Accelerating Ecological Data Extraction with AI

By Dr Silpaja Chandrasekar, PhDReviewed by Susha Cheriyedath, M.Sc.May 27 2024

In a paper published in the journal Npj Biodiversity, researchers formally tested the speed and accuracy of an artificial intelligence (AI) based large language model (LLM) compared to a human reviewer for extracting various ecological data from the scientific literature.

They found that the LLM extracted relevant data much faster than the reviewer and achieved high accuracy in extracting discrete and categorical data. However, it could have performed better with certain quantitative data. The study demonstrated that LLMs had great potential for creating large ecological databases rapidly, but additional quality assurance steps were needed to ensure data integrity.

Related Work

Past work has shown that the public release of AI-based language-generating chatbots has attracted significant attention due to their ability to quickly process and synthesize large amounts of text. However, their tendency to generate incorrect information raises concerns about their reliability.

Despite these challenges, researchers continue to explore ways to improve the accuracy and reliability of AI systems for various applications. Efforts are underway to develop robust quality assurance measures and enhance transparency in AI training data to address these concerns and unlock the full potential of AI technology.

LM Data Extraction

The researchers utilized reports from a recent study on the global accumulation of emerging infectious tree diseases to assess the ability of an LLM to extract ecological information. They focused on reports of emerging infectious diseases (EIDs), defined as diseases occurring in new geographic regions, on new hosts, or showing recent increases in impact.

These reports often provide short yet valuable ecological information and were chosen for their suitability in testing the LLM's capabilities. Specifically, the researchers used the first 100 reports from the study, which represented unique hosts and pathogens reported in new regions.

The researchers employed the publicly available text-bison-001 generative text model from Google for the LLM data extraction. This model was chosen for its ability to return only relevant text requested without additional conversational text. The LLM was prompted to extract various information from the disease reports, including the scientific names of the pathogen and hosts, the incidence of the pathogen, and details on when and where the pathogen was detected. The prompt underwent iterative refinement to ensure accurate and consistent data extraction, including specifying desired formats for variables and delimiting columns in the response table.

Interaction with the LLM was facilitated through Google's developer application programming interface (API),  which was accessed using the httr package in the R statistical program. The data extracted from each report were returned as a single text string, with rows and columns delimited for further processing.

The researchers encountered issues with some reports being flagged as "derogatory" or "toxic" by the LLM, which required adjustments to response thresholds. Additionally, the team set the LLM's response temperature to zero to improve repeatability to ensure deterministic responses.

Validation of the extracted data involved comparing results from the LLM with those from an independent human reviewer who had not previously worked with the data. The analysts calculated validation statistics for discrete and quantitative variables, including overall accuracy metrics, Cohen's Kappa for discrete variables, and percentage accuracy and absolute differences for quantitative variables. Flexibility was allowed for minor disagreements between the reviewer and the LLM, such as variations in species identification conventions. The researchers carefully assessed any discrepancies to ensure accuracy.

LLM Data Extraction

The researchers conducted data extraction via the LLM and found it significantly faster than human review, with a notable over 50-fold difference in processing time for 100 reports. The LLM demonstrated strong accuracy in identifying pathogens, hosts, years, and countries in the reports, with high matches to the reviewer's identifications.

However, challenges arose with pathogen incidence data, where the LLM tended to assign 100% incidence when data were not provided, indicating potential limitations in handling quantitative information. Despite these challenges, the automated workflow showcased the potential for LLMs to compile large databases rapidly. However, caution is advised due to uncertainties regarding data accuracy and LLM performance on more complex tasks.

The study underscores the promising yet nuanced role of LLMs in ecological research. While they offer unprecedented speed and scale in data extraction, ensuring accuracy for quantitative data and more complex tasks remains a concern. Further refinements and assessments of LLM capabilities, including language variety interpretation and environmental impact considerations, are necessary to harness their full potential effectively in ecological studies.

Conclusion

To sum up, the study highlighted the significant potential of LLMs in expediting data extraction processes within ecological research. While the LLM demonstrated remarkable efficiency in identifying pathogens, hosts, and geographic locations, challenges were encountered in accurately processing quantitative information.

Despite these limitations, the automated workflow underscored LLMs' transformative role in rapidly compiling extensive databases. Further refinements and assessments of LLM capabilities are essential to ensure accurate and reliable data extraction in ecological studies.