By Hopcroft J.E.
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5 Applications to Gene Expression Profiles 47 attributes that affect the system, such as experimental conditions, temporal indicators, and exogenous cellular conditions. As a result, we can model simultaneously the biological mechanisms we are interested in and the external conditions influencing them in a single, comprehensive network. 1 Model Averaging Consider, for example, the protein signaling data studied in Sachs et al. (2005). The data consist in the simultaneous measurements of 11 phosphorylated proteins and phospholypids derived from thousands of individual primary immune system cells, subjected to both general and specific molecular interventions.
Some examples from this class of algorithms are the following: • Greedy search algorithms such as hill-climbing with random restarts or tabu search (Bouckaert, 1995). 2). , 1997). In this case the search space is explored through the crossover (which combines the structure of two networks) and mutation (which introduces random alterations) stochastic operators. • Simulated annealing (Bouckaert, 1995). This algorithm performs a stochastic local search by accepting changes that increase the network score and, at the same time, allowing changes that decrease it with a probability inversely proportional to the score decrease.
This design choice makes network structures not as easy to modify as in bnlearn, because the parameters of the local distributions must be modified at the same time to preserve the coherence of the R object. Furthermore, in some cases the lack of accessor functions forces the user to work directly on the internals of the class, which increases the complexity of even simple tasks. , 2012). Consider, for instance, the undirected graph and the DAG shown in Fig. 2. With the deal package we can again create an empty network, which in this case is an object of class network.
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