A Bayesian adaptive marker‐stratified design for molecularly targeted agents with customized hierarchical modeling

It is well known that the treatment effect of a molecularly targeted agent (MTA) may vary dramatically, depending on each patient's biomarker profile. Therefore, for a clinical trial evaluating MTA, it is more reasonable to evaluate its treatment effect within different marker subgroups rather than evaluating the average treatment effect for the overall population. The marker‐stratified design (MSD) provides a useful tool to evaluate the subgroup treatment effects of MTAs. Under the Bayesian framework, the beta‐binomial model is conventionally used under the MSD to estimate the response rate and test the hypothesis. However, this conventional model ignores the fact that the biomarker used in the MSD is, in general, predictive only for the MTA. The response rates for the standard treatment can be approximately consistent across different subgroups stratified by the biomarker. In this paper, we proposed a Bayesian hierarchical model incorporating this biomarker information into consideration. The proposed model uses a hierarchical prior to borrow strength across different subgroups of patients receiving the standard treatment and, therefore, improve the efficiency of the design. Prior informativeness is determined by solving a “customized” equation reflecting the physician's professional opinion. We developed a Bayesian adaptive design based on the proposed hierarchical model to guide the treatment allocation and test the subgroup treatment effect as well as the predictive marker effect. Simulation studies and a real trial application demonstrate that the proposed design yields desirable operating characteristics and outperforms the existing designs

A clustering linear combination method for multiple phenotype association studies based on GWAS summary statistics

There is strong evidence showing that joint analysis of multiple phenotypes in genome-wide association studies (GWAS) can increase statistical power when detecting the association between genetic variants and human complex diseases. We previously developed the Clustering Linear Combination (CLC) method and a computationally efficient CLC (ceCLC) method to test the association between multiple phenotypes and a genetic variant, which perform very well. However, both of these methods require individual-level genotypes and phenotypes that are often not easily accessible. In this research, we develop a novel method called sCLC for association studies of multiple phenotypes and a genetic variant based on GWAS summary statistics. We use the LD score regression to estimate the correlation matrix among phenotypes. The test statistic of sCLC is constructed by GWAS summary statistics and has an approximate Cauchy distribution. We perform a variety of simulation studies and compare sCLC with other commonly used methods for multiple phenotype association studies using GWAS summary statistics. Simulation results show that sCLC can control Type I error rates well and has the highest power in most scenarios. Moreover, we apply the newly developed method to the UK Biobank GWAS summary statistics from the XIII category with 70 related musculoskeletal system and connective tissue phenotypes. The results demonstrate that sCLC detects the most number of significant SNPs, and most of these identified SNPs can be matched to genes that have been reported in the GWAS catalog to be associated with those phenotypes. Furthermore, sCLC also identifies some novel signals that were missed by standard GWAS, which provide new insight into the potential genetic factors of the musculoskeletal system and connective tissue phenotypes

Physical Deep Reinforcement Learning Towards Safety Guarantee

Deep reinforcement learning (DRL) has achieved tremendous success in many complex decision-making tasks of autonomous systems with high-dimensional state and/or action spaces. However, the safety and stability still remain major concerns that hinder the applications of DRL to safety-critical autonomous systems. To address the concerns, we proposed the Phy-DRL: a physical deep reinforcement learning framework. The Phy-DRL is novel in two architectural designs: i) Lyapunov-like reward, and ii) residual control (i.e., integration of physics-model-based control and data-driven control). The concurrent physical reward and residual control empower the Phy-DRL the (mathematically) provable safety and stability guarantees. Through experiments on the inverted pendulum, we show that the Phy-DRL features guaranteed safety and stability and enhanced robustness, while offering remarkably accelerated training and enlarged reward.Comment: Working Pape

