arXiv subjects

Ziyu Xu

Publications and source records attributed to Ziyu Xu.

At least 19 recordsLinked to original sources

arXiv2026

Nuisance-Aware Muon Tomography

Cosmic-ray muon scattering tomography can image dense, shielded, or inaccessible objects without an artificial radiation source. In a compact magnet-free tracker, however, each accepted muon provides only a few hit positions and no event-by-event momentum measurement. The downstream hit residual is therefore a compound observable: target scattering, muon momentum, detector resolution, support material, air scattering, and track extrapolation all enter the same measured displacement. We introduce Nuisance-Aware Muon Tomography (NAMT), a residual-likelihood reconstruction method for magnet-free trackers. The upstream hits define the incident track, downstream hit residuals carry the scattering signal, and a radiation-length density field $\lambda=1/X_0$ predicts their material-induced variance through a path integral. NAMT marginalizes the unmeasured momentum with a shared event-level scattering scale and uses open-field blank scans to fix detector and environmental residuals before object reconstruction. On eight Geant4 benchmark scenes spanning strong, weak, and negative scattering contrast, NAMT-4P reaches a mean area under the ROC curve (AUC) of $0.916$ at $120$k effective muons and $1$ mm hit error, compared with $0.784$ for ASR, $0.749$ for MLS-EM, and $0.643$ for PoCA. NAMT-3P uses one downstream hit plane in reconstruction and still reaches $0.909$ mean AUC at the reference setting, while giving the highest reference mean contrast-to-noise ratio (CNR) and the best mean AUC at $30$k muons.

physics.ins-det↗

arXiv2026

Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design

When reliable target structures are unavailable at scale or phenotypes arise from dysregulated pathways, transcriptomic perturbations provide a system-level functional readout for drug action. In this work, we formalize \emph{Transcriptome-based Drug Design (TBDD)} as a generative inverse problem: designing drug molecules conditioned on desired transcriptomic state transitions. We analyze the inherently ill-posed nature of this task, which is further complicated by the profound domain gap between biology and chemistry and by the sparsity of transcriptomic signals. To address these challenges, we propose \textbf{\themodel{}} (A \textbf{C}ell\textbf{U}lar \textbf{R}esponse \textbf{E}ngine), a multi-resolution transcriptome-guided diffusion framework. \themodel{} features a specialized \textbf{Transcriptome Perturbation Functional Feature Extractor (TFE)} that (1) distills function-oriented perturbation embeddings from pre/post states, (2) aligns these signatures to dual chemical views to bridge the cross-modal gap, and (3) performs heterogeneity-aware aggregation to extract robust state-specific signals from noisy transcriptomic data. Extensive evaluations on both standard benchmarks and rigorous out-of-distribution protocols demonstrate that \themodel{} consistently outperforms strong baselines in structural quality and functional consistency. Furthermore, we validate its practical utility via a zero-shot gene-inhibitor design task, highlighting the potential of phenotype-driven generative discovery.

cs.LG↗

arXiv2026

Improving online FDR procedures via online analogs of e-closure and compound e-values

In many scientific applications, hypotheses are generated and tested continuously in a stream. We develop a framework for improving online multiple testing procedures with false discovery rate (FDR) control under arbitrary dependence. Our approach is two-fold: we construct methods via the online e-closure principle, as well as a novel formulation of online compound e-values that is defined through donations. This yields strict power improvements over state-of-the-art e-value and p-value procedures while retaining FDR control. We further derive algorithms that compute the decision at time $t$ in $O(\log t)$ time, and we demonstrate improved empirical performance on synthetic and real data.

