arXiv subjects

Zhi Zhao

Publications and source records attributed to Zhi Zhao.

At least 19 recordsLinked to original sources

arXiv2026

Impedance-Guided Programmable Transmission of Localized Deformation in Modular Soft Metamaterials

Soft metamaterials provide a promising platform for robotics, biomedical devices, and flexible electronics. The localized mechanical responses by nonuniform excitation are ubiquitous in soft materials, yet their controlled transmission across assemblies remains largely overlooked in metamaterial design, which critically constrains nontrivial functionalities with end-to-end and long-range deformation transmission. Here, we introduce an impedance-guided design framework that enables programmable transmission of localized deformation in modular soft metamaterials, achieving behaviors unattainable by intuitive design. By establishing a nonlinear model considering position-dependent interactions and integrating the concept of mechanical impedance within metamaterials, we regulate assembly-level transmission solely through unit-cell topology optimization. The resulting framework enables effective synthesis of module families, allowing both homogeneous and heterogeneous assemblies to be custom-built with markedly enhanced transmission characteristics. Leveraging the highly combinatorial and extensible design space, we physically realize diverse on-demand displacement manipulation architectures, including obstacle-bypassing modular soft-metamaterial assemblies, defect-tolerant soft gripping, and embodied signal processing. Beyond deformation programming, the reconfigurability and reassemblability of these soft modules can embed electric logic signals, enabling energy-efficient and low-latency information processing through compliant-switch-controlled mechanical LED displays and wearable finger-motion-sensing controllers. Our method provides fundamental insights into localized deformation transmission in modular soft metamaterials and establishes a scalable route toward embodied-intelligence material systems, particularly for soft-metamaterial-centric actuation, sensing, and collective computing.

cs.CE↗

arXiv2026

AliyunConsoleAgent: Training Web Agents in Real-World Cloud Environments via Distillation and Reinforcement Learning

We present AliyunConsoleAgent, a web agent framework for automated documentation verification in real-world cloud consoles. Major cloud platforms encompass hundreds of products with rapid feature iteration, causing console UIs to frequently diverge from their corresponding documentation. Verifying that documented procedures accurately reflect the current console and can be executed end-to-end demands an estimated 4 million recurring inspections annually, yet manual coverage remains below 1%. While agent systems built on frontier proprietary models achieve high success rates, their prohibitive cost and data privacy constraints preclude large-scale deployment. We propose a two-stage training paradigm: supervised fine-tuning (SFT) on distilled frontier-model trajectories, followed by reinforcement learning using Group Relative Policy Optimization (GRPO) and a dual-channel outcome reward model in real cloud environments. To support large-scale RL training, we construct a high-determinism rollout system featuring Terraform-based resource pre-provisioning and LLM-driven on-demand provisioning, which effectively isolates environment noise from the training signal. We further introduce a rule-based reward evaluation protocol grounded in backend audit logs, providing objective, reward-hacking-resistant outcome judgment. Our model evolves from mechanical instruction following to autonomous decision-making with cloud console and product-specific understanding. Experiments on a challenging 278-task benchmark where the best frontier model achieves only 65.34% demonstrate that AliyunConsoleAgent-32B achieves a 63.52% mean success rate -- a 20.24 percentage-point improvement over the base model, narrowing the gap to the best frontier proprietary model to 1.82 pp (bootstrap 95% CI [-1.27, 7.39]) -- at 92% lower inference cost.

cs.AI↗

arXiv2026

PliableBVS: A flexible Bayesian variable selection method for modeling interactions with mandatory modifying variables

High-dimensional interaction models are useful for studying, for example, how a large set of variables of interest, such as gene expression or other omics features, interact with a smaller set of modifying variables, such as clinical covariates. In this context, the pliable lasso has recently been proposed as an efficient method for screening large numbers of potential interaction terms under an asymmetric weak hierarchical constraint. In this work, we extend this framework by introducing PliableBVS, a Bayesian variable selection approach that preserves the hierarchical structure of the pliable lasso while inducing sparsity through spike-and-slab priors. The proposed model combines the continuous shrinkage effect of Bayesian lasso with a hierarchical spike-and-slab prior formulation that has two layers of decision variables: one governing the inclusion of main effects and another controlling the inclusion of interaction effects which is conditional on the inclusion of the corresponding main effects. This structure enables simultaneous selection of high-dimensional main and interaction effects within a coherent probabilistic framework. In simulation studies the proposed method outperforms the original pliable lasso in identifying active main and interaction effects, reducing false discoveries, and improving prediction accuracy in most scenarios. Applications with data from a labor onset study and a preeclampsia study demonstrate that PliableBVS selects biologically meaningful features and interactions.

