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Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

Why is the Winner the Best?

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Why is the Winner the Best?

Conference on Computer Vision and Pattern Recognition (CVPR)

作者： M. Eisenmann A. Reinke V. Weru M. D. Tizabi F. Isensee T. J. Adler S. Ali V. Andrearczyk M. Aubreville U. Baid S. Bakas N. Balu S. Bano J. Bernal S. Bodenstedt A. Casella V. Cheplygina M. Daum M. De Bruijne A. Depeursinge R. Dorent J. Egger D. G. Ellis S. Engelhardt M. Ganz N. Ghatwary G. Girard P. Godau A. Gupta L. Hansen K. Harada M. Heinrich N. Heller A. Hering A. Huaulmé P. Jannin A. E. Kavur O. Kodym M. Kozubek J. Li H. Li J. Ma C. Martín-Isla B. Menze A. Noble V. Oreiller N. Padoy S. Pati K. Payette T. Rädsch J. Rafael-Patiño V. Singh Bawa S. Speidel C. H. Sudre K. Van Wijnen M. Wagner D. Wei A. Yamlahi M. H. Yap C. Yuan M. Zenk A. Zia D. Zimmerer D. Aydogan B. Bhattarai L. Bloch R. Brüngel J. Cho C. Choi Q. Dou I. Ezhov C. M. Friedrich C. Fuller R. R. Gaire A. Galdran Á. García Faura M. Grammatikopoulou S. Hong M. Jahanifar I. Jang A. Kadkhodamohammadi I. Kang F. Kofler S. Kondo H. Kuijf M. Li M. Luu T. Martinčič P. Morais M. A. Naser B. Oliveira D. Owen S. Pang J. Park S. Park S. Płotka E. Puybareau N. Rajpoot K. Ryu N. Saeed A. Shephard P. Shi D. Štepec R. Subedi G. Tochon H. R. Torres H. Urien J. L. Vilaça K. A. Wahid H. Wang J. Wang L. Wang X. Wang B. Wiestler M. Wodzinski F. Xia J. Xie Z. Xiong S. Yang Y. Yang Z. Zhao K. Maier-Hein P. F. Jäger A. Kopp-Schneider L. Maier-Hein Division of Intelligent Medical Systems German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Imaging German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Engineering and Physical Sciences School of Computing University of Leeds Leeds UK Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany Center for Artificial Intelligence and Data Science for Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology University of Washington Seattle WA USA Department of Computer Science Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS) University College London London UK Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Division of Translational Surgical Oncology National Center for Tumor Diseases (NCT/UCC) Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Department of Radiology and Nuc

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and post-processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

关键词：

Text generation based on generative adversarial nets with latent variable

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arXiv 2017年

作者： Wang, Heng Qin, Zengchang Wan, Tao Intelligent Computing and Machine Learning Lab School of ASEE Beihang University Beijing100191 China School of Biological Science and Medical Engineering Beihang University Beijing100191 China

In this paper, we propose a model using generative adver- sarial net (GAN) to generate realistic text. Instead of using standard GAN, we combine variational autoencoder (VAE) with generative ad- versarial net. The use of high-level latent random variables is helpful to learn the data distribution and solve the problem that generative adver- sarial net always emits the similar data. We propose the VGAN model where the generative model is composed of recurrent neural network and VAE. The discriminative model is a convolutional neural network. We train the model via policy gradient. We apply the proposed model to the task of text generation and compare it to other recent neural network based models, such as recurrent neural network language model and Seq- GAN. We evaluate the performance of the model by calculating negative log-likelihood and the BLEU score. We conduct experiments on three benchmark datasets, and results show that our model outperforms other previous models. Copyright © 2017, The Authors. All rights reserved.

关键词： Recurrent neural networks

Logical parsing from natural language based on a neural translation model

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arXiv 2017年

作者： Li, Liang Li, Pengyu Liu, Yifan Wan, Tao Qin, Zengchang Intelligent Computing and Machine Learning Lab School of ASEE Beihang University Beijing100191 China Biomedical Imaging and Informatics Lab School of Biological Science and Medical Engineering Beihang University Beijing100191 China

Semantic parsing has emerged as a significant and powerful paradigm for natural language interface and question answering systems. Traditional methods of building a semantic parser rely on high-quality lexicons, hand-crafted grammars and linguistic features which are limited by applied domain or representation. In this paper, we propose a general approach to learn from denotations based on Seq2Seq model augmented with attention mechanism. We encode input sequence into vectors and use dynamic programming to infer candidate logical forms. We utilize the fact that similar utterances should have similar logical forms to help reduce the searching space. Under our learning policy, the Seq2Seq model can learn mappings gradually with noises. Curriculum learning is adopted to make the learning smoother. We test our method on the arithmetic domain which shows our model can successfully infer the correct logical forms and learn the word meanings, compositionality and operation orders simultaneously. Copyright © 2017, The Authors. All rights reserved.

