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arXiv 2025年

作者： Tang, Sophia Zhang, Yinuo Tong, Alexander Chatterjee, Pranam Department of Biomedical Engineering Duke University United States Management and Technology Program University of Pennsylvania United States Center of Computational Biology Duke-NUS Medical School Singapore Mila Quebec AI Institute Canada Université de Montréal Canada Department of Computer Science Duke University United States Department of Biostatistics and Bioinformatics Duke University United States

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment. © 2025, CC BY-NC-ND.

关键词： Velocity distribution

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CHARACTERISTICS OF JUNCTIONS MADE BETWEEN PB AND BI2SR2CACU2O8+X

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IEEE TRANSACTIONS ON MAGNETICS 1991年第2期27卷 935-938页

作者： YANG, YF NORDMAN, JE Materials Science Program Department of Electrical and Computer Engineering University of Wisconsin Madison Madison WI USA

Investigations on the junctions made between Pb and polycrystalline Bi2Sr2CaCu2O8+x (BSCCO) are reported. The BSCCO surfaces were treated with number of methods including mechanically scraping, plasma sputtering, plasma oxidation, and Br etch before junctions were fabricated. The current-voltage characteristics and dynamic resistance (dV/dI) vs voltage have been measured at both 77K and 4.2K. We observed, among other features, a Pb gap structure similar to that seen in Pb/YBa2Cu3O7-delta junctions, a magnetic dependent supercurrent, an asymmetric I-V curve, and narrow resistance peaks. Properties of junctions prepared in different manners are compared. Both XPS and electrical studies indicated that Br etch is not suitable for the BiSrCaCuO system in spite of its successful application in YBa2Cu3O7-delta.

关键词： Plasma measurements Bismuth compounds Plasma applications Plasma properties Strontium Surface resistance Surface treatment Sputtering Oxidation Sputter etching

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Glaucoma identification with retinal fundus images using deep learning: Systematic review

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Informatics in Medicine Unlocked 2025年 56卷

作者： Meedeniya, Dulani Shyamalee, Thisara Lim, Gilbert Yogarajah, Pratheepan Department of Computer Science and Engineering University of Moratuwa Moratuwa 10400 Sri Lanka First-Year Division Faculty of Computing Sri Lanka Institute of Information Technology Malabe 10115 Sri Lanka SingHealth AI Health Program SingHealth Group Singapore 168582 Singapore School of Computing Engineering and Intelligent System Ulster University Londonderry BT48 7JL United Kingdom

Glaucoma is a leading cause of blindness, affecting millions of people worldwide. It is a chronic eye condition that damages the optic nerve and, if left untreated, can lead to vision loss and a decreased quality of life. Therefore, there is a need to explore practical and reliable mechanisms for glaucoma identification. This study systematically reviews deep-learning approaches for glaucoma identification using retinal fundus images from 2018 to 2024. Compared to existing survey studies, we cover the latest research, including several public retinal fundus image datasets, and focus on segmentation, classification based on convolutional neural networks and vision transformers, and explainability. The findings of this study, including comparisons of existing methods and key insights, will assist researchers and developers in identifying the most suitable techniques for glaucoma detection. © 2025 The Authors

关键词： Artificial intelligence Classification Deep learning Explainability Glaucoma Segmentation Trustworthiness

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Pan-cancer analysis of CDC7 in human tumors: Integrative multi-omics insights and discovery of novel marine-based inhibitors through machine learning and computational approaches

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computers in Biology and Medicine 2025年 190卷 110044-110044页

作者： Saif, Ahmed Islam, Md. Tarikul Raihan, Md. Obayed Yousefi, Niloofar Rahman, Md. Ajijur Faridi, Hafeez Hasan, Al Riyad Hossain, Mirza Mahfuj Saleem, Rasha Mohammed Albadrani, Ghadeer M. Al-Ghadi, Muath Q. Ahasan Setu, Md. Ali Kamel, Mohamed Abdel-Daim, Mohamed M. Aktaruzzaman, Md. Department of Pharmacy Faculty of Science University of Rajshahi Rajshahi6205 Bangladesh Department of Genetic Engineering and Biotechnology Faculty of Biological Science and Technology Jashore University of Science and Technology Jashore7408 Bangladesh Jashore7408 Bangladesh Department of Pharmaceutical Sciences College of Health Sciences and Pharmacy Chicago State University ChicagoIL United States Department of Industrial Engineering and Management Systems University of Central Florida USA OrlandoFL United States Department of Pharmacy Faculty of Biological Science and Technology Jashore University of Science and Technology Jashore7408 Bangladesh Department of Computer Science and Engineering Faculty of Engineering and Technology Jashore University of Science and Technology Jashore7408 Bangladesh Department of Laboratory Medicine Faculty of Applied Medical Sciences Al-Baha University Al-Baha65431 Saudi Arabia Department of Biology College of Science Princess Nourah bint Abdulrahman University 84428 Riyadh11671 Saudi Arabia Department of Zoology College of Science King Saud University P.O. Box 2455 Riyadh11451 Saudi Arabia Department of Microbiology Faculty of Biological Science and Technology Jashore University of Science and Technology Jashore7408 Bangladesh Department of Medicine and Infectious Diseases Faculty of Veterinary Medicine Cairo University Giza12211 Egypt Department of Pharmaceutical Sciences Pharmacy Program Batterjee Medical College P.O. Box 6231 Jeddah21442 Saudi Arabia Pharmacology Department Faculty of Veterinary Medicine Suez Canal University Ismailia41522 Egypt

