Results of the seventh edition of the BioASQ Challenge

The results of the seventh edition of the BioASQ challenge are presented in this paper. The aim of the BioASQ challenge is the promotion of systems and methodologies through the organization of a challenge on the tasks of large-scale biomedical semantic indexing and question answering. In total, 30 teams with more than 100 systems participated in the challenge this year. As in previous years, the best systems were able to outperform the strong baselines. This suggests that state-of-the-art systems are continuously improving, pushing the frontier of research.Comment: 17 pages, 2 figure

Overview of BioASQ 2021-MESINESP track. Evaluation of advance hierarchical classification techniques for scientific literature, patents and clinical trials

CLEF 2021 – Conference and Labs of the Evaluation Forum, September 21–24, 2021, Bucharest, Romania,There is a pressing need to exploit recent advances in natural language processing technologies, in particular language models and deep learning approaches, to enable improved retrieval, classification and ultimately access to information contained in multiple, heterogeneous types of documents. This is particularly true for the field of biomedicine and clinical research, where medical experts and scientists need to carry out complex search queries against a variety of document collections, including literature, patents, clinical trials or other kind of content like EHRs. Indexing documents with structured controlled vocabularies used for semantic search engines and query expansion purposes is a critical task for enabling sophisticated user queries and even cross-language retrieval. Due to the complexity of the medical domain and the use of very large hierarchical indexing terminologies, implementing efficient automatic systems to aid manual indexing is extremely difficult. This paper provides a summary of the MESINESP task results on medical semantic indexing in Spanish (BioASQ/ CLEF 2021 Challenge). MESINESP was carried out in direct collaboration with literature content databases and medical indexing experts using the DeCS vocabulary, a similar resource as MeSH terms. Seven participating teams used advanced technologies including extreme multilabel classification and deep language models to solve this challenge which can be viewed as a multi-label classification problem. MESINESP resources, we have released a Gold Standard collection of 243,000 documents with a total of 2179 manual annotations divided in train, development and test subsets covering literature, patents as well as clinical trial summaries, under a cross-genre training and data labeling scenario. Manual indexing of the evaluation subsets was carried out by three independent experts using a specially developed indexing interface called ASIT. Additionally, we have published a collection of large-scale automatic semantic annotations based on NER systems of these documents with mentions of drugs/medications (170,000), symptoms (137,000), diseases (840,000) and clinical procedures (415,000). In addition to a summary of the used technologies by the teams, this paperS

Large scale biomedical texts classification: a kNN and an ESA-based approaches

With the large and increasing volume of textual data, automated methods for identifying significant topics to classify textual documents have received a growing interest. While many efforts have been made in this direction, it still remains a real challenge. Moreover, the issue is even more complex as full texts are not always freely available. Then, using only partial information to annotate these documents is promising but remains a very ambitious issue. MethodsWe propose two classification methods: a k-nearest neighbours (kNN)-based approach and an explicit semantic analysis (ESA)-based approach. Although the kNN-based approach is widely used in text classification, it needs to be improved to perform well in this specific classification problem which deals with partial information. Compared to existing kNN-based methods, our method uses classical Machine Learning (ML) algorithms for ranking the labels. Additional features are also investigated in order to improve the classifiers' performance. In addition, the combination of several learning algorithms with various techniques for fixing the number of relevant topics is performed. On the other hand, ESA seems promising for this classification task as it yielded interesting results in related issues, such as semantic relatedness computation between texts and text classification. Unlike existing works, which use ESA for enriching the bag-of-words approach with additional knowledge-based features, our ESA-based method builds a standalone classifier. Furthermore, we investigate if the results of this method could be useful as a complementary feature of our kNN-based approach.ResultsExperimental evaluations performed on large standard annotated datasets, provided by the BioASQ organizers, show that the kNN-based method with the Random Forest learning algorithm achieves good performances compared with the current state-of-the-art methods, reaching a competitive f-measure of 0.55% while the ESA-based approach surprisingly yielded reserved results.ConclusionsWe have proposed simple classification methods suitable to annotate textual documents using only partial information. They are therefore adequate for large multi-label classification and particularly in the biomedical domain. Thus, our work contributes to the extraction of relevant information from unstructured documents in order to facilitate their automated processing. Consequently, it could be used for various purposes, including document indexing, information retrieval, etc.Comment: Journal of Biomedical Semantics, BioMed Central, 201