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genetics, genomics, opioid, machine learning, artificial intelligence, evolution, QTL, eQTL, NLP
United States

Biography

I am currently a project scientist at Cedars-Sinai Medical Center in Lost Angeles, CA. My research aims to identify risk factors of complex human diseases and poor clinical outcomes, with a primary focus on opioid use disorder (OUD) by identifying multilevel (individual, social, genetic, epigenetic, transcriptomic, clinical, and environmental) predictors using machine learning (ML) and artificial intelligence (AI). OUD and problematic opioid use have been shown to be associated with a host of other poor clinical outcomes. Thus, the identification of causative factors of OUD and problematic opioid use can assist in the development of risk assessment protocols and tools that can inform patients and clinicians of potential consequences of undergoing surgery or other medical procedures. To this end, I make extensive use of clinical notes, electronic health record (EHR) data, demographic information, societal data (including biometric and social media), and omics data to accurately predict poor clinical outcomes (including OUD) and identify predictors not usually captured using standard inference-based statistical approaches by employing various AI techniques including automated machine learning and natural language processing. I aim to create comprehensive patient profiles by combining diverse sources of available data to identify new dimensions of risk so accurate and broadly applicable risk assessment tools can be developed and applied to many diagnoses and medical procedures. My primary research goal is to reduce incidences of poor clinical outcomes to limit their adverse impacts on patients, families, and society.

Alongside my interests in predictive/precision medicine, I am currently engaged in the active development of automated machine learning techniques aimed at establishing associations between genotypes and phenotypes, as well as identifying sources of non-additive genetic variation, such as epistasis.

Activities

Employment (4)

Cedars-Sinai Medical Center: Los Angeles, California, US

2022-01-07 to present | Postdoctoral Scientist (Computational Biomedicine)
Employment
Source: Self-asserted source
Philip J. Freda

University of Pennsylvania: Philadelphia, PA, US

2019-05-01 to 2022-01-16 | Postdoctoral Researcher (Biostatistics, Epidemiology, and Informatics)
Employment
Source: Self-asserted source
Philip J. Freda

Kansas State University: Manhattan, KS, US

2014-08-01 to 2018-12-21 | Ph.D. Candidate (Entomology)
Employment
Source: Self-asserted source
Philip J. Freda

Saint Joseph's University: Philadelphia, PA, US

2010-08-15 to 2014-05-15 | Graduate Student (Biology)
Employment
Source: Self-asserted source
Philip J. Freda

Education and qualifications (4)

Kansas State University: Manhattan, KS, US

2014-08 to 2018-12 | Ph.D. (Entomology)
Education
Source: Self-asserted source
Philip J. Freda

Saint Joseph's University: Philadelphia, PA, US

2012-08 to 2014-05 | M.S. (Biology)
Education
Source: Self-asserted source
Philip J. Freda

Pennsylvania State University: State College, Pennsylvania, US

2001-08 to 2005-12 | B.S. (Administration of Justice)
Education
Source: Self-asserted source
Philip J. Freda

Pennsylvania State University: State College, Pennsylvania, US

2001 to 2005 | Minor (Sociology)
Education
Source: Self-asserted source
Philip J. Freda

Professional activities (4)

Golden Key International Honour Society: Atlanta, GA, US

2016 to present | Member
Membership
Source: Self-asserted source
Philip J. Freda

Alpha Epsilon Lambda: LaBelle, FL, US

2014 to present | Lifetime Member (Graduate Students Honor Society)
Membership
Source: Self-asserted source
Philip J. Freda

Sigma Xi: Durham, North Carolina, US

2012-08 to 2018-12 | Associate Member
Membership
Source: Self-asserted source
Philip J. Freda

Saint Joseph's University: Philadelphia, PA, US

2014-05 | Biology Graduate Award (Biology)
Distinction
Source: Self-asserted source
Philip J. Freda

Funding (11)

Ruth L. Kirschstein Institutional National Research Service Award

2018-05 to 2020-05 | Grant
National Institutes of Health (Md., Md., US)
GRANT_NUMBER: HG009495
Source: Self-asserted source
Philip J. Freda

Kansas State University, Department of Entomology, Travel Award

2017 to 2017 | Award
Kansas State University (KS, KS, US)
GRANT_NUMBER:

3

Source: Self-asserted source
Philip J. Freda

Roger C. Smith Ph.D. Award in Entomology

2017 to 2017 | Award
Kansas State University (KS, KS, US)
GRANT_NUMBER: 2
Source: Self-asserted source
Philip J. Freda

Don C. Warren Genetics Scholarship

2016 to 2017 | Award
Kansas State University (KS, KS, US)
GRANT_NUMBER: 6
Source: Self-asserted source
Philip J. Freda

Kansas State University, Department of Entomology, Travel Award

2016 to 2016 | Award
Kansas State University (KS, KS, US)
GRANT_NUMBER:

4

Source: Self-asserted source
Philip J. Freda

Grants-in-aid-of-research (GIAR)

