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Yuxi Chen

Publications and source records attributed to Yuxi Chen.

At least 37 records · Page 2Linked to original sources

Top-$k$ Feature Importance Ranking

Accurate ranking of important features is a fundamental challenge in interpretable machine learning with critical applications in scientific discovery and decision-making. Unlike feature selection and feature importance, the specific problem of ranking important features has received considerably less attention. We introduce RAMPART (Ranked Attributions with MiniPatches And Recursive Trimming), a framework that utilizes any existing feature importance measure in a novel algorithm specifically tailored for ranking the top-$k$ features. Our approach combines an adaptive sequential halving strategy that progressively focuses computational resources on promising features with an efficient ensembling technique using both observation and feature subsampling. Unlike existing methods that convert importance scores to ranks as post-processing, our framework explicitly optimizes for ranking accuracy. We provide theoretical guarantees showing that RAMPART achieves the correct top-$k$ ranking with high probability under mild conditions, and demonstrate through extensive simulation studies that RAMPART consistently outperforms popular feature importance methods, concluding with a high-dimensional genomics case study.

cs.LG↗

Knowing or Guessing? Robust Medical Visual Question Answering via Joint Consistency and Contrastive Learning

In high-stakes medical applications, consistent answering across diverse question phrasings is essential for reliable diagnosis. However, we reveal that current Medical Vision-Language Models (Med-VLMs) exhibit concerning fragility in Medical Visual Question Answering, as their answers fluctuate significantly when faced with semantically equivalent rephrasings of medical questions. We attribute this to two limitations: (1) insufficient alignment of medical concepts, leading to divergent reasoning patterns, and (2) hidden biases in training data that prioritize syntactic shortcuts over semantic understanding. To address these challenges, we construct RoMed, a dataset built upon original VQA datasets containing 144k questions with variations spanning word-level, sentence-level, and semantic-level perturbations. When evaluating state-of-the-art (SOTA) models like LLaVA-Med on RoMed, we observe alarming performance drops (e.g., a 40\% decline in Recall) compared to original VQA benchmarks, exposing critical robustness gaps. To bridge this gap, we propose Consistency and Contrastive Learning (CCL), which integrates two key components: (1) knowledge-anchored consistency learning, aligning Med-VLMs with medical knowledge rather than shallow feature patterns, and (2) bias-aware contrastive learning, mitigating data-specific priors through discriminative representation refinement. CCL achieves SOTA performance on three popular VQA benchmarks and notably improves answer consistency by 50\% on the challenging RoMed test set, demonstrating significantly enhanced robustness. Code will be released.

cs.CL↗

Omnidirectionally manipulated skyrmions in an orientationally chiral system

Skyrmions, originally from condensed matter physics, have been widely explored in various physical systems, including soft matter. A crucial challenge in manipulating topological solitary waves like skyrmions is controlling their flow on demand. Here, we control the arbitrary moving direction of skyrmions in a chiral liquid crystal system by adjusting the bias of the applied alternate current electric field. Specifically, the velocity, including both moving direction and speed can be continuously changed. The motion control of skyrmions originates from the symmetry breaking of the topological structure induced by flexoelectric-polarization effect. The omnidirectional control of topological solitons opens new avenues in light-steering and racetrack memories.

cond-mat.soft↗

Characterising Bugs in Jupyter Platform

As a representative literate programming platform, Jupyter is widely adopted by developers, data analysts, and researchers for replication, data sharing, documentation, interactive data visualization, and more. Understanding the bugs in the Jupyter platform is essential for ensuring its correctness, security, and robustness. Previous studies focused on code reuse, restoration, and repair execution environment for Jupyter notebooks. However, the bugs in Jupyter notebooks' hosting platform Jupyter are not investigated. In this paper, we investigate 387 bugs in the Jupyter platform. These Jupyter bugs are classified into 11 root causes and 11 bug symptoms. We identify 14 major findings for developers. More importantly, our study opens new directions in building tools for detecting and fixing bugs in the Jupyter platform.

cs.SE↗

Suppressing spurious oscillations and particle noise in particle-in-cell simulations

Particle-in-cell (PIC) simulations are essential for studying kinetic plasma processes, but they often suffer from statistical noise, especially in plasmas with fast flows. We have also found that the typical central difference scheme used in PIC codes to solve Maxwell's equations produces spurious oscillations near discontinuities, which can lead to unphysical solutions. In this work, we present numerical techniques to address these challenges within the semi-implicit PIC code FLEKS, which is based on the Gauss's Law-satisfying Energy-Conserving Semi-Implicit Particle-in-Cell method (GL-ECSIM). First, we introduce a Lax-Friedrichs-type diffusion term with a flux limiter into the Maxwell solver to suppress unphysical oscillations near discontinuities. Second, we propose a novel approach for calculating the current density in the comoving frame, which significantly reduces particle noise in simulations with fast plasma flows. Numerical tests are presented to demonstrate the effectiveness of these methods in mitigating spurious oscillations and noise in shock and magnetic reconnection simulations.

