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Nov 10

AgriField3D: A Curated 3D Point Cloud and Procedural Model Dataset of Field-Grown Maize from a Diversity Panel

The application of artificial intelligence (AI) in three-dimensional (3D) agricultural research, particularly for maize, has been limited by the scarcity of large-scale, diverse datasets. While 2D image datasets are abundant, they fail to capture essential structural details such as leaf architecture, plant volume, and spatial arrangements that 3D data provide. To address this limitation, we present AgriField3D (https://baskargroup.github.io/AgriField3D/), a curated dataset of 3D point clouds of field-grown maize plants from a diverse genetic panel, designed to be AI-ready for advancing agricultural research. Our dataset comprises over 1,000 high-quality point clouds collected using a Terrestrial Laser Scanner, complemented by procedural models that provide structured, parametric representations of maize plants. These procedural models, generated using Non-Uniform Rational B-Splines (NURBS) and optimized via a two-step process combining Particle Swarm Optimization (PSO) and differentiable programming, enable precise, scalable reconstructions of leaf surfaces and plant architectures. To enhance usability, we performed graph-based segmentation to isolate individual leaves and stalks, ensuring consistent labeling across all samples. We also conducted rigorous manual quality control on all datasets, correcting errors in segmentation, ensuring accurate leaf ordering, and validating metadata annotations. The dataset further includes metadata detailing plant morphology and quality, alongside multi-resolution subsampled versions (100k, 50k, 10k points) optimized for various computational needs. By integrating point cloud data of field grown plants with high-fidelity procedural models and ensuring meticulous manual validation, AgriField3D provides a comprehensive foundation for AI-driven phenotyping, plant structural analysis, and 3D applications in agricultural research.

  • 9 authors
·
Mar 10

SurgLaVi: Large-Scale Hierarchical Dataset for Surgical Vision-Language Representation Learning

Vision-language pre-training (VLP) offers unique advantages for surgery by aligning language with surgical videos, enabling workflow understanding and transfer across tasks without relying on expert-labeled datasets. However, progress in surgical VLP remains constrained by the limited scale, procedural diversity, semantic quality, and hierarchical structure of existing datasets. In this work, we present SurgLaVi, the largest and most diverse surgical vision-language dataset to date, comprising nearly 240k clip-caption pairs from more than 200 procedures, and comprising hierarchical levels at phase-, step-, and task-level. At the core of SurgLaVi lies a fully automated pipeline that systematically generates fine-grained transcriptions of surgical videos and segments them into coherent procedural units. To ensure high-quality annotations, it applies dual-modality filtering to remove irrelevant and noisy samples. Within this framework, the resulting captions are enriched with contextual detail, producing annotations that are both semantically rich and easy to interpret. To ensure accessibility, we release SurgLaVi-eta, an open-source derivative of 113k clip-caption pairs constructed entirely from public data, which is over four times larger than existing surgical VLP datasets. To demonstrate the value of SurgLaVi datasets, we introduce SurgCLIP, a CLIP-style video-text contrastive framework with dual encoders, as a representative base model. SurgCLIP achieves consistent improvements across phase, step, action, and tool recognition, surpassing prior state-of-the-art methods, often by large margins. These results validate that large-scale, semantically rich, and hierarchically structured datasets directly translate into stronger and more generalizable representations, establishing SurgLaVi as a key resource for developing surgical foundation models.

  • 5 authors
·
Sep 9

BioProBench: Comprehensive Dataset and Benchmark in Biological Protocol Understanding and Reasoning

Biological protocols are fundamental to reproducible and safe life science research. While LLMs excel on general tasks, their systematic evaluation on these highly specialized, accuracy-critical, and inherently procedural texts remains limited. In this work, we present BioProBench, the first large-scale, integrated multi-task benchmark for biological protocol understanding and reasoning. While limited benchmarks have touched upon specific aspects like protocol QA, BioProBench provides a comprehensive suite of five core tasks: Protocol Question Answering, Step Ordering, Error Correction, Protocol Generation, and Protocol Reasoning, enabling a holistic evaluation of LLMs on procedural biological texts. Built upon 27K original protocols, it yields nearly 556K high-quality structured instances. We evaluate 12 mainstream open/closed-source LLMs on BioProBench. Experimental results reveal that while top models preform well on surface understanding tasks, struggle significantly with deep reasoning and structured generation tasks like ordering and generation. Furthermore, model comparisons reveal diverse performance: certain open-source models approach closed-source levels on some tasks, yet bio-specific small models lag behind general LLMs, indicating limitations on complex procedural content. Overall, our findings underscore that procedural reasoning within biological protocols represents a significant challenge for current LLMs. BioProBench serves as a standardized framework to diagnose these specific limitations and guide the development of AI systems better equipped for safely automating complex scientific procedures. The code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/GreatCaptainNemo/BioProBench.

  • 5 authors
·
May 11

ROOM: A Physics-Based Continuum Robot Simulator for Photorealistic Medical Datasets Generation

Continuum robots are advancing bronchoscopy procedures by accessing complex lung airways and enabling targeted interventions. However, their development is limited by the lack of realistic training and test environments: Real data is difficult to collect due to ethical constraints and patient safety concerns, and developing autonomy algorithms requires realistic imaging and physical feedback. We present ROOM (Realistic Optical Observation in Medicine), a comprehensive simulation framework designed for generating photorealistic bronchoscopy training data. By leveraging patient CT scans, our pipeline renders multi-modal sensor data including RGB images with realistic noise and light specularities, metric depth maps, surface normals, optical flow and point clouds at medically relevant scales. We validate the data generated by ROOM in two canonical tasks for medical robotics -- multi-view pose estimation and monocular depth estimation, demonstrating diverse challenges that state-of-the-art methods must overcome to transfer to these medical settings. Furthermore, we show that the data produced by ROOM can be used to fine-tune existing depth estimation models to overcome these challenges, also enabling other downstream applications such as navigation. We expect that ROOM will enable large-scale data generation across diverse patient anatomies and procedural scenarios that are challenging to capture in clinical settings. Code and data: https://github.com/iamsalvatore/room.

  • 7 authors
·
Sep 16 2