Dataset Information

Tool recommender system in Galaxy using deep learning.

ABSTRACT:

Background

Galaxy is a web-based and open-source scientific data-processing platform. Researchers compose pipelines in Galaxy to analyse scientific data. These pipelines, also known as workflows, can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To help researchers with creating workflows, a system is developed to recommend tools that can facilitate further data analysis.

Findings

A model is developed to recommend tools using a deep learning approach by analysing workflows composed by researchers on the European Galaxy server. The higher-order dependencies in workflows, represented as directed acyclic graphs, are learned by training a gated recurrent units neural network, a variant of a recurrent neural network. In the neural network training, the weights of tools used are derived from their usage frequencies over time and the sequences of tools are uniformly sampled from training data. Hyperparameters of the neural network are optimized using Bayesian optimization. Mean accuracy of 98% in recommending tools is achieved for the top-1 metric.

Conclusions

The model is accessed by a Galaxy API to provide researchers with recommended tools in an interactive manner using multiple user interface integrations on the European Galaxy server. High-quality and highly used tools are shown at the top of the recommendations. The scripts and data to create the recommendation system are available under MIT license at https://github.com/anuprulez/galaxy_tool_recommendation.

SUBMITTER: Kumar A

PROVIDER: S-EPMC7786169 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Publications

Tool recommender system in Galaxy using deep learning.

Kumar Anup A Rasche Helena H Grüning Björn B Backofen Rolf R

GigaScience 20210101 1

<h4>Background</h4>Galaxy is a web-based and open-source scientific data-processing platform. Researchers compose pipelines in Galaxy to analyse scientific data. These pipelines, also known as workflows, can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To help researchers with creating workflows, a system is developed to recommend tools that can facilitate further data analysis.<h4>Findings</h4>A model is developed to recommend tools using ...[more]

PMID: 33404053

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Project description:Expert assessments with pre-defined numerical or language terms can limit the scope of decision-making models. We propose that decision-making models can incorporate expert judgments expressed in natural language through sentiment analysis. To help make more informed choices, we present the Sentiment Analysis in Recommender Systems with Multi-person, Multi-criteria Decision Making (SAR-MCMD) method. This method compiles the opinions of several experts by analyzing their written reviews and, if applicable, their star ratings. The growth of online applications and the sheer amount of available information have made it difficult for users to decide which information or products to select from the Internet. Intelligent decision-support technologies, known as recommender systems, leverage users' preferences to suggest what they might find interesting. Recommender systems are one of the many approaches to dealing with information overload issues. These systems have traditionally relied on single-grading algorithms to predict and communicate users' opinions for observed items. To boost their predictive and recommendation abilities, multi-criteria recommender systems assign numerous ratings to various qualities of products. We created, manually annotated, and released the technique in a case study of restaurant selection using 'TripAdvisor reviews', 'TMDB 5000 movies', and an 'Amazon dataset'. In various areas, cutting-edge deep learning approaches have led to breakthrough progress. Recently, researchers have begun to focus on applying these methods to recommendation systems, and different deep learning-based recommendation models have been suggested. Due to its proficiency with sparse data in large data systems and its ability to construct complex models that characterize user performance for the recommended procedure, deep learning is a formidable tool. In this article, we introduce a model for a multi-criteria recommender system that combines the best of both deep learning and multi-criteria decision-making. According to our findings, the suggested system may give customers very accurate suggestions with a sentiment analysis accuracy of 98%. Additionally, the metrics, accuracy, precision, recall, and F1 score are where the system truly shines, much above what has been achieved in the past.

Dataset Information

Tool recommender system in Galaxy using deep learning.

Background

Findings

Conclusions

Publications

Tool recommender system in Galaxy using deep learning.

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