BayesiaLab Specifications en

BayesiaLab Professional Edition 5.
0
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BayesiaLab 5.0 Professional Edition

Technical Specifications
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BAYESIA - SAS with a capital of 148 460 RCS Laval 433 996 519 6, rue Lonard de Vinci - BP 0119 - 53001 Laval Cedex - France - Tel.: +33(0)2 43 49 75 69 - Fax: +33(0)2 43 49 75 83 www.bayesia.com
BayesiaLab Professional Edition 5.0

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Table of Contents
1 Introduction ..................................................................................................3 2 Network........................................................................................................3 3 Expert Knowledge Elicitation .......................................................................6 4 Learning.......................................................................................................6 5 Network Analysis .........................................................................................8 6 Inference....................................................................................................10 7 Tools ..........................................................................................................12 8 Dynamic Bayesian networks......................................................................14 9 Documentation...........................................................................................14 10 Technical specifications ...........................................................................15 11 Protection with logical keys ......................................................................15 12 Bayesia License Server............................................................................16 13 Delivery ....................................................................................................17 14 Technical Support ....................................................................................17
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Introduction
Developed by Bayesia, BayesiaLab Professional Edition 5.0 is the worlds only comprehensive Software package for learning, editing and analyzing Bayesian Networks. It offers a broad set of tools for: Developing static and dynamic Bayesian networks by using Expert Knowledge and/or Machine Learning; Independent Expert Knowledge assessment by using a user-friendly web interface hosted on our secured web-site; Observational inference (simulation and/or diagnosis reasoning) and Causal Inference (intervention); Quickly assimilating the represented knowledge using a set of original analytical tools; Utilizing the models in interactive mode or in batch mode; Searching for optimal action policies by using dynamic programming for static Bayesian network and reinforcement learning for dynamic Bayesian network. As a Java based program, BayesiaLab is works under Windows, OS X, Linux/Unix. It is available in English, Japanese, Chinese, Spanish and French.
Network
BayesiaLab allows to easily designing networks by hand thanks to it user-friendly graphical interface. Various kinds of nodes are available: Chance node o Discrete o Continuous Constraint node Utility node Decision node Target node Hidden node Temporal node Excluded node (to temporarily exclude nodes from learning). A very intuitive graphical development of the networks: Node creation with a simple click Arc drawing with a simple drag Magnetic grid Alignment tools Powerful layout algorithms to improve the readability of the networks o Symmetric algorithm based on repulsive and attractive forces o Dynamic algorithm based on repulsive and attractive forces o Genetic algorithm that takes into account user defined esthetic characteristics o Mutual information mapping
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o Random layouting Arc inversion tools.
Quick access to all the necessary information related to the nodes using the editing window: Name Type (Discrete for symbolic state nodes and Continuous for discretized continuous variables) Automatic state creation Possibility to change the discretization (manually or automatically) Possibility to change the order of the states of a variable Probability distribution o Probabilistic mode o Deterministic mode o Equation editor Discrete probability distributions Continuous probability distributions, Special functions Arithmetic functions Transformation functions Trigonometric functions, Relational operators Boolean operators Arithmetic operators User function thanks to a plugin system Expert assessments (probabilities, confidence and comments) Possibility to dynamically change to order of the parents in the conditional probability table Properties o Color o Image o Temporal index o Cost of observation Classes (to define groups of nodes sharing some properties) Values (to associate numerical values to the modalities) State names (to associate long names to the modalities) Filtered state (to define a state of a variable that represents a filtered/censored value) HTML comment with hypertext links. HTML comments can also be associated to arcs and networks. During learning, the comments associated to the network are automatically updated for a traceability purposes. They contains The author name The creation date The used database Some characteristics of the database (number of lines, missing values, weight) The used learning algorithm The obtained score The used missing value processing.
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BayesiaLab also comes with full Cut&Paste functionalities inside BayesiaLab and with all the external applications that support the clipboard (eg. Word, Excel, PowerPoint, ): network, node, table, equation, chart, report can then be efficiently copied. Dictionaries are available for automatically carrying out actions on: Arcs o Arc definition o Forbidden arcs o Comments o Colors o Fixed arcs Nodes o Renaming o Classes o Comments o Colors o Images o Costs o Temporal indices o Local structural coefficients o State virtual numbers o Locations States o Renaming o Value o Names o Filtered.
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Expert Knowledge Elicitation

