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Constraint-Guided Learning of Data-driven Health Indicator Models: An Application on the Pronostia Bearing Dataset

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arXiv 2025年

作者： Tefera, Yonas Van Baelen, Quinten Meire, Maarten Luca, Stijn Karsmakers, Peter KU Leuven Dept. of Computer Science ADVISE-DTAI Kleinhoefstraat 4 GeelB-2440 Belgium Leuven.AI - KU Leuven Institute for AI Belgium Flanders Make @ KU Leuven Belgium Addis Ababa University School of Electrical and Computer Engineering Addis Ababa Ethiopia Ghent University Department of Data Analysis and Mathematical Modelling Coupure Links 653 Gent9000 Belgium

This paper presents a constraint-guided deep learning framework to develop physically consistent health indicators in bearing prognostics and health management. Conventional data-driven approaches often lack physical plausibility, while physics-based models are limited by incomplete knowledge of complex systems. To address this, we integrate domain knowledge into deep learning models via constraints, ensuring monotonicity, bounding output ranges between 1 and 0 (representing healthy to failed states respectively), and maintaining consistency between signal energy trends and health indicator estimates. This eliminates the need for complex loss term balancing to incorporate domain knowledge. We implement a constraint-guided gradient descent optimization within an autoencoder architecture, creating a constrained autoencoder. However, the framework is flexible and can be applied to other architectures as well. Using time-frequency representations of accelerometer signals from the Pronostia dataset, the constrained model generates more accurate and reliable representations of bearing health compared to conventional methods. It produces smoother degradation profiles that align with the expected physical behavior. Model performance is assessed using three metrics: trendability, robustness, and consistency. When compared to a conventional baseline model, the constrained model shows significant improvement in all three metrics. Another baseline incorporated the monotonicity behavior directly into the loss function using a soft-ranking approach. While this approach outperforms the constrained model in trendability, due to its explicit monotonicity enforcement, the constrained model performed better in robustness and consistency, providing stable and interpretable health indicator estimates over time. The results of the ablation study confirm that the monotonicity constraint enhances trendability, the boundary constraint ensures consistency, and the energy-health indicator con

关键词： Electronic health record

On inertia and ratio type bounds for the k-independence number of a graph and their relationship

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arXiv 2022年

作者： Abiad, Aida Dalfó, Cristina Fiol, Miquel Àngel Zeijlemaker, Sjanne Dept. of Mathematics and Computer Science Eindhoven University of Technology Netherlands Dept. of Mathematics: Analysis Logic and Discrete Mathematics Ghent University Belgium Dept. of Mathematics and Data Science Vrije Universiteit Brussel Belgium Dept. de Matemàtica Universitat de Lleida Catalonia Spain Dept. de Matemàtiques Universitat Politècnica de Catalunya Catalonia Spain Barcelona Graduate School of Mathematics Catalonia Spain Spain

For k ≥ 1, the k-independence number αk of a graph is the maximum number of vertices that are mutually at distance greater than k. The well-known inertia and ratio bounds for the (1-)independence number α(= α1) of a graph, due to Cvetković and Hoffman, respectively, were generalized recently for every value of k. We show that, for graphs with enough regularity, the polynomials involved in such generalizations are closely related and give exact values for αk, showing a new relationship between the inertia and ratio type bounds. Additionally, we investigate the existence and properties of the extremal case of sets of vertices that are mutually at maximum distance for walk-regular graphs. Finally, we obtain new sharp inertia and ratio type bounds for partially walk-regular graphs by using the predistance polynomials. © 2022, CC BY.

