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A hybrid multi-instance learning-based identification of gastric adenocarcinoma differentiation on whole-slide images

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BioMedical Engineering OnLine 2025年第1期24卷 1-14页

作者： Zhang, Mudan Sun, Xinhuan Li, Wuchao Cao, Yin Liu, Chen Tu, Guilan Wang, Jian Wang, Rongpin Department of Radiology Guizhou Provincial Key Laboratory of Intelligent Medical Image Analysis and Precision Diagnosis Guizhou Provincial People’s Hospital Guiyang China Engineering Research Center of Text Computing & Cognitive Intelligence Ministry of Education Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province State Key Laboratory of Public Big Data College of Computer Science and Technology Guizhou University Guiyang China Department of pathology Guizhou Provincial People’s Hospital Guiyang China Department of Radiology Southwest Hospital Army Medical University (Third Military Medical University) Chongqing China Laboratory department Guizhou Provincial Center for Clinical Laboratory Guiyang China Medical college of Guizhou University Guiyang China

To investigate the potential of a hybrid multi-instance learning model (TGMIL) combining Transformer and graph attention networks for classifying gastric adenocarcinoma differentiation on whole-slide images (WSIs) without manual annotation. A hybrid multi-instance learning model is proposed based on the Transformer and the graph attention network, called TGMIL, to classify the differentiation of gastric adenocarcinoma. A total of 613 WSIs from patients with gastric adenocarcinoma were retrospectively collected from two different hospitals. According to the differentiation of gastric adenocarcinoma, the data were divided into four groups: normal group (n = 254), well differentiation group (n = 166), moderately differentiation group (n = 75), and poorly differentiation group (n = 118). The gold standard of differentiation classification was blindly established by two gastrointestinal pathologists. The WSIs were randomly split into a training dataset consisting of 494 images and a testing dataset consisting of 119 images. Within the training set, the WSI count of the normal, well, moderately, and poorly differential groups was 203, 131, 62, and 98 individuals, respectively. Within the test set, the corresponding WSI count was 51, 35, 13, and 20 individuals. The TGMIL model developed for the differential prediction task exhibited remarkable efficiency when considering sensitivity, specificity, and the area under the curve (AUC) values. We also conducted a comparative analysis to assess the efficiency of five other models, namely MIL, CLAM_SB, CLAM_MB, DSMIL, and TransMIL, in classifying the differentiation of gastric cancer. The TGMIL model achieved a sensitivity of 73.33% and a specificity of 91.11%, with an AUC value of 0.86. The hybrid multi-instance learning model TGMIL could accurately classify the differentiation of gastric adenocarcinoma using WSI without the need for labor-intensive and time-consuming manual annotations, w

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cognitive modelling with multilayer networks: Insights, advancements and future challenges

arXiv

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arXiv 2022年

作者： Stella, Massimo Citraro, Salvatore Rossetti, Giulio Marinazzo, Daniele Kenett, Yoed N. Vitevitch, Michael S. CogNosco Lab Department of Computer Science University of Exeter Exeter United Kingdom Department of Computer Science University of Pisa Pisa Italy Institute of Information Science and Technologies National Research Council Pisa Italy Faculty of Psychology and Educational Sciences Department of Data Analysis University of Ghent Ghent Belgium Cognitive Complexity Lab Faculty of Industrial Engineering and Management Technion Israel Institute of Technology Israel Department of Psychology University of Kansas LawrenceKS United States