physics.comp-ph↗

Estimation of Tissue Deformation and Interactive Force in Robotic Surgery through Vision-based Learning

Goal: A limitation in robotic surgery is the lack of force feedback, due to challenges in suitable sensing techniques. To enhance the perception of the surgeons and precise force rendering, estimation of these forces along with tissue deformation level is presented here. Methods: An experimental test bed is built for studying the interaction, and the forces are estimated from the raw data. Since tissue deformation and stiffness are non-linearly related, they are independently computed for enhanced reliability. A Convolutional Neural Network (CNN) based vision model is deployed, and both classification and regression models are developed. Results: The forces applied on the tissue are estimated, and the tissue is classified based on its deformation. The exact deformation of the tissue is also computed. Conclusions: The surgeons can render precise forces and detect tumors using the proposed method. The rarely discussed efficacy of computing the deformation level is also demonstrated.

eess.SY↗

MT-PCR: Leveraging Modality Transformation for Large-Scale Point Cloud Registration with Limited Overlap

Large-scale scene point cloud registration with limited overlap is a challenging task due to computational load and constrained data acquisition. To tackle these issues, we propose a point cloud registration method, MT-PCR, based on Modality Transformation. MT-PCR leverages a BEV capturing the maximal overlap information to improve the accuracy and utilizes images to provide complementary spatial features. Specifically, MT-PCR converts 3D point clouds to BEV images and eastimates correspondence by 2D image keypoints extraction and matching. Subsequently, the 2D correspondence estimates are then transformed back to 3D point clouds using inverse mapping. We have applied MT-PCR to Terrestrial Laser Scanning and Aerial Laser Scanning point cloud registration on the GrAco dataset, involving 8 low-overlap, square-kilometer scale registration scenarios. Experiments and comparisons with commonly used methods demonstrate that MT-PCR can achieve superior accuracy and robustness in large-scale scenes with limited overlap.

cs.RO↗

CNSv2: Probabilistic Correspondence Encoded Neural Image Servo

Visual servo based on traditional image matching methods often requires accurate keypoint correspondence for high precision control. However, keypoint detection or matching tends to fail in challenging scenarios with inconsistent illuminations or textureless objects, resulting significant performance degradation. Previous approaches, including our proposed Correspondence encoded Neural image Servo policy (CNS), attempted to alleviate these issues by integrating neural control strategies. While CNS shows certain improvement against error correspondence over conventional image-based controllers, it could not fully resolve the limitations arising from poor keypoint detection and matching. In this paper, we continue to address this problem and propose a new solution: Probabilistic Correspondence Encoded Neural Image Servo (CNSv2). CNSv2 leverages probabilistic feature matching to improve robustness in challenging scenarios. By redesigning the architecture to condition on multimodal feature matching, CNSv2 achieves high precision, improved robustness across diverse scenes and runs in real-time. We validate CNSv2 with simulations and real-world experiments, demonstrating its effectiveness in overcoming the limitations of detector-based methods in visual servo tasks.

cs.CV↗

BATSRUS GPU: Faster-than-Real-Time Magnetospheric Simulations with a Block-Adaptive Grid Code

BATSRUS, our state-of-the-art extended magnetohydrodynamic code, is the most used and one of the most resource-consuming models in the Space Weather Modeling Framework. It has always been our objective to improve its efficiency and speed with emerging techniques, such as GPU acceleration. To utilize the GPU nodes on modern supercomputers, we port BATSRUS to GPUs with the OpenACC API. Porting the code to a single GPU requires rewriting and optimizing the most used functionalities of the original code into a new solver, which accounts for around 1% of the entire program in length. To port it to multiple GPUs, we implement a new message passing algorithm to support its unique block-adaptive grid feature. We conduct weak scaling tests on as many as 256 GPUs and find good performance. The program has 50-60% parallel efficiency on up to 256 GPUs, and up to 95% efficiency within a single node (4 GPUs). Running large problems on more than one node has reduced efficiency due to hardware bottlenecks. We also demonstrate our ability to run representative magnetospheric simulations on GPUs. The performance for a single A100 GPU is about the same as 270 AMD "Rome" CPU cores, and it runs 3.6 times faster than real time. The simulation can run 6.9 times faster than real time on four A100 GPUs.

