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Rui Qiu

Publications and source records attributed to Rui Qiu.

At least 19 recordsLinked to original sources

Marginal Coordinate Test for Fr\'echet Regression with Random Objects

We develop a marginal coordinate test for regression with Euclidean predictors and a random-object response in a separable metric space. The goal is to test whether a predictor provides additional information about the response conditional on the remaining predictors. In a semi-supervised design, an unlabeled sample is used to estimate predictor conditional means, while an independent labeled sample is reserved for inference. The resulting residuals are combined with a product-space kernel to form a kernel conditional mean dependence (KCMD) U-statistic without requiring a response residual. The primary identity-based test targets a necessary conditional mean restriction, while a multiple-transformation extension probes broader alternatives. We establish a weighted centered chi-square null limit, wild bootstrap validity, consistency against fixed detectable alternatives, and local power under mean-element alternatives. For simultaneous inference, truncated p-to-e calibration combined with e-BH provides asymptotic false discovery rate control under general dependence. Simulations with Euclidean and non-Euclidean responses, together with a New York City taxi-flow analysis, illustrate the method.

stat.ME

DetMesh-Gadep: Triangulated Surface Modeling and GPU-based Monte Carlo Efficiency Calibration of High-Purity Germanium Detectors

Sourceless efficiency calibration of high-purity germanium (HPGe) detectors can provide accurate detector-response information without experiments using radioactive calibration sources, offering advantages in both convenience and safety. In many practical implementations, this process is performed using Monte Carlo simulation; however, its performance is constrained by the accuracy of detector modeling, the operational complexity of simulation frameworks, and the computational-resource requirements associated with CPU-based parallelization. In this study, a complete detector modeling and simulation framework is proposed. The detector modeling program DetMesh can generate triangulated surface geometry from parameterized detector models, providing advantages in the representation of complex geometric boundaries. It incorporates standard geometric operations and a geometric library, and is lightweight with strong extensibility. The generated geometry is then input into Gadep, a GPU-based Monte Carlo computational kernel, to enable rapid simulation. For $1\times 10^8$ particles, a single RTX 4090 achieved a speedup factor of 13.53 compared with simultaneous computation using 60 CPU cores. The proposed framework has low implementation cost and broad applicability, providing a complete solution for refined detector modeling and calibration.

physics.ins-det

A Wideband Composite Sequence Impedance Model for Evaluation of Interactions in Unbalanced Power-Electronic-Based Power Systems

This paper proposes a wideband composite sequence impedance model (WCSIM)-based analysis method to evaluate the interactions in power-electronic-based power systems subjected to unbalanced grid faults or with unbalanced loads. The WCSIM-based method intuitively assesses the impact of the small-signal interconnection among the positive-, negative-, and zero-sequence circuits on the interaction stability of unbalanced power systems. The effectiveness of this method is demonstrated using a permanent magnet synchronous generator-based weak grid system under a single-line-to-ground fault (SLGF). Frequency scanning results and controller hardware-in-loop tests validate both the correctness of the WCSIM and the effectiveness of the WCSIM-based analysis method.

eess.SY

Completing A Systematic Review in Hours instead of Months with Interactive AI Agents

Systematic reviews (SRs) are vital for evidence-based practice in high stakes disciplines, such as healthcare, but are often impeded by intensive labors and lengthy processes that can take months to complete. Due to the high demand for domain expertise, existing automatic summarization methods fail to accurately identify relevant studies and generate high-quality summaries. To that end, we introduce InsightAgent, a human-centered interactive AI agent powered by large language models that revolutionize this workflow. InsightAgent partitions a large literature corpus based on semantics and employs a multi-agent design for more focused processing of literature, leading to significant improvement in the quality of generated SRs. InsightAgent also provides intuitive visualizations of the corpus and agent trajectories, allowing users to effortlessly monitor the actions of the agent and provide real-time feedback based on their expertise. Our user studies with 9 medical professionals demonstrate that the visualization and interaction mechanisms can effectively improve the quality of synthesized SRs by 27.2%, reaching 79.7% of human-written quality. At the same time, user satisfaction is improved by 34.4%. With InsightAgent, it only takes a clinician about 1.5 hours, rather than months, to complete a high-quality systematic review.

cs.HC

VADIS: A Visual Analytics Pipeline for Dynamic Document Representation and Information-Seeking

