Coronavirus disease 2019 (COVID-19) is a global pandemic. Although much has been learned about the novel coronavirus since its emergence, there are many open questions related to tracking its spread, describing symptomology, predicting the severity of infection, and forecasting healthcare utilization. Free-text clinical notes contain critical information for resolving these questions. Data-driven, automatic information extraction models are needed to use this text-encoded information in large-scale studies. This work presents a new clinical corpus, referred to as the COVID-19 Annotated Clinical Text (CACT) Corpus, which comprises 1,472 notes with detailed annotations characterizing COVID-19 diagnoses, testing, and clinical presentation. We introduce a span-based event extraction model that jointly extracts all annotated phenomena, achieving high performance in identifying COVID-19 and symptom events with associated assertion values (0.83-0.97 F1 for events and 0.73-0.79 F1 for assertions). In a secondary use application, we explored the prediction of COVID-19 test results using structured patient data (e.g. vital signs and laboratory results) and automatically extracted symptom information. The automatically extracted symptoms improve prediction performance, beyond structured data alone.
We propose a novel strategy for extracting features in supervised learning that can be used to construct a classifier which is more robust to small perturbations in the input space. Our method builds upon the idea of the information bottleneck by introducing an additional penalty term that encourages the Fisher information of the extracted features to be small, when parametrized by the inputs. By tuning the regularization parameter, we can explicitly trade off the opposing desiderata of robustness and accuracy when constructing a classifier. We derive the optimal solution to the robust information bottleneck when the inputs and outputs are jointly Gaussian, proving that the optimally robust features are also jointly Gaussian in that setting. Furthermore, we propose a method for optimizing a variational bound on the robust information bottleneck objective in general settings using stochastic gradient descent, which may be implemented efficiently in neural networks. Our experimental results for synthetic and real data sets show that the proposed feature extraction method indeed produces classifiers with increased robustness to perturbations.
The use of electronic health records in medical research is difficult because of the unstructured format. Extracting information within reports and summarising patient presentations in a way amenable to downstream analysis would be enormously beneficial for operational and clinical research. In this work we present a natural language processing pipeline for information extraction of radiological reports in neurology. Our pipeline uses a hybrid sequence of rule-based and artificial intelligence models to accurately extract and summarise neurological reports. We train and evaluate a custom language model on a corpus of 150000 radiological reports from National Hospital for Neurology and Neurosurgery, London MRI imaging. We also present results for standard NLP tasks on domain-specific neuroradiology datasets. We show our pipeline, called `neuroNLP', can reliably extract clinically relevant information from these reports, enabling downstream modelling of reports and associated imaging on a heretofore unprecedented scale.
Clinical notes contain an abundance of important but not-readily accessible information about patients. Systems to automatically extract this information rely on large amounts of training data for which their exists limited resources to create. Furthermore, they are developed dis-jointly; meaning that no information can be shared amongst task-specific systems. This bottle-neck unnecessarily complicates practical application, reduces the performance capabilities of each individual solution and associates the engineering debt of managing multiple information extraction systems. We address these challenges by developing Multitask-Clinical BERT: a single deep learning model that simultaneously performs eight clinical tasks spanning entity extraction, PHI identification, language entailment and similarity by sharing representations amongst tasks. We find our single system performs competitively with all state-the-art task-specific systems while also benefiting from massive computational benefits at inference.
Document information extraction tasks performed by humans create data consisting of a PDF or document image input, and extracted string outputs. This end-to-end data is naturally consumed and produced when performing the task because it is valuable in and of itself. It is naturally available, at no additional cost. Unfortunately, state-of-the-art word classification methods for information extraction cannot use this data, instead requiring word-level labels which are expensive to create and consequently not available for many real life tasks. In this paper we propose the Attend, Copy, Parse architecture, a deep neural network model that can be trained directly on end-to-end data, bypassing the need for word-level labels. We evaluate the proposed architecture on a large diverse set of invoices, and outperform a state-of-the-art production system based on word classification. We believe our proposed architecture can be used on many real life information extraction tasks where word classification cannot be used due to a lack of the required word-level labels.