Cancer remains a significant global health challenge, with the Cell Division Cycle 7 (CDC7) protein emerging as a potential therapeutic target due to its critical role in tumor proliferation, survival, and resistance. However, a comprehensive analysis of CDC7 across multiple cancers is lacking, and existing therapeutic options have come with limited clinical success. The aim of this is to integrate a comprehensive pan-cancer analysis of CDC7 with the identification of novel marine-derived inhibitors, bridging the understanding of CDC7's role as a prognostic biomarker and therapeutic target across diverse cancer types. In this study, we conducted a pan-cancer analysis of CDC7 across 33 tumor types using publicly available datasets to evaluate its expression, genetic alterations, immune interactions, survival, and prognostic significance. Additionally, a marine-derived compound library of 31,492 molecules was screened to identify potential CDC7 inhibitors using chemoinformatics and machine learning. The top candidates underwent rigorous evaluations, including molecular docking, pharmacokinetics, toxicity, Density Functional Theory (DFT) calculations, and Molecular Dynamics (MD) simulations. The findings revealed that CDC7 is overexpressed in several cancers and is associated with poor survival outcomes and unfavorable prognosis. Enrichment analysis linked CDC7 to critical DNA replication pathways, while its role in modulating tumor-immune interactions highlighted its potential as a target for immunotherapy. Among all tested compounds, Tetrahydroaltersolanol D (CMNPD21999) exhibited the strongest binding affinity and stability, along with better drug-likeness and zero toxicity. These attributes highlight its potential as a promising drug candidate for CDC7 inhibition and future cancer treatment development. Furthermore, additional in vitro and in vivo studies are required to confirm the effectiveness of this drug candidate against the CDC7 protein. © 2025

关键词： Gene expression

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Testing the Inference Accuracy of Accelerator-Friendly Approximate Phylogeny Tracking

Testing the Inference Accuracy of Accelerator-Friendly Appro...

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Computational Intelligence in Artificial Life and Cooperative Intelligent Systems (ALIFE-CIS), IEEE Symposium on

作者： Matthew Andres Moreno Anika Ranjan Emily Dolson Luis Zaman Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and AI in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

ISBN: (数字)9798331508371

ISBN: (纸本)9798331508388

computer simulations are an important tool for studying the mechanics of biological evolution. In particular, agent-based approaches provide an opportunity to collect high-quality records of ancestry relationships. Such phylogenies can provide insight into evolutionary dynamics within these simulations. Previous work generally tracks lineages directly, yielding an exact phylogenetic record of evolutionary history. However, challenges exist in scaling direct ancestrytracking approaches to highly-distributed, many-processor evolution in silico. An alternative approach is to estimate phylogenetic history via noncoding annotations on digital genomes, akin to how bioinformaticians build phylogenies by assessing genetic similarities between organisms. Recent work has extended this “hereditary stratigraphy” approach to support powerful hardware accelerator platforms, such as the Cerebras Wafer-Scale Engine. Although these second-generation “surface”-based hereditary stratigraphy algorithms have demonstrated order-ofmagnitude speedups over first-generation “column”-based algorithms, it remains unknown how they impact the accuracy of reconstructed phylogenies. To address this question, we assessed reconstruction accuracy under alternative configurations across a matrix of evolutionary conditions varying in selection pressure, spatial structure, and ecological dynamics. Encouragingly, we find that the second-generation approaches provide higher reconstruction quality across most surveyed conditions.

关键词： Surface reconstruction Accuracy Annotations Heuristic algorithms Computational modeling Biological system modeling Stratigraphy Phylogeny History Bars

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Testing the Inference Accuracy of Accelerator-Friendly Approximate Phylogeny Tracking

Testing the Inference Accuracy of Accelerator-Friendly Appro...

