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stClinic dissects clinically relevant niches by integrating spatial multi-slice multi-omics data in dynamic graphs

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Nature communications 2025年第1期16卷 5317页

作者： Chunman Zuo Junjie Xia Yupeng Xu Ying Xu Pingting Gao Jing Zhang Yan Wang Luonan Chen School of Life Sciences Sun Yat-sen University Guangzhou China. zuochm@***. Institute of Artificial Intelligence Donghua University Shanghai China. zuochm@***. Shanghai Collaborative Innovation Center of Endoscopy Fudan University Shanghai China. zuochm@***. Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun China. zuochm@***. Institute of Artificial Intelligence Donghua University Shanghai China. System Biology Lab for Metabolic Reprogramming Department of Human Genetics and Cell Biology School of Medicine Southern University of Science and Technology Shenzhen China. Shanghai Collaborative Innovation Center of Endoscopy Fudan University Shanghai China. Department of Pathology Changzheng Hospital Secondary Military Medical University Shanghai China. College of Computer Science and Technology Jilin University Changchun China. School of Mathematical Sciences Shanghai Jiao Tong University Shanghai China. lnchen@***. School of AI Shanghai Jiao Tong University Shanghai China. lnchen@***. Key Laboratory of Systems Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China. lnchen@***. Key Laboratory of Systems Health Science of Zhejiang Province School of Life Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Chinese Academy of Sciences Hangzhou China. lnchen@***. West China Biomedical Big Data Center Med-X Center for Informatics West China Hospital Sichuan University Chengdu China. lnchen@***.

Spatial multi-slice multi-omics (SMSMO) integration has transformed our understanding of cellular niches, particularly in tumors. However, challenges like data scale and diversity, disease heterogeneity, and limited sample population size, impede the derivation of clinical insights. Here, we propose stClinic, a dynamic graph model that integrates SMSMO and phenotype data to uncover clinically relevant niches. stClinic aggregates information from evolving neighboring nodes with similar-profiles across slices, aided by a Mixture-of-Gaussians prior on latent features. Furthermore, stClinic directly links niches to clinical manifestations by characterizing each slice with attention-based geometric statistical measures, relative to the population. In cancer studies, stClinic uses survival time to assess niche malignancy, identifying aggressive niches enriched with tumor-associated macrophages, alongside favorable prognostic niches abundant in B and plasma cells. Additionally, stClinic identifies a niche abundant in SPP1+ MTRNR2L12+ myeloid cells and cancer-associated fibroblasts driving colorectal cancer cell adaptation and invasion in healthy liver tissue. These findings are supported by independent functional and clinical data. Notably, stClinic excels in label annotation through zero-shot learning and facilitates multi-omics integration by relying on other tools for latent feature initialization.

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Master stability functions for complete, intralayer, and interlayer synchronization in multiplex networks of coupled Rössler oscillators

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Physical Review E 2019年第1期99卷 012304-012304页

作者： Longkun Tang Xiaoqun Wu Jinhu Lü Jun-an Lu Raissa M. D'Souza Fujian Province University Key Laboratory of Computation Science School of Mathematical Science Huaqiao University Quanzhou 362021 China School of Mathematics and Statistics Wuhan University Wuhan 430072 China Department of Computer Science University of California Davis California 95616 USA School of Automation Science and Electrical Engineering State Key Laboratory of Software Development Environment and Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University Beijing 100191 China

Synchronization phenomena are of broad interest across disciplines and increasingly of interest in a multiplex network setting. For the multiplex network of coupled Rössler oscillators, here we show how the master stability function, a celebrated framework for analyzing synchronization on a single network, can be extended to certain classes of multiplex networks with different intralayer and interlayer coupling functions. We derive three master stability equations that determine, respectively, the necessary regions of complete synchronization, intralayer synchronization, and interlayer synchronization. We calculate these three regions explicitly for the case of a two-layer network of Rössler oscillators and show that the overlap of the regions determines the type of synchronization achieved. In particular, if the interlayer or intralayer coupling function is such that the interlayer or intralayer synchronization region is empty, complete synchronization cannot be achieved regardless of the coupling strength. Furthermore, for any network structure, the occurrence of intralayer and interlayer synchronization depends mainly on the coupling functions of nodes within a layer and across layers, respectively. Our mathematical analysis requires that the intralayer and interlayer supra-Laplacians commute. But, we show this is only a sufficient, and not necessary, condition and that the results can be applied more generally.

关键词： Collective dynamics Synchronization Synchronization transition

Identifying Laguerre-Gaussian Modes using Convolutional neural Network

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Identifying Laguerre-Gaussian Modes using Convolutional Neur...

