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

Cryo-electron microscopy (cryo-EM) offers near-atomic resolution imaging of macromolecules, but developing robust models for downstream analysis is hindered by the scarcity of high-quality annotated data. While synthetic data generation has emerged as a potential solution, existing methods often fail to capture both the structural diversity of biological specimens and the complex, spatially varying noise inherent in cryo-EM imaging. To overcome these limitations, we propose CryoCCD, a synthesis framework that integrates biophysical modeling with generative techniques. Specifically, CryoCCD produces multi-scale cryo-EM micrographs that reflect realistic biophysical variability through compositional heterogeneity, cellular context, and physics-informed imaging. To generate realistic noise, we employ a conditional diffusion model, enhanced by cycle consistency to preserve structural fidelity and mask-aware contrastive learning to capture spatially adaptive noise patterns. Extensive experiments show that CryoCCD generates structurally accurate micrographs and enhances performance in downstream tasks, outperforming state-of-the-art baselines in both particle picking and reconstruction.

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.

AutoMiSeg: Automatic Medical Image Segmentation via Test-Time Adaptation of Foundation Models

Medical image segmentation is vital for clinical diagnosis, yet current deep learning methods often demand extensive expert effort, i.e., either through annotating large training datasets or providing prompts at inference time for each new case. This paper introduces a zero-shot and automatic segmentation pipeline that combines off-the-shelf vision-language and segmentation foundation models. Given a medical image and a task definition (e.g., "segment the optic disc in an eye fundus image"), our method uses a grounding model to generate an initial bounding box, followed by a visual prompt boosting module that enhance the prompts, which are then processed by a promptable segmentation model to produce the final mask. To address the challenges of domain gap and result verification, we introduce a test-time adaptation framework featuring a set of learnable adaptors that align the medical inputs with foundation model representations. Its hyperparameters are optimized via Bayesian Optimization, guided by a proxy validation model without requiring ground-truth labels. Our pipeline offers an annotation-efficient and scalable solution for zero-shot medical image segmentation across diverse tasks. Our pipeline is evaluated on seven diverse medical imaging datasets and shows promising results. By proper decomposition and test-time adaptation, our fully automatic pipeline performs competitively with weakly-prompted interactive foundation models.

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.

SetONet: A Deep Set-based Operator Network for Solving PDEs with permutation invariant variable input sampling

Neural operators, particularly the Deep Operator Network (DeepONet), have shown promise in learning mappings between function spaces for solving differential equations. However, standard DeepONet requires input functions to be sampled at fixed locations, limiting its applicability in scenarios with variable sensor configurations, missing data, or irregular grids. We introduce the Set Operator Network (SetONet), a novel architecture that integrates Deep Sets principles into the DeepONet framework to address this limitation. The core innovation lies in the SetONet branch network, which processes the input function as an unordered \emph{set} of location-value pairs. This design ensures permutation invariance with respect to the input points, making SetONet inherently robust to variations in the number and locations of sensors. SetONet learns richer, spatially-aware input representations by explicitly processing spatial coordinates and function values. We demonstrate SetONet's effectiveness on several benchmark problems, including derivative/anti-derivative operators, 1D Darcy flow, and 2D elasticity. Results show that SetONet successfully learns operators under variable input sampling conditions where standard DeepONet fails. Furthermore, SetONet is architecturally robust to sensor drop-off; unlike standard DeepONet, which requires methods like interpolation to function with missing data. Notably, SetONet can achieve comparable or improved accuracy over DeepONet on fixed grids, particularly for nonlinear problems, likely due to its enhanced input representation. SetONet provides a flexible and robust extension to the neural operator toolkit, significantly broadening the applicability of operator learning to problems with variable or incomplete input data.

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.

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.

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.

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.

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.