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Analysis of -omics data: Graphical interpretation- and validation tools in multi-block methods

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS 2010年第1期104卷 140-153页

作者： Hassani, Sahar Martens, Harald Qannari, El Mostafa Hanafi, Mohamed Borge, Grethe Iren Kohler, Achim Nofima Mat AS Ctr Biospect & Data Modelling N-1430 As Norway Univ Life Sci CIGENE Ctr Integrat Genet N-1432 As Norway Norwegian Univ Life Sci Dept Math Sci & Technol IMT N-1432 As Norway ONIRIS Unite Sensometrie & Chimiometrie F-44322 Nantes 3 France

As systems biology develops, various types of high-throughput -omics data become rapidly available. An increasing challenge is to analyze such massive data, interpret the results and validate the findings. Data analysis for most of the omics-techniques is in a fledgling immature stage. Alone the dimensionality of the data tables calls for new ways to reveal structure in the data, without cognitive overflow and excessive false discovery rate. Multi-block methods have been developed and adapted in order to find common variation patterns in data and depict these findings on graphical displays while providing tools to enhance the interpretation of the outcomes. In particular, multi-block methods based on latent variables are powerful tools to study block and global variation patterns, e.g. by inspecting block and global score plots. These methods can be used to achieve a graphical overview over sample and variable variation patterns in an efficient way. However, a visual detection of patterns may be subjective and, therefore, there is a need for validation tools. In this paper tools for validation of visually identified patterns in multi-block results are presented. Cross-validated estimates of Root Mean Square Error (RMSE) for block results are introduced for estimating the number of relevant PCs of the Consensus Principal Component Analysis (CPCA) models. Furthermore, important variables are identified by approximate t-tests based on Procrustes-corrected jackknifing. For the assessment of the stability of score patterns, block stability plots are introduced. Outliers can be revealed graphically on block and global level by stability plots. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Omics data Multi-block methods validation tools

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A survey of tools for the validation and verification of knowledge-based systems: 1985-1995

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DECISION SUPPORT SYSTEMS 1997年第4期21卷 307-323页

作者： Murrell, S Plant, RT Univ Miami Dept Comp & Informat Sci Coral Gables FL 33124 USA Univ Miami Dept Elect & Comp Engn Coral Gables FL 33124 USA

This paper presents the findings of a survey of software tools built to assist in the verification and validation of knowledge-based systems. The tools were identified from literature sources from the period 1985-1995. The tool builders were contacted and asked to complete and return a survey that identified which testing and analysis techniques were utilised and covered by their tool. From these survey results it is possible to identify trends in tool development, technique coverage and areas for future research. (C) 1997 Elsevier Science B.V.

关键词： verification validation verification tools validation tools testing knowledge-based system testing

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THE ESTEREL LANGUAGE

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PROCEEDINGS OF THE IEEE 1991年第9期79卷 1293-1304页

作者： BOUSSINOT, F DESIMONE, R ECOLE NATL SUPER MINES APPL MATH CTR LABVALBONNEFRANCE INST NATL RECH INFORMAT & AUTOMAT F-06560 VALBONNEFRANCE

We present the basics of the ESTEREL reactive model of synchronous parallel systems. We illustrate the ESTEREL programming style, based on "instantaneous communications and decisions" through the example of a mouse handler. We briefly describe the ESTEREL formal semantics and show how programs can be compiled into finite states sequential machines for efficient execution. The up to date implementation is described together with the ESTEREL environment, including simulation, and verification and validation tools. Finally, we report on some ESTEREL uses in various contexts.

关键词： ESTEREL environment ESTEREL formal semantics ESTEREL reactive model finite state sequential machines instantaneous communications mouse handler parallel programming program compilers program verification programming environments simulation synchronous parallel systems validation tools verification

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validation of intelligent systems: a critical study and a tool

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EXPERT SYSTEMS WITH APPLICATIONS 2000年第1期18卷 1-16页

作者： Mosqueira-Rey, E Moret-Bonillo, V Univ A Coruna Dept Comp Sci Lab Res & Dev Artificial Intelligence A Coruna 15071 Spain

One of the most important phases in the methodology for the development of intelligent systems is that corresponding to the evaluation of the performance of the implemented product. This process is popularly known as verification and validation (V&V). The majority of tools designed to support the V&V process are preferentially directed at verification in detriment to validation, and limited to an analysis of the internal structures of the system. The authors of this article propose a methodology for the development of a results-oriented validation, and a tool (SHIVA) is presented which facilitates the fulfilment of the tasks included in the methodology, whilst covering quantitative as well as heuristic aspects. The result is an intelligent tool for the validation of intelligent systems. (C) 2000 Elsevier Science Ltd. All rights reserved.

