Electronic health records (EHRs) hold significant value for research and applications. As a new way of information extraction, question answering (QA) can extract more flexible information than conventional methods and is more accessible to clinical researchers, but its progress is impeded by the scarcity of annotated data. In this paper, we propose a novel approach that automatically generates training data for transfer learning of QA models. Our pipeline incorporates a preprocessing module to handle challenges posed by extraction types that are not readily compatible with extractive QA frameworks, including cases with discontinuous answers and many-to-one relationships. The obtained QA model exhibits excellent performance on subtasks of information extraction in EHRs, and it can effectively handle few-shot or zero-shot settings involving yes-no questions. Case studies and ablation studies demonstrate the necessity of each component in our design, and the resulting model is deemed suitable for practical use.
Recently, there has been increasing interest in exploring the capabilities of advanced large language models (LLMs) in the field of information extraction (IE), specifically focusing on tasks related to named entity recognition (NER) and relation extraction (RE). Although researchers are exploring the use of few-shot information extraction through in-context learning with LLMs, they tend to focus only on using correct or positive examples for demonstration, neglecting the potential value of incorporating incorrect or negative examples into the learning process. In this paper, we present c-ICL, a novel few-shot technique that leverages both correct and incorrect sample constructions to create in-context learning demonstrations. This approach enhances the ability of LLMs to extract entities and relations by utilizing prompts that incorporate not only the positive samples but also the reasoning behind them. This method allows for the identification and correction of potential interface errors. Specifically, our proposed method taps into the inherent contextual information and valuable information in hard negative samples and the nearest positive neighbors to the test and then applies the in-context learning demonstrations based on LLMs. Our experiments on various datasets indicate that c-ICL outperforms previous few-shot in-context learning methods, delivering substantial enhancements in performance across a broad spectrum of related tasks. These improvements are noteworthy, showcasing the versatility of our approach in miscellaneous scenarios.
Extracting semantic information from generated text is a useful tool for applications such as automated fact checking or retrieval augmented generation. Currently, this requires either separate models during inference, which increases computational cost, or destructive fine-tuning of the language model. Instead, we propose directly embedding information extraction capabilities into pre-trained language models using probing classifiers, enabling efficient simultaneous text generation and information extraction. For this, we introduce an approach called EMBER and show that it enables named entity recognition in decoder-only language models without fine-tuning them and while incurring minimal additional computational cost at inference time. Specifically, our experiments using GPT-2 show that EMBER maintains high token generation rates during streaming text generation, with only a negligible decrease in speed of around 1% compared to a 43.64% slowdown measured for a baseline using a separate NER model. Code and data are available at https://github.com/nicpopovic/EMBER.
This paper proposes LayoutLLM, a more flexible document analysis method for understanding imaged documents. Visually Rich Document Understanding tasks, such as document image classification and information extraction, have gained significant attention due to their importance. Existing methods have been developed to enhance document comprehension by incorporating pre-training awareness of images, text, and layout structure. However, these methods require fine-tuning for each task and dataset, and the models are expensive to train and operate. To overcome this limitation, we propose a new LayoutLLM that integrates these with large-scale language models (LLMs). By leveraging the strengths of existing research in document image understanding and LLMs' superior language understanding capabilities, the proposed model, fine-tuned with multimodal instruction datasets, performs an understanding of document images in a single model. Our experiments demonstrate improvement over the baseline model in various document analysis tasks.
Relation extraction is an efficient way of mining the extraordinary wealth of human knowledge on the Web. Existing methods rely on domain-specific training data or produce noisy outputs. We focus here on extracting targeted relations from semi-structured web pages given only a short description of the relation. We present GraphScholarBERT, an open-domain information extraction method based on a joint graph and language model structure. GraphScholarBERT can generalize to previously unseen domains without additional data or training and produces only clean extraction results matched to the search keyword. Experiments show that GraphScholarBERT can improve extraction F1 scores by as much as 34.8\% compared to previous work in a zero-shot domain and zero-shot website setting.
