LLM_Relations

This is the documentation for the Reading papers: Extraction of molecular interaction networks with large language models study.

Questions about the study can be addressed to Enio Gjerga, Philipp Wiesenbach or Prof. Christoph Dieterich or feel free to open an Issue for anything related to the code.

This study makes use of the RegulaTome corpus of literature, so we suggest to have a look at this study first.

License

Distributed under the GNU GPLv3 License.

Code Organization

The code and results have been organized in the following direcotries:

llm_files

Here we provide the structured JSON files for each case study:

• PPI evaluations over the RegulaTome corpus (regulatome_eval_ppi)
• Synonyms of entities participating in PPI interactions from the RegulaTome corpus (regulatome_synonyms)
• PPI evaluations over the selected Manuscript corpus (manuscript_eval_ppi)

The JSON files being contained in each of these directories have been named according to the type as well as the LLM model used for evaluation (Please refer to the study manuscript for the nomenclature).

llm_evaluations

Here we provide the scripts that were used to calculate and visualize the precision-recall values for PPI relation extraction in the RegulaTome and the selected manuscript corpus.

PPI Evaluation over the RegulaTome and Cardiac-related corpus (llm_evaluations)

The following R-scripts can be found in the dirctory and which should be run in the order presented in this documentation.

1. data_preparation.R Here are provided the scripts that Read through the RegulaTome resource and then generate tables of PPI and GRN/TF-Gene annotated relations as well as entities in the src/ directory. For this the RegulaTome courpus can be read from the devel/, test/ and train/ direcotries and which can be downloaded from the Zenodo link published in RegulaTome.

2. regulatome_eval_ppi.R This script is used to calculate the RE precision-recall metrics for PPI relations. Evaluation results have been stored in the output/ directory.

3. manuscript_eval_ppi.R Here we evaluate PPI RE's over the manually annotated corpus of the selected 5 cardiac manuscripts. Evaluation results have been stored in the output/ directory.