Jacob Antunes

Senior Research Scientist at MIM Software Inc.
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Contact Information
us****@****om
(386) 825-5501
Location
Cleveland, Ohio, United States, US
Languages
  • English -

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Experience

    • United States
    • Software Development
    • 200 - 300 Employee
    • Senior Research Scientist
      • Sep 2020 - Present

      ● Lead investigator on multiple imaging research projects requiring advanced algorithmic or image processing solutions ● Constructed various machine learning and deep learning pipelines for CAD, OAR segmentation, lesion classification, and image-to-image translation ● Developed in-house suite of 2D and 3D voxel-wise radiomic texture and kinematic features ● Lead author on 3 abstracts for synthetic CT generation for MR-only guided radiation therapy ● Coordinate with KOLs… Show more ● Lead investigator on multiple imaging research projects requiring advanced algorithmic or image processing solutions ● Constructed various machine learning and deep learning pipelines for CAD, OAR segmentation, lesion classification, and image-to-image translation ● Developed in-house suite of 2D and 3D voxel-wise radiomic texture and kinematic features ● Lead author on 3 abstracts for synthetic CT generation for MR-only guided radiation therapy ● Coordinate with KOLs, stakeholders for investigating potential radiation oncology solutions ● Supervising 3-4 team members or interns Show less ● Lead investigator on multiple imaging research projects requiring advanced algorithmic or image processing solutions ● Constructed various machine learning and deep learning pipelines for CAD, OAR segmentation, lesion classification, and image-to-image translation ● Developed in-house suite of 2D and 3D voxel-wise radiomic texture and kinematic features ● Lead author on 3 abstracts for synthetic CT generation for MR-only guided radiation therapy ● Coordinate with KOLs… Show more ● Lead investigator on multiple imaging research projects requiring advanced algorithmic or image processing solutions ● Constructed various machine learning and deep learning pipelines for CAD, OAR segmentation, lesion classification, and image-to-image translation ● Developed in-house suite of 2D and 3D voxel-wise radiomic texture and kinematic features ● Lead author on 3 abstracts for synthetic CT generation for MR-only guided radiation therapy ● Coordinate with KOLs, stakeholders for investigating potential radiation oncology solutions ● Supervising 3-4 team members or interns Show less

    • United States
    • Higher Education
    • 700 & Above Employee
    • Graduate Research Assistant
      • May 2016 - Sep 2020

      During my Ph.D., I developed novel computerized methods and applications in the context of medical imaging data. My mentors were Drs. Satish Viswanath and Anant Madabhushi. I worked on a variety of projects primarily focused on predicting and evaluating treatment response in rectal cancers from in vivo multi-parametric MRI, improving personalized management of patients. My projects utilized state-of-the-art machine learning algorithms for quantitative data fusion and analysis. I also… Show more During my Ph.D., I developed novel computerized methods and applications in the context of medical imaging data. My mentors were Drs. Satish Viswanath and Anant Madabhushi. I worked on a variety of projects primarily focused on predicting and evaluating treatment response in rectal cancers from in vivo multi-parametric MRI, improving personalized management of patients. My projects utilized state-of-the-art machine learning algorithms for quantitative data fusion and analysis. I also developed my own set of novel quantitative imaging descriptors and co-registration techniques for advanced disease characterization by recognizing tissue signatures from ex vivo pathology specimens on the in vivo imaging. Thus far, key findings from my research have resulted in 2 first authors journal publications, 1 first author conference publication, and 9 presentations at national and international scientific meetings, both poster and oral presentation formats. In the course of my work, I developed and implemented software wand algorithms for various medical imaging tasks such as noise filtering, texture analysis, co-registration, classification, dimensionality reduction, pattern recognition, image visualization, and other data analysis techniques; using languages include MATLAB and R. I am also familiar with Java and C++. My position involved closely collaborating with a multi-disciplinary team of clinicians and academic researchers at University Hospitals Cleveland Medical Center, Cleveland Clinic, and Louis Stokes Veterans Affairs Medical Center. Additionally, I worked with a team of expert radiologists, radiation oncologists, surgeons, and pathologists to develop a user-friendly software package for the computer-aided risk score assessment of rectal cancer patients following treatment who may be candidates for avoiding additional surgery and the associated poor quality-of-life issues. Show less During my Ph.D., I developed novel computerized methods and applications in the context of medical imaging data. My mentors were Drs. Satish Viswanath and Anant Madabhushi. I worked on a variety of projects primarily focused on predicting and evaluating treatment response in rectal cancers from in vivo multi-parametric MRI, improving personalized management of patients. My projects utilized state-of-the-art machine learning algorithms for quantitative data fusion and analysis. I also… Show more During my Ph.D., I developed novel computerized methods and applications in the context of medical imaging data. My mentors were Drs. Satish Viswanath and Anant Madabhushi. I worked on a variety of projects primarily focused on predicting and evaluating treatment response in rectal cancers from in vivo multi-parametric MRI, improving personalized management of patients. My projects utilized state-of-the-art machine learning algorithms for quantitative data fusion and analysis. I also developed my own set of novel quantitative imaging descriptors and co-registration techniques for advanced disease characterization by recognizing tissue signatures from ex vivo pathology specimens on the in vivo imaging. Thus far, key findings from my research have resulted in 2 first authors journal publications, 1 first author conference publication, and 9 presentations at national and international scientific meetings, both poster and oral presentation formats. In the course of my work, I developed and implemented software wand algorithms for various medical imaging tasks such as noise filtering, texture analysis, co-registration, classification, dimensionality reduction, pattern recognition, image visualization, and other data analysis techniques; using languages include MATLAB and R. I am also familiar with Java and C++. My position involved closely collaborating with a multi-disciplinary team of clinicians and academic researchers at University Hospitals Cleveland Medical Center, Cleveland Clinic, and Louis Stokes Veterans Affairs Medical Center. Additionally, I worked with a team of expert radiologists, radiation oncologists, surgeons, and pathologists to develop a user-friendly software package for the computer-aided risk score assessment of rectal cancer patients following treatment who may be candidates for avoiding additional surgery and the associated poor quality-of-life issues. Show less

