Clinical studies often require understanding elements of a patient's narrative that exist only in free text clinical notes. To transform notes into structured data for downstream use, these elements are commonly extracted and normalized to medical vocabularies. In this work, we audit the performance of and indicate areas of improvement for state-of-the-art systems. We find that high task accuracies for clinical entity normalization systems on the 2019 n2c2 Shared Task are misleading, and underlying performance is still brittle. Normalization accuracy is high for common concepts (95.3%), but much lower for concepts unseen in training data (69.3%). We demonstrate that current approaches are hindered in part by inconsistencies in medical vocabularies, limitations of existing labeling schemas, and narrow evaluation techniques. We reformulate the annotation framework for clinical entity extraction to factor in these issues to allow for robust end-to-end system benchmarking. We evaluate concordance of annotations from our new framework between two annotators and achieve a Jaccard similarity of 0.73 for entity recognition and an agreement of 0.83 for entity normalization. We propose a path forward to address the demonstrated need for the creation of a reference standard to spur method development in entity recognition and normalization.
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.
We build a common-knowledge concept recognition system for a Systems Engineer's Virtual Assistant (SEVA) which can be used for downstream tasks such as relation extraction, knowledge graph construction, and question-answering. The problem is formulated as a token classification task similar to named entity extraction. With the help of a domain expert and text processing methods, we construct a dataset annotated at the word-level by carefully defining a labelling scheme to train a sequence model to recognize systems engineering concepts. We use a pre-trained language model and fine-tune it with the labeled dataset of concepts. In addition, we also create some essential datasets for information such as abbreviations and definitions from the systems engineering domain. Finally, we construct a simple knowledge graph using these extracted concepts along with some hyponym relations.
This research on data extraction methods applies recent advances in natural language processing to evidence synthesis based on medical texts. Texts of interest include abstracts of clinical trials in English and in multilingual contexts. The main focus is on information characterized via the Population, Intervention, Comparator, and Outcome (PICO) framework, but data extraction is not limited to these fields. Recent neural network architectures based on transformers show capacities for transfer learning and increased performance on downstream natural language processing tasks such as universal reading comprehension, brought forward by this architecture's use of contextualized word embeddings and self-attention mechanisms. This paper contributes to solving problems related to ambiguity in PICO sentence prediction tasks, as well as highlighting how annotations for training named entity recognition systems are used to train a high-performing, but nevertheless flexible architecture for question answering in systematic review automation. Additionally, it demonstrates how the problem of insufficient amounts of training annotations for PICO entity extraction is tackled by augmentation. All models in this paper were created with the aim to support systematic review (semi)automation. They achieve high F1 scores, and demonstrate the feasibility of applying transformer-based classification methods to support data mining in the biomedical literature.
Joint extraction of entities and relations has received significant attention due to its potential of providing higher performance for both tasks. Among existing methods, CopyRE is effective and novel, which uses a sequence-to-sequence framework and copy mechanism to directly generate the relation triplets. However, it suffers from two fatal problems. The model is extremely weak at differing the head and tail entity, resulting in inaccurate entity extraction. It also cannot predict multi-token entities (e.g. \textit{Steven Jobs}). To address these problems, we give a detailed analysis of the reasons behind the inaccurate entity extraction problem, and then propose a simple but extremely effective model structure to solve this problem. In addition, we propose a multi-task learning framework equipped with copy mechanism, called CopyMTL, to allow the model to predict multi-token entities. Experiments reveal the problems of CopyRE and show that our model achieves significant improvement over the current state-of-the-art method by 9% in NYT and 16% in WebNLG (F1 score). Our code is available at https://github.com/WindChimeRan/CopyMTL
The task of named entity recognition (NER) is normally divided into nested NER and flat NER depending on whether named entities are nested or not. Models are usually separately developed for the two tasks, since sequence labeling models, the most widely used backbone for flat NER, are only able to assign a single label to a particular token, which is unsuitable for nested NER where a token may be assigned several labels. In this paper, we propose a unified framework that is capable of handling both flat and nested NER tasks. Instead of treating the task of NER as a sequence labeling problem, we propose to formulate it as a machine reading comprehension (MRC) task. For example, extracting entities with the \textsc{per} label is formalized as extracting answer spans to the question "{\it which person is mentioned in the text?}". This formulation naturally tackles the entity overlapping issue in nested NER: the extraction of two overlapping entities for different categories requires answering two independent questions. Additionally, since the query encodes informative prior knowledge, this strategy facilitates the process of entity extraction, leading to better performances for not only nested NER, but flat NER. We conduct experiments on both {\em nested} and {\em flat} NER datasets. Experimental results demonstrate the effectiveness of the proposed formulation. We are able to achieve vast amount of performance boost over current SOTA models on nested NER datasets, i.e., +1.28, +2.55, +5.44, +6.37, respectively on ACE04, ACE05, GENIA and KBP17, along with SOTA results on flat NER datasets, i.e.,+0.24, +1.95, +0.21, +1.49 respectively on English CoNLL 2003, English OntoNotes 5.0, Chinese MSRA, Chinese OntoNotes 4.0.