关键词： Polynomials

Improved Prediction Of Ligand-Protein Binding Affinities By Meta-Modeling

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arXiv 2023年

作者： Lee, Ho-Joon Emani, Prashant S. Gerstein, Mark B. Dept. of Genetics and Yale University New HavenCT06510 United States Yale Center for Genome Analysis Yale University New HavenCT06510 United States Dept. of Molecular Biophysics & Biochemistry Yale University New HavenCT06520 United States Program in Computational Biology & Bioinformatics Yale University New HavenCT06520 United States Dept. of Computer Science Yale University New HavenCT06520 United States Dept. of Statistics & Data Science Yale University New HavenCT06520 United States Dept. of Biomedical Informatics & Data Science Yale University New HavenCT06520 United States

The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity between ligands and proteins. Many computational models for binding affinity prediction have been developed, but with varying results across targets. Given that ensembling or meta-modeling approaches have shown great promise in reducing model-specific biases, we develop a framework to integrate published force-field-based empirical docking and sequence-based deep learning models. In building this framework, we evaluate many combinations of individual base models, training databases, and several meta-modeling approaches. We show that many of our meta-models significantly improve affinity predictions over base models. Our best meta-models achieve comparable performance to state-of-the-art deep learning tools exclusively based on 3D structures, while allowing for improved database scalability and flexibility through the explicit inclusion of features such as physicochemical properties or molecular descriptors. We further demonstrate improved generalization capability by our models using a large-scale benchmark of affinity prediction as well as a virtual screening application benchmark. Overall, we demonstrate that diverse modeling approaches can be ensembled together to gain meaningful improvement in binding affinity prediction. © 2023, CC BY-NC-SA.

关键词： Prediction models

Full-atom protein pocket design via iterative refinement 23

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Full-atom protein pocket design via iterative refinement

Proceedings of the 37th International Conference on Neural Information Processing Systems

作者： Zaixi Zhang Zepu Lu Zhongkai Hao Marinka Zitnik Qi Liu Anhui Province Key Lab of Big Data Analysis and Application School of Computer Science and Technology University of Science and Technology of China and State Key Laboratory of Cognitive Intelligence Hefei Anhui China and Harvard University Anhui Province Key Lab of Big Data Analysis and Application School of Computer Science and Technology University of Science and Technology of China and State Key Laboratory of Cognitive Intelligence Hefei Anhui China Dept. of Comp. Sci. and Tech. Institute for AI THBI Lab BNRist Center Tsinghua-Bosch Joint ML Center Tsinghua Harvard University

The design and optimization of functional proteins that bind specific ligand molecules is paramount in therapeutics and bio-engineering. A critical yet formidable task in this endeavor is the design of the protein pocket, which is the cavity region of the protein where the ligand binds. Current methods are plagued by inefficient generation, inadequate context modeling of the ligand molecule, and the inability to generate side-chain atoms. Here, we present the Full-Atom Iterative Refinement (FAIR) method, designed to address these challenges by facilitating the co-design of protein pocket sequences, specifically residue types, and their corresponding 3D structures. FAIR operates in two steps, proceeding in a coarse-to-fine manner (transitioning from protein backbone to atoms, including side chains) for a full-atom generation. In each iteration, all residue types and structures are simultaneously updated, a process termed full-shot refinement. In the initial stage, the residue types and backbone coordinates are refined using a hierarchical context encoder, complemented by two structure refinement modules that capture both inter-residue and pocket-ligand interactions. The subsequent stage delves deeper, modeling the side-chain atoms of the pockets and updating residue types to ensure sequence-structure congruence. Concurrently, the structure of the binding ligand is refined across iterations to accommodate its inherent flexibility. Comprehensive experiments show that FAIR surpasses existing methods in designing superior pocket sequences and structures, producing average improvement exceeding 10% in AAR and RMSD metrics.

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Learning superconductivity from ordered and disordered material structures 24

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Learning superconductivity from ordered and disordered mater...

