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Information Extraction from Electronic Medical Records Using Multitask Recurrent Neural Network with Contextual Word Embedding
applied sciences Article Information Extraction from Electronic Medical Records Using Multitask Recurrent Neural Network with Contextual Word Embedding Jianliang Yang 1 , Yuenan Liu 1, Minghui Qian 1,*, Chenghua Guan 2 and Xiangfei Yuan 2 1 School of Information Resource Management, Renmin University of China, 59 Zhongguancun Avenue, Beijing 100872, China 2 School of Economics and Resource Management, Beijing Normal University, 19 Xinjiekou Outer Street, Beijing 100875, China * Correspondence: [email protected]; Tel.: +86-139-1031-3638 Received: 13 August 2019; Accepted: 26 August 2019; Published: 4 September 2019 Abstract: Clinical named entity recognition is an essential task for humans to analyze large-scale electronic medical records efficiently. Traditional rule-based solutions need considerable human effort to build rules and dictionaries; machine learning-based solutions need laborious feature engineering. For the moment, deep learning solutions like Long Short-term Memory with Conditional Random Field (LSTM–CRF) achieved considerable performance in many datasets. In this paper, we developed a multitask attention-based bidirectional LSTM–CRF (Att-biLSTM–CRF) model with pretrained Embeddings from Language Models (ELMo) in order to achieve better performance. In the multitask system, an additional task named entity discovery was designed to enhance the model’s perception of unknown entities. Experiments were conducted on the 2010 Informatics for Integrating Biology & the Bedside/Veterans Affairs (I2B2/VA) dataset. Experimental results show that our model outperforms the state-of-the-art solution both on the single model and ensemble model. Our work proposes an approach to improve the recall in the clinical named entity recognition task based on the multitask mechanism. -
Mlpack: Or, How I Learned to Stop Worrying and Love C++ Ryan R
mlpack: or, How I Learned To Stop Worrying and Love C++ Ryan R. Curtin March 21, 2018 speed programming languages machine learning C++ mlpack fast Introduction Why are we here? programming languages machine learning C++ mlpack fast Introduction Why are we here? speed machine learning C++ mlpack fast Introduction Why are we here? speed programming languages C++ mlpack fast Introduction Why are we here? speed programming languages machine learning mlpack fast Introduction Why are we here? speed programming languages machine learning C++ fast Introduction Why are we here? speed programming languages machine learning C++ mlpack Introduction Why are we here? speed programming languages machine learning C++ mlpack fast Java JS INTERCAL Scala Python C++ C Go Ruby C# Tcl ASM PHP Lua VB low-level high-level fast easy specific portable Note: this is not a scientific or particularly accurate representation. Graph #1 Java JS INTERCAL Scala Python C++ C Go Ruby C# Tcl ASM PHP Lua VB fast easy specific portable Note: this is not a scientific or particularly accurate representation. Graph #1 low-level high-level Java JS INTERCAL Scala Python C++ C Go Ruby C# Tcl PHP Lua VB fast easy specific portable Note: this is not a scientific or particularly accurate representation. Graph #1 ASM low-level high-level Java JS INTERCAL Scala Python C++ C Go Ruby C# Tcl PHP Lua VB fast easy specific portable Note: this is not a scientific or particularly accurate representation. Graph #1 ASM low-level high-level Java JS INTERCAL Scala Python C++ C Go Ruby C# Tcl PHP Lua fast easy specific portable Note: this is not a scientific or particularly accurate representation. -
Data Mining – Intro
