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Predicting gastric cancer response to anti-HER2 therapy or anti-HER2 combined immunotherapy based on multimodal data

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Signal Transduction and Targeted Therapy 2024年第9期9卷 4137-4148页

作者： Zifan Chen Yang Chen Yu Sun Lei Tang Li Zhang Yajie Hu Meng He Zhiwei Li Siyuan Cheng Jiajia Yuan Zhenghang Wang Yakun Wang Jie Zhao Jifang Gong Liying Zhao Baoshan Cao Guoxin Li Xiaotian Zhang Bin Dong Lin Shen Center for Data Science Peking UniversityBeijingChina Department of Gastrointestinal Oncology Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education)Peking University Cancer Hospital and InstituteBeijingChina Department of Pathology Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education)Peking University Cancer Hospital and InstituteBeijingChina Department of Radiology Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education)Peking University Cancer Hospital and InstituteBeijingChina National Biomedical Imaging Center Peking UniversityBeijingChina Department of General Surgery Nanfang HospitalSouthern Medical UniversityGuangzhouChina Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor GuangzhouChina Department of Medical Oncology and Radiation Sickness Peking University Third HospitalBeijingChina National Engineering Laboratory for Big Data Analysis and Applications Peking UniversityBeijingChina Beijing International Center for Mathematical Research(BICMR) Peking UniversityBeijingChina Center for Machine Learning Research Peking UniversityBeijingChina

The sole use of single modality data often fails to capture the complex heterogeneity among patients,including the variability in resistance to anti-HER2 therapy and outcomes of combined treatment regimens,for the treatment of HER2-positive gastric cancer(GC).This modality deficit has not been fully considered in many ***,the application of artificial intelligence in predicting the treatment response,particularly in complex diseases such as GC,is still in its ***,this study aimed to use a comprehensive analytic approach to accurately predict treatment responses to anti-HER2 therapy or anti-HER2 combined immunotherapy in patients with HER2-positive *** collected multi-modal data,comprising radiology,pathology,and clinical information from a cohort of 429 patients:310 treated with anti-HER2 therapy and 119 treated with a combination of anti-HER2 and anti-PD-1/PD-L1 inhibitors *** introduced a deep learning model,called the Multi-Modal model(MuMo),that integrates these data to make precise treatment response *** achieved an area under the curve score of 0.821 for anti-HER2 therapy and 0.914 for combined ***,patients classified as low-risk by MuMo exhibited significantly prolonged progression-free survival and overall survival(log-rank test,P<0.05).These findings not only highlight the significance of multi-modal data analysis in enhancing treatment evaluation and personalized medicine for HER2-positive gastric cancer,but also the potential and clinical value of our model.

关键词： immunotherapy HER2 cancer

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Deep Reinforcement learning for Beam Angle Optimization of Intensity-Modulated Radiation Therapy

arXiv

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arXiv 2023年

作者： Bao, Peng Wang, Gong Yang, Ruijie Dong, Bin The Center for Data Science Peking University the Department of Radiation Oncology Peking University Third Hospital Beijing China The Department of Radiation Oncology Peking University Third Hospital Beijing China Beijing International Center for Mathematical Research Center for Machine Learning Research National Biomedical Imaging Center Peking University Beijing China

