Yassine Mrabet

Text mining for pharmacovigilance

Pharmacovigilance (PV) is defined by the World Health Organization as the science and activities related to the detection, assessment, understanding and prevention of adverse effects or any other drug-related problem. An essential aspect in PV is to acquire knowledge about Drug-Drug Interactions (DDIs). The shared tasks on DDI-Extraction organized in 2011 and 2013 have pointed out the importance of this issue and provided benchmarks for: Drug Name Recognition, DDI extraction and DDI classification. In this paper, we present our text mining systems for these tasks and evaluate their results on the DDI-Extraction benchmarks. Our systems rely on machine learning techniques using both feature-based and kernel-based methods. The obtained results for drug name recognition are encouraging. For DDI-Extraction, our hybrid system combining a feature-based method and a kernel-based method was ranked second in the DDI-Extraction-2011 challenge, and our two-step system for DDI detection and classification was ranked first in the DDI-Extraction-2013 task at SemEval. We discuss our methods and results and give pointers to future work.

TextFlow: A Text Similarity Measure based on Continuous Sequences

Text similarity measures are used in multiple tasks such as plagiarism detection, information ranking and recognition of paraphrases and textual entailment. While recent advances in deep learning highlighted the relevance of sequential models in natural language generation, existing similarity measures do not fully exploit the sequential nature of language. Examples of such similarity measures include n-grams and skip-grams overlap which rely on distinct slices of the input texts. In this paper we present a novel text similarity measure inspired from a common representation in DNA sequence alignment algorithms. The new measure, called TextFlow, represents input text pairs as continuous curves and uses both the actual position of the words and sequence matching to compute the similarity value. Our experiments on 8 different datasets show very encouraging results in paraphrase detection, textual entailment recognition and ranking relevance.

Towards natural language question generation for the validation of ontologies and mappings

BackgroundThe increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the validation of ontologies from a domain point-of-view. However, the growing number of ontologies and their fast evolution over time make manual validation challenging.MethodsWe propose a novel semi-automatic approach based on the generation of natural language (NL) questions to support the validation of ontologies and their evolution. The proposed approach includes the automatic generation, factorization and ordering of NL questions from medical ontologies. The final validation and correction is performed by submitting these questions to domain experts and automatically analyzing their feedback. We also propose a second approach for the validation of mappings impacted by ontology changes. The method exploits the context of the changes to propose correction alternatives presented as Multiple Choice Questions.ResultsThis research provides a question optimization strategy to maximize the validation of ontology entities with a reduced number of questions. We evaluate our approach for the validation of three medical ontologies. We also evaluate the feasibility and efficiency of our mappings validation approach in the context of ontology evolution. These experiments are performed with different versions of SNOMED-CT and ICD9.ConclusionsThe obtained experimental results suggest the feasibility and adequacy of our approach to support the validation of interconnected and evolving ontologies. Results also suggest that taking into account RDFS and OWL entailment helps reducing the number of questions and validation time. The application of our approach to validate mapping evolution also shows the difficulty of adapting mapping evolution over time and highlights the importance of semi-automatic validation.

Semantic Analysis and Automatic Corpus Construction for Entailment Recognition in Medical Texts

Textual Entailment Recognition (RTE) consists in detecting inference relationships between natural language sentences. It has a wide range of applications such as machine translation, question answering or text summarization. Significant interest has been brought to RTE with several challenges. However, most of current approaches are dedicated to open domains. The major challenge facing RTE in specialized domains is the lack of relevant training corpora and resources. In this paper we present an automatic corpus construction approach for RTE in the medical domain. We also quantify the impact of using (open-)domain RDF datasets on supervised learning based RTE. We evaluate the relevance of our corpus construction method by comparing the results obtained by an efficient memory based learning algorithm on PASCAL RTE corpora and on our automatically constructed corpus. The results show an accuracy increase of +6 to +28% and an improvement of +8 to +23% in terms of F-measure. We also found that semantic annotations from large open-domain datasets increased F1 score by 6%, while smaller medical RDF datasets actually decreased the overall performance. We discuss these findings and give some pointers to future investigations.

Semantic annotation of consumer health questions

BackgroundConsumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health information needs are complex and can only fully be expressed in natural language. Consumer health question answering (QA) systems aim to fill this gap. A major challenge in developing consumer health QA systems is extracting relevant semantic content from the natural language questions (question understanding). To develop effective question understanding tools, question corpora semantically annotated for relevant question elements are needed. In this paper, we present a two-part consumer health question corpus annotated with several semantic categories: named entities, question triggers/types, question frames, and question topic. The first part (CHQA-email) consists of relatively long email requests received by the U.S. National Library of Medicine (NLM) customer service, while the second part (CHQA-web) consists of shorter questions posed to MedlinePlus search engine as queries. Each question has been annotated by two annotators. The annotation methodology is largely the same between the two parts of the corpus; however, we also explain and justify the differences between them. Additionally, we provide information about corpus characteristics, inter-annotator agreement, and our attempts to measure annotation confidence in the absence of adjudication of annotations.ResultsThe resulting corpus consists of 2614 questions (CHQA-email: 1740, CHQA-web: 874). Problems are the most frequent named entities, while treatment and general information questions are the most common question types. Inter-annotator agreement was generally modest: question types and topics yielded highest agreement, while the agreement for more complex frame annotations was lower. Agreement in CHQA-web was consistently higher than that in CHQA-email. Pairwise inter-annotator agreement proved most useful in estimating annotation confidence.ConclusionsTo our knowledge, our corpus is the first focusing on annotation of uncurated consumer health questions. It is currently used to develop machine learning-based methods for question understanding. We make the corpus publicly available to stimulate further research on consumer health QA.

LIST-LUX: Disorder Identification from Clinical Texts

This paper describes our participation in task 14 of SemEval 2015. This task focuses on the analysis of clinical texts and includes: (i) the recognition of the span of a disorder mention and (ii) its normalization to a unique concept identifier in the UMLS/SNOMEDCT terminology. We propose a two-step approach which relies first on Conditional Random Fields to detect textual mentions of disorders using different lexical, syntactic, orthographic and semantic features such as ontologies and, second, on a similarity measure and SNOMED to determine the relevant CUI. We present and discuss the obtained results on the development corpus and the official test corpus.