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arXiv 2023年

作者： Karandashev, Konstantin Weinreich, Jan Heinen, Stefan Arrieta, Daniel Jose Arismendi von Rudorff, Guido Falk Hermansson, Kersti von Lilienfeld, O. Anatole University of Vienna Faculty of Physics Kolingasse 14-16 WienAT-1090 Austria Vector Institute for Artificial Intelligence TorontoONM5S 1M1 Canada Department of Chemistry-Angström Laboratory Uppsala University Box 538 UppsalaSE-75121 Sweden University Kassel Department of Chemistry Heinrich-Plett-Str.40 Kassel34132 Germany Heinrich-Plett-Strase 40 Kassel34132 Germany Departments of Chemistry Materials Science and Engineering and Physics University of Toronto St. George Campus TorontoON Canada Machine Learning Group Technische Universität Berlin Institute for the Foundations of Learning and Data Berlin10587 Germany

Optimizing a target function over the space of organic molecules is an important problem appearing in many fields of applied science, but also a very difficult one due to the vast number of possible molecular systems. We propose an Evolutionary Monte Carlo algorithm for solving such problems which is capable of straightforwardly tuning both exploration and exploitation characteristics of an optimization procedure while retaining favourable properties of genetic algorithms. The method, dubbed MOSAiCS (Metropolis Optimization by Sampling Adaptively in Chemical Space), is tested on problems related to optimizing components of battery electrolytes, namely minimizing solvation energy in water or maximizing dipole moment while enforcing a lower bound on the HOMO-LUMO gap;optimization was done over sets of molecular graphs inspired by QM9 and Electrolyte Genome Project (EGP) datasets. MOSAiCS reliably generated molecular candidates with good target quantity values, which were in most cases better than the ones found in QM9 or EGP. While the optimization results presented in this work sometimes required up to 106 QM calculations and were thus only feasible thanks to computationally efficient ab initio approximations of properties of interest, we discuss possible strategies for accelerating MOSAiCS using machine learning approaches. Copyright © 2023, The Authors. All rights reserved.

关键词： Electrolytes

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Towards deployment-centric multimodal AI beyond vision and language

arXiv

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arXiv 2025年

作者： Liu, Xianyuan Zhang, Jiayang Zhou, Shuo van der Plas, Thijs L. Vijayaraghavan, Avish Grishina, Anastasiia Zhuang, Mengdie Schofield, Daniel Tomlinson, Christopher Wang, Yuhan Li, Ruizhe van Zeeland, Louisa Tabakhi, Sina Demeocq, Cyndie Li, Xiang Das, Arunav Timmerman, Orlando Baldwin-McDonald, Thomas Wu, Jinge Bai, Peizhen Al Sahili, Zahraa Alwazzan, Omnia Do, Thao N. Suvon, Mohammod N.I. Wang, Angeline Cipolina-Kun, Lucia Moretti, Luigi A. Farndale, Lucas Jain, Nitisha Efremova, Natalia Ge, Yan Varela, Marta Lam, Hak-Keung Celiktutan, Oya Evans, Ben R. Coca-Castro, Alejandro Wu, Honghan Abdallah, Zahraa S. Chen, Chen Danchev, Valentin Tkachenko, Nataliya Lu, Lei Zhu, Tingting Slabaugh, Gregory G. Moore, Roger K. Cheung, William K. Charlton, Peter H. Lu, Haiping Centre for Machine Intelligence University of Sheffield Sheffield United Kingdom School of Computer Science University of Sheffield Sheffield United Kingdom The Alan Turing Institute London United Kingdom Department of Metabolism Digestion and Reproduction Imperial College London London United Kingdom Department of Applied AI Simula Research Laboratory Oslo Norway Information School University of Sheffield Sheffield United Kingdom NHS England Leeds United Kingdom Institute of Health Informatics University College London London United Kingdom Department of Engineering King’s College London London United Kingdom Department of Computing Science University of Aberdeen Aberdeen United Kingdom School of Informatics University of Edinburgh Edinburgh United Kingdom School of Engineering Mathematics and Technology University of Bristol Bristol United Kingdom Department of Informatics King’s College London London United Kingdom Department of Earth Sciences University of Cambridge Cambridge United Kingdom Department of Computer Science University of Manchester Manchester United Kingdom Department of Computer Science Queen Mary University of London London United Kingdom Digital Environment Research Institute Queen Mary University of London London United Kingdom Department of Computer Science University of Bath Bath United Kingdom Department of Classics King’s College London London United Kingdom School of Electrical Electronic and Mechanical Engineering University of Bristol Bristol United Kingdom School of Engineering University of the West of England Bristol United Kingdom Cancer Research UK Scotland Institute Glasgow United Kingdom School of Business and Management Queen Mary University of London London United Kingdom City St George’s University of London London United Kingdom British Antarctic Survey Cambridge United Kingdom School of Health and Wellbeing University of Glasgow Glasgow United Kingdom Chief Data & AI Office Lloyds Banking Group Lo

