cubic: CUDA-accelerated 3D Bioimage Computing

Quantitative analysis of multidimensional biological images is useful for understanding complex cellular phenotypes and accelerating advances in biomedical research. As modern microscopy generates ever-larger 2D and 3D datasets, existing computational approaches are increasingly limited by their scalability, efficiency, and integration with modern scientific computing workflows. Existing bioimage analysis tools often lack application programmable interfaces (APIs), do not support graphics processing unit (GPU) acceleration, lack broad 3D image processing capabilities, and/or have poor interoperability for compute-heavy workflows. Here, we introduce cubic, an open-source Python library that addresses these challenges by augmenting widely used SciPy and scikit-image APIs with GPU-accelerated alternatives from CuPy and RAPIDS cuCIM. cubic's API is device-agnostic and dispatches operations to GPU when data reside on the device and otherwise executes on CPU, seamlessly accelerating a broad range of image processing routines. This approach enables GPU acceleration of existing bioimage analysis workflows, from preprocessing to segmentation and feature extraction for 2D and 3D data. We evaluate cubic both by benchmarking individual operations and by reproducing existing deconvolution and segmentation pipelines, achieving substantial speedups while maintaining algorithmic fidelity. These advances establish a robust foundation for scalable, reproducible bioimage analysis that integrates with the broader Python scientific computing ecosystem, including other GPU-accelerated methods, enabling both interactive exploration and automated high-throughput analysis workflows. cubic is openly available at https://github$.$com/alxndrkalinin/cubic

A methodology for clinically driven interactive segmentation evaluation

Interactive segmentation is a promising strategy for building robust, generalisable algorithms for volumetric medical image segmentation. However, inconsistent and clinically unrealistic evaluation hinders fair comparison and misrepresents real-world performance. We propose a clinically grounded methodology for defining evaluation tasks and metrics, and built a software framework for constructing standardised evaluation pipelines. We evaluate state-of-the-art algorithms across heterogeneous and complex tasks and observe that (i) minimising information loss when processing user interactions is critical for model robustness, (ii) adaptive-zooming mechanisms boost robustness and speed convergence, (iii) performance drops if validation prompting behaviour/budgets differ from training, (iv) 2D methods perform well with slab-like images and coarse targets, but 3D context helps with large or irregularly shaped targets, (v) performance of non-medical-domain models (e.g. SAM2) degrades with poor contrast and complex shapes.

Memory as Action: Autonomous Context Curation for Long-Horizon Agentic Tasks

Large Language Models face challenges in long-horizon agentic tasks as their constrained memory is easily overwhelmed by distracting or irrelevant context. Existing working memory methods typically rely on external, heuristic mechanisms that are decoupled from the agent's core policy. In this work, we reframe working memory management as a learnable, intrinsic capability. We propose a novel framework, Memory-as-Action, where an agent actively manages its working memory by executing explicit editing operations as part of a unified policy. This formulation allows an agent, trained via reinforcement learning, to balance memory curation against long-term task objectives under given resource constraints. However, such memory editing actions break the standard assumption of a continuously growing prefix in LLM interactions, leading to what we call trajectory fractures. These non-prefix changes disrupt the causal continuity required by standard policy gradient methods, making those methods inapplicable. To address this, we propose a new algorithm, Dynamic Context Policy Optimization, which enables stable end-to-end reinforcement learning by segmenting trajectories at memory action points and applying trajectory-level advantages to the resulting action segments. Our results demonstrate that jointly optimizing for task reasoning and memory management in an end-to-end fashion not only reduces overall computational consumption but also improves task performance, driven by adaptive context curation strategies tailored to the model's intrinsic capabilities.

What If : Understanding Motion Through Sparse Interactions

Understanding the dynamics of a physical scene involves reasoning about the diverse ways it can potentially change, especially as a result of local interactions. We present the Flow Poke Transformer (FPT), a novel framework for directly predicting the distribution of local motion, conditioned on sparse interactions termed "pokes". Unlike traditional methods that typically only enable dense sampling of a single realization of scene dynamics, FPT provides an interpretable directly accessible representation of multi-modal scene motion, its dependency on physical interactions and the inherent uncertainties of scene dynamics. We also evaluate our model on several downstream tasks to enable comparisons with prior methods and highlight the flexibility of our approach. On dense face motion generation, our generic pre-trained model surpasses specialized baselines. FPT can be fine-tuned in strongly out-of-distribution tasks such as synthetic datasets to enable significant improvements over in-domain methods in articulated object motion estimation. Additionally, predicting explicit motion distributions directly enables our method to achieve competitive performance on tasks like moving part segmentation from pokes which further demonstrates the versatility of our FPT. Code and models are publicly available at https://compvis.github.io/flow-poke-transformer.

ChartAgent: A Multimodal Agent for Visually Grounded Reasoning in Complex Chart Question Answering

Recent multimodal LLMs have shown promise in chart-based visual question answering, but their performance declines sharply on unannotated charts, those requiring precise visual interpretation rather than relying on textual shortcuts. To address this, we introduce ChartAgent, a novel agentic framework that explicitly performs visual reasoning directly within the chart's spatial domain. Unlike textual chain-of-thought reasoning, ChartAgent iteratively decomposes queries into visual subtasks and actively manipulates and interacts with chart images through specialized actions such as drawing annotations, cropping regions (e.g., segmenting pie slices, isolating bars), and localizing axes, using a library of chart-specific vision tools to fulfill each subtask. This iterative reasoning process closely mirrors human cognitive strategies for chart comprehension. ChartAgent achieves state-of-the-art accuracy on the ChartBench and ChartX benchmarks, surpassing prior methods by up to 16.07% absolute gain overall and 17.31% on unannotated, numerically intensive queries. Furthermore, our analyses show that ChartAgent is (a) effective across diverse chart types, (b) achieve the highest scores across varying visual and reasoning complexity levels, and (c) serves as a plug-and-play framework that boosts performance across diverse underlying LLMs. Our work is among the first to demonstrate visually grounded reasoning for chart understanding using tool-augmented multimodal agents.

