{"id":1154,"date":"2023-03-30T12:29:17","date_gmt":"2023-03-30T12:29:17","guid":{"rendered":"https:\/\/amirsafavi.com\/?page_id=1154"},"modified":"2023-08-14T20:53:42","modified_gmt":"2023-08-14T20:53:42","slug":"research-projects","status":"publish","type":"page","link":"https:\/\/amirsafavi.com\/index.php\/my-background-experience\/research-projects\/","title":{"rendered":"Research Projects"},"content":{"rendered":"\t\t
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Brief Description of My Past and Current Projects<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t
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As part of my MD thesis, I started my first research in 2017 on time series analysis of\u00a0<\/span>the national cancer<\/strong><\/span>\u00a0registry<\/strong><\/span> database. As COVID-19 emerged, I was assigned to coordinate the “<\/span>Tehran COVID-19 Cohort<\/strong><\/span>“, during which I started coding in Python and Visual Basic. In 2019 I co-founded a\u00a0<\/span>start-up<\/span><\/a>\u00a0aimed at developing CAD systems in CXRs. In 2021 our business plan failed, and I joined a medical imaging company as an R&D associate. After graduation in 2021, my research fellowship started on a joint project between\u00a0<\/span>Research Institute for Gastroenterology and Liver Diseases<\/span><\/em>\u00a0&\u00a0<\/span>Bioinformatics and Computational Biology Laboratory<\/span><\/em>. My main project aims to develop a multi-purpose ML model for pancreas cancer<\/span> imaging. I initiated two side projects on capsule endoscopy<\/span> and 3D visualization of the perianal fistula<\/span>. I also participated in other projects if they attracted my attention, could boost my skills, or were interesting to my mentees.<\/span><\/p>

During all these projects, I mentored 12 junior students as a peer mentor, of which I am deeply proud. I also gave lectures on “Introduction to ML Logic,” “Research Methodology,” “Visualization in Research Paper,” “Vision, Long-Term Goals, Daily Tasks,” and “From Medical Problem to ML Tasks” at the Shahid Beheshti University of Science and Tehran University of Medical Science as a teaching assistant or workshop lecturer.<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t

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Perianal fistula is an ancient health problem and high failure in treatment. In the first step, we visualized the path of the fistula using 3D reconstruction of manually segmented perianal fistula in MRI images and generated a reporting manual. In the next stage, we perform RCT on the effectiveness of 3D visualization to decrease the surgery and surgeon evaluation time. At last, we will try ML models such as EfficientNetV2 and ResNet to examine automated segmentation of the perianal fistula and anal sphincters.<\/span><\/p>

My Supervisors: Dr. Khorsanizadeh (MD, Radiologist) and Prof. Keshvari (Colorectal Surgeon)<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t

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This image is from the article by Saraiva et al. (http:\/\/dx.doi.org\/10.1136\/bmjgast-2021-000753)<\/figcaption>\n\t\t\t\t\t\t\t\t\t\t<\/figure>\n\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t
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A capsule endoscopy of 260 patients were collected. We aim to develop ML model to detect anatomic region and abnormal lesions.\u00a0<\/p>

My Supervisors: Dr. Shabnam Shahrokh (MD, Gastroenterologist)<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t

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Pancreas cancer is among deadliest cancers. As my interest for pancreas cancer early detection growed, I proposed my title to start an joint project between four universities. I collected CT scan of pathologically confirmed PDAC and PNET cancers. We get them segmented by two radiologists, and then a follow-up call was made to find 1-year survival. Seven projects were defined on the dataset, and the protocol of this study is under review in PLOS journal.<\/p>\n

My ultimate goal is to deploy these models, and get them freely available for all patients. <\/p>\n

My Supervisors: Prof. Hamid Assadzadeh (MD-PhD, Gastroenterologist), and Prof. Mohammad Reza Zali (MD-ACG-AGA Gastroenterologist).<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t

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As a coordinator of “Tehran COVID-19 Cohort” I managed 20 collaborators from 5 medical centers. After data collection, I examined the quality, cleaned the data, and get it ready for analysis. The dataset currently consist 10,000 COVID-19 inpatients, and 1-year follow-up data of 1000 patients. We belive in Open Science, and the data will be published for public use on March 2023 (Scientific Data). This pictures is from our project for developing an generalizable ML model to predict prognosis of COVID-19. We tried to implement it in collaborator hospitals, which we failed.<\/p>

My Supervisor: Prof. Mohammad Amin Pourhoseingholi (PhD Biostatistics)<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t

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As my thesis, I handled national cancer registry data. I used pairwise comparison using JointPoint Software to compare HPV-related and HPV-unrelated oral cancers.<\/p>

My Supervisor: Dr. Ali Safavi (MD, ENT)<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t

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Brief Description of My Past and Current Projects As part of my MD thesis, I started my first research in 2017 on time series analysis of\u00a0the national cancer\u00a0registry database. As COVID-19 emerged, I was assigned to coordinate the “Tehran COVID-19 Cohort“, during which I started coding in Python and Visual Basic. In 2019 I co-founded […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":1080,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1154","page","type-page","status-publish","hentry","entry"],"_links":{"self":[{"href":"https:\/\/amirsafavi.com\/index.php\/wp-json\/wp\/v2\/pages\/1154","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/amirsafavi.com\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/amirsafavi.com\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/amirsafavi.com\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/amirsafavi.com\/index.php\/wp-json\/wp\/v2\/comments?post=1154"}],"version-history":[{"count":11,"href":"https:\/\/amirsafavi.com\/index.php\/wp-json\/wp\/v2\/pages\/1154\/revisions"}],"predecessor-version":[{"id":1485,"href":"https:\/\/amirsafavi.com\/index.php\/wp-json\/wp\/v2\/pages\/1154\/revisions\/1485"}],"up":[{"embeddable":true,"href":"https:\/\/amirsafavi.com\/index.php\/wp-json\/wp\/v2\/pages\/1080"}],"wp:attachment":[{"href":"https:\/\/amirsafavi.com\/index.php\/wp-json\/wp\/v2\/media?parent=1154"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}