stat.ME↗

arXiv2025

Active multiple testing with proxy p-values and e-values

Researchers often lack the resources to test every hypothesis of interest directly or compute test statistics comprehensively, but often possess auxiliary data from which we can compute an estimate of the experimental outcome. We introduce a novel approach for selecting which hypotheses to query a statistic (e.g., run an experiment, perform expensive computation, etc.) in a hypothesis testing setup by leveraging estimates to compute proxy statistics. Our framework allows a scientist to propose a proxy statistic and then query the true statistic with some probability based on the value of the proxy. We make no assumptions about how the proxy is derived, and it can be arbitrarily dependent on the true statistic. If the true statistic is not queried, the proxy is used in its place. We characterize "active" methods that produce valid p-values and e-values in this setting and utilize this framework in the multiple testing setting to create procedures with false discovery rate (FDR) control. Through simulations and real data analysis of causal effects in scCRISPR screen experiments, we empirically demonstrate that our proxy framework has both high power and low resource usage when our proxies are accurate estimates of the respective true statistics.

stat.ME↗

arXiv2025

More powerful multiple testing under dependence via randomization

We develop a technique to improve the power of any e-value by a simple randomization involving one independent uniform random variable. Using this framework, we show that two procedures for false discovery rate (FDR) control -- the Benjamini-Yekutieli procedure for dependent p-values, and the e-Benjamini-Hochberg procedure for dependent e-values -- can be improved through randomization. We also improve the Hommel test under dependence, and post-selection inference procedures for confidence intervals with false coverage rate (FCR) that allow for arbitrary selection rules and dependence. Importantly, our randomized improvements are never worse than the originals and are typically strictly more powerful, with marked improvements in simulations.

stat.ME↗

arXiv2025

Systematic Evaluation and Guidelines for Segment Anything Model in Surgical Video Analysis

Surgical video segmentation is critical for AI to interpret spatial-temporal dynamics in surgery, yet model performance is constrained by limited annotated data. The SAM2 model, pretrained on natural videos, offers potential for zero-shot surgical segmentation, but its applicability in complex surgical environments, with challenges like tissue deformation and instrument variability, remains unexplored. We present the first comprehensive evaluation of the zero-shot capability of SAM2 in 9 surgical datasets (17 surgery types), covering laparoscopic, endoscopic, and robotic procedures. We analyze various prompting (points, boxes, mask) and {finetuning (dense, sparse) strategies}, robustness to surgical challenges, and generalization across procedures and anatomies. Key findings reveal that while SAM2 demonstrates notable zero-shot adaptability in structured scenarios (e.g., instrument segmentation, {multi-organ segmentation}, and scene segmentation), its performance varies under dynamic surgical conditions, highlighting gaps in handling temporal coherence and domain-specific artifacts. These results highlight future pathways to adaptive data-efficient solutions for the surgical data science field.

cs.CV↗

arXiv2025

Robust Trajectory Tracking of Autonomous Surface Vehicle via Lie Algebraic Online MPC

Autonomous surface vehicles (ASVs) are influenced by environmental disturbances such as wind and waves, making accurate trajectory tracking a persistent challenge in dynamic marine conditions. In this paper, we propose an efficient controller for trajectory tracking of marine vehicles under unknown disturbances by combining a convex error-state MPC on the Lie group augmented by an online learning module to compensate for these disturbances in real time. This design enables adaptive and robust tracking control while maintaining computational efficiency. Extensive evaluations in the Virtual RobotX (VRX) simulator, and real-world field experiments demonstrate that our method achieves superior tracking accuracy under various disturbance scenarios compared with existing approaches.

cs.RO↗

arXiv2025

Human-Machine Ritual: Synergic Performance through Real-Time Motion Recognition

We introduce a lightweight, real-time motion recognition system that enables synergic human-machine performance through wearable IMU sensor data, MiniRocket time-series classification, and responsive multimedia control. By mapping dancer-specific movement to sound through somatic memory and association, we propose an alternative approach to human-machine collaboration, one that preserves the expressive depth of the performing body while leveraging machine learning for attentive observation and responsiveness. We demonstrate that this human-centered design reliably supports high accuracy classification (<50 ms latency), offering a replicable framework to integrate dance-literate machines into creative, educational, and live performance contexts.

