arXiv subjects

Junan Chen

Publications and source records attributed to Junan Chen.

12 recordsLinked to original sources

arXiv2026

Differentiable Jitter Correction using Deep Learning-based Image Quality Metric for Phase-Contrast Micro-CT

This paper proposes a fully differentiable jitter correction method for X-ray phase-contrast micro computed tomography using a deep learning-based image quality metric that estimates and compensates per-projection rigid jitter directly from the acquired projection data, without a pre-scan motion-free reference. The approach builds on a gradient-based auto-focus strategy adapted to parallel-beam geometry. A set of candidate objective functions is benchmarked in a controlled study, and the sensitivity of the visual information fidelity (VIF) metric to the jitter artifact is verified with the target phase-contrast data. To operate without a clean reference, a compact 3D convolutional neural network is trained to predict the VIF score from a single corrupted volume. A spatially selective total variation penalty applied exclusively to the image background is introduced to penalize spurious high-frequency structures that otherwise emerge during optimization. Experiments on biological specimens acquired at different synchrotron beamlines are conducted. Evaluation uses jitter motion applied to simulated and experimentally acquired projection data. The result confirms that the integrated pipeline reliably recovers fine structural detail lost due to jitter, with generalization demonstrated across morphologically distinct samples.

cs.CV↗

arXiv2026

Can Multimodal Large Language Models Truly Understand Small Objects?

Multimodal Large Language Models (MLLMs) have shown promising potential in diverse understanding tasks, e.g., image and video analysis, math and physics olympiads. However, they remain blank and unexplored for Small Object Understanding (SOU) tasks. To fill this gap, we introduce SOUBench, the first and comprehensive benchmark for exploring the small objects understanding capability of existing MLLMs. Specifically, we first design an effective and automatic visual question-answer generation strategy, constructing a new SOU-VQA evaluation dataset, with 18,204 VQA pairs, six relevant sub-tasks, and three dominant scenarios (i.e., Driving, Aerial, and Underwater). Then, we conduct a comprehensive evaluation on 15 state-of-the-art MLLMs and reveal their weak capabilities in small object understanding. Furthermore, we develop SOU-Train, a multimodal training dataset with 11,226 VQA pairs, to improve the SOU capabilities of MLLMs. Through supervising fine-tuning of the latest MLLM, we demonstrate that SOU-Train can effectively enhance the latest MLLM's ability to understand small objects. Comprehensive experimental results demonstrate that, the proposed SOUBench, along with the SOU-VQA and SOU-Train datasets, provides a crucial empirical foundation to the community for further developing models with enhanced small object understanding capabilities. Datasets and Code: https://github.com/Hanfj-X/SOU.

cs.CV↗

arXiv2026

When More Thinking Hurts: Overthinking in LLM Test-Time Compute Scaling

Scaling test-time compute through extended chains of thought has become a dominant paradigm for improving large language model reasoning. However, existing research implicitly assumes that longer thinking always yields better results. This assumption remains largely unexamined. We systematically investigate how the marginal utility of additional reasoning tokens changes as compute budgets increase. We find that marginal returns diminish substantially at higher budgets and that models exhibit ``overthinking'', where extended reasoning is associated with abandoning previously correct answers. Furthermore, we show that optimal thinking length varies across problem difficulty, suggesting that uniform compute allocation is suboptimal. Our cost-aware evaluation framework reveals that stopping at moderate budgets can reduce computation significantly while maintaining comparable accuracy.

cs.AI↗

arXiv2025

Q-Adapter: Visual Query Adapter for Extracting Textually-related Features in Video Captioning

Recent advances in video captioning are driven by large-scale pretrained models, which follow the standard "pre-training followed by fine-tuning" paradigm, where the full model is fine-tuned for downstream tasks. Although effective, this approach becomes computationally prohibitive as the model size increases. The Parameter-Efficient Fine-Tuning (PEFT) approach offers a promising alternative, but primarily focuses on the language components of Multimodal Large Language Models (MLLMs). Despite recent progress, PEFT remains underexplored in multimodal tasks and lacks sufficient understanding of visual information during fine-tuning the model. To bridge this gap, we propose Query-Adapter (Q-Adapter), a lightweight visual adapter module designed to enhance MLLMs by enabling efficient fine-tuning for the video captioning task. Q-Adapter introduces learnable query tokens and a gating layer into Vision Encoder, enabling effective extraction of sparse, caption-relevant features without relying on external textual supervision. We evaluate Q-Adapter on two well-known video captioning datasets, MSR-VTT and MSVD, where it achieves state-of-the-art performance among the methods that take the PEFT approach across BLEU@4, METEOR, ROUGE-L, and CIDEr metrics. Q-Adapter also achieves competitive performance compared to methods that take the full fine-tuning approach while requiring only 1.4% of the parameters. We further analyze the impact of key hyperparameters and design choices on fine-tuning effectiveness, providing insights into optimization strategies for adapter-based learning. These results highlight the strong potential of Q-Adapter in balancing caption quality and parameter efficiency, demonstrating its scalability for video-language modeling.