International Conference on Machine Learning and Applications (ICMLA)

作者： Safura Sharifi Yaser Banadaki Elisha Siddiqui Savannah Cuzzo Narayan Bhusal Lior Cohen Austin Kalasky Nik Prajapati Rachel Soto-Garcia Sofia Brown Irina Novikova Eugeniy Mikhailov Georgios Veronis Jonathan Dowling School of Electrical Engineering & Computer Science Center for Computation and Technology Hearne Institute for Theoretical Physics Louisiana State University Baton Rouge Louisiana USA School of Computer Science Southern University and A&M College Baton Rouge Louisiana USA Department of Physics College of William and Marry Williamburg Virginia USA

关键词： Laser beams Training Optical beams Laser modes Mathematical model Feature extraction Data models

Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

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Database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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ADCMO: An Anomaly Detection Approach Based on Local Outlier Factor for Continuously Monitored Object

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ADCMO: An Anomaly Detection Approach Based on Local Outlier ...

IEEE International Conference on Big Data and Cloud Computing (BdCloud)

作者： Shubin Su Limin Xiao Li Ruan Rongbin Xu Shupan Li Zhaokai Wang Qigong He Wei Li State Key Laboratory of Software Development Environment Beihang University School of Computer Science and Engineering Beihang University Beijing China School of Electronics and Information Engineering Beihang University Beijing China The Classified Information Carrier Safety Management Engineering Technology Research Center of Beijing Beijing Jinghang Computation and Communication Research Institute Beijing China

ISBN: (数字)9781728143286

ISBN: (纸本)9781728143293

Since the existing works in data stream anomaly detection mainly locate abnormal objects from data sequences instead of detecting the abnormal state of a monitored object in real-time. And they need a set of empirical predefined thresholds, which may affect the flexibility of the detection models. These limitations make the existing solutions no longer suitable for the real-time detection of the changes in the status of the monitored object. In this paper, we propose a new Abnormal conditions Detection approach (ADCMO) on the Continuously Monitored Object. ADCMO incorporates the data distribution property to carry out the anomaly quantification for the data in the data stream, and then the abnormal conditions of the monitored object are quantified by the anomaly information of the current data and historical data. Finally, the anomaly state is adaptively determined by the distribution of anomaly coefficients. ADCMO can detect the changes in the status by calculating the outlier coefficient of the object at each moment and adaptively make the abnormal early warning. The experiments show that ADCMO can do this any-time, dynamically, efficiently and effectively.

关键词： Monitoring Biomedical monitoring Anomaly detection Real-time systems Transient analysis Laboratories Software

Robust classification with sparse representation fusion on diverse data subsets

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arXiv 2019年

作者： Feng, Chun-Mei Xu, Yong Li, Zuoyong Yang, Jian Bio-Computing Research Center Harbin Institute of Technology Shenzhen Guangdong518055 China Key Laboratory of Network Oriented Intelligent Computation Shenzhen Guangdong518055 China Fuzhou350121 China School of Computer Science and Engineering Nanjing University of Science and Technology Nanjing Jiangsu210094 China

Sparse Representation (SR) techniques encode the test samples into a sparse linear combination of all training samples and then classify the test samples into the class with the minimum residual. The classification of SR techniques depends on the representation capability on the test samples. However, most of these models view the representation problem of the test samples as a deterministic problem, ignoring the uncertainty of the representation. The uncertainty is caused by two factors, random noise in the samples and the intrinsic randomness of the sample set, which means that if we capture a group of samples, the obtained set of samples will be different in different conditions. In this paper, we propose a novel method based upon Collaborative Representation that is a special instance of SR and has closed-form solution. It performs Sparse Representation Fusion based on the Diverse Subset of training samples (SRFDS), which reduces the impact of randomness of the sample set and enhances the robustness of classification results. The proposed method is suitable for multiple types of data and has no requirement on the pattern type of the tasks. In addition, SRFDS not only preserves a closed-form solution but also greatly improves the classification performance. Promising results on various datasets serve as the evidence of better performance of SRFDS than other SR-based methods. The Matlab code of SRFDS will be accessible at http://***/***. Copyright © 2019, The Authors. All rights reserved.

