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bioRxiv · 10.1101/2024.04.19.590278

Benchmarking Large Language Models for Bio-Image Analysis Code Generation

Haase, R.·Tischer, C.·Scherf, N.
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Abstract

In the computational age, life-scientists often have to write Python code to solve bio-image analysis (BIA) problems. Many of them have not been formally trained in programming though. Code-generation, or coding assistance in general, with Large Language Models (LLMs) can have a clear impact on BIA. To the best of our knowledge, the quality of the generated code in this domain has not been studied. We present a quantitative benchmark to estimate the capability of LLMs to generate code for solving common BIA tasks. Our benchmark currently consists of 57 human-written prompts with corresponding reference solutions in Python, and unit-tests to evaluate functional correctness of potential solutions. We demonstrate our benchmark here and compare 18 state-of-the-art LLMs. To ensure that we will cover most of our community needs we also outline mid- and long-term strategies to maintain and extend the benchmark by the BIA open-source community. This work should support users in deciding for an LLM and also guide LLM developers in improving the capabilities of LLMs in the BIA domain.

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Haase, R., Tischer, C., Scherf, N.. 2024-04-21. Benchmarking Large Language Models for Bio-Image Analysis Code Generation. https://doi.org/10.1101/2024.04.19.590278

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