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arXiv 2024年

作者： Zhou, Peng Wang, Jianmin Li, Chunyan Wang, Zixu Liu, Yiping Sun, Siqi Lin, Jianxin Wei, Leyi Cai, Xibao Lai, Houtim Liu, Wei Wang, Longyue Liu, Yuansheng Zeng, Xiangxiang College of Information Science and Engineering Hunan University Changsha China The Interdisciplinary Graduate Program in Integrative Biotechnology Yonsei University Incheon21983 Korea Republic of School of Informatics Yunnan Normal University Kunming650500 China Department of Computer Science University of Tsukuba Tsukuba3058577 Japan Research Institute of Intelligent Complex Systems Fudan University Shanghai200433 China Shanghai AI Laboratory Shanghai200232 China Centre for Artificial Intelligence driven Drug Discovery Faculty of Applied Science Macao Polytechnic University China School of Informatics Xiamen University Xiamen China Tencent AI Lab China

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science. Copyright © 2024, The Authors. All rights reserved.

关键词： Students

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The effect of stereochemical constraints on the radius of gyration of folded proteins

arXiv

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arXiv 2025年

作者： Logan, Jack A. Sumner, Jacob Grigas, Alex T. Shattuck, Mark D. O'Hern, Corey S. Department of Mechanical Engineering Yale University New HavenCT06520 United States Graduate Program in Computational Biology & Biomedical Informatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Benjamin Levich Institute and Physics Department The City College of New York New YorkNY10031 United States Department of Applied Physics Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States

Proteins are composed of linear chains of amino acids that fold into complex three-dimensional structures. A general feature of folded proteins is that they are compact with a radius of gyration Rg(N) ∼ Nν that obeys power-law scaling with the number of amino acids N in each protein and ν ∼ 1/3. In this study, we investigate the internal scaling of the radius of gyration Rg(n) versus the chemical separation n between amino acids for all subchains of length n. We show that for globular proteins Rg(n) ∼ nν1,2 with a larger exponent ν1 > 1/3 for small n and a smaller exponent ν2 g(N) ∝ Nν. To describe this scaling behavior for Rg(n), we carry out folding simulations for a series of coarse-grained models for proteins beginning with the freely-jointed and freely-rotating chain models composed of spherical monomers and varying degrees of stereochemical constraints. We show that a minimal model, which coarse-grains amino acids into a single spherical backbone atom and one variable-sized spherical side-chain atom, and enforces bend- and dihedral-angle constraints, can recapitulate Rg(n) for x-ray crystal structures of globular proteins. In addition, this model predicts the correct average packing fraction and size of the hydrophobic core, which are two key physical features that can be used to distinguish between computational 'decoys' and correctly folded proteins in protein design applications. © 2025, CC BY.

关键词： Spheres

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Road-Width-Aware Network Optimisation for Bike Lane Planning

arXiv

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arXiv 2025年

作者： Basilone, Riccardo Bruno, Matteo Melo, Hygor Piaget Monteiro Avalle, Michele Loreto, Vittorio Sapienza Univ. of Rome Physics Dept Piazzale A. Moro 2 Rome00185 Italy Sony Computer Science Laboratories - Rome Joint Initiative CREF-SONY Centro Ricerche Enrico Fermi Via Panisperna 89/A Rome00184 Italy Via Panisperna 89/A Rome00184 Italy Postgraduate Program in Applied Informatics University of Fortaleza Ceará Fortaleza60811-905 Brazil Complexity Science Hub Josefstädter Strasse 39 ViennaA 1080 Austria

Active mobility is becoming an essential component of the green transition in modern cities. However, the challenge of designing an efficient network of protected bike lanes without disrupting existing road networks for motorised vehicles remains unsolved. This paper focuses on the specific case of Milan, using a network approach that considers street widths to optimise the placement of dedicated bike lanes at the edges of the network. Unlike other network approaches in this field, our method considers the actual shapes of the streets, which introduces a realistic aspect lacking in current studies. We used these data to simulate cycling networks that maximise connectivity while minimising the impact of bike lane placement on the drivable network. Our mixed simulation strategies optimise for edge betweenness and width. Furthermore, we quantify the impact of dedicated bike lane infrastructure on the existing road network, demonstrating that it is feasible to create highly effective cycling networks with minimal disruption caused by lane width reductions. This paper illustrates how realistic cycling lanes can be simulated using road width data and discusses the challenges and benefits of moving beyond one-dimensional road data in network studies. Copyright © 2025, The Authors. All rights reserved.

