A Survey of Embeddings in Clinical Natural Language Processing Kalyan KS, S
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Information Retrieval Application of Text Mining Also on Bio-Medical Fields
JOURNAL OF CRITICAL REVIEWS ISSN- 2394-5125 VOL 7, ISSUE 8, 2020 INFORMATION RETRIEVAL APPLICATION OF TEXT MINING ALSO ON BIO-MEDICAL FIELDS Charan Singh Tejavath1, Dr. Tryambak Hirwarkar2 1Research Scholar, Dept. of Computer Science & Engineering, Sri Satya Sai University of Technology & Medical Sciences, Sehore, Bhopal-Indore Road, Madhya Pradesh, India. 2Research Guide, Dept. of Computer Science & Engineering, Sri Satya Sai University of Technology & Medical Sciences, Sehore, Bhopal Indore Road, Madhya Pradesh, India. Received: 11.03.2020 Revised: 21.04.2020 Accepted: 27.05.2020 ABTRACT: Electronic clinical records contain data on all parts of health care. Healthcare data frameworks that gather a lot of textual and numeric data about patients, visits, medicines, doctor notes, and so forth. The electronic archives encapsulate data that could prompt an improvement in health care quality, advancement of clinical and exploration activities, decrease in clinical mistakes, and decrease in healthcare costs. In any case, the reports that contain the health record are wide-going in multifaceted nature, length, and utilization of specialized jargon, making information revelation complex. The ongoing accessibility of business text mining devices gives a one of a kind chance to remove basic data from textual information files. This paper portrays the biomedical text-mining technology. KEYWORDS: Text-mining technology, Bio-medical fields, Textual information files. © 2020 by Advance Scientific Research. This is an open-access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) DOI: http://dx.doi.org/10.31838/jcr.07.08.357 I. INTRODUCTION The corpus of biomedical data is becoming quickly. New and helpful outcomes show up each day in research distributions, from diary articles to book parts to workshop and gathering procedures. -
Barriers to Retrieving Patient Information from Electronic Health Record Data: Failure Analysis from the TREC Medical Records Track
Barriers to Retrieving Patient Information from Electronic Health Record Data: Failure Analysis from the TREC Medical Records Track Tracy Edinger, ND, Aaron M. Cohen, MD, MS, Steven Bedrick, PhD, Kyle Ambert, BA, William Hersh, MD Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA Abstract Objective: Secondary use of electronic health record (EHR) data relies on the ability to retrieve accurate and complete information about desired patient populations. The Text Retrieval Conference (TREC) 2011 Medical Records Track was a challenge evaluation allowing comparison of systems and algorithms to retrieve patients eligible for clinical studies from a corpus of de-identified medical records, grouped by patient visit. Participants retrieved cohorts of patients relevant to 35 different clinical topics, and visits were judged for relevance to each topic. This study identified the most common barriers to identifying specific clinic populations in the test collection. Methods: Using the runs from track participants and judged visits, we analyzed the five non-relevant visits most often retrieved and the five relevant visits most often overlooked. Categories were developed iteratively to group the reasons for incorrect retrieval for each of the 35 topics. Results: Reasons fell into nine categories for non-relevant visits and five categories for relevant visits. Non-relevant visits were most often retrieved because they contained a non-relevant reference to the topic terms. Relevant visits were most often infrequently retrieved because they used a synonym for a topic term. Conclusions : This failure analysis provides insight into areas for future improvement in EHR-based retrieval with techniques such as more widespread and complete use of standardized terminology in retrieval and data entry systems. -
Arxiv:2002.06235V1
Semantic Relatedness and Taxonomic Word Embeddings Magdalena Kacmajor John D. Kelleher Innovation Exchange ADAPT Research Centre IBM Ireland Technological University Dublin [email protected] [email protected] Filip Klubickaˇ Alfredo Maldonado ADAPT Research Centre Underwriters Laboratories Technological University Dublin [email protected] [email protected] Abstract This paper1 connects a series of papers dealing with taxonomic word embeddings. It begins by noting that there are different types of semantic relatedness and that different lexical representa- tions encode different forms of relatedness. A particularly important distinction within semantic relatedness is that of thematic versus taxonomic relatedness. Next, we present a number of ex- periments that analyse taxonomic embeddings that have been trained on a synthetic corpus that has been generated via a random walk over a taxonomy. These experiments demonstrate how the properties of the synthetic corpus, such as the percentage of rare words, are affected by the shape of the knowledge graph the corpus is generated from. Finally, we explore the interactions between the relative sizes of natural and synthetic corpora on the performance of embeddings when taxonomic and thematic embeddings are combined. 1 Introduction Deep learning has revolutionised natural language processing over the last decade. A key enabler of deep learning for natural language processing has been the development of word embeddings. One reason for this is that deep learning intrinsically involves the use of neural network models and these models only work with numeric inputs. Consequently, applying deep learning to natural language processing first requires developing a numeric representation for words. Word embeddings provide a way of creating numeric representations that have proven to have a number of advantages over traditional numeric rep- resentations of language. -
