arXiv subjects

Xingjian Li

Publications and source records attributed to Xingjian Li.

At least 55 records · Page 3Linked to original sources

arXiv2025

CryoCCD: Conditional Cycle-consistent Diffusion with Biophysical Modeling for Cryo-EM Synthesis

Single-particle cryo-electron microscopy (cryo-EM) has become a cornerstone of structural biology, enabling near-atomic resolution analysis of macromolecules through advanced computational methods. However, the development of cryo-EM processing tools is constrained by the scarcity of high-quality annotated datasets. Synthetic data generation offers a promising alternative, but existing approaches lack thorough biophysical modeling of heterogeneity and fail to reproduce the complex noise observed in real imaging. To address these limitations, we present CryoCCD, a synthesis framework that unifies versatile biophysical modeling with the first conditional cycle-consistent diffusion model tailored for cryo-EM. The biophysical engine provides multi-functional generation capabilities to capture authentic biological organization, and the diffusion model is enhanced with cycle consistency and mask-guided contrastive learning to ensure realistic noise while preserving structural fidelity. Extensive experiments demonstrate that CryoCCD generates structurally faithful micrographs, enhances particle picking and pose estimation, as well as achieves superior performance over state-of-the-art baselines, while also generalizing effectively to held-out protein families.

cs.CV↗

arXiv2025

Towards Foundation Models for Cryo-ET Subtomogram Analysis

Cryo-electron tomography (cryo-ET) enables in situ visualization of macromolecular structures, where subtomogram analysis tasks such as classification, alignment, and averaging are critical for structural determination. However, effective analysis is hindered by scarce annotations, severe noise, and poor generalization. To address these challenges, we take the first step towards foundation models for cryo-ET subtomograms. First, we introduce CryoEngine, a large-scale synthetic data generator that produces over 904k subtomograms from 452 particle classes for pretraining. Second, we design an Adaptive Phase Tokenization-enhanced Vision Transformer (APT-ViT), which incorporates adaptive phase tokenization as an equivariance-enhancing module that improves robustness to both geometric and semantic variations. Third, we introduce a Noise-Resilient Contrastive Learning (NRCL) strategy to stabilize representation learning under severe noise conditions. Evaluations across 24 synthetic and real datasets demonstrate state-of-the-art (SOTA) performance on all three major subtomogram tasks and strong generalization to unseen datasets, advancing scalable and robust subtomogram analysis in cryo-ET.

cs.CV↗

arXiv2025

TextCAM: Explaining Class Activation Map with Text

Deep neural networks (DNNs) have achieved remarkable success across domains but remain difficult to interpret, limiting their trustworthiness in high-stakes applications. This paper focuses on deep vision models, for which a dominant line of explainability methods are Class Activation Mapping (CAM) and its variants working by highlighting spatial regions that drive predictions. We figure out that CAM provides little semantic insight into what attributes underlie these activations. To address this limitation, we propose TextCAM, a novel explanation framework that enriches CAM with natural languages. TextCAM combines the precise spatial localization of CAM with the semantic alignment of vision-language models (VLMs). Specifically, we derive channel-level semantic representations using CLIP embeddings and linear discriminant analysis, and aggregate them with CAM weights to produce textual descriptions of salient visual evidence. This yields explanations that jointly specify where the model attends and what visual attributes likely support its decision. We further extend TextCAM to generate feature channels into semantically coherent groups, enabling more fine-grained visual-textual explanations. Experiments on ImageNet, CLEVR, and CUB demonstrate that TextCAM produces faithful and interpretable rationales that improve human understanding, detect spurious correlations, and preserve model fidelity.

cs.CV↗

arXiv2025

Semi-MoE: Mixture-of-Experts meets Semi-Supervised Histopathology Segmentation

Semi-supervised learning has been employed to alleviate the need for extensive labeled data for histopathology image segmentation, but existing methods struggle with noisy pseudo-labels due to ambiguous gland boundaries and morphological misclassification. This paper introduces Semi-MOE, to the best of our knowledge, the first multi-task Mixture-of-Experts framework for semi-supervised histopathology image segmentation. Our approach leverages three specialized expert networks: A main segmentation expert, a signed distance field regression expert, and a boundary prediction expert, each dedicated to capturing distinct morphological features. Subsequently, the Multi-Gating Pseudo-labeling module dynamically aggregates expert features, enabling a robust fuse-and-refine pseudo-labeling mechanism. Furthermore, to eliminate manual tuning while dynamically balancing multiple learning objectives, we propose an Adaptive Multi-Objective Loss. Extensive experiments on GlaS and CRAG benchmarks show that our method outperforms state-of-the-art approaches in low-label settings, highlighting the potential of MoE-based architectures in advancing semi-supervised segmentation. Our code is available at https://github.com/vnlvi2k3/Semi-MoE.