    • United States
    • Software Development
    • 200 - 300 Employee
    • Algorithms Development and Research Intern
      • Jun 2019 - Sep 2019

      Summer industry experience in the medical imaging field during my graduate studies. • Constructed and evaluated machine learning pipelines for identifying clinically significant prostate lesions off multi-parametric MRI, including data pre-processing, feature extraction and selection, and ML/DL models • Developed and tested in-house suite of 2D pixel-wise radiomic texture and kinematic features • Implemented XmasNET-styled CNNs for prostate lesion-wise classification in Python… Show more Summer industry experience in the medical imaging field during my graduate studies. • Constructed and evaluated machine learning pipelines for identifying clinically significant prostate lesions off multi-parametric MRI, including data pre-processing, feature extraction and selection, and ML/DL models • Developed and tested in-house suite of 2D pixel-wise radiomic texture and kinematic features • Implemented XmasNET-styled CNNs for prostate lesion-wise classification in Python, TensorFlow Show less Summer industry experience in the medical imaging field during my graduate studies. • Constructed and evaluated machine learning pipelines for identifying clinically significant prostate lesions off multi-parametric MRI, including data pre-processing, feature extraction and selection, and ML/DL models • Developed and tested in-house suite of 2D pixel-wise radiomic texture and kinematic features • Implemented XmasNET-styled CNNs for prostate lesion-wise classification in Python… Show more Summer industry experience in the medical imaging field during my graduate studies. • Constructed and evaluated machine learning pipelines for identifying clinically significant prostate lesions off multi-parametric MRI, including data pre-processing, feature extraction and selection, and ML/DL models • Developed and tested in-house suite of 2D pixel-wise radiomic texture and kinematic features • Implemented XmasNET-styled CNNs for prostate lesion-wise classification in Python, TensorFlow Show less

    • United States
    • Higher Education
    • 700 & Above Employee
    • Undergraduate Teaching Assistant
      • Aug 2014 - May 2015

      TA for the freshman course "ENGR 131: Introduction to Programming." • Instructed first-year students how to implement beginner-level programming in MATLAB • Provided additional 10 hours outside of lab reserved for helping individual students • Responsible for assessing the performance of each student

    • Undergraduate Research Assistant
      • Feb 2014 - May 2015

      Part-time research at the Center for Computational Imaging and Personalized Diagnostics (CCIPD) at Case Western Reserve University while I pursued my undergraduate degree in Biomedical Engineering. • Developed strategies for extracting quantifiable information from medical images • Investigate parameters for co-registration of 3D MRI and CT volumes • 2 conference poster presentations on PET/MRI features reflective of early treatment response for renal cell carcinoma • 1 manuscript… Show more Part-time research at the Center for Computational Imaging and Personalized Diagnostics (CCIPD) at Case Western Reserve University while I pursued my undergraduate degree in Biomedical Engineering. • Developed strategies for extracting quantifiable information from medical images • Investigate parameters for co-registration of 3D MRI and CT volumes • 2 conference poster presentations on PET/MRI features reflective of early treatment response for renal cell carcinoma • 1 manuscript on analytic framework for evaluating early treatment response using integrated PET/MRI protocols.