cs.LG↗

arXiv2025

Bringing closure to FDR control: beating the e-Benjamini-Hochberg procedure

False discovery rate (FDR) has been a key metric for error control in multiple hypothesis testing, and many methods have developed for FDR control across a diverse cross-section of settings and applications. We develop a closure principle for all FDR controlling procedures, i.e., we provide a characterization based on e-values for all admissible FDR controlling procedures. A general version of this closure principle can recover any multiple testing error metric and allows one to choose the error metric post-hoc. We leverage this idea to formulate the closed eBH procedure, a (usually strict) improvement over the eBH procedure for FDR control when provided with e-values. This also yields a closed BY procedure that dominates the Benjamini-Yekutieli (BY) procedure for FDR control with arbitrarily dependent p-values, thus proving that the latter is inadmissibile. We demonstrate the practical performance of our new procedures in simulations.

stat.ME↗

arXiv2025

Bringing Closure to False Discovery Rate Control: A General Principle for Multiple Testing

We present a novel necessary and sufficient principle for multiple testing methods controlling an expected loss. This principle asserts that every such multiple testing method is a special case of a general closed testing procedure based on e-values. It generalizes the Closure Principle, known to underlie all methods controlling familywise error and tail probabilities of false discovery proportions, to a large class of error rates -- in particular to the false discovery rate (FDR). By writing existing methods as special cases of this procedure, we can achieve uniform improvements, as we demonstrate for the e-Benjamini-Hochberg and the Benjamini-Yekutieli procedures, and the self-consistent method of Su (2018). We also show that methods derived using our novel e-Closure Principle generally control their error rate not just for one rejected set, but simultaneously over many, allowing post hoc flexibility for the researcher. Moreover, because all multiple testing methods for the expected loss error metrics covered by our framework are derived from the same procedure, researchers may even choose the error metric post hoc. Under certain conditions, this flexibility even extends to post hoc choice of the nominal error rate.

stat.ME↗

arXiv2025

Don't Overthink It: A Survey of Efficient R1-style Large Reasoning Models

Recently, Large Reasoning Models (LRMs) have gradually become a research hotspot due to their outstanding performance in handling complex tasks. Among them, DeepSeek R1 has garnered significant attention for its exceptional performance and open-source nature, driving advancements in the research of R1-style LRMs. Unlike traditional Large Language Models (LLMs), these models enhance logical deduction and decision-making capabilities during reasoning by incorporating mechanisms such as long chain-of-thought and self-reflection through reinforcement learning. However, with the widespread application of these models, the problem of overthinking has gradually emerged. Specifically, when generating answers, these models often construct excessively long reasoning chains with redundant or repetitive steps, which leads to reduced reasoning efficiency and may affect the accuracy of the final answer. To this end, various efficient reasoning methods have been proposed, aiming to reduce the length of reasoning paths without compromising model performance and reasoning capability. By reviewing the current research advancements in the field of efficient reasoning methods systematically, we categorize existing works into two main directions based on the lens of single-model optimization versus model collaboration: (1) Efficient Reasoning with Single Model, which focuses on improving the reasoning efficiency of individual models; and (2) Efficient Reasoning with Model Collaboration, which explores optimizing reasoning paths through collaboration among multiple models. Besides, we maintain a public GitHub repository that tracks the latest progress in efficient reasoning methods.

cs.AI↗

arXiv2025

OrthoInsight: Rib Fracture Diagnosis and Report Generation Based on Multi-Modal Large Models

The growing volume of medical imaging data has increased the need for automated diagnostic tools, especially for musculoskeletal injuries like rib fractures, commonly detected via CT scans. Manual interpretation is time-consuming and error-prone. We propose OrthoInsight, a multi-modal deep learning framework for rib fracture diagnosis and report generation. It integrates a YOLOv9 model for fracture detection, a medical knowledge graph for retrieving clinical context, and a fine-tuned LLaVA language model for generating diagnostic reports. OrthoInsight combines visual features from CT images with expert textual data to deliver clinically useful outputs. Evaluated on 28,675 annotated CT images and expert reports, it achieves high performance across Diagnostic Accuracy, Content Completeness, Logical Coherence, and Clinical Guidance Value, with an average score of 4.28, outperforming models like GPT-4 and Claude-3. This study demonstrates the potential of multi-modal learning in transforming medical image analysis and providing effective support for radiologists.

