arXiv subjects

Shu Yang

Publications and source records attributed to Shu Yang.

At least 145 records · Page 8Linked to original sources

arXiv2025

Doubly robust omnibus sensitivity analysis of externally controlled trials with intercurrent events

Externally controlled trials are crucial in clinical development when randomized controlled trials are unethical or impractical. These trials consist of a full treatment arm with the experimental treatment and a full external control arm. However, they present significant challenges in learning the treatment effect due to the lack of randomization and a parallel control group. Besides baseline incomparability, outcome mean non-exchangeability, caused by differences in conditional outcome distributions between external controls and counterfactual concurrent controls, is infeasible to test and may introduce biases in evaluating the treatment effect. Sensitivity analysis of outcome mean non-exchangeability is thus critically important to assess the robustness of the study's conclusions against such assumption violations. Moreover, intercurrent events, which are ubiquitous and inevitable in clinical studies, can further confound the treatment effect and hinder the interpretation of the estimated treatment effects. This paper establishes a semi-parametric framework for externally controlled trials with intercurrent events, offering doubly robust and locally optimal estimators for primary and sensitivity analyses. We develop an omnibus sensitivity analysis that accounts for both outcome mean non-exchangeability and the impacts of intercurrent events simultaneously, ensuring root-n consistency and asymptotic normality under specified conditions. The performance of the proposed sensitivity analysis is evaluated in simulation studies and a real-data problem.

stat.ME↗

arXiv2025

Double Machine Learning Methods for Estimating Average Treatment Effects: A Comparative Study

Observational cohort studies are increasingly being used for comparative effectiveness research to assess the safety of therapeutics. Recently, various doubly robust methods have been proposed for average treatment effect estimation by combining the treatment model and the outcome model via different vehicles, such as matching, weighting, and regression. The key advantage of doubly robust estimators is that they require either the treatment model or the outcome model to be correctly specified to obtain a consistent estimator of average treatment effects, and therefore lead to a more accurate and often more precise inference. However, little work has been done to understand how doubly robust estimators differ due to their unique strategies of using the treatment and outcome models and how machine learning techniques can be combined to boost their performance, which we call double machine learning estimators. Here we examine multiple popular doubly robust methods and compare their performance using different treatment and outcome modeling via extensive simulations and a real-world application. We found that incorporating machine learning with doubly robust estimators such as the targeted maximum likelihood estimator gives the best overall performance. Practical guidance on how to apply doubly robust estimators is provided.

stat.ME↗

arXiv2025

Geometrically Templated Dynamic Wrinkling from Suspended Poly(vinyl alcohol) Soap Films

Wrinkling is commonly observed as mechanical instability when a stiff thin film bound on a compliant thick substrate undergoes in-plane compression exceeding a threshold. Despite significant efforts to create a broad range of surface patterns via wrinkling, little has been studied about a dynamic and transient wrinkling process, where a suspended polymer thin film undergoes liquid-to-solid phase transitions. Here, a spontaneous wrinkling process is reported, when drying poly(vinyl alcohol) (PVA) soap films suspended on 3D printed wireframes with near zero or negative Gaussian curvatures. As water evaporates, a thickness gradient across the sample is developed, leading to non-uniform drying rates, and a concentration gradient between the inner and outer sides (exposed to air) of the suspended PVA soap film induces a differential osmotic pressure. Together, these effects contribute to an in-plane compressive stress, leading to the formation of surface wrinkles, whose growth is guided by the geometry of the frame. Importantly, the wrinkles evolve dynamically: the wavelength and number of the wrinkles can be tuned by altering the concentration of the PVA aqueous solutions, the initial mass, the relative humidity of the drying environment; the patterns of the resulting wrinkles can be programmed by the geometry of the wireframe.

cond-mat.soft↗

arXiv2025

Emergent Continuous Time Crystal in Dissipative Quantum Spin System without Driving