cs.CV↗

arXiv2025

Quantitative Stain Mapping in X-ray Virtual Histology

Virtual histology is an emerging field in biomedicine that enables three-dimensional tissue visualization using X-ray micro-computed tomography. However, the method still lacks the specificity of conventional histology, in which parts of the tissue are selectively highlighted using targeted stains. Though some first X-ray stains have been developed to address this issue, their precise location and quantity inside the tissue volume remain largely unknown. In this work, we present a novel approach to virtual histology that simultaneously captures electron number density and X-ray attenuation values through modulation-based X-ray imaging with a structured phase modulator. These complementary measurements enable decomposition of tissue volumes into basis materials, which allows the extraction of three-dimensional maps of molar contrast agent distribution alongside morphological details on the micrometer scale -- here demonstrated on murine kidneys. The concentration values are validated against the established method of K-edge subtraction imaging. We also create a direct bridge from X-ray to visible light imaging by detecting the same stain both using classical histology and our proposed X-ray approach. Our methodology opens new possibilities for biomedical research into disease progression by providing quantitative three-dimensional stain mapping across entire tissue volumes alongside high-contrast morphology, enabling deeper insights into disease mechanisms.

physics.med-ph↗

arXiv2025

Bacterial dimensions sensitively regulate surface diffusivity and residence time

Run-and-tumble is a common but vital strategy that bacteria employ to explore environment suffused with boundaries, as well as to escape from entrapment. In this study we reveal how this strategy and the resulting dynamical behavior can be sensitively regulated by bacterial dimensions. Our results demonstrate that the logarithm of the surface residence time for bacteria with constant tumble bias is linearly related to a dimensionless parameter of bacterial intrinsic size characteristics, where a small variation in bacterial dimensions, which is natural in a suspension, reproduces well the experimentally observed large variation in bacterial residence time. Furthermore, our results predict that the optimal tumble bias corresponding to the maximum surface diffusivity depends strongly on bacterial dimensions, where the same small variation in bacterial dimensions gives rise to a strongly diversified optimal tumble bias and an order of magnitude change in surface diffusivity.

cond-mat.soft↗

arXiv2024

2D-3D Deformable Image Registration of Histology Slide and Micro-CT with ML-based Initialization

Recent developments in the registration of histology and micro-computed tomography ({\mu}CT) have broadened the perspective of pathological applications such as virtual histology based on {\mu}CT. This topic remains challenging because of the low image quality of soft tissue CT. Additionally, soft tissue samples usually deform during the histology slide preparation, making it difficult to correlate the structures between histology slide and {\mu}CT. In this work, we propose a novel 2D-3D multi-modal deformable image registration method. The method uses a machine learning (ML) based initialization followed by the registration. The registration is finalized by an analytical out-of-plane deformation refinement. The method is evaluated on datasets acquired from tonsil and tumor tissues. {\mu}CTs of both phase-contrast and conventional absorption modalities are investigated. The registration results from the proposed method are compared with those from intensity- and keypoint-based methods. The comparison is conducted using both visual and fiducial-based evaluations. The proposed method demonstrates superior performance compared to the other two methods.

eess.IV↗

arXiv2024

Extending the field of view in modulation-based X-ray phase microtomography

Recent advances in propagation-based phase-contrast imaging, such as hierarchical imaging, have enabled the visualization of internal structures in large biological specimens and material samples. However, modulation-based techniques, which provide quantitative electron density information, face challenges when imaging larger objects due to stringent beam stability requirements and detector distortions. Extending the field of view of these methods is crucial for obtaining comparable quantitative results across beamlines and adapting to the smaller beam profiles of fourth-generation synchrotron sources. We introduce a novel image processing technique combining an eigenflat optimization with deformable image registration to address the challenges and enable quantitative high-resolution scans of centimeter-sized objects with multiple-micrometer resolution. We demonstrate the potential of the method by obtaining an electron density map of a rat brain sample 15 mm in diameter despite the limited horizontal field of view of 6 mm of the beamline. This showcases the technique's ability to significantly widen the range of applications of modulation-based techniques in both biological and materials science research.

