Runmin Jiang

Runmin Jiang, Zhaoxin Fan, Junhao Wu et al.

3D medical image segmentation is a challenging task with crucial implications for disease diagnosis and treatment planning. Recent advances in deep learning have significantly enhanced fully supervised medical image segmentation. However, this approach heavily relies on labor-intensive and time-consuming fully annotated ground-truth labels, particularly for 3D volumes. To overcome this limitation, we propose a novel probabilistic-aware weakly supervised learning pipeline, specifically designed for 3D medical imaging. Our pipeline integrates three innovative components: a Probability-based Pseudo Label Generation technique for synthesizing dense segmentation masks from sparse annotations, a Probabilistic Multi-head Self-Attention network for robust feature extraction within our Probabilistic Transformer Network, and a Probability-informed Segmentation Loss Function to enhance training with annotation confidence. Demonstrating significant advances, our approach not only rivals the performance of fully supervised methods but also surpasses existing weakly supervised methods in CT and MRI datasets, achieving up to 18.1% improvement in Dice scores for certain organs. The code is available at https://github.com/runminjiang/PW4MedSeg.

Yang Liu, Jiyao Yang, Hongjin Zhao et al.

Large vision-language models (LVLMs) demonstrate strong performance in dermatology; however, evaluating diagnostic reasoning for rare conditions remains largely unexplored. Existing benchmarks focus on common diseases and assess only final accuracy, overlooking the clinical reasoning process, which is critical for complex cases. We address this gap by constructing DermCase, a long-context benchmark derived from peer-reviewed case reports. Our dataset contains 26,030 multi-modal image-text pairs and 6,354 clinically challenging cases, each annotated with comprehensive clinical information and step-by-step reasoning chains. To enable reliable evaluation, we establish DermLIP-based similarity metrics that achieve stronger alignment with dermatologists for assessing differential diagnosis quality. Benchmarking 22 leading LVLMs exposes significant deficiencies across diagnosis accuracy, differential diagnosis, and clinical reasoning. Fine-tuning experiments demonstrate that instruction tuning substantially improves performance while Direct Preference Optimization (DPO) yields minimal gains. Systematic error analysis further reveals critical limitations in current models' reasoning capabilities.

Runmin Jiang, Genpei Zhang, Yuntian Yang et al. · cmu, harvard

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.

Penghao Rao, Runmin Jiang, Min Xu

Approximating training-point influence on test predictions is critical for deploying deep-learning vision models, essential for locating noisy data. Though the influence function was proposed for attributing how infinitesimal up-weighting or removal of individual training examples affects model outputs, its implementation is still challenging in deep-learning vision models: inverse-curvature computations are expensive, and training non-stationarity invalidates static approximations. Prior works use iterative solvers and low-rank surrogates to reduce cost, but offline computation lags behind training dynamics, and missing confidence calibration yields fragile rankings that misidentify critical examples. To address these challenges, we introduce a Stability-Guided Online Influence Framework (SG-OIF), the first framework that treats algorithmic stability as a real-time controller, which (i) maintains lightweight anchor IHVPs via stochastic Richardson and preconditioned Neumann; (ii) proposes modular curvature backends to modulate per-example influence scores using stability-guided residual thresholds, anomaly gating, and confidence. Experimental results show that SG-OIF achieves SOTA (State-Of-The-Art) on noise-label and out-of-distribution detection tasks across multiple datasets with various corruption. Notably, our approach achieves 91.1\% accuracy in the top 1\% prediction samples on the CIFAR-10 (20\% asym), and gets 99.8\% AUPR score on MNIST, effectively demonstrating that this framework is a practical controller for online influence estimation.

Hong Wang, Jie Wang, Jian Luo et al.

Eigenvalue problems are among the most important topics in many scientific disciplines. With the recent surge and development of machine learning, neural eigenvalue methods have attracted significant attention as a forward pass of inference requires only a tiny fraction of the computation time compared to traditional solvers. However, a key limitation is the requirement for large amounts of labeled data in training, including operators and their eigenvalues. To tackle this limitation, we propose a novel method, named Sorting Chebyshev Subspace Filter (SCSF), which significantly accelerates eigenvalue data generation by leveraging similarities between operators -- a factor overlooked by existing methods. Specifically, SCSF employs truncated fast Fourier transform sorting to group operators with similar eigenvalue distributions and constructs a Chebyshev subspace filter that leverages eigenpairs from previously solved problems to assist in solving subsequent ones, reducing redundant computations. To the best of our knowledge, SCSF is the first method to accelerate eigenvalue data generation. Experimental results show that SCSF achieves up to a $3.5\times$ speedup compared to various numerical solvers.

Runmin Jiang, Wanyue Feng, Yuntian Yang et al. · cmu, harvard

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.

Xingjian Li, Qifeng Wu, Adithya S. Ubaradka et al.

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 not only substantially surpasses the previously best-performing method, yielding a 69\% relative improvement in accuracy (Dice Score from 42.53 to 71.81), but also performs competitively with weakly-prompted interactive foundation models.