Proceedings of the 38th International Conference on Neural Information Processing Systems

作者： Pin Chen Luoxuan Peng Rui Jiao Qing Mo Zhen Wang Wenbing Huang Yang Liu Yutong Lu National Supercomputer Center in Guangzhou School of Computer Science and Engineering Sun Yat-sen University Dept. of Comp. Sci. & Tech. Institute for AI BNRist Center Tsinghua University and Institute for AIR Tsinghua University Gaoling School of Artificial Intelligence Renmin University of China and Beijing Key Laboratory of Big Data Management and Analysis Methods Beijing China

ISBN: (纸本)9798331314385

Superconductivity is a fascinating phenomenon observed in certain materials under certain conditions. However, some critical aspects of it, such as the relationship between superconductivity and materials' chemical/structural features, still need to be understood. Recent successes of data-driven approaches in material science strongly inspire researchers to study this relationship with them, but a corresponding dataset is still lacking. Hence, we present a new dataset for data-driven approaches, namely SuperCon3D, containing both 3D crystal structures and experimental superconducting transition temperature (Tc) for the first time. Based on SuperCon3D, we propose two deep learning methods for designing high Tc superconductors. The first is SODNet, a novel equivariant graph attention model for screening known structures, which differs from existing models in incorporating both ordered and disordered geometric content. The second is a diffusion generative model DiffCSP-SC for creating new structures, which enables high Tc-targeted generation. Extensive experiments demonstrate that both our proposed dataset and models are advantageous for designing new high Tc superconducting candidates.

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Intelligent Facility Layout Planning for Emergency Department: A Multi-Agent System and Particle Swarm Optimization Approach

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Intelligent Facility Layout Planning for Emergency Departmen...

International Conference on Intelligent Systems: Theories and Applications (SITA)

作者： Khalil Bouramtane Said Kharraja Jamal Riffi Omar Elbeqqali Saïd Boujraf Laboratory of Signal and Industrial Process Analysis (LASPI) University of Saint-Etienne Roanne France Faculty of Science Dhar El Mahraz Laboratory of Computer Science Signals Automation and Cognitivism (LISAC) University Sidi Mohamed Ben Abdellah Fez Morocco Dept. Biophysics & Clinical MRI Methods Faculty of Medicine Clinical Neuroscience Laboratory University of Sidi Mohamed Ben Abdellah Fez Morocco

The efficient design of facility layouts for emergency services represents a major challenge due to the dynamic and complex nature of their operations. Within this paper, a fresh approach is introduced to tackle this particular challenge, drawing upon the collaborative power of multi-agent systems along with the principles of particle swarm optimization. Moreover, the utilization of simulation technique is incorporated to enrich the comprehension and depiction of the analyzed *** the proposed framework, agents representing different entities within the emergency department collaborate through a particle swarm optimization algorithm, working collectively towards an optimal facility layout. The main aim is to minimize travel costs and improve workflow efficiency. The results highlight the superiority of the multi-agent particle swarm optimization approach in the realization of intelligent layouts for emergency services. This research contributes to the advancement of facility planning by providing an innovative and efficient solution applicable to dynamic operational environments.

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Time series ordinal classification via shapelets

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Time series ordinal classification via shapelets

International Joint Conference on Neural Networks (IJCNN)

作者： David Guijo-Rubio Pedro A. Gutiérrez Anthony Bagnall César Hervás-Martínez Dept. of Computer Science and Numerical Analysis University of Córdoba Córdoba Spain School of Computing Sciences University of East Anglia Norwich United Kingdom

ISBN: (数字)9781728169262

ISBN: (纸本)9781728169279

Nominal time series classification has been widely developed over the last years. However, to the best of our knowledge, ordinal classification of time series is an unexplored field, and this paper proposes a first approach in the context of the shapelet transform (ST). For those time series dataset where there is a natural order between the labels and the number of classes is higher than 2, nominal classifiers are not capable of achieving the best results, because the models impose the same cost of misclassification to all the errors, regardless the difference between the predicted and the ground-truth. In this sense, we consider four different evaluation metrics to do so, three of them of an ordinal nature. The first one is the widely known Information Gain (IG), proved to be very competitive for ST methods, whereas the remaining three measures try to boost the order information by refining the quality measure. These three measures are a reformulation of the Fisher score, the Spearman's correlation coefficient (ρ), and finally, the Pearson's correlation coefficient (R 2 ). An empirical evaluation is carried out, considering 7 ordinal datasets from the UEA & UCR time series classification repository, 4 classifiers (2 of them of nominal nature, whereas the other 2 are of ordinal nature) and 2 performance measures (correct classification rate, CCR, and average mean absolute error, AMAE). The results show that, for both performance metrics, the ST quality metric based on R 2 is able to obtain the best results, specially for AMAE, for which the differences are statistically significant in favour of R 2 .