关键词： Bicycles

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ReViT: A Hybrid Approach for BCLC Staging of Hepatocellular Carcinoma Using 3D CT with Multiple Instance Learning

ReViT: A Hybrid Approach for BCLC Staging of Hepatocellular ...

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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： Shun-Cheng Chang Hsin-Pei Yu Yi-Hsien Hsieh Pochuang Wang Weichung Wang Tung-Hung Su Jia-Horng Kao Che Lin Graduate Institute of Communication Engineering National Taiwan University (NTU) Taipei Taiwan Department of Computer Science and Information Engineering NTU Taipei Taiwan Institute of Applied Mathematical Sciences NTU Taipei Taiwan Department of Internal Medicine Division of Gastroenterology and Hepatology National Taiwan University Hospital Taipei Taiwan Department of Electrical Engineering NTU Taipei Taiwan Center for Advanced Computing and Imaging in Biomedicine NTU Taipei Taiwan Smart Medicine and Health Informatics Program NTU Taipei Taiwan

ISBN: (数字)9798350351552

ISBN: (纸本)9798350351569

Deep learning has revolutionized medical imaging, offering advanced methods for accurate diagnosis and treatment planning. The BCLC staging system is crucial for staging Hepatocellular Carcinoma (HCC), a high-mortality cancer. An automated BCLC staging system could significantly enhance diagnosis and treatment planning efficiency. However, we found that BCLC staging, which is directly related to the size and number of liver tumors, aligns well with the principles of the Multiple Instance Learning (MIL) framework. To effectively achieve this, we proposed a new preprocessing technique called Masked Cropping and Padding(MCP), which addresses the variability in liver volumes and ensures consistent input sizes. This technique preserves the structural integrity of the liver, facilitating more effective learning. Furthermore, we introduced Re ViT, a novel hybrid model that integrates the local feature extraction capabilities of Convolutional Neural Networks (CNNs) with the global context modeling of Vision Transformers (ViTs). Re ViT leverages the strengths of both architectures within the MIL framework, enabling a robust and accurate approach for BCLC staging. We will further explore the trade-off between performance and interpretability by employing TopK Pooling strategies, as our model focuses on the most informative instances within each bag.

关键词： Visualization Accuracy Three-dimensional displays Liver Transformers Planning Convolutional neural networks Context modeling Biomedical imaging Tumors

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Revealing the core-periphery structure of cities

arXiv

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arXiv 2024年

作者： Fanelli, Federica Melo, Hygor P.M. Bruno, Matteo Loreto, Vittorio Sapienza Univ. of Rome Physics Dept Piazzale A. Moro 2 Rome00185 Italy Sony Computer Science Laboratories - Rome Joint Initiative CREF-Sony Centro Ricerche Enrico Fermi Via Panisperna 89/A Rome00184 Italy Via Panisperna 89/A Rome00184 Italy Postgraduate Program in Applied Informatics University of Fortaleza CE Fortaleza60811-905 Brazil Complexity Science Hub Josefstädter Strasse 39 A 1080 Vienna Austria

The distribution of urban services reveals critical patterns of human activity and accessibility. Proximity to amenities like restaurants, banks, and hospitals can reduce access barriers, but these services are often unevenly distributed, exacerbating spatial inequalities and socioeconomic disparities. In this study, we present a novel accessibility measure based on the spatial distribution of Points of Interest (POIs) within cities. Using the radial distribution function from statistical physics, we analyze the dispersion of services across different urban zones, combining local and remote access to services. This approach allows us to identify a city’s central core, intermediate areas or secondary cores, and its periphery. Comparing the areas that we find with the resident population distribution highlights clusters of urban services and helps uncover disparities in access to opportunities. Copyright © 2024, The Authors. All rights reserved.

