A Brief Survey of Text Mining: Classification, Clustering and Extraction Techniques

The amount of text that is generated every day is increasing dramatically. This tremendous volume of mostly unstructured text cannot be simply processed and perceived by computers. Therefore, efficient and effective techniques and algorithms are required to discover useful patterns. Text mining is the task of extracting meaningful information from text, which has gained significant attentions in recent years. In this paper, we describe several of the most fundamental text mining tasks and techniques including text pre-processing, classification and clustering. Additionally, we briefly explain text mining in biomedical and health care domains.Comment: some of References format have update

Scientific Discovery by Machine Intelligence: A New Avenue for Drug Research

The majority of big data is unstructured and of this majority the largest chunk is text. While data mining techniques are well developed and standardized for structured, numerical data, the realm of unstructured data is still largely unexplored. The general focus lies on information extraction, which attempts to retrieve known information from text. The Holy Grail, however is knowledge discovery, where machines are expected to unearth entirely new facts and relations that were not previously known by any human expert. Indeed, understanding the meaning of text is often considered as one of the main characteristics of human intelligence. The ultimate goal of semantic artificial intelligence is to devise software that can understand the meaning of free text, at least in the practical sense of providing new, actionable information condensed out of a body of documents. As a stepping stone on the road to this vision I will introduce a totally new approach to drug research, namely that of identifying relevant information by employing a self-organizing semantic engine to text mine large repositories of biomedical research papers, a technique pioneered by Merck with the InfoCodex software. I will describe the methodology and a first successful experiment for the discovery of new biomarkers and phenotypes for diabetes and obesity on the basis of PubMed abstracts, public clinical trials and Merck internal documents. The reported approach shows much promise and has potential to impact fundamentally pharmaceutical research as a way to shorten time-to-market of novel drugs, and for early recognition of dead ends

Fuzzy Approach Topic Discovery in Health and Medical Corpora

The majority of medical documents and electronic health records (EHRs) are in text format that poses a challenge for data processing and finding relevant documents. Looking for ways to automatically retrieve the enormous amount of health and medical knowledge has always been an intriguing topic. Powerful methods have been developed in recent years to make the text processing automatic. One of the popular approaches to retrieve information based on discovering the themes in health & medical corpora is topic modeling, however, this approach still needs new perspectives. In this research we describe fuzzy latent semantic analysis (FLSA), a novel approach in topic modeling using fuzzy perspective. FLSA can handle health & medical corpora redundancy issue and provides a new method to estimate the number of topics. The quantitative evaluations show that FLSA produces superior performance and features to latent Dirichlet allocation (LDA), the most popular topic model.Comment: 12 Pages, International Journal of Fuzzy Systems, 201

Text2Node: a Cross-Domain System for Mapping Arbitrary Phrases to a Taxonomy

Electronic health record (EHR) systems are used extensively throughout the healthcare domain. However, data interchangeability between EHR systems is limited due to the use of different coding standards across systems. Existing methods of mapping coding standards based on manual human experts mapping, dictionary mapping, symbolic NLP and classification are unscalable and cannot accommodate large scale EHR datasets. In this work, we present Text2Node, a cross-domain mapping system capable of mapping medical phrases to concepts in a large taxonomy (such as SNOMED CT). The system is designed to generalize from a limited set of training samples and map phrases to elements of the taxonomy that are not covered by training data. As a result, our system is scalable, robust to wording variants between coding systems and can output highly relevant concepts when no exact concept exists in the target taxonomy. Text2Node operates in three main stages: first, the lexicon is mapped to word embeddings; second, the taxonomy is vectorized using node embeddings; and finally, the mapping function is trained to connect the two embedding spaces. We compared multiple algorithms and architectures for each stage of the training, including GloVe and FastText word embeddings, CNN and Bi-LSTM mapping functions, and node2vec for node embeddings. We confirmed the robustness and generalisation properties of Text2Node by mapping ICD-9-CM Diagnosis phrases to SNOMED CT and by zero-shot training at comparable accuracy. This system is a novel methodological contribution to the task of normalizing and linking phrases to a taxonomy, advancing data interchangeability in healthcare. When applied, the system can use electronic health records to generate an embedding that incorporates taxonomical medical knowledge to improve clinical predictive models

