AutoSAM: an Agentic Framework for Automating Input File Generation for the SAM Code with Multi-Modal Retrieval-Augmented Generation

In the design and safety analysis of advanced reactor systems, constructing input files for system-level thermal-hydraulics codes such as the System Analysis Module (SAM) remains a labor-intensive task. Analysts must extract and reconcile design data from heterogeneous engineering documents and manually translate it into solver-specific syntax. In this paper, we present AutoSAM, an agentic framework that automates SAM input file generation. The framework combines a large language model agent with retrieval-augmented generation over the solver's user guide and theory manual, together with specialized tools for analyzing PDFs, images, spreadsheets, and text files. AutoSAM ingests unstructured engineering documents, including system diagrams, design reports, and data tables, extracts simulation-relevant parameters into a human-auditable intermediate representation, and synthesizes validated, solver-compatible input decks. Its multimodal retrieval pipeline integrates scientific text extraction, vision-based figure interpretation, semantic embedding, and query answering. We evaluate AutoSAM on four case studies of increasing complexity: a single-pipe steady-state model, a solid-fuel channel with temperature reactivity feedback, the Advanced Burner Test Reactor core, and the Molten Salt Reactor Experiment primary loop. Across all cases, the agent produces runnable SAM models consistent with expected thermal-hydraulic behavior while explicitly identifying missing data and labeling assumed values. The framework achieves 100% utilization of structured inputs, about 88% extraction from PDF text, and 100% completeness in vision-based geometric extraction. These results demonstrate a practical path toward prompt-driven reactor modeling, in which analysts provide system descriptions and supporting documentation while the agent translates them into transparent, and executable, SAM simulations.

MERIT: Multi-domain Efficient RAW Image Translation

RAW images captured by different camera sensors exhibit substantial domain shifts due to varying spectral responses, noise characteristics, and tone behaviors, complicating their direct use in downstream computer vision tasks. Prior methods address this problem by training domain-specific RAW-to-RAW translators for each source-target pair, but such approaches do not scale to real-world scenarios involving multiple types of commercial cameras. In this work, we introduce MERIT, the first unified framework for multi-domain RAW image translation, which leverages a single model to perform translations across arbitrary camera domains. To address domain-specific noise discrepancies, we propose a sensor-aware noise modeling loss that explicitly aligns the signal-dependent noise statistics of the generated images with those of the target domain. We further enhance the generator with a conditional multi-scale large kernel attention module for improved context and sensor-aware feature modeling. To facilitate standardized evaluation, we introduce MDRAW, the first dataset tailored for multi-domain RAW image translation, comprising both paired and unpaired RAW captures from five diverse camera sensors across a wide range of scenes. Extensive experiments demonstrate that MERIT outperforms prior models in both quality (5.56 dB improvement) and scalability (80% reduction in training iterations).

Mamba-driven MRI-to-CT Synthesis for MRI-only Radiotherapy Planning

Radiotherapy workflows for oncological patients increasingly rely on multi-modal medical imaging, commonly involving both Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). MRI-only treatment planning has emerged as an attractive alternative, as it reduces patient exposure to ionizing radiation and avoids errors introduced by inter-modality registration. While nnU-Net-based frameworks are predominantly used for MRI-to-CT synthesis, we explore Mamba-based architectures for this task, aiming to showcase the advantages of state-space modeling for cross-modality translation compared to standard convolutional neural networks. Specifically, we adapt both the U-Mamba and the SegMamba architecture, originally proposed for segmentation, to perform cross-modality image generation. Our 3D Mamba architecture effectively captures complex volumetric features and long-range dependencies, thus allowing accurate CT synthesis while maintaining fast inference times. Experiments were conducted on a subset of SynthRAD2025 dataset, comprising registered single-channel MRI-CT volume pairs across three anatomical regions. Quantitative evaluation is performed via a combination of image similarity metrics computed in Hounsefield Units (HU) and segmentation-based metrics obtained from TotalSegmentator to ensure geometric consistency is preserved. The findings pave the way for the integration of state-space models into radiotherapy workflows.