Objective: Intensity-modulated radiation therapy (IMRT) beam angle optimization (BAO) is a challenging combinatorial optimization problem that is NP-hard. In this study, we aim to develop a personalized BAO algorithm for IMRT that improves the quality of the final treatment. Methods: To improve the quality of IMRT treatment planning, we propose a deep reinforcement learning (DRL)based approach for IMRT BAO. We consider the task as a sequential decision-making problem and formulate it as a Markov Decision Process. To facilitate the training process, a 3D-Unet is designed to predict the dose distribution for the different number of beam angles, ranging from 1 to 9, to simulate the IMRT environment. By leveraging the simulation model, double deep-Q network (DDQN) and proximal policy optimization (PPO) are used to train agents to select the personalized beam angle sequentially within a few seconds. Results: The treatment plans with beam angles selected by DRL outperform those with clinically used evenly distributed beam angles. For DDQN, the overall average improvement of the CIs is 0.027, 0.032, and 0.03 for 5, 7, and 9 beam angles respectively. For PPO, the overall average improvement of CIs is 0.045, 0.051, and 0.025 for 5, 7, and 9 beam angles respectively. Conclusion: The proposed DRL-based beam angle selection strategy can generate personalized beam angles within a few seconds, and the resulting treatment plan is superior to that obtained using evenly distributed angles. Significance: A fast and automated personalized beam angle selection approach is been proposed for IMRT BAO. © 2023, CC BY.

关键词： Reinforcement learning

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Embarrassingly Simple Scribble Supervision for 3D Medical Segmentation

arXiv

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arXiv 2024年

作者： Gotkowski, Karol Lüth, Carsten Jäger, Paul F. Ziegler, Sebastian Krämer, Lars Denner, Stefan Xiao, Shuhan Disch, Nico Maier-Hein, Klaus H. Isensee, Fabian Division of Medical Image Computing DKFZ Heidelberg Germany Helmholtz Imaging DKFZ Heidelberg Germany Interactive Machine Learning Group DKFZ Heidelberg Germany Medical Faculty Heidelberg University of Heidelberg Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Germany HIDSS4Health - Helmholtz Information and Data Science School for Health Germany

Traditionally, segmentation algorithms require dense annotations for training, demanding significant annotation efforts, particularly within the 3D medical imaging field. Scribble-supervised learning emerges as a possible solution to this challenge, promising a reduction in annotation efforts when creating large-scale datasets. Recently, a plethora of methods for optimized learning from scribbles have been proposed, but have so far failed to position scribble annotation as a beneficial alternative. We relate this shortcoming to two major issues: 1) the complex nature of many methods which deeply ties them to the underlying segmentation model, thus preventing a migration to more powerful state-of-the-art models as the field progresses and 2) the lack of a systematic evaluation to validate consistent performance across the broader medical domain, resulting in a lack of trust when applying these methods to new segmentation problems. To address these issues, we propose a comprehensive scribble supervision benchmark consisting of seven datasets covering a diverse set of anatomies and pathologies imaged with varying modalities. We furthermore propose the systematic use of partial losses, i.e. losses that are only computed on annotated voxels. Contrary to most existing methods, these losses can be seamlessly integrated into state-of-the-art segmentation methods, enabling them to learn from scribble annotations while preserving their original loss formulations. Our evaluation using nnU-Net reveals that while most existing methods suffer from a lack of generalization, the proposed approach consistently delivers state-of-the-art performance. Thanks to its simplicity, our approach presents an embarrassingly simple yet effective solution to the challenges of scribble supervision. Source code as well as our extensive scribble benchmarking suite will be made publicly available upon publication. © 2024, CC BY.

关键词： Medical imaging

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Explainability and transparency in the realm of digital humanities: toward a historian XAI

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International Journal of Digital Humanities 2023年第2期5卷 299-331页

作者： El-Hajj, Hassan Eberle, Oliver Merklein, Anika Siebold, Anna Shlomi, Noga Büttner, Jochen Martinetz, Julius Müller, Klaus-Robert Montavon, Grégoire Valleriani, Matteo Max Planck Institute for the History of Science Berlin Germany BIFOLD – Berlin Institute for the Foundations of Learning and Data Berlin Germany Machine Learning Group Technische Universität Berlin Berlin Germany German Center for Art History Paris (DFK Paris) Paris France The Cohn Institute for the History and Philosophy of Science and Ideas Faculty of Humanities Tel-Aviv University Tel-Aviv Israel Department of Artificial Intelligence Korea University Seoul South Korea Max Planck Institute for Informatics Saarbrüken Germany Department of Mathematics and Computer Science Freie Universität Berlin Berlin Germany

