Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape

From Text to Knowledge with Graphs: modelling, querying and exploiting textual content

This paper highlights the challenges, current trends, and open issues related to the representation, querying and analytics of content extracted from texts. The internet contains vast text-based information on various subjects, including commercial documents, medical records, scientific experiments, engineering tests, and events that impact urban and natural environments. Extracting knowledge from this text involves understanding the nuances of natural language and accurately representing the content without losing information. This allows knowledge to be accessed, inferred, or discovered. To achieve this, combining results from various fields, such as linguistics, natural language processing, knowledge representation, data storage, querying, and analytics, is necessary. The vision in this paper is that graphs can be a well-suited text content representation once annotated and the right querying and analytics techniques are applied. This paper discusses this hypothesis from the perspective of linguistics, natural language processing, graph models and databases and artificial intelligence provided by the panellists of the DOING session in the MADICS Symposium 2022

A Survey on Semantic Processing Techniques

Semantic processing is a fundamental research domain in computational linguistics. In the era of powerful pre-trained language models and large language models, the advancement of research in this domain appears to be decelerating. However, the study of semantics is multi-dimensional in linguistics. The research depth and breadth of computational semantic processing can be largely improved with new technologies. In this survey, we analyzed five semantic processing tasks, e.g., word sense disambiguation, anaphora resolution, named entity recognition, concept extraction, and subjectivity detection. We study relevant theoretical research in these fields, advanced methods, and downstream applications. We connect the surveyed tasks with downstream applications because this may inspire future scholars to fuse these low-level semantic processing tasks with high-level natural language processing tasks. The review of theoretical research may also inspire new tasks and technologies in the semantic processing domain. Finally, we compare the different semantic processing techniques and summarize their technical trends, application trends, and future directions.Comment: Published at Information Fusion, Volume 101, 2024, 101988, ISSN 1566-2535. The equal contribution mark is missed in the published version due to the publication policies. Please contact Prof. Erik Cambria for detail

A knowledge-based framework for information extraction and exploration

Harnessing insights from the colossal amount of online information requires the computerised processing of unstructured text in order to satisfy the information need of particular applications such as recommender systems and sentiment analysis. The increasing availability of online documents that describe domain-specific information provides an opportunity in employing a knowledge-based approach in extracting information from Web data. In this thesis, a novel comprehensive knowledge-based framework is proposed to construct and exploit a domain-specific semantic knowledgebase. The proposed framework introduces a methodology for linking several components of different techniques and tools. It focuses on providing reusable and configurable data and application templates, which allow developers to apply it in diversity of domains. The objectives of this framework are: extracting information from unstructured data, constructing a semantic knowledgebase from the extracted information, enriching the resultant semantic knowledgebase by sourcing appropriate semi-structured and structured datasets, and consuming the resultant semantic knowledgebase to facilitate the intelligent exploration and search of information. For the purpose of investigating the challenges of extracting and modelling information in a specific domain, the financial domain was employed as a use-case in the context of a stock investment motivating scenario. The developed knowledge-based approach exploits the semantic and syntactic characteristics of the problem domain knowledge in implementing a hybrid approach of Rule-based and Machine Learning based relation classification. The rule-based approach is adopted in the Natural Language Processing tasks associated with linguistic and structural features, Named Entity Recognition, instances labelling and feature generation processes. The results of these tasks are used to classify the relations between the named entities by employing the Machine Learning based relation classification. In addition, the domain knowledge is analysed to benefit knowledge modelling by translating the domain key concepts into a formal ontology. This ontology is employed in constructing semantic knowledgebase from unstructured online data of a specific domain, enriching the resulting semantic knowledgebase by sourcing semi-structured and structured online data sources and applying advanced classifications and inference technologies to infer new and interesting facts to improve the decision-making and intelligent exploration activities. However, most relations are non-binary in the problem domain knowledge because of its specific characteristic hence an appropriate N-ary relation patterns technique were adopted and investigated. A serious of a novel experiments were conducted to implement and configure a Machine Learning based relation classification. The experimental evaluation evidenced that the developed knowledge-assisted ML relation classification model, which was further boosted by our implementation of GAs to reduce the feature space, has resulted in significant improvement in the process of relation extraction. The experimental results also indicate that amongst the implemented ML algorithms, SVM exhibited the best relation classification accuracy in the majority of the training datasets, while retaining acceptable levels of accuracy in the rest in the remaining training datasets. Web Ontology Language (OWL) reasoning and rule-based reasoning on the resultant semantic knowledgebase were applied to derive stock investment specific recommendations. In addition, SPARQL query language was employed to explore the semantic knowledgebase. Moreover, taking into consideration the problem domain's requirements for modelling non-binary relations, a relation-as-class N-ary relations pattern was implemented, and the reasoning axioms and query language were adjusted to fit the intermediate resources in the N-ary relations requirements. In this thesis also the experience on addressing the challenges of implementing the proposed knowledge-based framework for constructing and exploiting a semantic knowledgebase were summarised. These challenges can be considered by domain experts and knowledge engineers as a novel methodology for employing the Semantic Web Technologies for the knowledge user to intelligently exploit knowledge in similar problem domains. The evaluation of knowledge accessibility by utilising Semantic Web Technologies in the developed application includes the ability of data retrieval to obtain either the entire or some portion of the data from the semantic knowledgebase for a particular use-case scenario. Investigating the tasks of reasoning, accessing and querying the semantic knowledgebase evidences that Semantic Web Technologies can perform an accurate and complex knowledge representation to share Knowledge from a diversity of data sources and, improve the decision‑making process and the intelligent exploration of the semantic knowledgebase