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Development and Validation of a Computable Radiotherapy Phenotype

International journal of radiation oncology, biology, physics 2025年

作者： Cecelia J Madison Julie A Lynch Scott L Duvall Patrick R Alba Elizabeth Hanchrow Fatai Y Agiri Kathryn M Pridgen Ryan J Burri Reid F Thompson Maria Kelly Evangelia Katsoulakis VA Informatics and Computing Infrastructure VA Salt Lake City Health Care System Salt Lake City UT USA. Electronic address: Cecilia.madison@va.gov. VA Informatics and Computing Infrastructure VA Salt Lake City Health Care System Salt Lake City UT USA Division of Epidemiology Department of Internal Medicine University of Utah School of Medicine Salt Lake City UT USA. Electronic address: julie.lynch@va.gov. Division of Epidemiology Department of Internal Medicine University of Utah School of Medicine Salt Lake City UT USA. VA Informatics and Computing Infrastructure VA Salt Lake City Health Care System Salt Lake City UT USA. Radiation Bay Pines VA Healthcare System Bay Pines Florida USA. VA National Radiation Oncology Program Richmond VA USA Division of Hospital and Specialty Medicine VA Portland Healthcare System Portland OR USA Department of Radiation Medicine Oregon Health & Science University Portland OR USA. VA National Radiation Oncology Program Richmond VA USA.

BACKGROUND:This study aims to develop a robust methodology using structured and semi-structured health data to identify patients who have undergone radiation therapy, thereby facilitating future research on treatment outcomes. METHODS:In this retrospective cohort study, we identified Veterans receiving radiation oncology care through documentation of referrals, encounters, and billing codes from 2014 through 2023. We classified administrative codes based on process of care and type of radiation received, and then analyzed utilization patterns. Unstructured data analysis was performed using keyword search of relevant clinical notes in the metadata fields and categorizing those notes by radiation oncology processes. To validate our algorithm, we compared the cohort we developed using existing data sources to a cohort that was chart reviewed. RESULTS:The final cohort included 589,318 Veterans with radiation oncology care. Among these, 355,276 had codes indicating radiotherapy delivery. The most common treatments were image guided (IGRT), three-dimensional conformal (3DCRT), intensity-modulated (IMRT), and stereotactic radiosurgery/stereotactic body (SRS/SBRT). Anatomy-specific billing codes were underutilized. Clinical note analysis identified 1,341 unique labels for radiation oncology content, with 947,928 notes found for 204,064 patients. Validation against chart-reviewed datasets showed strong concordance and confirmed the accuracy of our algorithm in identifying radiation oncology care. CONCLUSION:Automated extraction of medical records can be used to identify cohorts of patients who have undergone radiotherapy. Employing this algorithm may facilitate more precise phenotyping of radiotherapy cases and thus significantly enhance our understanding of these cohorts.

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Hadamard matrix guided online hashing

arXiv

引用

arXiv 2019年

作者： Lin, Mingbao Ji, Rongrong Liu, Hong Sun, Xiaoshuai Chen, Shen Tian, Qi Media Analytics and Computing Laboratory Department of Cognitive Science School of Informatics Xiamen University China Peng Cheng Laboratory Shenzhen China Huawei Noah's Art Lab China

Online image hashing has attracted increasing research attention recently, which receives large-scale data in a streaming manner to update the hash functions on-the-fly. Its key challenge lies in the difficulty of balancing the learning timeliness and model accuracy. To this end, most works follow a supervised setting, i.e., using class labels to boost the hashing performance, which defects in two aspects: First, strong constraints, e.g., orthogonal or similarity preserving, are used, which however are typically relaxed and lead to large accuracy drop. Second, large amounts of training batches are required to learn the up-to-date hash functions, which largely increase the learning complexity. To handle the above challenges, a novel supervised online hashing scheme termed Hadamard Matrix Guided Online Hashing (HMOH) is proposed in this paper. Our key innovation lies in introducing Hadamard matrix, which is an orthogonal binary matrix built via Sylvester method. In particular, to release the need of strong constraints, we regard each column of Hadamard matrix as the target code for each class label, which by nature satisfies several desired properties of hashing codes. To accelerate the online training, LSH is first adopted to align the lengths of target code and to-be-learned binary code. We then treat the learning of hash functions as a set of binary classification problems to fit the assigned target code. Finally, extensive experiments on four widely-used datasets demonstrate the superior accuracy and efficiency of the proposed method over various state-of-the-art methods. Copyright © 2019, The Authors. All rights reserved.