Data warehouse& Data Mining UNIT-3 Syllabus • UNIT 3 • Classification: Introduction, decision tree, tree induction algorithm – split algorithm based on information theory, split algorithm based on Gini index; naïve Bayes method; estimating predictive accuracy of classification method; classification software, software for association rule mining; case study; KDD Insurance Risk Assessment What is Data Mining? • Data Mining is: (1) The efficient discovery of previously unknown, valid, potentially useful, understandable patterns in large datasets (2) Data mining is the analysis step of the "knowledge discovery in databases" process, or KDD (2) The analysis of (often large) observational data sets to find unsuspected relationships and to summarize the data in novel ways that are both understandable and useful to the data owner Knowledge Discovery Examples of Large Datasets • Government: IRS, NGA, … • Large corporations • WALMART: 20M transactions per day • MOBIL: 100 TB geological databases • AT&T 300 M calls per day • Credit card companies • Scientific • NASA, EOS project: 50 GB per hour • Environmental datasets KDD The Knowledge Discovery in Databases (KDD) process is commonly defined with the stages: (1) Selection (2) Pre-processing (3) Transformation (4) Data Mining (5) Interpretation/Evaluation Data Mining Methods 1. Decision Tree Classifiers: Used for modeling, classification 2. Association Rules: Used to find associations between sets of attributes 3. Sequential patterns: Used to find temporal associations in time series 4. Hierarchical -
Text Mining Course for KNIME Analytics Platform
Text Mining Course for KNIME Analytics Platform KNIME AG Copyright © 2018 KNIME AG Table of Contents 1. The Open Analytics Platform 2. The Text Processing Extension 3. Importing Text 4. Enrichment 5. Preprocessing 6. Transformation 7. Classification 8. Visualization 9. Clustering 10. Supplementary Workflows Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 2 Noncommercial-Share Alike license 1 https://creativecommons.org/licenses/by-nc-sa/4.0/ Overview KNIME Analytics Platform Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 3 Noncommercial-Share Alike license 1 https://creativecommons.org/licenses/by-nc-sa/4.0/ What is KNIME Analytics Platform? • A tool for data analysis, manipulation, visualization, and reporting • Based on the graphical programming paradigm • Provides a diverse array of extensions: • Text Mining • Network Mining • Cheminformatics • Many integrations, such as Java, R, Python, Weka, H2O, etc. Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 4 Noncommercial-Share Alike license 2 https://creativecommons.org/licenses/by-nc-sa/4.0/ Visual KNIME Workflows NODES perform tasks on data Not Configured Configured Outputs Inputs Executed Status Error Nodes are combined to create WORKFLOWS Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 5 Noncommercial-Share Alike license 3 https://creativecommons.org/licenses/by-nc-sa/4.0/ Data Access • Databases • MySQL, MS SQL Server, PostgreSQL • any JDBC (Oracle, DB2, …) • Files • CSV, txt -
The Shogun Machine Learning Toolbox
The Shogun Machine Learning Toolbox Heiko Strathmann, Gatsby Unit, UCL London Open Machine Learning Workshop, MSR, NY August 22, 2014 A bit about Shogun I Open-Source tools for ML problems I Started 1999 by SÖren Sonnenburg & GUNnar Rätsch, made public in 2004 I Currently 8 core-developers + 20 regular contributors I Purely open-source community driven I In Google Summer of Code since 2010 (29 projects!) Ohloh - Summary Ohloh - Code Supervised Learning Given: x y n , want: y ∗ x ∗ I f( i ; i )gi=1 j I Classication: y discrete I Support Vector Machine I Gaussian Processes I Logistic Regression I Decision Trees I Nearest Neighbours I Naive Bayes I Regression: y continuous I Gaussian Processes I Support Vector Regression I (Kernel) Ridge Regression I (Group) LASSO Unsupervised Learning Given: x n , want notion of p x I f i gi=1 ( ) I Clustering: I K-Means I (Gaussian) Mixture Models I Hierarchical clustering I Latent Models I (K) PCA I Latent Discriminant Analysis I Independent Component Analysis I Dimension reduction I (K) Locally Linear Embeddings I Many more... And many more I Multiple Kernel Learning I Structured Output I Metric Learning I Variational Inference I Kernel hypothesis testing I Deep Learning (whooo!) I ... I Bindings to: LibLinear, VowpalWabbit, etc.. http://www.shogun-toolbox.org/page/documentation/ notebook Some Large-Scale Applications I Splice Site prediction: 50m examples of 200m dimensions I Face recognition: 20k examples of 750k dimensions ML in Practice I Modular data represetation I Dense, Sparse, Strings, Streams, ... I Multiple types: 8-128 bit word size I Preprocessing tools I Evaluation I Cross-Validation I Accuracy, ROC, MSE, .. -
A Survey of Clustering with Deep Learning: from the Perspective of Network Architecture