关键词： Dynamic programming

Auto-painter: Cartoon image generation from sketch by using conditional generative adversarial networks

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arXiv 2017年

作者： Liu, Yifan Qin, Zengchang Luo, Zhenbo Wang, Hua Intelligent Computing and Machine Learning Lab School of ASEE Beihang University Beijing100191 China Samsung RandD Institute China Beijing 18F TaiTangGong Plaza Beijing100028 China

Recently, realistic image generation using deep neural networks has become a hot topic in machine learning and computer vision. Images can be generated at the pixel level by learning from a large collection of images. learning to generate colorful cartoon images from black-and-white sketches is not only an interesting research problem, but also a potential application in digital entertainment. In this paper, we investigate the sketch-to-image synthesis problem by using conditional generative adversarial networks (cGAN). We propose the auto-painter model which can automatically generate compatible colors for a sketch. The new model is not only capable of painting hand-draw sketch with proper colors, but also allowing users to indicate preferred colors. Experimental results on two sketch datasets show that the auto-painter performs better that existing image-to-image methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Generative adversarial networks

Motif iteration model for network representation

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arXiv 2017年

作者： Lv, Lintao Qin, Zengchang Wan, Tao Intelligent Computing and Machine Learning Lab School of Automation Science and Electrical Engineering Beihang University Beijing Beijing100191 China School of Biological Science and Medical Engineering Beihang University Beijing Beijing100191 China

Social media mining has become one of the most popular research areas in Big Data with the explosion of social networking information from Facebook, Twitter, LinkedIn,Weibo and so on. Understanding and representing the structure of a social network is a key in social media mining. In this paper, we propose the Motif Iteration Model (MIM) to represent the structure of a social network. As the name suggested, the new model is based on iteration of basic network motifs. In order to better show the properties of the model, a heuristic and greedy algorithm called Vertex Reordering and Arranging (VRA) is proposed by studying the adjacency matrix of the three-vertex undirected network motifs. The algorithm is for mapping from the adjacency matrix of a network to a binary image, it shows a new perspective of network structure visualization. In summary, this model provides a useful approach towards building link between images and networks and offers a new way of representing the structure of a social network. Copyright © 2017, The Authors. All rights reserved.

关键词： Social networking (online)

Biomedical image analysis competitions: The state of current participation practice

