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Probabilistic genotype-phenotype maps reveal mutational robustness of RNA folding, spin glasses, and quantum circuits

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Physical Review Research 2025年第1期7卷 013118-013118页

作者： Anna Sappington Vaibhav Mohanty Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Harvard-MIT Program in Health Sciences and Technology Harvard Medical School Boston Massachusetts 02115 USA and Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Harvard/MIT MD-PhD Program Harvard Medical School Boston Massachusetts 02115 USA and Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Department of Chemistry and Chemical Biology Harvard University Cambridge Massachusetts 02138 USA

Recent studies of genotype-phenotype maps have reported universally enhanced phenotypic robustness to genotype mutations, a feature essential to evolution. Virtually all of these studies make a simplifying assumption that each genotype—represented as a sequence—maps deterministically to a single phenotype, such as a discrete structure. Here we introduce probabilistic genotype-phenotype (PrGP) maps, where each genotype maps to a vector of phenotype probabilities, as a more realistic and universal language for investigating robustness in a variety of physical, biological, and computational systems. We study three model systems to show that PrGP maps offer a generalized framework which can handle uncertainty emerging from various physical sources: (1) thermal fluctuation in RNA folding, (2) external field disorder in the spin-glass ground state search problem, and (3) superposition and entanglement in quantum circuits, which are realized experimentally on IBM quantum computers. In all three cases, we observe a biphasic robustness scaling which is enhanced relative to random expectation for more frequent phenotypes and approaches random expectation for less frequent phenotypes. We derive an analytical theory for the behavior of PrGP robustness, and we demonstrate that the theory is highly predictive of empirical robustness.

关键词： Quantum computers

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Correction: Materials laboratories of the future for alloys, amorphous, and composite materials (MRS Bulletin, (2025), 50, 2, (190-207), 10.1557/s43577-024-00846-y)

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MRS Bulletin 2025年 1-2页

作者： Banerjee, Sarbajit Meng, Y. Shirley Minor, Andrew M. Zhang, Minghao Zaluzec, Nestor J. Chan, Maria K.Y. Seidler, Gerald McComb, David W. Agar, Joshua Mukherjee, Partha P. Melot, Brent Chapman, Karena Guiton, Beth S. Klie, Robert F. McCue, Ian D. Voyles, Paul M. Robertson, Ian Li, Ling Chi, Miaofang Destino, Joel F. Devaraj, Arun Marquis, Emmanuelle A. Segre, Carlo U. Liu, Huinan H. Yang, Judith C. Momeni, Kasra Misra, Amit Abdolrahim, Niaz Medvedeva, Julia E. Cai, Wenjun Sehirlioglu, Alp Dizbay-Onat, Melike Mehta, Apurva Graham-Brady, Lori Maruyama, Benji Rajan, Krishna Warner, Jamie H. Taheri, Mitra L. Kalinin, Sergei V. Reeja-Jayan, B. Schwarz, Udo D. Simon, Sindee L. Brown, Craig M. Department of Chemistry and Department of Materials Science & Engineering Texas A & M University College Station United States Pritzker School of Molecular Engineering The University of Chicago Chicago United States Department of Materials Science & Engineering University of California Berkeley Berkeley United States National Center for Electron Microscopy Molecular Foundry Lawrence Berkeley National Laboratory Berkeley United States Center for Nanoscale Materials Argonne National Laboratory Lemont United States Department of Physics University of Washington Seattle United States Department of Materials Science & Engineering The Ohio State University Columbus United States Department of Mechanical Engineering and Mechanics Drexel University Philadelphia United States School of Mechanical Engineering Purdue University West Lafayette United States Department of Chemistry University of Southern California Los Angeles United States Department of Chemistry Stony Brook University The State University of New York Stony Brook United States Department of Chemistry University of Kentucky Lexington United States Department of Physics University of Illinois at Chicago Chicago United States Department of Materials Science & Engineering Northwestern University Evanston Bangladesh Department of Materials Science & Engineering University of Wisconsin–Madison Madison United States Department of Materials Science and Engineering University of Pennsylvania Philadelphia United States Department of Mechanical Engineering and Materials Science Duke University Durham United States Department of Chemistry Creighton University Omaha United States Physical and Computational Sciences Directorate Pacific Northwest National Laboratory Richland United States Department of Materials Science & Engineering University of Michigan–Ann Arbor Ann Arbor United States Department of Physics Illinois Institute of Technology Chicago United States Department of Bioengineering and the Mater

