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arXiv 2025年

作者： Neeley, Matthew B. Qi, Guantong Wang, Guanchu Tang, Ruixiang Mao, Dongxue Liu, Chaozhong Pasupuleti, Sasidhar Yuan, Bo Xia, Fan Liu, Pengfei Liu, Zhandong Hu, Xia Jan and Dan Duncan Neurological Research Institute Texas Children’s Hospital Houston United States Graduate School of Biomedical Sciences Program in Quantitative and Computational Biosciences Baylor College of Medicine Houston United States Graduate School of Biomedical Sciences Program in Genetics and Genomics Baylor College of Medicine Houston United States Department of Computer Science Rice University Houston United States Department of Computer Science Rutgers University NJ United States Department of Pediatrics Baylor College of Medicine Houston United States Department of Molecular and Human Genetics Baylor College of Medicine Houston United States Human Genome Sequencing Center Baylor College of Medicine Houston United States Baylor Genetics Houston United States

Background Rare diseases can be difficult to diagnose due to limited patient data and broad genetic diversity. Despite the advances in variant prioritization tools, many rare disease cases remain undiagnosed. While large language models (LLMs) have performed well in medical exams, their accuracy in diagnosing rare genetic diseases has not yet been evaluated. Methods To identify causal genes for genetic diseases, we benchmarked various LLMs for gene prioritization. We employed multi-agent and Human Phenotype Ontology (HPO) classification approaches to identify patient case groups based on phenotypes categorizing them into different levels of solvability. To address LLM limitations in ranking large gene sets, we used a divide-and-conquer strategy to break down the ranking task into smaller subsets. Mini-batching inputs and limiting the number of generated tokens improved efficiency. Results In its vanilla form, GPT-4 consistently outperformed the other LLMs with an accuracy around 30%. Multi-agent and HPO classification approaches aided us in distinguishing between confidently-solved and challenging cases. In addition, we observed bias towards well-studied genes and input order sensitivity which are drawbacks of LLMs in disease-causal gene prioritization. Our divide-and-conquer strategy enhanced accuracy by overcoming positional and gene frequency biases in literature. This framework, based on benchmarking insights and novel techniques, significantly optimizes the overall process when identifying disease-causal genes for genetic diseases when compared to our baseline evaluation, and thereby better enables the development of targeted diagnostic and therapeutic interventions. Conclusions Using HPO classification and our novel multi-agent techniques, and our LLM divide-and-conquer strategy (1) highlighted the importance of accounting for differences in patient case solvability and (2) yielded improved performance in identifying causal genes for rare diseases when compare

关键词： Gene Ontology

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

arXiv

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arXiv 2025年

作者： Kimara, Elvis Hadadi, Mozhgan Godbersen, Jackson Balu, Aditya Jubery, Talukder Li, Yawei Krishnamurthy, Adarsh Schnable, Patrick S. Ganapathysubramanian, Baskar Department of Computer Science Iowa State University Ames United States Translational AI Research and Education Center Ames United States Department of Mechanical Engineering Iowa State University Ames United States Plant Science Institute Iowa State University Ames United States Interdepartmental Genetics and Genomics Graduate Program Iowa State University Ames United States Department of Agronomy Iowa State University Ames United States

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 (website), 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. © 2025, CC BY-NC-SA.

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Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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Advantages of two quantum programming platforms in quantum computing and quantum chemistry

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Journal of cheminformatics 2025年第1期17卷 77页

作者： Pei-Hua Wang Wei-Yeh Wu Che-Yu Lee Jia-Cheng Hong Yufeng Jane Tseng Undergraduate Program in Intelligent Computing and Big Data Chung Yuan Christian University No. 200 Zhongbei Road Taoyuan 320314 Taiwan. Quantum Information Center Chung Yuan Christian University No. 200 Zhongbei Road Taoyuan 320314 Taiwan. Department of Computer Science and Information Engineering National Taiwan University No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan. Graduate Institute of Biomedical Electronics and Bioinformatics College of Electrical Engineering and Computer Science National Taiwan University No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan. Department of Computer Science and Information Engineering National Taiwan University No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan. yjtseng@csie.ntu.edu.tw. Graduate Institute of Biomedical Electronics and Bioinformatics College of Electrical Engineering and Computer Science National Taiwan University No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan. yjtseng@csie.ntu.edu.tw. Physics Division National Center for Theoretical Sciences No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan. yjtseng@csie.ntu.edu.tw. Center for Quantum Science and Engineering National Taiwan University No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan. yjtseng@csie.ntu.edu.tw.