    • Design Projects
      • Sep 2011 - May 2015

      Fall 2014 - Spring 2015: Senior project aimed at designing a device which gives quadriplegics the ability to control navigation on a smartphone using only EMGs generated from facial muscle movement Spring 2012: Requested as a freshman by BME Department faculty to join a senior project focused on designing a new mechanical component for quick attachment and removal of a prosthetic foot at the ankle Fall 2011: Selected as a freshman through interview process by BME Department… Show more Fall 2014 - Spring 2015: Senior project aimed at designing a device which gives quadriplegics the ability to control navigation on a smartphone using only EMGs generated from facial muscle movement Spring 2012: Requested as a freshman by BME Department faculty to join a senior project focused on designing a new mechanical component for quick attachment and removal of a prosthetic foot at the ankle Fall 2011: Selected as a freshman through interview process by BME Department faculty to join a senior project focused on building and testing a mechanism to simulate lifting a paraplegic from a chair to a bed

    • Teaching Assistant
      • Aug 2013 - Dec 2013

      Instructed students how to implement programming in MATLAB. Provided additional 10 hours outside of lab reserved for helping individual students. Evaluated the performance of each student.

    • Undergraduate Laboratory Assistant
      • Nov 2012 - Dec 2013

      Conducted standard aerobic experiments with cystic fibrosis rodents. Compiled data into spreadsheets and graphs for analysis and modeling. Automated a process for characterizing mitochondrial morphology in electron microscopy images of rodent skeletal muscle using Java and ImageJ.

    • Netherlands
    • Hospitals and Health Care
    • 700 & Above Employee
    • Co-op, Physics/Software Engineer, AMI Department
      • Jan 2014 - Aug 2014

      8-month co-op opportunity with one of the world's largest medical imaging suppliers. • Created technical reports of results, led presentations of findings to engineering team managers • Segmented whole body PET images to establish ground truth in PET/MRI truncation research • Developed and tested series of scanning sequences on a new, digitized PET/CT system • Performed independent analyses on PET image quality and PET/CT alignment 8-month co-op opportunity with one of the world's largest medical imaging suppliers. • Created technical reports of results, led presentations of findings to engineering team managers • Segmented whole body PET images to establish ground truth in PET/MRI truncation research • Developed and tested series of scanning sequences on a new, digitized PET/CT system • Performed independent analyses on PET image quality and PET/CT alignment

    • United States
    • Restaurants
    • 700 & Above Employee
    • Crew Member
      • Jun 2013 - Aug 2013

      Summer college job enjoying making some great food! • Efficiently prepared, cooked,and served all-natural food while providing a friendly and energetic atmosphere • Actively motivated employees around me in a fast-paced, high-stress environment. Summer college job enjoying making some great food! • Efficiently prepared, cooked,and served all-natural food while providing a friendly and energetic atmosphere • Actively motivated employees around me in a fast-paced, high-stress environment.

    • IT Services and IT Consulting
    • 1 - 100 Employee
    • Intern, Audio-visual Technician
      • May 2012 - Aug 2012

      Summer working for a private technology firm specializing in the design and installation of audio-visual networks. • Installed software, set IP addresses, and tested audio-visual equipment • Wired audio-visual technology racks and carts for 30 college classrooms • Deployed cable networks in corporate buildings Summer working for a private technology firm specializing in the design and installation of audio-visual networks. • Installed software, set IP addresses, and tested audio-visual equipment • Wired audio-visual technology racks and carts for 30 college classrooms • Deployed cable networks in corporate buildings

    • United States
    • Food and Beverage Services
    • 500 - 600 Employee
    • Production
      • Apr 2011 - May 2012

      First job, summer after graduating high school • Drive-thru, Kitchen, Cashier • Successfully provided friendly and timely customer service while working multiple positions First job, summer after graduating high school • Drive-thru, Kitchen, Cashier • Successfully provided friendly and timely customer service while working multiple positions

Education

  • Case Western Reserve University
    Ph.D., Biomedical Engineering
    2016 - 2020
  • Case Western Reserve University
    M.S., Biomedical Engineering
    2014 - 2016
  • Case Western Reserve University
    B.S., Biomedical Engineering- Computing and Analysis
    2011 - 2015
  • Turpin High School
    2007 - 2011

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