Re4: Scientific Computing Agent with Rewriting, Resolution, Review and Revision

Large language models (LLMs) serve as an active and promising field of generative artificial intelligence and have demonstrated abilities to perform complex tasks in multiple domains, including mathematical and scientific reasoning. In this work, we construct a novel agent framework for solving representative problems in scientific computing. The proposed agent, incorporating a "rewriting-resolution-review-revision" logical chain via three reasoning LLMs (functioning as the Consultant, Reviewer, and Programmer, respectively), is integrated in a collaborative and interactive manner. The Consultant module endows the agent with knowledge transfer capabilities to link problems to professional domain insights, thereby rewriting problem descriptions through text augmentation. The Programmer module is responsible for generating and executing well-structured code to deliver the problem resolution. The Reviewer module equips the agent with the capacity for self-debugging and self-refinement through interactive feedback with code runtime outputs. By leveraging the end-to-end review mechanism, the executable code provided by the Programmer attains the iterative revision. A comprehensive evaluation is conducted on the performance of the proposed agent framework in solving PDEs, ill-conditioned linear systems, and data-driven physical analysis problems. Compared to single-model, this collaborative framework significantly improves the bug-free code generation rate and reduces the occurrence of non-physical solutions, thereby establishing a highly reliable framework for autonomous code generation based on natural language descriptions. The review mechanism improved the average execution success (bug-free code and non-NaN solutions) rate of the latest reasoning models. In summary, our agent framework establishes automatic code generation and review as a promising scientific computing paradigm.

AxonCallosumEM Dataset: Axon Semantic Segmentation of Whole Corpus Callosum cross section from EM Images

The electron microscope (EM) remains the predominant technique for elucidating intricate details of the animal nervous system at the nanometer scale. However, accurately reconstructing the complex morphology of axons and myelin sheaths poses a significant challenge. Furthermore, the absence of publicly available, large-scale EM datasets encompassing complete cross sections of the corpus callosum, with dense ground truth segmentation for axons and myelin sheaths, hinders the advancement and evaluation of holistic corpus callosum reconstructions. To surmount these obstacles, we introduce the AxonCallosumEM dataset, comprising a 1.83 times 5.76mm EM image captured from the corpus callosum of the Rett Syndrome (RTT) mouse model, which entail extensive axon bundles. We meticulously proofread over 600,000 patches at a resolution of 1024 times 1024, thus providing a comprehensive ground truth for myelinated axons and myelin sheaths. Additionally, we extensively annotated three distinct regions within the dataset for the purposes of training, testing, and validation. Utilizing this dataset, we develop a fine-tuning methodology that adapts Segment Anything Model (SAM) to EM images segmentation tasks, called EM-SAM, enabling outperforms other state-of-the-art methods. Furthermore, we present the evaluation results of EM-SAM as a baseline.