arXiv subjects

Xiaoxia Liu

Publications and source records attributed to Xiaoxia Liu.

12 recordsLinked to original sources

arXiv2026

CODESKILL: Learning Self-Evolving Skills for Coding Agents

Coding agents produce rich trajectories while solving software-engineering tasks. To enable agent self-evolution, these trajectories can be distilled into reusable procedural skills that compactly encode experience to guide future behavior. However, existing skill construction and maintenance methods often rely on fixed prompts and heuristic update rules, leaving it unclear how knowledge should be selected, abstracted, and maintained to best serve downstream agents. We propose CODESKILL, an LLM-based framework that reformulates skill extraction and skill-bank maintenance as a learnable management policy. CODESKILL extracts multi-granularity procedural skills from coding-agent trajectories, evolves skills with new experience, and maintains a compact skill bank for future task solving. We train CODESKILL with reinforcement learning, using a hybrid reward that combines dense rubric-based skill-quality feedback with sparse verifiable execution feedback from the frozen downstream agent. Experiments on EnvBench, SWE-Bench Verified, and Terminal-Bench 2 show that CODESKILL improves average pass rate by 9.69 over the no-skill baseline and by 4.01 over the strongest prompt-based or memory baseline, while maintaining the skill bank at a stable size during iterative construction.

cs.AI↗

arXiv2025

Efficient Function Orchestration for Large Language Models

Function calling is a fundamental capability of today's large language models, but sequential function calling posed efficiency problems. Recent studies have proposed to request function calls with parallelism support in order to alleviate this issue. However, they either delegate the concurrent function calls to users for execution which are conversely executed sequentially, or overlook the relations among various function calls, rending limited efficiency. This paper introduces LLMOrch, an advanced framework for automated, parallel function calling in large language models. The key principle behind LLMOrch is to identify an available processor to execute a function call while preventing any single processor from becoming overburdened. To this end, LLMOrch models the data relations (i.e., def-use) among different function calls and coordinates their executions by their control relations (i.e., mutual-exclusion) as well as the working status of the underlying processors. When comparing with state-of-the-art techniques, LLMOrch demonstrated comparable efficiency improvements in orchestrating I/O-intensive functions, while significantly outperforming (2$\times$) them with compute-intensive functions. LLMOrch's performance even showed a linear correlation to the number of allocated processors. We believe that these results highlight the potential of LLMOrch as an efficient solution for parallel function orchestration in the context of large language models.

cs.SE↗

arXiv2025

Orthogonal Constrained Minimization with Tensor $\ell_{2,p}$ Regularization for HSI Denoising and Destriping

Hyperspectral images~(HSIs) are often contaminated by a mixture of noise such as Gaussian noise, dead lines, stripes, and so on. In this paper, we propose a multi-scale low-rank tensor regularized $\ell_{2,p}$ (MLTL2p) approach for HSI denoising and destriping, which consists of an orthogonal constrained minimization model and an iterative algorithm with convergence guarantees. The model of the proposed MLTL2p approach is built based on a new sparsity-enhanced Multi-scale Low-rank Tensor regularization and a tensor $\ell_{2,p}$ norm with $p\in (0,1)$. The multi-scale low-rank regularization for HSI denoising utilizes the global and local spectral correlation as well as the spatial nonlocal self-similarity priors of HSIs. The corresponding low-rank constraints are formulated based on independent higher-order singular value decomposition with sparsity enhancement on its core tensor to prompt more low-rankness. The tensor $\ell_{2,p}$ norm for HSI destriping is extended from the matrix $\ell_{2,p}$ norm. A proximal block coordinate descent algorithm is proposed in the MLTL2p approach to solve the resulting nonconvex nonsmooth minimization with orthogonal constraints. We show any accumulation point of the sequence generated by the proposed algorithm converges to a first-order stationary point, which is defined using three equalities of substationarity, symmetry, and feasibility for orthogonal constraints. In the numerical experiments, we compare the proposed method with state-of-the-art methods including a deep learning based method, and test the methods on both simulated and real HSI datasets. Our proposed MLTL2p method demonstrates outperformance in terms of metrics such as mean peak signal-to-noise ratio as well as visual quality.

math.OC↗

arXiv2025

Provably Convergent Plug-and-play Proximal Block Coordinate Descent Method for Hyperspectral Anomaly Detection

Hyperspectral anomaly detection refers to identifying pixels in the hyperspectral images that have spectral characteristics significantly different from the background. In this paper, we introduce a novel model that represents the background information using a low-rank representation. We integrate an implicit proximal denoiser prior, associated with a deep learning based denoiser, within a plug-and-play (PnP) framework to effectively remove noise from the eigenimages linked to the low-rank representation. Anomalies are characterized using a generalized group sparsity measure, denoted as $\|\cdot\|_{2,ψ}$. To solve the resulting orthogonal constrained nonconvex nonsmooth optimization problem, we develop a PnP-proximal block coordinate descent (PnP-PBCD) method, where the eigenimages are updated using a proximal denoiser within the PnP framework. We prove that any accumulation point of the sequence generated by the PnP-PBCD method is a stationary point. We evaluate the effectiveness of the PnP-PBCD method on hyperspectral anomaly detection in scenarios with and without Gaussian noise contamination. The results demonstrate that the proposed method can effectively detect anomalous objects, outperforming the competing methods that may mistakenly identify noise as anomalies or misidentify the anomalous objects due to noise interference.