A Study of Recent Contributions on Information Extraction

This paper reports on modern approaches in Information Extraction (IE) and its two main sub-tasks of Named Entity Recognition (NER) and Relation Extraction (RE). Basic concepts and the most recent approaches in this area are reviewed, which mainly include Machine Learning (ML) based approaches and the more recent trend to Deep Learning (DL) based methods

Unsupervised Extraction of Phenotypes from Cancer Clinical Notes for Association Studies

The recent adoption of Electronic Health Records (EHRs) by health care providers has introduced an important source of data that provides detailed and highly specific insights into patient phenotypes over large cohorts. These datasets, in combination with machine learning and statistical approaches, generate new opportunities for research and clinical care. However, many methods require the patient representations to be in structured formats, while the information in the EHR is often locked in unstructured texts designed for human readability. In this work, we develop the methodology to automatically extract clinical features from clinical narratives from large EHR corpora without the need for prior knowledge. We consider medical terms and sentences appearing in clinical narratives as atomic information units. We propose an efficient clustering strategy suitable for the analysis of large text corpora and to utilize the clusters to represent information about the patient compactly. To demonstrate the utility of our approach, we perform an association study of clinical features with somatic mutation profiles from 4,007 cancer patients and their tumors. We apply the proposed algorithm to a dataset consisting of about 65 thousand documents with a total of about 3.2 million sentences. We identify 341 significant statistical associations between the presence of somatic mutations and clinical features. We annotated these associations according to their novelty, and report several known associations. We also propose 32 testable hypotheses where the underlying biological mechanism does not appear to be known but plausible. These results illustrate that the automated discovery of clinical features is possible and the joint analysis of clinical and genetic datasets can generate appealing new hypotheses

Deep EHR: A Survey of Recent Advances in Deep Learning Techniques for Electronic Health Record (EHR) Analysis

The past decade has seen an explosion in the amount of digital information stored in electronic health records (EHR). While primarily designed for archiving patient clinical information and administrative healthcare tasks, many researchers have found secondary use of these records for various clinical informatics tasks. Over the same period, the machine learning community has seen widespread advances in deep learning techniques, which also have been successfully applied to the vast amount of EHR data. In this paper, we review these deep EHR systems, examining architectures, technical aspects, and clinical applications. We also identify shortcomings of current techniques and discuss avenues of future research for EHR-based deep learning.Comment: Accepted for publication with Journal of Biomedical and Health Informatics: http://ieeexplore.ieee.org/abstract/document/8086133

Toward Interpretable Topic Discovery via Anchored Correlation Explanation

Many predictive tasks, such as diagnosing a patient based on their medical chart, are ultimately defined by the decisions of human experts. Unfortunately, encoding experts' knowledge is often time consuming and expensive. We propose a simple way to use fuzzy and informal knowledge from experts to guide discovery of interpretable latent topics in text. The underlying intuition of our approach is that latent factors should be informative about both correlations in the data and a set of relevance variables specified by an expert. Mathematically, this approach is a combination of the information bottleneck and Total Correlation Explanation (CorEx). We give a preliminary evaluation of Anchored CorEx, showing that it produces more coherent and interpretable topics on two distinct corpora.Comment: presented at 2016 ICML Workshop on #Data4Good: Machine Learning in Social Good Applications, New York, N

Relation Extraction : A Survey

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

Scientific Article Summarization Using Citation-Context and Article's Discourse Structure

We propose a summarization approach for scientific articles which takes advantage of citation-context and the document discourse model. While citations have been previously used in generating scientific summaries, they lack the related context from the referenced article and therefore do not accurately reflect the article's content. Our method overcomes the problem of inconsistency between the citation summary and the article's content by providing context for each citation. We also leverage the inherent scientific article's discourse for producing better summaries. We show that our proposed method effectively improves over existing summarization approaches (greater than 30% improvement over the best performing baseline) in terms of \textsc{Rouge} scores on TAC2014 scientific summarization dataset. While the dataset we use for evaluation is in the biomedical domain, most of our approaches are general and therefore adaptable to other domains.Comment: EMNLP 201