Transformer-based tool recommendation system in Galaxy

• Published in: BMC bioinformatics Vol. 24; no. 1; pp. 1 - 446
• Main Authors: Kumar, Anup, Grüning, Björn, Backofen, Rolf
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 27.11.2023; BioMed Central; BMC
• Subjects: Accuracy; Artificial intelligence; Comparative analysis; Convergence; Data analysis; Galaxies; Galaxy; Neural networks; Open source software; Proteins; Recommendation system; Recommender systems; Recurrent neural networks; Training; Transformer; Transformers; Workflows; Europe
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-023-05573-w

Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a collection of tools that can be used to extend an analysis. In this work, a tool recommender system is developed by training a transformer on workflows available on Galaxy Europe and its performance is compared to other neural networks such as recurrent, convolutional and dense neural networks. The transformer neural network achieves two times faster convergence, has significantly lower model usage (model reconstruction and prediction) time and shows a better generalisation that goes beyond training workflows than the older tool recommender system created using RNN in Galaxy. In addition, the transformer also outperforms CNN and DNN on several key indicators. It achieves a faster convergence time, lower model usage time, and higher quality tool recommendations than CNN. Compared to DNN, it converges faster to a higher precision@k metric (approximately 0.98 by transformer compared to approximately 0.9 by DNN) and shows higher quality tool recommendations. Our work shows a novel usage of transformers to recommend tools for extending scientific workflows. A more robust tool recommendation model, created using a transformer, having significantly lower usage time than RNN and CNN, higher precision@k than DNN, and higher quality tool recommendations than all three neural networks, will benefit researchers in creating scientifically significant workflows and exploratory data analysis in Galaxy. Additionally, the ability to train faster than all three neural networks imparts more scalability for training on larger datasets consisting of millions of tool sequences. Open-source scripts to create the recommendation model are available under MIT licence at https://github.com/anuprulez/galaxy_tool_recommendation_transformers