This article was updated to correct Minghao Zhang’s affiliation from "Pritzker School of Molecular engineering, The University of Chicago, Chicago, USA" to "Pritzker School of Molecular engineering, The University of Chicago, Chicago, USA;Argonne National Laboratory, Lemont, USA." Argonne National Laboratory was left off the original publication. © The Author(s) 2025.

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Molecular architecture of mammalian pyruvate dehydrogenase complex

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Protein & Cell 2025年第1期16卷 72-78页

作者： Maofei Chen Yutong Song Sensen Zhang Yitang Zhang Xudong Chen Minghui Zhang Meng Han Xin Gao Sai Li Maojun Yang Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological StructureSchool of Life SciencesTsinghua UniversityBeijing 100084China Ministry of Education Key Laboratory of Protein Science Tsinghua UniversityBeijing 100084China State Key Laboratory of Membrane Biology Tsinghua UniversityBeijing 100084China Department of Biochemistry and Molecular Biology School of Basic Medical SciencesShenzhen University Health Science CenterShenzhen 518060China Protein Research Technology Center Protein Chemistry and Omics PlatformSchool of Life SciencesTsinghua UniversityBeijing 100084China Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Kingdom of Saudi Arabia Computational Bioscience Research Center King Abdullah University of Science and TechnologyThuwal 23955-6900Kingdom of Saudi Arabia Cryo-EM Facility Center Southern University of Science and TechnologyShenzhen 518055China Beijing Life Science Academy Beijing 102209China

Dear Editor,Pyruvate dehydrogenase complex(PDHc) is a large multienzyme assembly(Mr = 4–10 million Daltons) consisting of three essential components: pyruvate dehydrogenase(E1p), dihydrolipoyl transacetylase(E2p), and dihydrolipoyl dehydrogenase(E3). These three enzymes perform distinct functions sequentially to catalyze the oxidative decarboxylation of pyruvate with formation of nicotinamide adenine dinucleotide(NADH) and acetyl-coenzyme A(Patel and Roche, 1990).

关键词： sequentially oxidative Dalton

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A Finite Difference Method for a Normalized Time-Fractional Black–Scholes Equation

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International Journal of Applied and Computational Mathematics 2025年第3期11卷 1-17页

作者： Nam, Yunjae Wang, Jian Lee, Chaeyoung Choi, Yongho Bang, Minjoon Li, Zhengang Kim, Junseok Program in Actuarial Science and Financial Engineering Korea University Seoul 02841 South Korea School of Mathematics and Statistics Nanjing University of Information Science and Technology Nanjing 210044 China Department of Mathematics Kyonggi University Suwon 16227 South Korea Computer and Information Engineering Daegu University Gyeongsan 38453 South Korea Department of Mathematics Korea University Seoul 02841 South Korea

In this article, we propose a normalized time-fractional Black–Scholes (TFBS) equation. The proposed model uses a normalized time-fractional derivative which has a distinctive feature wherein a weight function possesses the property that its integral with respect to time is always equal to one. This feature ensures a well-balanced integration over time and provides a fair comparison between different fractional orders. An implicit finite difference method is used for the numerical solution of the TFBS equation. We perform several standard numerical tests to examine the effect of the fractional parameter on the option pricing. These experiments are designed to investigate how variations in the fractional parameter influence pricing outcomes and provide valuable insights into the model’s behavior under different conditions. The computational results demonstrate the model’s potential for capturing more intricate market dynamics, which makes the proposed model a promising tool for financial analysis. In the appendix, we provide a computer program that implements the numerical methods discussed in the paper for interested readers. © The Author(s), under exclusive licence to Springer Nature India Private Limited 2025.