An expert is defined by: Name Credibility level Photo Comment (e.g. a description of his/her position in the company, or his/her expertise domain). Each expert can assess each probability of the probability tables. He can express his knowledge (probability, confidence and commentary on the assessment) directly by using the BayesiaLabs node editor or via the Bayesias web interface for knowledge elicitation (cf. http://www.bayesia.com/en/products/bayesialab/resources/tutorials/bayesiaLab-knowledge-elicitationenvironment.php for a complete overview of this environment). The use of this web interface is only available under subscription. A mathematical consensus is automatically computed by using the assessments weighted by the credibility and the confidence of each expert.
Learning
A data importation wizard allows to: Access the initial statistical information about data (text file or data base) Sample the data Discard the useless variables Define a Row Identifier variable Define a weight variable Define the missing values Define the filtered/censored values Define a data type variable for indicating the lines that have to be used for learning and those that have to be used for testing Select a subset of lines by defining filters based on the states of some variables. Discretize continuous variables o Manual discretization with a interactive graphical interface o Automatic discretization: Equal distances Equal frequencies K-Means for a discretization that fits the density function Decision trees for an intelligent discretization that focus on a target variable Aggregate some states o Manual aggregation o Automatic aggregation with decision trees for an intelligent aggregation that focus on a target variable Define the missing values processing o Filtering o Replacement with
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A specific value The modal value for the discrete variables The mean value for the continuous variables o Bayesian inference Static imputation Dynamic imputation Structural Expectation-Maximization. Parameter-learning algorithms and a broad set of score based structural learning algorithms are available: Estimation of the probabilities of a Bayesian network from new cases (maximum likelihood) Bayesian updating Unsupervised learning for inducing the most compact probabilistic representation of the Joint Probability Distribution (association discovery) o Maximum Weight Spanning tree (based on the Minimum Description Length score or on the Pearson correlation) o Taboo learning o EQ and SopLEQ (greedy search algorithms in the space defined by all set of the equivalence classes) o Taboo Order (search algorithm in the space defined by all the possible orders of the nodes) Bayesian data clustering (segmentation): o Automatic search of the number of clusters o Automatic report edition with the clusters purity, the 2D visualization of the obtained clusters and the probabilistic profile of each cluster o Possibility to take into account a priori relations, as for example structural dependencies between variables or strong relations o Semi-supervised clustering using weighted variables K-Means clustering to create new variables summarizing a subset of (numerical) variables Bayesian variable clustering (segmentation): o Automatic search of the number of clusters o Dynamic Dendrogram Multiple clustering to automatically generate one latent variable per cluster of variables (factors, useful for probabilistic structural equations or hierarchical data clustering), Supervised learning for the probabilistic characterization of a target variable o Nave learning o Tree Augmented Nave learning o Augmented Nave learning o Son and Spouse learning o Markov Blanket learning to characterize the target variable with the minimal subset of variables o Augmented Markov Blanket learning o Minimal Augmented Markov Blanket learning o Stratification Semi supervised learning to induce a network centered on a seed variable.
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All those learning algorithms take into account missing values, filtered/censored states, user-defined constraints (e.g. arcs forbidden between nodes or classes of nodes, arc fixed). A Structural Complexity parameter is available to module the complexity of the obtained networks with respect to the data available. It can be compared to a significance threshold. When a Bayesian network contains Decision nodes and Utility nodes, BayesiaLab can be used for learning the optimal action policy with: Dynamic programming for the static networks Reinforcement learning for the compact form of the dynamic networks.
Network Analysis
BayesiaLab makes it easy to understand the Bayesian networks thanks to its various analytical tools and its algorithms for the automatic layout of the nodes. Network Descriptive report o Use of the Time in the Dynamic Networks o Classes o Forbidden arcs o Structural compression o Number of nodes (Discrete, Continuous, Constraint, Decision, Utility) o Number of states (average, minimum and maximum) o Number of arcs (total, fixed and temporal) o Number of parents (average and maximum) o Number of children (average and maximum) o Connectivity (average, minimum and maximum) o Conditional probability tables Evidence analysis (hard and soft) o Joint probability o Impact of each evidence on the Uncertainty and Likelihood variations o Highlighting of the impact of each evidence on the marginal probabilities o Global and local contradiction/consistency analysis o Bayes Factors o Difference Decomposition Analysis between two scenarios (Causal analysis) Arc analysis o Global strength of the probabilistic relation computed with the Kullback-Liebler distortion. The arc thickness is proportional to its force. It is also possible to display the mutual information value on the arc o Strength of the arc based on the mutual information. The arc thickness is proportional to its force. It is also possible to display the mutual information value on the arc o Linear correlation computed to the Pearson Correlation R. The arc thickness is proportional to its force and its color depends on the sign of the relation; possibility to display the correlation value R on the arc o Node force computed with respect to the strength of its entering and outing arcs Mosac Analysis:
