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Most neurons involved in perceptual judgments are at least two synapses removed from sensory receptors. Psychophysical models that link perception to the physical qualities of external stimuli are thus black boxes. Opening these black boxes is challenging and requires comprehensive estimates of activity in many neurons carrying perceptually relevant signals. Because sensory representations are distributed over large numbers of neurons, such estimates have generally remained elusive. Here, we take advantage of the well-characterized olfactory system of fruit flies to relate knowledge of the neuronal population representations of odors to behavioral measures of odor discrimination. Flies detect odors using ~50 types of olfactory receptor neurons (ORNs). ORN axons segregate anatomically by receptor type and transmit signals via separate synaptic relays, to discrete classes of excitatory projection neurons (ePNs). Previously, ORN responses to odors and a transformation estimating PN spike rates from measured ORN spike rates were presented. ePNs project to the mushroom body, and the lateral horn (LH). The LH, thought to be responsible of naïve behavior, also receives input from a functionally uncharacterized group of GABAergic inhibitory PNs (iPNs). The fact that iPNs target exclusively the LH hints at a possible function of these inhibitory neurons in naïve behavior. We formulate and test a simple model of innate odor discrimination that takes as its input the estimated PN signals projected onto the LH and generates as its output a prediction of whether two odors can be distinguished. We show that the main determinant of discriminability is the distance between the PN activity patterns evoked by two odors. Experimental manipulations of this distance have graded predictable perceptual consequences. We further show that, inhibition by iPNs makes closely related odors easier to distinguish, in all likelihood by imposing a high-pass filter on ePN output that stretches the distances between partially overlapping odor representations.