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Ontological Fuzzy Rule System (OFRS)

Dans le document Data Mining in Biomedicine Using Ontologies (Page 134-137)

Mapping Genes to Biological Pathways Using Ontological Fuzzy Rule Systems

6.3 Ontological Fuzzy Rule System (OFRS)

weights is that T1 is T3 to the extent of 0.9, but T3 is T2 only to the extent of 0.4.

The weight values (0.4 and 0.9) were chosen arbitrarily (as in [1]), but they can be learned from a corpus based on term co-occurrences [17].

Example 6.1 Consider the ontology snippet from Figure 6.3 with two terms, T1 and T2, that have a common parent T3. There are two ways of getting from T1 to T2, (T1,T3,T2) and (T1,T3,T4,T3,T2), hence the similarity between T1 and T2 is according to (1) s12=max{w(T1→T3) × w(T3→T2), w(T1→T3) × w(T3→T4) × w(T4→T3) × w(T3→T2)} = max{0.9 × 0.4, 0.9 × 0.9 × 0.4 × 0.4}=0.36.

A more general case is when C1 is an object that has some properties described by a set of terms (such as T1 and T2). The question is then to compute the similar-ity, s(C1,C2), of the object C1 to another object C2, described by terms from the same ontology. The resulting similarity is interpreted as the object C2 is a C1 to the extent of s(C1,C2). One method for computing the similarity between two objects C1={T11,..., T1n} and C2={T21, ...,T2m}, described by ontology terms, is the

where s(t1i, T2j) is computed using (6.1). The normalization of the average ensures that s(C1,C1)=1. Other possible similarity measures are described in Chapter 2.

Example 6.2 Let us compute the similarity between two objects, C1={T1, T2} and C2={T3, T4}. First, observe that if we do not consider the ontological relations be-tween the terms Ti, i∈{1,2,3,4}, the similarity between the two objects is 0. Assume that, using some term-similarity measure, such as Formula (1) in some ontology, we have: s(T1,T2) = 0.2, s(T1,T3) = 0.3, s(T1,T4) = 0.4, s(T2,T3) = 0.5, s(T2,T4) = 0.6, s(T3,T4) = 0.7, and s(Ti,Ti) = 1 for any i∈{1,2,3,4}. Then, using (6.2), we ob-tain sa(C1,C2) = 0.45, sa(C1,C1) = 0.8, sa(C2,C2) = 0.85 and, fi nally, s(C1,C2)=0.45/

max{0.8, 0.85} = 0.53.

An interesting method for defi ning the distance between entities in fi rst-order logic (FOL) was found in [3]. The method was based on comparing the predicates used to describe two objects, and it was used in the conceptual clustering system, KBG.

6.3 Ontological Fuzzy Rule System (OFRS)

We defi ne an ontological fuzzy rule system (OFRS) by analogy to a Mamdani fuzzy rule system (FRS). A typical Mamdani FRS with n inputs and 1 output variable has the following form [6]:

where Gij and Pi, i∈ [1,m], and j∈ [1,n], are fuzzy sets, {xi} is the inputs variable, and y is the output variable, respectively. The fuzzy sets Gij are possible values for the variable xi, while Pi is a possible value for the output y. Gij and Pi are usually represented using membership functions of the type shown in Figure 6.1. A Mam-dani FRS for m = 2 and n = 2 is shown in Figure 6.4.

The computation of the FRS output, y0 ∈ R, for two inputs x10, x20 ∈ R, is performed as follows:

The memberships, wij=Gij(xi0), are computed for each rule i and input j, i,j∈{1,2}.

Second, the activation, ai, of rule i is computed as ai = wi1⊕wi2, where ⊕ is an AND type operator. In most applications ⊕ is minimum (that is, ai = min{wi1,wi2}), but other choices are possible (see [6]). It is also possible for the variables in the rule antecedent (left-hand side) to be joined by an OR type operator. In this case, the typical operator employed is maximum, that is, ai = max{wi1,wi2}. After computing the activation, the output of each rule is computed as aiPi,which is the shaded area of each output membership Pi shown in Figure 6.4. The fuzzy output of the system, Psum, is computed by aggregating the individual rule outputs as Psum = max{a1P1, a2P2}. Here, too, more choices of aggregating operators, other than max, are pos-sible. The fi nal step of the computation is called defuzzifi cation, and it consists of reducing the output fuzzy set Psum to a number. Among the most used defuzzifi -cation procedures are the center of gravity (COG, y0 in Figure 6.4) and mean of maximum (MOM, y1 in Figure 6.4). Using the COG procedure, the output of the FRS, y0, is computed as the center of the area under the membership function Psum. By employing the MOM algorithm, the output y1 is computed as the center of the region where the membership Psum is the maximum.

