Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2606.00472

CodeCytos: AI-assisted spatial molecular imaging analysis via code-augmented agent action space

Hung Q. Vo·Huy Q. Vo·Son T. Ly·Zhihao Wan·Anh-Vu Nguyen·Hong Zhao·Jianting Sheng·Stephen T. C. Wong·Hien V. Nguyen
View original source ↗Read source document ↗Export metadata ↓

Abstract

Conventional tissue image analysis software provides foundational capabilities for cellular analysis, including segmentation, basic morphological feature extraction, and spatial organization analysis. However, these tools often require manual intervention and are not well integrated with code-driven automation, limiting efficiency and scalability for complex spatial tissue studies. In addition, they offer limited flexibility for custom analyses, as they typically support only a fixed set of pre-implemented spatial cellular features. To address these limitations, we propose CodeCytos, a coding-based reasoning agent framework that enables dynamic, programmable interaction with spatial molecular imaging data to improve automation and customization. CodeCytos is designed to streamline the exploration of custom spatial cellular features and adapt to diverse research needs. We demonstrate its utility through case studies on four expert-curated datasets from distinct tissue types: frontal cortex, non-small-cell lung cancer, pancreas, and tonsil. We evaluate CodeCytos under a realistic minimal prompt setting, where bioscientists pose simple questions without task-specific instructions or contextual information about spatial cellular analysis, and benchmark multiple LLM backbones with strong coding capabilities. We further show that incorporating tailored, domain-agnostic few-shot in-context coding-reasoning examples (randomly sampled demonstrations outside the spatial analysis domain) can substantially improve performance without requiring costly, expert-crafted in-domain demonstrations. Overall, CodeCytos outperforms baseline approaches, highlighting the potential of code-action agents to assist with custom feature exploration in spatial molecular imaging and to accelerate biomarker discovery.

Explore related subjects

cs.CVcs.AIcs.HCcs.LG

Keep this discovery

BibTeXRIS

Hung Q. Vo, Huy Q. Vo, Son T. Ly, Zhihao Wan, Anh-Vu Nguyen, Hong Zhao, Jianting Sheng, Stephen T. C. Wong, Hien V. Nguyen. 2026-05-30. CodeCytos: AI-assisted spatial molecular imaging analysis via code-augmented agent action space. https://arxiv.org/abs/2606.00472

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

HiPerViT: A Hierarchical Perceiver-Vision Transformer Architecture for Multi-Scale Texture Recognition

Texture recognition remains challenging for modern vision models because discriminative evidence is often carried by higher-order spatial statistics rather than by object shape alone. While Vision Transformers provide strong long-range modeling capacity, their standard object-centric representations do not explicitly expose such statistical structure, which limits texture sensitivity in fine-grained recognition settings. We present HiPerViT, a compact vision-only architecture that injects an explicit second-order statistical prior into a transformer-based recognition pipeline. The method combines global and local image views with a compact bilinear descriptor encoded as a statistical token, and integrates this token with first-order spatial representations through Perceiver-style latent distillation. This design enables direct interaction between spatial tokens and second-order feature co-occurrence statistics, providing the model with explicit access to texture-relevant information without requiring multimodal pretraining or ensemble construction. Across six texture recognition benchmarks, HiPerViT achieves consistent improvements over strong vision-only baselines under the reported evaluation protocols, including gains of +3.05 percentage points on DTD, +10.48 on GTOS-Mobile, and +10.10 on 1200Tex. Beyond benchmark performance, our analyses show that these gains are largely invariant to the backbone depth used to extract second-order statistics and to the ordering of interaction and distillation stages. This pattern suggests that the primary source of improvement is not a specific fusion topology, but the explicit availability of second-order statistical information as a first-class representational signal. These results support explicit statistical tokenization as an effective and robust design principle for texture-centric visual recognition.

cs.CV↗
arXiv2026

CamPilot: A Multi-Agent Cinematic Assistant for Camera-Controlled Movie Generation

The integration of large language models (LLMs) into video generation has enabled rapid text-to-video creation and improved visual quality. However, it still falls short of professional filmmaking, where cinematographic language is less refined than human-crafted camera work and multi-shot continuity remains challenging. To address these limitations, we introduce CamPilot, a multi-agent framework that integrates cinematographic planning and camera-work control to produce more coherent, logically structured, and human-aesthetic movies. CamPilot adopts a GRPO-based learning paradigm to learn camera work planning from 14K real-world professional movies, internalizing motion patterns and composition principles that support reasoning over shooting techniques (e.g., camera angle, motion, and focal behavior) and cross-shot relationships for controllable camera-viewpoint generation. Multiple agents further collaborate and evolve to improve overall output quality. To support this work and further studies in this domain, we establish CamEval, a benchmark for evaluating camera work quality and cinematic engagement. Empirical results show that CamPilot outperforms state-of-the-art text-to-movie generation methods on cinematographic control and quality, highlighting the impact of professional camera design on movie generation.

cs.CV↗
arXiv2026

New Evidence, Same Choice: Testing Physical Experiment Selection in Vision Language Models

A model first sees an image from one physical measurement experiment, such as how far a block coasted, and must answer a question about a new trial, such as whether the block will pass a target after a fixed push. The initial experiment may provide enough information to answer, or the model may need another measurement, such as the object's mass, friction, restitution, or spring stiffness. We study whether vision language models can decide when to answer immediately and, when more evidence is needed, which experiment to perform. Current physical reasoning benchmarks usually evaluate only the final answer, so they do not directly measure this decision-making ability. We introduce a controlled evaluation where each problem provides one measurement image and four possible physical worlds created by combining two possible masses and two possible values of another relevant property. The model must either stop and answer or select the cheapest additional experiment that can resolve the question. We construct matched problem pairs where changing either the observed measurement or the question changes the optimal action. Since all possible worlds and experiment costs are known, we can explicitly determine the optimal choice. Across six open models and 144 physical parameter sets, direct responses repeat the same action for 95.1% to 100% of image pairs even when the correct action changes. Brief reasoning improves action switching, but the best model makes both decisions correctly for only 5.9% of image pairs. Additional analysis reveals failures in measurement interpretation, physical reasoning, and response formatting. By evaluating evidence selection separately from final answers, our benchmark reveals limitations in physical reasoning that conventional answer accuracy can overlook.

cs.CV↗