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Weisfeiler and Leman go machine learning: the story so far

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The Journal of Machine Learning Research

The Journal of Machine Learning Research 2023年第1期24卷 15865-15923页

作者： Christopher Morris Yaron Lipman Haggai Maron Bastian Rieck Nils M. Kriege Martin Grohe Matthias Fey Karsten Borgwardt Department of Computer Science RWTH Aachen University Aachen Germany Meta AI Research Department of Computer Science and Applied Mathematics Weizmann Institute of Science Rehovot Israel NVIDIA Research Tel Aviv Israel AIDOS Lab Institute of AI for Health Helmholtz Zentrum München and Technical University of Munich Munich Germany Faculty of Computer Science and Research Network Data Science University of Vienna Vienna Austria Kumo.AI Mountain View CA Machine Learning & Computational Biology Lab Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland and Swiss Institute of Bioinformatics Lausanne Switzerland

In recent years, algorithms and neural architectures based on the Weisfeiler-Leman algorithm, a well-known heuristic for the graph isomorphism problem, have emerged as a powerful tool for machine learning with graphs and relational data. Here, we give a comprehensive overview of the algorithm's use in a machine-learning setting, focusing on the supervised regime. We discuss the theoretical background, show how to use it for supervised graph and node representation learning, discuss recent extensions, and outline the algorithm's connection to (permutation-)equivariant neural architectures. Moreover, we give an overview of current applications and future directions to stimulate further research.

关键词： machine learning for graphs graph neural networks Weisfeiler-Leman algorithm expressivity equivariance

Empowering Precision Medicine: AI-Driven Schizophrenia Diagnosis via EEG Signals: A Comprehensive Review from 2002-2023

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arXiv 2023年

作者： Jafari, Mahboobeh Sadeghi, Delaram Shoeibi, Afshin Alinejad-Rokny, Hamid Beheshti, Amin García, David López Chen, Zhaolin Acharya, U. Rajendra Gorriz, Juan M. 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 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 Health Data Analytics Program Centre for Applied Artificial Intelligence Macquarie University Sydney2109 Australia Data Science Lab School of Computing Macquarie University SydneyNSW2109 Australia Monash University Melbourne Australia School of Mathematics Physics and Computing University of Southern Queensland Springfield Australia Department of Psychiatry University of Cambridge United Kingdom

Schizophrenia (SZ) is a prevalent mental disorder characterized by cognitive, emotional, and behavioral changes. Symptoms of SZ include hallucinations, illusions, delusions, lack of motivation, and difficulties in concentration. While the exact causes of SZ remain unproven, factors such as brain injuries, stress, and psychotropic drugs have been implicated in its development. SZ can be classified into different types, including paranoid, disorganized, catatonic, undifferentiated, and residual. Diagnosing SZ involves employing various tools, including clinical interviews, physical examinations, psychological evaluations, the Diagnostic and Statistical Manual of Mental Disorders (DSM), and neuroimaging techniques. Electroencephalography (EEG) recording is a significant functional neuroimaging modality that provides valuable insights into brain function during SZ. However, EEG signal analysis poses challenges for neurologists and scientists due to the presence of artifacts, long-term recordings, and the utilization of multiple channels. To address these challenges, researchers have introduced artificial intelligence (AI) techniques, encompassing conventional machine learning (ML) and deep learning (DL) methods, to aid in SZ diagnosis. This study reviews papers focused on SZ diagnosis utilizing EEG signals and AI methods. The introduction section provides a comprehensive explanation of SZ diagnosis methods and intervention techniques. Subsequently, review papers in this field are discussed, followed by an introduction to the AI methods employed for SZ diagnosis and a summary of relevant papers presented in tabular form. Additionally, this study reports on the most significant challenges encountered in SZ diagnosis, as identified through a review of papers in this field. Future directions to overcome these challenges are also addressed. The discussion section examines the specific details of each paper, culminating in the presentation of conclusions and findings. © 2023,

关键词： Electroencephalography

Transfer Learning for Bayesian Optimization: A Survey

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arXiv 2023年

作者： Bai, Tianyi Li, Yang Shen, Yu Zhang, Xinyi Zhang, Wentao Cui, Bin School of Mathematics and Statistics Beijing Institute of Technology Beijing China Data Platform TEG Tencent Inc. Beijing China Key Lab of High Confidence Software Technologies Peking University Beijing China Mila - Québec AI Institute Montréal Canada Institute of Computational Social Science Peking University Qingdao China

