A knowledge-based approach to information extraction for semantic interoperability in the archaeology domain

The paper presents a method for automatic semantic indexing of archaeological grey-literature reports using empirical (rule-based) Information Extraction techniques in combination with domain-specific knowledge organization systems. Performance is evaluated via the Gold Standard method. The semantic annotation system (OPTIMA) performs the tasks of Named Entity Recognition, Relation Extraction, Negation Detection and Word Sense disambiguation using hand-crafted rules and terminological resources for associating contextual abstractions with classes of the standard ontology (ISO 21127:2006) CIDOC Conceptual Reference Model (CRM) for cultural heritage and its archaeological extension, CRM-EH, together with concepts from English Heritage thesauri and glossaries.Relation Extraction performance benefits from a syntactic based definition of relation extraction patterns derived from domain oriented corpus analysis. The evaluation also shows clear benefit in the use of assistive NLP modules relating to word-sense disambiguation, negation detection and noun phrase validation, together with controlled thesaurus expansion.The semantic indexing results demonstrate the capacity of rule-based Information Extraction techniques to deliver interoperable semantic abstractions (semantic annotations) with respect to the CIDOC CRM and archaeological thesauri. Major contributions include recognition of relevant entities using shallow parsing NLP techniques driven by a complimentary use of ontological and terminological domain resources and empirical derivation of context-driven relation extraction rules for the recognition of semantic relationships from phrases of unstructured text. The semantic annotations have proven capable of supporting semantic query, document study and cross-searching via the ontology framework

Few-Shot Relation Extraction with Hybrid Visual Evidence

The goal of few-shot relation extraction is to predict relations between name entities in a sentence when only a few labeled instances are available for training. Existing few-shot relation extraction methods focus on uni-modal information such as text only. This reduces performance when there are no clear contexts between the name entities described in text. We propose a multi-modal few-shot relation extraction model (MFS-HVE) that leverages both textual and visual semantic information to learn a multi-modal representation jointly. The MFS-HVE includes semantic feature extractors and multi-modal fusion components. The MFS-HVE semantic feature extractors are developed to extract both textual and visual features. The visual features include global image features and local object features within the image. The MFS-HVE multi-modal fusion unit integrates information from various modalities using image-guided attention, object-guided attention, and hybrid feature attention to fully capture the semantic interaction between visual regions of images and relevant texts. Extensive experiments conducted on two public datasets demonstrate that semantic visual information significantly improves the performance of few-shot relation prediction.Comment: 16 pages, 5 figure

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

Discovering Relations by Entity Search in Lightweight Semantic Text Graphs

Entity search is becoming a popular alternative for full text search. Recently Google released its entity search based on confirmed, human-generated data such as Wikipedia. In spite of these developments, the task of entity discovery, search, or relation search in unstructured text remains a major challenge in the fields of information retrieval and information extraction. This paper tries to address that challenge, focusing specifically on entity relation discovery. This is achieved by processing unstructured text using simple information extraction methods, building lightweight semantic graphs and reusing them for entity relation discovery by applying algorithms from graph theory. An important part is also user interaction with semantic graphs, which can significantly improve information extraction results and entity relation search. Entity relations can be discovered by various text mining methods, but the advantage of the presented method lies in the similarity between the lightweight semantics extracted from a text and the information networks available as structured data. Both graph structures have similar properties and similar relation discovery algorithms can be applied. In addition, we can benefit from the integration of such graph data. We provide both a relevance and performance evaluations of the approach and showcase it in several use case applications

Enhancing Biomedical Text Summarization Using Semantic Relation Extraction

Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1) We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2) We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3) For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization

LANGUAGE MODELS FOR RARE DISEASE INFORMATION EXTRACTION: EMPIRICAL INSIGHTS AND MODEL COMPARISONS

End-to-end relation extraction (E2ERE) is a crucial task in natural language processing (NLP) that involves identifying and classifying semantic relationships between entities in text. This thesis compares three paradigms for end-to-end relation extraction (E2ERE) in biomedicine, focusing on rare diseases with discontinuous and nested entities. We evaluate Named Entity Recognition (NER) to Relation Extraction (RE) pipelines, sequence-to-sequence models, and generative pre-trained transformer (GPT) models using the RareDis information extraction dataset. Our findings indicate that pipeline models are the most effective, followed closely by sequence-to-sequence models. GPT models, despite having eight times as many parameters, perform worse than sequence-to-sequence models and significantly lag pipeline models. Our results also hold for a second E2ERE dataset for chemical-protein interactions