A direct unified wave-particle method for simulating non-equilibrium flows

In this work, the Navier-Stokes (NS) solver is combined with the Direct simulation Monte Carlo (DSMC) solver in a direct way, under the wave-particle formulation [J. Comput. Phys. 401, 108977 (2020)]. Different from the classical domain decomposition method with buffer zone for overlap, in the proposed direct unified wave-particle (DUWP) method, the NS solver is coupled with DSMC solver on the level of algorithm. Automatically, in the rarefied flow regime, the DSMC solver leads the simulation, while the NS solver leads the continuum flow simulation. Thus advantages of accuracy and efficiency are both taken. At internal flow regimes, like the transition flow regime, the method is accurate as well because a kind of mesoscopic modeling is proposed in this work, which gives the DUWP method the multi-scale property. Specifically, as to the collision process, at $t < \tau$, it is supposed that only single collision happens, and the collision term of DSMC is just used. At $t > \tau$, it is derived that $1-\tau/\Delta t$ of particles should experience multiple collisions, which will be absorbed into the wave part and calculated by the NS solver. Then the DSMC and NS solver can be coupled in a direct and simple way, bringing about multi-scale property. The governing equation is derived and named as multi-scale Boltzmann equation. Different from the original wave-particle method, in the proposed DUWP method, the wave-particle formulation is no more restricted by the Boltzmann-BGK type model and the enormous research findings of DSMC and NS solvers can be utilized into much more complicated flows, like the thermochemical non-equilibrium flow. In this work, one-dimensional cases in monatomic argon gas are preliminarily tested, such as shock structures and Sod shock tubes

Gene-based association tests using GWAS summary statistics and incorporating eQTL

Although genome-wide association studies (GWAS) have been successfully applied to a variety of complex diseases and identified many genetic variants underlying complex diseases via single marker tests, there is still a considerable heritability of complex diseases that could not be explained by GWAS. One alternative approach to overcome the missing heritability caused by genetic heterogeneity is gene-based analysis, which considers the aggregate effects of multiple genetic variants in a single test. Another alternative approach is transcriptome-wide association study (TWAS). TWAS aggregates genomic information into functionally relevant units that map to genes and their expression. TWAS is not only powerful, but can also increase the interpretability in biological mechanisms of identified trait associated genes. In this study, we propose a powerful and computationally efficient gene-based association test, called Overall. Using extended Simes procedure, Overall aggregates information from three types of traditional gene-based association tests and also incorporates expression quantitative trait locus (eQTL) information into a gene-based association test using GWAS summary statistics. We show that after a small number of replications to estimate the correlation among the integrated gene-based tests, the p values of Overall can be calculated analytically. Simulation studies show that Overall can control type I error rates very well and has higher power than the tests that we compared with. We also apply Overall to two schizophrenia GWAS summary datasets and two lipids GWAS summary datasets. The results show that this newly developed method can identify more significant genes than other methods we compared with

Dynamic update of shortest path tree in OSPF

2003-2004 > Academic research: refereed > Refereed conference paperVersion of RecordPublishe

Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name

It has been observed that both cancer tissue cells and normal proliferating cells (NPCs) have the Warburg effect. Our goal here is to demonstrate that they do this for different reasons. To accomplish this, we have analyzed the transcriptomic data of over 7000 cancer and control tissues of 14 cancer types in TCGA and data of five NPC types in GEO. Our analyses reveal that NPCs accumulate large quantities of ATPs produced by the respiration process before starting the Warburg effect, to raise the intracellular pH from ∼6.8 to ∼7.2 and to prepare for cell division energetically. Once cell cycle starts, the cells start to rely on glycolysis for ATP generation followed by ATP hydrolysis and lactic acid release, to maintain the elevated intracellular pH as needed by cell division since together the three processes are pH neutral. The cells go back to the normal respiration-based ATP production once the cell division phase ends. In comparison, cancer cells have reached their intracellular pH at ∼7.4 from top down as multiple acid-loading transporters are up-regulated and most acid-extruding ones except for lactic acid exporters are repressed. Cancer cells use continuous glycolysis for ATP production as way to acidify the intracellular space since the lactic acid secretion is decoupled from glycolysis-based ATP generation and is pH balanced by increased expressions of acid-loading transporters. Co-expression analyses suggest that lactic acid secretion is regulated by external, non-pH related signals. Overall, our data strongly suggest that the two cell types have the Warburg effect for very different reasons