Publications by authors named "Ana Garcia-Serrano"

In this paper, we present the results of a research experience of implementing andragogy in a learning environment designed to better meet the needs of adult learners studying part-time at a distance university. The learning environment was composed of a learning experience on a formal distance university online course that has been enriched with a non-formal component based on students' participation in a Massive Online Open Course (MOOC) related to the same topic. The non-formal experience was designed to consolidate the learning of specific content that involved difficult concepts and foster collaborative skills.

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This registered report introduces the largest, and for the first time, reproducible experimental survey on biomedical sentence similarity with the following aims: (1) to elucidate the state of the art of the problem; (2) to solve some reproducibility problems preventing the evaluation of most current methods; (3) to evaluate several unexplored sentence similarity methods; (4) to evaluate for the first time an unexplored benchmark, called Corpus-Transcriptional-Regulation (CTR); (5) to carry out a study on the impact of the pre-processing stages and Named Entity Recognition (NER) tools on the performance of the sentence similarity methods; and finally, (6) to bridge the lack of software and data reproducibility resources for methods and experiments in this line of research. Our reproducible experimental survey is based on a single software platform, which is provided with a detailed reproducibility protocol and dataset as supplementary material to allow the exact replication of all our experiments and results. In addition, we introduce a new aggregated string-based sentence similarity method, called LiBlock, together with eight variants of current ontology-based methods, and a new pre-trained word embedding model trained on the full-text articles in the PMC-BioC corpus.

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Background: Ontology-based semantic similarity measures based on SNOMED-CT, MeSH, and Gene Ontology are being extensively used in many applications in biomedical text mining and genomics respectively, which has encouraged the development of semantic measures libraries based on the aforementioned ontologies. However, current state-of-the-art semantic measures libraries have some performance and scalability drawbacks derived from their ontology representations based on relational databases, or naive in-memory graph representations. Likewise, a recent reproducible survey on word similarity shows that one hybrid IC-based measure which integrates a shortest-path computation sets the state of the art in the family of ontology-based semantic measures.

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Measuring semantic similarity between sentences is a significant task in the fields of Natural Language Processing (NLP), Information Retrieval (IR), and biomedical text mining. For this reason, the proposal of sentence similarity methods for the biomedical domain has attracted a lot of attention in recent years. However, most sentence similarity methods and experimental results reported in the biomedical domain cannot be reproduced for multiple reasons as follows: the copying of previous results without confirmation, the lack of source code and data to replicate both methods and experiments, and the lack of a detailed definition of the experimental setup, among others.

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Article Synopsis
  • The article presents a reproducibility dataset aimed at replicating experiments and results from the authors' earlier work on ontology-based semantic similarity and Word Embeddings.
  • The dataset compiles raw word-similarity values from various methods, all processed using a script to generate key evaluation metrics and tables.
  • Additionally, it offers tools to conduct new word similarity benchmarks, enabling further exploration of the topic using different methods or datasets.
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