In the biomedical domain, visualizing the document embeddings of an extensive corpus has been widely used in information-seeking tasks. However, three key challenges with existing visualizations make it difficult for clinicians to find information efficiently. First, the document embeddings used in these visualizations are generated statically by pretrained language models, which cannot adapt to the user's evolving interest. Second, existing document visualization techniques cannot effectively display how the documents are relevant to users' interest, making it difficult for users to identify the most pertinent information. Third, existing embedding generation and visualization processes suffer from a lack of interpretability, making it difficult to understand, trust and use the result for decision-making. In this paper, we present a novel visual analytics pipeline for user driven document representation and iterative information seeking (VADIS). VADIS introduces a prompt-based attention model (PAM) that generates dynamic document embedding and document relevance adjusted to the user's query. To effectively visualize these two pieces of information, we design a new document map that leverages a circular grid layout to display documents based on both their relevance to the query and the semantic similarity. Additionally, to improve the interpretability, we introduce a corpus-level attention visualization method to improve the user's understanding of the model focus and to enable the users to identify potential oversight. This visualization, in turn, empowers users to refine, update and introduce new queries, thereby facilitating a dynamic and iterative information-seeking experience. We evaluated VADIS quantitatively and qualitatively on a real-world dataset of biomedical research papers to demonstrate its effectiveness.

cs.HC

Impact of Oxygen on DNA Damage Distribution in 3D Genome and its Correlation to Oxygen Enhancement Ratio after High-LET Irradiation

The variation of the oxygen enhancement ratio (OER) across linear energy transfer (LET) currently lacks a comprehensive mechanistic interpretation and a mechanistic model. Our earlier research revealed a significant correlation between the distribution of double-strand breaks (DSBs) within 3D genome and radiation-induced cell death, which offers valuable insights into the oxygen effect. We propose a model where the reaction of oxygen is represented as the probability of inducing DNA strand breaks. Then it is integrated into a track-structure Monte Carlo simulation to investigate the impact of oxygen on the distribution of DSBs within 3D genome. Using the parameters from our previous study, we calculate the OER values related to cell survival. Results show that the incidence ratios of clustered DSBs within a single topologically associating domain (TAD) (case 2) and within frequently interacting TADs (case 3) under aerobic and hypoxic conditions align with the trend in the OER of cell survival across LET. Our OER curves exhibit good correspondence with experimental data. This study provides a potentially mechanistic explanation for changes in OER across LET. High-LET irradiation leads to dense ionization events, resulting in an overabundance of lesions that readily induce case 2 and case 3, which have substantially higher probabilities of cell killing than other damage patterns. This may contribute to the main mechanism governing the variation of OER for high LET. Our study further underscores the importance of the DSB distribution within 3D genome in the context of radiation-induced cell death.

physics.bio-ph

Correlation Between DNA Double-Strand Break Distribution in 3D Genome and Radiation-Induced Cell Death

The target theory is the most classical hypothesis explaining radiation-induced cell death, the physical or biological nature of the "target" remains ambiguous. This study hypothesizes that the distribution of DNA double-strand breaks (DSBs) within the 3D genome is a pivotal factor affecting the probability of radiation-induced cell death. We propose that clustered DSBs in DNA segments with high interaction frequencies are more susceptible to leading to cell death than isolated DSBs. Topologically associating domains (TAD) can be regarded as the reference unit for evaluating the impact of DSB clustering in the 3D genome. To quantify this correlation between the DSB distribution in 3D genome and radiation-induced effect, we developed a simplified model considering the DSB distribution across TADs. Utilizing track-structure Monte Carlo codes to simulate the electron and carbon ion irradiation, we calculated the incidence of each case across a variety of radiation doses and LETs. Our simulation results indicate that DSBs in TADs with frequent interactions (case 3) are significantly more likely to induce cell death than clustered DSBs within a single TAD (case 2). Moreover, case 2 is significantly more likely to induce cell death than isolated DSBs (case 1). The curves of the incidence of case 2 and case 3 versus LETs have a similar shape to the radiation quality factor used in radiation protection. This indicates that these two cases are also associated with the stochastic effects induced by high LET irradiation. Our study underscores the significance of the 3D genome structure in the fundamental mechanisms of radiobiological effects. The hypothesis in our research offers novel perspectives on the mechanisms that regulate radiobiological effects. Moreover, it serves as a valuable reference for establishing mechanistic models that can predict cell survival under different doses and LETs.