cs.CV↗

arXiv2025

Describe Anything Model for Visual Question Answering on Text-rich Images

Recent progress has been made in region-aware vision-language modeling, particularly with the emergence of the Describe Anything Model (DAM). DAM is capable of generating detailed descriptions of any specific image areas or objects without the need for additional localized image-text alignment supervision. We hypothesize that such region-level descriptive capability is beneficial for the task of Visual Question Answering (VQA), especially in challenging scenarios involving images with dense text. In such settings, the fine-grained extraction of textual information is crucial to producing correct answers. Motivated by this, we introduce DAM-QA, a framework with a tailored evaluation protocol, developed to investigate and harness the region-aware capabilities from DAM for the text-rich VQA problem that requires reasoning over text-based information within images. DAM-QA incorporates a mechanism that aggregates answers from multiple regional views of image content, enabling more effective identification of evidence that may be tied to text-related elements. Experiments on six VQA benchmarks show that our approach consistently outperforms the baseline DAM, with a notable 7+ point gain on DocVQA. DAM-QA also achieves the best overall performance among region-aware models with fewer parameters, significantly narrowing the gap with strong generalist VLMs. These results highlight the potential of DAM-like models for text-rich and broader VQA tasks when paired with efficient usage and integration strategies. Our code is publicly available at https://github.com/Linvyl/DAM-QA.git.

cs.CV↗

arXiv2025

Visual Instance-aware Prompt Tuning

Visual Prompt Tuning (VPT) has emerged as a parameter-efficient fine-tuning paradigm for vision transformers, with conventional approaches utilizing dataset-level prompts that remain the same across all input instances. We observe that this strategy results in sub-optimal performance due to high variance in downstream datasets. To address this challenge, we propose Visual Instance-aware Prompt Tuning (ViaPT), which generates instance-aware prompts based on each individual input and fuses them with dataset-level prompts, leveraging Principal Component Analysis (PCA) to retain important prompting information. Moreover, we reveal that VPT-Deep and VPT-Shallow represent two corner cases based on a conceptual understanding, in which they fail to effectively capture instance-specific information, while random dimension reduction on prompts only yields performance between the two extremes. Instead, ViaPT overcomes these limitations by balancing dataset-level and instance-level knowledge, while reducing the amount of learnable parameters compared to VPT-Deep. Extensive experiments across 34 diverse datasets demonstrate that our method consistently outperforms state-of-the-art baselines, establishing a new paradigm for analyzing and optimizing visual prompts for vision transformers.

cs.CV↗

arXiv2025

SaSi: A Self-augmented and Self-interpreted Deep Learning Approach for Few-shot Cryo-ET Particle Detection

Cryo-electron tomography (cryo-ET) has emerged as a powerful technique for imaging macromolecular complexes in their near-native states. However, the localization of 3D particles in cellular environments still presents a significant challenge due to low signal-to-noise ratios and missing wedge artifacts. Deep learning approaches have shown great potential, but they need huge amounts of data, which can be a challenge in cryo-ET scenarios where labeled data is often scarce. In this paper, we propose a novel Self-augmented and Self-interpreted (SaSi) deep learning approach towards few-shot particle detection in 3D cryo-ET images. Our method builds upon self-augmentation techniques to further boost data utilization and introduces a self-interpreted segmentation strategy for alleviating dependency on labeled data, hence improving generalization and robustness. As demonstrated by experiments conducted on both simulated and real-world cryo-ET datasets, the SaSi approach significantly outperforms existing state-of-the-art methods for particle localization. This research increases understanding of how to detect particles with very few labels in cryo-ET and thus sets a new benchmark for few-shot learning in structural biology.