关键词： Implicit finite difference method Memory effect Normalized time-fractional Black–Scholes equation

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Reachability Analysis of Nonlinear Discrete-Time Systems Using Polyhedral Relaxations and Constrained Zonotopes

arXiv

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arXiv 2025年

作者： Rego, Brenner S. Raffo, Guilherme V. Terra, Marco H. Scott, Joseph K. Department of Chemical and Biomolecular Engineering Georgia Institute of Technology 311 Ferst Dr. AtlantaGA30318 United States Department of Electrical and Computer Engineering University of São Paulo SP São Carlos13566-590 Brazil Department of Electronics Engineering the Graduate Program in Electrical Engineering Federal University of Minas Gerais MG Belo Horizonte31270-901 Brazil

This paper presents a novel algorithm for reachability analysis of nonlinear discrete-time systems. The proposed method combines constrained zonotopes (CZs) with polyhedral relaxations of factorable representations of nonlinear functions to propagate CZs through nonlinear functions, which is normally done using conservative linearization techniques. The new propagation method provides better approximations than those resulting from linearization procedures, leading to significant improvements in the computation of reachable sets in comparison to other CZ methods from the literature. Numerical examples highlight the advantages of the proposed algorithm. © 2025, CC BY-NC-ND.

关键词： Numerical methods

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AVTENet: A Human-Cognition-Inspired Audio-Visual Transformer-Based Ensemble Network for Video Deepfake Detection

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IEEE Transactions on Cognitive and Developmental Systems 2025年

作者： Hashmi, Ammarah Shahzad, Sahibzada Adil Lin, Chia-Wen Tsao, Yu Wang, Hsin-Min Taiwan International Graduate Program Academia Sinica Social Networks and Human-Centered Computing Program Taipei11529 Taiwan National Tsing Hua University Institute of Information Systems and Applications Hsinchu30013 Taiwan National Chengchi University Department of Computer Science Taipei11605 Taiwan National Tsing Hua University Department of Electrical Engineering Institute of Communications Engineering Hsinchu300044 Taiwan Academia Sinica Research Center for Information Technology Innovation Taipei11529 Taiwan

The recent proliferation of hyper-realistic deepfake videos has drawn attention to the threat of audio and visual forgeries. Most previous studies on detecting artificial intelligence-generated fake videos only utilize visual modality or audio modality. While some methods exploit audio and visual modalities to detect forged videos, they have not been comprehensively evaluated on multimodal datasets of deepfake videos involving acoustic and visual manipulations, and are mostly based on convolutional neural networks with low detection accuracy. Considering that human cognition instinctively integrates multisensory information including audio and visual cues to perceive and interpret content and the success of transformer in various fields, this study introduces the audio-visual transformer-based ensemble network (AVTENet). This innovative framework tackles the complexities of deepfake technology by integrating both acoustic and visual manipulations to enhance the accuracy of video forgery detection. Specifically, the proposed model integrates several purely transformer-based variants that capture video, audio, and audio-visual salient cues to reach a consensus in prediction. For evaluation, we use the recently released benchmark multimodal audio-video FakeAVCeleb dataset. For a detailed analysis, we evaluate AVTENet, its variants, and several existing methods on multiple test sets of the FakeAVCeleb dataset. Experimental results show that the proposed model outperforms all existing methods and achieves state-of-the-art performance on Testset-I and Testset-II of the FakeAVCeleb dataset. We also compare AVTENet against humans in detecting video forgery. The results show that AVTENet significantly outperforms humans. © 2016 IEEE.

