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Motif-aware Graph Neural Networks for Networked Time Series Imputation 39

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Motif-aware Graph Neural Networks for Networked Time Series ...

39th Annual AAAI Conference on Artificial Intelligence, AAAI 2025

作者： Ahmed, Nourhan Yalavarthi, Vijaya Krishna Schmidt-Thieme, Lars Information Systems and Machine Learning Lab (ISMLL) University of Hildesheim Germany VWFS Data Analytics Research Center Germany

ISBN: (纸本)157735897X

Networked time series are time series on a graph, one for each node, with applications in traffic and weather monitoring. Graph neural networks are natural candidates for networked time series imputation and have recently outperformed existing alternatives such as recurrent and generative models for time series imputation as they utilize a relational inductive bias for imputation. However, existing GNN-based approaches fail to capture the higher-order topological structure between sensors, which are shaped by recurring substructures in the graph, referred to as temporal motifs. In addition, it remains uncertain which motifs are the most pivotal motifs guiding the imputation task in networked time series. In this paper, we fill in this gap by proposing a graph neural network designed to leverage motif structures within the network by employing weighted motif adjacency matrices to capture higher-order neighborhood information. In particular, (1) we design a motif-wise multi-view attention module that explicitly captures various higher-order structures along with an attention mechanism that automatically assigns high weights to informative ones in order to maximize the use of higher-order information. (2) We introduce a gated fusion module by merging gated recurrent networks and graph convolutional networks to capture the spatial and temporal dependency in order to reflect the intricate impacts of temporal and spatial influence. Experimental results demonstrate that when compared to state-of-the-art models for time-series imputation tasks, our proposed model can reduce the error by around 19%. Copyright © 2025, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

关键词： Graph neural networks

Hyperparameter Tuning MLP's for Probabilistic Time Series Forecasting

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arXiv 2024年

作者： Madhusudhanan, Kiran Jawed, Shayan Schmidt-Thieme, Lars Information Systems and Machine Learning Lab VWFS Data Analytics Research Center University of Hildesheim Hildesheim Germany

Time series forecasting attempts to predict future events by analyzing past trends and patterns. Although well researched, certain critical aspects pertaining to the use of deep learning in time series forecasting remain ambiguous. Our research primarily focuses on examining the impact of specific hyperparameters related to time series, such as context length and validation strategy, on the performance of the state-of-the-art MLP model in time series forecasting. We have conducted a comprehensive series of experiments involving 4800 configurations per dataset across 20 time series forecasting datasets, and our findings demonstrate the importance of tuning these parameters. Furthermore, in this work, we introduce the largest metadataset for time series forecasting to date, named TSBench, comprising 97200 evaluations, which is a twentyfold increase compared to previous works in the field. Finally, we demonstrate the utility of the created metadataset on multi-fidelity hyperparameter optimization tasks. © 2024, CC BY.

关键词： Forecasting

ProbSAINT: Probabilistic Tabular Regression for Used Car Pricing

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ProbSAINT: Probabilistic Tabular Regression for Used Car Pri...

IEEE International Conference on Big data

作者： Kiran Madhusudhanan Gunnar Behrens Maximilian Stubbemann Lars Schmidt-Thieme Information Systems and Machine Learning Lab VWFS Data Analytics Research Center University Of Hildesheim Data Analytics & AI Engineering Volkswagen Financial Services AG

ISBN: (数字)9798350362480

ISBN: (纸本)9798350362497

关键词： Industries Accuracy Uncertainty machine learning algorithms Pricing Predictive models Probabilistic logic Prediction algorithms Automobiles Vehicle dynamics

Channel Dependence, Limited Lookback Windows, and the Simplicity of datasets: How Biased is Time Series Forecasting?

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arXiv 2025年

作者： Abdelmalak, Ibram Madhusudhanan, Kiran Choi, Jungmin Stubbemann, Maximilian Schmidt-Thieme, Lars Information Science and Machine Learning Lab VWFS Data Analytics Research Center University of Hildesheim Niedersachsen Hildesheim Germany

Time-series forecasting research has converged to a small set of datasets and a standardized collection of evaluation scenarios. Such a standardization is to a specific extent needed for comparable research. However, the underlying assumption is, that the considered setting is a representative for the problem as a whole. In this paper, we challenge this assumption and show that the current scenario gives a strongly biased perspective on the state of time-series forecasting research. To be more detailed, we show that the current evaluation scenario is heavily biased by the simplicity of the current datasets. We furthermore emphasize, that when the lookback-window is properly tuned, current models usually do not need any information flow across channels. However, when using more complex benchmark data, the situation changes: Here, modeling channel-interactions in a sophisticated manner indeed enhances performances. Furthermore, in this complex evaluation scenario, Crossformer, a method regularly neglected as an important baseline, is the SOTA method for time series forecasting. Based on this, we present the Fast Channel-dependent Transformer (FaCT), a simplified version of Crossformer which closes the runtime gap between Crossformer and TimeMixer, leading to an efficient model for complex forecasting datasets. © 2025, CC BY.