Received May 12, 2018, accepted July 2, 2018, date of publication July 17, 2018, date of current version August 7, 2018. Digital Object Identifier 10.1109/ACCESS.2018.2855437 A Survey of Clustering With Deep Learning: From the Perspective of Network Architecture ERXUE MIN , XIFENG GUO, QIANG LIU , (Member, IEEE), GEN ZHANG , JIANJING CUI, AND JUN LONG College of Computer, National University of Defense Technology, Changsha 410073, China Corresponding authors: Erxue Min ([email protected]) and Qiang Liu ([email protected]) This work was supported by the National Natural Science Foundation of China under Grant 60970034, Grant 61105050, Grant 61702539, and Grant 6097003. ABSTRACT Clustering is a fundamental problem in many data-driven application domains, and clustering performance highly depends on the quality of data representation. Hence, linear or non-linear feature transformations have been extensively used to learn a better data representation for clustering. In recent years, a lot of works focused on using deep neural networks to learn a clustering-friendly representation, resulting in a significant increase of clustering performance. In this paper, we give a systematic survey of clustering with deep learning in views of architecture. Specifically, we first introduce the preliminary knowledge for better understanding of this field. Then, a taxonomy of clustering with deep learning is proposed and some representative methods are introduced. Finally, we propose some interesting future opportunities of clustering with deep learning and give some conclusion remarks. INDEX TERMS Clustering, deep learning, data representation, network architecture. I. INTRODUCTION property of highly non-linear transformation. For the sim- Data clustering is a basic problem in many areas, such as plicity of description, we call clustering methods with deep machine learning, pattern recognition, computer vision, data learning as deep clustering1 in this paper. -
A Tree-Based Dictionary Learning Framework
A Tree-based Dictionary Learning Framework Renato Budinich∗ & Gerlind Plonka† June 11, 2020 We propose a new outline for adaptive dictionary learning methods for sparse encoding based on a hierarchical clustering of the training data. Through recursive application of a clustering method the data is organized into a binary partition tree representing a multiscale structure. The dictionary atoms are defined adaptively based on the data clusters in the partition tree. This approach can be interpreted as a generalization of a discrete Haar wavelet transform. Furthermore, any prior knowledge on the wanted structure of the dictionary elements can be simply incorporated. The computational complex- ity of our proposed algorithm depends on the employed clustering method and on the chosen similarity measure between data points. Thanks to the multi- scale properties of the partition tree, our dictionary is structured: when using Orthogonal Matching Pursuit to reconstruct patches from a natural image, dic- tionary atoms corresponding to nodes being closer to the root node in the tree have a tendency to be used with greater coefficients. Keywords. Multiscale dictionary learning, hierarchical clustering, binary partition tree, gen- eralized adaptive Haar wavelet transform, K-means, orthogonal matching pursuit 1 Introduction arXiv:1909.03267v2 [cs.LG] 9 Jun 2020 In many applications one is interested in sparsely approximating a set of N n-dimensional data points Y , columns of an n N real matrix Y = (Y1;:::;Y ). Assuming that the data j × N ∗R. Budinich is with the Fraunhofer SCS, Nordostpark 93, 90411 Nürnberg, Germany, e-mail: re- [email protected] †G. Plonka is with the Institute for Numerical and Applied Mathematics, University of Göttingen, Lotzestr. -
Getting Started with Machine Learning