Multimodal artificial intelligence (AI) integrates diverse types of data via machine learning to improve understanding, prediction, and decision-making across disciplines such as healthcare, science, and engineering. However, most multimodal AI advances focus on models for vision and language data, while their deployability remains a key challenge. We advocate a deployment-centric workflow that incorporates deployment constraints early to reduce the likelihood of undeployable solutions, complementing data-centric and model-centric approaches. We also emphasise deeper integration across multiple levels of multimodality and multidisciplinary collaboration to significantly broaden the research scope beyond vision and language. To facilitate this approach, we identify common multimodal-AI-specific challenges shared across disciplines and examine three real-world use cases: pandemic response, self-driving car design, and climate change adaptation, drawing expertise from healthcare, social science, engineering, science, sustainability, and finance. By fostering multidisciplinary dialogue and open research practices, our community can accelerate deployment-centric development for broad societal impact. © 2025, CC BY.

关键词： Decision making

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T-Cell Receptor Optimization with Reinforcement learning and Mutation Policies for Precision Immunotherapy

arXiv

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arXiv 2023年

作者： Chen, Ziqi Min, Martin Renqiang Guo, Hongyu Cheng, Chao Clancy, Trevor Ning, Xia Computer Science and Engineering The Ohio State University ColumbusOH43210 United States Machine Learning Department NEC Labs PrincetonNJ08540 United States Digital Technologies Research Centre National Research Council Canada ON Canada Department of Medicine Baylor College of Medicine HoustonTX77030 United States NEC Oncolmmunity AS Oslo Cancer Cluster Innovation Park Ullernchausséen 64 Oslo0379 Norway Biomedical Informatics The Ohio State University ColumbusOH43210 United States Translational Data Analytics Institute The Ohio State University ColumbusOH43210 United States

T cells monitor the health status of cells by identifying foreign peptides displayed on their surface. T-cell receptors (TCRs), which are protein complexes found on the surface of T cells, are able to bind to these peptides. This process is known as TCR recognition and constitutes a key step for immune response. Optimizing TCR sequences for TCR recognition represents a fundamental step towards the development of personalized treatments to trigger immune responses killing cancerous or virus-infected cells. In this paper, we formulated the search for these optimized TCRs as a reinforcement learning (RL) problem, and presented a framework TCRPPO with a mutation policy using proximal policy optimization. TCRPPO mutates TCRs into effective ones that can recognize given peptides. TCRPPO leverages a reward function that combines the likelihoods of mutated sequences being valid TCRs measured by a new scoring function based on deep autoencoders, with the probabilities of mutated sequences recognizing peptides from a peptide-TCR interaction predictor. We compared TCRPPO with multiple baseline methods and demonstrated that TCRPPO significantly outperforms all the baseline methods to generate positive binding and valid TCRs. These results demonstrate the potential of TCRPPO for both precision immunotherapy and peptide-recognizing TCR motif discovery. © 2023, CC BY.

关键词： Reinforcement learning

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Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?

