourse. Computational Linguistics 43(1), pp. 125-17