stat.ME↗

arXiv2026

Mixture-of-experts Wishart model for covariance matrices with an application to Cancer drug screening

Covariance matrices arise naturally in different scientific fields, including finance, genomics, and neuroscience, where they encode dependence structures and reveal essential features of complex multivariate systems. In this work, we introduce a comprehensive Bayesian framework for analyzing heterogeneous covariance data through both classical mixture models and a novel mixture-of-experts Wishart (MoE-Wishart) model. The proposed MoE-Wishart model extends standard Wishart mixtures by allowing mixture weights to depend on predictors through a multinomial logistic gating network. This formulation enables the model to capture complex, nonlinear heterogeneity in covariance structures and to adapt subpopulation membership probabilities to covariate-dependent patterns. To perform inference, we develop an efficient Gibbs-within-Metropolis-Hastings sampling algorithm tailored to the geometry of the Wishart likelihood and the gating network. We additionally derive an Expectation-Maximization algorithm for maximum likelihood estimation in the mixture-of-experts setting. Extensive simulation studies demonstrate that the proposed Bayesian and maximum likelihood estimators achieve accurate subpopulation recovery and estimation under a range of heterogeneous covariance scenarios. Finally, we present an innovative application of our methodology to a challenging dataset: cancer drug sensitivity profiles, illustrating the ability of the MoE-Wishart model to leverage covariance across drug dosages and replicate measurements. Our methods are implemented in the \texttt{R} package \texttt{moewishart} available at https://github.com/zhizuio/moewishart .

stat.ME↗

arXiv2025

PHWSOA: A Pareto-based Hybrid Whale-Seagull Scheduling for Multi-Objective Tasks in Cloud Computing

Task scheduling is a critical research challenge in cloud computing, a transformative technology widely adopted across industries. Although numerous scheduling solutions exist, they predominantly optimize singular or limited metrics such as execution time or resource utilization often neglecting the need for comprehensive multi-objective optimization. To bridge this gap, this paper proposes the Pareto-based Hybrid Whale-Seagull Optimization Algorithm (PHWSOA). This algorithm synergistically combines the strengths of the Whale Optimization Algorithm (WOA) and the Seagull Optimization Algorithm (SOA), specifically mitigating WOA's limitations in local exploitation and SOA's constraints in global exploration. Leveraging Pareto dominance principles, PHWSOA simultaneously optimizes three key objectives: makespan, virtual machine (VM) load balancing, and economic cost. Key enhancements include: Halton sequence initialization for superior population diversity, a Pareto-guided mutation mechanism to avert premature convergence, and parallel processing for accelerated convergence. Furthermore, a dynamic VM load redistribution mechanism is integrated to improve load balancing during task execution. Extensive experiments conducted on the CloudSim simulator, utilizing real-world workload traces from NASA-iPSC and HPC2N, demonstrate that PHWSOA delivers substantial performance gains. Specifically, it achieves up to a 72.1% reduction in makespan, a 36.8% improvement in VM load balancing, and 23.5% cost savings. These results substantially outperform baseline methods including WOA, GA, PEWOA, and GCWOA underscoring PHWSOA's strong potential for enabling efficient resource management in practical cloud environments.

cs.DC↗

arXiv2025

Generalized promotion time cure model: A new modeling framework to identify cell-type-specific genes and improve survival prognosis

Single-cell technologies provide an unprecedented opportunity for dissecting the interplay between the cancer cells and the associated tumor microenvironment, and the produced high-dimensional omics data should also augment existing survival modeling approaches for identifying tumor cell type-specific genes predictive of cancer patient survival. However, there is no statistical model to integrate multiscale data including individual-level survival data, multicellular-level cell composition data and cellular-level single-cell omics covariates. We propose a class of Bayesian generalized promotion time cure models (GPTCMs) for the multiscale data integration to identify cell-type-specific genes and improve cancer prognosis. We demonstrate with simulations in both low- and high-dimensional settings that the proposed Bayesian GPTCMs are able to identify cell-type-associated covariates and improve survival prediction.

