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Kevin Arvai
Washington, United States
I am a data scientist with experience in clinical genomics. I am also a Python enthusiast and an open-source advocate. My ambition is to create software that leverages data to improve human health. Experience: Creating machine learning models with scikit-learn and deep learning models using Keras and TensorFlow. Delivering natural language processing solutions for named entity recognition. Collaborating on software projects using git for version control. Optimizing algorithms on high-performance computing platforms. Python, R, Perl, SQL, shell scripting, and cloud computing. Personal: I developed and currently maintain Imputer, an open-source genome imputation application that performs genotype imputation for members of the non-profit organization, Open Humans. I am active in the open-source community, frequently developing and contributing to open-source repositories on GitHub. Occasionally I compete in machine learning challenges or write kernels on Kaggle (https://www.kaggle.com/kevinarvai/kernels). I also enjoy participating in hackathons and local coding meetups.
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List your work history, including any contracts or internships
DataRobot Full-time
Jan 2021 - Jun 2021 (5 months)
Senior Data Scientist, Team Lead
GeneDx
5 years 9 months
Senior Data Scientist
Apr 2018 - Jan 2021 (2 years 9 months)
Developed software to assess the semantic similarity between two or more sets of phenotypes.
https://github.com/genedx/phenopy
Significantly reduced the amount of time genetic counselors spend abstracting patient phenotypes from pdfs by implementing named entity recognition with natural language processing tools.
Developed a calculator that determines the classification of genetic variants given a list of ACMG criteria.
Serve as an internal resource for data preprocessing and feature engineering techniques.
https://github.com/genedx/phenopy
Significantly reduced the amount of time genetic counselors spend abstracting patient phenotypes from pdfs by implementing named entity recognition with natural language processing tools.
Developed a calculator that determines the classification of genetic variants given a list of ACMG criteria.
Serve as an internal resource for data preprocessing and feature engineering techniques.
Scientist
Apr 2015 - Apr 2018 (3 years)
Develop and implement machine learning models to support decision making for next-generation sequencing (NGS) assays. Models include gene prioritization in clinical exomes, NGS quality control improvements and natural language processing for named entity recognition.
Performed study design, programming and analysis for genetic association studies from hereditary cancer multi-gene panel testing assays.
Created semantic similarity algorithms that compare phenotypic similarity between cases, diseases, and genes using phenotype terms from the Human Phenotype Ontology.
Validate new bioinformatics software and, when necessary, integrate them into existing pipelines.
Performed study design, programming and analysis for genetic association studies from hereditary cancer multi-gene panel testing assays.
Created semantic similarity algorithms that compare phenotypic similarity between cases, diseases, and genes using phenotype terms from the Human Phenotype Ontology.
Validate new bioinformatics software and, when necessary, integrate them into existing pipelines.
Quest Diagnostics
6 years 3 months
Scientist
Jan 2012 - Apr 2015 (3 years 3 months)
Member of a small research and development team focused on designing new molecular diagnostic assays for the clinical anatomic pathology laboratory. Principle investigator on a study that led to publication. The publication describes the role of stem cells and cancer pathways on tumor progression in colorectal cancer. Methods included in the study were immunohistochemistry, fluorescent in-situ hybridization, oligo-snp arrays and NGS. Developed bioinformatics workflows for hematopoietic and solid tumor NGS assays. Validated clinical NGS mutation-calling pipeline with current open-source software tools. Investigated the role of somatic mutations in hematopoietic disorders using multi-gene NGS panels.
Histotechnologist
Jun 2011 - Jan 2012 (7 months)
Performed quality control by microscopic examination of immunohistochemical tissue slides in a high-throughput setting.
Validated and optimized new antibodies on multiple automated staining platforms. Company-wide validation of a new, automated staining platform.
Validated and optimized new antibodies on multiple automated staining platforms. Company-wide validation of a new, automated staining platform.
Lab Associate III
Jan 2009 - Jun 2011 (2 years 5 months)
Worked closely with pathologists and clinical directors to validate immunohistochemistry and fluorescent in-situ hybridization image analysis algorithms.
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