eess.IV↗

arXiv2025

Seg2Box: 3D Object Detection by Point-Wise Semantics Supervision

LiDAR-based 3D object detection and semantic segmentation are critical tasks in 3D scene understanding. Traditional detection and segmentation methods supervise their models through bounding box labels and semantic mask labels. However, these two independent labels inherently contain significant redundancy. This paper aims to eliminate the redundancy by supervising 3D object detection using only semantic labels. However, the challenge arises due to the incomplete geometry structure and boundary ambiguity of point-cloud instances, leading to inaccurate pseudo labels and poor detection results. To address these challenges, we propose a novel method, named Seg2Box. We first introduce a Multi-Frame Multi-Scale Clustering (MFMS-C) module, which leverages the spatio-temporal consistency of point clouds to generate accurate box-level pseudo-labels. Additionally, the Semantic?Guiding Iterative-Mining Self-Training (SGIM-ST) module is proposed to enhance the performance by progressively refining the pseudo-labels and mining the instances without generating pseudo-labels. Experiments on the Waymo Open Dataset and nuScenes Dataset show that our method significantly outperforms other competitive methods by 23.7\% and 10.3\% in mAP, respectively. The results demonstrate the great label-efficient potential and advancement of our method.

cs.CV↗

arXiv2025

L4DR: LiDAR-4DRadar Fusion for Weather-Robust 3D Object Detection

LiDAR-based vision systems are integral for 3D object detection, which is crucial for autonomous navigation. However, they suffer from performance degradation in adverse weather conditions due to the quality deterioration of LiDAR point clouds. Fusing LiDAR with the weather-robust 4D radar sensor is expected to solve this problem. However, the fusion of LiDAR and 4D radar is challenging because they differ significantly in terms of data quality and the degree of degradation in adverse weather. To address these issues, we introduce L4DR, a weather-robust 3D object detection method that effectively achieves LiDAR and 4D Radar fusion. Our L4DR includes Multi-Modal Encoding (MME) and Foreground-Aware Denoising (FAD) technique to reconcile sensor gaps, which is the first exploration of the complementarity of early fusion between LiDAR and 4D radar. Additionally, we design an Inter-Modal and Intra-Modal ({IM}2 ) parallel feature extraction backbone coupled with a Multi-Scale Gated Fusion (MSGF) module to counteract the varying degrees of sensor degradation under adverse weather conditions. Experimental evaluation on a VoD dataset with simulated fog proves that L4DR is more adaptable to changing weather conditions. It delivers a significant performance increase under different fog levels, improving the 3D mAP by up to 20.0% over the traditional LiDAR-only approach. Moreover, the results on the K-Radar dataset validate the consistent performance improvement of L4DR in real-world adverse weather conditions.

cs.CV↗

arXiv2024

Active, anytime-valid risk controlling prediction sets

Rigorously establishing the safety of black-box machine learning models concerning critical risk measures is important for providing guarantees about model behavior. Recently, Bates et. al. (JACM '24) introduced the notion of a risk controlling prediction set (RCPS) for producing prediction sets that are statistically guaranteed low risk from machine learning models. Our method extends this notion to the sequential setting, where we provide guarantees even when the data is collected adaptively, and ensures that the risk guarantee is anytime-valid, i.e., simultaneously holds at all time steps. Further, we propose a framework for constructing RCPSes for active labeling, i.e., allowing one to use a labeling policy that chooses whether to query the true label for each received data point and ensures that the expected proportion of data points whose labels are queried are below a predetermined label budget. We also describe how to use predictors (i.e., the machine learning model for which we provide risk control guarantees) to further improve the utility of our RCPSes by estimating the expected risk conditioned on the covariates. We characterize the optimal choices of label policy and predictor under a fixed label budget and show a regret result that relates the estimation error of the optimal labeling policy and predictor to the wealth process that underlies our RCPSes. Lastly, we present practical ways of formulating label policies and empirically show that our label policies use fewer labels to reach higher utility than naive baseline labeling strategies on both simulations and real data.