physics.med-ph

PIG: Prompt Images Guidance for Night-Time Scene Parsing

Night-time scene parsing aims to extract pixel-level semantic information in night images, aiding downstream tasks in understanding scene object distribution. Due to limited labeled night image datasets, unsupervised domain adaptation (UDA) has become the predominant method for studying night scenes. UDA typically relies on paired day-night image pairs to guide adaptation, but this approach hampers dataset construction and restricts generalization across night scenes in different datasets. Moreover, UDA, focusing on network architecture and training strategies, faces difficulties in handling classes with few domain similarities. In this paper, we leverage Prompt Images Guidance (PIG) to enhance UDA with supplementary night knowledge. We propose a Night-Focused Network (NFNet) to learn night-specific features from both target domain images and prompt images. To generate high-quality pseudo-labels, we propose Pseudo-label Fusion via Domain Similarity Guidance (FDSG). Classes with fewer domain similarities are predicted by NFNet, which excels in parsing night features, while classes with more domain similarities are predicted by UDA, which has rich labeled semantics. Additionally, we propose two data augmentation strategies: the Prompt Mixture Strategy (PMS) and the Alternate Mask Strategy (AMS), aimed at mitigating the overfitting of the NFNet to a few prompt images. We conduct extensive experiments on four night-time datasets: NightCity, NightCity+, Dark Zurich, and ACDC. The results indicate that utilizing PIG can enhance the parsing accuracy of UDA.

cs.CV

Semi-supervised Fr\'echet Regression

This paper explores the field of semi-supervised Fr\'echet regression, driven by the significant costs associated with obtaining non-Euclidean labels. Methodologically, we propose two novel methods: semi-supervised NW Fr\'echet regression and semi-supervised kNN Fr\'echet regression, both based on graph distance acquired from all feature instances. These methods extend the scope of existing semi-supervised Euclidean regression methods. We establish their convergence rates with limited labeled data and large amounts of unlabeled data, taking into account the low-dimensional manifold structure of the feature space. Through comprehensive simulations across diverse settings and applications to real data, we demonstrate the superior performance of our methods over their supervised counterparts. This study addresses existing research gaps and paves the way for further exploration and advancements in the field of semi-supervised Fr\'echet regression.

math.ST

Mathematical Analysis of FLASH Effect Models Based on Theoretical Hypotheses

Clinical applications of FLASH radiotherapy require formulas to describe how the FLASH radiation features and other related factors determine the FLASH effect. Mathematical analysis of the models can connect the theoretical hypotheses with the radiobiological effect, which provides the foundation for establishing clinical application models. We abstract the complex models of the oxygen depletion hypothesis and radical recombination-antioxidants hypothesis into concise mathematical equations. The equations are solved to analyze how the radiation features and other factors influence the FLASH effect. Then we propose methodologies for determining the parameters in the models and utilizing the models to predict the FLASH effect.The formulas linking the physical, chemical and biological factors to the FLASH effect are obtained through mathematical derivation of the equation. The analysis indicates that the initial oxygen concentration, radiolytic oxygen consumption and oxygen recovery are key factors for the oxygen depletion hypothesis and that the level of antioxidants is the key factor for the radical recombination-antioxidants hypothesis. According to the model derivations and analysis, the methodologies for determining parameters and predicting the FLASH effect are proposed: the criteria for data filtration, the strategy of hybrid FLASH and conventional dose rate irradiation to ensure the acquisition of effective experimental data across a wide dose range, the pipelines of fitting parameters and predicting the FLASH effect. The derived formulas can be used to calculate the FLASH effect in future clinical FLASH radiotherapy. The proposed methodologies guide to obtain sufficient high-quality datasets and utilize them to predict the FLASH effect. Furthermore, this study indicates the key factors of the FLASH effect and offers clues to further explore the FLASH mechanism.

physics.med-ph

SKG: A Versatile Information Retrieval and Analysis Framework for Academic Papers with Semantic Knowledge Graphs

The number of published research papers has experienced exponential growth in recent years, which makes it crucial to develop new methods for efficient and versatile information extraction and knowledge discovery. To address this need, we propose a Semantic Knowledge Graph (SKG) that integrates semantic concepts from abstracts and other meta-information to represent the corpus. The SKG can support various semantic queries in academic literature thanks to the high diversity and rich information content stored within. To extract knowledge from unstructured text, we develop a Knowledge Extraction Module that includes a semi-supervised pipeline for entity extraction and entity normalization. We also create an ontology to integrate the concepts with other meta information, enabling us to build the SKG. Furthermore, we design and develop a dataflow system that demonstrates how to conduct various semantic queries flexibly and interactively over the SKG. To demonstrate the effectiveness of our approach, we conduct the research based on the visualization literature and provide real-world use cases to show the usefulness of the SKG. The dataset and codes for this work are available at https://osf.io/aqv8p/?view_only=2c26b36e3e3941ce999df47e4616207f.

