Social media mining for identification and exploration of health-related information from pregnant women

Widespread use of social media has led to the generation of substantial amounts of information about individuals, including health-related information. Social media provides the opportunity to study health-related information about selected population groups who may be of interest for a particular study. In this paper, we explore the possibility of utilizing social media to perform targeted data collection and analysis from a particular population group -- pregnant women. We hypothesize that we can use social media to identify cohorts of pregnant women and follow them over time to analyze crucial health-related information. To identify potentially pregnant women, we employ simple rule-based searches that attempt to detect pregnancy announcements with moderate precision. To further filter out false positives and noise, we employ a supervised classifier using a small number of hand-annotated data. We then collect their posts over time to create longitudinal health timelines and attempt to divide the timelines into different pregnancy trimesters. Finally, we assess the usefulness of the timelines by performing a preliminary analysis to estimate drug intake patterns of our cohort at different trimesters. Our rule-based cohort identification technique collected 53,820 users over thirty months from Twitter. Our pregnancy announcement classification technique achieved an F-measure of 0.81 for the pregnancy class, resulting in 34,895 user timelines. Analysis of the timelines revealed that pertinent health-related information, such as drug-intake and adverse reactions can be mined from the data. Our approach to using user timelines in this fashion has produced very encouraging results and can be employed for other important tasks where cohorts, for which health-related information may not be available from other sources, are required to be followed over time to derive population-based estimates.Comment: 9 page

Linking social media, medical literature, and clinical notes using deep learning.

Researchers analyze data, information, and knowledge through many sources, formats, and methods. The dominant data format includes text and images. In the healthcare industry, professionals generate a large quantity of unstructured data. The complexity of this data and the lack of computational power causes delays in analysis. However, with emerging deep learning algorithms and access to computational powers such as graphics processing unit (GPU) and tensor processing units (TPUs), processing text and images is becoming more accessible. Deep learning algorithms achieve remarkable results in natural language processing (NLP) and computer vision. In this study, we focus on NLP in the healthcare industry and collect data not only from electronic medical records (EMRs) but also medical literature and social media. We propose a framework for linking social media, medical literature, and EMRs clinical notes using deep learning algorithms. Connecting data sources requires defining a link between them, and our key is finding concepts in the medical text. The National Library of Medicine (NLM) introduces a Unified Medical Language System (UMLS) and we use this system as the foundation of our own system. We recognize social media’s dynamic nature and apply supervised and semi-supervised methodologies to generate concepts. Named entity recognition (NER) allows efficient extraction of information, or entities, from medical literature, and we extend the model to process the EMRs’ clinical notes via transfer learning. The results include an integrated, end-to-end, web-based system solution that unifies social media, literature, and clinical notes, and improves access to medical knowledge for the public and experts

Accurate and budget-efficient text, image, and video analysis systems powered by the crowd

Crowdsourcing systems empower individuals and companies to outsource labor-intensive tasks that cannot currently be solved by automated methods and are expensive to tackle by domain experts. Crowdsourcing platforms are traditionally used to provide training labels for supervised machine learning algorithms. Crowdsourced tasks are distributed among internet workers who typically have a range of skills and knowledge, differing previous exposure to the task at hand, and biases that may influence their work. This inhomogeneity of the workforce makes the design of accurate and efficient crowdsourcing systems challenging. This dissertation presents solutions to improve existing crowdsourcing systems in terms of accuracy and efficiency. It explores crowdsourcing tasks in two application areas, political discourse and annotation of biomedical and everyday images. The first part of the dissertation investigates how workers' behavioral factors and their unfamiliarity with data can be leveraged by crowdsourcing systems to control quality. Through studies that involve familiar and unfamiliar image content, the thesis demonstrates the benefit of explicitly accounting for a worker's familiarity with the data when designing annotation systems powered by the crowd. The thesis next presents Crowd-O-Meter, a system that automatically predicts the vulnerability of crowd workers to believe \enquote{fake news} in text and video. The second part of the dissertation explores the reversed relationship between machine learning and crowdsourcing by incorporating machine learning techniques for quality control of crowdsourced end products. In particular, it investigates if machine learning can be used to improve the quality of crowdsourced results and also consider budget constraints. The thesis proposes an image analysis system called ICORD that utilizes behavioral cues of the crowd worker, augmented by automated evaluation of image features, to infer the quality of a worker-drawn outline of a cell in a microscope image dynamically. ICORD determines the need to seek additional annotations from other workers in a budget-efficient manner. Next, the thesis proposes a budget-efficient machine learning system that uses fewer workers to analyze easy-to-label data and more workers for data that require extra scrutiny. The system learns a mapping from data features to number of allocated crowd workers for two case studies, sentiment analysis of twitter messages and segmentation of biomedical images. Finally, the thesis uncovers the potential for design of hybrid crowd-algorithm methods by describing an interactive system for cell tracking in time-lapse microscopy videos, based on a prediction model that determines when automated cell tracking algorithms fail and human interaction is needed to ensure accurate tracking

Bootstrapping Named Entity Annotation by Means of Active Machine Learning: A Method for Creating Corpora