physics.med-ph↗

arXiv2023

Probabilistic Uncertainty Quantification of Prediction Models with Application to Visual Localization

The uncertainty quantification of prediction models (e.g., neural networks) is crucial for their adoption in many robotics applications. This is arguably as important as making accurate predictions, especially for safety-critical applications such as self-driving cars. This paper proposes our approach to uncertainty quantification in the context of visual localization for autonomous driving, where we predict locations from images. Our proposed framework estimates probabilistic uncertainty by creating a sensor error model that maps an internal output of the prediction model to the uncertainty. The sensor error model is created using multiple image databases of visual localization, each with ground-truth location. We demonstrate the accuracy of our uncertainty prediction framework using the Ithaca365 dataset, which includes variations in lighting, weather (sunny, snowy, night), and alignment errors between databases. We analyze both the predicted uncertainty and its incorporation into a Kalman-based localization filter. Our results show that prediction error variations increase with poor weather and lighting condition, leading to greater uncertainty and outliers, which can be predicted by our proposed uncertainty model. Additionally, our probabilistic error model enables the filter to remove ad hoc sensor gating, as the uncertainty automatically adjusts the model to the input data

cs.RO↗

arXiv2022

Ithaca365: Dataset and Driving Perception under Repeated and Challenging Weather Conditions

Advances in perception for self-driving cars have accelerated in recent years due to the availability of large-scale datasets, typically collected at specific locations and under nice weather conditions. Yet, to achieve the high safety requirement, these perceptual systems must operate robustly under a wide variety of weather conditions including snow and rain. In this paper, we present a new dataset to enable robust autonomous driving via a novel data collection process - data is repeatedly recorded along a 15 km route under diverse scene (urban, highway, rural, campus), weather (snow, rain, sun), time (day/night), and traffic conditions (pedestrians, cyclists and cars). The dataset includes images and point clouds from cameras and LiDAR sensors, along with high-precision GPS/INS to establish correspondence across routes. The dataset includes road and object annotations using amodal masks to capture partial occlusions and 3D bounding boxes. We demonstrate the uniqueness of this dataset by analyzing the performance of baselines in amodal segmentation of road and objects, depth estimation, and 3D object detection. The repeated routes opens new research directions in object discovery, continual learning, and anomaly detection. Link to Ithaca365: https://ithaca365.mae.cornell.edu/

cs.CV↗

arXiv2022

Hindsight is 20/20: Leveraging Past Traversals to Aid 3D Perception

Self-driving cars must detect vehicles, pedestrians, and other traffic participants accurately to operate safely. Small, far-away, or highly occluded objects are particularly challenging because there is limited information in the LiDAR point clouds for detecting them. To address this challenge, we leverage valuable information from the past: in particular, data collected in past traversals of the same scene. We posit that these past data, which are typically discarded, provide rich contextual information for disambiguating the above-mentioned challenging cases. To this end, we propose a novel, end-to-end trainable Hindsight framework to extract this contextual information from past traversals and store it in an easy-to-query data structure, which can then be leveraged to aid future 3D object detection of the same scene. We show that this framework is compatible with most modern 3D detection architectures and can substantially improve their average precision on multiple autonomous driving datasets, most notably by more than 300% on the challenging cases.

cs.CV↗

arXiv2019

Dual Learning-based Video Coding with Inception Dense Blocks

In this paper, a dual learning-based method in intra coding is introduced for PCS Grand Challenge. This method is mainly composed of two parts: intra prediction and reconstruction filtering. They use different network structures, the neural network-based intra prediction uses the full-connected network to predict the block while the neural network-based reconstruction filtering utilizes the convolutional networks. Different with the previous filtering works, we use a network with more powerful feature extraction capabilities in our reconstruction filtering network. And the filtering unit is the block-level so as to achieve a more accurate filtering compensation. To our best knowledge, among all the learning-based methods, this is the first attempt to combine two different networks in one application, and we achieve the state-of-the-art performance for AI configuration on the HEVC Test sequences. The experimental result shows that our method leads to significant BD-rate saving for provided 8 sequences compared to HM-16.20 baseline (average 10.24% and 3.57% bitrate reductions for all-intra and random-access coding, respectively). For HEVC test sequences, our model also achieved a 9.70% BD-rate saving compared to HM-16.20 baseline for all-intra configuration.

eess.IV↗