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Dynamic graphical representation of the joint probability distribution of a subset of variables. The standardized Pearson residuals associated to each cell allow to accurately analyzing the statistical significance of the probabilistic relations between the variable states. or G-test are used to measure the statistical significance of the global relation Target variable analysis: o Correlation of each node with the target node: the brightness of the square inside the node is proportional to the amount of information it brings to the target. The monitor associated to the nodes can be automatically displayed by using an automatic ranking based on the amount of information brought by the corresponding node to the target o Correlation of each node with a target state: the brightness of the smiley inside the node is proportional to the amount of information it brings to the target state. The monitor associated to the nodes can be automatically displayed by using an automatic ranking based on the amount of information brought by the corresponding node to the target state o Influence analysis to graphically illustrate the impact of a set of nodes on the states of the target node o Sensitivity analysis to measure the impact of each variable on the target (Hano tour) o Sensitivity analysis of the conditional probabilities with respect to the target modality o Mean value analysis: graphical visualization of the target expected numerical value with respect to the values of the selected nodes o Target Dynamic Profile: incremental procedure for the optimization (maximization or minimization) of the selected criterion (State Probability, Variable Mean or Probability Difference between two States). This (driver) analysis can be based observations/interventions: Hard evidence Value variations (positives and negatives) expressed in percentage of: The current mean value The domain of the variable The progress margin Costs can be taken into account during the optimization o Optimization tree: returns the set of optimization policies (generalization of the Target Dynamic Profile that only returns the optimal one) o Exhaustive search of the tuples that optimize the target variable (generalization of the Target Dynamic Profile that only returns the optimal one) o Interpretation tree based on mutual information (generalization of the Adaptive Questionnaire) o Total Effects: computation of the effect of small variations on the variable values on the target variable expected value o Quadrant analysis (opportunity plot): 2D graph with a priori expected value of the variables on the X-axis and the strength of their relation with the target on the Y- axis (mutual information, total effect, standardized total effect) Sensibility analysis to measure the impact of the uncertainty (the probability distribution) associated to a set of Parameter nodes on a set of Target nodes o Possibility to save the simulation points in a file o Representation of the probability distribution/density functions for each state of the Target nodes o
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Sensibility analysis of the experts assessments to measure the impact of the uncertainty associated to the consensual probability distribution of the Parameter nodes on a set of Target nodes o Random selection of one expert per network o Random selection of one expert per node o Random selection of one expert per conditional probability distribution Graphical Neighborhood Analysis to highlight the neighborhood of the selected node (Markov Blanket, parents, children, spouses, distance). Most Probable Explanation to get the configuration that has the greatest joint probability distribution Causal analysis by using essential graphs Edition of complete HTML analysis reports Performance analysis o Targeted analysis Global precision of the prediction of the target node values with respect to the associated file or the test cases Coefficients R, R2, Gini and Lift Confusion matrix Gain curve Lift curve ROC curve o Global analysis Distribution and repartition functions of the network log-likelihood with respect to each data point of the learning and test sets Contingency Table Fit to measure the precision of the representation of the Joint Probability Distribution Kolmogorov-Smirnov test to compare the results obtained on learning and test sets BayesiaLab also comes with a graphical module: Bar chart Occurrence matrix with or G-test computation Distribution function Scatter of points (2D) 2D plot of the temporal evolution of a variable, colored with respect to the states of another variable Scatter of points (3D) Bubble chart
Inference
BayesiaLab comes with exact and approximate inference algorithms for both the static and dynamic Bayesian networks: Exact inference with the Junction Tree algorithm Approximate inference
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o o
Likelihood Weighting algorithm Automatic simplification of the graph to allow exact inference (on approximate networks)
BayesiaLab is the first commercial tool that comes with Causal inference (Pearls Do-Calculus). The Causal Intervention is compatible with all the analysis tools that are available in BayesiaLab, and with all the kinds of evidence (hard, soft, probability distribution, mean value). The type of inference, observation or intervention, can be set for each variable. Various kinds of evidence (observations/interventions) can be set: Positive evidence Negative evidence Likelihood distribution Fixed and unfixed probability distributions Fixed and unfixed target mean Inference can be: Interactive o Manual evidence setting by using the monitors associated to the nodes o Automatic evidence setting with respect to cases described in a database o Automatic evidence through scenario files Realized in a batch mode on cases described in a database o Prediction of the target value o Probability distributions of the unobservable nodes o Most probable explanation of the unobservable nodes o Likelihood distribution computed with the most probable explanation of the unobservable nodes o Joint probability o Missing values imputation Maximum likelihood Sampling in the posterior probability distribution. Each node can have an associated monitor. Those monitors are used for: Displaying the marginal probability distribution of its associated node given the set of observations/interventions defined on the other nodes o Probabilities expressed in percentage or with the scientific notation o Curves or bars Setting the inference mode, i.e. observation or intervention Setting the evidence The monitors are also used as analysis tools: They can be sorted with respect to the correlation with the target node/state The monitors corresponding to nodes with evidence can be sorted with respect to their impact on the joint probability Marginal probability variations are highlighted after each new evidence (with respect to the past distribution or a defined reference distribution).