Biomedical Text Mining: a Survey of Recent Progress
Chapter 14 BIOMEDICAL TEXT MINING: A SURVEY OF RECENT PROGRESS Matthew S. Simpson Lister Hill National Center for Biomedical Communications United States National Library of Medicine, National Institutes of Health [email protected] Dina Demner-Fushman Lister Hill National Center for Biomedical Communications United States National Library of Medicine, National Institutes of Health [email protected] Abstract The biomedical community makes extensive use of text mining tech- nology. In the past several years, enormous progress has been made in developing tools and methods, and the community has been witness to some exciting developments. Although the state of the community is regularly reviewed, the sheer volume of work related to biomedical text mining and the rapid pace in which progress continues to be made make this a worthwhile, if not necessary, endeavor. This chapter pro- vides a brief overview of the current state of text mining in the biomed- ical domain. Emphasis is placed on the resources and tools available to biomedical researchers and practitioners, as well as the major text mining tasks of interest to the community. These tasks include the recognition of explicit facts from biomedical literature, the discovery of previously unknown or implicit facts, document summarization, and question answering. For each topic, its basic challenges and methods are outlined and recent and influential work is reviewed. Keywords: Biomedical information extraction, named entity recognition, relations, events, summarization, question answering, literature-based discovery C.C. Aggarwal and C.X. Zhai (eds.), Mining Text Data, DOI 10.1007/978-1-4614-3223-4_14, 465 © Springer Science+Business Media, LLC 2012 466 MINING TEXT DATA 1. -
Automatic Correction of Real-Word Errors in Spanish Clinical Texts
sensors Article Automatic Correction of Real-Word Errors in Spanish Clinical Texts Daniel Bravo-Candel 1,Jésica López-Hernández 1, José Antonio García-Díaz 1 , Fernando Molina-Molina 2 and Francisco García-Sánchez 1,* 1 Department of Informatics and Systems, Faculty of Computer Science, Campus de Espinardo, University of Murcia, 30100 Murcia, Spain; [email protected] (D.B.-C.); [email protected] (J.L.-H.); [email protected] (J.A.G.-D.) 2 VÓCALI Sistemas Inteligentes S.L., 30100 Murcia, Spain; [email protected] * Correspondence: [email protected]; Tel.: +34-86888-8107 Abstract: Real-word errors are characterized by being actual terms in the dictionary. By providing context, real-word errors are detected. Traditional methods to detect and correct such errors are mostly based on counting the frequency of short word sequences in a corpus. Then, the probability of a word being a real-word error is computed. On the other hand, state-of-the-art approaches make use of deep learning models to learn context by extracting semantic features from text. In this work, a deep learning model were implemented for correcting real-word errors in clinical text. Specifically, a Seq2seq Neural Machine Translation Model mapped erroneous sentences to correct them. For that, different types of error were generated in correct sentences by using rules. Different Seq2seq models were trained and evaluated on two corpora: the Wikicorpus and a collection of three clinical datasets. The medicine corpus was much smaller than the Wikicorpus due to privacy issues when dealing Citation: Bravo-Candel, D.; López-Hernández, J.; García-Díaz, with patient information. -
Combining Word Embeddings with Semantic Resources
AutoExtend: Combining Word Embeddings with Semantic Resources Sascha Rothe∗ LMU Munich Hinrich Schutze¨ ∗ LMU Munich We present AutoExtend, a system that combines word embeddings with semantic resources by learning embeddings for non-word objects like synsets and entities and learning word embeddings that incorporate the semantic information from the resource. The method is based on encoding and decoding the word embeddings and is flexible in that it can take any word embeddings as input and does not need an additional training corpus. The obtained embeddings live in the same vector space as the input word embeddings. A sparse tensor formalization guar- antees efficiency and parallelizability. We use WordNet, GermaNet, and Freebase as semantic resources. AutoExtend achieves state-of-the-art performance on Word-in-Context Similarity and Word Sense Disambiguation tasks. 1. Introduction Unsupervised methods for learning word embeddings are widely used in natural lan- guage processing (NLP). The only data these methods need as input are very large corpora. However, in addition to corpora, there are many other resources that are undoubtedly useful in NLP, including lexical resources like WordNet and Wiktionary and knowledge bases like Wikipedia and Freebase. We will simply refer to these as resources. In this article, we present AutoExtend, a method for enriching these valuable resources with embeddings for non-word objects they describe; for example, Auto- Extend enriches WordNet with embeddings for synsets. The word embeddings and the new non-word embeddings live in the same vector space. Many NLP applications benefit if non-word objects described by resources—such as synsets in WordNet—are also available as embeddings. -
