Robust Biomedical Publication Type and Study Design Classification with Knowledge-Guided Perturbations

Accurately and consistently indexing biomedical literature by publication type and study design is essential for supporting evidence synthesis and knowledge discovery. Prior work on automated publication type and study design indexing has primarily focused on expanding label coverage, enriching feature representations, and improving in-domain accuracy, with evaluation typically conducted on data drawn from the same distribution as training. Although pretrained biomedical language models achieve strong performance under these settings, models optimized for in-domain accuracy may rely on superficial lexical or dataset-specific cues, resulting in reduced robustness under distributional shift. In this study, we introduce an evaluation framework based on controlled semantic perturbations to assess the robustness of a publication type classifier and investigate robustness-oriented training strategies that combine entity masking and domain-adversarial training to mitigate reliance on spurious topical correlations. Our results show that the commonly observed trade-off between robustness and in-domain accuracy can be mitigated when robustness objectives are designed to selectively suppress non-task-defining features while preserving salient methodological signals. We find that these improvements arise from two complementary mechanisms: (1) increased reliance on explicit methodological cues when such cues are present in the input, and (2) reduced reliance on spurious domain-specific topical features. These findings highlight the importance of feature-level robustness analysis for publication type and study design classification and suggest that refining masking and adversarial objectives to more selectively suppress topical information may further improve robustness. Data, code, and models are available at: https://github.com/ScienceNLP-Lab/MultiTagger-v2/tree/main/ICHI

Multi-label Sequential Sentence Classification via Large Language Model

Sequential sentence classification (SSC) in scientific publications is crucial for supporting downstream tasks such as fine-grained information retrieval and extractive summarization. However, current SSC methods are constrained by model size, sequence length, and single-label setting. To address these limitations, this paper proposes LLM-SSC, a large language model (LLM)-based framework for both single- and multi-label SSC tasks. Unlike previous approaches that employ small- or medium-sized language models, the proposed framework utilizes LLMs to generate SSC labels through designed prompts, which enhance task understanding by incorporating demonstrations and a query to describe the prediction target. We also present a multi-label contrastive learning loss with auto-weighting scheme, enabling the multi-label classification task. To support our multi-label SSC analysis, we introduce and release a new dataset, biorc800, which mainly contains unstructured abstracts in the biomedical domain with manual annotations. Experiments demonstrate LLM-SSC's strong performance in SSC under both in-context learning and task-specific tuning settings. We release biorc800 and our code at: https://github.com/ScienceNLP-Lab/LLM-SSC.