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Adaptive questionnaires generate a dynamic ranking of the monitors that takes into account the information brought by the corresponding nodes to the target (or target state), and possibly costs to get information for those nodes. Each new piece of evidence on a node triggers the updating of the monitor order. BayesiaLab also allows generating cases (internal or external data base) corresponding to the joint probability distribution encoded by the Bayesian network, possibly taking into account evidence on a subset of nodes. Evidence scenario files can be created interactively by storing the current set of evidence (hard and soft) in a text file, that can be saved, edited, and loaded. They can be used in interactive algorithms and in batch instead of the classical databases.
Tools
BayesiaLab offers a set of tools: Network structural comparison: o HTML report listing the common and different arcs of the two compared networks o Graphical interface to see the synthesis network and the two networks Comparison of the joint probability distributions obtained on two data bases (computed with the Batch inference tool), usually with the same network. The analysis is then identical as the one described in section 5.: o Distribution and repartition functions of the network log-likelihood with respect to each data point of the learning and test sets o Kolmogorov-Smirnov test to compare the results obtained on learning and test sets Cross-Validation: o Arc confidence: the confidence of an arc is measured as its frequency in the set of generated networks (jack-knife) HTML report listing the common and different arcs of the generated networks Graphical interface to see the synthesis network, the generated networks, and, for extracting a new network based on constraints expressed on frequencies o Data perturbation: a Gaussian noise is added to the weight of each data line Optimization the learned networks by trying to escape from score local minima Measurement of the robustness of the learning algorithms HTML report listing the common and different arcs of the generated networks Graphical interface to see the synthesis network, the generated networks, and, for extracting a new network based on constraints expressed on frequencies o Targeted evaluation carried out on the set of generated networks (k-folds) Global precision of the prediction of the target node values with respect to the associated file or the test cases Coefficients R, R2, Gini and Lift Confusion matrix Gain curve Lift curve ROC curve
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HTML report listing the variables that are used in the generated models, as well as the common and different arcs Graphical interface to see the synthesis network, the generated networks, and, for extracting a new network based on constraints expressed on frequencies, and save the numerical values predicted by each network on its associated test set o Structural coefficient analysis: induction of a set of networks with the selected learning algorithm by using different structural coefficient HTML report listing the common and different arcs of the generated networks Graphical interface to see the synthesis network, the generated networks, and, for extracting a new network based on constraints expressed on frequencies 2D graph with the structural coefficient on the X-axis, and where the Y-axis can be: The ratio Structure/Data The precision of the prediction The ratio Structure/Precision A validation measure taking into account the mean log-likelihood obtained on the test set and the training set Multi-Quadrant analysis: o Induction of a set of networks that have the same structure as the reference network, but where the parameters are estimated on the subsets of data defined buy the states of the so called Break-out variable (e.g. a product, a country). o The analysis can be based on Mutual Information, Total Effect, and Standardized Total Effect o Relations with the target variable can be linearized by reorganizing the values associated to the states o The values associated to the states can be updated with the mean value of the state on each data subset o Global Opportunity graph (quadrant) for comparing the quadrants of each network (data set) o Export of the variation percentage to apply to each variable to achieve the minimum and maximum values actually observed on the global data set. This file can then be used by the Target Dynamic Profile, the Target Optimization Tree, and the Target Optimization, cf. section 5. o Whereas the network structure remains the same, the parameters are learnt on each subset. A typical application of this tool is the analysis of a total market. It is possible to export the variations that have to be applied to each driver for reaching the best value of the market. These variations can then be used in the Dynamic Profile tool. Assessment: o Export of one network per Expert o Export of the all set of elicited probabilities o Export of the Experts assessments
The code allowing carrying out inference on the Markov Blanket of the target node can be exported in: SAS macro JavaScript
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PHP These export functions are available on subscription only.
Dynamic Bayesian networks

