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

Supervised Machine Learning Techniques to Detect TimeML Events in French and English

International audienceIdentifying events from texts is an information extraction task necessary for many NLP applications. Through the TimeML specifications and TempEval challenges, it has received some attention in the last years; yet, no reference result is available for French. In this paper, we try to fill this gap by proposing several event extraction systems, combining for instance Conditional Random Fields, language modeling and k-nearest-neighbors. These systems are evaluated on French corpora and compared with state-of-the-art methods on English. The very good results obtained on both languages validate our whole approach

Event extraction and representation: A case study for the portuguese language

Text information extraction is an important natural language processing (NLP) task, which aims to automatically identify, extract, and represent information from text. In this context, event extraction plays a relevant role, allowing actions, agents, objects, places, and time periods to be identified and represented. The extracted information can be represented by specialized ontologies, supporting knowledge-based reasoning and inference processes. In this work, we will describe, in detail, our proposal for event extraction from Portuguese documents. The proposed approach is based on a pipeline of specialized natural language processing tools; namely, a part-of-speech tagger, a named entities recognizer, a dependency parser, semantic role labeling, and a knowledge extraction module. The architecture is language-independent, but its modules are language-dependent and can be built using adequate AI (i.e., rule-based or machine learning) methodologies. The developed system was evaluated with a corpus of Portuguese texts and the obtained results are presented and analysed. The current limitations and future work are discussed in detail

Event extraction from biomedical texts using trimmed dependency graphs

This thesis explores the automatic extraction of information from biomedical publications. Such techniques are urgently needed because the biosciences are publishing continually increasing numbers of texts. The focus of this work is on events. Information about events is currently manually curated from the literature by biocurators. Biocuration, however, is time-consuming and costly so automatic methods are needed for information extraction from the literature. This thesis is dedicated to modeling, implementing and evaluating an advanced event extraction approach based on the analysis of syntactic dependency graphs. This work presents the event extraction approach proposed and its implementation, the JReX (Jena Relation eXtraction) system. This system was used by the University of Jena (JULIE Lab) team in the "BioNLP 2009 Shared Task on Event Extraction" competition and was ranked second among 24 competing teams. Thereafter JReX was the highest scorer on the worldwide shared U-Compare event extraction server, outperforming the competing systems from the challenge. This success was made possible, among other things, by extensive research on event extraction solutions carried out during this thesis, e.g., exploring the effects of syntactic and semantic processing procedures on solving the event extraction task. The evaluations executed on standard and community-wide accepted competition data were complemented by real-life evaluation of large-scale biomedical database reconstruction. This work showed that considerable parts of manually curated databases can be automatically re-created with the help of the event extraction approach developed. Successful re-creation was possible for parts of RegulonDB, the world's largest database for E. coli. In summary, the event extraction approach justified, developed and implemented in this thesis meets the needs of a large community of human curators and thus helps in the acquisition of new knowledge in the biosciences

Schema-aware Reference as Prompt Improves Data-Efficient Relational Triple and Event Extraction

Information Extraction, which aims to extract structural relational triple or event from unstructured texts, often suffers from data scarcity issues. With the development of pre-trained language models, many prompt-based approaches to data-efficient information extraction have been proposed and achieved impressive performance. However, existing prompt learning methods for information extraction are still susceptible to several potential limitations: (i) semantic gap between natural language and output structure knowledge with pre-defined schema; (ii) representation learning with locally individual instances limits the performance given the insufficient features. In this paper, we propose a novel approach of schema-aware Reference As Prompt (RAP), which dynamically leverage schema and knowledge inherited from global (few-shot) training data for each sample. Specifically, we propose a schema-aware reference store, which unifies symbolic schema and relevant textual instances. Then, we employ a dynamic reference integration module to retrieve pertinent knowledge from the datastore as prompts during training and inference. Experimental results demonstrate that RAP can be plugged into various existing models and outperforms baselines in low-resource settings on four datasets of relational triple extraction and event extraction. In addition, we provide comprehensive empirical ablations and case analysis regarding different types and scales of knowledge in order to better understand the mechanisms of RAP. Code is available in https://github.com/zjunlp/RAP.Comment: Work in progres

Event Parsing In Narrative: Trials And Tribulations Of Archaic English Fairy Tales

While event extraction and automatic summarization have taken great strides in the realm of news stories, fictional narratives like fairy tales have not been so fortunate. A number of challenges arise from the literary elements present in fairy tales that are not found in more straightforward corpora of natural language, such as archaic expressions and sentence structures. To aid in summarization of fictional texts, I created an class - a template for a digital object, in this case a semantic and story event - that captures elements predicted to help classify events as important for inclusion. I wrote a processor to run over a new corpus of fairy tales and parse them into events, then to be manually annotated for importance and clustered to create a classifier that could be used on novel texts. These two latter steps could not be completed before publication of this paper, but my proposed approach is covered extensively, as is future work along the same lines. Along with this paper, supplementary materials encompassing the event class, processor code, corpus in full text, and corpus as un-annotated event data are included

Scale Up Event Extraction Learning via Automatic Training Data Generation

The task of event extraction has long been investigated in a supervised learning paradigm, which is bound by the number and the quality of the training instances. Existing training data must be manually generated through a combination of expert domain knowledge and extensive human involvement. However, due to drastic efforts required in annotating text, the resultant datasets are usually small, which severally affects the quality of the learned model, making it hard to generalize. Our work develops an automatic approach for generating training data for event extraction. Our approach allows us to scale up event extraction training instances from thousands to hundreds of thousands, and it does this at a much lower cost than a manual approach. We achieve this by employing distant supervision to automatically create event annotations from unlabelled text using existing structured knowledge bases or tables.We then develop a neural network model with post inference to transfer the knowledge extracted from structured knowledge bases to automatically annotate typed events with corresponding arguments in text.We evaluate our approach by using the knowledge extracted from Freebase to label texts from Wikipedia articles. Experimental results show that our approach can generate a large number of highquality training instances. We show that this large volume of training data not only leads to a better event extractor, but also allows us to detect multiple typed events