The recent advancements in the field of Artificial Intelligence (AI) translated to an increased adoption of AI technology in the humanities, which is often challenged by the limited amount of annotated data, as well as its heterogeneity. Despite the scarcity of data it has become common practice to design increasingly complex AI models, usually at the expense of human readability, explainability, and trust. This in turn has led to an increased need for tools to help humanities scholars better explain and validate their models as well as their hypotheses. In this paper, we discuss the importance of employing Explainable AI (XAI) methods within the humanities to gain insights into historical processes as well as ensure model reproducibility and a trustworthy scientific result. To drive our point, we present several representative case studies from the Sphaera project where we analyze a large, well-curated corpus of early modern textbooks using an AI model, and rely on the XAI explanatory outputs to generate historical insights concerning their visual content. More specifically, we show that XAI can be used as a partner when investigating debated subjects in the history of science, such as what strategies were used in the early modern period to showcase mathematical instruments and machines.

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Audio Enhancement for Computer Audition – An Iterative Training Paradigm Using Sample Importance

arXiv

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arXiv 2024年

作者： Milling, Manuel Liu, Shuo Triantafyllopoulos, Andreas Aslan, Ilhan Schuller, Björn W. EIHW – Embedded Intelligence for Health Care & Wellbeing University of Augsburg Germany MRI Technical University of Munich Germany MCML – Munich Center for Machine Learning Germany Huawei Technologies Munich Germany MDSI – Munich Data Science Institute Germany GLAM – The Group on Language Audio & Music Imperial College London United Kingdom

Neural network models for audio tasks, such as automatic speech recognition (ASR) and acoustic scene classification (ASC), are susceptible to noise contamination for real-life applications. To improve audio quality, an enhancement module, which can be developed independently, is explicitly used at the front-end of the target audio applications. In this paper, we present an end-to-end learning solution to jointly optimise the models for audio enhancement (AE) and the subsequent applications. To guide the optimisation of the AE module towards a target application, and especially to overcome difficult samples, we make use of the sample-wise performance measure as an indication of sample importance. In experiments, we consider four representative applications to evaluate our training paradigm, i.e., ASR, speech command recognition (SCR), speech emotion recognition (SER), and ASC. These applications are associated with speech and non-speech tasks concerning semantic and non-semantic features, transient and global information, and the experimental results indicate that our proposed approach can considerably boost the noise robustness of the models, especially at low signal-to-noise ratios (SNRs), for a wide range of computer audition tasks in everyday-life noisy environments. © 2024, CC BY-NC-SA.

关键词： Semantics

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Ranking-based convolutional neural network models for peptide-MHC binding prediction

arXiv

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arXiv 2020年

作者： Chen, Ziqi Min, Martin Renqiang Ning, Xia Computer Science and Engineering Department Ohio State University ColumbusOH United States Machine Learning Department NEC Labs America PrincetonNJ United States Biomedical Informatics Department Ohio State University ColumbusOH United States Translational Data Analytics Institute Ohio State University ColumbusOH United States

T-cell receptors can recognize foreign peptides bound to major histocompatibility complex (MHC) class-I proteins, and thus trigger the adaptive immune response. Therefore, identifying peptides that can bind to MHC class-I molecules plays a vital role in the design of peptide vaccines. Many computational methods, for example, the state-of-the-art allele-specific method MHCflurry, have been developed to predict the binding affinities between peptides and MHC molecules. In this manuscript, we develop two allele-specific Convolutional Neural Network (CNN)based methods named ConvM and SpConvM to tackle the binding prediction problem. Specifically, we formulate the problem as to optimize the rankings of peptide-MHC bindings via ranking-based learning objectives. Such optimization is more robust and tolerant to the measurement inaccuracy of binding affinities, and therefore enables more accurate prioritization of binding peptides. In addition, we develop a new position encoding method in ConvM and SpConvM to better identify the most important amino acids for the binding events. We conduct a comprehensive set of experiments using the latest Immune Epitope database (IEDB) datasets. Our experimental results demonstrate that our models significantly outperform the state-of-the-art methods including MHCflurry with an average percentage improvement of 6.70% on AUC and 17.10% on ROC5 across 128 alleles. © 2020, CC BY.