stat.ML↗

arXiv2024

An online generalization of the (e-)Benjamini-Hochberg procedure

In online multiple testing, the hypotheses arrive one by one, and at each time we must immediately reject or accept the current hypothesis solely based on the data and hypotheses observed so far. Many online procedures have been proposed, but none of them are generalizations of the Benjamini-Hochberg (BH) procedure based on p-values, or of the e-BH procedure that uses e-values. In this paper, we consider a relaxed problem setup that allows the current hypothesis to be rejected at any later step. We show that this relaxation allows us to define -- what we justify extensively to be -- the natural and appropriate online extension of the BH and e-BH procedures. We show that the FDR guarantees for BH (resp. e-BH) and online BH (resp. online e-BH) are identical under positive, negative or arbitrary dependence, at fixed and stopping times. Further, the online BH (resp. online e-BH) rule recovers the BH (resp. e-BH) rule as a special case when the number of hypotheses is known to be fixed. Of independent interest, our proof techniques also allow us to prove that numerous existing online procedures, which were known to control the FDR at fixed times, also control the FDR at stopping times.

stat.ME↗

arXiv2024

Geometric Visualizations of Single and Entangled Qubits

The Bloch Sphere visualization of the possible states of a single qubit has proved a useful pedagogical and conceptual tool as a one-to-one map between qubit states and points in a 3-D space. However, understanding many important concepts of quantum mechanics, such as entanglement, requires developing intuitions about states with a minimum of two qubits, which map one-to-one to unvisualizable spaces of 6 dimensions and higher. In this paper we circumvent this visualization issue by creating maps of subspaces of 1- and 2-qubit systems that quantitatively and qualitatively encode properties of these states in their geometries. For the 1-qubit case, the subspace approach allows one to visualize how mixed states relate to different choices of measurement in a basis-independent way and how to read off the entries in a density matrix representation of these states from lengths in a simple diagram. For the 2-qubit case, a toroidal map of 2-qubit states illuminates the non-trivial topology of the state space while allowing one to simultaneously read off, in distances and angles, the level of entanglement in the 2-qubit state and the mixed-state properties of its constituent qubits. By encoding states and their evolutions through quantum logic gates with little to no need of mathematical formalism, these maps may prove particularly useful for understanding fundamental concepts of quantum mechanics and quantum information at the introductory level. Interactive versions of the visualizations introduced in this paper are available at https://quantum.bard.edu/.

quant-ph↗

arXiv2024

Post-selection inference for e-value based confidence intervals

Suppose that one can construct a valid $(1-δ)$-confidence interval (CI) for each of $K$ parameters of potential interest. If a data analyst uses an arbitrary data-dependent criterion to select some subset $S$ of parameters, then the aforementioned CIs for the selected parameters are no longer valid due to selection bias. We design a new method to adjust the intervals in order to control the false coverage rate (FCR). The main established method is the "BY procedure" by Benjamini and Yekutieli (JASA, 2005). The BY guarantees require certain restrictions on the selection criterion and on the dependence between the CIs. We propose a new simple method which, in contrast, is valid under any dependence structure between the original CIs, and any (unknown) selection criterion, but which only applies to a special, yet broad, class of CIs that we call e-CIs. To elaborate, our procedure simply reports $(1-δ|S|/K)$-CIs for the selected parameters, and we prove that it controls the FCR at $δ$ for confidence intervals that implicitly invert e-values; examples include those constructed via supermartingale methods, via universal inference, or via Chernoff-style bounds, among others. The e-BY procedure is admissible, and recovers the BY procedure as a special case via a particular calibrator. Our work also has implications for post-selection inference in sequential settings, since it applies at stopping times, to continuously-monitored confidence sequences, and under bandit sampling. We demonstrate the efficacy of our procedure using numerical simulations and real A/B testing data from Twitter.

math.ST↗