Francisco M. Couto

Pedro Ruas, Diana F. Sousa, André Neves et al.

Biomedical Natural Language Processing (NLP) tends to become cumbersome for most researchers, frequently due to the amount and heterogeneity of text to be processed. To address this challenge, the industry is continuously developing highly efficient tools and creating more flexible engineering solutions. This work presents the integration between industry data engineering solutions for efficient data processing and academic systems developed for Named Entity Recognition (LasigeUnicage\_NER) and Relation Extraction (BiOnt). Our design reflects an integration of those components with external knowledge in the form of additional training data from other datasets and biomedical ontologies. We used this pipeline in the 2022 LitCoin NLP Challenge, where our team LasigeUnicage was awarded the 7th Prize out of approximately 200 participating teams, reflecting a successful collaboration between the academia (LASIGE) and the industry (Unicage). The software supporting this work is available at \url{https://github.com/lasigeBioTM/Litcoin-Lasige_Unicage}.

Pedro Ruas, Fernando Gallego, Francisco J. Veredas et al.

State-of-the-art deep learning entity linking methods rely on extensive human-labelled data, which is costly to acquire. Current datasets are limited in size, leading to inadequate coverage of biomedical concepts and diminished performance when applied to new data. In this work, we propose to automatically generate data to create large-scale training datasets, which allows the exploration of approaches originally developed for the task of extreme multi-label ranking in the biomedical entity linking task. We propose the hybrid X-Linker pipeline that includes different modules to link disease and chemical entity mentions to concepts in the MEDIC and the CTD-Chemical vocabularies, respectively. X-Linker was evaluated on several biomedical datasets: BC5CDR-Disease, BioRED-Disease, NCBI-Disease, BC5CDR-Chemical, BioRED-Chemical, and NLM-Chem, achieving top-1 accuracies of 0.8307, 0.7969, 0.8271, 0.9511, 0.9248, and 0.7895, respectively. X-Linker demonstrated superior performance in three datasets: BC5CDR-Disease, NCBI-Disease, and BioRED-Chemical. In contrast, SapBERT outperformed X-Linker in the remaining three datasets. Both models rely only on the mention string for their operations. The source code of X-Linker and its associated data are publicly available for performing biomedical entity linking without requiring pre-labelled entities with identifiers from specific knowledge organization systems.

Luís Campos, Francisco Couto

MRA (Multilingual Report Annotator) is a web application that translates Radiology text and annotates it with RadLex terms. Its goal is to explore the solution of translating non-English Radiology reports as a way to solve the problem of most of the Text Mining tools being developed for English. In this brief paper we explain the language barrier problem and shortly describe the application. MRA can be found at https://github.com/lasigeBioTM/MRA .

Sérgio Nunes, Suzanne Little, Sumit Bhatia et al.

ECIR 2020 https://ecir2020.org/ was one of the many conferences affected by the COVID-19 pandemic. The Conference Chairs decided to keep the initially planned dates (April 14-17, 2020) and move to a fully online event. In this report, we describe the experience of organizing the ECIR 2020 Workshops in this scenario from two perspectives: the workshop organizers and the workshop participants. We provide a report on the organizational aspect of these events and the consequences for participants. Covering the scientific dimension of each workshop is outside the scope of this article.

Marcia Barros, André Moitinho, Francisco M. Couto

Recommending Chemical Compounds of interest to a particular researcher is a poorly explored field. The few existent datasets with information about the preferences of the researchers use implicit feedback. The lack of Recommender Systems in this particular field presents a challenge for the development of new recommendations models. In this work, we propose a Hybrid recommender model for recommending Chemical Compounds. The model integrates collaborative-filtering algorithms for implicit feedback (Alternating Least Squares (ALS) and Bayesian Personalized Ranking(BPR)) and semantic similarity between the Chemical Compounds in the ChEBI ontology (ONTO). We evaluated the model in an implicit dataset of Chemical Compounds, CheRM. The Hybrid model was able to improve the results of state-of-the-art collaborative-filtering algorithms, especially for Mean Reciprocal Rank, with an increase of 6.7% when comparing the collaborative-filtering ALS and the Hybrid ALS_ONTO.

Diana Sousa, Andre Lamurias, Francisco M. Couto

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.

Miguel J. Rodrigues, Miguel Falé, Andre Lamurias et al.