astro-ph.IM↗

Simulation Models for Exploring Magnetic Reconnection

Simulations have played a critical role in the advancement of our knowledge of magnetic reconnection. However, due to the inherently multiscale nature of reconnection, it is impossible to simulate all physics at all scales. For this reason, a wide range of simulation methods have been crafted to study particular aspects and consequences of magnetic reconnection. This chapter reviews many of these methods, laying out critical assumptions, numerical techniques, and giving examples of scientific results. Plasma models described include magnetohydrodynamics (MHD), Hall MHD, Hybrid, kinetic particle-in-cell (PIC), kinetic Vlasov, Fluid models with embedded PIC, Fluid models with direct feedback from energetic populations, and the Rice Convection Model (RCM).

physics.plasm-ph↗

Earth's Alfvén wings driven by the April 2023 Coronal Mass Ejection

We report a rare regime of Earth's magnetosphere interaction with sub-Alfvénic solar wind in which the windsock-like magnetosphere transforms into one with Alfvén wings. In the magnetic cloud of a Coronal Mass Ejection (CME) on April 24, 2023, NASA's Magnetospheric Multiscale mission distinguishes the following features: (1) unshocked and accelerated cold CME plasma coming directly against Earth's dayside magnetosphere; (2) dynamical wing filaments representing new channels of magnetic connection between the magnetosphere and foot points of the Sun's erupted flux rope; (3) cold CME ions observed with energized counter-streaming electrons, evidence of CME plasma captured due to reconnection between magnetic-cloud and Alfvén-wing field lines. The reported measurements advance our knowledge of CME interaction with planetary magnetospheres, and open new opportunities to understand how sub-Alfvénic plasma flows impact astrophysical bodies such as Mercury, moons of Jupiter, and exoplanets close to their host stars.

physics.space-ph↗

MESSENGER observations of Mercury's planetary ion escape rates and their dependence on true anomaly angle

This study investigates the escape of Mercury's sodium-group ions (Na+-group, including ions with m/q from 21 to 30 amu/e) and their dependence on true anomaly angle (TAA), i.e., Mercury's orbital phase around the Sun, using measurements from MESSENGER. The measurements are categorized into solar wind, magnetosheath, and magnetosphere, and further divided into four TAA intervals. Na+-group ions form escape plumes in the solar wind and magnetosheath, with higher fluxes along the solar wind's motional electric field. The total escape rates vary from 0.2 to 1 times 10^{25} atoms/s with the magnetosheath being the main escaping region. These rates exhibit a TAA dependence, peaking near the perihelion and similar during Mercury's remaining orbit. Despite Mercury's tenuous exosphere, Na+-group ions escape rate is comparable to other inner planets. This can be attributed to several processes, including that Na+-group ions may include several ion species, efficient photoionization frequency for elements within Na+-group, etc.

physics.space-ph↗

A kinetic-magnetohydrodynamic model with adaptive mesh refinement for modeling heliosphere neutral-plasma interaction

The charge exchange between the interstellar medium (ISM) and the solar wind plasma is crucial for determining the structures of the heliosphere. Since both the neutral-ion and neutral-neutral collision mean free paths are either comparable to or larger than the size of the heliosphere, the neutral phase space distribution can deviate far away from the Maxwellian distribution. A kinetic description for the neutrals is crucial for accurately modeling the heliosphere. It is computationally challenging to run three-dimensional (3D) time-dependent kinetic simulations due to the large number of macro-particles. In this paper, we present the new highly efficient SHIELD-2 model with a kinetic model of neutrals and a magnetohydrodynamic (MHD) model for the ions and electrons. To improve the simulation efficiency, we implement adaptive mesh refinement (AMR) and particle splitting and merging algorithms for the neutral particles to reduce the particle number that is required for an accurate simulation. We present several tests to verify and demonstrate the capabilities of the model.

physics.space-ph↗

Field-Aligned Current Structures during the Terrestrial Magnetosphere's Transformation into Alfven Wings and Recovery

On April 24th, 2023, a CME event caused the solar wind to become sub-Alfvenic, leading to the development of an Alfven Wing configuration in the Earth's Magnetosphere. Alfven Wings have previously been observed as cavities of low flow in Jupiter's magnetosphere, but the observing satellites did not have the ability to directly measure the Alfven Wings' current structures. Through in situ measurements made by the Magnetospheric Multiscale (MMS) spacecraft, the April 24th event provides us with the first direct measurements of current structures during an Alfven Wing configuration. We have found two distinct types of current structures associated with the Alfven Wing transformation as well as the magnetosphere recovery. These structures are observed to be significantly more anti-field-aligned and electron-driven than typical magnetopause currents, indicating the disruptions caused to the magnetosphere current system by the Alfven Wing formation.

physics.space-ph↗

Interplanetary magnetic field $B_y$ controlled Alfvén wings at Earth during encounter of a coronal mass ejection

