Federated Learning (FL) faces major challenges regarding communication overhead and model privacy when training large language models (LLMs), especially in healthcare applications. To address these, we introduce Selective Attention Federated Learning (SAFL), a novel approach that dynamically fine-tunes only those transformer layers identified as attention-critical. By employing attention patterns to determine layer importance, SAFL significantly reduces communication bandwidth and enhances differential privacy resilience. Evaluations on clinical NLP benchmarks (i2b2 Clinical Concept Extraction and MIMIC-III discharge summaries) demonstrate that SAFL achieves competitive performance with centralized models while substantially improving communication efficiency and privacy preservation.
Breast ultrasound is essential for detecting and diagnosing abnormalities, with radiology reports summarizing key findings like lesion characteristics and malignancy assessments. Extracting this critical information is challenging due to the unstructured nature of these reports, with varied linguistic styles and inconsistent formatting. While proprietary LLMs like GPT-4 are effective, they are costly and raise privacy concerns when handling protected health information. This study presents a pipeline for developing an in-house LLM to extract clinical information from radiology reports. We first use GPT-4 to create a small labeled dataset, then fine-tune a Llama3-8B model on it. Evaluated on clinician-annotated reports, our model achieves an average F1 score of 84.6%, which is on par with GPT-4. Our findings demonstrate the feasibility of developing an in-house LLM that not only matches GPT-4's performance but also offers cost reductions and enhanced data privacy.
Objective: To develop a natural language processing system that solves both clinical concept extraction and relation extraction in a unified prompt-based machine reading comprehension (MRC) architecture with good generalizability for cross-institution applications. Methods: We formulate both clinical concept extraction and relation extraction using a unified prompt-based MRC architecture and explore state-of-the-art transformer models. We compare our MRC models with existing deep learning models for concept extraction and end-to-end relation extraction using two benchmark datasets developed by the 2018 National NLP Clinical Challenges (n2c2) challenge (medications and adverse drug events) and the 2022 n2c2 challenge (relations of social determinants of health [SDoH]). We also evaluate the transfer learning ability of the proposed MRC models in a cross-institution setting. We perform error analyses and examine how different prompting strategies affect the performance of MRC models. Results and Conclusion: The proposed MRC models achieve state-of-the-art performance for clinical concept and relation extraction on the two benchmark datasets, outperforming previous non-MRC transformer models. GatorTron-MRC achieves the best strict and lenient F1-scores for concept extraction, outperforming previous deep learning models on the two datasets by 1%~3% and 0.7%~1.3%, respectively. For end-to-end relation extraction, GatorTron-MRC and BERT-MIMIC-MRC achieve the best F1-scores, outperforming previous deep learning models by 0.9%~2.4% and 10%-11%, respectively. For cross-institution evaluation, GatorTron-MRC outperforms traditional GatorTron by 6.4% and 16% for the two datasets, respectively. The proposed method is better at handling nested/overlapped concepts, extracting relations, and has good portability for cross-institute applications.
There is an increasing interest in developing artificial intelligence (AI) systems to process and interpret electronic health records (EHRs). Natural language processing (NLP) powered by pretrained language models is the key technology for medical AI systems utilizing clinical narratives. However, there are few clinical language models, the largest of which trained in the clinical domain is comparatively small at 110 million parameters (compared with billions of parameters in the general domain). It is not clear how large clinical language models with billions of parameters can help medical AI systems utilize unstructured EHRs. In this study, we develop from scratch a large clinical language model - GatorTron - using >90 billion words of text (including >82 billion words of de-identified clinical text) and systematically evaluate it on 5 clinical NLP tasks including clinical concept extraction, medical relation extraction, semantic textual similarity, natural language inference (NLI), and medical question answering (MQA). We examine how (1) scaling up the number of parameters and (2) scaling up the size of the training data could benefit these NLP tasks. GatorTron models scale up the clinical language model from 110 million to 8.9 billion parameters and improve 5 clinical NLP tasks (e.g., 9.6% and 9.5% improvement in accuracy for NLI and MQA), which can be applied to medical AI systems to improve healthcare delivery. The GatorTron models are publicly available at: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/models/gatortron_og.