关键词： Binary codes

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Hierarchical policy learning is sensitive to goal space design

arXiv

引用

arXiv 2019年

作者： Dwiel, Zach Candadai, Madhavun Phielipp, Mariano Bansal, Arjun K. Intel AI Lab BloomingtonIN United States Program in Cognitive Science School of Informatics Computing and Engineering BloomingtonIN United States Intel AI Lab PhoenixAZ United States Intel AI Lab San DiegoCA United States

Hierarchy in reinforcement learning agents allows for control at multiple time scales yielding improved sample efficiency, the ability to deal with long time horizons and transferability of sub-policies to tasks outside the training distribution. It is often implemented as a master policy providing goals to a sub-policy. Ideally, we would like the goal-spaces to be learned, however, properties of optimal goal spaces still remain unknown and consequently there is no method yet to learn optimal goal spaces. Motivated by this, we systematically analyze how various modifications to the ground-truth goal-space affect learning in hierarchical models with the aim of identifying important properties of optimal goal spaces. Our results show that, while rotation of ground-truth goal spaces and noise had no effect, having additional unnecessary factors significantly impaired learning in hierarchical models. Copyright © 2019, The Authors. All rights reserved.

关键词： Hierarchical systems

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Homoharringtonine as a PHGDH inhibitor: Unraveling metabolic dependencies and developing a potent therapeutic strategy for high-risk neuroblastoma

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Biomedicine and Pharmacotherapy 2023年第1期166卷 115429-115429页

作者： Hsieh, Chiao-Hui Huang, Chen-Tsung Cheng, Yi-Sheng Hsu, Chun-Hua Hsu, Wen-Ming Chung, Yun-Hsien Liu, Yen-Lin Yang, Tsai-Shan Chien, Chia-Yu Lee, Yu-Hsuan Huang, Hsuan-Cheng Juan, Hsueh-Fen Department of Life Science National Taiwan University Taipei Taiwan Center for Computational and Systems Biology National Taiwan University Taipei Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Institute of Plant Biology National Taiwan University Taipei Taiwan Genome and Systems Biology Degree Program National Taiwan University and Academia Sinica Taipei Taiwan Department of Agricultural Chemistry National Taiwan University Taipei Taiwan Department of Surgery National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan Department of Pediatrics School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei Taiwan Center for Advanced Computing and Imaging in Biomedicine Taipei Taiwan

Neuroblastoma, a childhood cancer affecting the sympathetic nervous system, continues to challenge the development of potent treatments due to the limited availability of druggable targets for this aggressive illness. Recent investigations have uncovered that phosphoglycerate dehydrogenase (PHGDH), an essential enzyme for de novo serine synthesis, serves as a non-oncogene dependency in high-risk neuroblastoma. In this study, we show that homoharringtonine (HHT) acts as a PHGDH inhibitor, inducing intricate alterations in cellular metabolism, and thus providing an efficient treatment for neuroblastoma. We have experimentally verified the reliance of neuroblastoma on PHGDH and employed molecular docking, thermodynamic evaluations, and X-ray crystallography techniques to determine the bond interactions between HHT and PHGDH. Administering HHT to treat neuroblastoma resulted in effective cell elimination in vitro and tumor reduction in vivo. Metabolite and functional assessments additionally disclosed that HHT treatment suppressed de novo serine synthesis, initiating intricate metabolic reconfiguration and oxidative stress in neuroblastoma. Collectively, these discoveries highlight the potential of targeting PHGDH using HHT as a potent approach for managing high-risk neuroblastoma. © 2023 The Authors

关键词： Computational molecular docking Drug discovery High-risk neuroblastoma Metabolic reprogramming Molecular target therapy Phosphoglycerate dehydrogenase

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Dispensed transformer network for unsupervised domain adaptation

arXiv

引用

arXiv 2021年

作者： Li, Yunxiang Li, Jingxiong Dan, Ruilong Wang, Shuai Jin, Kai Zeng, Guodong Wang, Jun Pan, Xiangji Zhang, Qianni Zhou, Huiyu Jin, Qun Wang, Li Wang, Yaqi College of Computer Science and Technology Hangzhou Dianzi University Hangzhou China Artificial Intelligence and Biomedical Image Analysis Lab Westlake University Hangzhou China School of Mechanical Electrical and Information Engineering Shandong University Weihai China Department of Ophthalmology Hospital of Zhejiang University Hangzhou China sitem Center for Translational Medicine and Biomedical Entrepreneurship University of Bern Bern Switzerland School of Biomedical Engineering Shanghai Jiao Tong University Shanghai China School of Electronic Engineering and Computer Science Queen Mary University of London London United Kingdom School of Computing and Mathematical Sciences University of Leicester United Kingdom Department of Human Informatics and Cognitive Sciences Faculty of Human Sciences Waseda University Tokyo Japan Department of Radiology and Biomedical Research Imaging Center University of North Carolina at Chapel Hill Chapel Hill United States College of Media Engineering Communication University of Zhejiang Hangzhou China

