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Table 7

From: Identifying protein complexes directly from high-throughput TAP data with Markov random fields

Algorithm: Mean field annealing

\SetKwInOut{Input}{Input}

\SetKwInOut{Output}{Output}

\Input{A set of observations (t ij , s ij ) for each pair (i, j), ψ, a number of clusters K}

\Output{A probability q ik for a node i belonging to a cluster k for all i and for all k}

Initialize q to random values;

Initialize annealing factor γ;

While γ <γmax Repeat q converges

ForAll i ∈ V

ForAll k ∈ K

C i k = ∑ j ∈ N e i g h b o r ( i ) q j k ( t i j − s i j ) + ( 1 − q j k ) ψ s i j MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@6230@

ForAll k ∈ K

q ^ i k = exp ( − γ C i k ) ∑ l = 1 K exp ( − γ C i l ) MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGafmyCaeNbaKaadaWgaaWcbaGaemyAaKMaem4AaSgabeaakiabg2da9KqbaoaalaaabaGagiyzauMaeiiEaGNaeiiCaaNaeiikaGIaeyOeI0ccciGae83SdCMaem4qam0aaSbaaeaacqWGPbqAcqWGRbWAaeqaaiabcMcaPaqaamaaqahabaGagiyzauMaeiiEaGNaeiiCaaNaeiikaGIaeyOeI0Iae83SdCMaem4qam0aaSbaaeaacqWGPbqAcqWGSbaBaeqaaiabcMcaPaqaaiabdYgaSjabg2da9iabigdaXaqaaiabdUealbGaeyyeIuoaaaaaaa@514E@

ForAll k ∈ K

q ik = q ^ i k MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGafmyCaeNbaKaadaWgaaWcbaGaemyAaKMaem4AaSgabeaaaaa@3034@

Increase γ;