stat.ME↗

arXiv2025

Bayesian Cox model with graph-structured variable selection priors for multi-omics biomarker identification

An important goal in cancer research is the survival prognosis of a patient based on a minimal panel of genomic and molecular markers such as genes or proteins. Purely data-driven models without any biological knowledge can produce non-interpretable results. We propose a penalized semiparametric Bayesian Cox model with graph-structured selection priors for sparse identification of multi-omics features by making use of a biologically meaningful graph via a Markov random field (MRF) prior to capturing known relationships between multi-omics features. Since the fixed graph in the MRF prior is for the prior probability distribution, it is not a hard constraint to determine variable selection, so the proposed model can verify known information and has the potential to identify new and novel biomarkers for drawing new biological knowledge. Our simulation results show that the proposed Bayesian Cox model with graph-based prior knowledge results in more trustable and stable variable selection and non-inferior survival prediction, compared to methods modeling the covariates independently without any prior knowledge. The results also indicate that the performance of the proposed model is robust to a partially correct graph in the MRF prior, meaning that in a real setting where not all the true network information between covariates is known, the graph can still be useful. The proposed model is applied to the primary invasive breast cancer patients data in The Cancer Genome Atlas project.

stat.ME↗

arXiv2024

A note on promotion time cure models with a new biological consideration

We introduce a generalized promotion time cure model motivated by a new biological consideration. The new approach is flexible to model heterogeneous survival data, in particular for addressing intra-sample heterogeneity. We also indicate that the new approach is suited to model a series or parallel system consisting of multiple subsystems in reliability analysis.

stat.ME↗

arXiv2024

Comparison of the LASSO and Integrative LASSO with Penalty Factors (IPF-LASSO) methods for multi-omics data: Variable selection with Type I error control

Variable selection in relation to regression modeling has constituted a methodological problem for more than 60 years. Especially in the context of high-dimensional regression, developing stable and reliable methods, algorithms, and computational tools for variable selection has become an important research topic. Omics data is one source of such high-dimensional data, characterized by diverse genomic layers, and an additional analytical challenge is how to integrate these layers into various types of analyses. While the IPF-LASSO model has previously explored the integration of multiple omics modalities for feature selection and prediction by introducing distinct penalty parameters for each modality, the challenge of incorporating heterogeneous data layers into variable selection with Type I error control remains an open problem. To address this problem, we applied stability selection as a method for variable selection with false positives control in both IPF-LASSO and regular LASSO. The objective of this study was to compare the LASSO algorithm with IPF-LASSO, investigating whether introducing different penalty parameters per omics modality could improve statistical power while controlling false positives. Two high-dimensional data structures were investigated, one with independent data and the other with correlated data. The different models were also illustrated using data from a study on breast cancer treatment, where the IPF-LASSO model was able to select some highly relevant clinical variables.

stat.ME↗

arXiv2024

Tutorial on survival modeling with applications to omics data

Motivation: Identification of genomic, molecular and clinical markers prognostic of patient survival is important for developing personalized disease prevention, diagnostic and treatment approaches. Modern omics technologies have made it possible to investigate the prognostic impact of markers at multiple molecular levels, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, and how these potential risk factors complement clinical characterization of patient outcomes for survival prognosis. However, the massive sizes of the omics data sets, along with their correlation structures, pose challenges for studying relationships between the molecular information and patients' survival outcomes. Results: We present a general workflow for survival analysis that is applicable to high-dimensional omics data as inputs when identifying survival-associated features and validating survival models. In particular, we focus on the commonly used Cox-type penalized regressions and hierarchical Bayesian models for feature selection in survival analysis, which are are especially useful for high-dimensional data, but the framework is applicable more generally. Availability and implementation: A step-by-step R tutorial using The Cancer Genome Atlas survival and omics data for the execution and evaluation of survival models has been made available at https://ocbe-uio.github.io/survomics/survomics.html.

