Automatic ICD coding is the task of assigning codes from the International Classification of Diseases (ICD) to medical notes. These codes describe the state of the patient and have multiple applications, e.g., computer-assisted diagnosis or epidemiological studies. ICD coding is a challenging task due to the complexity and length of medical notes. Unlike the general trend in language processing, no transformer model has been reported to reach high performance on this task. Here, we investigate in detail ICD coding using PubMedBERT, a state-of-the-art transformer model for biomedical language understanding. We find that the difficulty of fine-tuning the model on long pieces of text is the main limitation for BERT-based models on ICD coding. We run extensive experiments and show that despite the gap with current state-of-the-art, pretrained transformers can reach competitive performance using relatively small portions of text. We point at better methods to aggregate information from long texts as the main need for improving BERT-based ICD coding.
This paper achieves state of the art results for the ICD code prediction task using the MIMIC-III dataset. This was achieved through the use of Clinical BERT (Alsentzer et al., 2019). embeddings and text augmentation and label balancing to improve F1 scores for both ICD Chapter as well as ICD disease codes. We attribute the improved performance mainly to the use of novel text augmentation to shuffle the order of sentences during training. In comparison to the Top-32 ICD code prediction (Keyang Xu, et. al.) with an F1 score of 0.76, we achieve a final F1 score of 0.75 but on a total of the top …
Clinical interactions are initially recorded and documented in free text medical notes. ICD coding is the task of classifying and coding all diagnoses, symptoms and procedures associated with a patient's visit. The process is often manual and extremely time-consuming and expensive for hospitals. In this paper, we propose a machine learning model, BERT-XML, for large scale automated ICD coding from EHR notes, utilizing recently developed unsupervised pretraining that have achieved state of the art performance on a variety of NLP tasks. We train a BERT model from scratch on EHR notes, learning w…
Transformer models have achieved great success across many NLP problems. However, previous studies in automated ICD coding concluded that these models fail to outperform some of the earlier solutions such as CNN-based models. In this paper we challenge this conclusion. We present a simple and scalable method to process long text with the existing transformer models such as BERT. We show that this method significantly improves the previous results reported for transformer models in ICD coding, and is able to outperform one of the prominent CNN-based methods.
Medical document understanding has gained much attention recently. One representative task is the International Classification of Disease (ICD) diagnosis code assignment. Existing work adopts either RNN or CNN as the backbone network because the vanilla BERT cannot handle well long documents (>2000 to kens). One issue shared across all these approaches is that they are over specific to the ICD code assignment task, losing generality to give the whole document-level and sentence-level embedding. As a result, it is not straight-forward to direct them to other downstream NLU tasks. Motivated by t…
Learning to represent free text is a core task in many clinical machine learning (ML) applications, as clinical text contains observations and plans not otherwise available for inference. State-of-the-art methods use large language models developed with immense computational resources and training data; however, applying these models is challenging because of the highly varying syntax and vocabulary in clinical free text. Structured information such as International Classification of Disease (ICD) codes often succinctly abstracts the most important facts of a clinical encounter and yields good…
Sberbank Artificial Intelligence Laboratory（俄罗斯联邦储蓄银行人工智能实验室）；New York University（纽约大学）
In this paper we study the problem of predicting clinical diagnoses from textual Electronic Health Records (EHR) data. We show the importance of this problem in medical community and present comprehensive historical review of the problem and proposed methods. As the main scientific contributions we present a modification of Bidirectional Encoder Representations from Transformers (BERT) model for sequence classification that implements a novel way of Fully-Connected (FC) layer composition and a BERT model pretrained only on domain data. To empirically validate our model, we use a large-scale Ru…
Vicomtech Foundation, Basque Research and Technology Alliance (BRTA)（维康特克基金会，巴斯克研究与技术联盟（BRTA））
Massive digital data processing provides a wide range of opportunities and benefits, but at the cost of endangering personal data privacy. Anonymisation consists in removing or replacing sensitive information from data, enabling its exploitation for different purposes while preserving the privacy of individuals. Over the years, a lot of automatic anonymisation systems have been proposed; however, depending on the type of data, the target language or the availability of training documents, the task remains challenging still. The emergence of novel deep-learning models during the last two years …
The University of Melbourne（墨尔本大学）；Amazon Research（亚马逊研究院）；University of Edinburgh（爱丁堡大学）