Getting Started with Machine Learning CSC131 The Beauty & Joy of Computing Cornell College 600 First Street SW Mount Vernon, Iowa 52314 September 2018 ii Contents 1 Applications: where machine learning is helping1 1.1 Sheldon Branch............................1 1.2 Bram Dedrick.............................4 1.3 Tony Ferenzi.............................5 1.3.1 Benefits of Machine Learning................5 1.4 William Golden............................7 1.4.1 Humans: The Teachers of Technology...........7 1.5 Yuan Hong..............................9 1.6 Easton Jensen............................. 11 1.7 Rodrigo Martinez........................... 13 1.7.1 Machine Learning in Medicine............... 13 1.8 Matt Morrical............................. 15 1.9 Ella Nelson.............................. 16 1.10 Koichi Okazaki............................ 17 1.11 Jakob Orel.............................. 19 1.12 Marcellus Parks............................ 20 1.13 Lydia Sanchez............................. 22 1.14 Tiff Serra-Pichardo.......................... 24 1.15 Austin Stala.............................. 25 1.16 Nicole Trenholm........................... 26 1.17 Maddy Weaver............................ 28 1.18 Peter Weber.............................. 29 iii iv CONTENTS 2 Recommendations: How to learn more about machine learning 31 2.1 Sheldon Branch............................ 31 2.1.1 Course 1: Machine Learning................. 31 2.1.2 Course 2: Robotics: Vision Intelligence and Machine Learn- ing............................... 33 2.1.3 Course -
Python Libraries, Development Frameworks and Algorithms for Machine Learning Applications
Published by : International Journal of Engineering Research & Technology (IJERT) http://www.ijert.org ISSN: 2278-0181 Vol. 7 Issue 04, April-2018 Python Libraries, Development Frameworks and Algorithms for Machine Learning Applications Dr. V. Hanuman Kumar, Sr. Assoc. Prof., NHCE, Bangalore-560 103 Abstract- Nowadays Machine Learning (ML) used in all sorts numerical values and is of the form y=A0+A1*x, for input of fields like Healthcare, Retail, Travel, Finance, Social Media, value x and A0, A1 are the coefficients used in the etc., ML system is used to learn from input data to construct a representation with the data that we have. The classification suitable model by continuously estimating, optimizing and model helps to identify the sentiment of a particular post. tuning parameters of the model. To attain the stated, For instance a user review can be classified as positive or python programming language is one of the most flexible languages and it does contain special libraries for negative based on the words used in the comments. Emails ML applications namely SciPy, NumPy, etc., which great for can be classified as spam or not, based on these models. The linear algebra and getting to know kernel methods of machine clustering model helps when we are trying to find similar learning. The python programming language is great to use objects. For instance If you are interested in read articles when working with ML algorithms and has easy syntax about chess or basketball, etc.., this model will search for the relatively. When taking the deep-dive into ML, choosing a document with certain high priority words and suggest framework can be daunting. -
Rcppmlpack: R Integration with MLPACK Using Rcpp
RcppMLPACK: R integration with MLPACK using Rcpp Qiang Kou [email protected] April 20, 2020 1 MLPACK MLPACK[1] is a C++ machine learning library with emphasis on scalability, speed, and ease-of-use. It outperforms competing machine learning libraries by large margins, for detailed results of benchmarking, please refer to Ref[1]. 1.1 Input/Output using Armadillo MLPACK uses Armadillo as input and output, which provides vector, matrix and cube types (integer, floating point and complex numbers are supported)[2]. By providing Matlab-like syntax and various matrix decompositions through integration with LAPACK or other high performance libraries (such as Intel MKL, AMD ACML, or OpenBLAS), Armadillo keeps a good balance between speed and ease of use. Armadillo is widely used in C++ libraries like MLPACK. However, there is one point we need to pay attention to: Armadillo matrices in MLPACK are stored in a column-major format for speed. That means observations are stored as columns and dimensions as rows. So when using MLPACK, additional transpose may be needed. 1.2 Simple API Although MLPACK relies on template techniques in C++, it provides an intuitive and simple API. For the standard usage of methods, default arguments are provided. The MLPACK paper[1] provides a good example: standard k-means clustering in Euclidean space can be initialized like below: 1 KMeans<> k(); Listing 1: k-means with all default arguments If we want to use Manhattan distance, a different cluster initialization policy, and allow empty clusters, the object can be initialized with additional arguments: 1 KMeans<ManhattanDistance, KMeansPlusPlusInitialization, AllowEmptyClusters> k(); Listing 2: k-means with additional arguments 1 1.3 Available methods in MLPACK Commonly used machine learning methods are all implemented in MLPACK. -
