Joseph Menke
2026
Divide-Prompt-Refine: a Training-Free, Structure-Aware Framework for Biomedical Abstract Generation
Sylvey Lin | Joseph Menke | Shufan Ming | Dongin Nam | Neil Smalheiser | Halil Kilicoglu
BioNLP 2026
Sylvey Lin | Joseph Menke | Shufan Ming | Dongin Nam | Neil Smalheiser | Halil Kilicoglu
BioNLP 2026
Biomedical abstracts play a critical role in downstream NLP applications, such as information retrieval, biocuration, and biomedical knowledge discovery. However, a non-trivial number of biomedical articles do not have abstracts, diminishing the utility of these articles for downstream tasks. We propose DPR-BAG (Divide, Prompt, and Refine for Biomedical Abstract Generation), a training-free, zero-shot framework that generates coherent and factually grounded abstracts for biomedical articles with full text but no abstract. DPR-BAG decomposes full-text documents into structured rhetorical facets following the Background-Objective-Methods-Results-Conclusions (BOMRC) schema, performs parallel LLM-based summarization for each facet, and applies a final refinement stage to restore global discourse coherence. On PMC-MAD, a distribution-aligned dataset of 46,309 biomedical articles, DPR-BAG improves abstractive novelty over strong extractive and fine-tuned baselines, while maintaining factual consistency. Our ablation study reveals a counterintuitive finding: increasing prompt complexity or explicitly injecting entity-level guidance can degrade factual alignment, highlighting the importance of controlled prompting strategies. These findings underscore the potential of training-free, structure-aware frameworks for scalable biomedical abstract generation in low-resource settings. Our data and code are available at https://huggingface.co/datasets/pmc-mad/PMC-MAD and https://github.com/ScienceNLP-Lab/MultiTagger-v2/tree/main/DPR-BAG.
2021
Detecting Anatomical and Functional Connectivity Relations in Biomedical Literature via Language Representation Models
Ibrahim Burak Ozyurt | Joseph Menke | Anita Bandrowski | Maryann Martone
Proceedings of the Second Workshop on Scholarly Document Processing
Ibrahim Burak Ozyurt | Joseph Menke | Anita Bandrowski | Maryann Martone
Proceedings of the Second Workshop on Scholarly Document Processing
Understanding of nerve-organ interactions is crucial to facilitate the development of effective bioelectronic treatments. Towards the end of developing a systematized and computable wiring diagram of the autonomic nervous system (ANS), we introduce a curated ANS connectivity corpus together with several neural language representation model based connectivity relation extraction systems. We also show that active learning guided curation for labeled corpus expansion significantly outperforms randomly selecting connectivity relation candidates minimizing curation effort. Our final relation extraction system achieves F1 = 72.8% on anatomical connectivity and F1 = 74.6% on functional connectivity relation extraction.