stat.AP↗

arXiv2023

Multivariate Bayesian structured variable selection for pharmacogenomic studies

Precision cancer medicine aims to determine the optimal treatment for each patient. In-vitro cancer drug sensitivity screens combined with multi-omics characterization of the cancer cells have become an important tool to achieve this aim. Analyzing such pharmacogenomic studies requires flexible and efficient joint statistical models for associating drug sensitivity with high-dimensional multi-omics data. We propose a multivariate Bayesian structured variable selection model for sparse identification of omics features associated with multiple correlated drug responses. Since many anti-cancer drugs are designed for specific molecular targets, our approach makes use of known structure between responses and predictors, e.g. molecular pathways and related omics features targeted by specific drugs, via a Markov random field (MRF) prior for the latent indicator variables of the coefficients in sparse seemingly unrelated regression. The structure information included in the MRF prior can improve the model performance, i.e. variable selection and response prediction, compared to other common priors. In addition, we employ random effects to capture heterogeneity between cancer types in a pan-cancer setting. The proposed approach is validated by simulation studies and applied to the Genomics of Drug Sensitivity in Cancer data, which includes pharmacological profiling and multi-omics characterization of a large set of heterogeneous cell lines.

stat.ME↗

arXiv2023

Some Tucker-like approximations based on the modal semi-tensor product

Approximating higher-order tensors by the Tucker format has been applied in many fields such as psychometrics, chemometrics, signal processing, pattern classification, and so on. In this paper, we propose some new Tucker-like approximations based on the modal semi-tensor product (STP), especially, a new singular value decomposition (SVD) and a new higher-order SVD (HOSVD) are derived. Algorithms for computing new decompositions are provided. We also give some numerical examples to illustrate our theoretical results.

math.NA↗

arXiv2021

A Riemannian Inexact Newton Dogleg Method for Constructing a Symmetric Nonnegative Matrix with Prescribed Spectrum

This paper is concerned with the inverse problem of constructing a symmetric nonnegative matrix from realizable spectrum. We reformulate the inverse problem as an underdetermined nonlinear matrix equation over a Riemannian product manifold. To solve it, we develop a Riemannian underdetermined inexact Newton dogleg method for solving a general underdetermined nonlinear equation defined between Riemannian manifolds and Euclidean spaces. The global and quadratic convergence of the proposed method is established under some mild assumptions. Then we solve the inverse problem by applying the proposed method to its equivalent nonlinear matrix equation and a preconditioner for the perturbed normal Riemannian Newton equation is also constructed. Numerical tests show the efficiency of the proposed method for solving the inverse problem.

math.NA↗

arXiv2021

BayesSUR: An R package for high-dimensional multivariate Bayesian variable and covariance selection in linear regression

In molecular biology, advances in high-throughput technologies have made it possible to study complex multivariate phenotypes and their simultaneous associations with high-dimensional genomic and other omics data, a problem that can be studied with high-dimensional multi-response regression, where the response variables are potentially highly correlated. To this purpose, we recently introduced several multivariate Bayesian variable and covariance selection models, e.g., Bayesian estimation methods for sparse seemingly unrelated regression for variable and covariance selection. Several variable selection priors have been implemented in this context, in particular the hotspot detection prior for latent variable inclusion indicators, which results in sparse variable selection for associations between predictors and multiple phenotypes. We also propose an alternative, which uses a Markov random field (MRF) prior for incorporating prior knowledge about the dependence structure of the inclusion indicators. Inference of Bayesian seemingly unrelated regression (SUR) by Markov chain Monte Carlo methods is made computationally feasible by factorisation of the covariance matrix amongst the response variables. In this paper we present BayesSUR, an R package, which allows the user to easily specify and run a range of different Bayesian SUR models, which have been implemented in C++ for computational efficiency. The R package allows the specification of the models in a modular way, where the user chooses the priors for variable selection and for covariance selection separately. We demonstrate the performance of sparse SUR models with the hotspot prior and spike-and-slab MRF prior on synthetic and real data sets representing eQTL or mQTL studies and in vitro anti-cancer drug screening studies as examples for typical applications.

stat.ME↗

arXiv2021

Deterministic Assembly of Single Emitters in Sub-5 Nanometer Optical Cavity Formed by Gold Nanorod Dimers on Three-Dimensional DNA Origami