cs.IR

ChameleMon: Shifting Measurement Attention as Network State Changes

Flow-level network measurement is critical to many network applications. Among various measurement tasks, packet loss detection and heavy-hitter detection are two most important measurement tasks, which we call the two key tasks. In practice, the two key tasks are often required at the same time, but existing works seldom handle both tasks. In this paper, we design ChameleMon to support the two key tasks simultaneously. One key design/novelty of ChameleMon is to shift measurement attention as network state changes, through two dimensions of dynamics: 1) dynamically allocating memory between the two key tasks; 2) dynamically monitoring the flows of importance. To realize the key design, we propose a key technique, leveraging Fermat's little theorem to devise a flexible data structure, namely FermatSketch. FermatSketch is dividable, additive, and subtractive, supporting the two key tasks. We have fully implemented a ChameleMon prototype on a testbed with a Fat-tree topology. We conduct extensive experiments and the results show ChameleMon supports the two key tasks with low memory/bandwidth overhead, and more importantly, it can automatically shift measurement attention as network state changes.

cs.NI

3D Random Occlusion and Multi-Layer Projection for Deep Multi-Camera Pedestrian Localization

Although deep-learning based methods for monocular pedestrian detection have made great progress, they are still vulnerable to heavy occlusions. Using multi-view information fusion is a potential solution but has limited applications, due to the lack of annotated training samples in existing multi-view datasets, which increases the risk of overfitting. To address this problem, a data augmentation method is proposed to randomly generate 3D cylinder occlusions, on the ground plane, which are of the average size of pedestrians and projected to multiple views, to relieve the impact of overfitting in the training. Moreover, the feature map of each view is projected to multiple parallel planes at different heights, by using homographies, which allows the CNNs to fully utilize the features across the height of each pedestrian to infer the locations of pedestrians on the ground plane. The proposed 3DROM method has a greatly improved performance in comparison with the state-of-the-art deep-learning based methods for multi-view pedestrian detection.

cs.CV

Random Forest Weighted Local Fr\'echet Regression with Random Objects

Statistical analysis is increasingly confronted with complex data from metric spaces. Petersen and M\"uller (2019) established a general paradigm of Fr\'echet regression with complex metric space valued responses and Euclidean predictors. However, the local approach therein involves nonparametric kernel smoothing and suffers from the curse of dimensionality. To address this issue, we in this paper propose a novel random forest weighted local Fr\'echet regression paradigm. The main mechanism of our approach relies on a locally adaptive kernel generated by random forests. Our first method uses these weights as the local average to solve the conditional Fr\'echet mean, while the second method performs local linear Fr\'echet regression, both significantly improving existing Fr\'echet regression methods. Based on the theory of infinite order U-processes and infinite order $M_{m_n}$-estimator, we establish the consistency, rate of convergence, and asymptotic normality for our local constant estimator, which covers the current large sample theory of random forests with Euclidean responses as a special case. Numerical studies show the superiority of our methods with several commonly encountered types of responses such as distribution functions, symmetric positive-definite matrices, and sphere data. The practical merits of our proposals are also demonstrated through the application to New York taxi data and human mortality data.

stat.ML

Intercomparison of micro- and nanodosimetry Monte Carlo simulations: an approach to assess the influence of different cross-sections for low-energy electrons on the dispersion of results

An intercomparison of microdosimetric and nanodosimetric quantities simulated Monte Carlo codes is in progress with the goal of assessing the uncertainty contribution to simulated results due to the uncertainties of the electron interaction cross-sections used in the codes. In the first stage of the intercomparison, significant discrepancies were found for nanodosimetric quantities as well as for microdosimetric simulations of a radiation source placed at the surface of a spherical water scoring volume. This paper reports insight gained from further analysis, including additional results for the microdosimetry case where the observed discrepancies in the simulated distributions could be traced back to the difference between track-structure and condensed-history approaches. Furthermore, detailed investigations into the sensitivity of nanodosimetric distributions to alterations in inelastic electron scattering cross-sections are presented which were conducted in the lead up to the definition of an approach to be used in the second stage of the intercomparison to come. The suitability of simulation results for assessing the sought uncertainty contributions from cross-sections is discussed and a proposed framework is described.