Accurate segmentation is a crucial step in medical image analysis and applying supervised machine learning to segment the organs or lesions has been substantiated effective. However, it is costly to perform data annotation that provides ground truth labels for training the supervised algorithms, and the high variance of data that comes from different domains tends to severely degrade system performance over cross-site or cross-modality datasets. To mitigate this problem, a novel unsupervised domain adaptation (UDA) method named dispensed Transformer network (DTNet) is introduced in this paper. Our novel DTNet contains three modules. First, a dispensed residual transformer block is designed, which realizes global attention by dispensed interleaving operation and deals with the excessive computational cost and GPU memory usage of the Transformer. Second, a multi-scale consistency regularization is proposed to alleviate the loss of details in the low-resolution output for better feature alignment. Finally, a feature ranking discriminator is introduced to automatically assign different weights to domain-gap features to lessen the feature distribution distance, reducing the performance shift of two domains. The proposed method is evaluated on large fluorescein angiography (FA) retinal nonperfusion (RNP) cross-site dataset with 676 images and a wide used cross-modality dataset from the MM-WHS challenge. Extensive results demonstrate that our proposed network achieves the best performance in comparison with several state-of-the-art techniques. © 2021, CC BY.

关键词： Supervised learning

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A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge

arXiv

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arXiv 2024年

作者： de la Rosa, Ezequiel Reyes, Mauricio Liew, Sook-Lei Hutton, Alexandre Wiest, Roland Kaesmacher, Johannes Hanning, Uta Hakim, Arsany Zubal, Richard Valenzuela, Waldo Robben, David Sima, Diana M. Anania, Vincenzo Brys, Arne Meakin, James A. Mickan, Anne Broocks, Gabriel Heitkamp, Christian Gao, Shengbo Liang, Kongming Zhang, Ziji Siddiquee, Md Mahfuzur Rahman Myronenko, Andriy Ashtari, Pooya Van Huffel, Sabine Jeong, Hyun-Su Yoon, Chi-Ho Kim, Chulhong Huo, Jiayu Ourselin, Sebastien Sparks, Rachel Clèrigues, Albert Oliver, Arnau Lladó, Xavier Chalcroft, Liam Pappas, Ioannis Bertels, Jeroen Heylen, Ewout Moreau, Juliette Hatami, Nima Frindel, Carole Qayyum, Abdul Mazher, Moona Puig, Domenec Lin, Shao-Chieh Juan, Chun-Jung Hu, Tianxi Boone, Lyndon Goubran, Maged Liu, Yi-Jui Wegener, Susanne Kofler, Florian Ezhov, Ivan Shit, Suprosanna Hernandez Petzsche, Moritz R. Menze, Bjoern Kirschke, Jan S. Wiestler, Benedikt Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Informatics Technical University Munich Germany Icometrix Leuven Belgium ARTORG Center for Biomedical Research University of Bern Bern Switzerland Department of Radiation Oncology University Hospital Bern University of Bern Switzerland University of Bern Bern Switzerland Chan Division of Occupational Science and Occupational Therapy University of Southern California Los AngelesCA United States Stevens Neuroimaging and Informatics Institute Department of Neurology Keck School of Medicine University of Southern California United States University Institute of Diagnostic and Interventional Neuroradiology Inselspital Bern Switzerland University Institute of Diagnostic and Interventional Neuroradiology University Hospital Bern Inselspital University of Bern Bern Switzerland Department of Diagnostic and Interventional neuroradiology University Medical Center Hamburg-Eppendorf Hamburg Germany Department of Medical Imaging Radboud University Medical Center Institute for Health Sciences Nijmegen Netherlands Deepwise AI Lab Beijing China Beijing University of Posts and Telecommunications Bejing China School of Computing and Augmented Intelligence Arizona State University TempeAZ United States NVIDIA Santa ClaraCA United States STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Pohang Korea Republic of School of Biomedical Engineering & Imaging Sciences King’s College London United Kingdom Institute of Computer Vision and Robotics University of Girona Spain Wellcome Centre for Human Neuroimaging University College London London United Kingdom Laboratory of Neuro Imaging Stevens Institute for Neuroimaging and Informatics Keck School of Medicine University of Southern California Los Angeles United States KU Leuven Leuven Belgium CREATIS Université Lyon1 CNRS UMR5220 INSERM U1206 INSA-Lyon Villeurbanne696

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES’22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. By assessing them against a hidden test set, we identified strengths, weaknesses, and potential biases. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model combines the individual algorithms’ strengths and achieved superior ischemic lesion detection and segmentation accuracy (median Dice score: 0.82, median lesion-wise F1 score: 0.86) on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers like lesion types and affected vascular territories. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm’s segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model’s generalizability (median Dice score: 0.82, median lesion-wise F1 score: 0.86). The algorithm’s outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)rad