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ProbSAINT: Probabilistic Tabular Regression for Used Car Pricing

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arXiv 2024年

作者： Madhusudhanan, Kiran Behrens, Gunnar Stubbemann, Maximilian Schmidt-Thieme, Lars Information Systems and Machine Learning Lab VWFS Data Analytics Research Center University of Hildesheim Hildesheim Germany Data Analytics & AI Engineering Volkswagen Financial Services AG Braunschweig Germany

Used car pricing is a critical aspect of the automotive industry, influenced by many economic factors and market dynamics. With the recent surge in online marketplaces and increased demand for used cars, accurate pricing would benefit both buyers and sellers by ensuring fair transactions. However, the transition towards automated pricing algorithms using machine learning necessitates the comprehension of model uncertainties, specifically the ability to flag predictions that the model is unsure about. Although recent literature proposes the use of boosting algorithms or nearest neighbor-based approaches for swift and precise price predictions, encapsulating model uncertainties with such algorithms presents a complex challenge. We introduce ProbSAINT, a model that offers a principled approach for uncertainty quantification of its price predictions, along with accurate point predictions that are comparable to state-of-the-art boosting techniques. Furthermore, acknowledging that the business prefers pricing used cars based on the number of days the vehicle was listed for sale, we show how ProbSAINT can be used as a dynamic forecasting model for predicting price probabilities for different expected offer duration. Our experiments further indicate that ProbSAINT is especially accurate on instances where it is highly certain. This proves the applicability of its probabilistic predictions in real-world scenarios where trustworthiness is crucial. © 2024, CC BY.

关键词： Costs

Reproducibility and Geometric Intrinsic Dimensionality: An Investigation on Graph Neural Network research

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arXiv 2024年

作者： Hille, Tobias Stubbemann, Maximilian Hanika, Tom Knowledge & Data Engineering Group University of Kassel Kassel Germany Interdisciplinary Research Center for Information System Design University of Kassel Kassel Germany Information Systems and Machine Learning Lab University of Hildesheim Hildesheim Germany Institute of Computer Science University of Hildesheim Hildesheim Germany

Difficulties in replication and reproducibility of empirical evidences in machine learning research have become a prominent topic in recent years. Ensuring that machine learning research results are sound and reliable requires reproducibility, which verifies the reliability of research findings using the same code and data. This promotes open and accessible research, robust experimental workflows, and the rapid integration of new findings. Evaluating the degree to which research publications support these different aspects of reproducibility is one goal of the present work. For this we introduce an ontology of reproducibility in machine learning and apply it to methods for graph neural networks. Building on these efforts we turn towards another critical challenge in machine learning, namely the curse of dimensionality, which poses challenges in data collection, representation, and analysis, making it harder to find representative data and impeding the training and inference processes. Using the closely linked concept of geometric intrinsic dimension we investigate to which extend the used machine learning models are influenced by the intrinsic dimension of the data sets they are trained *** Codes 68T01 68T07 68T09 51F99 Copyright © 2024, The Authors. All rights reserved.

关键词： Graph neural networks

Accurately predicting anticancer peptide using an ensemble of heterogeneously trained classifiers

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Informatics in Medicine Unlocked 2023年 42卷

作者： Azim, Sayed Mehedi Sabab, Noor Hossain Nuri Noshadi, Iman Alinejad-Rokny, Hamid Sharma, Alok Shatabda, Swakkhar Dehzangi, Iman Center for Computational and Integrative Biology Rutgers University Camden 08102 NJ United States Department of Computer Science and Engineering United International University Plot 2 United City Madani Avenue BaddaDhaka 1212 Bangladesh Department of Bioengineering University of California Riverside 92507 CA United States BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering The University of New South Wales (UNSW Sydney) Sydney NSW 2052 Australia UNSW Data Science Hub UNSW Sydney Sydney NSW 2052 Australia Health Data Analytics Program AI-enabled Processes Research Centre Macquarie University Sydney 2109 Australia Institute for Integrated and Intelligent Systems Griffith University Brisbane Australia Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama 230-0045 Japan Department of Computer Science Rutgers University Camden 08102 NJ United States