Time crystals are a nonequilibrium phase of matter that extend fundamental spontaneous symmetry breaking into the temporal dimension, typically requiring external driving for their realization. Here, we explore the nonequilibrium phase diagram of a two-dimensional dissipative Heisenberg spin system without external coherent or incoherent driving. Through numerical analysis of spin dynamics, we identify nonstationary steady states, some of which are limit cycles with persistent periodic oscillations, while others exhibit chaotic, aperiodic behavior. The emergence of limit cycle steady states breaks the continuous time-translation symmetry of this time-independent many-body system, classifying them as continuous time crystals. We further validate these oscillatory behaviors by testing their stability against local perturbations and assess the robustness of the emergent continuous time crystals by introducing isotropic Gaussian white noise. This work provides insights into the intricate interplay between the dissipation and spin interaction, and opens possibilities for realizing dissipation-induced, heating-immune time crystals.

quant-ph↗

arXiv2025

Who Wrote This? The Key to Zero-Shot LLM-Generated Text Detection Is GECScore

The efficacy of detectors for texts generated by large language models (LLMs) substantially depends on the availability of large-scale training data. However, white-box zero-shot detectors, which require no such data, are limited by the accessibility of the source model of the LLM-generated text. In this paper, we propose a simple yet effective black-box zero-shot detection approach based on the observation that, from the perspective of LLMs, human-written texts typically contain more grammatical errors than LLM-generated texts. This approach involves calculating the Grammar Error Correction Score (GECScore) for the given text to differentiate between human-written and LLM-generated text. Experimental results show that our method outperforms current state-of-the-art (SOTA) zero-shot and supervised methods, achieving an average AUROC of 98.62% across XSum and Writing Prompts dataset. Additionally, our approach demonstrates strong reliability in the wild, exhibiting robust generalization and resistance to paraphrasing attacks. Data and code are available at: https://github.com/NLP2CT/GECScore.

cs.CL↗

arXiv2025

Exploring the Personality Traits of LLMs through Latent Features Steering

Large language models (LLMs) have significantly advanced dialogue systems and role-playing agents through their ability to generate human-like text. While prior studies have shown that LLMs can exhibit distinct and consistent personalities, the mechanisms through which these models encode and express specific personality traits remain poorly understood. To address this, we investigate how various factors, such as cultural norms and environmental stressors, encoded within LLMs, shape their personality traits, guided by the theoretical framework of social determinism. Inspired by related work on LLM interpretability, we propose a training-free approach to modify the model's behavior by extracting and steering latent features corresponding to factors within the model, thereby eliminating the need for retraining. Furthermore, we analyze the implications of these factors for model safety, focusing on their impact through the lens of personality.

cs.CL↗

arXiv2025

EAP-GP: Mitigating Saturation Effect in Gradient-based Automated Circuit Identification

Understanding the internal mechanisms of transformer-based language models remains challenging. Mechanistic interpretability based on circuit discovery aims to reverse engineer neural networks by analyzing their internal processes at the level of computational subgraphs. In this paper, we revisit existing gradient-based circuit identification methods and find that their performance is either affected by the zero-gradient problem or saturation effects, where edge attribution scores become insensitive to input changes, resulting in noisy and unreliable attribution evaluations for circuit components. To address the saturation effect, we propose Edge Attribution Patching with GradPath (EAP-GP), EAP-GP introduces an integration path, starting from the input and adaptively following the direction of the difference between the gradients of corrupted and clean inputs to avoid the saturated region. This approach enhances attribution reliability and improves the faithfulness of circuit identification. We evaluate EAP-GP on 6 datasets using GPT-2 Small, GPT-2 Medium, and GPT-2 XL. Experimental results demonstrate that EAP-GP outperforms existing methods in circuit faithfulness, achieving improvements up to 17.7%. Comparisons with manually annotated ground-truth circuits demonstrate that EAP-GP achieves precision and recall comparable to or better than previous approaches, highlighting its effectiveness in identifying accurate circuits.

cs.LG↗

arXiv2025

Dissecting Representation Misalignment in Contrastive Learning via Influence Function