The superior performance of supervised classification methods in the information extraction (IE) area heavily relies on a large amount of gold standard data. Recent zero-shot classification methods converted the task to other NLP tasks (e.g., textual entailment) and used off-the-shelf models of these NLP tasks to directly perform inference on the test data without using a large amount of IE annotation data. A potentially valuable by-product of these methods is the large-scale silver standard data, i.e., pseudo-labeled data by the off-the-shelf models of other NLP tasks. However, there is no further investigation into the use of these data. In this paper, we propose a new framework, Clean-LaVe, which aims to utilize silver standard data to enhance the zero-shot performance. Clean-LaVe includes four phases: (1) Obtaining silver data; (2) Identifying relatively clean data from silver data; (3) Finetuning the off-the-shelf model using clean data; (4) Inference on the test data. The experimental results show that Clean-LaVe can outperform the baseline by 5% and 6% on TACRED and Wiki80 dataset in the zero-shot relation classification task, and by 3%-7% on Smile (Korean and Polish) in the zero-shot cross-lingual relation classification task, and by 8% on ACE05-E+ in the zero-shot event argument classification task. The code is share in https://github.com/wjw136/Clean_LaVe.git.
A critical challenge in deploying unmanned aerial vehicles (UAVs) for autonomous tasks is their ability to navigate in an unknown environment. This paper introduces a novel vision-depth fusion approach for autonomous navigation on nano-UAVs. We combine the visual-based PULP-Dronet convolutional neural network for semantic information extraction, i.e., serving as the global perception, with 8x8px depth maps for close-proximity maneuvers, i.e., the local perception. When tested in-field, our integration strategy highlights the complementary strengths of both visual and depth sensory information. We achieve a 100% success rate over 15 flights in a complex navigation scenario, encompassing straight pathways, static obstacle avoidance, and 90{\deg} turns.
This paper explores the development and application of an automated system designed to extract information from semi-structured interview transcripts. Given the labor-intensive nature of traditional qualitative analysis methods, such as coding, there exists a significant demand for tools that can facilitate the analysis process. Our research investigates various topic modeling techniques and concludes that the best model for analyzing interview texts is a combination of BERT embeddings and HDBSCAN clustering. We present a user-friendly software prototype that enables researchers, including those without programming skills, to efficiently process and visualize the thematic structure of interview data. This tool not only facilitates the initial stages of qualitative analysis but also offers insights into the interconnectedness of topics revealed, thereby enhancing the depth of qualitative analysis.
Biomedical event extraction is an information extraction task to obtain events from biomedical text, whose targets include the type, the trigger, and the respective arguments involved in an event. Traditional biomedical event extraction usually adopts a pipelined approach, which contains trigger identification, argument role recognition, and finally event construction either using specific rules or by machine learning. In this paper, we propose an n-ary relation extraction method based on the BERT pre-training model to construct Binding events, in order to capture the semantic information about an event's context and its participants. The experimental results show that our method achieves promising results on the GE11 and GE13 corpora of the BioNLP shared task with F1 scores of 63.14% and 59.40%, respectively. It demonstrates that by significantly improving theperformance of Binding events, the overall performance of the pipelined event extraction approach or even exceeds those of current joint learning methods.
The progress in natural language processing (NLP) using large language models (LLMs) has greatly improved patient information extraction from clinical narratives. However, most methods based on the fine-tuning strategy have limited transfer learning ability for cross-domain applications. This study proposed a novel approach that employs a soft prompt-based learning architecture, which introduces trainable prompts to guide LLMs toward desired outputs. We examined two types of LLM architectures, including encoder-only GatorTron and decoder-only GatorTronGPT, and evaluated their performance for the extraction of social determinants of health (SDoH) using a cross-institution dataset from the 2022 n2c2 challenge and a cross-disease dataset from the University of Florida (UF) Health. The results show that decoder-only LLMs with prompt tuning achieved better performance in cross-domain applications. GatorTronGPT achieved the best F1 scores for both datasets, outperforming traditional fine-tuned GatorTron by 8.9% and 21.8% in a cross-institution setting, and 5.5% and 14.5% in a cross-disease setting.