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

Using domain specific language and sequence to sequence models as a hybrid framework for a natural language interface to a database solution

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonThe aim of this project is to provide a new approach to solving the problem of converting natural language into a language capable of querying a database or data repository. This problem has been around for a while, in the 1970's the US Navy developed a solution called LADDER and since then there have been an array of solutions, approaches and tweaks that have kept the research community busy. The introduction of electronic assistants into the smart phone in 2010 has given new impetus to this problem. With the increasingly pervasive nature of data and its ever expanding use to answer questions within business science, medicine extracting data is becoming more important. The idea behind this project is to make data more democratised by allowing access to it without the need for specialist languages. The performance and reliability of converting natural language into structured query language can be problematic in handling nuances that are prevalent in natural language. Relational databases are not designed to understand language nuance. This project introduces the following components as part of a holistic approach to improving the conversion of a natural language statement into a language capable of querying a data repository. ● The idea proposed in this project combines the use of sequence to sequence models in conjunction with the natural language part of speech technologies and domain specific languages to convert natural language queries into SQL. The approach being proposed by this chapter is to use natural language processing to perform an initial shallow pass of the incoming query and then use Google's Tensor Flow to refine the query with the use of a sequence to sequence model. ● This thesis is also proposing to use a Domain Specific Language (DSL) as part of the conversion process. The use of the DSL has the potential to allow the natural language query to be translated into more than just an SQL statement, but any query language such as NoSQL or XQuery

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

Coreference resolution in clinical discharge summaries, progress notes, surgical and pathology reports: a unified lexical approach

We developed a lexical rule-based system that uses a unified approach to resolving coreference across a wide variety of clinical records comprising discharge summaries, progress notes, pathology, radiology and surgical reports from two corpora (Ontology Development and Information Extraction (ODIE) and i2b2/VA) provided for the fifth i2b2/VA shared task. Taking the unweighted mean between 4 coreference metrics, validation of the system against the i2b2/VA corpus attained an overall F-score of 87.7% across all mention classes, with a maximum of 93.1% for coreference of persons, and a minimum of 77.2% for coreference of tests. For the ODIE corpus the overall F-score across all mention classes was 79.4%, with a maximum of 82.0% for coreference of persons and a minimum of 13.1% for coreference of diagnostic reagents. For the ODIE corpus our results are comparable to the mean reported inter-annotator agreement with the gold standard. We discuss the four categories of errors we identified, and how these might be addressed. The system uses a number of reusable modules and techniques that may be of benefit to the research community

Semantic chunking

Long sentences pose a challenge for natural language processing (NLP) applications. They are associated with a complex information structure leading to increased requirements for processing resources. Although the issue is present in many areas of research, there is little uniformity in the solutions used by research communities dedicated to individual NLP applications. Different aspects of the problem are addressed by different tasks, such as sentence simplification or shallow chunking. The main contribution of this thesis is the introduction of the task of semantic chunking as a general approach to reducing the cost of processing long sentences. The goal of semantic chunking is to find semantically contained fragments of a sentence representation that can be processed independently and recombined without loss of information. We anchor its principles in established concepts of semantic theory, in particular event and situation semantics. Most of the experiments in this thesis focus on semantic chunking defined on complex semantic representations in Dependency Minimal Recursion Semantics (DMRS), but we also demonstrate that the task can be performed on sentence strings. We present three chunking models: a) rule-based proof-of-concept DMRS chunking system; b) a semi-supervised sequence labelling neural model for surface semantic chunking; c) a system capable of finding semantic chunk boundaries based on the inherent structure of DMRS graphs, generalisable in the form of descriptive templates. We show how semantic chunking can be applied within a divide-and-conquer processing paradigm, using as an example the task of realization from DMRS. The application of semantic chunking yields noticeable efficiency gains without decreasing the quality of results

Toward a Neural Semantic Parsing System for EHR Question Answering

Clinical semantic parsing (SP) is an important step toward identifying the exact information need (as a machine-understandable logical form) from a natural language query aimed at retrieving information from electronic health records (EHRs). Current approaches to clinical SP are largely based on traditional machine learning and require hand-building a lexicon. The recent advancements in neural SP show a promise for building a robust and flexible semantic parser without much human effort. Thus, in this paper, we aim to systematically assess the performance of two such neural SP models for EHR question answering (QA). We found that the performance of these advanced neural models on two clinical SP datasets is promising given their ease of application and generalizability. Our error analysis surfaces the common types of errors made by these models and has the potential to inform future research into improving the performance of neural SP models for EHR QA.Comment: Accepted at the AMIA Annual Symposium 2022 (10 pages, 5 tables, 1 figure