cs.CV↗

arXiv2025

Describe Anything in Medical Images

Localized image captioning has made significant progress with models like the Describe Anything Model (DAM), which can generate detailed region-specific descriptions without explicit region-text supervision. However, such capabilities have yet to be widely applied to specialized domains like medical imaging, where diagnostic interpretation relies on subtle regional findings rather than global understanding. To mitigate this gap, we propose MedDAM, the first comprehensive framework leveraging large vision-language models for region-specific captioning in medical images. MedDAM employs medical expert-designed prompts tailored to specific imaging modalities and establishes a robust evaluation benchmark comprising a customized assessment protocol, data pre-processing pipeline, and specialized QA template library. This benchmark evaluates both MedDAM and other adaptable large vision-language models, focusing on clinical factuality through attribute-level verification tasks, thereby circumventing the absence of ground-truth region-caption pairs in medical datasets. Extensive experiments on the VinDr-CXR, LIDC-IDRI, and SkinCon datasets demonstrate MedDAM's superiority over leading peers (including GPT-4o, Claude 3.7 Sonnet, LLaMA-3.2 Vision, Qwen2.5-VL, GPT-4Rol, and OMG-LLaVA) in the task, revealing the importance of region-level semantic alignment in medical image understanding and establishing MedDAM as a promising foundation for clinical vision-language integration.

cs.CV↗

arXiv2025

MLPs and KANs for data-driven learning in physical problems: A performance comparison

There is increasing interest in solving partial differential equations (PDEs) by casting them as machine learning problems. Recently, there has been a spike in exploring Kolmogorov-Arnold Networks (KANs) as an alternative to traditional neural networks represented by Multi-Layer Perceptrons (MLPs). While showing promise, their performance advantages in physics-based problems remain largely unexplored. Several critical questions persist: Can KANs capture complex physical dynamics and under what conditions might they outperform traditional architectures? In this work, we present a comparative study of KANs and MLPs for learning physical systems governed by PDEs. We assess their performance when applied in deep operator networks (DeepONet) and graph network-based simulators (GNS), and test them on physical problems that vary significantly in scale and complexity. Drawing inspiration from the Kolmogorov Representation Theorem, we examine the behavior of KANs and MLPs across shallow and deep network architectures. Our results reveal that although KANs do not consistently outperform MLPs when configured as deep neural networks, they demonstrate superior expressiveness in shallow network settings, significantly outpacing MLPs in accuracy over our test cases. This suggests that KANs are a promising choice, offering a balance of efficiency and accuracy in applications involving physical systems.

cs.LG↗

arXiv2025

Visual Variational Autoencoder Prompt Tuning

Parameter-efficient fine-tuning (PEFT) has emerged as a crucial approach for adapting large vision transformers to downstream tasks without the prohibitive computational costs of full fine-tuning. While existing visual prompt tuning (VPT) methods have made significant strides, they predominantly rely on static, domain-specific prompts that fail to capture the rich visual diversity within individual instances. This paper introduces V$^2$APT (Visual Variational Autoencoder Prompt Tuning), a novel framework that generates dynamic, input-dependent prompts using a variational autoencoder architecture. By learning a latent representation of image-specific features and decoding them into customized prompts, V$^2$APT adapts to the unique visual characteristics of each input. Extensive experiments on FGVC, HTA, and VTAB-1k benchmarks demonstrate that our approach consistently outperforms state-of-the-art PEFT methods. Notably, V$^2$APT achieves +3.2\% improvement over VPT-Deep on HTA, with an average performance gain of +2.0\% across all three datasets.

cs.CV↗

arXiv2025

OT-Transformer: A Continuous-time Transformer Architecture with Optimal Transport Regularization

Transformers have achieved state-of-the-art performance in numerous tasks. In this paper, we propose a continuous-time formulation of transformers. Specifically, we consider a dynamical system whose governing equation is parametrized by transformer blocks. We leverage optimal transport theory to regularize the training problem, which enhances stability in training and improves generalization of the resulting model. Moreover, we demonstrate in theory that this regularization is necessary as it promotes uniqueness and regularity of solutions. Our model is flexible in that almost any existing transformer architectures can be adopted to construct the dynamical system with only slight modifications to the existing code. We perform extensive numerical experiments on tasks motivated by natural language processing, image classification, and point cloud classification. Our experimental results show that the proposed method improves the performance of its discrete counterpart and outperforms relevant comparing models.