关键词： Time series analysis Shape measurement Time measurement Correlation computer science numerical analysis

Equivariant diffusion for crystal structure prediction 24

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Equivariant diffusion for crystal structure prediction

Proceedings of the 41st International Conference on Machine Learning

作者： Peijia Lin Pin Chen Rui Jiao Qing Mo Jianhuan Cen Wenbing Huang Yang Liu Dan Huang Yutong Lu School of Computer Science and Engineering Sun Yat-sen University Guangzhou China School of Computer Science and Engineering Sun Yat-sen University Guangzhou China and National Supercomputer Center in Guangzhou China Dept. of Comp. Sci. Tech. Institute for AI Tsinghua University Beijing China and Institute for AIR Tsinghua University Beijing China National Supercomputer Center in Guangzhou China Gaoling School of Artificial Intelligence Renmin University of China Beijing China and Beijing Key Laboratory of Big Data Management and Analysis Methods Beijing China

In addressing the challenge of Crystal Structure Prediction (CSP), symmetry-aware deep learning models, particularly diffusion models, have been extensively studied, which treat CSP as a conditional generation task. However, ensuring permutation, rotation, and periodic translation equivariance during diffusion process remains incompletely addressed. In this work, we propose EquiCSP, a novel equivariant diffusion-based generative model. We not only address the overlooked issue of lattice permutation equivariance in existing models, but also develop a unique noising algorithm that rigorously maintains periodic translation equivariance throughout both training and inference processes. Our experiments indicate that EquiCSP significantly surpasses existing models in terms of generating accurate structures and demonstrates faster convergence during the training process. Code is available at https://***/EmperorJia/EquiCSP.

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Full-Atom Protein Pocket Design via Iterative Refinement

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arXiv 2023年

作者： Zhang, Zaixi Lu, Zepu Hao, Zhongkai Zitnik, Marinka Liu, Qi Anhui Province Key Lab of Big Data Analysis and Application School of Computer Science and Technology University of Science and Technology of China China State Key Laboratory of Cognitive Intelligence Anhui Hefei China Dept. of Comp. Sci. and Tech. Institute for AI THBI Lab BNRist Center Tsinghua-Bosch Joint ML Center Tsinghua China Harvard University United States

The design of de novo functional proteins that bind specific ligand molecules is paramount in therapeutics and bio-engineering. A critical yet formidable task in this endeavor is the design of the protein pocket, which is the cavity region of the protein where the ligand binds. Current methods are plagued by inefficient generation, inadequate context modeling of the ligand molecule, and the inability to generate side-chain atoms. Here, we present the Full-Atom Iterative Refinement (FAIR) method, designed to address these challenges by facilitating the co-design of protein pocket sequences, specifically residue types, and their corresponding 3D structures. FAIR operates in two steps, proceeding in a coarse-to-fine manner (transitioning from protein backbone to atoms, including side chains) for a full-atom generation. In each iteration, all residue types and structures are simultaneously updated, a process termed full-shot refinement. In the initial stage, the residue types and backbone coordinates are refined using a hierarchical context encoder, complemented by two structure refinement modules that capture both inter-residue and pocket-ligand interactions. The subsequent stage delves deeper, modeling the side-chain atoms of the pockets and updating residue types to ensure sequence-structure congruence. Concurrently, the structure of the binding ligand is refined across iterations to accommodate its inherent flexibility. Comprehensive experiments show that FAIR surpasses existing methods in designing superior pocket sequences and structures, producing average improvement exceeding 10% in AAR and RMSD metrics. FAIR is available at https://***/zaixizhang/FAIR. © 2023, CC BY.

关键词： Atoms