With its temporal arcs, BayesiaLab integrates the notion of time in Bayesian networks and then allow to model dynamic systems with a compact form of Dynamic Bayesian networks. It is possible to: Follow the temporal evolution of the probability distributions of a subset of variables o step by step o over a time period graphically in a file Evaluate the consequences of action policies (e.g. preventive maintenance policies or risk management policies) in terms of expected mean of gains/costs per time steps over a chosen period.
Documentation
BayesiaLab has an online help that is available though the Help menu or by pressing the F1 key. The F2 key also allows getting contextual helps. A PDF version of this help file can also be downloaded from our web site. There are also a lot of case studies available as static and/or dynamic presentations on our web site (http://www.bayesia.com/en/products/bayesialab/resources.php) : Introductory presentation Analysis toolbox Bayesian Network Learning Decision support Dynamic Bayesian networks and Action Policy Learning Filtered/Censored States Probabilistic Structural Equations and Path Analysis Expert Knowledge Elicitation Environment Modeling and Simulation of Dynamic Systems Production Optimization through Experience Feedback analysis Analysis of a perfume market Identifying drivers of liking Studying Consumer Drivers Consumer Segmentation Customer Characterization, development of Profiles Satisfaction Questionnaire analysis Implementation of a Bayesian score Difficult intubations analysis Salmonella isolation Transcriptome analysis
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Soccer World-Cup 2010 Health Trajectory analysis Employees satisfaction analysis Analysis of the French Presidential Elections of April 2007 Risk analysis and Safety Policy Cyber-Crimes detection Organization name identification
10 Technical specifications
Our software work under all the Operating Systems that implement a Java Virtual Machine (JRE 1.6): Windows Solaris Linux Mac Here are different computer configurations depending on the use of our software.
Configuration Minimum OS Processor Memory Disk Type JVM 32 bits Intel Pentium E/Intel Core 2 E /AMD Athlon A64 X2/AMD Athlon X2 512 MB HDD 32 bits Default 32/64 bits Intel Core 2 E/Intel Core 2 Q /AMD Athlon II/AMD Phenom 2 or 4 2GB or 4 GB HDD 32/64 bits Advanced 64 bits Intel Core I7/AMD Phenom II X4 4 or sup 4GB or sup HDD or SSD 64 bits
Core number 1 or 2

