Browsing HMS Scholarly Articles by Keyword "Algorithms"

Now showing items 1-20 of 28

    • ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes 

      Mosaliganti, Kishore Rao; Noche, Ramil; Xiong, Fengzhu; Swinburne, Ian A; Megason, Sean G. (Public Library of Science, 2012)
      The quantification of cell shape, cell migration, and cell rearrangements is important for addressing classical questions in developmental biology such as patterning and tissue morphogenesis. Time-lapse microscopic imaging ...

    • An Active Learning Approach for Rapid Characterization of Endothelial Cells in Human Tumors 

      Padmanabhan, Raghav K.; Somasundar, Vinay H.; Griffith, Sandra D.; Zhu, Jianliang; Samoyedny, Drew; Tan, Kay See; Hu, Jiahao; Liao, Xuejun; Carin, Lawrence; Yoon, Sam S.; Flaherty, Keith T.; DiPaola, Robert S.; Heitjan, Daniel F.; Lal, Priti; Feldman, Michael D.; Roysam, Badrinath; Lee, William M. F. (Public Library of Science, 2014)
      Currently, no available pathological or molecular measures of tumor angiogenesis predict response to antiangiogenic therapies used in clinical practice. Recognizing that tumor endothelial cells (EC) and EC activation and ...

    • Automatic Prediction of Rheumatoid Arthritis Disease Activity from the Electronic Medical Records 

      Lin, Chen; Karlson, Elizabeth W.; Canhao, Helena; Miller, Timothy A.; Dligach, Dmitriy; Chen, Pei Jun; Perez, Raul Natanael Guzman; Shen, Yuanyan; Weinblatt, Michael E.; Shadick, Nancy A.; Plenge, Robert M.; Savova, Guergana K. (Public Library of Science, 2013)
      Objective: We aimed to mine the data in the Electronic Medical Record to automatically discover patients' Rheumatoid Arthritis disease activity at discrete rheumatology clinic visits. We cast the problem as a document ...

    • Biological Time Series Analysis Using a Context Free Language: Applicability to Pulsatile Hormone Data 

      Dean, Dennis A.; Adler, Gail K.; Nguyen, David P.; Klerman, Elizabeth B. (Public Library of Science, 2014)
      We present a novel approach for analyzing biological time-series data using a context-free language (CFL) representation that allows the extraction and quantification of important features from the time-series. This ...

    • The Complexity of Standing Postural Control in Older Adults: A Modified Detrended Fluctuation Analysis Based upon the Empirical Mode Decomposition Algorithm 

      Zhou, Junhong; Manor, Bradley David; Liu, Dongdong; Hu, Kun; Zhang, Jue; Fang, Jing (Public Library of Science, 2013)
      Human aging into senescence diminishes the capacity of the postural control system to adapt to the stressors of everyday life. Diminished adaptive capacity may be reflected by a loss of the fractal-like, multiscale complexity ...

    • Conic Sampling: An Efficient Method for Solving Linear and Quadratic Programming by Randomly Linking Constraints within the Interior 

      Serang, Oliver R. (Public Library of Science, 2012)
      Linear programming (LP) problems are commonly used in analysis and resource allocation, frequently surfacing as approximations to more difficult problems. Existing approaches to LP have been dominated by a small group of ...

    • Deconvolution of Serum Cortisol Levels by Using Compressed Sensing 

      Faghih, Rose T.; Dahleh, Munther A.; Adler, Gail K.; Klerman, Elizabeth B.; Brown, Emery N. (Public Library of Science, 2014)
      The pulsatile release of cortisol from the adrenal glands is controlled by a hierarchical system that involves corticotropin releasing hormone (CRH) from the hypothalamus, adrenocorticotropin hormone (ACTH) from the ...

    • Determinants of Smoking and Quitting in HIV-Infected Individuals 

      Regan, Susan; Meigs, James B.; Grinspoon, Steven K.; Triant, Virginia A. (Public Library of Science, 2016)
      Background: Cigarette smoking is widespread among HIV-infected patients, who confront increased risk of smoking-related co-morbidities. The effects of HIV infection and HIV-related variables on smoking and smoking cessation ...

    • Efficient Universal Computing Architectures for Decoding Neural Activity 

      Rapoport, Benjamin Isaac; Turicchia, Lorenzo; Wattanapanitch, Woradorn; Davidson, Thomas J.; Sarpeshkar, Rahul (Public Library of Science, 2012)
      The ability to decode neural activity into meaningful control signals for prosthetic devices is critical to the development of clinically useful brain– machine interfaces (BMIs). Such systems require input from tens to ...

    • Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder 

      Lingren, Todd; Chen, Pei; Bochenek, Joseph; Doshi-Velez, Finale; Manning-Courtney, Patty; Bickel, Julie; Wildenger Welchons, Leah; Reinhold, Judy; Bing, Nicole; Ni, Yizhao; Barbaresi, William; Mentch, Frank; Basford, Melissa; Denny, Joshua; Vazquez, Lyam; Perry, Cassandra; Namjou, Bahram; Qiu, Haijun; Connolly, John; Abrams, Debra; Holm, Ingrid A.; Cobb, Beth A.; Lingren, Nataline; Solti, Imre; Hakonarson, Hakon; Kohane, Isaac S.; Harley, John; Savova, Guergana (Public Library of Science, 2016)
      Objective: Cohort selection is challenging for large-scale electronic health record (EHR) analyses, as International Classification of Diseases 9th edition (ICD-9) diagnostic codes are notoriously unreliable disease ...

    • Identifying Cases of Type 2 Diabetes in Heterogeneous Data Sources: Strategy from the EMIF Project 

      Roberto, Giuseppe; Leal, Ingrid; Sattar, Naveed; Loomis, A. Katrina; Avillach, Paul; Egger, Peter; van Wijngaarden, Rients; Ansell, David; Reisberg, Sulev; Tammesoo, Mari-Liis; Alavere, Helene; Pasqua, Alessandro; Pedersen, Lars; Cunningham, James; Tramontan, Lara; Mayer, Miguel A.; Herings, Ron; Coloma, Preciosa; Lapi, Francesco; Sturkenboom, Miriam; van der Lei, Johan; Schuemie, Martijn J.; Rijnbeek, Peter; Gini, Rosa (Public Library of Science, 2016)
      Due to the heterogeneity of existing European sources of observational healthcare data, data source-tailored choices are needed to execute multi-data source, multi-national epidemiological studies. This makes transparent ...

    • Indication Alerts Intercept Drug Name Confusion Errors during Computerized Entry of Medication Orders 

      Galanter, William L.; Bryson, Michelle L.; Falck, Suzanne; Rosenfield, Rachel; Laragh, Marci; Shrestha, Neeha; Schiff, Gordon D.; Lambert, Bruce L. (Public Library of Science, 2014)
      Background: Confusion between similar drug names is a common cause of potentially harmful medication errors. Interventions to prevent these errors at the point of prescribing have had limited success. The purpose of this ...

    • Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models 

      Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn; Zucker, Jeremy Daniel Hofeld; Colijn, Caroline; Weiner, Brian; Galagan, James E. (Public Library of Science, 2012)
      Background: Bacteria have evolved the ability to efficiently and resourcefully adapt to changing environments. A key means by which they optimize their use of available nutrients is through adjustments in gene expression ...

    • Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems 

      Gerber, Georg Kurt; Onderdonk, Andrew Bruce; Bry, Lynn (Public Library of Science, 2012)
      The human gut microbiota comprise a complex and dynamic ecosystem that profoundly affects host development and physiology. Standard approaches for analyzing time-series data of the microbiota involve computation of measures ...

    • Integrated diagnostics: proceedings from the 9th biennial symposium of the International Society for Strategic Studies in Radiology 

      Krestin, G. P.; Grenier, P. A.; Hricak, H.; Jackson, V. P.; Khong, P. L.; Miller, Janet C.; Muellner, A.; Schwaiger, M.; Thrall, James Hunter (Springer-Verlag, 2012)
      The International Society for Strategic Studies in Radiology held its 9th biennial meeting in August 2011. The focus of the programme was integrated diagnostics and massive computing. Participants discussed the opportunities, ...

    • Investigation of Bias in Continuous Medical Image Label Fusion 

      Xing, Fangxu; Prince, Jerry L.; Landman, Bennett A. (Public Library of Science, 2016)
      Image labeling is essential for analyzing morphometric features in medical imaging data. Labels can be obtained by either human interaction or automated segmentation algorithms, both of which suffer from errors. The ...

    • Multi-Edge Gene Set Networks Reveal Novel Insights into Global Relationships between Biological Themes 

      Parikh, Jignesh R.; Xia, Yu; Marto, Jarrod (Public Library of Science, 2012)
      Curated gene sets from databases such as KEGG Pathway and Gene Ontology are often used to systematically organize lists of genes or proteins derived from high-throughput data. However, the information content inherent to ...

    • Oocyte Family Trees: Old Branches or New Stems? 

      Woods, Dori C.; Telfer, Evelyn E.; Tilly, Jonathan Lee (Public Library of Science, 2012)

    • Pituitary Adenoma Volumetry with 3D Slicer 

      Egger, Jan; Kapur, Tina; Nimsky, Christopher; Kikinis, Ron (Public Library of Science, 2012)
      In this study, we present pituitary adenoma volumetry using the free and open source medical image computing platform for biomedical research: (3D) Slicer. Volumetric changes in cerebral pathologies like pituitary adenomas ...

    • The Separatrix Algorithm for Synthesis and Analysis of Stochastic Simulations with Applications in Disease Modeling 

      Klein, Daniel J.; Baym, Michael; Eckhoff, Philip (Public Library of Science, 2014)
      Decision makers in epidemiology and other disciplines are faced with the daunting challenge of designing interventions that will be successful with high probability and robust against a multitude of uncertainties. To ...