Browsing by Subject "Semi-supervised learning"

Now showing 1 - 3 of 3
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    Keyphrase Identification Using Minimal Labeled Data with Hierarchical Context and Transfer Learning
    (medRxiv, 2023-05-26) Goli, Rohan; Hubig, Nina; Min, Hua; Gong, Yang; Sittig, Dean F.; Rennert, Lior; Robinson, David; Biondich, Paul; Wright, Adam; Nøhr, Christian; Law, Timothy; Faxvaag, Arild; Weaver, Aneesa; Gimbel, Ronald; Jing, Xia; Pediatrics, School of Medicine
    Interoperable clinical decision support system (CDSS) rules provide a pathway to interoperability, a well-recognized challenge in health information technology. Building an ontology facilitates creating interoperable CDSS rules, which can be achieved by identifying the keyphrases (KP) from the existing literature. However, KP identification for data labeling requires human expertise, consensus, and contextual understanding. This paper aims to present a semi-supervised KP identification framework using minimal labeled data based on hierarchical attention over the documents and domain adaptation. Our method outperforms the prior neural architectures by learning through synthetic labels for initial training, document-level contextual learning, language modeling, and fine-tuning with limited gold standard label data. To the best of our knowledge, this is the first functional framework for the CDSS sub-domain to identify KPs, which is trained on limited labeled data. It contributes to the general natural language processing (NLP) architectures in areas such as clinical NLP, where manual data labeling is challenging, and light-weighted deep learning models play a role in real-time KP identification as a complementary approach to human experts' effort.
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    Point process modeling of drug overdoses with heterogeneous and missing data
    (Institute of Mathematical Statistics, 2021) Liu, Xueying; Carter, Jeremy; Ray, Brad; Mohler, George; Computer and Information Science, School of Science
    Opioid overdose rates have increased in the United States over the past decade and reflect a major public health crisis. Modeling and prediction of drug and opioid hotspots, where a high percentage of events fall in a small percentage of space–time, could help better focus limited social and health services. In this work we present a spatial-temporal point process model for drug overdose clustering. The data input into the model comes from two heterogeneous sources: (1) high volume emergency medical calls for service (EMS) records containing location and time but no information on the type of nonfatal overdose, and (2) fatal overdose toxicology reports from the coroner containing location and high-dimensional information from the toxicology screen on the drugs present at the time of death. We first use nonnegative matrix factorization to cluster toxicology reports into drug overdose categories, and we then develop an EM algorithm for integrating the two heterogeneous data sets, where the mark corresponding to overdose category is inferred for the EMS data and the high volume EMS data is used to more accurately predict drug overdose death hotspots. We apply the algorithm to drug overdose data from Indianapolis, showing that the point process defined on the integrated data out-performs point processes that use only coroner data (AUC improvement 0.81 to 0.85). We also investigate the extent to which overdoses are contagious, as a function of the type of overdose, while controlling for exogenous fluctuations in the background rate that might also contribute to clustering. We find that drug and opioid overdose deaths exhibit significant excitation with branching ratio ranging from 0.72 to 0.98.
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    SSMD: a semi-supervised approach for a robust cell type identification and deconvolution of mouse transcriptomics data
    (Oxford University Press, 2021) Lu, Xiaoyu; Tu, Szu-Wei; Chang, Wennan; Wan, Changlin; Wang, Jiashi; Zang, Yong; Ramdas, Baskar; Kapur, Reuben; Lu, Xiongbin; Cao, Sha; Zhang, Chi; Medical and Molecular Genetics, School of Medicine
    Deconvolution of mouse transcriptomic data is challenged by the fact that mouse models carry various genetic and physiological perturbations, making it questionable to assume fixed cell types and cell type marker genes for different data set scenarios. We developed a Semi-Supervised Mouse data Deconvolution (SSMD) method to study the mouse tissue microenvironment. SSMD is featured by (i) a novel nonparametric method to discover data set-specific cell type signature genes; (ii) a community detection approach for fixing cell types and their marker genes; (iii) a constrained matrix decomposition method to solve cell type relative proportions that is robust to diverse experimental platforms. In summary, SSMD addressed several key challenges in the deconvolution of mouse tissue data, including: (i) varied cell types and marker genes caused by highly divergent genotypic and phenotypic conditions of mouse experiment; (ii) diverse experimental platforms of mouse transcriptomics data; (iii) small sample size and limited training data source and (iv) capable to estimate the proportion of 35 cell types in blood, inflammatory, central nervous or hematopoietic systems. In silico and experimental validation of SSMD demonstrated its high sensitivity and accuracy in identifying (sub) cell types and predicting cell proportions comparing with state-of-the-arts methods. A user-friendly R package and a web server of SSMD are released via https://github.com/xiaoyulu95/SSMD.