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Chromosome structure modeling tools and their evaluation in bacteria

BRIEFINGS IN BIOINFORMATICS 2024年第2期25卷 bbae044-bbae044页

作者： Liu, Tong Qiu, Qin-Tian Hua, Kang-Jian Ma, Bin-Guang Huazhong Agr Univ Bioinformat Ctr Wuhan Peoples R China Huazhong Agr Univ Coll Informat Wuhan Peoples R China Huazhong Agr Univ Bioinformat Dept Wuhan Peoples R China

The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained from Escherichia coli and Caulobacter crescentus, as well as simulated datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms.

关键词： prokaryotes chromatin interaction Hi-C chromosome modeling algorithm evaluation

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evaluation and comparison of the results of the NET-VISA seismic event association method based on Bayesian theory

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NATURAL HAZARDS 2021年第2期105卷 1521-1539页

作者： Li, Jian Wang, Juan Wang, Xiaoming Jiang, Changsheng Wang, Weidong Liu, Junmin Beijing Univ Posts & Telecommun Sch Elect Engn Informat & Elect Technol Lab Beijing 100876 Peoples R China CTBT Beijing Natl Data Ctr Beijing 100085 Peoples R China China Earthquake Adm Inst Geophys Beijing 100081 Peoples R China

Seismic monitoring is an important verification technique under the Comprehensive Nuclear-Test-Ban Treaty. Phase association technology, which is an important component of seismic data processing, associates signals generated from the same event source recorded at multiple stations and determines event information based on signal features. Seismic event association based on the historical seismic data feature model is a research hot spot in the field of seismic monitoring. In this paper, an event association method called NET-VISA based on Bayesian theory is introduced;then, the application of the historical data feature model in NET-VISA is analyzed. The NET-VISA method is evaluated using the International Data Centre LEB bulletins published by the Comprehensive Nuclear-Test-Ban Treaty Organization, the ISC Reviewed Bulletins, and the China Earthquake Networks Center bulletin as reference sets. The results show that for the global sparse network, NET-VISA is generally superior to the GA method currently used by the IDC, which verifies NET-VISA's effectiveness. However, NET-VISA misses some events detected by the GA. The reasons might be that these events are located in regions with low seismic activity and that insufficient historical event data exists, resulting in unreasonable scoring ***, the application method and research direction of NET-VISA in actual scenarios are discussed.

关键词： Seismology Probability model Bayesian inference algorithm evaluation

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Performance measure for sparse recovery algorithms in compressed sensing perspective

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INTERNATIONAL JOURNAL OF DATA SCIENCE AND ANALYTICS 2023年第4期15卷 391-406页

作者： Vivekanand, V. Mishra, Deepak Indian Space Res Org Vikram Sarabhai Space Ctr Thiruvananthapuram Kerala India Indian Inst Space Sci & Technol Dept Space Thiruvananthapuram Kerala India

The sparse signal recovery is of great interest in compressed sensed data recovery. Many sparse recovery algorithms were developed in the last decade. However, selection of an appropriate recovery algorithm is an important matter of concern in many applications. The recovery algorithms are generally compared in terms of computational complexity, computational time, recovery probability and recovery precision. Typically, absolute Mean Squared Error (MSE) and relative MSE are used to compare the recovery precision of various sparse recovery algorithms. However, these two metric alone may not qualify to assess all algorithms. This paper presents an algorithm evaluation strategy by ranking the algorithms concerning an observable similarity between the original and reconstructed signal. We aim to propose a recovery similarity measure and an empirically defined factor to compare the performance measure of sparse recovery algorithms.

关键词： Compressed sensing Sparse recovery Performance measure Performance metric algorithm evaluation

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METHODICAL ANALYSIS OF ADAPTIVE LOAD SHARING algorithmS

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IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 1992年第6期3卷 747-760页

作者： KREMIEN, O KRAMER, J UNIV LONDON IMPERIAL COLL SCI TECHNOL & MED DISTRIBUTED SOFTWARE ENGN RES SECTLONDON SW7 2BZENGLAND

This paper presents a method for qualitative and quantitative analysis of load sharing algorithms, using a number of well known examples as illustration. algorithm design choices are considered with respect to the main activities of information dissemination and allocation decision making. We argue that nodes must be capable of making local decisions, and for this efficient state dissemination techniques are necessary. Activities related to remote execution should be bounded and restricted to a small proportion of the activity in the system. The quantitative analysis provides both performance and efficiency measures, including consideration of the load and delay characteristics of the environment. To assess stability, which is also a precondition for scalability, we introduce and measure load sharing hit-ratio, the ratio of remote execution requests concluded successfully. Using our analysis method, we are able to suggest improvements to some published algorithms.

