As the number of scientific publications is growing at a rapid pace, it is difficult for laypeople to keep track of and understand the latest scientific advances, especially in the biomedical domain. While the summarization of scientific publications has been widely studied, research on summarization targeting laypeople has remained scarce. In this study, considering the lengthy input of biomedical articles, we have developed a lay summarization system through an extract-then-summarize framework with large language models (LLMs) to summarize biomedical articles for laypeople. Using a fine-tuned GPT-3.5 model, our approach achieves the highest overall ranking and demonstrates the best relevance performance in the BioLaySumm 2024 shared task.

As language models continue to be integrated into applications of personal and societal relevance, ensuring these models’ trustworthiness is crucial, particularly with respect to producing consistent outputs regardless of sensitive attributes. Given that first names may serve as proxies for (intersectional) socio-demographic representations, it is imperative to examine the impact of first names on commonsense reasoning capabilities. In this paper, we study whether a model’s reasoning given a specific input differs based on the first names provided. Our underlying assumption is that the reasoning about Alice should not differ from the reasoning about James. We propose and implement a controlled experimental framework to measure the causal effect of first names on commonsense reasoning, enabling us to distinguish between model predictions due to chance and caused by actual factors of interest. Our results indicate that the frequency of first names has a direct effect on model prediction, with less frequent names yielding divergent predictions compared to more frequent names. To gain insights into the internal mechanisms of models that are contributing to these behaviors, we also conduct an in-depth explainable analysis. Overall, our findings suggest that to ensure model robustness, it is essential to augment datasets with more diverse first names during the configuration stage.

We propose a cascade of neural models that performs sentence classification, phrase recognition, and triple extraction to automatically structure the scholarly contributions of NLP publications. To identify the most important contribution sentences in a paper, we used a BERT-based classifier with positional features (Subtask 1). A BERT-CRF model was used to recognize and characterize relevant phrases in contribution sentences (Subtask 2). We categorized the triples into several types based on whether and how their elements were expressed in text, and addressed each type using separate BERT-based classifiers as well as rules (Subtask 3). Our system was officially ranked second in Phase 1 evaluation and first in both parts of Phase 2 evaluation. After fixing a submission error in Pharse 1, our approach yields the best results overall. In this paper, in addition to a system description, we also provide further analysis of our results, highlighting its strengths and limitations. We make our code publicly available at https://github.com/Liu-Hy/nlp-contrib-graph.

Text similarity measures are used in multiple tasks such as plagiarism detection, information ranking and recognition of paraphrases and textual entailment. While recent advances in deep learning highlighted the relevance of sequential models in natural language generation, existing similarity measures do not fully exploit the sequential nature of language. Examples of such similarity measures include n-grams and skip-grams overlap which rely on distinct slices of the input texts. In this paper we present a novel text similarity measure inspired from a common representation in DNA sequence alignment algorithms. The new measure, called TextFlow, represents input text pairs as continuous curves and uses both the actual position of the words and sequence matching to compute the similarity value. Our experiments on 8 different datasets show very encouraging results in paraphrase detection, textual entailment recognition and ranking relevance.

We describe a corpus of consumer health questions annotated with named entities. The corpus consists of 1548 de-identified questions about diseases and drugs, written in English. We defined 15 broad categories of biomedical named entities for annotation. A pilot annotation phase in which a small portion of the corpus was double-annotated by four annotators was followed by a main phase in which double annotation was carried out by six annotators, and a reconciliation phase in which all annotations were reconciled by an expert. We conducted the annotation in two modes, manual and assisted, to assess the effect of automatic pre-annotation and calculated inter-annotator agreement. We obtained moderate inter-annotator agreement; assisted annotation yielded slightly better agreement and fewer missed annotations than manual annotation. Due to complex nature of biomedical entities, we paid particular attention to nested entities for which we obtained slightly lower inter-annotator agreement, confirming that annotating nested entities is somewhat more challenging. To our knowledge, the corpus is the first of its kind for consumer health text and is publicly available.

This paper presents a method for annotating question decomposition on complex medical questions. The annotations cover multiple syntactic ways that questions can be decomposed, including separating independent clauses as well as recognizing coordinations and exemplifications. We annotate a corpus of 1,467 multi-sentence consumer health questions about genetic and rare diseases. Furthermore, we label two additional medical-specific annotations: (1) background sentences are annotated with a number of medical categories such as symptoms, treatments, and family history, and (2) the central focus of the complex question (a disease) is marked. We present simple baseline results for automatic classification of these annotations, demonstrating the challenging but important nature of this task.