arXiv

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arXiv 2024年

作者： Bassi, Pedro R.A.S. Li, Wenxuan Tang, Yucheng Isensee, Fabian Wang, Zifu Chen, Jieneng Chou, Yu-Cheng Roy, Saikat Kirchhoff, Yannick Rokuss, Maximilian Huang, Ziyan Ye, Jin He, Junjun Wald, Tassilo Ulrich, Constantin Baumgartner, Michael Maier-Hein, Klaus H. Jaeger, Paul Ye, Yiwen Xie, Yutong Zhang, Jianpeng Chen, Ziyang Xia, Yong Xing, Zhaohu Zhu, Lei Sadegheih, Yousef Bozorgpour, Afshin Kumari, Pratibha Azad, Reza Merhof, Dorit Shi, Pengcheng Ma, Ting Du, Yuxin Bai, Fan Huang, Tiejun Zhao, Bo Wang, Haonan Li, Xiaomeng Gu, Hanxue Dong, Haoyu Yang, Jichen Mazurowski, Maciej A. Gupta, Saumya Wu, Linshan Zhuang, Jiaxin Chen, Hao Roth, Holger Xu, Daguang Blaschko, Matthew B. Decherchi, Sergio Cavalli, Andrea Yuille, Alan L. Zhou, Zongwei Department of Computer Science Johns Hopkins University United States Department of Pharmacy and Biotechnology University of Bologna Italy Center for Biomolecular Nanotechnologies Istituto Italiano di Tecnologia Italy NVIDIA United States Germany Germany ESAT-PSI KU Leuven Belgium Faculty of Mathematics and Computer Science Heidelberg University Germany HIDSS4Health - Helmholtz Information and Data Science School for Health Germany Shanghai Jiao Tong University China Shanghai Artificial Intelligence Laboratory China Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Germany DKFZ Germany School of Computer Science and Engineering Northwestern Polytechnical University China Australian Institute for Machine Learning The University of Adelaide Australia College of Computer Science and Technology Zhejiang University China Hong Kong University of Science and Technology Guangzhou China Hong Kong University of Science and Technology Hong Kong Faculty of Informatics and Data Science University of Regensburg Germany Faculty of Electrical Engineering and Information Technology RWTH Aachen University Germany Fraunhofer Institute for Digital Medicine MEVIS Germany Electronic & Information Engineering School Harbin Institute of Technology Shenzhen China China The Chinese University of Hong Kong Hong Kong Peking University China Department of Electrical and Computer Engineering Duke University United States Stony Brook University United States Department of Computer Science and Engineering Department of Chemical and Biological Engineering Division of Life Science Hong Kong University of Science and Technology Hong Kong Data Science and Computation Facility Fondazione Istituto Italiano di Tecnologia Italy Ecole Polytechnique Fédérale de Lausanne Switzerland

How can we test AI performance? This question seems trivial, but it isn’t. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms. In addition, we also evaluated pre-existing AI frameworks—which, differing from algorithms, are more flexible and can support different algorithms—including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain. Copyright © 2024, The Authors. All rights reserved.

关键词： Open systems

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

Advanced Process Control in Manufacturing Using IoT Devices ...

引用

Sustainable Expert Systems (ICSES), International Conference on

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

ISBN: (数字)9798331540364

ISBN: (纸本)9798331540371

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.

关键词： Performance evaluation Adaptation models Process control Artificial neural networks Predictive models Real-time systems Manufacturing Sensors Internet of Things Monitoring

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Insightful analysis of historical sources at scales beyond human capabilities using unsupervised machine learning and XAI

arXiv

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arXiv 2023年

作者： Eberle, Oliver Büttner, Jochen El-Hajj, Hassan Montavon, Grégoire Müller, Klaus-Robert Valleriani, Matteo Machine Learning Group Technische Universität Berlin Marchstr. 23 Berlin10587 Germany BIFOLD – Berlin Institute for the Foundations of Learning and Data Berlin10587 Germany Max Planck Institute for the History of Science Boltzmannstr. 22 Berlin14195 Germany Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 14 Berlin14195 Germany Department of Artificial Intelligence Korea University Seoul136-713 Korea Republic of Max Planck Institute for Informatics Stuhlsatzenhausweg 4 Saarbrücken66123 Germany Institute of History and Philosophy of Science Technology and Literature Faculty I - Humanities and Educational Sciences Technische Universität Berlin Straße des 17. Juni 135 Berlin10623 Germany The Cohn Institute for the History and Philosophy of Science and Ideas Faculty of Humanities Tel Aviv University P.O.B. 39040 Ramat Aviv Tel Aviv6139001 Israel

Historical materials are abundant. Yet, piecing together how human knowledge has evolved and spread both diachronically and synchronically remains a challenge that can so far only be very selectively addressed. The vast volume of materials precludes comprehensive studies, given the restricted number of human specialists. However, as large amounts of historical materials are now available in digital form there is a promising opportunity for AI-assisted historical analysis. In this work, we take a pivotal step towards analyzing vast historical corpora by employing innovative machine learning (ML) techniques, enabling in-depth historical insights on a grand scale. Our study centers on the evolution of knowledge within the ‘Sacrobosco Collection’ – a digitized collection of 359 early modern printed editions of textbooks on astronomy used at European universities between 1472 and 1650 – roughly 76,000 pages, many of which contain astronomic, computational tables. An ML based analysis of these tables helps to unveil important facets of the spatio-temporal evolution of knowledge and innovation in the field of mathematical astronomy in the period, as taught at European universities. Copyright © 2023, The Authors. All rights reserved.

