OBJECTIVE: Large language models (LLMs) have shown impressive ability in biomedical question-answering, but have not been adequately investigated for more specific biomedical applications. This study investigates ChatGPT family of models (GPT-3.5, GPT-4) in biomedical tasks beyond question-answering. MATERIALS AND METHODS: We evaluated model performance with 11 122 samples for two fundamental tasks in the biomedical domain-classification (n = 8676) and reasoning (n = 2446). The first task involves classifying health advice in scientific literature, while the second task is detecting causal relations in biomedical literature. We used 20% of the dataset for prompt development, including zero- and few-shot settings with and without chain-of-thought (CoT). We then evaluated the best prompts from each setting on the remaining dataset, comparing them to models using simple features (BoW with logistic regression) and fine-tuned BioBERT models. RESULTS: Fine-tuning BioBERT produced the best classification (F1: 0.800-0.902) and reasoning (F1: 0.851) results. Among LLM approaches, few-shot CoT achieved the best classification (F1: 0.671-0.770) and reasoning (F1: 0.682) results, comparable to the BoW model (F1: 0.602-0.753 and 0.675 for classification and reasoning, respectively). It took 78 h to obtain the best LLM results, compared to 0.078 and 0.008 h for the top-performing BioBERT and BoW models, respectively. DISCUSSION: The simple BoW model performed similarly to the most complex LLM prompting. Prompt engineering required significant investment. CONCLUSION: Despite the excitement around viral ChatGPT, fine-tuning for two fundamental biomedical natural language processing tasks remained the best strategy.

Space situational awareness typically makes use of physical measurements from radar, telescopes, and other assets to monitor satellites and other spacecraft for operational, navigational, and defense purposes. In this work we explore using textual input for the space situational awareness task. We construct a corpus of 48.5k news articles spanning all known active satellites between 2009 and 2020. Using a dependency-rule-based extraction system designed to target three high-impact events – spacecraft launches, failures, and decommissionings, we identify 1,787 space-event sentences that are then annotated by humans with 15.9k labels for event slots. We empirically demonstrate a state-of-the-art neural extraction system achieves an overall F1 between 53 and 91 per slot for event extraction in this low-resource, high-impact domain.

We propose a simple and effective strategy for data augmentation for low-resource machine reading comprehension (MRC). Our approach first pretrains the answer extraction components of a MRC system on the augmented data that contains approximate context of the correct answers, before training it on the exact answer spans. The approximate context helps the QA method components in narrowing the location of the answers. We demonstrate that our simple strategy substantially improves both document retrieval and answer extraction performance by providing larger context of the answers and additional training data. In particular, our method significantly improves the performance of BERT based retriever (15.12%), and answer extractor (4.33% F1) on TechQA, a complex, low-resource MRC task. Further, our data augmentation strategy yields significant improvements of up to 3.9% exact match (EM) and 2.7% F1 for answer extraction on PolicyQA, another practical but moderate sized QA dataset that also contains long answer spans.

The goal of text simplification (TS) is to transform difficult text into a version that is easier to understand and more broadly accessible to a wide variety of readers.In some domains, such as healthcare, fully automated approaches cannot be used since information must be accurately preserved.Instead, semi-automated approaches can be used that assist a human writer in simplifying text faster and at a higher quality.In this paper, we examine the application of autocomplete to text simplification in the medical domain.We introduce a new parallel medical data set consisting of aligned English Wikipedia with Simple English Wikipedia sentences and examine the application of pretrained neural language models (PNLMs) on this dataset.We compare four PNLMs (BERT, RoBERTa, XLNet, and GPT-2), and show how the additional context of the sentence to be simplified can be incorporated to achieve better results (6.17% absolute improvement over the best individual model).We also introduce an ensemble model that combines the four PNLMs and outperforms the best individual model by 2.1%, resulting in an overall word prediction accuracy of 64.52%.