关键词： Peptides

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Advanced Process Control in Manufacturing Using IoT Devices and Artificial Neural Networks 4

Advanced Process Control in Manufacturing Using IoT Devices ...

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4th International Conference on Sustainable Expert Systems, ICSES 2024

作者： Sumathi, V. Ramesh, S. Basavaraddi, Chethan Chandra S. Visumathi, J. Ishwarya, M.V. Srinivasan, S. Sri Sairam Engineering College Department of Mathematics Tamil Nadu Chennai India School of Computing College of Engineering and Technology Srm Institute of Science and Technology Department of Computing Technologies Kattankulathur Tamil Nadu Chennai India R&d Don Bosco Institute of Technology Vtu Department of Artificial Intelligence and Machine Learning Karnataka Belagavi India Veltech Rangarajan Dr. Sagunthala R&d Institute of Science and Technology Department of Information Technology Tamil Nadu Chennai India Agni College of Technology Artificial intelligence and Data science Department Tamil Nadu Chennai India Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Saveetha University Department of Biomedical Engineering Tamil Nadu Chennai India

ISBN: (纸本)9798331540364

Optimization of industrial activities is significantly helped by Advanced Process Control (APC), which increases efficiency, decreases costs, and improves product quality. Artificial Neural Networks (ANNs) and the Internet of Things (IoT) have greatly improved APC in manufacturing. It examines how APC systems may include ANNs and IoT devices in industrial processes. By connecting to a wide range of sensors placed strategically throughout a production facility, IoT devices may gather data in real time, allowing for managing and monitoring crucial parameters. To APC systems, ANNs are invaluable for predictive modeling and control due to their adaptability to changing process conditions and capacity to represent complicated nonlinear interactions. Manufacturers may gain better control over their operations, improving productivity and product quality, by using data from the IoT to train and update ANN models. Recent advances in APC using IoT devices and ANNs are reviewed in this study. Their applications in various industrial industries are discussed, and case examples are shown to demonstrate their usefulness. Further improvements in APC for manufacturing using IoT devices and ANNs may be guided by highlighting the field's problems and future research goals. Challenges with data security, integration challenges, and reliability impact the accuracy of predictive modeling, scalability, and performance of IoT systems. © 2024 IEEE.

关键词： Adaptive control systems

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Analyzing Atomic Interactions in Molecules as Learned by Neural Networks

arXiv

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arXiv 2024年

作者： Esders, Malte Schnake, Thomas Lederer, Jonas Kabylda, Adil Montavon, Grégoire Tkatchenko, Alexandre Müller, Klaus-Robert BIFOLD Berlin Institute for the Foundations of Learning and Data Germany Machine Learning Group Berlin Institute of Technology Berlin10587 Germany Department of Physics and Materials Science University of Luxembourg Luxembourg CityL-1511 Luxembourg Department of Mathematics and Computer Science Free University of Berlin Germany Google Deepmind Berlin Germany Department of Artificial Intelligence Korea University Seoul136-713 Korea Republic of Max Planck Institute for Informatics Saarbrücken66123 Germany

While machine learning (ML) models have been able to achieve unprecedented accuracies across various prediction tasks in quantum chemistry, it is now apparent that accuracy on a test set alone is not a guarantee for robust chemical modeling such as stable molecular dynamics (MD). To go beyond accuracy, we use explainable artificial intelligence (XAI) techniques to develop a general analysis framework for atomic interactions and apply it to the SchNet and PaiNN neural network models. We compare these interactions with a set of fundamental chemical principles to understand how well the models have learned the underlying physicochemical concepts from the data. We focus on the strength of the interactions for different atomic species, how predictions for intensive and extensive quantum molecular properties are made, and analyze the decay and many-body nature of the interactions with interatomic distance. Models that deviate too far from known physical principles produce unstable MD trajectories, even when they have very high energy and force prediction accuracy. We also suggest further improvements to the ML architectures to better account for the polynomial decay of atomic interactions. Copyright © 2024, The Authors. All rights reserved.