Extracting entity from images is a crucial part of many OCR applications, such as entity recognition of cards, invoices, and receipts. Most of the existing works employ classical detection and recognition paradigm. This paper proposes an Entity-aware Attention Text Extraction Network called EATEN, which is an end-to-end trainable system to extract the entities without any post-processing. In the proposed framework, each entity is parsed by its corresponding entity-aware decoder, respectively. Moreover, we innovatively introduce a state transition mechanism which further improves the robustness of entity extraction. In consideration of the absence of public benchmarks, we construct a dataset of almost 0.6 million images in three real-world scenarios (train ticket, passport and business card), which is publicly available at https://github.com/beacandler/EATEN. To the best of our knowledge, EATEN is the first single shot method to extract entities from images. Extensive experiments on these benchmarks demonstrate the state-of-the-art performance of EATEN.
Most existing methods determine relation types only after all the entities have been recognized, thus the interaction between relation types and entity mentions is not fully modeled. This paper presents a novel paradigm to deal with relation extraction by regarding the related entities as the arguments of a relation. We apply a hierarchical reinforcement learning (HRL) framework in this paradigm to enhance the interaction between entity mentions and relation types. The whole extraction process is decomposed into a hierarchy of two-level RL policies for relation detection and entity extraction respectively, so that it is more feasible and natural to deal with overlapping relations. Our model was evaluated on public datasets collected via distant supervision, and results show that it gains better performance than existing methods and is more powerful for extracting overlapping relations.
This work addresses challenges arising from extracting entities from textual data, including the high cost of data annotation, model accuracy, selecting appropriate evaluation criteria, and the overall quality of annotation. We present a framework that integrates Entity Set Expansion (ESE) and Active Learning (AL) to reduce the annotation cost of sparse data and provide an online evaluation method as feedback. This incremental and interactive learning framework allows for rapid annotation and subsequent extraction of sparse data while maintaining high accuracy. We evaluate our framework on three publicly available datasets and show that it drastically reduces the cost of sparse entity annotation by an average of 85% and 45% to reach 0.9 and 1.0 F-Scores respectively. Moreover, the method exhibited robust performance across all datasets.
Timely analysis of cyber-security information necessitates automated information extraction from unstructured text. While state-of-the-art extraction methods produce extremely accurate results, they require ample training data, which is generally unavailable for specialized applications, such as detecting security related entities; moreover, manual annotation of corpora is very costly and often not a viable solution. In response, we develop a very precise method to automatically label text from several data sources by leveraging related, domain-specific, structured data and provide public access to a corpus annotated with cyber-security entities. Next, we implement a Maximum Entropy Model trained with the average perceptron on a portion of our corpus ($\sim$750,000 words) and achieve near perfect precision, recall, and accuracy, with training times under 17 seconds.
Events and entities are closely related; entities are often actors or participants in events and events without entities are uncommon. The interpretation of events and entities is highly contextually dependent. Existing work in information extraction typically models events separately from entities, and performs inference at the sentence level, ignoring the rest of the document. In this paper, we propose a novel approach that models the dependencies among variables of events, entities, and their relations, and performs joint inference of these variables across a document. The goal is to enable access to document-level contextual information and facilitate context-aware predictions. We demonstrate that our approach substantially outperforms the state-of-the-art methods for event extraction as well as a strong baseline for entity extraction.
Output-agreement mechanisms such as ESP Game have been widely used in human computation to obtain reliable human-generated labels. In this paper, we argue that a "time-limited" output-agreement mechanism can be used to create a fast and robust crowd-powered component in interactive systems, particularly dialogue systems, to extract key information from user utterances on the fly. Our experiments on Amazon Mechanical Turk using the Airline Travel Information System (ATIS) dataset showed that the proposed approach achieves high-quality results with an average response time shorter than 9 seconds.
Existing studies of how information diffuses across social networks have thus far concentrated on analysing and recovering the spread of deterministic innovations such as URLs, hashtags, and group membership. However investigating how mentions of real-world entities appear and spread has yet to be explored, largely due to the computationally intractable nature of performing large-scale entity extraction. In this paper we present, to the best of our knowledge, one of the first pieces of work to closely examine the diffusion of named entities on social media, using Reddit as our case study platform. We first investigate how named entities can be accurately recognised and extracted from discussion posts. We then use these extracted entities to study the patterns of entity cascades and how the probability of a user adopting an entity (i.e. mentioning it) is associated with exposures to the entity. We put these pieces together by presenting a parallelised diffusion model that can forecast the probability of entity adoption, finding that the influence of adoption between users can be characterised by their prior interactions -- as opposed to whether the users propagated entity-adoptions beforehand. Our findings have important implications for researchers studying influence and language, and for community analysts who wish to understand entity-level influence dynamics.