Controllable strong interactions between a nanocavity and a single emitter is important to manipulating optical emission in a nanophotonic systems but challenging to achieve. Here a three-dimensional DNA origami, named as DNA rack (DR) is proposed and demonstrated to deterministically and precisely assemble single emitters within ultra-small plasmonic nanocavities formed by closely coupled gold nanorods (AuNRs). The DR uniquely possesses a saddle shape with two tubular grooves that geometrically allows a snug fit and linearly align two AuNRs with a bending angle <10°. It also includes a spacer at the saddle point to maintain the gap between AuNRs as small as 2-3 nm, forming a nanocavity estimated to be 20 nm3 and an experimentally measured Q factor of 7.3. A DNA docking strand is designed at the spacer to position a single fluorescent emitter at nanometer accuracy within the cavity. Using Cy5 as a model emitter, a ~30-fold fluorescence enhancement and a significantly reduced emission lifetime (from 1.6 ns to 670 ps) were experimentally verified, confirming significant emitter-cavity interactions. This DR-templated assembly method is capable of fitting AuNRs of variable length-to-width aspect ratios to form anisotropic nanocavities and deterministically incorporating different single emitters, thus enabling flexible design of both cavity resonance and emission wavelengths to tailor light-matter interactions at nanometer scale.

physics.optics↗

arXiv2020

Riemannian Newton-CG Methods for Constructing a Positive Doubly Stochastic Matrix From Spectral Data

In this paper, we consider the inverse eigenvalue problem for the positive doubly stochastic matrices, which aims to construct a positive doubly stochastic matrix from the prescribed realizable spectral data. By using the real Schur decomposition, the inverse problem is written as a nonlinear matrix equation on a matrix product manifold. We propose monotone and nonmonotone Riemannian inexact Newton-CG methods for solving the nonlinear matrix equation. The global and quadratic convergence of the proposed methods is established under some assumptions. We also provide invariant subspaces of the constructed solution to the inverse problem based on the computed real Schur decomposition. Finally, we report some numerical tests, including an application in digraph, to illustrate the effectiveness of the proposed methods.

math.NA↗

arXiv2020

Structured penalized regression for drug sensitivity prediction

Large-scale {\it in vitro} drug sensitivity screens are an important tool in personalized oncology to predict the effectiveness of potential cancer drugs. The prediction of the sensitivity of cancer cell lines to a panel of drugs is a multivariate regression problem with high-dimensional heterogeneous multi-omics data as input data and with potentially strong correlations between the outcome variables which represent the sensitivity to the different drugs. We propose a joint penalized regression approach with structured penalty terms which allow us to utilize the correlation structure between drugs with group-lasso-type penalties and at the same time address the heterogeneity between omics data sources by introducing data-source-specific penalty factors to penalize different data sources differently. By combining integrative penalty factors (IPF) with tree-guided group lasso, we create the IPF-tree-lasso method. We present a unified framework to transform more general IPF-type methods to the original penalized method. Because the structured penalty terms have multiple parameters, we demonstrate how the interval-search Efficient Parameter Selection via Global Optimization (EPSGO) algorithm can be used to optimize multiple penalty parameters efficiently. Simulation studies show that IPF-tree-lasso can improve the prediction performance compared to other lasso-type methods, in particular for heterogenous data sources. Finally, we employ the new methods to analyse data from the Genomics of Drug Sensitivity in Cancer project.

stat.ME↗

arXiv2019

Composite local low-rank structure in learning drug sensitivity

The molecular characterization of tumor samples by multiple omics data sets of different types or modalities (e.g. gene expression, mutation, CpG methylation) has become an invaluable source of information for assessing the expected performance of individual drugs and their combinations. Merging the relevant information from the omics data modalities provides the statistical basis for determining suitable therapies for specific cancer patients. Different data modalities may each have their specific structures that need to be taken into account during inference. In this paper, we assume that each omics data modality has a low-rank structure with only few relevant features that affect the prediction and we propose to use a composite local nuclear norm penalization for learning drug sensitivity. Numerical results show that the composite low-rank structure can improve the prediction performance compared to using a global low-rank approach or elastic net regression.

stat.AP↗