A Machine Learning Based Analytical Framework for Semantic Annotation Requirements

The Semantic Web is an extension of the current web in which information is given well-defined meaning. The perspective of Semantic Web is to promote the quality and intelligence of the current web by changing its contents into machine understandable form. Therefore, semantic level information is one of the cornerstones of the Semantic Web. The process of adding semantic metadata to web resources is called Semantic Annotation. There are many obstacles against the Semantic Annotation, such as multilinguality, scalability, and issues which are related to diversity and inconsistency in content of different web pages. Due to the wide range of domains and the dynamic environments that the Semantic Annotation systems must be performed on, the problem of automating annotation process is one of the significant challenges in this domain. To overcome this problem, different machine learning approaches such as supervised learning, unsupervised learning and more recent ones like, semi-supervised learning and active learning have been utilized. In this paper we present an inclusive layered classification of Semantic Annotation challenges and discuss the most important issues in this field. Also, we review and analyze machine learning applications for solving semantic annotation problems. For this goal, the article tries to closely study and categorize related researches for better understanding and to reach a framework that can map machine learning techniques into the Semantic Annotation challenges and requirements

Classification of protein interaction sentences via gaussian processes

The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

Evaluating automated and hybrid neural disambiguation for African historical named entities

Documents detailing South African history contain ambiguous names. Ambiguous names may be due to people having the same name or the same person being referred to by multiple different names. Thus when searching for or attempting to extract information about a particular person, the name used may affect the results. This problem may be alleviated by using a Named Entity Disambiguation (NED) system to disambiguate names by linking them to a knowledge base. In recent years, transformer-based language models have led to improvements in NED systems. Furthermore, multilingual language models have shown the ability to learn concepts across languages, reducing the amount of training data required in low-resource languages. Thus a multilingual language model-based NED system was developed to disambiguate people's names within a historical South African context using documents written in English and isiZulu from the 500 Year Archive (FHYA). The multilingual language model-based system substantially improved on a probability-based baseline and achieved a micro F1-score of 0.726. At the same time, the entity linking component was able to link 81.9% of the mentions to the correct entity. However, the system's performance on documents written in isiZulu was significantly lower than on the documents written in English. Thus the system was augmented with handcrafted rules to improve its performance. The addition of handcrafted rules resulted in a small but significant improvement in performance when compared to the unaugmented NED system

Negation’s Not Solved: Generalizability Versus Optimizability in Clinical Natural Language Processing

A review of published work in clinical natural language processing (NLP) may suggest that the negation detection task has been “solved.” This work proposes that an optimizable solution does not equal a generalizable solution. We introduce a new machine learning-based Polarity Module for detecting negation in clinical text, and extensively compare its performance across domains. Using four manually annotated corpora of clinical text, we show that negation detection performance suffers when there is no in-domain development (for manual methods) or training data (for machine learning-based methods). Various factors (e.g., annotation guidelines, named entity characteristics, the amount of data, and lexical and syntactic context) play a role in making generalizability difficult, but none completely explains the phenomenon. Furthermore, generalizability remains challenging because it is unclear whether to use a single source for accurate data, combine all sources into a single model, or apply domain adaptation methods. The most reliable means to improve negation detection is to manually annotate in-domain training data (or, perhaps, manually modify rules); this is a strategy for optimizing performance, rather than generalizing it. These results suggest a direction for future work in domain-adaptive and task-adaptive methods for clinical NLP