Fig. 1

Flow chart of binary interaction network model. a Experimental AP-MS data. It includes two type of observations: bait-prey observations and prey-prey observations. b Co-complex interaction network (W _obs ). It can be derived from AP-MS data using some scoring schemes. It often contains both direct physical interactions and indirect interactions with no clear separation. This map illustrates the Collins and Friedel datasets. c Schematic overview of BINM model. Our model captures topological relationships between direct physical interactions and observed co-complex interactions in terms of the following assumptions: 1) the observed co-complex interactions are the sum of both direct physical interactions and indirect interactions; 2) the indirect interactions are captured by direct interactions through the common neighbors. Then the binary interaction detection problem can be transformed into a nonnegative constrained optimization problem. d Binary interaction network (W _dir ) identified by BINM. After finding an optimal solution for the BINM model, the observed interactions are ranked by their BINM scores (e.g., W _dir ). Top ranked interactions can be predicted as direct physical interactions. The map depicts binary networks induced by the top 2562 and 3018 interactions for the Collins and Friedel datasets, respectively. We discuss how to determine the rank cutoffs in the Results section