Free disk space Java version Internet > 250MB 1.6 Recommended for activating BayesiaLab
11 Protection with logical keys

Concerning the Single User Single Machine BayesiaLab licenses, a client identifier is given to the BayesiaLabs user. During the first execution, the user has to enter this identifier. If this identifier is correct, BayesiaLab will connect itself to the Bayesias Web Site and activate the logical key associated
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to the machine. If the firewall does not allow such automatic activation, this activation has to be realized manually by using the URL that is specified in the BayesiaLab activation window. The key is based on the HOSTNAME. Concerning the tokens (floating licenses), this activation procedure has to be realized with BayesiaLicenseServer (BLS). BLS has to be installed on a machine which IP and port 2424 is available. It manages the tokens that define the number of concurrent use of BayesiaLab. When launching BayesiaLab, the user, defined by a username and a password, sends a request to BLS for a license token. If BLS has an available token, the request is granted, and the software is launched. A used token can also be released (by ending the corresponding session) if the priority of the user is greater than one of the current users.
12 Bayesia License Server

The BayesiaLicenseServer (BLS) software allows managing floating licenses for the different software offered by Bayesia SAS. It must be installed on a machine accessible through a network by the machines on which the Bayesias software is installed. It doesnt have its own GUI. It can be managed remotely by a console having a graphic user interface. Its main features are : Licenses: BLS can manage leasing or purchase licenses. Each installed license can allow from 1 to n concurrent tokens. Such access must be made from computers connected to the server via a network. It can be necessary to configure the firewalls for allowing the connection on the 2424 server machine port Automatic activation: BLS needs an Internet connexion (directly or through a Proxy) in order to install licenses and to automatically update them (leasing). It can be necessary to configure the firewalls to establish the connection with the Bayesias website. Authentified access to the licenses: For each license, it is possible to register one or more users in order to obtain a token for this license giving a user name and a password. It is possible to obtain, at the same time, several tokens with the same user name and the same password. It allows managing a group of users with only one user name and only one password. Priority management: When a new user is registered, a priority from 0 to 100 is given to him. So, a user with a high priority will obtain a token even if all the tokens of the license are used and if one of the connected users has a lower priority than him. This user will lose its token and the new user will retrieve it. The user with the lower priority will have to close its application and wait for a free token. Log file: A log file (CSV format) is automatically generated. It is saved in the BLS running directory. It describes the transaction between the client applications and BLS. The following information are saved for each transaction: ID, date, hour, name and IP of the host, name and priority of the user, origin (server or client) and type (open, close, invalid) of the transaction, name, edition and version of the software corresponding to the license, user group, client ID, message associated to the transaction, session length, transaction result. Management console: A management console allows managing the whole license server. It is independent and can be executed on the server or remotely on a distant machine. The console is connected to the license server and displays in real time (except network latency) different server information. It is connected to the server via the port 9999 which can be changed. It allows adding or
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removing licenses, managing tokens, user names and priorities, as well as configuring the different server settings. Real time Information: The number of users that are using a token is displayed in the BLSs user interface. Windows service: when BLS is executed as a Windows service, it is launched and closed automatically with Windows. If BLS suffers from an unexpected stop, BLS will be launched again automatically. Once the server is started, the console can be connected to it in order to manage it. UNIX, Linux and Solaris daemon: BLS can be launched as a daemon. In that case, the user interface is not available. Once the server is started, the console can be connected to it in order to manage it. Client Application: the Client Application, i.e. the application that requests BLS for a token, has to stay connected with BLS to be able to keep its token. If the connection is broken, the Client Application receives a message that indicates that the application will be closed. It is then possible to save the current work.
13 Delivery
BayesiaLab is exclusively delivered by Internet. As soon as the order is validated, two mails are sent to the purchase contact. The first one contains the URL to download the software package; the second one contains the information necessary to access to that URL and to activate the software.
14 Technical Support
Technical support is based on a yearly subscription. It includes product update, with the possibility of downloading, free of charge, the last public version of the software, and technical support by telephone, email and e-conference. It comes automatically with the rented licenses. When several licenses of the same kind of software are purchased, the Technical Support cannot be subscribed for a subset of these licenses.
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BayesiaLab Professional Edition 5.

BayesiaLab 5.0 Professional Edition

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

o Random layouting Arc inversion tools.

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

Expert Knowledge Elicitation

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

BayesiaLab Professional Edition 5.0

PHP These export functions are available on subscription only.

Dynamic Bayesian networks

BayesiaLab Professional Edition 5.0

11 Protection with logical keys

BayesiaLab Professional Edition 5.0

12 Bayesia License Server

BayesiaLab Professional Edition 5.0

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