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2025 IEEE Symposium on Computational Intelligence in Artificial Life and Cooperative Intelligent Systems, ALIFE-CIS 2025

作者： Moreno, Matthew Andres Ranjan, Anika Dolson, Emily Zaman, Luis University of Michigan Department of Ecology and Evolutionary Biology Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and Ai in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Michigan State University Department of Computer Science and Engineering East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

ISBN: (纸本)9798331508371

computer simulations are an important tool for studying the mechanics of biological evolution. In particular, agent-based approaches provide an opportunity to collect high-quality records of ancestry relationships. Such phylogenies can provide insight into evolutionary dynamics within these simulations. Previous work generally tracks lineages directly, yielding an exact phylogenetic record of evolutionary history. However, challenges exist in scaling direct ancestrytracking approaches to highly-distributed, many-processor evolution in silico. An alternative approach is to estimate phylogenetic history via noncoding annotations on digital genomes, akin to how bioinformaticians build phylogenies by assessing genetic similarities between organisms. Recent work has extended this 'hereditary stratigraphy' approach to support powerful hardware accelerator platforms, such as the Cerebras Wafer-Scale Engine. Although these second-generation 'surface'-based hereditary stratigraphy algorithms have demonstrated order-ofmagnitude speedups over first-generation 'column'-based algorithms, it remains unknown how they impact the accuracy of reconstructed phylogenies. To address this question, we assessed reconstruction accuracy under alternative configurations across a matrix of evolutionary conditions varying in selection pressure, spatial structure, and ecological dynamics. Encouragingly, we find that the second-generation approaches provide higher reconstruction quality across most surveyed conditions. © 2025 IEEE.

关键词： Biostratigraphy

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Monitoring blood pressure through a single hybrid hemodynamic signal with a flexible optoelectronic patch

Device

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Device 2025年

作者： Zhong, Yizhou Zhang, Yongcao Pu, Jing Wustoni, Shofarul Uribe, Johana Lopez-Larrea, Naroa Marks, Adam McCulloch, Iain Mecerreyes, David Baran, Derya Inal, Sahika Organic Bioelectronics Laboratory Biological and Environmental Science and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Materials Science and Engineering Program (MSE) Physical Sciences and Engineering Division (PSE) KAUST Thuwal 23955-6900 Saudi Arabia POLYMAT University of the Basque Country UPV/EHU Avenida Tolosa 72 Guipuzcoa Donostia-San Sebastian 20018 Spain Department of Chemistry University of Oxford Oxford OX1 3TF United Kingdom Andlinger Center for Energy and the Environment and Department of Electrical and Computer Engineering Princeton University Princeton 08544 NJ United States IKERBASQUE Basque Foundation for Science Plaza Euskadi 5 Bilbao 48009 Spain

Hemodynamics, the study of blood flow and circulatory forces, is fundamental for assessing cardiovascular health, disease states, and therapeutic outcomes. Here, we introduce a skin-conformable organic optoelectronic thin-film patch (ePatch) designed to simultaneously capture electrocardiography (ECG) and photoplethysmography (PPG) signals as a single hybrid signal, named the electrocardio-photoplethysmogram (EC-PPG). The ePatch integrates an organic electrochemical transistor (OECT), an organic photodiode, surface-mounted light-emitting diodes, and electrochemical electrodes on a flexible, skin-conforming substrate. By training deep learning models on the hybrid EC-PPG data, we achieved accurate arterial blood pressure estimations, with mean errors of just 1.69 mmHg for systolic and 0.89 mmHg for diastolic blood pressure, outperforming traditional predictions that rely on individual physiological signals as inputs. Our findings underscore the potential of EC-PPG as a compound hemodynamic signal for AI-driven vital sign monitoring and integrated, solution-processable soft electronics for clinical and point-of-care applications. © 2025 The Authors

关键词： DTI-3: Develop electrocardiography electrophysiology flexible electronics OECT OPD organic electrochemical transistor photoplethysmography wearable electronics

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Accelerating adoption of species-agnostic plant sensors for precision farming

Nature Reviews Electrical Engineering

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Nature Reviews Electrical engineering 2025年 58-70页

作者： Abdullah Bukhamsin Khaled Nabil Salama Jürgen Kosel Ikram Blilou Bioengineering Program Biological and Environmental Science and Engineering (BESE) Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia Center of Excellence — Sustainable Food Security (SFS) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia Electrical and Computer Engineering Program Computer Electrical and Mathematical Sciences and Engineering (CEMSE) Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia Sensor Systems Division Silicon Austria Labs Villach Austria Plant Science Program Biological and Environmental Science and Engineering (BESE) Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia

Precision farming is an optimized management farming scheme that seeks to link the real-time needs of crops with the nutrients to be administered. Sensing platforms that can monitor the physiological status of crops in situ are key to enabling timely and localized interventions. However, the underdevelopment of plant sensing strategies limits the potential of precision farming. In this Review, we discuss the challenges and advancements in phyto-monitoring, focusing on strategies that are applicable to a wide range of plant species and suitable for field deployment. We explore species-agnostic sensors, including optical and electrochemical sensors, whose operation is based on principles that are widely applicable to all plant species. These platforms enable real-time monitoring of the physiological state of crops by assessing key biomarkers, such as plant hormones, and metabolites such as salicylic acid and reactive oxygen species. Evaluating these systems, we conclude that an integrative sensing approach is necessary to compensate for the limitations of the individual methods and can provide a holistic view of crop health. Cost-effective species-agnostic sensors are thus needed to provide information that can be used to minimize the resource footprint of farming and meet the growing global demand.

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Design and Performance Evaluation of Sequence Partition Algorithms

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Journal of computer science & Technology 2008年第5期23卷 711-718页

作者：杨兵陈菁吕恩月郑斯清 Cisco Systems 2200 East President George Bush Highway Telecom. Engineering Program University of Texas at Dallas Department of Mathematics and Computer Science Salisbury University Department of Computer Science University of Texas at Dallas

Tradeoffs between time complexities and solution optimalities are important when selecting algorithms for an NP-hard problem in different applications. Also, the distinction between theoretical upper bound and actual solution optimality for realistic instances of an NP-hard problem is a factor in selecting algorithms in practice. We consider the problem of partitioning a sequence of n distinct numbers into minimum number of monotone （increasing or decreasing） subsequences. This problem is NP-hard and the number of monotone subsequences can reach [√2n＋1/1-1/2]in the worst case. We introduce a new algorithm, the modified version of the Yehuda-Fogel algorithm, that computes a solution of no more than [√2n＋1/1-1/2]monotone subsequences in O（n^1.5） time. Then we perform a comparative experimental study on three algorithms, a known approximation algorithm of approximation ratio 1.71 and time complexity O（n^3）, a known greedy algorithm of time complexity O（n^1.5 log n）, and our new modified Yehuda-Fogel algorithm. Our results show that the solutions computed by the greedy algorithm and the modified Yehuda-Fogel algorithm are close to that computed by the approximation algorithm even though the theoretical worst-case error bounds of these two algorithms are not proved to be within a constant time of the optimal solution. Our study indicates that for practical use the greedy algorithm and the modified Yehuda-Fogel algorithm can be good choices if the running time is a major concern.

关键词： monotone subsequence permutation algorithm NP-complete approximation complexity

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Glacier runoff impacts the stoichiometry of riverine nutrient export from coastal Alaskan catchments

Communications Earth and Environment

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Communications Earth and Environment 2025年第1期6.0卷 1-9页

作者： Fellman, Jason B. Hood, Eran Munk, Lee Ann Jenckes, Jordan Whitney, Emily J. Klein, Eric S. Program on the Environment and Alaska Coastal Rainforest Center University of Alaska Southeast Juneau AK United States Geophysical Institute University of Alaska Fairbanks Fairbanks AK United States Department of Computer Science and Engineering University of Alaska Anchorage Anchorage AK United States Department of Geological Sciences University of Alaska Anchorage Anchorage AK United States

Understanding the impacts of glacier change on riverine ecosystems is limited by a lack of multi-year studies in glacierized mountain catchments quantifying the magnitude and stoichiometry of riverine biogeochemical yields. Here we evaluate riverine concentration-discharge relationships using the power function between daily runoff and element yields and stoichiometry across 10 catchments of varying glacial coverage within two climatically distinct regions in the Gulf of Alaska. Our multi-year study showed that biogeochemical stoichiometry and concentration-discharge relationships for dissolved carbon, nitrogen, and phosphorus varied significantly with catchment glacier coverage across both regions. This stoichiometric variability could drive regional differences in proglacial riverine food webs given that high trophic levels in low productivity rivers are generally driven by bottom-up controls. The coherence of our findings across the Gulf of Alaska suggests that observed patterns in concentration-discharge relationships are likely globally generalizable to catchments in which discharge is dominated by glacier ice and/or snowmelt. © The Author(s) 2025.

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