A Dependency Parsing Approach to Biomedical Text Mining

Biomedical research is currently facing a new type of challenge: an excess of information, both in terms of raw data from experiments and in the number of scientific publications describing their results. Mirroring the focus on data mining techniques to address the issues of structured data, there has recently been great interest in the development and application of text mining techniques to make more effective use of the knowledge contained in biomedical scientific publications, accessible only in the form of natural human language. This thesis describes research done in the broader scope of projects aiming to develop methods, tools and techniques for text mining tasks in general and for the biomedical domain in particular. The work described here involves more specifically the goal of extracting information from statements concerning relations of biomedical entities, such as protein-protein interactions. The approach taken is one using full parsing—syntactic analysis of the entire structure of sentences—and machine learning, aiming to develop reliable methods that can further be generalized to apply also to other domains. The five papers at the core of this thesis describe research on a number of distinct but related topics in text mining. In the first of these studies, we assessed the applicability of two popular general English parsers to biomedical text mining and, finding their performance limited, identified several specific challenges to accurate parsing of domain text. In a follow-up study focusing on parsing issues related to specialized domain terminology, we evaluated three lexical adaptation methods. We found that the accurate resolution of unknown words can considerably improve parsing performance and introduced a domain-adapted parser that reduced the error rate of theoriginal by 10% while also roughly halving parsing time. To establish the relative merits of parsers that differ in the applied formalisms and the representation given to their syntactic analyses, we have also developed evaluation methodology, considering different approaches to establishing comparable dependency-based evaluation results. We introduced a methodology for creating highly accurate conversions between different parse representations, demonstrating the feasibility of unification of idiverse syntactic schemes under a shared, application-oriented representation. In addition to allowing formalism-neutral evaluation, we argue that such unification can also increase the value of parsers for domain text mining. As a further step in this direction, we analysed the characteristics of publicly available biomedical corpora annotated for protein-protein interactions and created tools for converting them into a shared form, thus contributing also to the unification of text mining resources. The introduced unified corpora allowed us to perform a task-oriented comparative evaluation of biomedical text mining corpora. This evaluation established clear limits on the comparability of results for text mining methods evaluated on different resources, prompting further efforts toward standardization. To support this and other research, we have also designed and annotated BioInfer, the first domain corpus of its size combining annotation of syntax and biomedical entities with a detailed annotation of their relationships. The corpus represents a major design and development effort of the research group, with manual annotation that identifies over 6000 entities, 2500 relationships and 28,000 syntactic dependencies in 1100 sentences. In addition to combining these key annotations for a single set of sentences, BioInfer was also the first domain resource to introduce a representation of entity relations that is supported by ontologies and able to capture complex, structured relationships. Part I of this thesis presents a summary of this research in the broader context of a text mining system, and Part II contains reprints of the five included publications.Siirretty Doriast

Lessons Learned from EVALITA 2020 and Thirteen Years of Evaluation of Italian Language Technology

This paper provides a summary of the 7th Evaluation Campaign of Natural Language Processing and Speech Tools for Italian (EVALITA2020) which was held online on December 17th, due to the 2020 COVID-19 pandemic. The 2020 edition of Evalita included 14 different tasks belonging to five research areas, namely: (i) Affect, Hate, and Stance, (ii) Creativity and Style, (iii) New Challenges in Long-standing Tasks, (iv) Semantics and Multimodality, (v) Time and Diachrony. This paper provides a description of the tasks and the key findings from the analysis of participant outcomes. Moreover, it provides a detailed analysis of the participants and task organizers which demonstrates the growing interest with respect to this campaign. Finally, a detailed analysis of the evaluation of tasks across the past seven editions is provided; this allows to assess how the research carried out by the Italian community dealing with Computational Linguistics has evolved in terms of popular tasks and paradigms during the last 13 years

Evaluating contributions of natural language parsers to protein–protein interaction extraction

Motivation: While text mining technologies for biomedical research have gained popularity as a way to take advantage of the explosive growth of information in text form in biomedical papers, selecting appropriate natural language processing (NLP) tools is still difficult for researchers who are not familiar with recent advances in NLP. This article provides a comparative evaluation of several state-of-the-art natural language parsers, focusing on the task of extracting protein–protein interaction (PPI) from biomedical papers. We measure how each parser, and its output representation, contributes to accuracy improvement when the parser is used as a component in a PPI system

Natural Language Interfaces to Data

Recent advances in NLU and NLP have resulted in renewed interest in natural language interfaces to data, which provide an easy mechanism for non-technical users to access and query the data. While early systems evolved from keyword search and focused on simple factual queries, the complexity of both the input sentences as well as the generated SQL queries has evolved over time. More recently, there has also been a lot of focus on using conversational interfaces for data analytics, empowering a line of non-technical users with quick insights into the data. There are three main challenges in natural language querying (NLQ): (1) identifying the entities involved in the user utterance, (2) connecting the different entities in a meaningful way over the underlying data source to interpret user intents, and (3) generating a structured query in the form of SQL or SPARQL. There are two main approaches for interpreting a user's NLQ. Rule-based systems make use of semantic indices, ontologies, and KGs to identify the entities in the query, understand the intended relationships between those entities, and utilize grammars to generate the target queries. With the advances in deep learning (DL)-based language models, there have been many text-to-SQL approaches that try to interpret the query holistically using DL models. Hybrid approaches that utilize both rule-based techniques as well as DL models are also emerging by combining the strengths of both approaches. Conversational interfaces are the next natural step to one-shot NLQ by exploiting query context between multiple turns of conversation for disambiguation. In this article, we review the background technologies that are used in natural language interfaces, and survey the different approaches to NLQ. We also describe conversational interfaces for data analytics and discuss several benchmarks used for NLQ research and evaluation.Comment: The full version of this manuscript, as published by Foundations and Trends in Databases, is available at http://dx.doi.org/10.1561/190000007

Neural Unsupervised Domain Adaptation in NLP—A Survey

Deep neural networks excel at learning from labeled data and achieve state-of-the-art results on a wide array of Natural Language Processing tasks. In contrast, learning from unlabeled data, especially under domain shift, remains a challenge. Motivated by the latest advances, in this survey we review neural unsupervised domain adaptation techniques which do not require labeled target domain data. This is a more challenging yet a more widely applicable setup. We outline methods, from early approaches in traditional non-neural methods to pre-trained model transfer. We also revisit the notion of domain, and we uncover a bias in the type of Natural Language Processing tasks which received most attention. Lastly, we outline future directions, particularly the broader need for out-of-distribution generalization of future intelligent NLP