The mental lexicon is a complex cognitive system representing information about the words/concepts that one knows. Decades of psychological experiments have shown that conceptual associations across multiple, interactive cognitive levels can greatly influence word acquisition, storage, and processing. How can semantic, phonological, syntactic, and other types of conceptual associations be mapped within a coherent mathematical framework to study how the mental lexicon works? We here review cognitive multilayer networks as a promising quantitative and interpretative framework for investigating the mental lexicon. cognitive multilayer networks can map multiple types of information at once, thus capturing how different layers of associations might co-exist within the mental lexicon and influence cognitive processing. This review starts with a gentle introduction to the structure and formalism of multilayer networks. We then discuss quantitative mechanisms of psychological phenomena that could not be observed in single-layer networks and were only unveiled by combining multiple layers of the lexicon: (i) multiplex viability highlights language kernels and facilitative effects of knowledge processing in healthy and clinical populations;(ii) multilayer community detection enables contextual meaning reconstruction depending on psycholinguistic features;(iii) layer analysis can mediate latent interactions of mediation, suppression and facilitation for lexical access. By outlining novel quantitative perspectives where multilayer networks can shed light on cognitive knowledge representations, also in next-generation brain/mind models, we discuss key limitations and promising directions for cutting-edge future research. © 2022, CC BY.

关键词： Network layers

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Magnetic noise enabled biocompass

arXiv

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arXiv 2020年

作者： Xiao, Da-Wu Hu, Wen-Hui Cai, Yunfeng Zhao, Nan Beijing Computational Science Research Center Beijing100193 China Cognitive Computing Lab Baidu Research Beijing100085 China

The discovery of magnetic protein provides a new understanding of a biocompass at the molecular level. However, the mechanism by which magnetic protein enables a biocompass is still under debate, mainly because of the absence of permanent magnetism in the magnetic protein at room temperature. Here, based on a widely accepted radical pair model of a biocompass, we propose a microscopic mechanism that allows the biocompass to operate without a finite magnetization of the magnetic protein in a biological environment. With the structure of the magnetic protein, we show that the magnetic fluctuation, rather than the permanent magnetism, of the magnetic protein can enable geomagnetic field sensing. An analysis of the quantum dynamics of our microscopic model reveals the necessary conditions for optimal sensitivity. Our work clarifies the mechanism by which magnetic protein enables a biocompass. Copyright © 2020, The Authors. All rights reserved.

关键词： Proteins

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Hardware-Based Address-Centric Acceleration of Key-Value Store

Hardware-Based Address-Centric Acceleration of Key-Value Sto...

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IEEE Symposium on High-Performance Computer Architecture

作者： Chencheng Ye Yuanchao Xu Xipeng Shen Xiaofei Liao Hai Jin Yan Solihin National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China North Carolina State University Raleigh North Carolina USA Computer Science University of Central Florida Florida USA

Efficiently retrieving data is essential for key-value store applications. A major part of the retrieving time is on data addressing, that is, finding the location of the value in memory that corresponds to a key. This paper introduces an address-centric approach to speed up the addressing by creating a shortcut for the translation of a key to the physical address of the value. The new technique is materialized with a novel in-memory table, STLT, a virtual-physical address buffer, and two new instructions. It creates a fast path for data addressing and meanwhile opens up opportunities for the use of simpler and faster hash tables to strike a better tradeoff between hashing conflicts and hashing overhead. Together, the new technique brings up to 1.4× speedups on key-value store application Redis and up to 13× speedups on some widely used indexing data structures, consistently outperforming prior solutions significantly.

关键词： Production data structures Acceleration Indexing

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Generative Unfolding with Distribution Mapping

arXiv

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arXiv 2024年

作者： Butter, Anja Diefenbacher, Sascha Huetsch, Nathan Mikuni, Vinicius Nachman, Benjamin Schweitzer, Sofia Palacios Plehn, Tilman Institut für Theoretische Physik Universität Heidelberg Germany LPNHE Sorbonne Université Université Paris Cité CNRS IN2P3 Paris France Physics Division Lawrence Berkeley National Laboratory Berkeley United States National Energy Research Scientific Computing Center Berkeley Lab Berkeley94720 United States Berkeley Institute for Data Science University of California BerkeleyCA94720 United States Universität Heidelberg Germany

Machine learning enables unbinned, highly-differential cross section measurements. A recent idea uses generative models to morph a starting simulation into the unfolded data. We show how to extend two morphing techniques, Schrödinger Bridges and Direct Diffusion, in order to ensure that the models learn the correct conditional probabilities. This brings distribution mapping to a similar level of accuracy as the state-of-the-art conditional generative unfolding methods. Numerical results are presented with a standard benchmark dataset of single jet substructure as well as for a new dataset describing a 22-dimensional phase space of Z + 2-jets. © 2024, CC BY.