关键词： Population statistics

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A BCLC Staging System for Hepatocellular Carcinoma using Swin Transformer and CT Imaging

A BCLC Staging System for Hepatocellular Carcinoma using Swi...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Shun-Cheng Chang Pochuang Wang Weichung Wang Tung-Hung Su Jia-Horng Kao Che Lin Graduate Institute of Communication Engineering National Taiwan University (NTU) Taipei Taiwan Department of Computer Science and Information Engineering NTU Taipei Taiwan NTU Institute of Applied Mathematical Sciences Taipei Taiwan Department of Internal Medicine Division of Gastroenterology and Hepatology National Taiwan University Hospital Taipei Taiwan Department of Electrical Engineering NTU Taipei Taiwan NTU Center for Advanced Computing and Imaging in Biomedicine Taipei Taiwan NTU Smart Medicine and Health Informatics Program Taipei Taiwan

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

The Barcelona Clinic Liver Cancer (BCLC) staging system plays a crucial role in clinical planning, offering valuable insights for effectively managing hepatocellular carcinoma. Accurate prediction of BCLC stages can significantly ease the workload on radiologists. However, few datasets are explicitly designed for discerning BCLC stages. Despite the common practice of appending BCLC labels to clinical data within datasets, the inherent imbalance in BCLC distribution is further amplified by the diverse purposes for which datasets are curated. In this study, we aim to develop a BCLC staging system using the advanced Swin Transformer model. Additionally, we explore the integration of two datasets, each originally intended for separate objectives, highlighting the critical challenge of preserving class distribution in practical study designs. This exploration is pivotal for ensuring the applicability of our developed staging system in the designed clinical settings. Our resulting BCLC staging system demonstrates an accuracy of 55.81% (±7.8%), contributing to advancing medical image-based research for predicting BCLC stages.

关键词： Liver cancer Accuracy Computed tomography Biological system modeling Transformers Planning Biomedical imaging

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Relative magnetic field and slipping effect on Casson dusty fluid of two phase fluctuating flow over inclined parallel plate

引用

South African Journal of Chemical Engineering 2023年 44卷 135-146页

作者： khan, Dolat Kumam, Poom Kumam, Wiyada Suttiarporn, Panawan Rehman, Ali Fixed Point Research Laboratory Fixed Point Theory and Applications Research Group Center of Excellence in Theoretical and Computational Science (TaCS-CoE) Faculty of Science King Mongkut's University of Technology Thonburi (KMUTT) 126 Pracha Uthit Rd. Bang Mod Bangkok Thung Khru 10140 Thailand Center of Excellence in Theoretical and Computational Science (TaCS-CoE) Faculty of Science King Mongkut's University of Technology Thonburi (KMUTT) 126 Pracha Uthit Rd. Bang Mod Bangkok Thung Khru 10140 Thailand Applied Mathematics for Science and Engineering Research Unit (AMSERU) Program in Applied Statistics Department of Mathematics and Computer Science Faculty of Science and Technology Rajamangala University of Technology Thanyaburi (RMUTT) Pathum Thani 12110 Thailand Faculty of Science Energy and Environment King Mongkut's University of Technology North Bangkok Rayong Campus Rayong 21120 Thailand Special Interest Group for Modelling and Data Analytics Faculty of Ocean Engineering Technology and Informatics Universiti Malaysia Terengganu Terengganu Kuala Nerus 21030 Malaysia

Due to its significant applications in magnetic devices for cell separation, magnetic drugs for cancer tumor treatment, blood flow adjustment during surgery, magnetic endoscopy, and fluid pumping in industrial and engineering processes, magnetohydrodynamics (MHD) has a wide range of applications. Therefore, the aim of this study to investigate the Relative Magnetic Field and slipping effect on Casson dusty fluid of two-phase fluctuating flow over inclined parallel plate. More exactly, the relative magnetic phenomena are fixed relatively to the plate (MFFRP) or fixed relatively to the fluid (MFFRF). The mathematical modeling was established as the set of partial differential equations for dusty Casson fluid. Buckingham's pi theorem is used to find out the dimensionless variables, to make our system dimensionless. The solution in perturb form is to find out by incorporating Poincare–Lighthill perturbation technique (PLPT). To know in-depth different parameters the graphical results for both velocities are plotted with the help of software Mathcad- 15. It is clearly detected that the relative magnetic field performs a vital part in the fluid as well as particle motion. Moreover, the relative magnetic field play a vital role in the decreasing of skin friction of both plates. © 2023

关键词： Brinkman fluid Dust particles Fluctuating vertical plate Inclined relative magnetic field PLPT

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Model-Based Analysis of Microservice Resiliency Patterns

Model-Based Analysis of Microservice Resiliency Patterns

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Working IEEE/IFIP Conference on Software Architecture

作者： Nabor C. Mendonca Carlos M. Aderaldo Javier Camara David Garlan Post Graduate Program in Applied Informatics University of Fortaleza Brazil Post Graduate Program in Applied Informatics University of Fortaleza CE Brazil University of York York UK School of Computer Science Carnegie Mellon University Pittsburgh PA USA