关键词： ADAPTABILITY algorithm evaluation EFFICIENCY HIT-RATIO LOAD SHARING PERFORMANCE SCALABILITY STABILITY

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AN ELLIPSOID algorithm FOR NON-LINEAR PROGRAMMING

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MATHEMATICAL PROGRAMMING 1983年第1期27卷 83-106页

作者： ECKER, JG KUPFERSCHMID, M RENSSELAER POLYTECH INST ALAN M VOORHEES COMP CTRTROYNY 12181

We investigate an ellipsoid algorithm for nonlinear programming. After describing the basic steps of the algorithm, we discuss its computer implementation and present a method for measuring computational efficiency. The computational results obtained from experimenting with the algorithm are discussed and the algorithm's performance is compared with that of a widely used commercial code.

关键词： Ellipsoid algorithm Nonlinear Programming Computational Experiments algorithm evaluation

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A survey of methods for image annotation

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JOURNAL OF VISUAL LANGUAGES AND COMPUTING 2008年第5期19卷 617-627页

作者： Hanbury, Allan Inst Comp Aided Automat Pattern Recognit & Image Proc Grp PRIP A-1040 Vienna Austria

In order to evaluate automated image annotation and object recognition algorithms, ground truth in the form of a set of images correctly annotated with text describing each image is required. In this paper, three image annotation approaches are reviewed: free text annotation, keyword annotation and annotation based on ontologies. The practical aspects of image annotation are then considered. We discuss the creation of keyword vocabularies for use in automated image annotation evaluation. As direct manual annotation of images requires much time and effort, we also review various methods to make the creation of ground truth more efficient. An overview of annotated image datasets for computer vision research is provided. (C) 2008 Elsevier Ltd. All rights reserved.

关键词： image annotation object recognition computer vision ontology algorithm evaluation

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PERFORMANCE-MEASURES FOR EVALUATING algorithmS FOR SIMD-MACHINES

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IEEE TRANSACTIONS ON SOFTWARE ENGINEERING 1982年第4期8卷 319-331页

作者： SIEGEL, LJ SIEGEL, HJ SWAIN, PH School of Electrical Engineering Purdue University

An examination is conducted of measures for evaluating the performance of algorithms for single instruction stream-multiple data stream (SIMD) machines. The SIMD mode of parallelism involves the use of a large number of processors which are synchronized together. Although all processors execute the same instruction at the same time, each processor operates on a different data item. In general, the complexity of parallel algorithms is a function of the machine size, problem size, and type of interconnection network used to provide communications among the processors. Measures that quantify the effect of changing the machine-size/problem-size/network-type relationships are needed. Several such measures are presented and applied to an example SIMD algorithm from the image processing problem domain. Such measures include execution time, speed, parallel efficiency, overhead ratio, processor utilization, redundancy, cost effectiveness, speed-up of the parallel algorithm over the corresponding serial algorithm, and an additive measure called ''price'' which assigns a weighted value to computations and processors. Figures.

关键词： SIMD Machines algorithm evaluation Parallel Processing Performance Measures Reconfigurable Systems

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algorithms for network-based identification of differential regulators from transcriptome data: a systematic evaluation

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Science China(Life Sciences) 2014年第11期57卷 1090-1102页

作者： YU Hui MITRA Ramkrishna YANG Jing LI YuanYuan ZHAO ZhongMing Department of Biomedical Informatics Vanderbilt University School of Medicine School of Biotechnology East China University of Science and Technology Shanghai Center for Bioinformation Technology Department of Cancer Biology Vanderbilt University School of Medicine Department of Psychiatry Vanderbilt University School of Medicine Center for Quantitative Sciences Vanderbilt University