In the vicinity of Earth's orbit, the typical solar wind Alfvén Mach number exceeds 5, and the super-Alfvénic solar wind drives a conventional magnetosphere configuration. However, at the ejecta phase of an interplanetary coronal mass ejection (ICME) event, the Alfvén Mach number may experience a significant reduction due to the intensified interplanetary magnetic field (IMF) strength and decreased density. On 24 April 2023, an ICME reached Earth's orbit. The solar wind density dropped to as low as 0.3 amu/cc while the IMF strength is about 25 nT. As a result, the solar wind flow transitions to a sub-Alfvénic state with an Alfvén Mach number of 0.4, providing opportunities to investigate the interaction of planetary magnetospheres with low Mach number solar wind. We carry out global simulations to investigate the responses of Earth's magnetosphere to the sub-Alfvénic ICME ejecta. The global magnetohydrodynamic (MHD) simulation results show the formation of Alfvén wings as the solar wind becomes sub-Alfvénic. Furthermore, the sub-Alfvénic period was characterized by the dominance of IMF By component, causing the Alfvén wings to extend towards the dawn and dusk sides. In this paper, we present the structures of the magnetic field, plasma flow, and current system around the Alfvén wings. The global magnetospheric convection under the sub-Alfvénic solar wind condition is discussed in depth. Our results achieve a new level of understanding about the interaction between a magnetized body and sub-Alfvénic upstream conditions, and provide guidance for future observations.

physics.space-ph↗

From GPT-4 to Gemini and Beyond: Assessing the Landscape of MLLMs on Generalizability, Trustworthiness and Causality through Four Modalities

Multi-modal Large Language Models (MLLMs) have shown impressive abilities in generating reasonable responses with respect to multi-modal contents. However, there is still a wide gap between the performance of recent MLLM-based applications and the expectation of the broad public, even though the most powerful OpenAI's GPT-4 and Google's Gemini have been deployed. This paper strives to enhance understanding of the gap through the lens of a qualitative study on the generalizability, trustworthiness, and causal reasoning capabilities of recent proprietary and open-source MLLMs across four modalities: ie, text, code, image, and video, ultimately aiming to improve the transparency of MLLMs. We believe these properties are several representative factors that define the reliability of MLLMs, in supporting various downstream applications. To be specific, we evaluate the closed-source GPT-4 and Gemini and 6 open-source LLMs and MLLMs. Overall we evaluate 230 manually designed cases, where the qualitative results are then summarized into 12 scores (ie, 4 modalities times 3 properties). In total, we uncover 14 empirical findings that are useful to understand the capabilities and limitations of both proprietary and open-source MLLMs, towards more reliable downstream multi-modal applications.

cs.CV↗

Detection of magnetospheric ion drift patterns at Mars

Mars lacks a global magnetic field, and instead possesses small-scale crustal magnetic fields, making its magnetic environment fundamentally different from intrinsic magnetospheres like those of Earth or Saturn. Here we report the discovery of magnetospheric ion drift patterns, typical of intrinsic magnetospheres, at Mars usingmeasurements fromMarsAtmosphere and Volatile EvolutioNmission. Specifically, we observewedge-like dispersion structures of hydrogen ions exhibiting butterfly-shaped distributions within the Martian crustal fields, a feature previously observed only in planetary-scale intrinsic magnetospheres. These dispersed structures are the results of driftmotions that fundamentally resemble those observed in intrinsic magnetospheres. Our findings indicate that the Martian magnetosphere embodies an intermediate case where both the unmagnetized and magnetized ion behaviors could be observed because of the wide range of strengths and spatial scales of the crustal magnetic fields around Mars.

astro-ph.EP↗

Numerical Study of Magnetic Island Coalescence Using Magnetohydrodynamics With Adaptively Embedded Particle-In-Cell Model

Collisionless magnetic reconnection typically requires kinetic treatments that are, in general, computationally expensive compared to fluid-based models. In this study, we use the magnetohydrodynamics with adaptively embedded particle-in-cell (MHD-AEPIC) model to study the interaction of two magnetic flux ropes. This innovative model embeds one or more adaptive PIC regions into a global MHD simulation domain such that the kinetic treatment is only applied in regions where kinetic physics is prominent. We compare the simulation results among three cases: 1) MHD with adaptively embedded PIC regions, 2) MHD with statically (or fixed) embedded PIC regions, and 3) a full PIC simulation. The comparison yields good agreement when analyzing their reconnection rates and magnetic island separations, as well as the ion pressure tensor elements and ion agyrotropy. In order to reach a good agreement among the three cases, large adaptive PIC regions are needed within the MHD domain, which indicates that the magnetic island coalescence problem is highly kinetic in nature where the coupling between the macro-scale MHD and micro-scale kinetic physics is important.

physics.plasm-ph↗