math.OC↗

arXiv2025

S-Eval: Towards Automated and Comprehensive Safety Evaluation for Large Language Models

Generative large language models (LLMs) have revolutionized natural language processing with their transformative and emergent capabilities. However, recent evidence indicates that LLMs can produce harmful content that violates social norms, raising significant concerns regarding the safety and ethical ramifications of deploying these advanced models. Thus, it is both critical and imperative to perform a rigorous and comprehensive safety evaluation of LLMs before deployment. Despite this need, owing to the extensiveness of LLM generation space, it still lacks a unified and standardized risk taxonomy to systematically reflect the LLM content safety, as well as automated safety assessment techniques to explore the potential risk efficiently. To bridge the striking gap, we propose S-Eval, a novel LLM-based automated Safety Evaluation framework with a newly defined comprehensive risk taxonomy. S-Eval incorporates two key components, i.e., an expert testing LLM ${M}_t$ and a novel safety critique LLM ${M}_c$. ${M}_t$ is responsible for automatically generating test cases in accordance with the proposed risk taxonomy. ${M}_c$ can provide quantitative and explainable safety evaluations for better risk awareness of LLMs. In contrast to prior works, S-Eval is efficient and effective in test generation and safety evaluation. Moreover, S-Eval can be flexibly configured and adapted to the rapid evolution of LLMs and accompanying new safety threats, test generation methods and safety critique methods thanks to the LLM-based architecture. S-Eval has been deployed in our industrial partner for the automated safety evaluation of multiple LLMs serving millions of users, demonstrating its effectiveness in real-world scenarios. Our benchmark is publicly available at https://github.com/IS2Lab/S-Eval.

cs.CR↗

arXiv2024

ScAtt: an Attention based architecture to analyze Alzheimer's disease at cell type level from single-cell RNA-sequencing data

Alzheimer's disease (AD) is a pervasive neurodegenerative disorder that leads to memory and behavior impairment severe enough to interfere with daily life activities. Understanding this disease pathogenesis can drive the development of new targets and strategies to prevent and treat AD. Recent advances in high-throughput single-cell RNA sequencing technology (scRNA-seq) have enabled the generation of massive amounts of transcriptomic data at the single-cell level provided remarkable insights into understanding the molecular pathogenesis of Alzheimer's disease. In this study, we introduce ScAtt, an innovative Attention-based architecture, devised specifically for the concurrent identification of cell-type specific AD-related genes and their associated gene regulatory network. ScAtt incorporates a flexible model capable of capturing nonlinear effects, leading to the detection of AD-associated genes that might be overlooked by traditional differentially expressed gene (DEG) analyses. Moreover, ScAtt effectively infers a gene regulatory network depicting the combined influences of genes on the targeted disease, as opposed to examining correlations among genes in conventional gene co-expression networks. In an application to 95,186 single-nucleus transcriptomes from 17 hippocampus samples, ScAtt shows substantially better performance in modeling quantitative changes in expression levels between AD and healthy controls. Consequently, ScAtt performs better than existing methods in the identification of AD-related genes, with more unique discoveries and less overlap between cell types. Functional enrichments of the corresponding gene modules detected from gene regulatory network show significant enrichment of biologically meaningful AD-related pathways across different cell types.

q-bio.MN↗

arXiv2023

Prompting Frameworks for Large Language Models: A Survey

Since the launch of ChatGPT, a powerful AI Chatbot developed by OpenAI, large language models (LLMs) have made significant advancements in both academia and industry, bringing about a fundamental engineering paradigm shift in many areas. While LLMs are powerful, it is also crucial to best use their power where "prompt'' plays a core role. However, the booming LLMs themselves, including excellent APIs like ChatGPT, have several inherent limitations: 1) temporal lag of training data, and 2) the lack of physical capabilities to perform external actions. Recently, we have observed the trend of utilizing prompt-based tools to better utilize the power of LLMs for downstream tasks, but a lack of systematic literature and standardized terminology, partly due to the rapid evolution of this field. Therefore, in this work, we survey related prompting tools and promote the concept of the "Prompting Framework" (PF), i.e. the framework for managing, simplifying, and facilitating interaction with large language models. We define the lifecycle of the PF as a hierarchical structure, from bottom to top, namely: Data Level, Base Level, Execute Level, and Service Level. We also systematically depict the overall landscape of the emerging PF field and discuss potential future research and challenges. To continuously track the developments in this area, we maintain a repository at https://github.com/lxx0628/Prompting-Framework-Survey, which can be a useful resource sharing platform for both academic and industry in this field.