This paper describes our system, dubbed WS4A (Web Services for All), that participated in the fourth edition of the BioASQ challenge (2016). We used WS4A to perform the Question and Answering (QA) task 4b, which consisted on the retrieval of relevant concepts, documents, snippets, RDF triples, exact answers and ideal answers for each given question. The novelty in our approach consists on the maximum exploitation of existing web services in each step of WS4A, such as the annotation of text, and the retrieval of metadata for each annotation. The information retrieved included concept identifiers, ontologies, ancestors, and most importantly, PubMed identifiers. The paper describes the WS4A pipeline and also presents the precision, recall and f-measure values obtained in task 4b. Our system achieved two second places in two subtasks on one of the five batches.

Diogo Goncalves, Miguel Costa, Francisco M. Couto

Nowadays, Cable TV operators provide their users multiple ways to watch TV content, such as Live TV and Video on Demand (VOD) services. In the last years, Catch-up TV has been introduced, allowing users to watch recent broadcast content whenever they want to. Understanding how the users interact with such services is important to develop solutions that may increase user satisfaction , user engagement and user consumption. In this paper, we characterize, for the first time, how users interact with a large European Cable TV operator that provides Live TV, Catch-up TV and VOD services. We analyzed many characteristics, such as the service usage, user engagement, program type, program genres and time periods. This characterization will help us to have a deeper understanding on how users interact with these different services, that may be used to enhance the recommendation systems of Cable TV providers.

Diogo Goncalves, Miguel Costa, Francisco M. Couto

Recommendation systems are being explored by Cable TV operators to improve user satisfaction with services, such as Live TV and Video on Demand (VOD) services. More recently, Catch-up TV has been introduced, allowing users to watch recent broadcast content whenever they want to. These services give users a large set of options from which they can choose from, creating an information overflow problem. Thus, recommendation systems arise as essential tools to solve this problem by helping users in their selection, which increases not only user satisfaction but also user engagement and content consumption. In this paper we present a learning to rank approach that uses contextual information and implicit feedback to improve recommendation systems for a Cable TV operator that provides Live and Catch-up TV services. We compare our approach with existing state-of-the-art algorithms and show that our approach is superior in accuracy, while maintaining high scores of diversity and serendipity.

Francisco M Couto

This technical report presents a bibliometric analysis of the top 30 cited researchers from USA, UK and China. The analysis is based on Google Scholar data using CIDS. The researchers were identified using their email suffix: edu, uk and cn. This naïve approach was able to produce rankings consistent with the SCImago country rankings using mininal resources in a fully automated way.

Emanuel Santos, Daniel Faria, Cátia Pesquita et al.

Ontology Matching aims to find a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, most of the alignments produced for large ontologies are logically incoherent. It was only recently that the use of repair techniques to improve the quality of ontology alignments has been explored. In this paper we present a novel technique for detecting incoherent concepts based on ontology modularization, and a new repair algorithm that minimizes the incoherence of the resulting alignment and the number of matches removed from the input alignment. An implementation was done as part of a lightweight version of AgreementMaker system, a successful ontology matching platform, and evaluated using a set of four benchmark biomedical ontology matching tasks. Our results show that our implementation is efficient and produces better alignments with respect to their coherence and f-measure than the state of the art repairing tools. They also show that our implementation is a better alternative for producing coherent silver standard alignments.

Francisco M Couto, Daniel Faria, Bruno Tavares et al.

The increasing use of productivity and impact metrics for evaluation and comparison, not only of individual researchers but also of institutions, universities and even countries, has prompted the development of bibliometrics. Currently, metrics are becoming widely accepted as an easy and balanced way to assist the peer review and evaluation of scientists and/or research units, provided they have adequate precision and recall. This paper presents a benchmarking study of a selected list of representative Portuguese research units, based on a fairly complete set of parameters: bibliometric parameters, number of competitive projects and number of PhDs produced. The study aimed at collecting productivity and impact data from the selected research units in comparable conditions i.e., using objective metrics based on public information, retrievable on-line and/or from official sources and thus verifiable and repeatable. The study has thus focused on the activity of the 2003-06 period, where such data was available from the latest official evaluation. The main advantage of our study was the application of automatic tools, achieving relevant results at a reduced cost. Moreover, the results over the selected units suggest that this kind of analyses will be very useful to benchmark scientific productivity and impact, and assist peer review.