Contrastive learning, commonly applied in large-scale multimodal models, often relies on data from diverse and often unreliable sources, which can include misaligned or mislabeled text-image pairs. This frequently leads to robustness issues and hallucinations, ultimately causing performance degradation. Data valuation is an efficient way to detect and trace these misalignments. Nevertheless, existing methods are computationally expensive for large-scale models. Although computationally efficient, classical influence functions are inadequate for contrastive learning models, as they were initially designed for pointwise loss. Furthermore, contrastive learning involves minimizing the distance between positive sample modalities while maximizing the distance between negative sample modalities. This necessitates evaluating the influence of samples from both perspectives. To tackle these challenges, we introduce the Extended Influence Function for Contrastive Loss (ECIF), an influence function crafted for contrastive loss. ECIF considers both positive and negative samples and provides a closed-form approximation of contrastive learning models, eliminating the need for retraining. Building upon ECIF, we develop a series of algorithms for data evaluation, misalignment detection, and misprediction trace-back tasks. Experimental results demonstrate our ECIF advances the transparency and interpretability of CLIP-style embedding models by offering a more accurate assessment of data impact and model alignment compared to traditional baseline methods.

cs.LG↗

arXiv2025

Semiparametric Localized Principal Stratification Analysis with Continuous Strata

Principal stratification is essential for revealing causal mechanisms involving post-treatment intermediate variables, in real-world applications like surrogate marker evaluation. Principal stratification analysis with continuous intermediate variables is increasingly common but challenging due to the infinite principal strata and the nonidentifiability and nonregularity of principal causal effects. Inspired by recent research, we resolve these challenges by first using a flexible copula-based principal score model to identify principal causal effect under weak principal ignorability. We then target the local functional substitute of principal causal effect, which is statistically regular and can accurately approximate principal causal effect with vanishing bandwidth. We simplify the full efficient influence function of the local functional substitute by considering its oracle-scenario alternative. This leads to a computationally efficient and straightforward estimator for the local functional substitute and principal causal effect with vanishing bandwidth. We prove the double robustness of our proposed estimator, and derive its asymptotic normality for inferential purposes. With a vanishing bandwidth, our method attains minimax optimality for the nonparametric estimation of the principal causal effect. With a fixed bandwidth, it achieves semiparametric efficiency in estimating its local functional substitute. We demonstrate the strong performance of our proposed estimator through simulations and apply it to surrogate analysis of short-term CD4 count in ACTG 175.

stat.ME↗

arXiv2025

Evaluating Data Influence in Meta Learning

As one of the most fundamental models, meta learning aims to effectively address few-shot learning challenges. However, it still faces significant issues related to the training data, such as training inefficiencies due to numerous low-contribution tasks in large datasets and substantial noise from incorrect labels. Thus, training data attribution methods are needed for meta learning. However, the dual-layer structure of mata learning complicates the modeling of training data contributions because of the interdependent influence between meta-parameters and task-specific parameters, making existing data influence evaluation tools inapplicable or inaccurate. To address these challenges, based on the influence function, we propose a general data attribution evaluation framework for meta-learning within the bilevel optimization framework. Our approach introduces task influence functions (task-IF) and instance influence functions (instance-IF) to accurately assess the impact of specific tasks and individual data points in closed forms. This framework comprehensively models data contributions across both the inner and outer training processes, capturing the direct effects of data points on meta-parameters as well as their indirect influence through task-specific parameters. We also provide several strategies to enhance computational efficiency and scalability. Experimental results demonstrate the framework's effectiveness in training data evaluation via several downstream tasks.

cs.LG↗

arXiv2025

Accessing the topological properties of human brain functional sub-circuits in Echo State Networks

Recent years have witnessed an emerging trend in neuromorphic computing that centers around the use of brain connectomics as a blueprint for artificial neural networks. Connectomics-based neuromorphic computing has primarily focused on embedding human brain large-scale structural connectomes (SCs), as estimated from diffusion Magnetic Resonance Imaging (dMRI) modality, to echo-state networks (ESNs). A critical step in ESN embedding requires pre-determined read-in and read-out layers constructed by the induced subgraphs of the embedded reservoir. As \textit{a priori} set of functional sub-circuits are derived from functional MRI (fMRI) modality, it is unknown, till this point, whether the embedding of fMRI-induced sub-circuits/networks onto SCs is well justified from the neuro-physiological perspective and ESN performance across a variety of tasks. This paper proposes a pipeline to implement and evaluate ESNs with various embedded topologies and processing/memorization tasks. To this end, we showed that different performance optimums highly depend on the neuro-physiological characteristics of these pre-determined fMRI-induced sub-circuits. In general, fMRI-induced sub-circuit-embedded ESN outperforms simple bipartite and various null models with feed-forward properties commonly seen in MLP for different tasks and reservoir criticality conditions. We provided a thorough analysis of the topological properties of pre-determined fMRI-induced sub-circuits and highlighted their graph-theoretical properties that play significant roles in determining ESN performance.

