检索结果-内蒙古大学图书馆

Testing the Inference Accuracy of Accelerator-Friendly Approximate Phylogeny Tracking

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

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

来源：评论

学校读者我要写书评

暂无评论

Design and Performance Evaluation of Sequence Partition Algorithms

引用

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

来源：评论

学校读者我要写书评

暂无评论

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

引用

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

来源：评论

学校读者我要写书评

暂无评论

A Propositional Dynamic Logic for concurrent programs based on the π-Calculus

A Propositional Dynamic Logic for concurrent programs based ...

引用

作者： Benevides, Mario R. F. Schechter, L. Menasché Computer Science Department and Systems and Computer Engineering Program Federal University of Rio de Janeiro Brazil Systems and Computer Engineering Program Federal University of Rio de Janeiro Brazil

This work presents a Propositional Dynamic Logic (πDL) in which the programs are described in a language based on the π-Calculus without replication. Our goal is to build a dynamic logic that is suitable for the description and verification of properties of communicating concurrent systems, in a similar way as PDL is used for the sequential case. We build a simple Kripke semantics for this logic, provide a complete axiomatization for it and show that it has the finite model property. © 2010 Elsevier B.V. All rights reserved.

关键词： Semantics

来源：评论

学校读者我要写书评

暂无评论

SOME EFFICIENT ALGORITHMS FOR A CLASS OF ABSTRACT OPTIMIZATION PROBLEMS ARISING IN OPTIMAL CONTROL

引用

IEEE TRANSACTIONS ON AUTOMATIC CONTROL 1969年第6期AC14卷 640-+页

作者： BARR, RO GILBERT, EG Department of Electrical Engineering and Systems Science Michigan State University East Lansing MI USA Computer Information and Control Engineering Program University of Michigan Ann Arbor MI USA

Three abstract optimization problems are presented along with doubly iterative algorithms for their numerical solution. These algorithms are generalizations of particular algorithms described by Barr and Gilbert [19], [21] and Fujisawa and Yasuda [22]. The supporting theory is fully developed along with proofs of convergence. Practical aspects of computations are considered and procedures which insure rapid convergence are discussed. Two applications to discrete-time optimal control problems are described.

关键词： Optimal control Iterative algorithms Projection algorithms Dynamic programming Nonlinear equations Gradient methods Functional programming Boundary conditions Military computing Convergence of numerical methods

来源：评论

学校读者我要写书评

暂无评论

Accelerating adoption of species-agnostic plant sensors for precision farming

Nature Reviews Electrical Engineering

引用

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.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Using HMM in strategic games 9

Using HMM in strategic games

引用

9th International Workshop on Developments in Computational Models, DCM 2013

作者： Benevides, Mario Lima, Isaque Nader, Rafael Rougemont, Pedro Systems and Computer Engineering Program and Computer Science Department Federal University of Rio de Janeiro Brazil

In this paper we describe an approach to resolve strategic games in which players can assume different types along the game. Our goal is to infer which type the opponent is adopting at each moment so that we can increase the player's odds. To achieve that we use Markov games combined with hidden Markov model. We discuss a hypothetical example of a tennis game whose solution can be applied to any game with similar characteristics. © M. Benevides, I. Lima, R. Nader & P. Rougemont This work is licensed under the Creative Commons Attribution License.

关键词： Tennis

来源：评论

学校读者我要写书评

暂无评论

Emergent dimer-model topological order and quasi-particle excitations in liquid crystals: combinatorial vortex lattices

arXiv

引用

arXiv 2025年

作者： Meng, Cuiling Wu, Jin-Sheng Kos, Žiga Dunkel, Jörn Nisoli, Cristiano Smalyukh, Ivan I. Department of Physics and Chemical Physics Program University of Colorado BoulderCO80309 United States Hiroshima University Hiroshima Higashihiroshima Japan Department of Mathematics Massachusetts Institute of Technology CambridgeMA02139 United States Faculty of Mathematics and Physics University of Ljubljana Ljubljana Slovenia Department of Condensed Matter Physics Jožef Stefan Institute Ljubljana Slovenia Theoretical Division Physics of Condensed Matter and Complex Systems Center For Nonlinear Studies Los Alamos National Laboratory Los AlamosNM87545 United States Department of Electrical Computer and Energy Engineering Materials Science and Engineering Program University of Colorado BoulderCO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado BoulderCO80309 United States

