title: Probability state modeling theory.
abstract: As the technology of cytometry matures, there is mounting pressure to address two major issues with data analyses. The first issue is to develop new analysis methods for high-dimensional data that can directly reveal and quantify important characteristics associated with complex cellular biology. The other issue is to replace subjective and inaccurate gating with automated methods that objectively define subpopulations and account for population overlap due to measurement uncertainty. Probability state modeling (PSM) is a technique that addresses both of these issues. The theory and important algorithms associated with PSM are presented along with simple examples and general strategies for autonomous analyses. PSM is leveraged to better understand B-cell ontogeny in bone marrow in a companion Cytometry Part B manuscript. Three short relevant videos are available in the online supporting information for both of these papers. PSM avoids the dimensionality barrier normally associated with high-dimensionality modeling by using broadened quantile functions instead of frequency functions to represent the modulation of cellular epitopes as cells differentiate. Since modeling programs ultimately minimize or maximize one or more objective functions, they are particularly amenable to automation and, therefore, represent a viable alternative to subjective and inaccurate gating approaches.
authors.affiliation: Verity Software House, Topsham, Maine.
authors.forename: C Bruce
authors.initials: CB
authors.lastname: Bagwell
authors.affiliation: Verity Software House, Topsham, Maine.
authors.forename: Benjamin C
authors.initials: BC
authors.lastname: Hunsberger
authors.affiliation: Verity Software House, Topsham, Maine.
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Herbert
authors.affiliation: Verity Software House, Topsham, Maine.
authors.forename: Mark E
authors.initials: ME
authors.lastname: Munson
authors.affiliation: Verity Software House, Topsham, Maine.
authors.forename: Beth L
authors.initials: BL
authors.lastname: Hill
authors.affiliation: Verity Software House, Topsham, Maine.
authors.forename: Chris M
authors.initials: CM
authors.lastname: Bray
authors.affiliation: Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, 02114.
authors.forename: Frederic I
authors.initials: FI
authors.lastname: Preffer
mesh_terms: D000465:Algorithms; D001402:B-Lymphocytes / Q000166:cytology*; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D005434:Flow Cytometry / Q000379:methods*; D006801:Humans; D008962:Models, Theoretical; D011336:Probability; D013601:T-Lymphocytes / Q000166:cytology*
keywords: broadened quantile function modeling; cytometry; high-dimensional modeling; high-dimensional visualization; polychromatic