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 alert system, detecting prior evidence of antibiotic activity to prevent costly rediscoveries. The system integrates literature on organisms and chemicals 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 as well as the user interface for interactive exploration are available at https://github.com/idiap/abroad-kg-store and https://github.com/idiap/abroad-demo-webapp.

The sparsity of labeled data is an obstacle to the development of Relation Extraction (RE) models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the literature on natural products, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler, inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the text of input abstracts and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning (BioGPT, GPT-2, and Seq2rel) and few-shot learning with open Large Language Models (LLMs) (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open LLMs as synthetic data generators and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (F1-score = 59.0) BioGPT-Large model for end-to-end RE of natural products relationships along with all the training and evaluation datasets. See more details at https://github.com/idiap/abroad-re.