Fréjus A. A. Laleye

Qingyu Chen, Alexis Allot, Robert Leaman et al.

The COVID-19 pandemic has been severely impacting global society since December 2019. Massive research has been undertaken to understand the characteristics of the virus and design vaccines and drugs. The related findings have been reported in biomedical literature at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset, consisting of over 30,000 articles with manually reviewed topics, was created for training and testing. It is one of the largest multilabel classification datasets in biomedical scientific literature. 19 teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.

Loïc Rakotoson, Charles Letaillieur, Sylvain Massip et al.

With the explosive growth of scientific publications, making the synthesis of scientific knowledge and fact checking becomes an increasingly complex task. In this paper, we propose a multi-task approach for verifying the scientific questions based on a joint reasoning from facts and evidence in research articles. We propose an intelligent combination of (1) an automatic information summarization and (2) a Boolean Question Answering which allows to generate an answer to a scientific question from only extracts obtained after summarization. Thus on a given topic, our proposed approach conducts structured content modeling based on paper abstracts to answer a scientific question while highlighting texts from paper that discuss the topic. We based our final system on an end-to-end Extractive Question Answering (EQA) combined with a three outputs classification model to perform in-depth semantic understanding of a question to illustrate the aggregation of multiple responses. With our light and fast proposed architecture, we achieved an average error rate of 4% and a F1-score of 95.6%. Our results are supported via experiments with two QA models (BERT, RoBERTa) over 3 Million Open Access (OA) articles in the medical and health domains on Europe PMC.

Fréjus A. A. Laleye, Loïc Rakotoson, Sylvain Massip

Relation extraction task is a crucial and challenging aspect of Natural Language Processing. Several methods have surfaced as of late, exhibiting notable performance in addressing the task; however, most of these approaches rely on vast amounts of data from large-scale knowledge graphs or language models pretrained on voluminous corpora. In this paper, we hone in on the effective utilization of solely the knowledge supplied by a corpus to create a high-performing model. Our objective is to showcase that by leveraging the hierarchical structure and relational distribution of entities within a corpus without introducing external knowledge, a relation extraction model can achieve significantly enhanced performance. We therefore proposed a relation extraction approach based on the incorporation of pretrained knowledge graph embeddings at the corpus scale into the sentence-level contextual representation. We conducted a series of experiments which revealed promising and very interesting results for our proposed approach.The obtained results demonstrated an outperformance of our method compared to context-based relation extraction models.

D. Fortune Kponou, Frejus A. A. Laleye, Eugene C. Ezin

In this paper, we introduce the Fongbe to French Speech Translation Corpus (FFSTC) for the first time. This corpus encompasses approximately 31 hours of collected Fongbe language content, featuring both French transcriptions and corresponding Fongbe voice recordings. FFSTC represents a comprehensive dataset compiled through various collection methods and the efforts of dedicated individuals. Furthermore, we conduct baseline experiments using Fairseq's transformer_s and conformer models to evaluate data quality and validity. Our results indicate a score of 8.96 for the transformer_s model and 8.14 for the conformer model, establishing a baseline for the FFSTC corpus.

Loïc Rakotoson, Sylvain Massip, Fréjus A. A. Laleye

Information retrieval is a rapidly evolving field. However it still faces significant limitations in the scientific and industrial vast amounts of information, such as semantic divergence and vocabulary gaps in sparse retrieval, low precision and lack of interpretability in semantic search, or hallucination and outdated information in generative models. In this paper, we introduce a two-block approach to tackle these hurdles for long documents. The first block enhances language understanding in sparse retrieval by query expansion to retrieve relevant documents. The second block deepens the result by providing comprehensive and informative answers to the complex question using only the information spread in the long document, enabling bidirectional engagement. At various stages of the pipeline, intermediate results are presented to users to facilitate understanding of the system's reasoning. We believe this bidirectional approach brings significant advancements in terms of transparency, logical thinking, and comprehensive understanding in the field of scientific information retrieval.

Fréjus A. A. Laleye, Mikaël A. Mousse

One of the interests of modern poultry farming is the vocalization of laying hens which contain very useful information on health behavior. This information is used as health and well-being indicators that help breeders better monitor laying hens, which involves early detection of problems for rapid and more effective intervention. In this work, we focus on the sound analysis for the recognition of the types of calls of the laying hens in order to propose a robust system of characterization of their behavior for a better monitoring. To do this, we first collected and annotated laying hen call signals, then designed an optimal acoustic characterization based on the combination of time and frequency domain features. We then used these features to build the multi-label classification models based on recurrent neural network to assign a semantic class to the vocalization that characterize the laying hen behavior. The results show an overall performance with our model based on the combination of time and frequency domain features that obtained the highest F1-score (F1=92.75) with a gain of 17% on the models using the frequency domain features and of 8% on the compared approaches from the litterature.

Loïc Rakotoson, Charles Letaillieur, Sylvain Massip et al.

This paper describes our submission on the COVID-19 literature annotation task at Biocreative VII. We proposed an approach that exploits the knowledge of the globally non-optimal weights, usually rejected, to build a rich representation of each label. Our proposed approach consists of two stages: (1) A bagging of various initializations of the training data that features weakly trained weights, (2) A stacking of heterogeneous vocabulary models based on BERT and RoBERTa Embeddings. The aggregation of these weak insights performs better than a classical globally efficient model. The purpose is the distillation of the richness of knowledge to a simpler and lighter model. Our system obtains an Instance-based F1 of 92.96 and a Label-based micro-F1 of 91.35.

Fréjus A. A. Laleye, Antonia Blanié, Antoine Brouquet et al.

In medicine, a communicating virtual patient or doctor allows students to train in medical diagnosis and develop skills to conduct a medical consultation. In this paper, we describe a conversational virtual standardized patient system to allow medical students to simulate a diagnosis strategy of an abdominal surgical emergency. We exploited the semantic properties captured by distributed word representations to search for similar questions in the virtual patient dialogue system. We created two dialogue systems that were evaluated on datasets collected during tests with students. The first system based on hand-crafted rules obtains $92.29\%$ as $F1$-score on the studied clinical case while the second system that combines rules and semantic similarity achieves $94.88\%$. It represents an error reduction of $9.70\%$ as compared to the rules-only-based system.