The use of therapeutic peptides for the treatment of cancer has received tremendous attention in recent years. Anticancer peptides (ACPs) are considered new anticancer drugs which have several advantages over chemistry-based drugs including high specificity, strong tumor penetration capacity, and low toxicity level for normal cells. Due to the rise of experimentally verified bioactive peptides, several in silico approaches became imperative for the investigation of the characteristics of ACPs. In this paper, we proposed a new machine learning tool named iACP-RF that uses a combination of several sequence-based features and an ensemble of three heterogeneously trained Random Forest classifiers to accurately predict anticancer peptides. Experimental results show that our proposed model achieves an accuracy of 75.9% which outperforms other state-of-the-art methods by a significant margin. We also achieve 0.52, 75.6%, and 76.2% in terms of Matthews Correlation Coefficient (MCC), Sensitivity, and Specificity, respectively. iACP-RF as a standalone tool and its source code are publicly available at: https://***/MLBC-lab/iACP-RF. © 2023 The Authors

关键词： Anticancer peptides Ensemble learning Feature extraction Heterogeneous classifiers machine learning Random Forest

OLSR+: A new routing method based on fuzzy logic in flying ad-hoc networks (FANETs)

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Vehicular Communications 2022年 36卷

作者： Rahmani, Amir Masoud Ali, Saqib Yousefpoor, Efat Yousefpoor, Mohammad Sadegh Javaheri, Danial Lalbakhsh, Pooia Hassan Ahmed, Omed Hosseinzadeh, Mehdi Lee, Sang-Woong Future Technology Research Center National Yunlin University of Science and Technology Yunlin Taiwan Department of Information Systems College of Economics and Political Science Sultan Qaboos University Al Khoudh Muscat Oman Department of Computer Engineering Dezful Branch Islamic Azad University Dezful Iran Department of Computer Engineering Chosun University Gwangju 61452 South Korea Department of Data Science and Artificial Intelligence Faculty of Information Technology Monash University Clayton 3800 VIC Australia Department of Information Technology University of Human Development Sulaymaniyah Iraq Pattern Recognition and Machine Learning Lab Gachon University 1342 Seongnamdaero Sujeonggu Seongnam 13120 South Korea

Flying ad-hoc networks (FANETs) have many applications in military, industrial and agricultural areas. Due to specific features of FANETs, such as high-speed nodes, low density of nodes in the network, and rapid changes in the topology, most routing protocols designed for mobile ad hoc networks (MANETs) or vehicular ad hoc networks (VANETs) are not compatible with FANETs. In this paper, we propose a fuzzy logic-based routing approach called OLSR+ for FANETs. In this scheme, we seek to improve the optimized link state routing protocol (OLSR) so that it can efficiently be used in FANETs. OLSR+ includes four main phases: 1) Discovering neighboring nodes. In this phase, we propose a new and efficient technique for estimating the lifetime of the link between two unmanned ariel vehicles (UAVs) based on the link quality, distance, relative velocity, and movement direction. 2) Selecting multipoint relays (MPRs). In this phase, we present a fuzzy mechanism for selecting a set of MPR nodes. According to this mechanism, when a node has higher residual energy, higher link lifetime, and more neighborhood degree compared to others, it achieves more fitness to be selected as MPR. 3) Discovering the network topology. In this phase, we modify the format of the topology control (TC) message and add two fields, including route energy and route lifetime to this message. 4) Calculating the routing table. In OLSR+, we consider two parameters, including route energy and route lifetime, for establishing stable paths. Finally, we simulate OLSR+ using NS3 and compare its performance with two methods, namely greedy optimized link state routing (G-OLSR) and optimized link state routing (OLSR). The simulation results show that OLSR+ successfully reduces delay compared to G-OLSR and OLSR. In addition, it has higher packet delivery rate and throughput than others. Also, it improves energy consumption in the network. However, OLSR+ has more routing overhead than G-OLSR. © 2022 Elsevier Inc.

关键词： Artificial intelligence (AI) Flying ad hoc networks (FANETs) Fuzzy logic Routing Unmanned ariel vehicles (UAVs)

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