关键词： Sampling

Large language models surpass human experts in predicting neuroscience results

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arXiv 2024年

作者： Luo, Xiaoliang Rechardt, Akilles Sun, Guangzhi Nejad, Kevin K. Yáñez, Felipe Yilmaz, Bati Lee, Kangjoo Cohen, Alexandra O. Borghesani, Valentina Pashkov, Anton Marinazzo, Daniele Nicholas, Jonathan Salatiello, Alessandro Sucholutsky, Ilia Minervini, Pasquale Razavi, Sepehr Rocca, Roberta Yusifov, Elkhan Okalova, Tereza Gu, Nianlong Ferianc, Martin Khona, Mikail Patil, Kaustubh R. Lee, Pui-Shee Mata, Rui Myers, Nicholas E. Bizley, Jennifer K. Musslick, Sebastian Bilgin, Isil Poyraz Niso, Guiomar Ales, Justin M. Gaebler, Michael Murty, N. Apurva Ratan Loued-Khenissi, Leyla Behler, Anna Hall, Chloe M. Dafflon, Jessica Bao, Sherry Dongqi Love, Bradley C. Department of Experimental Psychology University College London London United Kingdom Department of Engineering University of Cambridge Cambridge United Kingdom Department of Physiology Anatomy & Genetics University of Oxford Oxford United Kingdom Max Planck Institute for Neurobiology of Behavior – caesar Bonn Germany Bilkent University Ankara Turkey Department of Computer Science University of Bristol Bristol United Kingdom The Alan Turing Institute London United Kingdom Department of Psychiatry Yale University New Haven United States Psychology Emory University Atlanta United States Faculty of Psychology and Educational Sciences Université de Genève Genève Switzerland Neurosurgery Novosibirsk State Medical University Novosibirsk Russia Federal Center of Neurosurgery FSBI Novosibirsk Russia Department of Data Collection and Processing Systems Novosibirsk State Technical University Novosibirsk Russia Department of Data Analysis Ghent University Ghent Belgium Psychology New York University New York United States Department of Cognitive Neurology University of Tübingen Tübingen Germany Computer Science Princeton University Princeton United States ILCC University of Edinburgh Edinburgh United Kingdom Philosophy Psychology and Language Sciences The University of Edinburgh Edinburgh United Kingdom Department of Culture Cognition and Computation Aarhus University Aarhus Denmark Department of Molecular Life Sciences University of Zurich Zurich Switzerland Bioengineering University of Pennsylvania Philadelphia United States Linguistic Research Infrastructure University of Zurich Zurich Switzerland Electronic and Electrical Engineering University College London London United Kingdom Brain and Cognitive Sciences Massachusetts Institute of Technology CambridgeMA United States Institute of Neuroscience and Medicine INM-7: Brain and Behaviour Research Centre Jülich Jülich Germany Medical Faculty Institute of Systems Neuroscience Heinrich Hein

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors. © 2024, CC BY.

关键词： Prediction models

An information-theoretic framework for non-linear canonical correlation analysis

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arXiv 2018年

作者： Painsky, Amichai Feder, Meir Tishby, Naftali School of Electrical Engineering Tel Aviv University Ramat Aviv Tel Aviv6997801 Israel School of Computer Science and Engineering Interdisciplinary Center for Neural Computation Hebrew University of Jerusalem Givat Ram Jerusalem9190401 Israel

Canonical Correlation Analysis (CCA) is a linear representation learning method that seeks maximally correlated variables in multi-view data. Non-linear CCA extends this notion to a broader family of transformations, which are more powerful for many real-world applications. Given the joint probability, the Alternating Conditional Expectation (ACE) provides an optimal solution to the non-linear CCA problem. However, it suffers from limited performance and an increasing computational burden when only a finite number of observations is available. In this work we introduce an information-theoretic framework for the non-linear CCA problem (ITCCA), which extends the classical ACE approach. Our suggested framework seeks compressed representations of the data that allow a maximal level of correlation. This way we control the trade-off between the flexibility and the complexity of the representation. Our approach demonstrates favorable performance at a reduced computational burden, compared to non-linear alternatives, in a finite sample size regime. Further, ITCCA provides theoretical bounds and optimality conditions, as we establish fundamental connections to rate-distortion theory, the information bottleneck and remote source coding. In addition, it implies a "soft" dimensionality reduction, as the compression level is measured (and governed) by the mutual information between the original noisy data and the signals that we extract. Copyright © 2018, The Authors. All rights reserved.

关键词： Signal distortion

Simultaneous spectral-spatial feature selection and extraction for hyperspectral images

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arXiv 2019年

作者： Zhang, Lefei Zhang, Qian Du, Bo Huang, Xin Tang, Yuan Yan Tao, Dacheng State Key Laboratory of Software Engineering School of Computer Wuhan University Wuhan430072 China Beijing Samsung Telecom R&D Center Beijing100028 China School of Remote Sensing and Information Engineering Wuhan University Wuhan430072 China Department of Computer and Information Science University of Macau Macau999078 China Centre for Quantum Computation and Intelligent Systems Faculty of Engineering and Information Technology University of Technology SydneyNSW2007 Australia

In hyperspectral remote sensing data mining, it is important to take into account of both spectral and spatial information, such as the spectral signature, texture feature and morphological property, to improve the performances, e.g., the image classification accuracy. In a feature representation point of view, a nature approach to handle this situation is to concatenate the spectral and spatial features into a single but high dimensional vector and then apply a certain dimension reduction technique directly on that concatenated vector before feed it into the subsequent classifier. However, multiple features from various domains definitely have different physical meanings and statistical properties, and thus such concatenation hasn't efficiently explore the complementary properties among different features, which should benefit for boost the feature discriminability. Furthermore, it is also difficult to interpret the transformed results of the concatenated vector. Consequently, finding a physically meaningful consensus low dimensional feature representation of original multiple features is still a challenging task. In order to address the these issues, we propose a novel feature learning framework, i.e., the simultaneous spectral-spatial feature selection and extraction algorithm, for hyperspectral images spectralspatial feature representation and classification. Specifically, the proposed method learns a latent low dimensional subspace by projecting the spectral-spatial feature into a common feature space, where the complementary information has been effectively exploited, and simultaneously, only the most significant original features have been transformed. Encouraging experimental results on three public available hyperspectral remote sensing datasets confirm that our proposed method is effective and efficient. Copyright © 2019, The Authors. All rights reserved.

关键词： Feature extraction