129,255 research outputs found
Mammalian gene expression variability is explained by underlying cell state.
Gene expression variability in mammalian systems plays an important role in physiological and pathophysiological conditions. This variability can come from differential regulation related to cell state (extrinsic) and allele-specific transcriptional bursting (intrinsic). Yet, the relative contribution of these two distinct sources is unknown. Here, we exploit the qualitative difference in the patterns of covariance between these two sources to quantify their relative contributions to expression variance in mammalian cells. Using multiplexed error robust RNA fluorescent in situ hybridization (MERFISH), we measured the multivariate gene expression distribution of 150 genes related to Ca2+ signaling coupled with the dynamic Ca2+ response of live cells to ATP. We show that after controlling for cellular phenotypic states such as size, cell cycle stage, and Ca2+ response to ATP, the remaining variability is effectively at the Poisson limit for most genes. These findings demonstrate that the majority of expression variability results from cell state differences and that the contribution of transcriptional bursting is relatively minimal
Nonlinear Hebbian learning as a unifying principle in receptive field formation
The development of sensory receptive fields has been modeled in the past by a
variety of models including normative models such as sparse coding or
independent component analysis and bottom-up models such as spike-timing
dependent plasticity or the Bienenstock-Cooper-Munro model of synaptic
plasticity. Here we show that the above variety of approaches can all be
unified into a single common principle, namely Nonlinear Hebbian Learning. When
Nonlinear Hebbian Learning is applied to natural images, receptive field shapes
were strongly constrained by the input statistics and preprocessing, but
exhibited only modest variation across different choices of nonlinearities in
neuron models or synaptic plasticity rules. Neither overcompleteness nor sparse
network activity are necessary for the development of localized receptive
fields. The analysis of alternative sensory modalities such as auditory models
or V2 development lead to the same conclusions. In all examples, receptive
fields can be predicted a priori by reformulating an abstract model as
nonlinear Hebbian learning. Thus nonlinear Hebbian learning and natural
statistics can account for many aspects of receptive field formation across
models and sensory modalities
Perceptual-based textures for scene labeling: a bottom-up and a top-down approach
Due to the semantic gap, the automatic interpretation of digital images is a very challenging task. Both the segmentation and classification are intricate because of the high variation of the data. Therefore, the application of appropriate features is of utter importance. This paper presents biologically inspired texture features for material classification and interpreting outdoor scenery images. Experiments show that the presented texture features obtain the best classification results for material recognition compared to other well-known texture features, with an average classification rate of 93.0%. For scene analysis, both a bottom-up and top-down strategy are employed to bridge the semantic gap. At first, images are segmented into regions based on the perceptual texture and next, a semantic label is calculated for these regions. Since this emerging interpretation is still error prone, domain knowledge is ingested to achieve a more accurate description of the depicted scene. By applying both strategies, 91.9% of the pixels from outdoor scenery images obtained a correct label
The Hough transform estimator
This article pursues a statistical study of the Hough transform, the
celebrated computer vision algorithm used to detect the presence of lines in a
noisy image. We first study asymptotic properties of the Hough transform
estimator, whose objective is to find the line that ``best'' fits a set of
planar points. In particular, we establish strong consistency and rates of
convergence, and characterize the limiting distribution of the Hough transform
estimator. While the convergence rates are seen to be slower than those found
in some standard regression methods, the Hough transform estimator is shown to
be more robust as measured by its breakdown point. We next study the Hough
transform in the context of the problem of detecting multiple lines. This is
addressed via the framework of excess mass functionals and modality testing.
Throughout, several numerical examples help illustrate various properties of
the estimator. Relations between the Hough transform and more mainstream
statistical paradigms and methods are discussed as well.Comment: Published at http://dx.doi.org/10.1214/009053604000000760 in the
Annals of Statistics (http://www.imstat.org/aos/) by the Institute of
Mathematical Statistics (http://www.imstat.org
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