MetaMP: Seamless Metadata Enrichment and AI Application Framework for Enhanced Membrane Protein Visualization and Analysis

Structural biology has made significant progress in determining membrane proteins, leading to a remarkable increase in the number of available structures in dedicated databases. The inherent complexity of membrane protein structures, coupled with challenges such as missing data, inconsistencies, and computational barriers from disparate sources, underscores the need for improved database integration. To address this gap, we present MetaMP, a framework that unifies membrane-protein databases within a web application and uses machine learning for classification. MetaMP improves data quality by enriching metadata, offering a user-friendly interface, and providing eight interactive views for streamlined exploration. MetaMP was effective across tasks of varying difficulty, demonstrating advantages across different levels without compromising speed or accuracy, according to user evaluations. Moreover, MetaMP supports essential functions such as structure classification and outlier detection. We present three practical applications of Artificial Intelligence (AI) in membrane protein research: predicting transmembrane segments, reconciling legacy databases, and classifying structures with explainable AI support. In a validation focused on statistics, MetaMP resolved 77% of data discrepancies and accurately predicted the class of newly identified membrane proteins 98% of the time and overtook expert curation. Altogether, MetaMP is a much-needed resource that harmonizes current knowledge and empowers AI-driven exploration of membrane-protein architecture.

Clink! Chop! Thud! -- Learning Object Sounds from Real-World Interactions

Can a model distinguish between the sound of a spoon hitting a hardwood floor versus a carpeted one? Everyday object interactions produce sounds unique to the objects involved. We introduce the sounding object detection task to evaluate a model's ability to link these sounds to the objects directly involved. Inspired by human perception, our multimodal object-aware framework learns from in-the-wild egocentric videos. To encourage an object-centric approach, we first develop an automatic pipeline to compute segmentation masks of the objects involved to guide the model's focus during training towards the most informative regions of the interaction. A slot attention visual encoder is used to further enforce an object prior. We demonstrate state of the art performance on our new task along with existing multimodal action understanding tasks.

VIRTUE: Visual-Interactive Text-Image Universal Embedder

Multimodal representation learning models have demonstrated successful operation across complex tasks, and the integration of vision-language models (VLMs) has further enabled embedding models with instruction-following capabilities. However, existing embedding models lack visual-interactive capabilities to specify regions of interest from users (e.g., point, bounding box, mask), which have been explored in generative models to broaden their human-interactive applicability. Equipping embedding models with visual interactions not only would unlock new applications with localized grounding of user intent, which remains unexplored, but also enable the models to learn entity-level information within images to complement their global representations for conventional embedding tasks. In this paper, we propose a novel Visual-InteRactive Text-Image Universal Embedder (VIRTUE) that extends the capabilities of the segmentation model and the vision-language model to the realm of representation learning. In VIRTUE, the segmentation model can process visual prompts that pinpoint specific regions within an image, thereby enabling the embedder to handle complex and ambiguous scenarios more precisely. To evaluate the visual-interaction ability of VIRTUE, we introduce a large-scale Segmentation-and-Scene Caption Retrieval (SCaR) benchmark comprising 1M samples that aims to retrieve the text caption by jointly considering the entity with a specific object and image scene. VIRTUE consistently achieves a state-of-the-art performance with significant improvements across 36 universal MMEB (3.1%-8.5%) and five visual-interactive SCaR (15.2%-20.3%) tasks.

Holistic Order Prediction in Natural Scenes

Even in controlled settings, understanding instance-wise geometries is a challenging task for a wide range of visual models. Although specialized systems exist, modern arts rely on expensive input formats (category labels, binary segmentation masks) and inference costs (a quadratic amount of forward passes). We mitigate these limitations by proposing InstaFormer, a network capable of holistic order prediction. That is, solely given an input RGB image, InstaFormer returns the full occlusion and depth orderings for all the instances in the scene in a single forward pass. At its core, InstaFormer relies on interactions between object queries and latent mask descriptors that semantically represent the same objects while carrying complementary information. We comprehensively benchmark and ablate our approach to highlight its effectiveness. Our code and models are open-source and available at this URL: https://github.com/SNU-VGILab/InstaOrder.

LangGrasp: Leveraging Fine-Tuned LLMs for Language Interactive Robot Grasping with Ambiguous Instructions

The existing language-driven grasping methods struggle to fully handle ambiguous instructions containing implicit intents. To tackle this challenge, we propose LangGrasp, a novel language-interactive robotic grasping framework. The framework integrates fine-tuned large language models (LLMs) to leverage their robust commonsense understanding and environmental perception capabilities, thereby deducing implicit intents from linguistic instructions and clarifying task requirements along with target manipulation objects. Furthermore, our designed point cloud localization module, guided by 2D part segmentation, enables partial point cloud localization in scenes, thereby extending grasping operations from coarse-grained object-level to fine-grained part-level manipulation. Experimental results show that the LangGrasp framework accurately resolves implicit intents in ambiguous instructions, identifying critical operations and target information that are unstated yet essential for task completion. Additionally, it dynamically selects optimal grasping poses by integrating environmental information. This enables high-precision grasping from object-level to part-level manipulation, significantly enhancing the adaptability and task execution efficiency of robots in unstructured environments. More information and code are available here: https://github.com/wu467/LangGrasp.