Biotext with SWeePtex: Bioinformatics Tricks to Perform Fast, Accurate, and Content-specific String Embedding

Diogo de J. S. Machado; Camilla R. De Pierri; Antonio C. da Silva Filho; Flávia de F. Costa; Nelson A. de M. Lemos; Camila P. Perico; Letícia G. C. Santos; Maricel G. Kann; Fábio de O. Pedrosa; Roberto T. Raittz

doi:10.5753/jbcs.2026.6198

Authors

Diogo de J. S. Machado Federal University of Paraná https://orcid.org/0009-0001-3885-6774
Camilla R. De Pierri Federal University of Paraná https://orcid.org/0000-0002-6114-1734
Antonio C. da Silva Filho Federal University of Paraná https://orcid.org/0000-0003-0669-4528
Flávia de F. Costa Federal University of Paraná https://orcid.org/0000-0003-4092-4673
Nelson A. de M. Lemos Federal University of Paraná https://orcid.org/0000-0001-9382-9982
Camila P. Perico Federal University of Paraná https://orcid.org/0000-0003-0186-4022
Letícia G. C. Santos Federal University of Paraná https://orcid.org/0000-0002-0206-2294
Maricel G. Kann University of Maryland https://orcid.org/0000-0003-0116-3883
Fábio de O. Pedrosa Federal University of Paraná https://orcid.org/0000-0003-3711-969X
Roberto T. Raittz Federal University of Paraná https://orcid.org/0000-0002-5271-991X

DOI:

https://doi.org/10.5753/jbcs.2026.6198

Keywords:

Text Mining, Vector Embedding, Bioinformatics, Random Projection

Abstract

The escalating demand for adaptable Artificial Intelligence (AI) systems presents a critical hurdle: generating efficient text embeddings tailored to specific problems. While Large Language Models (LLMs) excel in general contexts, they struggle in specialized domains due to their massive data requirements, opaque embedding strategies, and high computational costs. We introduce Biotext, featuring SWeePtex, a novel framework that adapts successful Bioinformatics techniques for text embedding. By converting text to the Biological Sequence-Like (BSL) format, our Python package enables the application of SWeeP, a tool originally developed for biological sequences, to create content-addressable vectors in natural language, employing the random projection paradigm. Using unsupervised machine learning, we validated this finding by analyzing data from 14,984 MEDLINE abstracts on the thioredoxin theme. Biotext, through SWeePtex, constructs a unified vector space for words and documents from scratch, capturing rich contextual relationships and offering scalable processing. Our usage example demonstrates that this Bioinformatics-inspired method effectively addresses key challenges in Natural Language Processing (NLP), providing interpretable, computationally efficient, and content-addressable linguistic representations for document exploration. Ultimately, Biotext demonstrates that bridging Bioinformatics and NLP yields powerful, efficient, and accessible text analysis tools that balance analytical power with interpretability, particularly valuable in specialized domains and resource-constrained environments. Biotext Python package is freely available at the PyPI repository.

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