关键词： audio-visual AVTENet Deepfake detection

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TextAI 3.0 (Multimodal): multimodal sentiment analysis using attention-enabled ensemble-based deep learning in hyperbolic space

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International Journal of Information technology (Singapore) 2025年 1-16页

作者： Singh, Jaskaran Sanga, Prabhav Khanna, Narendra N. Laird, John R. Singh, Inder M. Kalra, Mannudeep K. Mantella, Laura E. Johri, Amer M. Faa, Gavino Tiwari, Ekta Singh, Rajesh Abbas, Mohamed Saba, Luca Suri, Jasjit S. Stroke Monitoring and Diagnostic Division AtheroPoint™ Roseville 95661 CA United States Bharati Vidyapeeth’s College of Engineering New Delhi India Department of Cardiology Indraprastha APOLLO Hospitals New Delhi 110001 India Department of Neurology and Stroke Program University of Maryland School of Medicine Baltimore United States Department of Radiology Harvard Medical School Boston 02115 MA United States Department of Biomedical and Molecular Sciences Queen’s University Kingston ON Canada Division of Cardiology Department of Medicine Queen’s University Kingston ON Canada Department of Pathology University of Cagliari Cagliari Italy Department of Computer Science Visvesvaraya National Institute of Technology (VNIT) Nagpur 440010 India Department of Research and Innovation Uttaranchal Institute of Technology Uttaranchal University Dehradun 248007 India Central Labs King Khalid University P.O. Box 960 AlQura’a Abha Saudi Arabia Electrical Engineering Department College of Engineering King Khalid University Abha 61421 Saudi Arabia Department of Neurology University of Cagliari Cagliari Italy Department of ECE Idaho State University Pocatello 83209 ID United States Department of CE Graphic Era Deemed to Be University Dehradun 248002 India University Center for Research and Development Chandigarh University Mohali India Symbiosis Institute of Technology Symbiosis International (Deemed University) Nagpur Campus Pune India Department of Innovation Global Biomedical Technologies Inc. Roseville 95661 CA United States

The rising prevalence of depression presents a significant global health challenge, underscoring the need for effective early detection through sentiment analysis. Traditional multimodal sentiment analysis methods, which rely on Euclidean space for data representation, often fail to capture the complex hierarchical relationships and non-linear structures inherent in multimodal data. To address this limitation, we propose a novel multimodal architecture that operates in hyperbolic space and incorporates attention-based ensemble learning to enhance feature representation and model performance. We developed and evaluated ten AI models—five utilizing Euclidean space and five leveraging hyperbolic space—on the Spoken Language Understanding Evaluation (SLUE) benchmark dataset. The models were assessed using cross-validation techniques to ensure robustness, and statistical analyses were conducted to validate the findings. Our results indicate that hyperbolic-based multimodal models achieve a 2.32% improvement in accuracy compared to their Euclidean counterparts, while the integration of self-attention mechanisms further contributes an average accuracy gain of 0.96%. Additionally, we observed a 3.76% decline in performance when reducing the training-to-test data ratio from 90:10 to 50:50, highlighting the importance of data distribution in model training. These findings confirm that attention-enhanced multimodal models in hyperbolic space offer superior representations for sentiment analysis. © Bharati Vidyapeeth's Institute of computer Applications and Management 2025.

关键词： Attention-enabled Deep learning Euclidean space Hyperbolic space Multimodal Sentiment analysis

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Perovskite/Silicon Tandem Photovoltaics: Long-Term Stability through Interface engineering

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Energy & Fuels 2025年第22期39卷 10134-10149页

作者： Ahmed A. Said Xiaole Li Esma Ugur Furkan H. Isikgor Jiang Liu Randi Azmi Michele De Bastiani Erkan Aydin Shanshan Zhang Anand S. Subbiah Thomas G. Allen Gilles Lubineau Iain McCulloch Stefaan De Wolf Center for Renewable Energy and Storage Technologies (CREST) Physical Sciences and Engineering Division (PSE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Mechanical Engineering Program Physical Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Kingdom of Saudi Arabia Department of Chemistry University of Oxford Oxford OX1 2JD United Kingdom；Andlinger Center for Energy and the Environment and Department of Electrical and Computer Engineering Princeton University Princeton New Jersey 08544 United States

