Zhaobin Kuang, James Thomson, Michael Caldwell, Peggy Peissig, Ron Stewart, David Page
{"title":"Baseline Regularization for Computational Drug Repositioning with Longitudinal Observational Data.","authors":"Zhaobin Kuang, James Thomson, Michael Caldwell, Peggy Peissig, Ron Stewart, David Page","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Computational Drug Repositioning (CDR) is the knowledge discovery process of finding new indications for existing drugs leveraging heterogeneous drug-related data. Longitudinal observational data such as Electronic Health Records (EHRs) have become an emerging data source for CDR. To address the high-dimensional, irregular, subject and time-heterogeneous nature of EHRs, we propose Baseline Regularization (BR) and a variant that extend the one-way fixed effect model, which is a standard approach to analyze small-scale longitudinal data. For evaluation, we use the proposed methods to search for drugs that can lower Fasting Blood Glucose (FBG) level in the Marshfield Clinic EHR. Experimental results suggest that the proposed methods are capable of rediscovering drugs that can lower FBG level as well as identifying some potential blood sugar lowering drugs in the literature.</p>","PeriodicalId":73334,"journal":{"name":"IJCAI : proceedings of the conference","volume":"2016 ","pages":"2521-2528"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5382966/pdf/nihms786212.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34898673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Hidden Parameter Markov Decision Processes: A Semiparametric Regression Approach for Discovering Latent Task Parametrizations.","authors":"Finale Doshi-Velez, George Konidaris","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Control applications often feature tasks with similar, but not identical, dynamics. We introduce the Hidden Parameter Markov Decision Process (HiP-MDP), a framework that parametrizes a family of related dynamical systems with a low-dimensional set of latent factors, and introduce a semiparametric regression approach for learning its structure from data. We show that a learned HiP-MDP rapidly identifies the dynamics of new task instances in several settings, flexibly adapting to task variation.</p>","PeriodicalId":73334,"journal":{"name":"IJCAI : proceedings of the conference","volume":"2016 ","pages":"1432-1440"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466173/pdf/nihms859880.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35079547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"An Efficient Framework for Constructing Generalized Locally-Induced Text Metrics","authors":"S. Amizadeh, Shuguang Wang, M. Hauskrecht","doi":"10.5591/978-1-57735-516-8/IJCAI11-198","DOIUrl":"https://doi.org/10.5591/978-1-57735-516-8/IJCAI11-198","url":null,"abstract":"In this paper, we propose a new framework for constructing text metrics which can be used to compare and support inferences among terms and sets of terms. Our metric is derived from data-driven kernels on graphs that let us capture global relations among terms and sets of terms, regardless of their complexity and size. To compute the metric efficiently for any two subsets of terms, we develop an approximation technique that relies on the precompiled term-term similarities. To scale-up the approach to problems with huge number of terms, we develop and experiment with a solution that sub-samples the term space. We demonstrate the benefits of the whole framework on two text inference tasks: prediction of terms in the article from its abstract and query expansion in information retrieval.","PeriodicalId":73334,"journal":{"name":"IJCAI : proceedings of the conference","volume":"59 1","pages":"1159-1164"},"PeriodicalIF":0.0,"publicationDate":"2011-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79090536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"An Efficient Framework for Constructing Generalized Locally-Induced Text Metrics.","authors":"Saeed Amizadeh, Shuguang Wang, Milos Hauskrecht","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In this paper, we propose a new framework for constructing text metrics which can be used to compare and support inferences among terms and sets of terms. Our metric is derived from data-driven kernels on graphs that let us capture global relations among terms and sets of terms, regardless of their complexity and size. To compute the metric efficiently for any two subsets of terms, we develop an approximation technique that relies on the precompiled term-term similarities. To scale-up the approach to problems with huge number of terms, we develop and experiment with a solution that sub-samples the term space. We demonstrate the benefits of the whole framework on two text inference tasks: prediction of terms in the article from its abstract and query expansion in information retrieval.</p>","PeriodicalId":73334,"journal":{"name":"IJCAI : proceedings of the conference","volume":" ","pages":"1159-1164"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264061/pdf/nihms348372.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30414049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye, Zhi-Hua Zhou
{"title":"Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning.","authors":"Ying-Xin Li, Shuiwang Ji, Sudhir Kumar, Jieping Ye, Zhi-Hua Zhou","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The Berkeley Drosophila Genome Project (BDGP) has produced a large number of gene expression patterns, many of which have been annotated textually with anatomical and developmental terms. These terms spatially correspond to local regions of the images; however, they are attached collectively to groups of images, such that it is unknown which term is assigned to which region of which image in the group. This poses a challenge to the development of the computational method to automate the textual description of expression patterns contained in each image. In this paper, we show that the underlying nature of this task matches well with a new machine learning framework, Multi-Instance Multi-Label learning (MIML). We propose a new MIML support vector machine to solve the problems that beset the annotation task. Empirical study shows that the proposed method outperforms the state-of-the-art Drosophila gene expression pattern annotation methods.</p>","PeriodicalId":73334,"journal":{"name":"IJCAI : proceedings of the conference","volume":"2009 ","pages":"1445-1450"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932460/pdf/nihms110406.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29294296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}