关键词： artificial intelligence intelligent systems validation of intelligent systems validation tools

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DESIGN AND validation OF PROTOCOLS - A TUTORIAL

COMPUTER NETWORKS AND ISDN SYSTEMS

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COMPUTER NETWORKS AND ISDN SYSTEMS 1993年第9期25卷 981-1017页

作者： HOLZMANN, GJ AT & T Bell Laboratories Murray Hill NJ 07974 USA

It can be remarkably hard to design a good communications protocol, much harder than it is to write a sequential program. Unfortunately, when the design of a new protocol is complete, we usually have little trouble convincing ourselves that it is trivially correct. It can be a unreasonably hard to prove those facts formally and to convince also others. Faced with that dilemma, a designer usually decides to trust his or her instincts and forgo the formal proofs. The subtle logical flaws in a design thus get a chance to hide, and inevitably find the worst possible moment in the lifetime of the protocol to reveal themselves. Though few will admit it, most people design protocols by trial and error. There is a known set of trusted protocol standards, whose descriptions are faithfully copied in most textbooks, but there is little understanding of why some designs are correct and why others are not. To design and to analyze protocols you need tools. Until recently the right tools were simply not generally available. But that has changed. In this tutorial we introduce a state-of-the-art tool called SPIN and the specification language PROMELA. We show how the language and the tool can be used to design reliable protocols. The tool itself is available by anonymous ftp from ***, or by email from the author.

关键词： PROTOCOLS validation VERIFICATION DESIGN FORMAL DESCRIPTION TECHNIQUES DESIGN tools validation tools PROMELA SPIN

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Intelligent interpretation of validation data

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EXPERT SYSTEMS WITH APPLICATIONS 2002年第3期23卷 189-205页

作者： Mosqueira-Rey, E Moret-Bonillo, V Univ A Coruna Dept Comp Sci LIDIA Lab Res & Dev Artificial Intelligence La Coruna 15071 Spain

This paper describes the characteristics of an expert system that will make an intelligent interpretation of the quantitative data obtained following the usual validation process for intelligent systems. This expert system converts numerical data into information that will indicate whether the performance of the validated intelligent system is comparable to the performance of human experts from the domain taken as reference. The process is carried out in two parts: an algorithmic part which identifies the basic characteristics of the quantitative data;a heuristic part which analyses these characteristics so as to be able to draw conclusions as to the results of the system. Published by Elsevier Science Ltd.

关键词： artificial intelligence intelligent systems validation of intelligent systems validation tools

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An expert system to achieve fuzzy interpretations of validation data

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EXPERT SYSTEMS WITH APPLICATIONS 2008年第4期35卷 2089-2106页

作者： Mosqueira-Rey, Eduardo Moret-Bonillo, Vicente Fernandez-Leal, Angel Univ A Coruna Dept Comp Sci Lab Res & Dev Artificial Intelligence LIDIA La Coruna 15071 Spain

validation of an intelligent system consists, basically, of ensuring that the solutions proposed by the system inspire a level of confidence similar to that inspired by human experts in the application domain. We focus on a validation against a group of experts because represents the ideal balance between the simplicity of using a single expert and the complexity of arriving at a consensus between a number of domain experts. In this paper, a system for automated interpretation of validation data is described. This system is divided into two modules: an algorithmic module functioning with unprocessed data for the statistical measures, which produces output in the form of high-level information that takes working context into account;and a heuristic module, which processes this high-level information to produce the final interpretation. Previous works in the subject highlighted the importance of dealing with the imprecision inherent to the semantic labels fed into the heuristic module by the algorithmic module. One of the typical and most effective ways for handling this kind of imprecision is to use fuzzy logic. (C) 2007 Elsevier Ltd. All rights reserved.

