Abstracts or full text? Evaluating input scope and computational efficiency in biomedical lay summarization

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.

Abstractive summarization requires models to generate summaries that convey information in the source document. While large language models can generate summaries without fine-tuning, they often miss key details and include extraneous information. We propose BLooP (Bigram Lookahead Promotion), a simple training-free decoding intervention that encourages large language models (LLMs) to generate tokens that form bigrams from the source document. BLooP operates through a hash table lookup at each decoding step, requiring no training, fine-tuning, or model modification. We demonstrate improvements in ROUGE and BARTScore for Llama-3.1-8B-Instruct, Mistral-Nemo-Instruct-2407, and Gemma-2-9b-it on CNN/DM, CCSum, Multi-News, and SciTLDR. Human evaluation shows that BLooP significantly improves faithfulness without reducing readability. We make the code available at https://github.com/varuniyer/BLooP

Scientific long-document summarization datasets commonly treat author-written abstracts as gold reference summaries, although their quality and alignment with the source article vary. At the same time, publicly available scientific summarization datasets remain limited in scale and structure for modern long-context models. In this work, we address both challenges by a) constructing and releasing one of the largest biomedical and life science datasets for long-document summarization, containing 1.88 million PMC articles, and b) analyzing the reference quality of author-written abstracts with source-grounded and model-based metrics. We show that author-written abstracts vary in their alignment with the full article and that these quality signals can guide training-data selection. Training on selected high-quality subsets outperforms random sampling at matched training sizes and can match or exceed larger random subsets on factuality-oriented metrics. Our findings suggest that reference quality is an important factor in scientific summarization and that quality-aware data selection can improve training efficiency.