The field of natural language processing (NLP) has recently seen a large change towards using pre-trained language models for solving almost any task. Despite showing great improvements in benchmark datasets for various tasks, these models often perform sub-optimal in non-standard domains like the clinical domain where a large gap between pre-training documents and target documents is observed. In this paper, we aim at closing this gap with domain-specific training of the language model and we investigate its effect on a diverse set of downstream tasks and settings. We introduce the pre-trained CLIN-X (Clinical XLM-R) language models and show how CLIN-X outperforms other pre-trained transformer models by a large margin for ten clinical concept extraction tasks from two languages. In addition, we demonstrate how the transformer model can be further improved with our proposed task- and language-agnostic model architecture based on ensembles over random splits and cross-sentence context. Our studies in low-resource and transfer settings reveal stable model performance despite a lack of annotated data with improvements of up to 47 F1 points when only 250 labeled sentences are available. Our results highlight the importance of specialized language models as CLIN-X for concept extraction in non-standard domains, but also show that our task-agnostic model architecture is robust across the tested tasks and languages so that domain- or task-specific adaptations are not required.
Following the global COVID-19 pandemic, the number of scientific papers studying the virus has grown massively, leading to increased interest in automated literate review. We present a clinical text mining system that improves on previous efforts in three ways. First, it can recognize over 100 different entity types including social determinants of health, anatomy, risk factors, and adverse events in addition to other commonly used clinical and biomedical entities. Second, the text processing pipeline includes assertion status detection, to distinguish between clinical facts that are present, absent, conditional, or about someone other than the patient. Third, the deep learning models used are more accurate than previously available, leveraging an integrated pipeline of state-of-the-art pretrained named entity recognition models, and improving on the previous best performing benchmarks for assertion status detection. We illustrate extracting trends and insights, e.g. most frequent disorders and symptoms, and most common vital signs and EKG findings, from the COVID-19 Open Research Dataset (CORD-19). The system is built using the Spark NLP library which natively supports scaling to use distributed clusters, leveraging GPUs, configurable and reusable NLP pipelines, healthcare specific embeddings, and the ability to train models to support new entity types or human languages with no code changes.
The recognition and normalization of clinical information, such as tumor morphology mentions, is an important, but complex process consisting of multiple subtasks. In this paper, we describe our system for the CANTEMIST shared task, which is able to extract, normalize and rank ICD codes from Spanish electronic health records using neural sequence labeling and parsing approaches with context-aware embeddings. Our best system achieves 85.3 F1, 76.7 F1, and 77.0 MAP for the three tasks, respectively.
Due to the compelling improvements brought by BERT, many recent representation models adopted the Transformer architecture as their main building block, consequently inheriting the wordpiece tokenization system despite it not being intrinsically linked to the notion of Transformers. While this system is thought to achieve a good balance between the flexibility of characters and the efficiency of full words, using predefined wordpiece vocabularies from the general domain is not always suitable, especially when building models for specialized domains (e.g., the medical domain). Moreover, adopting a wordpiece tokenization shifts the focus from the word level to the subword level, making the models conceptually more complex and arguably less convenient in practice. For these reasons, we propose CharacterBERT, a new variant of BERT that drops the wordpiece system altogether and uses a Character-CNN module instead to represent entire words by consulting their characters. We show that this new model improves the performance of BERT on a variety of medical domain tasks while at the same time producing robust, word-level and open-vocabulary representations.
Recent studies on domain-specific BERT models show that effectiveness on downstream tasks can be improved when models are pretrained on in-domain data. Often, the pretraining data used in these models are selected based on their subject matter, e.g., biology or computer science. Given the range of applications using social media text, and its unique language variety, we pretrain two models on tweets and forum text respectively, and empirically demonstrate the effectiveness of these two resources. In addition, we investigate how similarity measures can be used to nominate in-domain pretraining data. We publicly release our pretrained models at https://bit.ly/35RpTf0.
