arXiv subjects

Stephen A. Ramsey

Publications and source records attributed to Stephen A. Ramsey.

4 recordsLinked to original sources

arXiv2022

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the interconnectedness between core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these "knowledge graphs" (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally-accepted, open-access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object-oriented classification and graph-oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates), representing biomedical entities such as gene, disease, chemical, anatomical structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

cs.DB↗

arXiv2021

Structural Generalizability: The Case of Similarity Search

Graph similarity search algorithms usually leverage the structural properties of a database. Hence, these algorithms are effective only on some structural variations of the data and are ineffective on other forms, which makes them hard to use. Ideally, one would like to design a data analytics algorithm that is structurally robust, i.e., it returns essentially the same accurate results over all possible structural variations of a dataset. We propose a novel approach to create a structurally robust similarity search algorithm over graph databases. We leverage the classic insight in the database literature that schematic variations are caused by having constraints in the database. We then present RelSim algorithm which is provably structurally robust under these variations. Our empirical studies show that our proposed algorithms are structurally robust while being efficient and as effective as or more effective than the state-of-the-art similarity search algorithms.

cs.DB↗

arXiv2002

Nonequilibrium dynamics of quantum fields in inflationary cosmology

The nonequilibrium dynamics of quantum fields is studied in inflationary cosmology, with particular emphasis on applications to the problem of post-inflation reheating. The Schwinger-Keldysh closed-time-path (CTP) formalism is utilized along with the two-particle-irreducible (2PI) effective action in order to obtain coupled, nonperturbative equations for the mean field and variance in a general curved background spacetime. For a model consisting of a quartically self-interacting O(N) field theory (with unbroken symmetry) in spatially flat FRW spacetime, the dynamics of the mean field is studied numerically, at leading order in the large-N expansion. The time evolution of the scale factor is determined self-consistently using the semiclassical Einstein equation. It is found that cosmic expansion can dramatically affect the efficiency of parametric resonance-induced particle production. The production of fermions due to the oscillating inflaton mean field is studied for the case of a scalar inflaton coupled to a fermion field via a Yukawa coupling $f$. The dissipation and noise kernels appearing at $O(f^2)$ in the one-loop CTP effective action are shown to satisfy a zero-temperature fluctuation-dissipation relation (FDR). The effective stochastic equation obeyed by the inflaton zero mode at $O(f^4)$ contains multiplicative noise. It is shown that stochasticity becomes important to the dynamics of the inflaton zero mode before the end of reheating. The thermalization problem is discussed, and a strategy is presented for obtaining time-local equations for equal-time correlation functions which goes beyond the Hartree-Fock approximation.

gr-qc↗

arXiv1999

One-loop $λϕ^4$ theory in Robertson-Walker spacetimes: adiabatic regularization and analytic approximation

The renormalization of a scalar field theory with a quartic self-coupling (a $λϕ^4$ theory) via adiabatic regularization in a general Robertson-Walker spacetime is discussed. The adiabatic counterterms are presented in a way that is most conducive to numerical computations. A variation of the adiabatic regularization method is presented which leads to analytic approximations for the energy-momentum tensor of the field and the quantum contribution to the effective mass of the mean field. Conservation of the energy-momentum tensor for the field is discussed and it is shown that the part of the energy-momentum tensor which depends only on the mean field is not conserved but the full renormalized energy-momentum tensor is conserved as expected and required by the semiclassical Einstein's equation. It is also shown that if the analytic approximations are used then the resulting approximate energy-momentum tensor is conserved. This allows a self-consistent backreaction calculation to be performed using the analytic approximations. The usefulness of the approximations is discussed.

gr-qc↗