Accelerating Antibiotic Discovery with Large Language Models and Knowledge Graphs

The discovery of novel antibiotics is critical to address the growing antimicrobial resistance (AMR). However, pharmaceutical industries face high costs (over $1 billion), long timelines, and a high failure rate, worsened by the rediscovery of known compounds. We propose an LLM-based pipeline that acts as an alarm system, detecting prior evidence of antibiotic activity to prevent costly rediscoveries. The system integrates organism and chemical literature into a Knowledge Graph (KG), ensuring taxonomic resolution, synonym handling, and multi-level evidence classification. We tested the pipeline on a private list of 73 potential antibiotic-producing organisms, disclosing 12 negative hits for evaluation. The results highlight the effectiveness of the pipeline for evidence reviewing, reducing false negatives, and accelerating decision-making. The KG for negative hits and the user interface for interactive exploration will be made publicly available.$

@article{delmas2025_2503.16655,
  title={ Accelerating Antibiotic Discovery with Large Language Models and Knowledge Graphs },
  author={ Maxime Delmas and Magdalena Wysocka and Danilo Gusicuma and André Freitas },
  journal={arXiv preprint arXiv:2503.16655},
  year={ 2025 }
}