关键词： intelligent systems validation of intelligent systems validation tools fuzzy logic

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Structure-based validation of rule-based systems

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DATA & KNOWLEDGE ENGINEERING 1998年第2期26卷 161-189页

作者： Preece, AD Grossner, C Chander, PG Radhakrishnan, T Univ Aberdeen Kings Coll Dept Comp Sci Aberdeen AB24 3UE Scotland Concordia Univ Dept Comp Sci Montreal PQ H3G 1M8 Canada

A central problem in validating rule-based systems is ensuring that the structural components of the system have been tested sufficiently thoroughly. In this paper, we present a method that can be used for structure-based testing of rule-based systems. Our method includes a model for determining the structural components in a rule base, a metric for quantifying coverage (the degree to which the structural components in a rule base have been tested) and techniques for analyzing the coverage obtained when a rule base is exercised on a given test set. We present the results produced by applying our method for structure-based testing to a complex rule-based system that had been previously subjected to functional testing. The results we obtained indicate that our method for structure-based testing reveals several types of faults not shown by previous testing, and quantifies the extent to which the rule base has been tested.

关键词： knowledge-based systems rule-based systems software engineering structural analysis testing validation tools

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Model validation and error estimation in multi-block partial least squares regression

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CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS 2012年 117卷 42-53页

作者： Hassani, Sahar Martens, Harald Qannari, El Mostafa Hanafi, Mohamed Kohler, Achim Nofima Mat AS Norwegian Food Res Inst N-1430 As Norway Norwegian Univ Life Sci Dept Math Sci & Technol IMT Ctr Integrat Genet CIGENE N-1432 As Norway ONIRIS INRA Unite Sensometrie & Chimiometrie F-44322 Nantes 3 France

While validation of Partial Least Squares Regression (PLSR) models has been discussed extensively, validation tools that are tailored to Multi-block Partial Least Squares Regression (MBPLSR) have not been discussed in literature yet. This paper introduces validation tools for estimating predictive ability and model stability in MBPLSR models on block level and on global level. Predictive ability on the block level and global level are estimated by calculating the predictive power of block and global parameters. Model stability is estimated by checking the stability of block model parameters and global parameters. By comparing error plots for model stability and predictive ability the user can decide on the number of component to be used. The number of components to be chosen depends on the data set and the purpose of the investigation. (C) 2011 Elsevier B.V. All rights reserved.

关键词： Multi-block methods Multi-block Partial Least Squares Regression (MBPLSR) validation tools Cross validation Number of components

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The physics of software tools: SWOT analysis and vision

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INTERNATIONAL JOURNAL ON SOFTWARE tools FOR TECHNOLOGY TRANSFER 2017年第1期19卷 1-7页

作者： Steffen, Bernhard TU Dortmund Univ Programming Syst D-44221 Dortmund Germany

This paper reviews the seemingly inevitable trend that software tools are no longer just a means for supporting the design, construction, and analysis of (large-scale) systems, but become so complex that each of them turns into a reality of their own, with its own "physics", that needs to be studied in its own right. The true effects of combining methodologies as diverse as classical static analysis, model checking, SAT and SMT solving, and dynamic methods such as simulation, runtime verification, testing, and learning, with their dedicated means of optimizations in terms of, e.g., BDD coding, parallelization, and various forms of abstraction and reduction, are very dependent on the particular tools and typically hardly predictable. Corresponding experimental investigations, today often supported by diverse and frequent tool challenges, provide interesting indications about the applied technology, but typically fail to provide sufficient evidence to transfer results to other settings and tools. Moreover, implementation-specific details often dominate the observed effects which thereby become invalid for drawing conceptual conclusions. On the other hand, requiring consequent in-depth analysis of any experimental observation in order to pinpoint the underlying conceptual consequences before publication would slow down the scientific exchange and also hinder the scientific progress. This paper analyzes the situation of today's software tools from a global perspective in terms of a SWOT (Strength, Weaknesses, Opportunities, Treats) analysis, identifies challenges, and establishes a global vision for overcoming current weaknesses.

关键词： validation tools Tool profiles Conceptual design SWOT analysis Open source Internet Exchange platform Tool competitions

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