physics.med-ph

Modeling of cellular response after FLASH irradiation: a quantitative analysis based on the radiolytic oxygen depletion hypothesis

Purpose: Recent studies suggest ultra-high dose rate (FLASH) irradiation can spare normal tissues from radiotoxicity, while efficiently controlling the tumor, and this is known as the FLASH effect. This study performed theoretical analyses about the impact of radiolytic oxygen depletion (ROD) on the cellular responses after FLASH irradiation. Methods: Monte Carlo simulation was used to model the ROD process, determine the DNA damage, and calculate the amount of oxygen depleted (LROD) during FLASH exposure. A mathematical model was applied to analyze oxygen tension (pO2) distribution in human tissues and the recovery of pO2 after FLASH irradiation. DNA damage and cell survival fractions (SFs) after FLASH irradiation were calculated. The impact of initial cellular pO2, FLASH pulse number, pulse interval, and radiation quality of the source particles on ROD and subsequent cellular responses were systematically evaluated. Results: The simulated electron LROD range was 0.38-0.43 {\mu}M/Gy when pO2 ranged from 7.5-160 mmHg. The calculated DNA damage and SFs show that radioprotective effect is only evident in cells with a lower pO2. Different irradiation setups alter the cellular responses by modifying the pO2. Single pulse delivery or multi-pulse delivery with pulse intervals shorter than 10-50 ms resulted in fewer DNA damages and higher SFs. Source particles with a low radiation quality have a higher capacity to deplete oxygen, and thus, lead to a more conspicuous radioprotective effect. Conclusions: The FLASH radioprotective effect due to ROD may only be observed in cells with a low pO2. Single pulse delivery or multi-pulse delivery with short pulse intervals are suggested for FLASH irradiation to avoid oxygen tension recovery during pulse intervals. Source particles with low radiation quality are preferred for their conspicuous radioprotective effects.

physics.med-ph

Oxygen depletion hypothesis remains controversial: a mathematical model of oxygen depletion during FLASH radiation

Background: Experiments have reported low normal tissue toxicities during FLASH radiation, but the mechanism has not been elaborated. Several hypotheses have been proposed to explain the mechanism. The oxygen depletion hypothesis has been introduced and mostly studied qualitatively. Methods: We present a computational model to describe the time-dependent change of oxygen concentration in the tissue. The kinetic equation of the model is solved numerically using the finite difference method. The model is used to analyze the FLASH effect with the oxygen depletion hypothesis, and the brain tissue is chosen as an example. Results: The oxygen distribution is determined by the oxygen consumption rate of the tissue and the distance between capillaries. The change of oxygen concentration with time after radiation has been found to follow a negative exponential function, and the time constant is determined by the distance between capillaries. When the dose rate is high enough, the same dose results in the same change of oxygen concentration regardless of dose rate. The analysis of FLASH effect in the brain tissue based on this model does not support the explanation of the oxygen depletion hypothesis. Conclusions: The oxygen depletion hypothesis remains controversial because oxygen in most normal tissues cannot be depleted by FLASH radiation according to the mathematical analysis with this model and experiments on the expression and distribution of the hypoxia-inducible factors.

physics.med-ph

Improved Algorithms and Coupled Neutron-Photon Transport for Auto-Importance Sampling Method

The Auto-Importance Sampling (AIS) method is a Monte Carlo variance reduction technique proposed for deep penetration problems, which can significantly improve computational efficiency without pre-calculations for importance distribution. However, the AIS method is only validated with several simple examples, and cannot be used for coupled neutron-photon transport. This paper presents the improved algorithms for the AIS method, including particle transport, fictitious particles creation and adjustment, fictitious surface geometry, random number allocation and calculation of the estimated relative error. These improvements allow the AIS method to be applicable to complicated deep penetration problems with complex geometry and multiple materials. A coupled Neutron-Photon Auto-Importance Sampling (NP-AIS) method is proposed to solve the deep penetration problems of coupled neutron-photon transport using the improved algorithms. The NUREG/CR-6115 PWR benchmark was calculated by using the methods of NP-AIS, geometry splitting with Russian roulette and the analog Monte Carlo, respectively. The calculation results of NP-AIS were in good agreement with those of geometry splitting with Russian roulette and the benchmark solutions. The computational efficiency of NP-AIS for both neutron and photon was much better than that of geometry splitting with Russian roulette in most cases, and increased by several orders of magnitude compared with that of the analog Monte Carlo.

nucl-th