arXiv subjects

Runmin Jiang

Publications and source records attributed to Runmin Jiang.

11 recordsLinked to original sources

arXiv2026

Does the Selected Object Reach the Reader? Auditing Identity Handoffs in Grounded Language-Model Pipelines

Grounded language-model pipelines can be divided into three stages: selecting an object, retrieving passages for it, and using that evidence to answer. If the selected object must reach the reader, losing it breaks the handoff. Benchmark recall checks the dataset-linked object, which can differ. We audit 600 HybridQA questions across three selector families. On 1,463 resolvable records where the selected object matches the dataset-traced passage, exact key lookup and exact title matching return the object every time. With every ranked rule given the same decoded selected title, body-only BM25 omits it on 389 records (26.6%) at cutoff five, while hybrid retrieval with reranking omits it on 14 (1.0%). The two identities differ on 329 of 1,792 resolvable records. With original-question rankings, their top-five checks disagree on 106 records (5.9%). Frozen reader comparisons associate the aligned object's presence with 28.6 to 31.0 points higher exact match. In a deliberately selected 64-item cohort, removing that passage sharply lowers exact match, while removing a similar-length comparison passage does not reproduce the drop. We release the Returned-Object Profile (ROP), an executable record of the target, returned-ID field, cutoff, membership rule, and complete expected population, with data and an offline replay.

cs.AI↗

arXiv2026

Adapting Vision Foundation Models with Cascaded Semantics

Prompt tuning, a leading parameter-efficient adaptation paradigm in NLP, has recently been extended to computer vision. Visual prompt tuning (VPT) adapts pre-trained vision transformers (ViTs) by updating a small set of additional prompt parameters. However, existing visual prompts are randomly initialized and do not exploit prior knowledge, such as instructions in NLP. We address this gap by injecting two complementary semantic priors into VPT. Fundamental image priors, including color, texture, and shape, are extracted with classical hand-crafted operators and injected into the input space, while self-attention maps provide instance-aware semantics in the feature space. We further propose a cascaded scheme that integrates both priors throughout ViT adaptation. Experiments on 34 challenging image classification datasets demonstrate superior downstream adaptation while tuning only 0.74% of ViT parameters. Project page: https://xixiaouab.github.io/Cascaded-Semantics/.

cs.CV↗

arXiv2026

Layer-Specific Prompt Fusion Discovery via Differentiable Search in Vision Foundation Models

Visual prompt tuning has emerged as a parameter-efficient fine-tuning approach for adapting large-scale Vision Transformers (ViTs) to downstream tasks. As its learnable prompts are applied in input and feature spaces, prior to jointly going through attention in transformer layers, the most commonly used scheme for fusing image and prompt tokens is concatenation or addition. In this paper, we aim to study a fundamental yet essential problem in visual prompt tuning: whether a single fusion scheme tends to yield better results, and whether that would be beneficial to develop a hybrid fusion scheme. To this end, we formulate the task as a bi-level optimization problem, and solve it leveraging differentiable architecture search. In this context, the learnable prompts and their fusion schemes are jointly optimized. To enrich the search space in the architecture search, we propose two additional fusion schemes, namely, affine transformation and cross-attention, in addition to concatenation and addition. Extensive experiments on 34 datasets spanning VTAB-1k, FGVC, and HTA show consistent gains over prompt-tuning baselines. With a frozen ViT backbone, our method delivers a favorable accuracy--latency--parameter trade-off compared with VPT-Deep and recent variants. Our findings reveal that how prompts fuse with image tokens plays a significant role in visual prompt tuning, and a hybrid fusion fashion can more effectively leverage layer semantics of ViTs, contributing a novel perspective for visual prompt-tuning research.

cs.CV↗

arXiv2026

SciTrace: Trajectory-Aware Safety Reasoning for Scientific Discovery Agents

LLM-based scientific agents have shown strong capacity for autonomous research, yet their safety layers remain structurally divorced from core reasoning: they inspect pipeline outputs rather than shaping the deliberation that produces them. This separation opens two failure modes: safety signals accumulated at one stage are discarded before the next, and sequences of individually benign tool calls can compose into harmful outcomes that no single-step filter detects. To address these challenges, we introduce \textbf{SciTrace}, a framework that weaves safety reasoning into every stage of the scientific agent pipeline. SciTrace couples two complementary mechanisms: a \textit{Safety-Intrinsic Reasoning Loop} (SIR) that maintains a cumulative risk state across the Thinker, Experimenter, Writer, and Reviewer stages through joint task-and-safety deliberation, and a \textit{Compositional Tool-Chain Verifier} (CTV) that performs trajectory-aware safety checks before execution, catching risks that surface only across multi-step tool sequences. Evaluated on 240 high-risk research tasks and 120 tool-related risk tasks spanning six scientific domains, SciTrace achieves state-of-the-art (\textbf{SOTA}) safety among compared frameworks across four backbone models: it consistently improves tool call safety and adversarial robustness while preserving scientific output quality, and it uncovers \textbf{78.8\%} of the compositional tool-chain escapes that single-step monitors miss. The project website is available at https://opensciagent.github.io/SciTrace/.

cs.AI↗

arXiv2026

Mind the Rarities: Can Rare Skin Diseases Be Reliably Diagnosed via Diagnostic Reasoning?

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.

cs.CV↗

arXiv2025

SG-OIF: A Stability-Guided Online Influence Framework for Reliable Vision Data

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.

cs.CV↗

arXiv2025

Accelerating Eigenvalue Dataset Generation via Chebyshev Subspace Filter

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.

cs.LG↗

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

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

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 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.

cs.CV↗

arXiv2024

Enhancing Weakly Supervised 3D Medical Image Segmentation through Probabilistic-aware Learning

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.

eess.IV↗