关键词： Phase space methods

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How does the primate brain combine generative and discriminative computations in vision?

arXiv

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arXiv 2024年

作者： Peters, Benjamin DiCarlo, James J. Gureckis, Todd Haefner, Ralf Isik, Leyla Tenenbaum, Joshua Konkle, Talia Naselaris, Thomas Stachenfeld, Kimberly Tavares, Zenna Tsao, Doris Yildirim, Ilker Kriegeskorte, Nikolaus Zuckerman Mind Brain Behavior Institute Columbia University United States School of Psychology & Neuroscience University of Glasgow United Kingdom Department of Brain and Cognitive Sciences MIT United States McGovern Institute for Brain Research MIT United States NSF Center for Brains Minds and Machines MIT United States Quest for Intelligence Schwarzman College of Computing MIT United States Department of Psychology New York University United States Brain and Cognitive Sciences University of Rochester United States Center for Visual Science University of Rochester United States Department of Cognitive Science Johns Hopkins University United States Computer Science and Artificial Intelligence Laboratory MIT United States Department of Psychology Harvard University United States Center for Brain Science Harvard University United States Kempner Institute for Natural and Artificial Intelligence Harvard University United States Department of Neuroscience University of Minnesota United States DeepMind United Kingdom Data Science Institute Columbia University United States Dept of Molecular & Cell Biology University of California Berkeley United States Howard Hughes Medical Institute United States Department of Psychology Yale University United States Department of Statistics and Data Science Yale University United States Department of Psychology Columbia University United States Department of Neuroscience Columbia University United States Department of Electrical Engineering Columbia University United States

Vision is widely understood as an inference problem. However, two contrasting conceptions of the inference process have each been influential in research on biological vision as well as the engineering of machine vision. The first emphasizes bottom-up signal flow, describing vision as a largely feedforward, discriminative inference process that filters and transforms the visual information to remove irrelevant variation and represent behaviorally relevant information in a format suitable for downstream functions of cognition and behavioral control. In this conception, vision is driven by the sensory data, and perception is direct because the processing proceeds from the data to the latent variables of interest. The notion of "inference" in this conception is that of the engineering literature on neural networks, where feedforward convolutional neural networks processing images are said to perform inference. The alternative conception is that of vision as an inference process in Helmholtz's sense, where the sensory evidence is evaluated in the context of a generative model of the causal processes that give rise to it. In this conception, vision inverts a generative model through an interrogation of the sensory evidence in a process often thought to involve top-down predictions of sensory data to evaluate the likelihood of alternative hypotheses. The authors include scientists rooted in roughly equal numbers in each of the conceptions and motivated to overcome what might be a false dichotomy between them and engage the other perspective in the realm of theory and experiment. The primate brain employs an unknown algorithm that may combine the advantages of both conceptions. We explain and clarify the terminology, review the key empirical evidence, and propose an empirical research program that transcends the dichotomy and sets the stage for revealing the mysterious hybrid algorithm of primate vision. © 2024, CC BY.

关键词： Feedforward neural networks

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Automatic Diagnosis of Myocarditis Disease in Cardiac MRI Modality using Deep Transformers and Explainable Artificial Intelligence

arXiv

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arXiv 2022年

作者： Jafari, Mahboobeh Shoeibi, Afshin Ghassemi, Navid Heras, Jonathan Ling, Sai Ho Beheshti, Amin Zhang, Yu-Dong Wang, Shui-Hua Alizadehsani, Roohallah Gorriz, Juan M. Acharya, U. Rajendra Rokny, Hamid Alinejad Internship in BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering UNSW Sydney SydneyNSW2052 Australia Data Science and Computational Intelligence Institute University of Granada Spain Department of Mathematics and Computer Science University of La Rioja La Rioja Spain Australia Data Analytics Lab Department of Computing Macquarie University SydneyNSW2109 Australia School of Computing and Mathematical Sciences University of Leicester Leicester United Kingdom Deakin University VIC3217 Australia Department of Psychiatry University of Cambridge United Kingdom School of Mathematics Physics and Computing University of Southern Queensland Springfield Australia BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering UNSW Sydney SydneyNSW2052 Australia UNSW Data Science Hub The University of New South Wales SydneyNSW2052 Australia Research Centre Macquarie University Sydney2109 Australia