Clinical concept extraction often begins with clinical Named Entity Recognition (NER). Often trained on annotated clinical notes, clinical NER models tend to struggle with tagging clinical entities in user queries because of the structural differences between clinical notes and user queries. User queries, unlike clinical notes, are often ungrammatical and incoherent. In many cases, user queries are compounded of multiple clinical entities, without comma or conjunction words separating them. By using as dataset a mixture of annotated clinical notes and synthesized user queries, we adapt a clinical NER model based on the BiLSTM-CRF architecture for tagging clinical entities in user queries. Our contribution are the following: 1) We found that when trained on a mixture of synthesized user queries and clinical notes, the NER model performs better on both user queries and clinical notes. 2) We provide an end-to-end and easy-to-implement framework for clinical concept extraction from user queries.
Background Concept extraction, a subdomain of natural language processing (NLP) with a focus on extracting concepts of interest, has been adopted to computationally extract clinical information from text for a wide range of applications ranging from clinical decision support to care quality improvement. Objectives In this literature review, we provide a methodology review of clinical concept extraction, aiming to catalog development processes, available methods and tools, and specific considerations when developing clinical concept extraction applications. Methods Based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a literature search was conducted for retrieving EHR-based information extraction articles written in English and published from January 2009 through June 2019 from Ovid MEDLINE In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid EMBASE, Scopus, Web of Science, and the ACM Digital Library. Results A total of 6,686 publications were retrieved. After title and abstract screening, 228 publications were selected. The methods used for developing clinical concept extraction applications were discussed in this review.
The text of clinical notes can be a valuable source of patient information and clinical assessments. Historically, the primary approach for exploiting clinical notes has been information extraction: linking spans of text to concepts in a detailed domain ontology. However, recent work has demonstrated the potential of supervised machine learning to extract document-level codes directly from the raw text of clinical notes. We propose to bridge the gap between the two approaches with two novel syntheses: (1) treating extracted concepts as features, which are used to supplement or replace the text of the note; (2) treating extracted concepts as labels, which are used to learn a better representation of the text. Unfortunately, the resulting concepts do not yield performance gains on the document-level clinical coding task. We explore possible explanations and future research directions.
Neural network-based representations ("embeddings") have dramatically advanced natural language processing (NLP) tasks, including clinical NLP tasks such as concept extraction. Recently, however, more advanced embedding methods and representations (e.g., ELMo, BERT) have further pushed the state-of-the-art in NLP, yet there are no common best practices for how to integrate these representations into clinical tasks. The purpose of this study, then, is to explore the space of possible options in utilizing these new models for clinical concept extraction, including comparing these to traditional word embedding methods (word2vec, GloVe, fastText). Both off-the-shelf open-domain embeddings and pre-trained clinical embeddings from MIMIC-III are evaluated. We explore a battery of embedding methods consisting of traditional word embeddings and contextual embeddings, and compare these on four concept extraction corpora: i2b2 2010, i2b2 2012, SemEval 2014, and SemEval 2015. We also analyze the impact of the pre-training time of a large language model like ELMo or BERT on the extraction performance. Last, we present an intuitive way to understand the semantic information encoded by contextual embeddings. Contextual embeddings pre-trained on a large clinical corpus achieves new state-of-the-art performances across all concept extraction tasks. The best-performing model outperforms all state-of-the-art methods with respective F1-measures of 90.25, 93.18 (partial), 80.74, and 81.65. We demonstrate the potential of contextual embeddings through the state-of-the-art performance these methods achieve on clinical concept extraction. Additionally, we demonstrate contextual embeddings encode valuable semantic information not accounted for in traditional word representations.