2015 to 2015 | Grant
Sigma Xi (NC, NC, US)
GRANT_NUMBER: 7
Source: Self-asserted source
Philip J. Freda

Reginald H. Painter Memorial Scholarship

2015 to 2015 | Award
Kansas State University (KS, KS, US)
GRANT_NUMBER:

5

Source: Self-asserted source
Philip J. Freda

Timothy R. Donoghue Graduate Scholarship

2014 to 2017 | Award
Kansas State University (KS, KS, US)
GRANT_NUMBER: 1
Source: Self-asserted source
Philip J. Freda

American Genetics Association - Ecological Genomics Travel Fellowship

2014 to 2014 | Award
American Genetics Association (South Beach, OR, US)
GRANT_NUMBER:

8

Source: Self-asserted source
Philip J. Freda

HHMI GK-12 Fellowship

2012 to 2014 | Grant
Howard Hughes Medical Institute (Md., Md., US)
GRANT_NUMBER:

10

Source: Self-asserted source
Philip J. Freda

HHMI Graduate Assistantship

2012 to 2014 | Grant
Howard Hughes Medical Institute (Md., Md., US)
GRANT_NUMBER:

9

Source: Self-asserted source
Philip J. Freda

Works (24)

Distinct network patterns emerge from Cartesian and XOR epistasis models: a comparative network science analysis

BioData Mining
2024-12-28 | Journal article
Part of ISSN: 1756-0381
Contributors: Zhendong Sha; Philip J. Freda; Priyanka Bhandary; Attri Ghosh; Nicholas Matsumoto; Jason H. Moore; Ting Hu
Source: Self-asserted source
Philip J. Freda

PAGER: A novel genotype encoding strategy for modeling deviations from additivity in complex trait association studies

BioData Mining
2024-10-11 | Journal article
Part of ISSN: 1756-0381
Contributors: Philip J. Freda; Attri Ghosh; Priyanka Bhandary; Nicholas Matsumoto; Apurva S. Chitre; Jiayan Zhou; Molly A. Hall; Abraham A. Palmer; Tayo Obafemi-Ajayi; Jason H. Moore
Source: Self-asserted source
Philip J. Freda

Realizing the potential of social determinants data in EHR systems: A scoping review of approaches for screening, linkage, extraction, analysis, and interventions

Journal of Clinical and Translational Science
2024-10-10 | Journal article | Writing - review & editing
Part of ISSN: 2059-8661
Contributors: Chenyu Li; Danielle Mowery; Xiaomeng Ma; RUI YANG; Ugurcan Vurgun; Sy Hwang; Hayoung Kim Donnelly; Harsh Bandhey; Yalini Senathirajah; Shyam Visweswaran et al.
Source: Self-asserted source
Philip J. Freda

Assessing the limitations of relief-based algorithms in detecting higher-order interactions.

BioData mining
2024-10-01 | Journal article
Contributors: Freda PJ; Ye S; Zhang R; Moore JH; Urbanowicz RJ
Source: Self-asserted source
Philip J. Freda

Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis

BioData Mining
2024-02-28 | Journal article
Part of ISSN: 1756-0381
Contributors: Sandra Batista; Vered Senderovich Madar; Philip J. Freda; Priyanka Bhandary; Attri Ghosh; Nicholas Matsumoto; Apurva S. Chitre; Abraham A. Palmer; Jason H. Moore
Source: Self-asserted source
Philip J. Freda

Realizing the Potential of Social Determinants Data: A Scoping Review of Approaches for Screening, Linkage, Extraction, Analysis and Interventions

2024-02-05 | Preprint
Contributors: Chenyu Li; Danielle L Mowery; Xiaomeng Ma; Rui Yang; Hayoung K Donnelly; Sy Hwang; Ugurcan Vurgun; Zohaib Akhtar; Harsh Bandhey; Phillip J Freda et al.
Source: check_circle
Crossref

Developing a Framework to Infer Opioid Use Disorder Severity From Clinical Notes to Inform Natural Language Processing Methods: Characterization Study

JMIR Mental Health
2024-01-15 | Journal article
Contributors: Melissa N Poulsen; Philip J Freda; Vanessa Troiani; Danielle L Mowery
Source: check_circle
Crossref

Cluster Analysis reveals Socioeconomic Disparities among Elective Spine Surgery Patients

Biocomputing 2024
2023-12 | Conference paper
Contributors: Alena Orlenko; Philip J. Freda; Attri Ghosh; Hyunjun Choi; Nicholas Matsumoto; Tiffani J. Bright; Corey T. Walker; Tayo Obafemi-Ajayi; Jason H. Moore
Source: Self-asserted source
Philip J. Freda

Developing a Framework to Infer Opioid Use Disorder Severity From Clinical Notes to Inform Natural Language Processing Methods: Characterization Study (Preprint)

2023-10-06 | Preprint
Contributors: Melissa N Poulsen; Philip J Freda; Vanessa Troiani; Danielle L Mowery
Source: check_circle
Crossref

Computational framework for statistical epistasis supports XOR penetrance function in a living system

2023-05-09 | Preprint
Contributors: Sandra Batista; Vered Senderovich Madar; Philip J. Freda; Priyanka Bhandary; Attri Ghosh; Apurva S. Chitre; Abraham A. Palmer; Jason H. Moore
Source: check_circle
Crossref

Identifying Barriers to Post-Acute Care Referral and Characterizing Negative Patient Preferences Among Hospitalized Older Adults Using Natural Language Processing.