Rigid Motion Estimation using Accelerated Iterative Coordinate Descent (REACT) for MR Imaging

Purpose: To develop a computationally viable autofocus method for estimating 3D rigid motion in MR imaging. Theory and Methods: The proposed method, REACT, assumes a piecewise-constant motion trajectory and estimates the rigid motion parameters of individual temporal segments by optimizing an image-quality metric. Coordinate descent is adopted to decompose the high-dimensional optimization problem into a series of subproblems, each updating the motion parameters of a single temporal segment. The cost function of each subproblem is assumed to be approximately locally convex under suitable acquisition conditions. Each subproblem is then solved using a derivative-free solver, thereby avoiding an exhaustive grid search. Numerical simulations were conducted to investigate the local convexity assumption. REACT was evaluated for respiratory motion correction on in vivo free-breathing coronary MR angiography datasets acquired using a 3D cones trajectory with image-based navigators (iNAVs). An autofocus nonrigid motion correction method was also evaluated for comparison. Coronary artery sharpness was quantified using unbounded image edge profile acutance (u-IEPA). Results: In numerical simulations, the objective surfaces of the subproblems were approximately locally convex when the current motion estimate was close to the desired solution. In the in vivo study, REACT yielded higher u-IEPA than the conventional iNAV-based translational motion-estimation method for both the left anterior descending artery (LAD) and right coronary artery. REACT also yielded higher u-IEPA for the LAD than the autofocus nonrigid motion correction method. Conclusion: This study demonstrates the feasibility of coordinate descent for autofocus motion correction in MR imaging.

6D Robotic OCT Scanning of Curved Tissue Surfaces

Optical coherence tomography (OCT) is a non-invasive volumetric imaging modality with high spatial and temporal resolution. For imaging larger tissue structures, OCT probes need to be moved to scan the respective area. For handheld scanning, stitching of the acquired OCT volumes requires overlap to register the images. For robotic scanning and stitching, a typical approach is to restrict the motion to translations, as this avoids a full hand-eye calibration, which is complicated by the small field of view of most OCT probes. However, stitching by registration or by translational scanning are limited when curved tissue surfaces need to be scanned. We propose a marker for full six-dimensional hand-eye calibration of a robot mounted OCT probe. We show that the calibration results in highly repeatable estimates of the transformation. Moreover, we evaluate robotic scanning of two phantom surfaces to demonstrate that the proposed calibration allows for consistent scanning of large, curved tissue surfaces. As the proposed approach is not relying on image registration, it does not suffer from a potential accumulation of errors along a scan path. We also illustrate the improvement compared to conventional 3D-translational robotic scanning.

PhotoAgent: A Robotic Photographer with Spatial and Aesthetic Understanding

Embodied agents for creative tasks like photography must bridge the semantic gap between high-level language commands and geometric control. We introduce PhotoAgent, an agent that achieves this by integrating Large Multimodal Models (LMMs) reasoning with a novel control paradigm. PhotoAgent first translates subjective aesthetic goals into solvable geometric constraints via LMM-driven, chain-of-thought (CoT) reasoning, allowing an analytical solver to compute a high-quality initial viewpoint. This initial pose is then iteratively refined through visual reflection within a photorealistic internal world model built with 3D Gaussian Splatting (3DGS). This ``mental simulation'' replaces costly and slow physical trial-and-error, enabling rapid convergence to aesthetically superior results. Evaluations confirm that PhotoAgent excels in spatial reasoning and achieves superior final image quality.

Improving Image-to-Image Translation via a Rectified Flow Reformulation

In this work, we propose Image-to-Image Rectified Flow Reformulation (I2I-RFR), a practical plug-in reformulation that recasts standard I2I regression networks as continuous-time transport models. While pixel-wise I2I regression is simple, stable, and easy to adapt across tasks, it often over-smooths ill-posed and multimodal targets, whereas generative alternatives often require additional components, task-specific tuning, and more complex training and inference pipelines. Our method augments the backbone input by channel-wise concatenation with a noise-corrupted version of the ground-truth target and optimizes a simple t-reweighted pixel loss. This objective admits a rectified-flow interpretation via an induced velocity field, enabling ODE-based progressive refinement at inference time while largely preserving the standard supervised training pipeline. In most cases, adopting I2I-RFR requires only expanding the input channels, and inference can be performed with a few explicit solver steps (e.g., 3 steps) without distillation. Extensive experiments across multiple image-to-image translation and video restoration tasks show that I2I-RFR generally improves performance across a wide range of tasks and backbones, with particularly clear gains in perceptual quality and detail preservation. Overall, I2I-RFR provides a lightweight way to incorporate continuous-time refinement into conventional I2I models without requiring a heavy generative pipeline.

