Processing Metonymy: a Domain-Model Heuristic Graph Traversal Approach

We address here the treatment of metonymic expressions from a knowledge representation perspective, that is, in the context of a text understanding system which aims to build a conceptual representation from texts according to a domain model expressed in a knowledge representation formalism. We focus in this paper on the part of the semantic analyser which deals with semantic composition. We explain how we use the domain model to handle metonymy dynamically, and more generally, to underlie semantic composition, using the knowledge descriptions attached to each concept of our ontology as a kind of concept-level, multiple-role qualia structure. We rely for this on a heuristic path search algorithm that exploits the graphic aspects of the conceptual graphs formalism. The methods described have been implemented and applied on French texts in the medical domain.Comment: 6 pages, LaTeX, one encapsulated PostScript figure, uses colap.sty (included) and epsf.sty (available from the cmp-lg macro library). To appear in Coling-9

Structured Named Entities in two distinct press corpora: Contemporary Broadcast News and Old Newspapers

International audienceThis paper compares the reference annotation of structured named entities in two corpora with different origins and properties. It ad- dresses two questions linked to such a comparison. On the one hand, what specific issues were raised by reusing the same annotation scheme on a corpus that differs from the first in terms of media and that predates it by more than a century? On the other hand, what contrasts were observed in the resulting annotations across the two corpora

Proposal for an Extension of Traditional Named Entitites: from Guidelines to Evaluation, an Overview

International audienceWithin the framework of the construction of a fact database, we defined guidelines to extract named entities, using a taxonomy based on an extension of the usual named entities defini- tion. We thus defined new types of entities with broader coverage including substantive- based expressions. These extended named en- tities are hierarchical (with types and compo- nents) and compositional (with recursive type inclusion and metonymy annotation). Human annotators used these guidelines to annotate a 1.3M word broadcast news corpus in French. This article presents the definition and novelty of extended named entity annotation guide- lines, the human annotation of a global corpus and of a mini reference corpus, and the evalu- ation of annotations through the computation of inter-annotator agreement. Finally, we dis- cuss our approach and the computed results, and outline further work

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

Natural language processing

Beginning with the basic issues of NLP, this chapter aims to chart the major research activities in this area since the last ARIST Chapter in 1996 (Haas, 1996), including: (i) natural language text processing systems - text summarization, information extraction, information retrieval, etc., including domain-specific applications; (ii) natural language interfaces; (iii) NLP in the context of www and digital libraries ; and (iv) evaluation of NLP systems

LIMSI@ CLEF eHealth 2015-task 2.

International audienceThis paper presents LIMSI’s participation in the User-Centered Health Information Retrieval task (task 2) at the CLEF eHealth 2015 workshop. In our contribution we explored two different strategies to query expansion, i.e. one based on entity recognition using MetaMap and the UMLS, and a second strategy based on disease hypothesis generation using self-constructed external resources such a corpus of Wikipedia pages describing diseases and conditions, and web pages from the Medline Plus health portal. Our best-scoring run was a weighed UMLS-based run which put emphasis on incorporating signs and symptoms recognized in the topic text by MetaMap. This run achieved a P@10 score of 0.262 and nDCG@10 of 0.196, respectively

SEME at SemEval-2024 Task 2: Comparing Masked and Generative Language Models on Natural Language Inference for Clinical Trials

This paper describes our submission to Task 2 of SemEval-2024: Safe Biomedical Natural Language Inference for Clinical Trials. The Multi-evidence Natural Language Inference for Clinical Trial Data (NLI4CT) consists of a Textual Entailment (TE) task focused on the evaluation of the consistency and faithfulness of Natural Language Inference (NLI) models applied to Clinical Trial Reports (CTR). We test 2 distinct approaches, one based on finetuning and ensembling Masked Language Models and the other based on prompting Large Language Models using templates, in particular, using Chain-Of-Thought and Contrastive Chain-Of-Thought. Prompting Flan-T5-large in a 2-shot setting leads to our best system that achieves 0.57 F1 score, 0.64 Faithfulness, and 0.56 Consistency

Clinical narrative analytics challenges

Precision medicine or evidence based medicine is based on the extraction of knowledge from medical records to provide individuals with the appropriate treatment in the appropriate moment according to the patient features. Despite the efforts of using clinical narratives for clinical decision support, many challenges have to be faced still today such as multilinguarity, diversity of terms and formats in different services, acronyms, negation, to name but a few. The same problems exist when one wants to analyze narratives in literature whose analysis would provide physicians and researchers with highlights. In this talk we will analyze challenges, solutions and open problems and will analyze several frameworks and tools that are able to perform NLP over free text to extract medical entities by means of Named Entity Recognition process. We will also analyze a framework we have developed to extract and validate medical terms. In particular we present two uses cases: (i) medical entities extraction of a set of infectious diseases description texts provided by MedlinePlus and (ii) scales of stroke identification in clinical narratives written in Spanish