Document-level information extraction is a flexible framework compatible with applications where information is not necessarily localized in a single sentence. For example, key features of a diagnosis in radiology a report may not be explicitly stated, but nevertheless can be inferred from the report's text. However, document-level neural models can easily learn spurious correlations from irrelevant information. This work studies how to ensure that these models make correct inferences from complex text and make those inferences in an auditable way: beyond just being right, are these models "right for the right reasons?" We experiment with post-hoc evidence extraction in a predict-select-verify framework using feature attribution techniques. While this basic approach can extract reasonable evidence, it can be regularized with small amounts of evidence supervision during training, which substantially improves the quality of extracted evidence. We evaluate on two domains: a small-scale labeled dataset of brain MRI reports and a large-scale modified version of DocRED (Yao et al., 2019) and show that models' plausibility can be improved with no loss in accuracy.
We cast a suite of information extraction tasks into a text-to-triple translation framework. Instead of solving each task relying on task-specific datasets and models, we formalize the task as a translation between task-specific input text and output triples. By taking the task-specific input, we enable a task-agnostic translation by leveraging the latent knowledge that a pre-trained language model has about the task. We further demonstrate that a simple pre-training task of predicting which relational information corresponds to which input text is an effective way to produce task-specific outputs. This enables the zero-shot transfer of our framework to downstream tasks. We study the zero-shot performance of this framework on open information extraction (OIE2016, NYT, WEB, PENN), relation classification (FewRel and TACRED), and factual probe (Google-RE and T-REx). The model transfers non-trivially to most tasks and is often competitive with a fully supervised method without the need for any task-specific training. For instance, we significantly outperform the F1 score of the supervised open information extraction without needing to use its training set.
With the advent of the Internet, large amount of digital text is generated everyday in the form of news articles, research publications, blogs, question answering forums and social media. It is important to develop techniques for extracting information automatically from these documents, as lot of important information is hidden within them. This extracted information can be used to improve access and management of knowledge hidden in large text corpora. Several applications such as Question Answering, Information Retrieval would benefit from this information. Entities like persons and organizations, form the most basic unit of the information. Occurrences of entities in a sentence are often linked through well-defined relations; e.g., occurrences of person and organization in a sentence may be linked through relations such as employed at. The task of Relation Extraction (RE) is to identify such relations automatically. In this paper, we survey several important supervised, semi-supervised and unsupervised RE techniques. We also cover the paradigms of Open Information Extraction (OIE) and Distant Supervision. Finally, we describe some of the recent trends in the RE techniques and possible future research directions. This survey would be useful for three kinds of readers - i) Newcomers in the field who want to quickly learn about RE; ii) Researchers who want to know how the various RE techniques evolved over time and what are possible future research directions and iii) Practitioners who just need to know which RE technique works best in various settings.
Event extraction (EE) is one of the core information extraction tasks, whose purpose is to automatically identify and extract information about incidents and their actors from texts. This may be beneficial to several domains such as knowledge bases, question answering, information retrieval and summarization tasks, to name a few. The problem of extracting event information from texts is longstanding and usually relies on elaborately designed lexical and syntactic features, which, however, take a large amount of human effort and lack generalization. More recently, deep neural network approaches have been adopted as a means to learn underlying features automatically. However, existing networks do not make full use of syntactic features, which play a fundamental role in capturing very long-range dependencies. Also, most approaches extract each argument of an event separately without considering associations between arguments which ultimately leads to low efficiency, especially in sentences with multiple events. To address the two above-referred problems, we propose a novel joint event extraction framework that aims to extract multiple event triggers and arguments simultaneously by introducing shortest dependency path (SDP) in the dependency graph. We do this by eliminating irrelevant words in the sentence, thus capturing long-range dependencies. Also, an attention-based graph convolutional network is proposed, to carry syntactically related information along the shortest paths between argument candidates that captures and aggregates the latent associations between arguments; a problem that has been overlooked by most of the literature. Our results show a substantial improvement over state-of-the-art methods.
Extractive methods have proven to be very effective in automatic document summarization. Previous works perform this task by identifying informative contents at sentence level. However, it is unclear whether performing extraction at sentence level is the best solution. In this work, we show that unnecessity and redundancy issues exist when extracting full sentences, and extracting sub-sentential units is a promising alternative. Specifically, we propose extracting sub-sentential units on the corresponding constituency parsing tree. A neural extractive model which leverages the sub-sentential information and extracts them is presented. Extensive experiments and analyses show that extracting sub-sentential units performs competitively comparing to full sentence extraction under the evaluation of both automatic and human evaluations. Hopefully, our work could provide some inspiration of the basic extraction units in extractive summarization for future research.