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.
Over the past years, there has been many efforts to curate and increase the added value of the raw data. Data curation has been defined as activities and processes an analyst undertakes to transform the raw data into contextualized data and knowledge. Data curation enables decision-makers and data analyst to extract value and derive insight from the raw data. However, to curate the raw data, an analyst needs to carry out various curation tasks including, extraction linking, classification, and indexing, which are error-prone, tedious and challenging. Besides, deriving insight require analysts to spend a long period of time to scan and analyze the curation environments. This problem is exacerbated when the curation environment is large, and the analyst needs to curate a varied and comprehensive list of data. To address these challenges, in this dissertation, we present techniques, algorithms and systems for augmenting analysts in curation tasks. We propose: ~(1) a feature-based and automated technique for curating the raw data. ~(2) We propose an autonomic approach for adapting data curation rules. ~(3) We provide a solution to augment users in formulating their preferences while curating data in large scale information spaces. ~(4) We implement a set of APIs for automating the basic curation tasks, including Named Entity extraction, POS tags, classification, and etc.
In the last decade, two paradigm shifts have reshaped the software industry - the move from boxed products to services and the widespread adoption of cloud computing. This has had a huge impact on the software development life cycle and the DevOps processes. Particularly, incident management has become critical for developing and operating large-scale services. Incidents are created to ensure timely communication of service issues and, also, their resolution. Prior work on incident management has been heavily focused on the challenges with incident triaging and de-duplication. In this work, we address the fundamental problem of structured knowledge extraction from service incidents. We have built SoftNER, a framework for unsupervised knowledge extraction from service incidents. We frame the knowledge extraction problem as a Named-entity Recognition task for extracting factual information. SoftNER leverages structural patterns like key,value pairs and tables for bootstrapping the training data. Further, we build a novel multi-task learning based BiLSTM-CRF model which leverages not just the semantic context but also the data-types for named-entity extraction. We have deployed SoftNER at Microsoft, a major cloud service provider and have evaluated it on more than 2 months of cloud incidents. We show that the unsupervised machine learning based approach has a high precision of 0.96. Our multi-task learning based deep learning model also outperforms the state of the art NER models. Lastly, using the knowledge extracted by SoftNER we are able to build significantly more accurate models for important downstream tasks like incident triaging.
We describe a named entity tagging system that requires minimal linguistic knowledge and can be applied to more target languages without substantial changes. The system is based on the ideas of the Brill's tagger which makes it really simple. Using supervised machine learning, we construct a series of automatons (or transducers) in order to tag a given text. The final model is composed entirely of automatons and it requires a lineal time for tagging. It was tested with the Spanish data set provided in the CoNLL-$2002$ attaining an overall $F_{\beta = 1}$ measure of $60\%.$ Also, we present an algorithm for the construction of the final transducer used to encode all the learned contextual rules.
The scale and scope of scholarly articles today are overwhelming human researchers who seek to timely digest and synthesize knowledge. In this paper, we seek to develop natural language processing (NLP) models to accelerate the speed of extraction of relationships from scholarly papers in social sciences, identify hypotheses from these papers, and extract the cause-and-effect entities. Specifically, we develop models to 1) classify sentences in scholarly documents in business and management as hypotheses (hypothesis classification), 2) classify these hypotheses as causal relationships or not (causality classification), and, if they are causal, 3) extract the cause and effect entities from these hypotheses (entity extraction). We have achieved high performance for all the three tasks using different modeling techniques. Our approach may be generalizable to scholarly documents in a wide range of social sciences, as well as other types of textual materials.
When comparing entities extracted by a medical entity recognition system with gold standard annotations over a test set, two types of mismatches might occur, label mismatch or span mismatch. Here we focus on span mismatch and show that its severity can vary from a serious error to a fully acceptable entity extraction due to the subjectivity of span annotations. For a domain-specific BERT-based NER system, we showed that 25% of the errors have the same labels and overlapping span with gold standard entities. We collected expert judgement which shows more than 90% of these mismatches are accepted or partially accepted by the user. Using the training set of the NER system, we built a fast and lightweight entity classifier to approximate the user experience of such mismatches through accepting or rejecting them. The decisions made by this classifier are used to calculate a learning-based F-score which is shown to be a better approximation of a forgiving user's experience than the relaxed F-score. We demonstrated the results of applying the proposed evaluation metric for a variety of deep learning medical entity recognition models trained with two datasets.
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.