AMIA ... Annual Symposium proceedings. AMIA Symposium
2023-04-29 | Journal article
Contributors: Kennedy EE; Davoudi A; Hwang S; Freda PJ; Urbanowicz R; Bowles KH; Mowery DL
Source: Self-asserted source
Philip J. Freda

Automated quantitative trait locus analysis (AutoQTL)

BioData Mining
2023-04-10 | Journal article
Part of ISSN: 1756-0381
Contributors: Philip J. Freda; Attri Ghosh; Elizabeth Zhang; Tianhao Luo; Apurva S. Chitre; Oksana Polesskaya; Celine L. St. Pierre; Jianjun Gao; Connor D. Martin; Hao Chen et al.
Source: Self-asserted source
Philip J. Freda

Automated quantitative trait locus analysis (AutoQTL)

2023-01-15 | Preprint
Contributors: Philip J. Freda; Attri Ghosh; Elizabeth Zhang; Tianhao Luo; Apurva Chitre; Oksana Polesskaya; Celine L. St. Pierre; Jianjun Gao; Connor D. Martin; Hao Chen et al.
Source: check_circle
Crossref

Novel digital approaches to the assessment of problematic opioid use

BioData Mining
2022-12 | Journal article
Contributors: Philip J. Freda, Jr; Henry R. Kranzler; Jason H. Moore
Source: check_circle
Crossref

Transcriptomic and functional genetic evidence for distinct ecophysiological responses across complex life cycle stages

Journal of Experimental Biology
2022-06-01 | Journal article
Contributors: Philip J. Freda; Jantina Toxopeus; Edwina J. Dowle; Zainab M. Ali; Nicholas Heter; Rebekah L. Collier; Isaiah Sower; Joseph C. Tucker; Theodore J. Morgan; Gregory J. Ragland
Source: check_circle
Crossref

Classifying Characteristics of Opioid Use Disorder From Hospital Discharge Summaries Using Natural Language Processing

Frontiers in Public Health
2022-05-09 | Journal article
Part of ISSN: 2296-2565
Source: Self-asserted source
Philip J. Freda

Transcriptomic and functional genetic evidence for distinct ecophysiological responses across complex life cycle stages

2022-01-19 | Preprint
Contributors: Philip J. Freda; Jantina Toxopeus; Edwina J. Dowle; Zainab M. Ali; Nicholas Heter; Rebekah L. Lambert-Collier; Isaiah Sower; Joseph C. Tucker; Theodore J. Morgan; Gregory J. Ragland
Source: check_circle
Crossref

The phenomics and genetics of addictive and affective comorbidity in opioid use disorder.

Drug and alcohol dependence
2021-02-22 | Journal article
Source: Self-asserted source
Philip J. Freda

Stage-specific genotype-by-environment interactions for cold and heat hardiness in Drosophila melanogaster

Heredity
2019-10 | Journal article
Part of ISSN: 0018-067X
Part of ISSN: 1365-2540
Source: Self-asserted source
Philip J. Freda

Ovary Development and Cold Tolerance of the Invasive Pest Drosophila suzukii (Matsumura) in the Central Plains of Kansas, United States

Environmental Entomology
2018-08-11 | Journal article
Part of ISSN: 0046-225X
Part of ISSN: 1938-2936
Source: Self-asserted source
Philip J. Freda

Genetic Decoupling of Thermal Hardiness across Metamorphosis in Drosophila melanogaster.

Integrative and comparative biology
2017-11-01 | Journal article
Source: Self-asserted source
Philip J. Freda

Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

G3 Genes|Genomes|Genetics
2015-05-01 | Journal article
Part of ISSN: 2160-1836
Source: Self-asserted source
Philip J. Freda

Drosophila suzukii, or Spotted Wing Drosophila, Recorded in Southeastern Pennsylvania, U.S.A.

Entomological News
2013-05 | Journal article
Part of ISSN: 0013-872X
Part of ISSN: 2162-3236
Source: Self-asserted source
Philip J. Freda

An efficient, pracitical, and reliable Drosophila trap

Drosophila Information Service
2013-01 | Journal article
Source: Self-asserted source
Philip J. Freda

Peer review (5 reviews for 4 publications/grants)

Review activity for Artificial intelligence in medicine. (2)
Review activity for Computers in biology and medicine. (1)
Review activity for Genetica. (1)
Review activity for Heredity (1)