Doctor of Philosophy

dissertationMost genes in a diploid organism are thought to be expressed and regulated equally by the two parental alleles. However, a subset of genes referred to as monoallelically-expressed genes are expressed preferentially only on the maternal or paternal allele. Monoallelically-expressed genes include imprinted genes, which express either the maternal or paternal allele p referentially, as well as random monoallelic genes that choose to express one allele at random. Examples of in vivo random monoallelic genes include X-linked genes in females, immunoglobulins in B cells, clustered protocadherins, and olfactory receptors. However, these examples generally are thought to be rare in the mammalian genome and confined to a few genes that have a uniquely clustered organization in the genome. In this dissertation, new genome-wide analysis methods were developed to reveal the lands cape of epigenetic allelic effects in the mous e. Chapter 2 details the discovery of novel, noncanonical genomic imprinting effects that are enriched uniquely in the brain. Chapter 3 details the development of new genomics and statistical methods to identif y genes that express their alleles differentially in vivo through nongenetic mechanisms. This novel screening strategy was applied to reveal the landscape of epigenetic allelic effects in the mouse brain at different ages and to p rofile different tissue types. The dissertation describes the discovery of diverse forms of nongenetic differential allelic expression in mouse, macaque, and human brains, and demonstrates that these effects interact with heterozygous mutations and shape genetic architecture at the allelic and cellular level in vivo. The results challenge current thinking in the fields of genetics and epigenetic by revealing a new landscape of epigenetic allelic effects in vivo, and describe new mechanisms that may shape phenotypic variation and susceptibility to disease. Although the functions of these allelic effects are unknown, and the regulatory mechanisms involved have yet to be defined, the future of the field is discussed

Condensate wave function and elementary excitations of bosonic polar molecules: beyond the first Born approximation

We investigate the condensate wave function and elementary excitations of strongly interacting bosonic polar molecules in a harmonic trap, treating the scattering amplitude beyond the standard first Born approximation (FBA). By using an appropriate trial wave function in the variational method, effects of the leading order correction beyond the FBA have been investigated and shown to be significantly enhanced when the system is close to the phase boundary of collapse. How such leading order effect of going beyond the FBA can be observed in a realistic experiment is also discussed.Comment: 7 pages, 4 figure

Multi-Relational Contrastive Learning for Recommendation

Personalized recommender systems play a crucial role in capturing users' evolving preferences over time to provide accurate and effective recommendations on various online platforms. However, many recommendation models rely on a single type of behavior learning, which limits their ability to represent the complex relationships between users and items in real-life scenarios. In such situations, users interact with items in multiple ways, including clicking, tagging as favorite, reviewing, and purchasing. To address this issue, we propose the Relation-aware Contrastive Learning (RCL) framework, which effectively models dynamic interaction heterogeneity. The RCL model incorporates a multi-relational graph encoder that captures short-term preference heterogeneity while preserving the dedicated relation semantics for different types of user-item interactions. Moreover, we design a dynamic cross-relational memory network that enables the RCL model to capture users' long-term multi-behavior preferences and the underlying evolving cross-type behavior dependencies over time. To obtain robust and informative user representations with both commonality and diversity across multi-behavior interactions, we introduce a multi-relational contrastive learning paradigm with heterogeneous short- and long-term interest modeling. Our extensive experimental studies on several real-world datasets demonstrate the superiority of the RCL recommender system over various state-of-the-art baselines in terms of recommendation accuracy and effectiveness.Comment: This paper has been published as a full paper at RecSys 202

CP Violation and Extra Dimensions

It is shown that the new sources of CP violation can be generated in the models with more than one extra dimensions. In the supersymmetric models on the space-time $M^4\times T^2/Z_2$, where the radius moduli have auxiliary vacuum expectation values and the supersymmetry breaking is mediated by the Kaluza-Klein states of gauge supermultiplets, we analyze the gaugino masses and trilinear couplings for two scenarios and obtain that there exist relative CP violating phases among the gaugino masses and trilinear couplings.Comment: Latex, 7 page