cs.SE↗

arXiv2023

Robust inference with GhostKnockoffs in genome-wide association studies

Genome-wide association studies (GWASs) have been extensively adopted to depict the underlying genetic architecture of complex diseases. Motivated by GWASs' limitations in identifying small effect loci to understand complex traits' polygenicity and fine-mapping putative causal variants from proxy ones, we propose a knockoff-based method which only requires summary statistics from GWASs and demonstrate its validity in the presence of relatedness. We show that GhostKnockoffs inference is robust to its input Z-scores as long as they are from valid marginal association tests and their correlations are consistent with the correlations among the corresponding genetic variants. The property generalizes GhostKnockoffs to other GWASs settings, such as the meta-analysis of multiple overlapping studies and studies based on association test statistics deviated from score tests. We demonstrate GhostKnockoffs' performance using empirical simulation and a meta-analysis of nine European ancestral genome-wide association studies and whole exome/genome sequencing studies. Both results demonstrate that GhostKnockoffs identify more putative causal variants with weak genotype-phenotype associations that are missed by conventional GWASs.

stat.ME↗

arXiv2022

Ensembling improves stability and power of feature selection for deep learning models

With the growing adoption of deep learning models in different real-world domains, including computational biology, it is often necessary to understand which data features are essential for the model's decision. Despite extensive recent efforts to define different feature importance metrics for deep learning models, we identified that inherent stochasticity in the design and training of deep learning models makes commonly used feature importance scores unstable. This results in varied explanations or selections of different features across different runs of the model. We demonstrate how the signal strength of features and correlation among features directly contribute to this instability. To address this instability, we explore the ensembling of feature importance scores of models across different epochs and find that this simple approach can substantially address this issue. For example, we consider knockoff inference as they allow feature selection with statistical guarantees. We discover considerable variability in selected features in different epochs of deep learning training, and the best selection of features doesn't necessarily occur at the lowest validation loss, the conventional approach to determine the best model. As such, we present a framework to combine the feature importance of trained models across different hyperparameter settings and epochs, and instead of selecting features from one best model, we perform an ensemble of feature importance scores from numerous good models. Across the range of experiments in simulated and various real-world datasets, we demonstrate that the proposed framework consistently improves the power of feature selection.

cs.LG↗

arXiv2022

Improving genetic risk prediction across diverse population by disentangling ancestry representations

Risk prediction models using genetic data have seen increasing traction in genomics. However, most of the polygenic risk models were developed using data from participants with similar (mostly European) ancestry. This can lead to biases in the risk predictors resulting in poor generalization when applied to minority populations and admixed individuals such as African Americans. To address this bias, largely due to the prediction models being confounded by the underlying population structure, we propose a novel deep-learning framework that leverages data from diverse population and disentangles ancestry from the phenotype-relevant information in its representation. The ancestry disentangled representation can be used to build risk predictors that perform better across minority populations. We applied the proposed method to the analysis of Alzheimer's disease genetics. Comparing with standard linear and nonlinear risk prediction methods, the proposed method substantially improves risk prediction in minority populations, particularly for admixed individuals.

cs.LG↗

arXiv2020

Multiplicative Noise Removal: Nonlocal Low-Rank Model and Its Proximal Alternating Reweighted Minimization Algorithm

The goal of this paper is to develop a novel numerical method for efficient multiplicative noise removal. The nonlocal self-similarity of natural images implies that the matrices formed by their nonlocal similar patches are low-rank. By exploiting this low-rank prior with application to multiplicative noise removal, we propose a nonlocal low-rank model for this task and develop a proximal alternating reweighted minimization (PARM) algorithm to solve the optimization problem resulting from the model. Specifically, we utilize a generalized nonconvex surrogate of the rank function to regularize the patch matrices and develop a new nonlocal low-rank model, which is a nonconvex nonsmooth optimization problem having a patchwise data fidelity and a generalized nonlocal low-rank regularization term. To solve this optimization problem, we propose the PARM algorithm, which has a proximal alternating scheme with a reweighted approximation of its subproblem. A theoretical analysis of the proposed PARM algorithm is conducted to guarantee its global convergence to a critical point. Numerical experiments demonstrate that the proposed method for multiplicative noise removal significantly outperforms existing methods such as the benchmark SAR-BM3D method in terms of the visual quality of the denoised images, and the PSNR (the peak-signal-to-noise ratio) and SSIM (the structural similarity index measure) values.

math.OC↗

arXiv2011

A Synthetic Error Analysis of Positioning Equation for Airborne Three-Dimensional Laser Imaging Sensor

This paper presents the exact error analysis of point positioning equation used for airborne three-dimensional(3D) imaging sensor. With differential calculus and principles of precision analysis a mathematics formula on the point position error and relative factors is derived to show how each error source affects both vertical and horizontal coordinates. A comprehensive analysis of the related error sources and their achievable accuracy are provided. At last, two example figures are shown to compare the position accuracy of elliptical trace scan and the line-trace scan are drawn under the same error source and some corresponding conclusions.

physics.optics↗