Quantum computing is at the forefront of technological advancement and has the potential to revolutionize various fields, including quantum chemistry. Choosing an appropriate quantum programming language becomes critical as quantum education and research increase. In this paper, we comprehensively compare two leading quantum programming languages, Qiskit and PennyLane, focusing on their suitability for teaching and research. We delve into their basic and advanced usage, examine their learning curves, and evaluate their capabilities in quantum computing experiments. We also demonstrate using a quantum programming language to build a half adder and a machine learning model. Our study reveals that each language has distinct advantages. While PennyLane excels in research applications due to its flexibility to adjust parameters in detail and access multiple sources of real quantum devices, Qiskit stands out in education because of its web-based graphical user interface and smaller code size. The codes and the dataset used in the studies are available at https://***/wangpeihua1231/quantum-programming-platform .

关键词： PennyLane Qiskit Quantum chemistry Quantum computing Quantum programming language

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Simultaneous Fuzzy Segmentation of Multiple Objects

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Electronic Notes in Discrete Mathematics 2003年 12卷 3-22页

作者： Carvalho, Bruno M. Herman, Gabor T. Kong, T.Yung Doctoral Program in Computer Science Graduate Center - CUNY New York NY 10016 United States Department of Computer Science Queens College CUNY Flushing NY 11367 United States

Fuzzy segmentation is a technique that assigns to each element in an image (corrupted by noise and/or shading) a grade of membership in an object (which is believed to be contained in the image). In an earlier work the first two authors extended this concept by presenting and illustrating an algorithm which simultaneously assigns to each element in an image a grade of membership in each one of a number of objects (which are believed to be contained in the image). In this paper we establish the correctness of this algorithm (in the sense of producing an output that is uniquely specified by a desirable mathematical property) and present a further example of its use in medical imaging. We also compare our method with two recently published related methods. © 2005 Elsevier Ltd. All rights reserved.

关键词： fuzzy graph fuzzy segmentation greedy algorithms

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Measurement of peripheral nerve magnetostimulation thresholds of a head solenoid coil between 200 Hz and 88.1 kHz

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IEEE Journal of Translational Engineering in Health and Medicine 2025年

作者： Barksdale, Alex C. Ferris, Natalie G. Mattingly, Eli Sliwiak, Monika Guerin, Bastien Wald, Lawrence L. Davids, Mathias Klein, Valerie MIT Department of Electrical Engineering and Computer Science Cambridge MA United States Martinos Center for Biomedical Imaging Charlestown MA United States Harvard University Harvard Graduate Program in Biophysics Cambridge MA United States Harvard-MIT Division of Health Sciences and Technology Boston MA United States Harvard Medical School Boston MA United States

Objective: Magnetic fields switching at kilohertz frequencies induce electric fields in the body, which can cause peripheral nerve stimulation (PNS). Although magnetostimulation has been extensively studied below 10 kHz, the behavior of PNS at higher frequencies remains poorly understood. This study aims to investigate PNS thresholds at frequencies up to 88.1 kHz and to explore deviations from the widely accepted hyperbolic strength-duration curve (SDC). Methods and procedures: PNS thresholds were measured in the head of 8 human volunteers using a solenoidal coil at 16 distinct frequencies, ranging from 200 Hz to 88.1 kHz. A hyperbolic SDC was used as a reference to compare the frequency-dependent behavior of PNS thresholds. Results: Contrary to the predictions of the hyperbolic SDC, PNS thresholds did not decrease monotonically with frequency. Instead, thresholds reached a minimum near 25 kHz, after which they increased by an average of 39% from 25 kHz to 88.1 kHz across subjects. This pattern indicates a significant deviation from previously observed behavior at lower frequencies. Conclusion: Our results suggest that PNS thresholds exhibit a non-monotonic frequency dependence at higher frequencies, diverging from the traditional hyperbolic SDC. These findings offer critical data for refining neurodynamic models and provide insights for setting PNS safety limits in applications like MRI gradient coils and magnetic particle imaging (MPI). Further investigation is needed to understand the biological mechanisms driving these deviations beyond 25 kHz. Clinical impact: These findings call for further basic research into biological mechanisms underlying high frequency PNS threshold trends, and supports refinement of safety guidelines for MRI and MPI systems for clinical implementation. © 2013 IEEE.

关键词： high frequency magnetostimulation magnetic particle imaging (MPI) magnetic resonance imaging (MRI) MRI gradient safety peripheral nerve stimulation

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A segmentation-based automatic navigation technique for virtual endoscopy

A segmentation-based automatic navigation technique for virt...

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2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano

作者： Carvalho, Bruno M. Herman, Gabor T. Dept. of Comp. and Info. Science University of Pennsylvania Doctoral Program in Computer Science Graduate Center City University of New York

ISBN: (纸本)0780383885

Virtual endoscopy (VE) mimics the examination consisting of introducing an endoscope into a tubular structure for diagnostic purposes. One of the main problems in VE is the computattion of the navigation path that the virtual camera will travel while producing the animation that will be viewed by the specialist. We propose a technique that allows the automatic computation of navigation paths connecting a starting and one or more end points inside the structure to be visualized. The computation of the path uses the connectedness map produced by the segmentation algorithm that has been used to identify the structure to be visualized in the image. A simple smoothing operation is then applied to this path to produce the final navigation path. © 2004 IEEE.

