Evidence map›Paper›PMID 36261805›Full record

ArticleBMC bioinformatics2022

Estimating the optimal linear combination of predictors using spherically constrained optimization.

Priyam Das, Debsurya De, Raju Maiti, Mona Kamal, Katherine A Hutcheson, Clifton D Fuller, Bibhas Chakraborty, Christine B Peterson

Open access · goldAbstract read
In one paragraph

Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.6field-weighted citation impact, top 32% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 8 citations in OpenAlex.

  1. Article
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  4. Article
  5. Clustering Sequence Data with Mixture Markov Chains with Covariates Using Multiple Simplex Constrained Optimization Routine (MSiCOR).Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America · 2024
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 4 institutions in 3 countries.

Priyam DasDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. pdasvcu@gmail.com.ORCID http://orcid.org/0000-0003-2384-0486
Debsurya DeIndian Statistical Institute, Kolkata, India.
Raju MaitiCentre for Quantitative Medicine, Duke-National University of Singapore Medical School, Singapore, Singapore.
Mona KamalDepartment of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Katherine A HutchesonDepartment of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Clifton D FullerDepartment of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Bibhas ChakrabortyCentre for Quantitative Medicine, Duke-National University of Singapore Medical School, Singapore, Singapore.
Christine B PetersonDepartment of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
The University of Texas MD Anderson Cancer Center · USNational University of Singapore · SGHarvard University · USIndian Statistical Institute · IN

Funding

Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Fabien Delerue · 1985 to 2026
$290.8M
Development of functional magnetic resonance imaging-guided adaptive radiotherapy for head and neck cancer patients using novel MR-Linac deviceR01DE028290 · NIDCR · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI CHRISTODOULEAS, JOHN PAUL, FULLER, CLIFTON DAVID · 2019 to 2023
$4.3M
Using Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) to Establish Objective Clinical Outcome Measures for Mandibular OsteoradionecrosisR01DE025248 · NIDCR · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI LAI, STEPHEN Y · 2016 to 2020
$2.9M
Longitudinal Spatial-Nonspatial Decision Support for Competing Outcomes in Head and Neck Cancer TherapyR01CA258827 · NCI · UNIVERSITY OF ILLINOIS AT CHICAGO · PI CANAHUATE, GUADALUPE, FULLER, CLIFTON DAVID · 2021 to 2025
$2.9M
Improving Recovery after Major Cancer Surgery using Patient-Reported OutcomesR01CA205146 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI WANG, XIN SHELLEY · 2016 to 2019
$2.6M
SCH: Personalized Rescheduling of Adaptive Radiation Therapy for Head & Neck CancerR01CA257814 · NCI · RICE UNIVERSITY · PI FULLER, CLIFTON DAVID, SCHAEFER, ANDREW J · 2021 to 2024
$1.8M
imaging Radiation-Associated Dysphagia (iRAD)R01CA218148 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI FULLER, CLIFTON DAVID, HUTCHESON, KATHERINE ARNOLD · 2017 to 2019
$810k
Fellow and Resident Radiation Oncology iNtensive Training in Imaging and Informatics to Empower Research Careers (FRONTI2ER)R25EB025787 · NIBIB · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI DAS, PRAJNAN, FULLER, CLIFTON DAVID · 2018 to 2022
$535k
Manual Therapy for Fibrosis-related Late Effect Dysphagia in Head and Neck Cancer Survivors: The MANTLE TrialR21CA226200 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI HUTCHESON, KATHERINE ARNOLD · 2018 to 2019
$378k
atos medical NAcancer prevention and research institute of texas RP150521cancer prevention and research institute of texas RP160668charles and daneen stiefel md anderson oropharynx program 00059189duke-nus medical school start-up grantelekta ab NAmd anderson cancer center support grant P30CA016672md anderson program in image-guided cancer therapy NAministry of education, singapore MOE2015-T2-2-056national institutes of health/national cancer center P30CA016672NCI NIH HHS P30 CA016672NCI NIH HHS R01 CA205146NCI NIH HHS R01 CA218148NCI NIH HHS R01 CA257814NCI NIH HHS R01 CA258827NCI NIH HHS R21 CA226200NCI NIH HHS R21CA226200-02nci parent research project grant R01CA258827nci parent rpg mechanism R01CA258827)NIBIB NIH HHS R25 EB025787nidcr academic industrial partnership grant R01DE028290NIDCR NIH HHS R01 DE025248NIDCR NIH HHS R01DE025248-05NIDCR NIH HHS R01 DE028290NIH HHS R01CA205146NIH HHS R21CA226200-02nih/nci cancer center support grant (ccsg) NAnih nibib research education programs for residents and clinical fellows grant R25EB025787-01nsf division of civil, mechanical, and manufacturing innovation (cmmi) grant NSF 1933369nsf/nih joint smart connected health program R01CA257814Patient-Centered Outcomes Research Institute NApilot research program award from the ut md anderson ccsg radiation oncology and cancer imaging program P30CA016672the multidisciplinary the radiation oncology/cancer imaging program P30CA016672-44the nci early phase clinical trials in imaging and image-guided interventions program 1R01CA218148thrive/hesi NA
6 · The paper itself

Abstract

backgroundIn the context of a binary classification problem, the optimal linear combination of continuous predictors can be estimated by maximizing the area under the receiver operating characteristic curve. For ordinal responses, the optimal predictor combination can similarly be obtained by maximization of the hypervolume under the manifold (HUM). Since the empirical HUM is discontinuous, non-differentiable, and possibly multi-modal, solving this maximization problem requires a global optimization technique. Estimation of the optimal coefficient vector using existing global optimization techniques is computationally expensive, becoming prohibitive as the number of predictors and the number of outcome categories increases.

resultsWe propose an efficient derivative-free black-box optimization technique based on pattern search to solve this problem, which we refer to as Spherically Constrained Optimization Routine (SCOR). Through extensive simulation studies, we demonstrate that the proposed method achieves better performance than existing methods including the step-down algorithm. Finally, we illustrate the proposed method to predict the severity of swallowing difficulty after radiation therapy for oropharyngeal cancer based on radiation dose to various structures in the head and neck.

conclusionsOur proposed method addresses an important challenge in combining multiple biomarkers to predict an ordinal outcome. This problem is particularly relevant to medical research, where it may be of interest to diagnose a disease with various stages of progression or a toxicity with multiple grades of severity. We provide the implementation of our proposed SCOR method as an R package, available online at https://CRAN.R-project.org/package=SCOR .

Indexed as

AlgorithmsBiomarkersComputer SimulationROC CurveBiomarkersArea under the curveClassificationGlobal optimizationHypervolume under the manifoldPattern searchROC curve

Identifiers

PMID36261805
PMCPMC9583504
OpenAlexW4306790221

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.