关键词： machine learning

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Roaming leads to amino acid photodamage: A deep learning study of tyrosine

arXiv

引用

arXiv 2021年

作者： Westermayr, Julia Gastegger, Michael Vörös, Dora Panzenboeck, Lisa Joerg, Florian González, Leticia Marquetand, Philipp University of Warwick Department of Chemistry Gibbet Hill Rd CoventryCV4 7AL United Kingdom Technical University of Berlin Machine Learning Group Berlin10587 Germany University of Vienna Faculty of Chemistry Institute of Theoretical Chemistry Währinger Str. 17 Vienna1090 Austria University of Vienna Vienna Research Platform on Accelerating Photoreaction Discovery Währinger Str. 17 Vienna1090 Austria University of Vienna Faculty of Chemistry Data Science @ Uni Vienna Währinger Str. 29 Vienna1090 Austria

Although the amino acid tyrosine is among the main building blocks of life, its photochemistry is not fully understood. Traditional theoretical simulations are neither accurate enough, nor computationally efficient to provide the missing puzzle pieces to the experimentally observed signatures obtained via time-resolved pump-probe spectroscopy or mass spectroscopy. In this work, we go beyond the realms of possibility with conventional quantum chemical methods and develop as well as apply a new technique to shed light on the photochemistry of tyrosine. By doing so, we discover roaming atoms in tyrosine, which is the first time such a reaction is discovered in biology. Our findings suggest that roaming atoms are radicals that could play a fundamental role in the photochemistry of peptides and proteins, offering a new perspective. Our novel method is based on deep learning, leverages the physics underlying the data, and combines different levels of theory. This combination of methods to obtain an accurate picture of excited molecules could shape how we study photochemical systems in the future and how we can overcome the current limitations that we face when applying quantum chemical methods. Copyright © 2021, The Authors. All rights reserved.

关键词： Amino acids

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Confidence intervals uncovered: Are we ready for real-world medical imaging AI?

arXiv

引用

arXiv 2024年

作者： Christodoulou, Evangelia Reinke, Annika Houhou, Rola Kalinowski, Piotr Erkan, Selen Sudre, Carole H. Burgos, Ninon Boutaj, Sofiène Loizillon, Sophie Solal, Maëlys Rieke, Nicola Cheplygina, Veronika Antonelli, Michela Mayer, Leon D. Tizabi, Minu D. Jorge Cardoso, M. Simpson, Amber Jäger, Paul F. Kopp-Schneider, Annette Varoquaux, Gaël Colliot, Olivier Maier-Hein, Lena Heidelberg Div. Intelligent Medical Systems Germany AI Health Innovation Cluster Germany NCT Heidelberg a partnership between DKFZ Heidelberg University Hospital Germany DKFZ Heidelberg Helmholtz Imaging Germany HIDSS4Health - Helmholtz Information and Data Science School for Health Germany DKFZ Heidelberg Interactive Machine Learning Group Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London United Kingdom Sorbonne Université Institut du Cerveau - Paris Brain Institute - ICM CNRS Inria Inserm AP-HP Hôpital de la Pitié-Salpêtrière France NVIDIA Germany Department of Computer Science IT University of Copenhagen Denmark Centre for Medical Image Computing University College London United Kingdom School of Computing Queen’s University Canada Department of Biomedical and Molecular Sciences Queen’s University Canada Division of Biostatistics DKFZ Germany Parietal project team INRIA Saclay-Île de France France Faculty of Mathematics and Computer Science Heidelberg University Germany Medical Faculty Heidelberg University Germany

