Jacob Antunes
Senior Research Scientist at MIM Software Inc.- Claim this Profile
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Topline Score
Bio
Experience
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MIM Software
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United States
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Software Development
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200 - 300 Employee
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Senior Research Scientist
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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
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Case Western Reserve University
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United States
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Higher Education
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700 & Above Employee
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Graduate Research Assistant
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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
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MIM Software
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United States
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Software Development
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200 - 300 Employee
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Algorithms Development and Research Intern
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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
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Case Western Reserve University
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United States
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Higher Education
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700 & Above Employee
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Undergraduate Teaching Assistant
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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
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Undergraduate Research Assistant
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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.
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Design Projects
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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
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Teaching Assistant
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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.
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Undergraduate Laboratory Assistant
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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.
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Philips
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Netherlands
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Hospitals and Health Care
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700 & Above Employee
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Co-op, Physics/Software Engineer, AMI Department
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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
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Chipotle Mexican Grill
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United States
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Restaurants
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700 & Above Employee
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Crew Member
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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.
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Premier Network Solutions
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IT Services and IT Consulting
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1 - 100 Employee
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Intern, Audio-visual Technician
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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
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Skyline Chili
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United States
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Food and Beverage Services
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500 - 600 Employee
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Production
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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
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Education
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Case Western Reserve University
Ph.D., Biomedical Engineering -
Case Western Reserve University
M.S., Biomedical Engineering -
Case Western Reserve University
B.S., Biomedical Engineering- Computing and Analysis -
Turpin High School