We present a system for answering questions based on the full text of books (BookQA), which first selects book passages given a question at hand, and then uses a memory network to reason and predict an answer. To improve generalization, we pretrain our memory network using artificial questions generated from book sentences. We experiment with the recently published NarrativeQA corpus, on the subset of Who questions, which expect book characters as answers. We experimentally show that BERT-based retrieval and pretraining improve over baseline results significantly. At the same time, we confirm …
In the last two decades, automatic extractive text summarization on lectures has demonstrated to be a useful tool for collecting key phrases and sentences that best represent the content. However, many current approaches utilize dated approaches, producing sub-par outputs or requiring several hours of manual tuning to produce meaningful results. Recently, new machine learning architectures have provided mechanisms for extractive summarization through the clustering of output embeddings from deep learning models. This paper reports on the project called Lecture Summarization Service, a python b…
University of Edinburgh（爱丁堡大学）；University College London（伦敦大学学院）；Health Data Research UK（英国健康数据研究所）
The identification of rare diseases from clinical notes with Natural Language Processing (NLP) is challenging due to the few cases available for machine learning and the need of data annotation from clinical experts. We propose a method using ontologies and weak supervision. The approach includes two steps: (i) Text-to-UMLS, linking text mentions to concepts in Unified Medical Language System (UMLS), with a named entity linking tool (e.g. SemEHR) and weak supervision based on customised rules and Bidirectional Encoder Representations from Transformers (BERT) based contextual representations, a…
A Comprehensive Survey on Pretrained Foundation Models: A History from BERT to ChatGPT
Michigan State University（密歇根州立大学）；Lehigh University（理海大学）；Beihang University（北京航空航天大学）；Macquarie University（麦考瑞大学）；Nanyang Technological University（南洋理工大学）；University of California San Diego（加利福尼亚大学圣地亚哥分校）；Salesforce AI Research（Salesforce人工智能研究院）；Duke University（杜克大学）；University of Illinois at Chicago（伊利诺伊大学芝加哥分校）
Environmental, Social, and Governance (ESG) are non-financial factors that are garnering attention from investors as they increasingly look to apply these as part of their analysis to identify material risks and growth opportunities. Some of this attention is also driven by clients who, now more aware than ever, are demanding for their money to be managed and invested responsibly. As the interest in ESG grows, so does the need for investors to have access to consumable ESG information. Since most of it is in text form in reports, disclosures, press releases, and 10-Q filings, we see a need for…
Harnessing Pre-Trained Sentence Transformers for Offensive Language Detection in Indian Languages
MKSSS Cummins College of Engineering for Women（MKSSS卡明斯女子工程学院）；Indian Institute of Technology Madras（印度理工学院马德拉斯分校）；Peoples' Friendship University of Russia (RUDN University)（俄罗斯人民友谊大学（RUDN大学））；Joint Institute for Nuclear Research（联合核研究所）；Vrije Universiteit Amsterdam（阿姆斯特丹自由大学）；University of Skövde（舍夫德大学）
Faculty of Informatics Kaunas University of Technology（考纳斯理工大学信息学院）；Kaunas University of Technology（考纳斯理工大学）
A recent introduction of Transformer deep learning architecture made breakthroughs in various natural language processing tasks. However, non-English languages could not leverage such new opportunities with the English text pre-trained models. This changed with research focusing on multilingual models, where less-spoken languages are the main beneficiaries. We compare pre-trained multilingual BERT, XLM-R, and older learned text representation methods as encodings for the task of Lithuanian news clustering. Our results indicate that publicly available pre-trained multilingual Transformer models…
Ontology-Driven and Weakly Supervised Rare Disease Identification from Clinical Notes
University of Edinburgh（爱丁堡大学）；Health Data Research UK（英国健康数据研究所）；University of Oxford（牛津大学）；University College London（伦敦大学学院）；The University of Manchester（曼彻斯特大学）
We present mSLAM, a multilingual Speech and LAnguage Model that learns cross-lingual cross-modal representations of speech and text by pre-training jointly on large amounts of unlabeled speech and text in multiple languages. mSLAM combines w2v-BERT pre-training on speech with SpanBERT pre-training on character-level text, along with Connectionist Temporal Classification (CTC) losses on paired speech and transcript data, to learn a single model capable of learning from and representing both speech and text signals in a shared representation space. We evaluate mSLAM on several downstream speech …
This open access book provides a comprehensive overview of the state of the art in research and applications of Foundation Models and is intended for readers familiar with basic Natural Language Processing (NLP) concepts. Over the recent years, a revolutionary new paradigm has been developed for training models for NLP. These models are first pre-trained on large collections of text documents to acquire general syntactic knowledge and semantic information. Then, they are fine-tuned for specific tasks, which they can often solve with superhuman accuracy. When the models are large enough, they c…