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arXiv 2022年

作者： Eisenmann, Matthias Reinke, Annika Weru, Vivienn Tizabi, Minu Dietlinde Isensee, Fabian Adler, Tim J. Godau, Patrick Cheplygina, Veronika Kozubek, Michal Maier-Hein, Klaus Jäger, Paul F. Kopp-Schneider, Annette Maier-Hein, Lena Ali, Sharib Gupta, Anubha Kybic, Jan Noble, Alison de Solórzano, Carlos Ortiz Pachade, Samiksha Petitjean, Caroline Sage, Daniel Wei, Donglai Wilden, Elizabeth Alapatt, Deepak Andrearczyk, Vincent Baid, Ujjwal Bakas, Spyridon Balu, Niranjan Bano, Sophia Bawa, Vivek Singh Bernal, Jorge Bodenstedt, Sebastian Casella, Alessandro Choi, Jinwook Commowick, Olivier Daum, Marie Depeursinge, Adrien Dorent, Reuben Egger, Jan Eichhorn, Hannah Engelhardt, Sandy Ganz, Melanie Girard, Gabriel Hansen, Lasse Heinrich, Mattias Heller, Nicholas Hering, Alessa Huaulmé, Arnaud Kim, Hyunjeong Li, Hongwei Bran Landman, Bennett Li, Jianning Ma, Jun Martel, Anne Martín-Isla, Carlos Menze, Bjoern Nwoye, Chinedu Innocent Oreiller, Valentin Padoy, Nicolas Pati, Sarthak Payette, Kelly Sudre, Carole van Wijnen, Kimberlin Vardazaryan, Armine Vercauteren, Tom Wagner, Martin Wang, Chuanbo Yap, Moi Hoon Yu, Zeyun Yuan, Chun Zenk, Maximilian Zia, Aneeq Zimmerer, David Bao, Rina Choi, Chanyeol Cohen, Andrew Dzyubachyk, Oleh Galdran, Adrian Gan, Tianyuan Guo, Tianqi Gupta, Pradyumna Haithami, Mahmood Ho, Edward Jang, Ikbeom Li, Zhili Luo, Zhengbo Lux, Filip Makrogiannis, Sokratis Müller, Dominik Oh, Young-Tack Pang, Subeen Pape, Constantin Polat, Gorkem Reed, Charlotte Rosalie Ryu, Kanghyun Scherr, Tim Thambawita, Vajira Wang, Haoyu Wang, Xinliang Xu, Kele Yeh, Hung Yeo, Doyeob Yuan, Yixuan Zeng, Yan Zhao, Xin Abbing, Julian Adam, Jannes Adluru, Nagesh Agethen, Niklas Ahmed, Salman Al Khalil, Yasmina Alenyà, Mireia Alhoniemi, Esa An, Chengyang Arega, Tewodros Weldebirhan Avisdris, Netanell Aydogan, Dogu Baran Bai, Yingbin Calisto, Maria Baldeon Basaran, Berke Doga Beetz, Marcel Bian, Hao Blansit, Kevin Bloch, Louise Bohnsack, Robert Bosticardo, Sara Breen, Jack Brudfors, Mikael Brüngel, Raphael Cabezas, Mariano Cacciola, Alb Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Biostatistics Germany Heidelberg Division of Medical Image Computing Germany Heidelberg HI Applied Vision Lab Germany IT University of Copenhagen Copenhagen Denmark Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Heidelberg Interactive Machine Learning Group Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg DKFZ University Hospital Heidelberg Germany School of Computing University of Leeds Leeds United Kingdom SBILab Department of ECE IIIT-Delhi India Faculty of Electrical Engineering Czech Technical University Prague Czech Republic Institute of Biomedical Engineering University of Oxford United Kingdom Center for Applied Medical Research Pamplona Spain Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Université de Rouen Normandie France Lausanne Switzerland School of Engineering and Applied Science Harvard University United States ICube University of Strasbourg CNRS France Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Techno-Pôle 3 Sierre3960 Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Rue du Bugnon 46 LausanneCH-1011 Switzerland University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington United States Wellcome EPSRC Centre for Interventional and Surgical Sciences University College London London United Kingdom Visual Artificial Intelligence Lab Oxford Brookes University Oxford United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Spain Dresden Fetscherstraße 74 PF 64 Dresden01307 Germany

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps. © 2022, CC BY.

关键词： Benchmarking

Stock volatility prediction using recurrent neural networks with sentiment analysis

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arXiv 2017年

作者： Liu, Yifan Qin, Zengchang Li, Pengyu Wan, Tao Intelligent Computing and Machine Learning Lab School of ASEE Beihang University Beijing100191 School of Mechanical Engineering and Automation Beihang University Beijing100191 School of Biological Science and Medical Engineering Beihang University Beijing100191 China

In this paper, we propose a model to analyze sentiment of online stock forum and use the information to predict the stock volatil-ity in the Chinese market. We have lab.led the sentiment of the online financial posts and make the dataset public availab.e for research. By generating a sentimental dictionary based on financial terms, we develop a model to compute the sentimental score of each online post related to a particular stock. Such sentimental information is represented by two sentiment indicators, which are fused to market data for stock volatility prediction by using the Recurrent Neural Networks (RNNs). Empirical study shows that, comparing to using RNN only, the model performs significantly better with sentimental indicators. Copyright © 2017, The Authors. All rights reserved.

关键词： Forecasting

Stable matching in structured networks 14th

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Stable matching in structured networks

14th International Workshop on Knowledge Management and Acquisition for intelligent Systems, PKAW2016

作者： Ling, Ying Wan, Tao Qin, Zengchang Intelligent Computing and Machine Learning Lab School of ASEE Beihang University Beijing100191 China School of Biological Science and Medical Engineering Beihang University Beijing100191 China

ISBN: (纸本)9783319427058

Stable matching studies how to pair members of two sets with the objective to achieve a matching that satisfies all participating agents based on their preferences. In this research, we consider the case of matching in a social network where agents are not fully connected. We propose the concept of D-neighbourhood associated with connective costs to investigate the matching quality in four types of well-used networks. A matching algorithm is proposed based on the classical Gale-Shapley algorithm under constraints of network topology. Through experimental studies, we find that the matching outcomes in scale-free networks yield the best average utility with least connective costs comparing to other structured networks. This research provides insights for understanding matching behavior in social networks like marriage, trade, partnership, online social and job search. © Springer International Publishing Switzerland 2016.

关键词： Costs