Intelligent assistants like Cortana, Siri, Alexa, and Google Assistant are trained to parse information when the conversation is synchronous and short; however, for email-based conversational agents, the communication is asynchronous, and often contains information irrelevant to the assistant. This makes it harder for the system to accurately detect intents, extract entities relevant to those intents and thereby perform the desired action. We present a neural model for scoping relevant information for the agent from a large query. We show that when used as a preprocessing step, the model improves performance of both intent detection and entity extraction tasks. We demonstrate the model's impact on Scheduler (Cortana is the persona of the agent, while Scheduler is the name of the service. We use them interchangeably in the context of this paper.) - a virtual conversational meeting scheduling assistant that interacts asynchronously with users through email. The model helps the entity extraction and intent detection tasks requisite by Scheduler achieve an average gain of 35% in precision without any drop in recall. Additionally, we demonstrate that the same approach can be used for component level analysis in large documents, such as signature block identification.
When it comes to factual knowledge about a wide range of domains, Wikipedia is often the prime source of information on the web. DBpedia and YAGO, as large cross-domain knowledge graphs, encode a subset of that knowledge by creating an entity for each page in Wikipedia, and connecting them through edges. It is well known, however, that Wikipedia-based knowledge graphs are far from complete. Especially, as Wikipedia's policies permit pages about subjects only if they have a certain popularity, such graphs tend to lack information about less well-known entities. Information about these entities is oftentimes available in the encyclopedia, but not represented as an individual page. In this paper, we present a two-phased approach for the extraction of entities from Wikipedia's list pages, which have proven to serve as a valuable source of information. In the first phase, we build a large taxonomy from categories and list pages with DBpedia as a backbone. With distant supervision, we extract training data for the identification of new entities in list pages that we use in the second phase to train a classification model. With this approach we extract over 700k new entities and extend DBpedia with 7.5M new type statements and 3.8M new facts of high precision.
We introduce the STEM (Science, Technology, Engineering, and Medicine) Dataset for Scientific Entity Extraction, Classification, and Resolution, version 1.0 (STEM-ECR v1.0). The STEM-ECR v1.0 dataset has been developed to provide a benchmark for the evaluation of scientific entity extraction, classification, and resolution tasks in a domain-independent fashion. It comprises abstracts in 10 STEM disciplines that were found to be the most prolific ones on a major publishing platform. We describe the creation of such a multidisciplinary corpus and highlight the obtained findings in terms of the following features: 1) a generic conceptual formalism for scientific entities in a multidisciplinary scientific context; 2) the feasibility of the domain-independent human annotation of scientific entities under such a generic formalism; 3) a performance benchmark obtainable for automatic extraction of multidisciplinary scientific entities using BERT-based neural models; 4) a delineated 3-step entity resolution procedure for human annotation of the scientific entities via encyclopedic entity linking and lexicographic word sense disambiguation; and 5) human evaluations of Babelfy returned encyclopedic links and lexicographic senses for our entities. Our findings cumulatively indicate that human annotation and automatic learning of multidisciplinary scientific concepts as well as their semantic disambiguation in a wide-ranging setting as STEM is reasonable.
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.
Biomedical documents such as Electronic Health Records (EHRs) contain a large amount of information in an unstructured format. The data in EHRs is a hugely valuable resource documenting clinical narratives and decisions, but whilst the text can be easily understood by human doctors it is challenging to use in research and clinical applications. To uncover the potential of biomedical documents we need to extract and structure the information they contain. The task at hand is Named Entity Recognition and Linking (NER+L). The number of entities, ambiguity of words, overlapping and nesting make the biomedical area significantly more difficult than many others. To overcome these difficulties, we have developed the Medical Concept Annotation Tool (MedCAT), an open-source unsupervised approach to NER+L. MedCAT uses unsupervised machine learning to disambiguate entities. It was validated on MIMIC-III (a freely accessible critical care database) and MedMentions (Biomedical papers annotated with mentions from the Unified Medical Language System). In case of NER+L, the comparison with existing tools shows that MedCAT improves the previous best with only unsupervised learning (F1=0.848 vs 0.691 for disease detection; F1=0.710 vs. 0.222 for general concept detection). A qualitative analysis of the vector embeddings learnt by MedCAT shows that it captures latent medical knowledge available in EHRs (MIMIC-III). Unsupervised learning can improve the performance of large scale entity extraction, but it has some limitations when working with only a couple of entities and a small dataset. In that case options are supervised learning or active learning, both of which are supported in MedCAT via the MedCATtrainer extension. Our approach can detect and link millions of different biomedical concepts with state-of-the-art performance, whilst being lightweight, fast and easy to use.
