Deep Learning (DL) techniques are increasingly applied in scientific studies across various domains to address complex research questions. However, the methodological details of these DL models are often hidden in the unstructured text. As a result, critical information about how these models are designed, trained, and evaluated is challenging to access and comprehend. To address this issue, in this work, we use five different open-source Large Language Models (LLMs): Llama-3 70B, Llama-3.1 70B, Mixtral-8x22B-Instruct-v0.1, Mixtral 8x7B, and Gemma 2 9B in combination with Retrieval-Augmented Generation (RAG) approach to extract and process DL methodological details from scientific publications automatically. We built a voting classifier from the outputs of five LLMs to accurately report DL methodological information. We tested our approach using biodiversity publications, building upon our previous research. To validate our pipeline, we employed two datasets of DL-related biodiversity publications: a curated set of 100 publications from our prior work and a set of 364 publications from the Ecological Informatics journal. Our results demonstrate that the multi-LLM, RAG-assisted pipeline enhances the retrieval of DL methodological information, achieving an accuracy of 69.5% (417 out of 600 comparisons) based solely on textual content from publications. This performance was assessed against human annotators who had access to code, figures, tables, and other supplementary information. Although demonstrated in biodiversity, our methodology is not limited to this field; it can be applied across other scientific domains where detailed methodological reporting is essential for advancing knowledge and ensuring reproducibility. This study presents a scalable and reliable approach for automating information extraction, facilitating better reproducibility and knowledge transfer across studies.

Machine learning algorithms abound in biodiversity research, but sometimes without the proper attribution or oversight. In an effort to raise the academic bar, Google says it will release an AI workflow for institutions, developed in collaboration with Global Biodiversity Information Facility (GBIF), iNaturalist, and Visipedia. Researchers at the tech giant say the workflow will support data aggregation and collaboration across teams while ensuring corpora follow standardized licensing terms, use compatible file formats, and provide fair and sufficient data coverage for the task at hand. "The promise of machine learning for species identification is coming to fruition, revealing its transformative potential in biodiversity research," wrote visiting faculty Serge Belongie and Google Research engineering director Hartwig Adam in a blog post published to coincide with the Biodiversity Next conference in Leiden, Netherlands. "International workshops … feature competitions to develop top performing classification algorithms for everything from wildlife camera trap images to pressed flower specimens on herbarium sheets. The encouraging results that have emerged from these competitions inspired us to expand the availability of biodiversity datasets and ML models from workshop-scale to global-scale."