Myocarditis is a significant cardiovascular disease (CVD) that poses a threat to the health of many individuals by causing damage to the myocardium. The occurrence of microbes and viruses, including the likes of HIV, plays a crucial role in the development of myocarditis disease (MCD). The images produced during cardiac magnetic resonance imaging (CMRI) scans are low contrast, which can make it challenging to diagnose cardiovascular diseases. In other hand, checking numerous CMRI slices for each CVD patient can be a challenging task for medical doctors. To overcome the existing challenges, researchers have suggested the use of artificial intelligence (AI)-based computer-aided diagnosis systems (CADS). The presented paper outlines a CADS for the detection of MCD from CMR images, utilizing deep learning (DL) methods. The proposed CADS consists of several steps, including dataset, preprocessing, feature extraction, classification, and post-processing. First, the Z-Alizadeh dataset was selected for the experiments. Subsequently, the CMR images underwent various preprocessing steps, including denoising, resizing, as well as data augmentation (DA) via CutMix and MixUp techniques. In the following, the most current deep pre-trained and transformer models are used for feature extraction and classification on the CMR images. The findings of our study reveal that transformer models exhibit superior performance in detecting MCD as opposed to pre-trained architectures. In terms of DL architectures, the Turbulence Neural Transformer (TNT) model exhibited impressive accuracy, reaching 99.73% utilizing a 10-fold cross-validation approach. Additionally, to pinpoint areas of suspicion for MCD in CMRI images, the Explainable-based Grad Cam method was employed. © 2022, CC BY-NC-ND.

关键词： Diseases

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A Learning-Exploring Method to Generate Diverse Paraphrases with Multi-Objective Deep Reinforcement Learning 28

A Learning-Exploring Method to Generate Diverse Paraphrases ...

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28th International Conference on Computational Linguistics, COLING 2020

作者： Liu, Mingtong Yang, Erguang Xiong, Deyi Zhang, Yujie Meng, Yao Hu, Changjian Xu, Jinan Chen, Yufeng School of Computer Science and Information Technology Beijing Key Lab of Traffic Data Analysis and Mining Beijing Jiaotong University Beijing China College of Intelligence and Computing Tianjin University Tianjin China Lenovo Research AI Lab. Beijing China

ISBN: (纸本)9781952148279

Paraphrase generation (PG) is of great importance to many downstream tasks in natural language processing. Diversity is an essential nature to PG for enhancing generalization capability and robustness of downstream applications. Recently, neural sequence-to-sequence (Seq2Seq) models have shown promising results in PG. However, traditional model training for PG focuses on optimizing model prediction against single reference and employs cross-entropy loss, which objective is unable to encourage model to generate diverse paraphrases. In this work, we present a novel approach with multi-objective learning to PG. We propose a learning-exploring method to generate sentences as learning objectives from the learned data distribution, and employ reinforcement learning to combine these new learning objectives for model training. We first design a sample-based algorithm to explore diverse sentences. Then we introduce several reward functions to evaluate the sampled sentences as learning signals in terms of expressive diversity and semantic fidelity, aiming to generate diverse and high-quality paraphrases. To effectively optimize model performance satisfying different evaluating aspects, we use a GradNorm-based algorithm that automatically balances these training objectives. Experiments and analyses on Quora and Twitter datasets demonstrate that our proposed method not only gains a significant increase in diversity but also improves generation quality over several state-of-the-art baselines. © 2020 COLING 2020 - 28th International Conference on Computational Linguistics, Proceedings of the Conference. All rights reserved.