A wide spectrum of design and decision problems, including parameter tuning, A/B testing and drug design, intrinsically are instances of black-box optimization. Bayesian optimization (BO) is a powerful tool that models and optimizes such expensive "black-box" functions. However, at the beginning of optimization, vanilla Bayesian optimization methods often suffer from slow convergence issue due to inaccurate modeling based on few trials. To address this issue, researchers in the BO community propose to incorporate the spirit of transfer learning to accelerate optimization process, which could borrow strength from the past tasks (source tasks) to accelerate the current optimization problem (target task). This survey paper first summarizes transfer learning methods for Bayesian optimization from four perspectives: initial points design, search space design, surrogate model, and acquisition function. Then it highlights its methodological aspects and technical details for each approach. Finally, it showcases a wide range of applications and proposes promising future directions. Copyright © 2023, The Authors. All rights reserved.

关键词： Learning systems

Coupling streaming AI and HPC ensembles to achieve 100–1000× faster biomolecular simulations

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Coupling streaming AI and HPC ensembles to achieve 100–1000...

International Symposium on Parallel and Distributed Processing (IPDPS)

作者： Alexander Brace Igor Yakushin Heng Ma Anda Trifan Todd Munson Ian Foster Arvind Ramanathan Hyungro Lee Matteo Turilli Shantenu Jha Data Science and Learning Division Argonne National Laboratory Lemont USA Department of Computer Science University of Chicago Chicago USA Data Science and Learning Division Argonne National LaboratoryLemontUSA Center For Biophysics University of Illinois Urbana-Champaign Champaign USA Mathematics and Computer Science Division Argonne National LaboratoryLemontUSA RADICAL-Lab Rutgers University New Brunswick USA Computational Science Initiative Brookhaven National Laboratory Upton USA

Machine learning (ML)-based steering can improve the performance of ensemble-based simulations by allowing for online selection of more scientifically meaningful computations. We present DeepDriveMD, a framework for ML-driven steering of scientific simulations that we have used to achieve orders-of-magnitude improvements in molecular dynamics (MD) performance via effective coupling of ML and HPC on large parallel computers. We discuss the design of DeepDriveMD and characterize its performance. We demonstrate that DeepDriveMD can achieve between 100-1000× acceleration for protein folding simulations relative to other methods, as measured by the amount of simulated time performed, while covering the same conformational landscape as quantified by the states sampled during a simulation. Experiments are performed on leadership-class platforms on up to 1020 nodes. The results establish DeepDriveMD as a high-performance framework for ML-driven HPC simulation scenarios, that supports diverse MD simulation and ML back-ends, and which enables new scientific insights by improving the length and time scales accessible with current computing capacity.

关键词： Proteins Couplings Computers Accelerometers Solid modeling Distributed processing computational modeling

Full wCDM analysis of KiDS-1000 weak lensing maps using deep learning

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Physical Review D 2022年第8期105卷 083518-083518页

作者： Janis Fluri Tomasz Kacprzak Aurelien Lucchi Aurel Schneider Alexandre Refregier Thomas Hofmann Institute of Particle Physics and Astrophysics Department of Physics ETH Zurich Wolfang-Pauli-Strasse 27 8093 Zurich Switzerland Data Analytics Lab Department of Computer Science ETH Zurich Universitätstrasse 6 8006 Zurich Switzerland Swiss Data Science Center Paul Scherrer Institute Forschungsstrasse 111 5232 Villigen Switzerland Department of Mathematics and Computer Science University of Basel Spiegelgasse 1 4051 Basel Switherland Center for Theoretical Astrophysics and Cosmology Institute for Computational Science University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland

We present a full forward-modeled wCDM analysis of the KiDS-1000 weak lensing maps using graph-convolutional neural networks (GCNN). Utilizing the cosmogrid, a novel massive simulation suite spanning six different cosmological parameters, we generate almost one million tomographic mock surveys on the sphere. Due to the large dataset size and survey area, we perform a spherical analysis while limiting our map resolution to HEALPix nside=512. We marginalize over systematics such as photometric redshift errors, multiplicative calibration and additive shear bias. Furthermore, we use a map-level implementation of the nonlinear intrinsic alignment model along with a novel treatment of baryonic feedback to incorporate additional astrophysical nuisance parameters. We also perform a spherical power spectrum analysis for comparison. The constraints of the cosmological parameters are generated using a likelihood-free inference method called Gaussian process approximate Bayesian computation (GPABC). Finally, we check that our pipeline is robust against choices of the simulation parameters. We find constraints on the degeneracy parameter of S8≡σ8ΩM/0.3=0.78−0.06+0.06 for our power spectrum analysis and S8=0.79−0.05+0.05 for our GCNN analysis, improving the former by 16%. This is consistent with earlier analyses of the 2-point function, albeit slightly higher. Baryonic corrections generally broaden the constraints on the degeneracy parameter by about 10%. These results offer great prospects for full machine learning based analyses of ongoing and future weak lensing surveys.

关键词： Cosmological parameters Large scale structure of the Universe Particle dark matter Numerical simulations in gravitation & astrophysics

A blind spot for large language models: Supradiegetic linguistic information

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arXiv 2023年

作者： Zimmerman, Julia Witte Hudon, Denis Cramer, Kathryn Onge, Jonathan St. Fudolig, Mikaela Trujillo, Milo Z. Danforth, Christopher M. Dodds, Peter Sheridan Computational Story Lab Vermont Advanced Computing Center University of Vermont BurlingtonVT05405 United States Vermont Complex Systems Center MassMutual Center of Excellence in Complex Systems and Data Science University of Vermont BurlingtonVT05405 United States Department of Mathematics & Statistics University of Vermont BurlingtonVT05405 United States Department of Computer Science University of Vermont BurlingtonVT05405 United States

Large Language Models (LLMs) like ChatGPT reflect profound changes in the field of Artificial Intelligence, achieving a linguistic fluency that is impressively, even shockingly, human-like. The extent of their current and potential capabilities is an active area of investigation by no means limited to scientific researchers. It is common for people to frame the training data for LLMs as "text" or even "language". We examine the details of this framing using ideas from several areas, including linguistics, embodied cognition, cognitive science, mathematics, and history. We propose that considering what it is like to be an LLM like ChatGPT, as Nagel might have put it, can help us gain insight into its capabilities in general, and in particular, that its exposure to linguistic training data can be productively reframed as exposure to the diegetic information encoded in language, and its deficits can be reframed as ignorance of extradiegetic information, including supradiegetic linguistic information. Supradiegetic linguistic information consists of those arbitrary aspects of the physical form of language that are not derivable from the one-dimensional relations of context—frequency, adjacency, proximity, co-occurrence—that LLMs like ChatGPT have access to. Roughly speaking, the diegetic portion of a word can be thought of as its function, its meaning, as the information in a theoretical vector in a word embedding, while the supradiegetic portion of the word can be thought of as its form, like the shapes of its letters or the sounds of its syllables. We use these concepts to investigate why LLMs like ChatGPT have trouble handling palindromes, the visual characteristics of symbols, translating Sumerian cuneiform, and continuing integer sequences. Copyright © 2023, The Authors. All rights reserved.

关键词： computational linguistics

Hollywood’s misrepresentation of death: A comparison of overall and by-gender mortality causes in film and the real world

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arXiv 2024年

作者： Beauregard, Calla Danforth, Christopher M. Dodds, Peter Sheridan Computational Story Lab Vermont Advanced Computing Center University of Vermont BurlingtonVT05405 United States Vermont Complex Systems Center MassMutual Center of Excellence for Complex Systems and Data Science University of Vermont BurlingtonVT05405 United States Department of Mathematics & Statistics University of Vermont BurlingtonVT05405 United States Department of Computer Science University of Vermont BurlingtonVT05405 United States Santa Fe Institute 1399 Hyde Park Rd Santa FeNM87501 United States

The common phrase ‘representation matters’ asserts that media has a measurable and important impact on civic society’s perception of self and others. The representation of health in media, in particular, may reflect and perpetuate a society’s disease burden. Here, for the top 10 major causes of death in the United States, we examine how cinematic representation of overall and by-gender mortality diverges from reality. Using crowd-sourced data on film deaths from Cinemorgue Wiki, we employ natural language processing (NLP) techniques to analyze shifts in representation of deaths in movies versus the 2021 National Vital Statistic Survey (NVSS) top ten mortality causes. Overall, movies strongly overrepresent suicide and, to a lesser degree, accidents. In terms of gender, movies overrepresent men and underrepresent women for nearly every major mortality cause, including heart disease and cerebrovascular disease. The two exceptions for which women are overrepresented are suicide and accidents. We discuss the implications of under- and over-representing causes of death overall and by gender, as well as areas of future research. © 2024, CC BY-SA.