This paper describes a machine learning and data science pipeline for structured information extraction from documents, implemented as a suite of open-source tools and extensions to existing tools. It centers around a methodology for extracting procedural information in the form of recipes, stepwise procedures for creating an artifact (in this case synthesizing a nanomaterial), from published scientific literature. From our overall goal of producing recipes from free text, we derive the technical objectives of a system consisting of pipeline stages: document acquisition and filtering, payload extraction, recipe step extraction as a relationship extraction task, recipe assembly, and presentation through an information retrieval interface with question answering (QA) functionality. This system meets computational information and knowledge management (CIKM) requirements of metadata-driven payload extraction, named entity extraction, and relationship extraction from text. Functional contributions described in this paper include semi-supervised machine learning methods for PDF filtering and payload extraction tasks, followed by structured extraction and data transformation tasks beginning with section extraction, recipe steps as information tuples, and finally assembled recipes. Measurable objective criteria for extraction quality include precision and recall of recipe steps, ordering constraints, and QA accuracy, precision, and recall. Results, key novel contributions, and significant open problems derived from this work center around the attribution of these holistic quality measures to specific machine learning and inference stages of the pipeline, each with their performance measures. The desired recipes contain identified preconditions, material inputs, and operations, and constitute the overall output generated by our computational information and knowledge management (CIKM) system.
The motivation, concept, design and implementation of latent semantic search for search engines have limited semantic search, entity extraction and property attribution features, have insufficient accuracy and response time of latent search, may impose privacy concerns and the search results are unavailable in offline mode for robotic search operations. The alternative suggestion involves autonomous search engine with adaptive storage consumption, configurable search scope and latent search response time with built-in options for entity extraction and property attribution available as open source platform for mobile, desktop and server solutions. The suggested architecture attempts to implement artificial general intelligence (AGI) principles as long as autonomous behaviour constrained by limited resources is concerned, and it is applied for specific task of enabling Web search for artificial agents implementing the AGI.
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
Entity extraction is an important task in text mining and natural language processing. A popular method for entity extraction is by comparing substrings from free text against a dictionary of entities. In this paper, we present several techniques as a post-processing step for improving the effectiveness of the existing entity extraction technique. These techniques utilise models trained with the web-scale corpora which makes our techniques robust and versatile. Experiments show that our techniques bring a notable improvement on efficiency and effectiveness.
More than 200 generic drugs approved by the U.S. Food and Drug Administration for non-cancer indications have shown promise for treating cancer. Due to their long history of safe patient use, low cost, and widespread availability, repurposing of generic drugs represents a major opportunity to rapidly improve outcomes for cancer patients and reduce healthcare costs worldwide. Evidence on the efficacy of non-cancer generic drugs being tested for cancer exists in scientific publications, but trying to manually identify and extract such evidence is intractable. In this paper, we introduce a system to automate this evidence extraction from PubMed abstracts. Our primary contribution is to define the natural language processing pipeline required to obtain such evidence, comprising the following modules: querying, filtering, cancer type entity extraction, therapeutic association classification, and study type classification. Using the subject matter expertise on our team, we create our own datasets for these specialized domain-specific tasks. We obtain promising performance in each of the modules by utilizing modern language modeling techniques and plan to treat them as baseline approaches for future improvement of individual components.
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.
Monitoring the administration of drugs and adverse drug reactions are key parts of pharmacovigilance. In this paper, we explore the extraction of drug mentions and drug-related information (reason for taking a drug, route, frequency, dosage, strength, form, duration, and adverse events) from hospital discharge summaries through deep learning that relies on various representations for clinical named entity recognition. This work was officially part of the 2018 n2c2 shared task, and we use the data supplied as part of the task. We developed two deep learning architecture based on recurrent neural networks and pre-trained language models. We also explore the effect of augmenting word representations with semantic features for clinical named entity recognition. Our feature-augmented BiLSTM-CRF model performed with F1-score of 92.67% and ranked 4th for entity extraction sub-task among submitted systems to n2c2 challenge. The recurrent neural networks that use the pre-trained domain-specific word embeddings and a CRF layer for label optimization perform drug, adverse event and related entities extraction with micro-averaged F1-score of over 91%. The augmentation of word vectors with semantic features extracted using available clinical NLP toolkits can further improve the performance. Word embeddings that are pre-trained on a large unannotated corpus of relevant documents and further fine-tuned to the task perform rather well. However, the augmentation of word embeddings with semantic features can help improve the performance (primarily by boosting precision) of drug-related named entity recognition from electronic health records.