ISBN: (数字)9781728146591

ISBN: (纸本)9781728146607

Microservice application developers try to mitigate the impact of partial outages typically by implementing service-to-service interactions that use well-known resiliency patterns, such as Retry, Fail Fast, and Circuit Breaker. However, those resiliency patterns-as well as their available open-source implementations-are often documented informally, leaving it up to application developers to figure out when and how to use those patterns in the context of a particular microservice application. In this paper, we take a first step towards improving on this situation by introducing a model checking-based approach in which we use the PRISM probabilistic model checker to analyze the behavior of the Retry and Circuit Breaker resiliency patterns as continuous-time Markov chains (CTMC). This approach has enabled us to quantify the impact of applying each resiliency pattern on multiple quality attributes, as well as to determine how to best tune their parameters to deal with varying service availability conditions, in the context of a simple client-service interaction scenario.

关键词： Circuit breakers Resilience Integrated circuit modeling Probabilistic logic Transient analysis Circuit faults Analytical models

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Principal Curvatures Estimation with Applications to Single Cell Data

arXiv

引用

arXiv 2025年

作者： Zhang, Yanlei Mezrag, Lydia Sun, Xingzhi Xu, Charles Macdonald, Kincaid Bhaskar, Dhananjay Krishnaswamy, Smita Wolf, Guy Rieck, Bastian Université de Montréal Dept. of Math. & Stat. QC Montréal Canada Mila – Quebec AI Institute MontréalQC Canada Yale University Dept. of Comp. Sci. New HavenCT United States Dept. of Genetics New HavenCT United States Applied Mathematics Program New HavenCT United States Université de Fribourg Department of Informatics Fribourg Switzerland Helmholtz Zentrum München Institute of AI for Health Munich Germany

The rapidly growing field of single-cell transcriptomic sequencing (scRNAseq) presents challenges for data analysis due to its massive datasets. A common method in manifold learning consists in hypothesizing that datasets lie on a lower dimensional manifold. This allows to study the geometry of point clouds by extracting meaningful descriptors like curvature. In this work, we will present Adaptive Local PCA (AdaL-PCA), a data-driven method for accurately estimating various notions of intrinsic curvature on data manifolds, in particular principal curvatures for surfaces. The model relies on local PCA to estimate the tangent spaces. The evaluation of AdaL-PCA on sampled surfaces shows state-of-the-art results. Combined with a PHATE embedding, the model applied to single-cell RNA sequencing data allows us to identify key variations in the cellular differentiation. © 2025, CC BY.

关键词： Spatio-temporal data

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A multicriteria approach to support task allocation in projects of distributed software development

A multicriteria approach to support task allocation in proje...

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作者： Simão Filho, Marum Pinheiro, Plácido R. Albuquerque, Adriano B. Simão, Régis P. S. Azevedo, Raimundo S. N. Nunes, Luciano C. Graduate Program in Applied Informatics University of Fortaleza Brazil Information Systems 7 de Setembro University Center Brazil

Organizations are increasingly investing in Distributed Software Development (DSD) over the years. A typical decision-making problem in the distributed scenario consists of deciding which team should be allocated each task. That decision takes into account a relative degree of subjectivity. That setting is suitable for applying Verbal Decision Analysis (VDA). This paper introduces an approach to support the allocation of tasks to distributed units in DSD projects, structured on the hybridisation of methods of Verbal Decision Analysis for classification and rank ordering applied to influencing factors and executing units. Firstly, a review of the literature was conducted aiming to identify the approaches to support the allocation of tasks in DSD contexts. Then, an approach was developed by applying VDA-based methods for classification and ordering. Bibliographic research and the application of surveys with professionals allowed identifying and characterising the main elements that influence task assignment in DSD projects. Afterwards, experiences were carried out in five real-world companies. In the end, the proposed approach has been submitted to the evaluation by the professionals of the participating companies and by some project management experts. The proposed approach comprises a workflow containing responsible actors and descriptions of the activities. Automated tools are also employed in automating the implementation of the approach. After applying the approach in five companies, task assignment recommendations are presented in groups for each company, according to the task type, i.e., requirements, architecture, coding, and testing, ranging from the most to the least preferable office. Results of the experiences and evaluations held during this work present evidence that the proposed approach is flexible, adaptable, and easy to understand and to use. Moreover, it helps to reduce decision subjectivity and to think of new aspects, supporting the task allocatio

关键词： Project management

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