PinPoint: Monocular Needle Pose Estimation for Robotic Suturing via Stein Variational Newton and Geometric Residuals

Reliable estimation of surgical needle 3D position and orientation is essential for autonomous robotic suturing, yet existing methods operate almost exclusively under stereoscopic vision. In monocular endoscopic settings, common in transendoscopic and intraluminal procedures, depth ambiguity and rotational symmetry render needle pose estimation inherently ill-posed, producing a multimodal distribution over feasible configurations, rather than a single, well-grounded estimate. We present PinPoint, a probabilistic variational inference framework that treats this ambiguity directly, maintaining a distribution of pose hypotheses rather than suppressing it. PinPoint combines monocular image observations with robot-grasp constraints through analytical geometric likelihoods with closed-form Jacobians. This framework enables efficient Gauss-Newton preconditioning in a Stein Variational Newton inference, where second-order particle transport deterministically moves particles toward high-probability regions while kernel-based repulsion preserves diversity in the multimodal structure. On real needle-tracking sequences, PinPoint reduces mean translational error by 80% (down to 1.00 mm) and rotational error by 78% (down to 13.80°) relative to a particle-filter baseline, with substantially better-calibrated uncertainty. On induced-rotation sequences, where monocular ambiguity is most severe, PinPoint maintains a bimodal posterior 84% of the time, almost three times the rate of the particle filter baseline, correctly preserving the alternative hypothesis rather than committing prematurely to one mode. Suturing experiments in ex vivo tissue demonstrate stable tracking through intermittent occlusion, with average errors during occlusion of 1.34 mm in translation and 19.18° in rotation, even when the needle is fully embedded.

Ontology-Guided Diffusion for Zero-Shot Visual Sim2Real Transfer

Bridging the simulation-to-reality (sim2real) gap remains challenging as labelled real-world data is scarce. Existing diffusion-based approaches rely on unstructured prompts or statistical alignment, which do not capture the structured factors that make images look real. We introduce Ontology- Guided Diffusion (OGD), a neuro-symbolic zero-shot sim2real image translation framework that represents realism as structured knowledge. OGD decomposes realism into an ontology of interpretable traits -- such as lighting and material properties -- and encodes their relationships in a knowledge graph. From a synthetic image, OGD infers trait activations and uses a graph neural network to produce a global embedding. In parallel, a symbolic planner uses the ontology traits to compute a consistent sequence of visual edits needed to narrow the realism gap. The graph embedding conditions a pretrained instruction-guided diffusion model via cross-attention, while the planned edits are converted into a structured instruction prompt. Across benchmarks, our graph-based embeddings better distinguish real from synthetic imagery than baselines, and OGD outperforms state-of-the-art diffusion methods in sim2real image translations. Overall, OGD shows that explicitly encoding realism structure enables interpretable, data-efficient, and generalisable zero-shot sim2real transfer.

Translating MRI to PET through Conditional Diffusion Models with Enhanced Pathology Awareness

Positron emission tomography (PET) is a widely recognized technique for diagnosing neurodegenerative diseases, offering critical functional insights. However, its high costs and radiation exposure hinder its widespread use. In contrast, magnetic resonance imaging (MRI) does not involve such limitations. While MRI also detects neurodegenerative changes, it is less sensitive for diagnosis compared to PET. To overcome such limitations, one approach is to generate synthetic PET from MRI. Recent advances in generative models have paved the way for cross-modality medical image translation; however, existing methods largely emphasize structural preservation while neglecting the critical need for pathology awareness. To address this gap, we propose PASTA, a novel image translation framework built on conditional diffusion models with enhanced pathology awareness. PASTA surpasses state-of-the-art methods by preserving both structural and pathological details through its highly interactive dual-arm architecture and multi-modal condition integration. Additionally, we introduce a novel cycle exchange consistency and volumetric generation strategy that significantly enhances PASTA's ability to produce high-quality 3D PET images. Our qualitative and quantitative results demonstrate the high quality and pathology awareness of the synthesized PET scans. For Alzheimer's diagnosis, the performance of these synthesized scans improves over MRI by 4%, almost reaching the performance of actual PET. Our code is available at https://github.com/ai-med/PASTA.