q-bio.NC↗

arXiv2025

Beyond Window-Based Detection: A Graph-Centric Framework for Discrete Log Anomaly Detection

Detecting anomalies in discrete event logs is critical for ensuring system reliability, security, and efficiency. Traditional window-based methods for log anomaly detection often suffer from context bias and fuzzy localization, which hinder their ability to precisely and efficiently identify anomalies. To address these challenges, we propose a graph-centric framework, TempoLog, which leverages multi-scale temporal graph networks for discrete log anomaly detection. Unlike conventional methods, TempoLog constructs continuous-time dynamic graphs directly from event logs, eliminating the need for fixed-size window grouping. By representing log templates as nodes and their temporal relationships as edges, the framework dynamically captures both local and global dependencies across multiple temporal scales. Additionally, a semantic-aware model enhances detection by incorporating rich contextual information. Extensive experiments on public datasets demonstrate that our method achieves state-of-the-art performance in event-level anomaly detection, significantly outperforming existing approaches in both accuracy and efficiency.

cs.SE↗

arXiv2025

Two-phase rejective sampling and its asymptotic properties

Rejective sampling improves design and estimation efficiency of single-phase sampling when auxiliary information in a finite population is available. When such auxiliary information is unavailable, we propose to use two-phase rejective sampling (TPRS), which involves measuring auxiliary variables for the sample of units in the first phase, followed by the implementation of rejective sampling for the outcome in the second phase. We explore the asymptotic design properties of double expansion and regression estimators under TPRS. We show that TPRS enhances the efficiency of the double expansion estimator, rendering it comparable to a regression estimator. We further refine the design to accommodate varying importance of covariates and extend it to multi-phase sampling. We start with the theory for the population mean and then extend the theory to parameters defined by general estimating equations. Our asymptotic results for TPRS immediately cover the existing single-phase rejective sampling, under which the asymptotic theory has not been fully established.

stat.ME↗

arXiv2025

Advances in RNA secondary structure prediction and RNA modifications: Methods, data, and applications

Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic. This review sets out to explore the computational prediction of RNA secondary structure and its connections to RNA modifications, which have emerged as an active domain in recent years. We first examine the progression of RNA secondary structure prediction methodology, focusing on a set of representative works categorized into thermodynamic, comparative, machine learning, and hybrid approaches. Next, we survey the advances in RNA modifications and computational methods for identifying RNA modifications, focusing on the prominent modification types. Subsequently, we highlight the interplay between RNA modifications and secondary structures, emphasizing how modifications such as m6A dynamically affect RNA folding and vice versa. In addition, we also review relevant data sources and provide a discussion of current challenges and opportunities in the field. Ultimately, we hope our review will be able to serve as a cornerstone to aid in the development of innovative methods for this emerging topic and foster therapeutic applications in the future.

q-bio.BM↗

arXiv2025

Transfer Learning for Individualized Treatment Rules: Application to Sepsis Patients Data from eICU-CRD and MIMIC-III Databases

Modern precision medicine aims to utilize real-world data to provide the best treatment for an individual patient. An individualized treatment rule (ITR) maps each patient's characteristics to a recommended treatment scheme that maximizes the expected outcome of the patient. A challenge precision medicine faces is population heterogeneity, as studies on treatment effects are often conducted on source populations that differ from the populations of interest in terms of the distribution of patient characteristics. Our research goal is to explore a transfer learning algorithm that aims to address the population heterogeneity problem and obtain targeted, optimal, and interpretable ITRs. The algorithm incorporates a calibrated augmented inverse probability weighting (CAIPW) estimator for the average treatment effect (ATE) and employs value function maximization for the target population using Genetic Algorithm (GA) to produce our desired ITR. To demonstrate its practical utility, we apply this transfer learning algorithm to two large medical databases, Electronic Intensive Care Unit Collaborative Research Database (eICU-CRD) and Medical Information Mart for Intensive Care III (MIMIC-III). We first identify the important covariates, treatment options, and outcomes of interest based on the two databases, and then estimate the optimal linear ITRs for patients with sepsis. Our research introduces and applies new techniques for data fusion to obtain data-driven ITRs that cater to patients' individual medical needs in a population of interest. By emphasizing generalizability and personalized decision-making, this methodology extends its potential application beyond medicine to fields such as marketing, technology, social sciences, and education.

