Clinical natural language processing faces challenges like complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation with LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 8 clinical NLP tasks and 18 datasets reveals that ClinGen consistently enhances performance across various tasks by 7.7%-8.7% on average, effectively aligning the distribution of real datasets and enriching the diversity of generated training instances.
Scientific information extraction (SciIE), which aims to automatically extract information from scientific literature, is becoming more important than ever. However, there are no existing SciIE datasets for polymer materials, which is an important class of materials used ubiquitously in our daily lives. To bridge this gap, we introduce POLYIE, a new SciIE dataset for polymer materials. POLYIE is curated from 146 full-length polymer scholarly articles, which are annotated with different named entities (i.e., materials, properties, values, conditions) as well as their N-ary relations by domain experts. POLYIE presents several unique challenges due to diverse lexical formats of entities, ambiguity between entities, and variable-length relations. We evaluate state-of-the-art named entity extraction and relation extraction models on POLYIE, analyze their strengths and weaknesses, and highlight some difficult cases for these models. To the best of our knowledge, POLYIE is the first SciIE benchmark for polymer materials, and we hope it will lead to more research efforts from the community on this challenging task. Our code and data are available on: https://github.com/jerry3027/PolyIE.
Hierarchical text classification (HTC) is a complex subtask under multi-label text classification, characterized by a hierarchical label taxonomy and data imbalance. The best-performing models aim to learn a static representation by combining document and hierarchical label information. However, the relevance of document sections can vary based on the hierarchy level, necessitating a dynamic document representation. To address this, we propose HiGen, a text-generation-based framework utilizing language models to encode dynamic text representations. We introduce a level-guided loss function to capture the relationship between text and label name semantics. Our approach incorporates a task-specific pretraining strategy, adapting the language model to in-domain knowledge and significantly enhancing performance for classes with limited examples. Furthermore, we present a new and valuable dataset called ENZYME, designed for HTC, which comprises articles from PubMed with the goal of predicting Enzyme Commission (EC) numbers. Through extensive experiments on the ENZYME dataset and the widely recognized WOS and NYT datasets, our methodology demonstrates superior performance, surpassing existing approaches while efficiently handling data and mitigating class imbalance. We release our code and dataset here: https://github.com/viditjain99/HiGen.
We present RAM-EHR, a Retrieval AugMentation pipeline to improve clinical predictions on Electronic Health Records (EHRs). RAM-EHR first collects multiple knowledge sources, converts them into text format, and uses dense retrieval to obtain information related to medical concepts. This strategy addresses the difficulties associated with complex names for the concepts. RAM-EHR then augments the local EHR predictive model co-trained with consistency regularization to capture complementary information from patient visits and summarized knowledge. Experiments on two EHR datasets show the efficacy of RAM-EHR over previous knowledge-enhanced baselines (3.4% gain in AUROC and 7.2% gain in AUPR), emphasizing the effectiveness of the summarized knowledge from RAM-EHR for clinical prediction tasks.
With the development of large language models (LLMs), zero-shot learning has attracted much attention for various NLP tasks. Different from prior works that generate training data with billion-scale natural language generation (NLG) models, we propose a retrieval-enhanced framework to create training data from a general-domain unlabeled corpus. To realize this, we first conduct contrastive pretraining to learn an unsupervised dense retriever for extracting the most relevant documents using class-descriptive verbalizers. We then further pro- pose two simple strategies, namely Verbalizer Augmentation with Demonstrations and Self- consistency Guided Filtering to improve the topic coverage of the dataset while removing noisy examples. Experiments on nine datasets demonstrate that ReGen achieves 4.3% gain over the strongest baselines and saves around 70% of the time when compared with baselines using large NLG models. Besides, REGEN can be naturally integrated with recently proposed large language models to boost performance.
We study the problem of extracting N-ary relation tuples from scientific articles. This task is challenging because the target knowledge tuples can reside in multiple parts and modalities of the document. Our proposed method ReSel decomposes this task into a two-stage procedure that first retrieves the most relevant paragraph/table and then selects the target entity from the retrieved component. For the high-level retrieval stage, ReSel designs a simple and effective feature set, which captures multi-level lexical and semantic similarities between the query and components. For the low-level selection stage, ReSel designs a cross-modal entity correlation graph along with a multi-view architecture, which models both semantic and document-structural relations between entities. Our experiments on three scientific information extraction datasets show that ReSel outperforms state-of-the-art baselines significantly.
Fine-tuned pre-trained language models can suffer from severe miscalibration for both in-distribution and out-of-distribution (OOD) data due to over-parameterization. To mitigate this issue, we propose a regularized fine-tuning method. Our method introduces two types of regularization for better calibration: (1) On-manifold regularization, which generates pseudo on-manifold samples through interpolation within the data manifold. Augmented training with these pseudo samples imposes a smoothness regularization to improve in-distribution calibration. (2) Off-manifold regularization, which encourages the model to output uniform distributions for pseudo off-manifold samples to address the over-confidence issue for OOD data. Our experiments demonstrate that the proposed method outperforms existing calibration methods for text classification in terms of expectation calibration error, misclassification detection, and OOD detection on six datasets. Our code can be found at https://github.com/Lingkai-Kong/Calibrated-BERT-Fine-Tuning.