BioCoder: A Benchmark for Bioinformatics Code Generation with Contextual Pragmatic Knowledge

Pre-trained large language models have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks and to be appropriately specialized to particular domains. Bioinformatics provides an important domain. In this field generating functional programs poses additional notable challenges due to the amount of specialized domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, GPT-3.5, and GPT-4. The results highlight two key aspects of successful models: 1) that they contain specific domain knowledge of bioinformatics (beyond just coding knowledge); 2) that they accommodate a long prompt with full context (i.e. functional dependencies). Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.