stat.AP↗

arXiv2024

Improving Quantization-aware Training of Low-Precision Network via Block Replacement on Full-Precision Counterpart

Quantization-aware training (QAT) is a common paradigm for network quantization, in which the training phase incorporates the simulation of the low-precision computation to optimize the quantization parameters in alignment with the task goals. However, direct training of low-precision networks generally faces two obstacles: 1. The low-precision model exhibits limited representation capabilities and cannot directly replicate full-precision calculations, which constitutes a deficiency compared to full-precision alternatives; 2. Non-ideal deviations during gradient propagation are a common consequence of employing pseudo-gradients as approximations in derived quantized functions. In this paper, we propose a general QAT framework for alleviating the aforementioned concerns by permitting the forward and backward processes of the low-precision network to be guided by the full-precision partner during training. In conjunction with the direct training of the quantization model, intermediate mixed-precision models are generated through the block-by-block replacement on the full-precision model and working simultaneously with the low-precision backbone, which enables the integration of quantized low-precision blocks into full-precision networks throughout the training phase. Consequently, each quantized block is capable of: 1. simulating full-precision representation during forward passes; 2. obtaining gradients with improved estimation during backward passes. We demonstrate that the proposed method achieves state-of-the-art results for 4-, 3-, and 2-bit quantization on ImageNet and CIFAR-10. The proposed framework provides a compatible extension for most QAT methods and only requires a concise wrapper for existing codes.

cs.LG↗

arXiv2024

Quantum Machine Learning in Log-based Anomaly Detection: Challenges and Opportunities

Log-based anomaly detection (LogAD) is the main component of Artificial Intelligence for IT Operations (AIOps), which can detect anomalous that occur during the system on-the-fly. Existing methods commonly extract log sequence features using classical machine learning techniques to identify whether a new sequence is an anomaly or not. However, these classical approaches often require trade-offs between efficiency and accuracy. The advent of quantum machine learning (QML) offers a promising alternative. By transforming parts of classical machine learning computations into parameterized quantum circuits (PQCs), QML can significantly reduce the number of trainable parameters while maintaining accuracy comparable to classical counterparts. In this work, we introduce a unified framework, \ourframework{}, for evaluating QML models in the context of LogAD. This framework incorporates diverse log data, integrated QML models, and comprehensive evaluation metrics. State-of-the-art methods such as DeepLog, LogAnomaly, and LogRobust, along with their quantum-transformed counterparts, are included in our framework.Beyond standard metrics like F1 score, precision, and recall, our evaluation extends to factors critical to QML performance, such as specificity, the number of circuits, circuit design, and quantum state encoding. Using \ourframework{}, we conduct extensive experiments to assess the performance of these models and their quantum counterparts, uncovering valuable insights and paving the way for future research in QML model selection and design for LogAD.

cs.LG↗

arXiv2024

Improve Sensitivity Analysis Synthesizing Randomized Clinical Trials With Limited Overlap

Randomized clinical trials are the gold standard when estimating the average treatment effect. However, they are usually not a random sample from the real-world population because of the inclusion/exclusion rules. Meanwhile, observational studies typically consist of representative samples from the real-world population. However, due to unmeasured confounding, sensitivity analysis is often used to estimate bounds for the average treatment effect without relying on stringent assumptions of other existing methods. This article introduces a synthesis estimator that improves sensitivity analysis in observational studies by incorporating randomized clinical trial data, even when overlap in covariate distribution is limited due to inclusion/exclusion criteria. We show that the proposed estimator will give a tighter bound when a "separability" condition holds for the sensitivity parameter. Theoretical proofs and simulations show that this method provides a tighter bound than the sensitivity analysis using only observational study. We apply this method to combine an observational study on drug effectiveness with a partially overlapping RCT dataset, yielding improved average treatment effect bounds.

stat.ME↗