An OFRS is similar to the FRS described above, except Some/all input fuzzy sets

1. Gij are replaced by ontology terms or by objects described by ontology terms. The variables related to these terms or objects are called symbolic variables. As opposed to the numeric variables, for

Figure 6.4 A Mamdani fuzzy rule system with n = 2 rules and m = 2 inputs. The inputs and the output of the system are real numbers.

6.3 Ontological Fuzzy Rule System (OFRS) 119

which the values are fuzzy sets represented by functions, the symbolic variables have values that consist of ontology terms or objects represented by ontology terms. Similarly, the output fuzzy sets Pi are replaced with terms from the same ontology (output ontology) in order to allow the assessment of relatedness (similarity). The output of the OFRS consists of a term or a set of terms from the output ontology.

The membership,

2. wij, of the input xi in the Gij is now computed, based on the similarity of the two terms (objects), using (6.1) or (6.2) as wij = s(xi, Gij).

The aggregation of the rule output has to take into account that the fi nal 3.

output of the OFRS should be a term or a set of terms. Consequently, the defuzzifi cation procedure has to summarize the output of the set of rules in few terms. Similar to the defuzzifi cation procedures described above for FRS, we mention two summarization procedures. The fi rst procedure, somewhat similar to MOM, chooses as output the term Pk, with the maximum activation, where k is given by

1,

{ }

arg max i

i m

k a

= = (6.4)

The wining rule activation ak may be used as the confi dence of the OFRS output.

This fi rst case does not use the term similarity as mentioned in item 2. The second procedure, denoted here as ontological COG (OCOG), tries to fi nd the

“center”of all output terms Pi. In this case, the output term Pk is chosen as

( )

1

The OCOG procedure has two desired properties. First, the ancestors of a term contribute to the term’s importance, and hence, to its chance of winning in (6.5).

Second, since the similarity relation is nonsymmetrical, that is s(ancestor, child) <

s(child, ancestor) (as explained in Figure 6.3), the child does not contribute as much to its ancestor. Hence, the OCOG procedure tends to choose the more specifi c term as the fi nal output. However, the average similarity value in (6.5) has a tendency of producing low membership values. A possible solution for this problem is to use an OWA-type operator [19], such as summing only the fi rst n’ most similar terms where n´ < n.

Example 6.3 Consider the following medical OFRS:

rule 1: IF x1=“back aches” AND x2=“high fever” THEN P1=“spinal meningitis”

rule 2: IF x1=“aches” AND x2=“moderate fever” THEN P2=“fl u”

In the above OFRS, x1 is a symbolic variable (a symptom), and x2 is a numeric one (the fever in degrees Fahrenheit). Assume, as in Figure 6.3, that s(“back aches,”

“aches”) = 0.9, s(“aches,” “back aches”) = 0.4, s(“fl u,” “spinal meningitis”) = 0.1, s(“spinal meningitis,” “fl u”) = 0.2, and all self-similarities s(Ti, Ti) = 1. Moreover,

assume that the memberships for fever (“moderate” and “high”) are similar to the ones from Figure 6.1, but adapted to the range of the fever. For the purpose of this example, we assume the following memberships: w(“moderate,” 100) = 0.9 and w(“high,”100) = 0.5.

For an input x = {x1 = “aches,” x2 = 100}, rule 1 will have an activation a1 = min{0.9,0.5} = 0.5 and rule 2 will have a2 = min{1,0.9}=0.9. Using (6.4), the output of the system is given by argmax{0.5, 0.9} = 2, that is, P2 = “fl u,” with confi dence 0.9. Note, that the activation of the fi rst rule is also signifi cant (0.5).

If we use (6.5) for the same input, we get argmax{(0.5*1+0.5*0.2)/2, (0.9*1+0.9*0.1)/2} = argmax{0.3, 0.49} = 2; hence, the output is P2, with confi -dence 0.49. Here we see the tendency of the average operator from (6.5) to produce low confi dence values (0.49 is much smaller than 0.9, which was obtained in the fi rst case.

Dans le document Data Mining in Biomedicine Using Ontologies (Page 134-137)