Comparison of Dimensionality Reduction Techniques on Audio Signals
Comparison of Dimensionality Reduction Techniques on Audio Signals Tamás Pál, Dániel T. Várkonyi Eötvös Loránd University, Faculty of Informatics, Department of Data Science and Engineering, Telekom Innovation Laboratories, Budapest, Hungary {evwolcheim, varkonyid}@inf.elte.hu WWW home page: http://t-labs.elte.hu Abstract: Analysis of audio signals is widely used and this work: car horn, dog bark, engine idling, gun shot, and very effective technique in several domains like health- street music [5]. care, transportation, and agriculture. In a general process Related work is presented in Section 2, basic mathe- the output of the feature extraction method results in huge matical notation used is described in Section 3, while the number of relevant features which may be difficult to pro- different methods of the pipeline are briefly presented in cess. The number of features heavily correlates with the Section 4. Section 5 contains data about the evaluation complexity of the following machine learning method. Di- methodology, Section 6 presents the results and conclu- mensionality reduction methods have been used success- sions are formulated in Section 7. fully in recent times in machine learning to reduce com- The goal of this paper is to find a combination of feature plexity and memory usage and improve speed of following extraction and dimensionality reduction methods which ML algorithms. This paper attempts to compare the state can be most efficiently applied to audio data visualization of the art dimensionality reduction techniques as a build- in 2D and preserve inter-class relations the most. ing block of the general process and analyze the usability of these methods in visualizing large audio datasets. -
Exploring the Role of Language in Two Systems for Categorization Kayleigh Ryherd University of Connecticut - Storrs, [email protected]
University of Connecticut OpenCommons@UConn Doctoral Dissertations University of Connecticut Graduate School 4-26-2019 Exploring the Role of Language in Two Systems for Categorization Kayleigh Ryherd University of Connecticut - Storrs, [email protected] Follow this and additional works at: https://opencommons.uconn.edu/dissertations Recommended Citation Ryherd, Kayleigh, "Exploring the Role of Language in Two Systems for Categorization" (2019). Doctoral Dissertations. 2163. https://opencommons.uconn.edu/dissertations/2163 Exploring the Role of Language in Two Systems for Categorization Kayleigh Ryherd, PhD University of Connecticut, 2019 Multiple theories of category learning converge on the idea that there are two systems for categorization, each designed to process different types of category structures. The associative system learns categories that have probabilistic boundaries and multiple overlapping features through iterative association of features and feedback. The hypothesis-testing system learns rule-based categories through explicit testing of hy- potheses about category boundaries. Prior research suggests that language resources are necessary for the hypothesis-testing system but not for the associative system. However, other research emphasizes the role of verbal labels in learning the probabilistic similarity-based categories best learned by the associative system. This suggests that language may be relevant for the associative system in a different way than it is relevant for the hypothesis-testing system. Thus, this study investigated the ways in which language plays a role in the two systems for category learning. In the first experiment, I tested whether language is related to an individual’s ability to switch between the associative and hypothesis-testing systems. I found that participants showed remarkable ability to switch between systems regardless of their language ability.