关键词： Molecular dynamics

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Exponential line-crossing inequalities

arXiv

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arXiv 2018年

作者： Howard, Steven R. Ramdas, Aaditya McAuliffe, Jon Sekhon, Jasjeet Departments of Statistics Political Science UC Berkeley Durant Hall 101 MC 2930 Berkeley CA 94704 US BerkeleyCA94704 United States Departments of Statistics and Data Science Machine Learning Carnegie Mellon 5000 Forbes Ave PittsburghPA15213 United States Voleon Group 2150 Dwight Way BerkeleyCA94704 United States

This paper develops a class of exponential bounds for the probability that a martingale sequence crosses a time-dependent linear threshold. Our key insight is that it is both natural and fruitful to formulate exponential concentration inequalities in this way. We illustrate this point by presenting a single assumption and a single theorem that together strengthen many tail bounds for martingales, including classical inequalities (1960-80) by Bernstein, Bennett, Hoeffding, and Freedman;contemporary inequalities (1980-2000) by Shorack and Wellner, Pinelis, Blackwell, van de Geer, and de la Peña;and several modern inequalities (post-2000) by Khan, Tropp, Bercu and Touati, Delyon, and others. In each of these cases, we give the strongest and most general statements to date, quantifying the time-uniform concentration of scalar, matrix, and Banach-space-valued martingales, under a variety of nonparametric assumptions in discrete and continuous time. In doing so, we bridge the gap between existing line-crossing inequalities, the sequential probability ratio test, the Cramér-Chernoff method, self-normalized processes, and other parts of the *** Codes 60E15, 60G17 (Primary) 60F10, 60B20 (Secondary) Copyright © 2018, The Authors. All rights reserved.

关键词： Banach spaces

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Weakly Supervised Object Detection with 2D and 3D Regression Neural Networks

arXiv

引用

arXiv 2019年

作者： Dubost, Florian Adams, Hieab Yilmaz, Pinar Bortsova, Gerda Van Tulder, Gijs Ikram, M. Arfan Niessen, Wiro Vernooij, Meike De Bruijne, Marleen Departments of Radiology and Medical Informatics Erasmus Medical Center Biomedical Imaging Group Rotterdam Rotterdam3015 GE Netherlands Departments of Radiology and Epidemiology Erasmus Medical Center Rotterdam3015 GE Netherlands Faculty of Applied Science Department of Imaging Physics Tu Delft Netherlands Department of Computer Science Machine Learning Section University of Copenhagen CopenhagenDK-2110 Denmark

Weakly supervised detection methods can infer the location of target objects in an image without requiring location or appearance information during training. We propose a weakly supervised deep learning method for the detection of objects that appear at multiple locations in an image. The method computes attention maps using the last feature maps of an encoder-decoder network optimized only with global labels: The number of occurrences of the target object in an image. In contrast with previous approaches, attention maps are generated at full input resolution thanks to the decoder part. The proposed approach is compared to multiple state-of-the-art methods in two tasks: The detection of digits in MNIST-based datasets, and the real life application of detection of enlarged perivascular spaces- A type of brain lesion-in four brain regions in a dataset of 2202 3D brain MRI scans. In MNIST-based datasets, the proposed method outperforms the other methods. In the brain dataset, several weakly supervised detection methods come close to the human intrarater agreement in each region. The proposed method reaches the lowest number of false positive detections in all brain regions at the operating point, while its average sensitivity is similar to that of the other best methods. Copyright © 2019, The Authors. All rights reserved.

关键词： Location

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