关键词： Diagnosis

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Multifunctionality in embodied agents: Three levels of neural reuse

arXiv

引用

arXiv 2018年

作者： Candadai, Madhavun Izquierdo, Eduardo J. Cognitive Science Program Indiana University BloomingtonIN47406 United States Cognitive Science Program School of Informatics Computing and Engineering Indiana University BloomingtonIN47406 United States

The brain in conjunction with the body is able to adapt to new environments and perform multiple behaviors through reuse of neural resources and transfer of existing behavioral traits. Although mechanisms that underlie this ability are not well understood, they are largely attributed to neuromodulation. In this work, we demonstrate that an agent can be multifunctional using the same sensory and motor systems across behaviors, in the absence of modulatory mechanisms. Further, we lay out the different levels at which neural reuse can occur through a dynamical filtering of the brain-body-environment system's operation: structural network, autonomous dynamics, and transient dynamics. Notably, transient dynamics reuse could only be explained by studying the brain-body-environment system as a whole and not just the brain. The multifunctional agent we present here demonstrates neural reuse at all three levels. Copyright © 2018, The Authors. All rights reserved.

关键词： Dynamical systems

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An Early Stage Researcher's Primer on Systems Medicine Terminology

Network and Systems Medicine

引用

Network and Systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the Systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

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Hadamard codebook based deep hashing

arXiv

引用

arXiv 2019年

作者： Chen, Shen Cao, Liujuan Lin, Mingbao Wang, Yan Sun, Xiaoshuai Wu, Chenglin Qiu, Jingfei Ji, Rongrong Fujian Laboratory of Sensing and Computing for Smart City Department Cognitive Science School of Informatics Xiamen University China Pinterest San Francisco United States Fuzhi Xiamen China Peng Cheng Laboratory Shenzhen China

As an approximate nearest neighbor search technique, hashing has been widely applied in large-scale image retrieval due to its excellent efficiency. Most supervised deep hashing methods have similar loss designs with embedding learning, while quantizing the continuous high-dim feature into compact binary space. We argue that the existing deep hashing schemes are defective in two issues that seriously affect the performance, i.e., bit independence and bit balance. The former refers to hash codes of different classes should be independent of each other, while the latter means each bit should have a balanced distribution of +1s and −1s. In this paper, we propose a novel supervised deep hashing method, termed Hadamard Codebook based Deep Hashing (HCDH), which solves the above two problems in a unified formulation. Specifically, we utilize an off-the-shelf algorithm to generate a binary Hadamard codebook to satisfy the requirement of bit independence and bit balance, which subsequently serves as the desired outputs of the hash functions learning. We also introduce a projection matrix to solve the inconsistency between the order of Hadamard matrix and the number of classes. Besides, the proposed HCDH further exploits the supervised labels by constructing a classifier on top of the outputs of hash functions. Extensive experiments demonstrate that HCDH can yield discriminative and balanced binary codes, which well outperforms many state-of-the-arts on three widely-used benchmarks. Copyright © 2019, The Authors. All rights reserved.

关键词： Hash functions

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Learning to reconstruct and understand indoor scenes from sparse views

arXiv

引用

arXiv 2019年

作者： Yang, Jingyu Xu, Ji Li, Kun Lai, Yu-Kun Yue, Huanjing Lu, Jianzhi Wu, Hao Liu, Yebin School of Electrical and Information Engineering Tianjin University Tianjin300072 China Tianjin Key Laboratory of Cognitive Computing and Application College of Intelligence and Computing Tianjin University Tianjin300350 China School of Computer Science and Informatics Cardiff University Wales United Kingdom 3vjia company Department of Automation Tsinghua University Beijing10084 China

This paper proposes a new method for simultaneous 3D reconstruction and semantic segmentation of indoor scenes. Unlike existing methods that require recording a video using a color camera and/or a depth camera, our method only needs a small number of (e.g., 3-5) color images from uncalibrated sparse views as input, which greatly simplifies data acquisition and extends applicable scenarios. Since different views have limited overlaps, our method allows a single image as input to discern the depth and semantic information of the scene. The key issue is how to recover relatively accurate depth from single images and reconstruct a 3D scene by fusing very few depth maps. To address this problem, we first design an iterative deep architecture, Iter-Net, that estimates depth and semantic segmentation alternately, so that they benefit each other. To deal with the little overlap and non-rigid transformation between views, we further propose a joint global and local registration method to reconstruct a 3D scene with semantic information from sparse *** also make available a new indoor synthetic dataset simultaneously providing photorealistic high-resolution RGB images, accurate depth maps and pixel-level semantic labels for thousands of complex layouts, useful for training and evaluation. Experimental results on public datasets and our dataset demonstrate that our method achieves more accurate depth estimation, smaller semantic segmentation errors and better 3D reconstruction results, compared with stateof-the-art methods. Copyright © 2019, The Authors. All rights reserved.

关键词： Cameras

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