cs.LG↗

arXiv2025

3D Printing of Near-Ambient Responsive Liquid Crystal Elastomers with Enhanced Nematic Order and Pluralized Transformation

Liquid Crystal Elastomers with near-ambient temperature-responsiveness (NAT-LCEs) have been extensively studied for building bio-compatible, low-power consumption devices and robotics. However, conventional manufacturing methods face limitations in programmability (e.g., molding) or low nematic order (e.g., DIW printing). Here, a hybrid cooling strategy is proposed for programmable 3D printing of NAT-LCEs with enhanced nematic order, intricate shape forming, and morphing capability. By integrating a low-temperature nozzle and a cooling platform into a 3D printer, the resulting temperature field synergistically facilitates mesogen alignment during extrusion and disruption-free UV cross-linking. This method achieves a nematic order 3000% higher than NAT-LCEs fabricated using traditional room temperature 3D printing. Enabled by shifting of transition temperature during hybrid cooling printing, printed sheets spontaneously turn into 3D structures after release from the platform, exhibiting bidirectional deformation with heating and cooling. By adjusting the nozzle and plate temperatures, NAT-LCEs with graded properties can be fabricated for intricate shape morphing. A wristband system with enhanced heart rate monitoring is also developed based on 3D-printed NAT-LCE. Our method may open new possibilities for soft robotics, biomedical devices, and wearable electronics.

cond-mat.soft↗

arXiv2024

Trustworthy Federated Learning: Privacy, Security, and Beyond

While recent years have witnessed the advancement in big data and Artificial Intelligence (AI), it is of much importance to safeguard data privacy and security. As an innovative approach, Federated Learning (FL) addresses these concerns by facilitating collaborative model training across distributed data sources without transferring raw data. However, the challenges of robust security and privacy across decentralized networks catch significant attention in dealing with the distributed data in FL. In this paper, we conduct an extensive survey of the security and privacy issues prevalent in FL, underscoring the vulnerability of communication links and the potential for cyber threats. We delve into various defensive strategies to mitigate these risks, explore the applications of FL across different sectors, and propose research directions. We identify the intricate security challenges that arise within the FL frameworks, aiming to contribute to the development of secure and efficient FL systems.

cs.CR↗

arXiv2024

Multimodal Generalized Category Discovery

Generalized Category Discovery (GCD) aims to classify inputs into both known and novel categories, a task crucial for open-world scientific discoveries. However, current GCD methods are limited to unimodal data, overlooking the inherently multimodal nature of most real-world data. In this work, we extend GCD to a multimodal setting, where inputs from different modalities provide richer and complementary information. Through theoretical analysis and empirical validation, we identify that the key challenge in multimodal GCD lies in effectively aligning heterogeneous information across modalities. To address this, we propose MM-GCD, a novel framework that aligns both the feature and output spaces of different modalities using contrastive learning and distillation techniques. MM-GCD achieves new state-of-the-art performance on the UPMC-Food101 and N24News datasets, surpassing previous methods by 11.5\% and 4.7\%, respectively.

cs.CV↗

arXiv2024

Advanced POD-Based Performance Evaluation of Classifiers Applied to Human Driver Lane Changing Prediction

Machine learning (ML) classifiers serve as essential tools facilitating classification and prediction across various domains. The performance of these algorithms should be known to ensure their reliable application. In certain fields, receiver operating characteristic and precision-recall curves are frequently employed to assess machine learning algorithms without accounting for the impact of process parameters. However, it may be essential to evaluate the performance of these algorithms in relation to such parameters. As a performance evaluation metric capable of considering the effects of process parameters, this paper uses a modified probability of detection (POD) approach to assess the reliability of ML-based algorithms. As an example, the POD-based approach is employed to assess ML models used for predicting the lane changing behavior of a vehicle driver. The time remaining to the predicted (and therefore unknown) lane changing event is considered as process parameter. The hit/miss approach to POD is taken here and modified by considering the probability of lane changing derived from ML algorithms at each time step, and obtaining the final result of the analysis accordingly. This improves the reliability of results compared to the standard hit/miss approach, which considers the outcome of the classifiers as either 0 or 1, while also simplifying evaluation compared to the â versus a approach. Performance evaluation results of the proposed approach are compared with those obtained with the standard hit/miss approach and a pre-developed â versus a approach to validate the effectiveness of the proposed method. The comparison shows that this method provides an averaging conservative behavior with the advantage of enhancing the reliability of the hit/miss approach to POD while retaining its simplicity.