关键词： Reinforcement learning

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RecycleNet: Latent Feature Recycling Leads to Iterative Decision Refinement

RecycleNet: Latent Feature Recycling Leads to Iterative Deci...

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IEEE Workshop on Applications of Computer Vision (WACV)

作者： Gregor Koehler Tassilo Wald Constantin Ulrich David Zimmerer Paul F. Jaeger Jörg K. H. Franke Simon Kohl Fabian Isensee Klaus H. Maier-Hein Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Information and Data Science School for Health Karlsruhe/Heidelberg Germany Helmholtz Imaging DKFZ National Center for Tumor Diseases (NCT) NCT Heidelberg a Partnership Between DKFZ University Medical Center Heidelberg Interactive Machine Learning Group DKFZ Machine Learning Lab University of Freiburg Freiburg Germany Latent Labs (***) London UK Applied Computer Vision Lab DKFZ Pattern Analysis and Learning Group Heidelberg University Hospital Heidelberg Germany

Despite the remarkable success of deep learning systems over the last decade, a key difference still remains between neural network and human decision-making: As humans, we can not only form a decision on the spot, but also ponder, revisiting an initial guess from different angles, distilling relevant information, arriving at a better decision. Here, we propose RecycleNet, a latent feature recycling method, instilling the pondering capability for neural networks to refine initial decisions over a number of recycling steps, where outputs are fed back into earlier network layers in an iterative fashion. This approach makes minimal assumptions about the neural network architecture and thus can be implemented in a wide variety of contexts. Using medical image segmentation as the evaluation environment, we show that latent feature recycling enables the network to iteratively refine initial predictions even beyond the iterations seen during training, converging towards an improved decision. We evaluate this across a variety of segmentation benchmarks and show consistent improvements even compared with top-performing segmentation methods. This allows trading increased computation time for improved performance, which can be beneficial, especially for safety-critical applications.

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Donut Modes in Space Wavelength Division Multiplexing: Multimode Optical Fiber Transmission based on Electrical Feedback Equalizer 5

Donut Modes in Space Wavelength Division Multiplexing: Multi...

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5th International Conference on Electronic Design, ICED 2020

作者： Ghazi, Alaan Aljunid, S.A. Idrus, Syed Zulkarnain Syed Endut, R. Ali, N. Amphawan, Angela Fareed, Alaa Al-Dawoodi, Aras Noori, Awab School of Human Development and Techno-communication University Malaysia Perlis Malaysia School of Computer and Communication Engineering University Malaysia Perlis Malaysia Computer Technical Engineering Al-Qalam University College Iraq Centre of Excellence Universiti Malaysia Perlis Malaysia Universiti Malaysia Perlis Perlis Malaysia Lightwave Laboratory School of Engineering and Technology Sunway University Petaling Jaya Selangor47500 Malaysia School of Computing University Utara Malaysia Malaysia Computer Science Department College of Computer Science and Information Technology Kirkuk University Iraq Data Science Research Lab School of Computing Universiti Utara Malaysia Malaysia

This study demonstrates the implementation of multi-input-multi-output (MIMO) transmission donut modes in space wavelength division multiplexing (SWDM) over multi-mode optical fiber (MMOF) and simulating the effect of mode coupling of the transmitted signal. However, during the data transmitted over MMF by using SWDM an issue is encountered, which is the inter symbol interference (ISI) due to mode coupling. ISI has been recognized as a major obstacle to high-speed data transmission. The signal processing in SDM of donut modes over MMOF with electrical feedback equalizer is used to improve the performance for increasing the bandwidth. A data rate 80 Gbit/s up for a distance of 1600 meters is achieved. SWDM topology was designed emitted from a spatial vertical cavity surface-emitting laser (VCSEL) through MMOF in conjunction with the configurations of electrical feedback equalizer. The parameters and values used in Opt-Sim simulation topology were listed. The performance measurement of this study based on bit-error rates (BER) and eye diagram before and after electrical feedback equalization were analysed. © 2021 Published under licence by IOP Publishing Ltd.

关键词： Space division multiple access

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