Perovskite solar cells (PSCs) have experienced a rapid increase in power conversion efficiency (PCE) over the past decade, positioning them as strong candidates for next-generation commercial photovoltaics (PVs). Their tunable bandgap makes them ideal for tandem configurations, especially when coupled with crystalline silicon (Si) bottom cells; this combination offers the potential to exceed the PCE limits of single-junction devices and is arguably essential for successful market entry of perovskite technologies. However, commercialization of perovskite/Si tandems also demands enhanced durability and reliable integration into PV modules, withstanding long-term outdoor exposure. Besides light, temperature, and voltage bias stress, difficulties to overcome involve the mechanical stability and performance of the interfaces within tandem devices, which may degrade over time under real-world operating conditions. This review explores the critical role of interface engineering in addressing these challenges, reviewing the latest advancements in interface materials, encapsulation strategies, and novel integration techniques. By identification of the critical issues and adequate solutions, this paper provides a vision for the future of perovskite/Si tandem solar cells, emphasizing the importance of advanced manufacturing techniques and interdisciplinary research but also policy support.

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Dynamics of COVID-19 Misinformation: An Analysis of Conspiracy Theories, Fake Remedies, and False Reports

arXiv

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arXiv 2025年

作者： Thakur, Nirmalya Shao, Mingchen Knieling, Victoria Su, Vanessa Bian, Andrew Jeong, Hongseok Department of Electrical Engineering and Computer Science South Dakota School of Mines and Technology Rapid CitySD57701 United States Department of Computer Science Emory University AtlantaGA30322 United States Program in Linguistics Emory University AtlantaGA30322 United States Goizueta Business School Emory University AtlantaGA30322 United States

This paper makes four scientific contributions to the area of misinformation detection and analysis on digital platforms, with a specific focus on investigating how conspiracy theories, fake remedies, and false reports emerge, propagate, and shape public perceptions in the context of COVID-19. A dataset of 5,614 posts on the internet that contained misinformation about COVID-19 was used for this study. These posts were published in 2020 on 427 online sources (such as social media platforms, news channels, and online blogs) from 193 countries and in 49 languages. First, this paper presents a structured, three-tier analytical framework that investigates how multiple motives - including fear, politics, and profit - can lead to a misleading claim. Second, it emphasizes the importance of narrative structures, systematically identifying and quantifying the thematic elements that drive conspiracy theories, fake remedies, and false reports. Third, it presents a comprehensive analysis of different sources of misinformation, highlighting the varied roles played by individuals, state-based organizations, media outlets, and other sources. Finally, it discusses multiple potential implications of these findings for public policy and health communication, illustrating how insights gained from motive, narrative, and source analyses can guide more targeted interventions in the context of misinformation detection on digital platforms. © 2025, CC BY.

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Transfer Learning for Keypoint Detection in Low-Resolution Thermal TUG Test Images

arXiv

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arXiv 2025年

作者： Chen, Wei-Lun Hsieh, Chia-Yeh Kao, Yu-Hsiang Liu, Kai-Chun Peng, Sheng-Yu Tsao, Yu Research Center for Information Technology Innovation Academic Sinica Taiwan Graduate Institute of Electrical Engineering National Taiwan University Taiwan Bachelor’s Program in Medical Informatics and Innovative Applications Fu Jen Catholic University Taiwan Department of Electrical Engineering National Taiwan University Taiwan College of Information and Computer Sciences University of Massachusetts AmherstMA01003 United States Department of Electrical Engineering National Taiwan University of Science of Technology Taiwan

This study presents a novel approach to human keypoint detection in low-resolution thermal images using transfer learning techniques. We introduce the first application of the Timed Up and Go (TUG) test in thermal image computer vision, establishing a new paradigm for mobility assessment. Our method leverages a MobileNetV3-Small encoder and a ViTPose decoder, trained using a composite loss function that balances latent representation alignment and heatmap accuracy. The model was evaluated using the Object Keypoint Similarity (OKS) metric from the COCO Keypoint Detection Challenge. The proposed model achieves better performance with AP, AP50, and AP75 scores of 0.861, 0.942, and 0.887 respectively, outperforming traditional supervised learning approaches like Mask R-CNN and ViTPose-Base. Moreover, our model demonstrates superior computational efficiency in terms of parameter count and FLOPS. This research lays a solid foundation for future clinical applications of thermal imaging in mobility assessment and rehabilitation monitoring. Copyright © 2025, The Authors. All rights reserved.

关键词： Thermography (imaging)

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