关键词： Endoscopy

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A Bayesian-based approach for extracting the pion charge radius from electron-electron scattering data

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Chinese Physics C 2021年第8期45卷 12-27页

作者： Alam A Hidayat Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara UniversityJakarta 11480Indonesia Computer Science Department BINUS Graduate Program-Master of Computer ScienceBina Nusantara UniversityJakarta 11480Indonesia

In this study,we utilize a potentially versatile Bayesian parameter approach to compute the value of the pion charge radius and quantify its uncertainty from several experimental e^(+)e^(-) datasets for the pion vector form *** employ dispersion relations to model the pion vector form factor to extract the *** model selection is used to determine the order of polynomial appearing in the form factor formulation that can be supported by the data,adapting the computation of Bayes evidence and Bayesian effective complexity based on Occam's *** findings indicate that five out of six used datasets favor the nine-parameter model for radius extraction,and accordingly,we average the radii from the *** some inconsistencies with the most updated radius values,our approach may serve as a more intuitive method of addressing parameter estimations in dispersion theory.

关键词： Bayesian complexity dispersion hadron pion

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Nonlocal flat optics for size-selective image processing and denoising

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Nature Communications 2025年第1期16卷 1-9页

作者： Chamoli, Sandeep Kumar Jin, Chunqi Fan, Yandong Kiani, Mehdi Goh, Heedong Huang, Chen Guo, Shuyu Wang, Yuntong Zhu, Fei Xing, Guohua Li, Bo Bai, Tian Alù, Andrea Li, Wei GPL Photonics Laboratory State Key Laboratory of Luminescence Science and Technology Changchun Institute of Optics Fine Mechanics and Physics Chinese Academy of Sciences Changchun Jilin 130033 China University of Chinese Academy of Sciences Beijing 100049 China Photonics Initiative Advanced Science Research Center City University of New York New York 10031 NY United States Physics Program Graduate Center of the City University of New York New York 10016 NY United States College of Computer Science and Technology Jilin University Changchun 130012 China

All-optical image processing based on metasurfaces is a swiftly advancing field of technology, due to its high speed, large integrability and inherently low energy requirements. So far, the proposed devices have been focusing on canonical operations, such as differentiations to perform edge detection across all objects in a complex scene. Yet, undesired background noise and clutter can hinder such operations, requiring target selection with digital post-processing which inherently limits the overall accuracy, efficiency and speed. Here, we introduce an optical solution for real-time size-selective image processing and experimentally demonstrate the concept with a metal-dielectric-metal film performing a spatial band-pass filter in momentum space. We show high-resolution (~0.9 μm) edge detection and real-time dynamic denoising, ideally suited for bio-imaging applications and target recognitions. Our demonstrated k-space filtering metasurface expands the scope of nonlocal flat optics for analog image processing, ushering in opportunities for ultra-compact, cost-effective, and multifunctional image processors. © The Author(s) 2025.

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Transfer Learning for Keypoint Detection in Low-Resolution Thermal TUG Test Images

arXiv

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arXiv 2025年

作者： Chen, Wei-Lun Hsieh, Chia-Yeh Kao, Yu-Hsiang Liu, Kai-Chun Peng, Sheng-Yu Tsao, Yu Research Center for Information Technology Innovation Academic Sinica Taiwan Graduate Institute of Electrical Engineering National Taiwan University Taiwan Bachelor’s Program in Medical Informatics and Innovative Applications Fu Jen Catholic University Taiwan Department of Electrical Engineering National Taiwan University Taiwan College of Information and Computer Sciences University of Massachusetts AmherstMA01003 United States Department of Electrical Engineering National Taiwan University of Science of Technology Taiwan

This study presents a novel approach to human keypoint detection in low-resolution thermal images using transfer learning techniques. We introduce the first application of the Timed Up and Go (TUG) test in thermal image computer vision, establishing a new paradigm for mobility assessment. Our method leverages a MobileNetV3-Small encoder and a ViTPose decoder, trained using a composite loss function that balances latent representation alignment and heatmap accuracy. The model was evaluated using the Object Keypoint Similarity (OKS) metric from the COCO Keypoint Detection Challenge. The proposed model achieves better performance with AP, AP50, and AP75 scores of 0.861, 0.942, and 0.887 respectively, outperforming traditional supervised learning approaches like Mask R-CNN and ViTPose-Base. Moreover, our model demonstrates superior computational efficiency in terms of parameter count and FLOPS. This research lays a solid foundation for future clinical applications of thermal imaging in mobility assessment and rehabilitation monitoring. Copyright © 2025, The Authors. All rights reserved.

关键词： Thermography (imaging)

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