关键词： Natural language processing systems

Connecting the Dots in Trustworthy Artificial Intelligence: From AI Principles, Ethics, and Key Requirements to Responsible AI Systems and Regulation

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arXiv 2023年

作者： Díaz-Rodríguez, Natalia Ser, Javier Del Coeckelbergh, Mark de Prado, Marcos López Herrera-Viedma, Enrique Herrera, Francisco Department of Computer Science and Artificial Intelligence DaSCI Andalusian Institute in Data Science and Computational Intelligence University of Granada Granada18071 Spain Derio48160 Spain Bilbao48013 Spain Department of Philosophy University of Vienna Vienna1010 Austria School of Engineering Cornell University IthacaNY14850 United States ADIA Lab Al Maryah Island Abu Dhabi United Arab Emirates Department of Mathematics Khalifa University of Science and Technology Abu Dhabi United Arab Emirates

MSC Codes 68T01Trustworthy Artificial Intelligence (AI) is based on seven technical requirements sustained over three main pillars that should be met throughout the system’s entire life cycle: it should be (1) lawful, (2) ethical, and (3) robust, both from a technical and a social perspective. However, attaining truly trustworthy AI concerns a wider vision that comprises the trustworthiness of all processes and actors that are part of the system’s life cycle, and considers previous aspects from different lenses. A more holistic vision contemplates four essential axes: the global principles for ethical use and development of AI-based systems, a philosophical take on AI ethics, a risk-based approach to AI regulation, and the mentioned pillars and requirements. The seven requirements (human agency and oversight;robustness and safety;privacy and data governance;transparency;diversity, non-discrimination and fairness;societal and environmental wellbeing;and accountability) are analyzed from a triple perspective: What each requirement for trustworthy AI is, Why it is needed, and How each requirement can be implemented in practice. On the other hand, a practical approach to implement trustworthy AI systems allows defining the concept of responsibility of AI-based systems facing the law, through a given auditing process. Therefore, a responsible AI system is the resulting notion we introduce in this work, and a concept of utmost necessity that can be realized through auditing processes, subject to the challenges posed by the use of regulatory sandboxes. Our multidisciplinary vision of trustworthy AI culminates in a debate on the diverging views published lately about the future of AI. Our reflections in this matter conclude that regulation is a key for reaching a consensus among these views, and that trustworthy and responsible AI systems will be crucial for the present and future of our society. © 2023, CC BY-NC-ND.

关键词： Artificial intelligence

Noncooperative dynamics in election interference

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Physical Review E 2020年第2期101卷 022307-022307页

作者： David Rushing Dewhurst Christopher M. Danforth Peter Sheridan Dodds MassMutual Center of Excellence in Complex Systems and Data Science Computational Story Lab Vermont Complex Systems Center and Department of Mathematics and Statistics University of Vermont Burlington Vermont 05405 USA

Foreign power interference in domestic elections is an existential threat to societies. Manifested through myriad methods from war to words, such interference is a timely example of strategic interaction between economic and political agents. We model this interaction between rational game players as a continuous-time differential game, constructing an analytical model of this competition with a variety of payoff structures. All-or-nothing attitudes by only one player regarding the outcome of the game lead to an arms race in which both countries spend increasing amounts on interference and counterinterference operations. We then confront our model with data pertaining to the Russian interference in the 2016 United States presidential election contest. We introduce and estimate a Bayesian structural time-series model of election polls and social media posts by Russian Twitter troll accounts. Our analytical model, while purposefully abstract and simple, adequately captures many temporal characteristics of the election and social media activity. We close with a discussion of our model's shortcomings and suggestions for future research.

关键词： Econophysics Brownian dynamics data analysis Fokker–Planck equation Monte Carlo methods