Area under curve (AUC) comparison at specific recalls.

<p>The AUCs are calculated in the recall (<i>x</i>)-precision (<i>y</i>) plane. The best precision at a specific recall is highlighted in bold.</p

Adjusted area under curve (AUC) comparison at specific recalls.

<p>The adjusted AUCs are the AUCs in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075940#pone-0075940-t002" target="_blank">Table 2</a> divided by the AUC that a perfect predictor can achieve at the corresponding recall. The best precision at a specific recall is highlighted in bold.</p

Comparison of the proposed two-stage approach to three PP-based techniques.

<p>The <i>y</i>-axis is the ratio of correct predictions predicted in the top <i>n</i> predictions (<i>x</i>-axis).</p

Performance using different reference collections.

<p>The <i>y</i>-axis is the ratio of correct predictions predicted in the top <i>n</i> predictions (<i>x</i>-axis).</p

Number of pairs that passed the non-zero filter and the first stage using different reference collections.

<p>This table reveals the number of pairs with reliable and similar PPs using different reference collections.</p

Schematic diagram of encoding a protein sequence into a feature vector.

<p>Step 1: Transform the amino acid sequence into the group sequence. Step 2: Scan the group sequence and count the triads in the occurrence vector <b>O</b>.</p

Workflow of the proposed two-stage framework of functional linkage prediction.

<p>Given a query protein pair, the first stage constructs and compares their phylogenetic profiles. A unique feature of the first stage is a non-zero filter (marked by an asterisk), which delivers no prediction (denoted as n/a) if either phylogenetic profile contains too less non-zero elements. A pair with similar phylogenetic profiles is submitted to the second stage for the final prediction.</p

The relationships among the number of predictions (<i>x</i>-axis), the non-zero thresholds (<i>y</i>-axis) and the prediction performance (color) with different reference collections of (a) 829 prokaryotes and (b) 132 eukaryotes.

<p>Since different applications might require different number of predictions, the colors of a specific abscissa were normalized from red to green. Thus, one can quickly identify the best non-zero threshold under a specific number of predictions.</p

Performance of the proposed two-stage approach and the individual stages.

<p>The <i>y</i>-axis is the ratio of correct predictions predicted in the top <i>n</i> predictions (<i>x</i>-axis).</p

Performance of using different non-zero (<i>nz</i>) thresholds.

<p>The <i>y</i>-axis is the ratio of correct predictions predicted in the top <i>n</i> predictions (<i>x</i>-axis).</p