This thesis describes the development and in-depth empirical investigation of a method, called BootMark, for bootstrapping the marking up of named entities in textual documents. The reason for working with documents, as opposed to for instance sentences or phrases, is that the BootMark method is concerned with the creation of corpora. The claim made in the thesis is that BootMark requires a human annotator to manually annotate fewer documents in order to produce a named entity recognizer with a given performance, than would be needed if the documents forming the basis for the recognizer were randomly drawn from the same corpus. The intention is then to use the created named en- tity recognizer as a pre-tagger and thus eventually turn the manual annotation process into one in which the annotator reviews system-suggested annotations rather than creating new ones from scratch. The BootMark method consists of three phases: (1) Manual annotation of a set of documents; (2) Bootstrapping – active machine learning for the purpose of selecting which document to an- notate next; (3) The remaining unannotated documents of the original corpus are marked up using pre-tagging with revision. Five emerging issues are identified, described and empirically investigated in the thesis. Their common denominator is that they all depend on the real- ization of the named entity recognition task, and as such, require the context of a practical setting in order to be properly addressed. The emerging issues are related to: (1) the characteristics of the named entity recognition task and the base learners used in conjunction with it; (2) the constitution of the set of documents annotated by the human annotator in phase one in order to start the bootstrapping process; (3) the active selection of the documents to annotate in phase two; (4) the monitoring and termination of the active learning carried out in phase two, including a new intrinsic stopping criterion for committee-based active learning; and (5) the applicability of the named entity recognizer created during phase two as a pre-tagger in phase three. The outcomes of the empirical investigations concerning the emerging is- sues support the claim made in the thesis. The results also suggest that while the recognizer produced in phases one and two is as useful for pre-tagging as a recognizer created from randomly selected documents, the applicability of the recognizer as a pre-tagger is best investigated by conducting a user study involving real annotators working on a real named entity recognition task

Understanding and Supporting Vocabulary Learners via Machine Learning on Behavioral and Linguistic Data

This dissertation presents various machine learning applications for predicting different cognitive states of students while they are using a vocabulary tutoring system, DSCoVAR. We conduct four studies, each of which includes a comprehensive analysis of behavioral and linguistic data and provides data-driven evidence for designing personalized features for the system. The first study presents how behavioral and linguistic interactions from the vocabulary tutoring system can be used to predict students' off-task states. The study identifies which predictive features from interaction signals are more important and examines different types of off-task behaviors. The second study investigates how to automatically evaluate students' partial word knowledge from open-ended responses to definition questions. We present a technique that augments modern word-embedding techniques with a classic semantic differential scaling method from cognitive psychology. We then use this interpretable semantic scale method for predicting students' short- and long-term learning. The third and fourth studies show how to develop a model that can generate more efficient training curricula for both human and machine vocabulary learners. The third study illustrates a deep-learning model to score sentences for a contextual vocabulary learning curriculum. We use pre-trained language models, such as ELMo or BERT, and an additional attention layer to capture how the context words are less or more important with respect to the meaning of the target word. The fourth study examines how the contextual informativeness model, originally designed to develop curricula for human vocabulary learning, can also be used for developing curricula for various word embedding models. We identify sentences predicted as low informative for human learners are also less helpful for machine learning algorithms. Having a rich understanding of user behaviors, responses, and learning stimuli is imperative to develop an intelligent online system. Our studies demonstrate interpretable methods with cross-disciplinary approaches to understand various cognitive states of students during learning. The analysis results provide data-driven evidence for designing personalized features that can maximize learning outcomes. Datasets we collected from the studies will be shared publicly to promote future studies related to online tutoring systems. And these findings can also be applied to represent different user states observed in other online systems. In the future, we believe our findings can help to implement a more personalized vocabulary learning system, to develop a system that uses non-English texts or different types of inputs, and to investigate how the machine learning outputs interact with students.PHDInformationUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/162999/1/sjnam_1.pd

Semantic Sort: A Supervised Approach to Personalized Semantic Relatedness

We propose and study a novel supervised approach to learning statistical semantic relatedness models from subjectively annotated training examples. The proposed semantic model consists of parameterized co-occurrence statistics associated with textual units of a large background knowledge corpus. We present an efficient algorithm for learning such semantic models from a training sample of relatedness preferences. Our method is corpus independent and can essentially rely on any sufficiently large (unstructured) collection of coherent texts. Moreover, the approach facilitates the fitting of semantic models for specific users or groups of users. We present the results of extensive range of experiments from small to large scale, indicating that the proposed method is effective and competitive with the state-of-the-art.Comment: 37 pages, 8 figures A short version of this paper was already published at ECML/PKDD 201

An Elastic-net Logistic Regression Approach to Generate Classifiers and Gene Signatures for Types of Immune Cells and T Helper Cell Subsets

Background: Host immune response is coordinated by a variety of different specialized cell types that vary in time and location. While host immune response can be studied using conventional low-dimensional approaches, advances in transcriptomics analysis may provide a less biased view. Yet, leveraging transcriptomics data to identify immune cell subtypes presents challenges for extracting informative gene signatures hidden within a high dimensional transcriptomics space characterized by low sample numbers with noisy and missing values. To address these challenges, we explore using machine learning methods to select gene subsets and estimate gene coefficients simultaneously. Results: Elastic-net logistic regression, a type of machine learning, was used to construct separate classifiers for ten different types of immune cell and for five T helper cell subsets. The resulting classifiers were then used to develop gene signatures that best discriminate among immune cell types and T helper cell subsets using RNA-seq datasets. We validated the approach using single-cell RNA-seq (scRNA-seq) datasets, which gave consistent results. In addition, we classified cell types that were previously unannotated. Finally, we benchmarked the proposed gene signatures against other existing gene signatures. Conclusions: Developed classifiers can be used as priors in predicting the extent and functional orientation of the host immune response in diseases, such as cancer, where transcriptomic profiling of bulk tissue samples and single cells are routinely employed. Information that can provide insight into the mechanistic basis of disease and therapeutic response. The so