Word-Like Character N-Gram Embedding
Word-like character n-gram embedding Geewook Kim and Kazuki Fukui and Hidetoshi Shimodaira Department of Systems Science, Graduate School of Informatics, Kyoto University Mathematical Statistics Team, RIKEN Center for Advanced Intelligence Project fgeewook, [email protected], [email protected] Abstract Table 1: Top-10 2-grams in Sina Weibo and 4-grams in We propose a new word embedding method Japanese Twitter (Experiment 1). Words are indicated called word-like character n-gram embed- by boldface and space characters are marked by . ding, which learns distributed representations FNE WNE (Proposed) Chinese Japanese Chinese Japanese of words by embedding word-like character n- 1 ][ wwww 自己 フォロー grams. Our method is an extension of recently 2 。␣ !!!! 。␣ ありがと proposed segmentation-free word embedding, 3 !␣ ありがと ][ wwww 4 .. りがとう 一个 !!!! which directly embeds frequent character n- 5 ]␣ ございま 微博 めっちゃ grams from a raw corpus. However, its n-gram 6 。。 うござい 什么 んだけど vocabulary tends to contain too many non- 7 ,我 とうござ 可以 うござい 8 !! ざいます 没有 line word n-grams. We solved this problem by in- 9 ␣我 がとうご 吗? 2018 troducing an idea of expected word frequency. 10 了, ください 哈哈 じゃない Compared to the previously proposed meth- ods, our method can embed more words, along tion tools are used to determine word boundaries with the words that are not included in a given in the raw corpus. However, these segmenters re- basic word dictionary. Since our method does quire rich dictionaries for accurate segmentation, not rely on word segmentation with rich word which are expensive to prepare and not always dictionaries, it is especially effective when the available. -
ACL 2019 Social Media Mining for Health Applications (#SMM4H)
ACL 2019 Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task Proceedings of the Fourth Workshop August 2, 2019 Florence, Italy c 2019 The Association for Computational Linguistics Order copies of this and other ACL proceedings from: Association for Computational Linguistics (ACL) 209 N. Eighth Street Stroudsburg, PA 18360 USA Tel: +1-570-476-8006 Fax: +1-570-476-0860 [email protected] ISBN 978-1-950737-46-8 ii Preface Welcome to the 4th Social Media Mining for Health Applications Workshop and Shared Task - #SMM4H 2019. The total number of users of social media continues to grow worldwide, resulting in the generation of vast amounts of data. Popular social networking sites such as Facebook, Twitter and Instagram dominate this sphere. According to estimates, 500 million tweets and 4.3 billion Facebook messages are posted every day 1. The latest Pew Research Report 2, nearly half of adults worldwide and two- thirds of all American adults (65%) use social networking. The report states that of the total users, 26% have discussed health information, and, of those, 30% changed behavior based on this information and 42% discussed current medical conditions. Advances in automated data processing, machine learning and NLP present the possibility of utilizing this massive data source for biomedical and public health applications, if researchers address the methodological challenges unique to this media. In its fourth iteration, the #SMM4H workshop takes place in Florence, Italy, on August 2, 2019, and is co-located with the -
Mapping the Hyponymy Relation of Wordnet Onto
Under review as a conference paper at ICLR 2019 MAPPING THE HYPONYMY RELATION OF WORDNET ONTO VECTOR SPACES Anonymous authors Paper under double-blind review ABSTRACT In this paper, we investigate mapping the hyponymy relation of WORDNET to feature vectors. We aim to model lexical knowledge in such a way that it can be used as input in generic machine-learning models, such as phrase entailment predictors. We propose two models. The first one leverages an existing mapping of words to feature vectors (fastText), and attempts to classify such vectors as within or outside of each class. The second model is fully supervised, using solely WORDNET as a ground truth. It maps each concept to an interval or a disjunction thereof. On the first model, we approach, but not quite attain state of the art performance. The second model can achieve near-perfect accuracy. 1 INTRODUCTION Distributional encoding of word meanings from the large corpora (Mikolov et al., 2013; 2018; Pen- nington et al., 2014) have been found to be useful for a number of NLP tasks. These approaches are based on a probabilistic language model by Bengio et al. (2003) of word sequences, where each word w is represented as a feature vector f(w) (a compact representation of a word, as a vector of floating point values). This means that one learns word representations (vectors) and probabilities of word sequences at the same time. While the major goal of distributional approaches is to identify distributional patterns of words and word sequences, they have even found use in tasks that require modeling more fine-grained relations between words than co-occurrence in word sequences. -
Pairwise Fasttext Classifier for Entity Disambiguation