Liquid crystals have proven to provide a versatile experimental and theoretical platform for studying topological objects such as vortices, skyrmions, and hopfions. In parallel, in hard condensed matter physics, the concept of topological phases and topological order has been introduced in the context of spin liquids to investigate emergent phenomena like quantum Hall effects and high-temperature superconductivity. Here, we bridge these two seemingly disparate perspectives on topology in physics. Combining experiments and simulations, we show how topological defects in liquid crystals can be used as versatile building blocks to create complex, highly degenerate topological phases, which we refer to as ‘Combinatorial Vortex Lattices’ (CVLs). CVLs exhibit extensive residual entropy and support locally stable quasi-particle excitations in the form of charge-conserving topological monopoles, which can act as mobile information carriers and be linked via Dirac strings. CLVs can be rewritten and reconfigured on demand, endowed with various symmetries, and modified through laser-induced topological surgery — an essential capability for information storage and retrieval. We demonstrate experimentally the realization, stability, and precise optical manipulation of CVLs, thus opening new avenues for understanding and technologically exploiting higher-hierarchy topology in liquid crystals and other ordered media. Copyright © 2025, The Authors. All rights reserved.

关键词： Laser surgery

来源：评论

学校读者我要写书评

暂无评论

Towards the conception of scientific workflows for in silico experiments in software engineering 10

Towards the conception of scientific workflows for in silico...

引用

Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software engineering and Measurement

作者： Pereira, Wallace M. Travassos, Guilherme H. Federal University of Rio de Janeiro/COPPE Systems Engineering and Computer Science Program Brazil

ISBN: (纸本)9781450300391

The evolution of science has been supported by complex computerized infrastructures with growing interest in simulation based experiments. This trend can also be observed in Software engineering. Our capacity of acquiring evidences to describe phenomena of interest in the field allowed the building of in silico models that can virtually replicate feasible software behaviors and improve our capacity of observation. In silico experiments demand additional concerns for its planning. One of them is regarding the scientific workflow conception. This task is not easy and to apply ad-hoc approaches can risky the experiment execution, validity and future replications. Regarding this topic, this paper presents some initial results from our research towards an approach to support the conception of scientific workflows for in silico experiments in Software engineering are presented. © 2010 ACM.

关键词： computer software

来源：评论

学校读者我要写书评

暂无评论

Towards supporting the specification of context-aware software system test cases 23

Towards supporting the specification of context-aware softwa...

引用

23rd Iberoamerican Conference on Software engineering, CIbSE 2020

作者： de Souza Doreste, Andréa Cristina Travassos, Guilherme Horta Systems Engineering and Computer Science Program COPPE Federal University of Rio de Janeiro Brazil

In Software engineering, context can be understood as the overall set of information used to characterize the situation of an entity. A software system is context-aware if it uses the context to provide relevant information or services to the user. Nowadays, different types of software systems with a profound impact on the user's life can be considered context-aware (e.g., ubiquitous and Internet of Things software systems). Therefore, it is crucial to guarantee that they behave correctly. Software Testing is the primary process for verifying system behavior. Because of the particularities of Context-Aware Software systems (CASS), conventional testing methods are not enough to test such systems. Based on that, we propose CATS#, a technique to support software engineers with the specification of CASS test cases and capture not only the context itself but its variation as well. CATS# is an evolution of the CATS (Context-Aware Test Suite) Design technique. It introduces two relevant evolutions: test case models and a new test template. The test case models were proposed after we searched for context-aware applications through the literature and realized that the context could affect the test process in different manners. The test template was proposed to capture the variation of context by specifying which variation should occur during the test case and when it should occur. We selected one example application to apply our technique, deriving different types of test cases and showing its relevance in these initial steps. © CIbSE 2020.

关键词： Software testing

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：