Medical imaging is spearheading the AI transformation of healthcare. Performance reporting is key to determine which methods should be translated into clinical practice. Frequently, broad conclusions are simply derived from mean performance values. In this paper, we argue that this common practice is often a misleading simplification as it ignores performance variability. Our contribution is threefold. (1) Analyzing all MICCAI segmentation papers (n = 221) published in 2023, we first observe that more than 50% of papers do not assess performance variability at all. Moreover, only one (0.5%) paper reported confidence intervals (CIs) for model performance. (2) To address the reporting bottleneck, we show that the unreported standard deviation (SD) in segmentation papers can be approximated by a second-order polynomial function of the mean Dice similarity coefficient (DSC). Based on external validation data from 56 previous MICCAI challenges, we demonstrate that this approximation can accurately reconstruct the CI of a method using information provided in publications. (3) Finally, we reconstructed 95% CIs around the mean DSC of MICCAI 2023 segmentation papers. The median CI width was 0.03 which is three times larger than the median performance gap between the first and second ranked method. For more than 60% of papers, the mean performance of the second-ranked method was within the CI of the first-ranked method. We conclude that current publications typically do not provide sufficient evidence to support which models could potentially be translated into clinical practice. © 2024, CC BY.

关键词： Medical imaging

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Author Correction: Efficient interatomic descriptors for accurate machine learning force fields of extended molecules

引用

Nature communications 2023年第1期14卷 4116页

作者： Adil Kabylda Valentin Vassilev-Galindo Stefan Chmiela Igor Poltavsky Alexandre Tkatchenko Department of Physics and Materials Science University of Luxembourg L-1511 Luxembourg City Luxembourg. Machine Learning Group Technische Universität Berlin 10587 Berlin Germany. BIFOLD - Berlin Institute for the Foundations of Learning and Data 10587 Berlin Germany. Department of Physics and Materials Science University of Luxembourg L-1511 Luxembourg City Luxembourg. alexandre.tkatchenko@uni.lu.

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Alchemical harmonic approximation based potential for iso-electronic diatomics: Foundational baseline for ∆-machine learning

arXiv

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arXiv 2024年

作者： Krug, Simon León Khan, Danish von Lilienfeld, O. Anatole Machine Learning Group Technische Universität Berlin Berlin Charlottenburg 10587 Germany Vector Institute for Artificial Intelligence TorontoONM5S 1M1 Canada Department of Chemistry University of Toronto St. George campus TorontoONM5S 3H6 Canada Berlin Institute for the Foundations of Learning and Data Charlottenburg Berlin10587 Germany Acceleration Consortium University of Toronto 80 St George St TorontoONM5S 3H6 Canada Department of Materials Science and Engineering University of Toronto St. George campus TorontoONM5S 3E4 Canada Department of Physics University of Toronto St. George campus TorontoONM5S 1A7 Canada

We introduce the alchemical harmonic approximation (AHA) of the absolute electronic energy for charge-neutral iso-electronic diatomics at fixed interatomic distance d0. To account for variations in distance, we combine AHA with this Ansatz for the electronic binding potential, E(d) = (Eu − Es)(formula presented), where Eu, Ec, Es correspond to the energies of united atom, calibration at d0, and sum of infinitely separated atoms, respectively. Our model covers the two-dimensional electronic potential energy surface spanned by distances of 0.7 to 2.5 Åand differences in nuclear charge from which only one single point (with elements of nuclear charge Z1, Z2 and distance d0) is drawn to calibrate Ec. Using reference data from pbe0/cc-pVDZ, we present numerical evidence for the electronic ground-state of all neutral diatomics with 8, 10, 12, 14 electrons. We assess the validity of our model by comparison to legacy interatomic potentials (Harmonic oscillator, Lennard-Jones, and Morse) within the most relevant range of binding (0.7-2.5 Å), and find comparable accuracy if restricted to single diatomics, and significantly better predictive power when extrapolating to the entire iso-electronic series. We also investigated ∆-learning of the electronic absolute energy using our model as baseline. This baseline model results in a systematic improvement, effectively reducing training data needs for reaching chemical accuracy by up to an order of magnitude from ∼1000 to ∼100. By contrast, using AHA+Morse as a baseline hardly leads to any improvement, and sometimes even deteriorates the predictive power. Inferring the energy of unseen CO converges to a prediction error of ∼0.1 Ha in direct learning, and ∼0.04 Ha with our baseline. © 2024, CC BY.

关键词： Harmonic analysis

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