Pairwise FastText Classifier for Entity Disambiguation a,b b b Cheng Yu , Bing Chu , Rohit Ram , James Aichingerb, Lizhen Qub,c, Hanna Suominenb,c a Project Cleopatra, Canberra, Australia b The Australian National University c DATA 61, Australia [email protected] {u5470909,u5568718,u5016706, Hanna.Suominen}@anu.edu.au [email protected] deterministically. Then we will evaluate PFC’s Abstract performance against a few baseline methods, in- cluding SVC3 with hand-crafted text features. Fi- For the Australasian Language Technology nally, we will discuss ways to improve disambig- Association (ALTA) 2016 Shared Task, we uation performance using PFC. devised Pairwise FastText Classifier (PFC), an efficient embedding-based text classifier, 2 Pairwise Fast-Text Classifier (PFC) and used it for entity disambiguation. Com- pared with a few baseline algorithms, PFC Our Pairwise FastText Classifier is inspired by achieved a higher F1 score at 0.72 (under the the FastText. Thus this section starts with a brief team name BCJR). To generalise the model, description of FastText, and proceeds to demon- we also created a method to bootstrap the strate PFC. training set deterministically without human labelling and at no financial cost. By releasing 2.1 FastText PFC and the dataset augmentation software to the public1, we hope to invite more collabora- FastText maps each vocabulary to a real-valued tion. vector, with unknown words having a special vo- cabulary ID. A document can be represented as 1 Introduction the average of all these vectors. Then FastText will train a maximum entropy multi-class classi- The goal of the ALTA 2016 Shared Task was to fier on the vectors and the output labels. -
Learned in Speech Recognition: Contextual Acoustic Word Embeddings
LEARNED IN SPEECH RECOGNITION: CONTEXTUAL ACOUSTIC WORD EMBEDDINGS Shruti Palaskar∗, Vikas Raunak∗ and Florian Metze Carnegie Mellon University, Pittsburgh, PA, U.S.A. fspalaska j vraunak j fmetze [email protected] ABSTRACT model [10, 11, 12] trained for direct Acoustic-to-Word (A2W) speech recognition [13]. Using this model, we jointly learn to End-to-end acoustic-to-word speech recognition models have re- automatically segment and classify input speech into individual cently gained popularity because they are easy to train, scale well to words, hence getting rid of the problem of chunking or requiring large amounts of training data, and do not require a lexicon. In addi- pre-defined word boundaries. As our A2W model is trained at the tion, word models may also be easier to integrate with downstream utterance level, we show that we can not only learn acoustic word tasks such as spoken language understanding, because inference embeddings, but also learn them in the proper context of their con- (search) is much simplified compared to phoneme, character or any taining sentence. We also evaluate our contextual acoustic word other sort of sub-word units. In this paper, we describe methods embeddings on a spoken language understanding task, demonstrat- to construct contextual acoustic word embeddings directly from a ing that they can be useful in non-transcription downstream tasks. supervised sequence-to-sequence acoustic-to-word speech recog- Our main contributions in this paper are the following: nition model using the learned attention distribution. On a suite 1. We demonstrate the usability of attention not only for aligning of 16 standard sentence evaluation tasks, our embeddings show words to acoustic frames without any forced alignment but also for competitive performance against a word2vec model trained on the constructing Contextual Acoustic Word Embeddings (CAWE). -
Fasttext.Zip: Compressing Text Classification Models
Under review as a conference paper at ICLR 2017 FASTTEXT.ZIP: COMPRESSING TEXT CLASSIFICATION MODELS Armand Joulin, Edouard Grave, Piotr Bojanowski, Matthijs Douze, Herve´ Jegou´ & Tomas Mikolov Facebook AI Research fajoulin,egrave,bojanowski,matthijs,rvj,[email protected] ABSTRACT We consider the problem of producing compact architectures for text classifica- tion, such that the full model fits in a limited amount of memory. After consid- ering different solutions inspired by the hashing literature, we propose a method built upon product quantization to store word embeddings. While the original technique leads to a loss in accuracy, we adapt this method to circumvent quan- tization artefacts. Combined with simple approaches specifically adapted to text classification, our approach derived from fastText requires, at test time, only a fraction of the memory compared to the original FastText, without noticeably sacrificing quality in terms of classification accuracy. Our experiments carried out on several benchmarks show that our approach typically requires two orders of magnitude less memory than fastText while being only slightly inferior with respect to accuracy. As a result, it outperforms the state of the art by a good margin in terms of the compromise between memory usage and accuracy. 1 INTRODUCTION Text classification is an important problem in Natural Language Processing (NLP). Real world use- cases include spam filtering or e-mail categorization. It is a core component in more complex sys- tems such as search and ranking. Recently, deep learning techniques based on neural networks have achieved state of the art results in various NLP applications. One of the main successes of deep learning is due to the effectiveness of recurrent networks for language modeling and their application to speech recognition and machine translation (Mikolov, 2012).