Automatic extraction of clinical concepts is an essential step for turning the unstructured data within a clinical note into structured and actionable information. In this work, we propose a clinical concept extraction model for automatic annotation of clinical problems, treatments, and tests in clinical notes utilizing domain-specific contextual word embedding. A contextual word embedding model is first trained on a corpus with a mixture of clinical reports and relevant Wikipedia pages in the clinical domain. Next, a bidirectional LSTM-CRF model is trained for clinical concept extraction using the contextual word embedding model. We tested our proposed model on the I2B2 2010 challenge dataset. Our proposed model achieved the best performance among reported baseline models and outperformed the state-of-the-art models by 3.4% in terms of F1-score.
Extraction of concepts present in patient clinical records is an essential step in clinical research. The 2010 i2b2/VA Workshop on Natural Language Processing Challenges for clinical records presented concept extraction (CE) task, with aim to identify concepts (such as treatments, tests, problems) and classify them into predefined categories. State-of-the-art CE approaches heavily rely on hand crafted features and domain specific resources which are hard to collect and tune. For this reason, this paper employs bidirectional LSTM with CRF decoding initialized with general purpose off-the-shelf word embeddings for CE. The experimental results achieved on 2010 i2b2/VA reference standard corpora using bidirectional LSTM CRF ranks closely with top ranked systems.
Automated extraction of concepts from patient clinical records is an essential facilitator of clinical research. For this reason, the 2010 i2b2/VA Natural Language Processing Challenges for Clinical Records introduced a concept extraction task aimed at identifying and classifying concepts into predefined categories (i.e., treatments, tests and problems). State-of-the-art concept extraction approaches heavily rely on handcrafted features and domain-specific resources which are hard to collect and define. For this reason, this paper proposes an alternative, streamlined approach: a recurrent neural network (the bidirectional LSTM with CRF decoding) initialized with general-purpose, off-the-shelf word embeddings. The experimental results achieved on the 2010 i2b2/VA reference corpora using the proposed framework outperform all recent methods and ranks closely to the best submission from the original 2010 i2b2/VA challenge.
Background. Previous state-of-the-art systems on Drug Name Recognition (DNR) and Clinical Concept Extraction (CCE) have focused on a combination of text "feature engineering" and conventional machine learning algorithms such as conditional random fields and support vector machines. However, developing good features is inherently heavily time-consuming. Conversely, more modern machine learning approaches such as recurrent neural networks (RNNs) have proved capable of automatically learning effective features from either random assignments or automated word "embeddings". Objectives. (i) To create a highly accurate DNR and CCE system that avoids conventional, time-consuming feature engineering. (ii) To create richer, more specialized word embeddings by using health domain datasets such as MIMIC-III. (iii) To evaluate our systems over three contemporary datasets. Methods. Two deep learning methods, namely the Bidirectional LSTM and the Bidirectional LSTM-CRF, are evaluated. A CRF model is set as the baseline to compare the deep learning systems to a traditional machine learning approach. The same features are used for all the models. Results. We have obtained the best results with the Bidirectional LSTM-CRF model, which has outperformed all previously proposed systems. The specialized embeddings have helped to cover unusual words in DDI-DrugBank and DDI-MedLine, but not in the 2010 i2b2/VA IRB Revision dataset. Conclusion. We present a state-of-the-art system for DNR and CCE. Automated word embeddings has allowed us to avoid costly feature engineering and achieve higher accuracy. Nevertheless, the embeddings need to be retrained over datasets that are adequate for the domain, in order to adequately cover the domain-specific vocabulary.
Clinical notes often describe important aspects of a patient's stay and are therefore critical to medical research. Clinical concept extraction (CCE) of named entities - such as problems, tests, and treatments - aids in forming an understanding of notes and provides a foundation for many downstream clinical decision-making tasks. Historically, this task has been posed as a standard named entity recognition (NER) sequence tagging problem, and solved with feature-based methods using handengineered domain knowledge. Recent advances, however, have demonstrated the efficacy of LSTM-based models for NER tasks, including CCE. This work presents CliNER 2.0, a simple-to-install, open-source tool for extracting concepts from clinical text. CliNER 2.0 uses a word- and character- level LSTM model, and achieves state-of-the-art performance. For ease of use, the tool also includes pre-trained models available for public use.