eess.SY↗

arXiv2024

Transform Arbitrary Good Quantum LDPC Codes into Good Geometrically Local Codes in Any Dimension

Geometrically local quantum codes, comprised of qubits and checks embedded in $\mathbb{R}^D$ with local check operators, have been a subject of significant interest. A key challenge is identifying the optimal code construction that maximizes both dimension and distance. Recent advancements have produced several constructions, but these either depend on specific good quantum low-density parity-check (qLDPC) codes or are limited to three dimensions. In this work, we introduce a construction that can transform any good qLDPC code into an optimal geometrically local quantum code. Our approach hinges on a novel procedure that extracts a two-dimensional structure from an arbitrary three-term chain complex. We expect that this procedure will find broader applications in areas such as weight reduction and the geometric realization of chain complexes.

quant-ph↗

arXiv2024

Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo Labeling

Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology facilitating the study of macromolecular structures at near-atomic resolution. Recent volumetric segmentation approaches on cryo-ET images have drawn widespread interest in biological sector. However, existing methods heavily rely on manually labeled data, which requires highly professional skills, thereby hindering the adoption of fully-supervised approaches for cryo-ET images. Some unsupervised domain adaptation (UDA) approaches have been designed to enhance the segmentation network performance using unlabeled data. However, applying these methods directly to cryo-ET images segmentation tasks remains challenging due to two main issues: 1) the source data, usually obtained through simulation, contain a certain level of noise, while the target data, directly collected from raw-data from real-world scenario, have unpredictable noise levels. 2) the source data used for training typically consists of known macromoleculars, while the target domain data are often unknown, causing the model's segmenter to be biased towards these known macromolecules, leading to a domain shift problem. To address these challenges, in this work, we introduce the first voxel-wise unsupervised domain adaptation approach, termed Vox-UDA, specifically for cryo-ET subtomogram segmentation. Vox-UDA incorporates a noise generation module to simulate target-like noises in the source dataset for cross-noise level adaptation. Additionally, we propose a denoised pseudo-labeling strategy based on improved Bilateral Filter to alleviate the domain shift problem. Experimental results on both simulated and real cryo-ET subtomogram datasets demonstrate the superiority of our proposed approach compared to state-of-the-art UDA methods.

cs.CV↗

arXiv2024

How (not) to Build Quantum PKE in Minicrypt

The seminal work by Impagliazzo and Rudich (STOC'89) demonstrated the impossibility of constructing classical public key encryption (PKE) from one-way functions (OWF) in a black-box manner. However, the question remains: can quantum PKE (QPKE) be constructed from quantumly secure OWF? A recent line of work has shown that it is indeed possible to build QPKE from OWF, but with one caveat -- they rely on quantum public keys, which cannot be authenticated and reused. In this work, we re-examine the possibility of perfect complete QPKE in the quantum random oracle model (QROM), where OWF exists. Our first main result: QPKE with classical public keys, secret keys and ciphertext, does not exist in the QROM, if the key generation only makes classical queries. Therefore, a necessary condition for constructing such QPKE from OWF is to have the key generation classically ``un-simulatable''. Previous discussions (Austrin et al. CRYPTO'22) on the impossibility of QPKE from OWF rely on a seemingly strong conjecture. Our work makes a significant step towards a complete and unconditional quantization of Impagliazzo and Rudich's results. Our second main result extends to QPKE with quantum public keys. The second main result: QPKE with quantum public keys, classical secret keys and ciphertext, does not exist in the QROM, if the key generation only makes classical queries and the quantum public key is either pure or ``efficiently clonable''. The result is tight due to all existing QPKEs constructions. Our result further gives evidence on why existing QPKEs lose reusability. To achieve these results, we use a novel argument based on conditional mutual information and quantum Markov chain by Fawzi and Renner (Communications in Mathematical Physics). We believe the techniques used in the work will find other usefulness in separations in quantum cryptography/complexity.

quant-ph↗