Identification of differential regulators is critical to understand the dynamics of cellular systems and molecular mechanisms of *** computational algorithms have recently been developed for this purpose by using transcriptome and network ***,it remains largely unclear which algorithm performs better under a specific *** knowledge is important for both appropriate application and future enhancement of these ***,we systematically evaluated seven main algorithms(TED,TDD,TFactS,RIF1,RIF2,dCSA_t2t,and dCSA_r2t),using both simulated and real *** our simulation evaluation,we artificially inactivated either a single regulator or multiple regulators and examined how well each algorithm detected known gold standard *** found that all these algorithms could effectively discern signals arising from regulatory network differences,indicating the validity of our simulation *** the seven tested algorithms,TED and TFactS were placed first and second when both discrimination accuracy and robustness against data variation were *** applied to two independent lung cancer datasets,both TED and TFactS replicated a substantial fraction of their respective differential *** TED and TFactS rely on two distinct features of transcriptome data,namely differential co-expression and differential expression,both may be applied as mutual references during practical application.

关键词： differential regulation differential co-expression differential expression simulation algorithm evaluation transcription factor

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VALUE OF SCATTER-GRAPHS FOR THE ASSESSMENT OF ECG COMPUTER MEASUREMENT RESULTS

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METHODS OF INFORMATION IN MEDICINE 1990年第4期29卷 413-423页

作者： MORLET, D RUBEL, P WILLEMS, JL CATHOLIC UNIV LEUVEN HOSP GASTHUISBERGCSE COORDINATING CTRB-3000 LOUVAINBELGIUM INST NATL SCI APPL DEPT INFORMATVILLEURBANNEFRANCE

A new method is presented, different from usual methods, for the discussion of the results of computer ECG measurement programs, based on a new graphical evaluation method. The proposed “scatter-graphs” both highlight the main program results and facilitate the comparison between various wave-recognition algorithms. They allow the distinction between the reliability of an algorithm, which is its capacity to provide a maximum of measurements with a minimum amount of errors, and its precision, i.e., the standard deviation of the differences between its point estimates and the reference. The method proves to be a powerful tool for the discussion of individual, as well as the median program results in CSE Measurement Study. It allows to highlight limitations induced in performance assessment by the variability of the reference itself, and to state that the median program is at least as close to the “Gold Standard” as the median of the referees.

关键词： ECG Processing Quantitative Electrocardiography Program evaluation Graphical evaluation Method algorithm evaluation

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Toward Advocacy-Free evaluation of Packet Classification algorithms

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IEEE TRANSACTIONS ON COMPUTERS 2011年第5期60卷 723-733页

作者： Song, Haoyu Turner, Jonathan S. Alcatel Lucent Bell Labs Holmdel NJ 07733 USA Washington Univ Dept Comp Sci & Engn St Louis MO 63130 USA

Understanding the real performance of a proposed algorithm is a basic requirement for both algorithm designers and implementers. However, this is sometimes difficult to achieve. Each new algorithm published is evaluated from different perspectives and based on different assumptions. Without a common ground, it is almost impossible to compare different algorithms directly. Choosing an incompetent algorithm for an application can incur significant cost. This is especially true for packet classification in network routers, since packet classification is intrinsically a hard problem and all existing algorithms are based on some heuristics and filter set characteristics. The performance of the packet classification subsystem is critical to the overall performance of the network routers. Although numerous algorithms have been proposed so far, a benchmark that can give them consistent evaluation and reveal their comparable performance is still missing. This paper summarizes our efforts toward improving this situation. First, we conduct a high-level survey on the existing algorithms and extract some insights on the general design ideas. Second, we describe an open-source platform dedicated for advocacy-free evaluation of packet classification algorithms. Many representative algorithms are actually implemented under a set of uniform conditions and assumptions. The freely available implementations allow other researchers to easily test them under different scenarios. We also enforce some consistent and fundamental criteria for the algorithm evaluation, so that their performance and potentials are directly comparable, regardless of the actual implementation platforms. This project serves dual purpose: It helps the researchers to accelerate the innovation in the area of packet classification algorithm development by relieving them from the labor of replicating the previous work and by enabling them to quickly compare and evaluate algorithms. Meanwhile, it also helps the system

关键词： Packet classification algorithm evaluation

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