NewsMeSH: A new classifier designed to annotate health news with MeSH headings

Automatic Classification and Visualization of Text Data on Rare Diseases

More than 7000 rare diseases affect over 400 million people, posing significant challenges for medical research and healthcare. The integration of precision medicine with artificial intelligence offers promising solutions. This work introduces a classifier developed to discern whether research and news articles pertain to rare or non-rare diseases. Our methodology involves extracting 709 rare disease MeSH terms from Mondo and MeSH to improve rare disease categorization. We evaluate our classifier on abstracts from PubMed/MEDLINE and an expert-annotated news dataset, which includes news articles on four selected rare neurodevelopmental disorders (NDDs)-considered the largest category of rare diseases-from a total of 16 analyzed. We achieved F1 scores of 85% for abstracts and 71% for news articles, demonstrating robustness across both datasets and highlighting the potential of integrating artificial intelligence and ontologies to improve disease classification. Although the results are promising, they also indicate the need for further refinement in managing data heterogeneity. Our classifier improves the identification and categorization of medical information, essential for advancing research, enhancing information access, influencing policy, and supporting personalized treatments. Future work will focus on expanding disease classification to distinguish between attributes such as infectious and hereditary diseases, addressing data heterogeneity, and incorporating multilingual capabilities.

Silva J, Almeida JR, Matos S. Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics

The identification of chemicals in articles has attracted a large interest in the biomedical scientific community, given its importance in drug development research. Most of previous research have focused on PubMed abstracts, and further investigation using full-text documents is required because these contain additional valuable information that must be explored. The manual expert task of indexing Medical Subject Headings (MeSH) terms to these articles later helps researchers find the most relevant publications for their ongoing work. The BioCreative VII NLM-Chem track fostered the development of systems for chemical identification and indexing in PubMed full-text articles. Chemical identification consisted in identifying the chemical mentions and linking these to unique MeSH identifiers. This manuscript describes our participation system and the post-challenge improvements we made. We propose a three-stage pipeline that individually performs chemical mention detection, entity normalization and indexing. Regarding chemical identification, we adopted a deep-learning solution that utilizes the PubMedBERT contextualized embeddings followed by a multilayer perceptron and a conditional random field tagging layer. For the normalization approach, we use a sieve-based dictionary filtering followed by a deep-learning similarity search strategy. Finally, for the indexing we developed rules for identifying the more relevant MeSH codes for each article. During the challenge, our system obtained the best official results in the normalization and indexing tasks despite the lower performance in the chemical mention recognition task. In a post-contest phase we boosted our results by improving our named entity recognition model with additional techniques. The final system achieved 0.8731, 0.8275 and 0.4849 in the chemical identification, normalization and indexing tasks, respectively. The code to reproduce our experiments and run the pipeline is publicly available.

Database URL

https://github.com/bioinformatics-ua/biocreativeVII_track2

AIDA: A knowledge graph about research dynamics in academia and industry

Academia and industry share a complex, multifaceted, and symbiotic relationship. Analyzing the knowledge flow between them, understanding which directions have the biggest potential, and discovering the best strategies to harmonize their efforts is a critical task for several stakeholders. Research publications and patents are an ideal medium to analyze this space, but current data sets of scholarly data cannot be used for such a purpose because they lack a high-quality characterization of the relevant research topics and industrial sectors. In this paper, we introduce the Academia/Industry DynAmics (AIDA) Knowledge Graph, which describes 21 million publications and 8 million patents according to the research topics drawn from the Computer Science Ontology. 5.1 million publications and 5.6 million patents are further characterized according to the type of the author’s affiliations and 66 industrial sectors from the proposed Industrial Sectors Ontology (INDUSO). AIDA was generated by an automatic pipeline that integrates data from Microsoft Academic Graph, Dimensions, DBpedia, the Computer Science Ontology, and the Global Research Identifier Database. It is publicly available under CC BY 4.0 and can be downloaded as a dump or queried via a triplestore. We evaluated the different parts of the generation pipeline on a manually crafted gold standard yielding competitive results.