Analysis tools for the interplay between genome layout and regulation

Genome layout and gene regulation appear to be interdependent. Understanding this interdependence is key to exploring the dynamic nature of chromosome conformation and to engineering functional genomes. Evidence for non-random genome layout, defined as the relative positioning of either co-functional or co-regulated genes, stems from two main approaches. Firstly, the analysis of contiguous genome segments across species, has highlighted the conservation of gene arrangement (synteny) along chromosomal regions. Secondly, the study of long-range interactions along a chromosome has emphasised regularities in the positioning of microbial genes that are co-regulated, co-expressed or evolutionarily correlated. While one-dimensional pattern analysis is a mature field, it is often powerless on biological datasets which tend to be incomplete, and partly incorrect. Moreover, there is a lack of comprehensive, user-friendly tools to systematically analyse, visualise, integrate and exploit regularities along genomes.Here we present the Genome REgulatory and Architecture Tools SCAN (GREAT:SCAN) software for the systematic study of the interplay between genome layout and gene expression regulation.SCAN is a collection of related and interconnected applications currently able to perform systematic analyses of genome regularities as well as to improve transcription factor binding sites (TFBS) and gene regulatory network predictions based on gene positional information.We demonstrate the capabilities of these tools by studying on one hand the regular patterns of genome layout in the major regulons of the bacterium Escherichia coli. On the other hand, we demonstrate the capabilities to improve TFBS prediction in microbes. Finally, we highlight, by visualisation of multivariate techniques, the interplay between position and sequence information for effective transcription regulation

A Convex Relaxation for Weakly Supervised Classifiers

This paper introduces a general multi-class approach to weakly supervised classification. Inferring the labels and learning the parameters of the model is usually done jointly through a block-coordinate descent algorithm such as expectation-maximization (EM), which may lead to local minima. To avoid this problem, we propose a cost function based on a convex relaxation of the soft-max loss. We then propose an algorithm specifically designed to efficiently solve the corresponding semidefinite program (SDP). Empirically, our method compares favorably to standard ones on different datasets for multiple instance learning and semi-supervised learning as well as on clustering tasks.Comment: Appears in Proceedings of the 29th International Conference on Machine Learning (ICML 2012

Annotating Synapses in Large EM Datasets

Reconstructing neuronal circuits at the level of synapses is a central problem in neuroscience and becoming a focus of the emerging field of connectomics. To date, electron microscopy (EM) is the most proven technique for identifying and quantifying synaptic connections. As advances in EM make acquiring larger datasets possible, subsequent manual synapse identification ({\em i.e.}, proofreading) for deciphering a connectome becomes a major time bottleneck. Here we introduce a large-scale, high-throughput, and semi-automated methodology to efficiently identify synapses. We successfully applied our methodology to the Drosophila medulla optic lobe, annotating many more synapses than previous connectome efforts. Our approaches are extensible and will make the often complicated process of synapse identification accessible to a wider-community of potential proofreaders

The cellular and synaptic architecture of the mechanosensory dorsal horn

The deep dorsal horn is a poorly characterized spinal cord region implicated in processing low-threshold mechanoreceptor (LTMR) information. We report an array of mouse genetic tools for defining neuronal components and functions of the dorsal horn LTMR-recipient zone (LTMR-RZ), a role for LTMR-RZ processing in tactile perception, and the basic logic of LTMR-RZ organization. We found an unexpectedly high degree of neuronal diversity in the LTMR-RZ: seven excitatory and four inhibitory subtypes of interneurons exhibiting unique morphological, physiological, and synaptic properties. Remarkably, LTMRs form synapses on between four and 11 LTMR-RZ interneuron subtypes, while each LTMR-RZ interneuron subtype samples inputs from at least one to three LTMR classes, as well as spinal cord interneurons and corticospinal neurons. Thus, the LTMR-RZ is a somatosensory processing region endowed with a neuronal complexity that rivals the retina and functions to pattern the activity of ascending touch pathways that underlie tactile perception

Multimodal MRI-based Imputation of the Aβ+ in Early Mild Cognitive Impairment.

ObjectiveTo identify brain atrophy from structural-MRI and cerebral blood flow(CBF) patterns from arterial spin labeling perfusion-MRI that are best predictors of the Aβ-burden, measured as composite 18F-AV45-PET uptake, in individuals with early mild cognitive impairment(MCI). Furthermore, to assess the relative importance of imaging modalities in classification of Aβ+/Aβ- early mild cognitive impairment.MethodsSixty-seven ADNI-GO/2 participants with early-MCI were included. Voxel-wise anatomical shape variation measures were computed by estimating the initial diffeomorphic mapping momenta from an unbiased control template. CBF measures normalized to average motor cortex CBF were mapped onto the template space. Using partial least squares regression, we identified the structural and CBF signatures of Aβ after accounting for normal cofounding effects of age, sex, and education.Results18F-AV45-positive early-MCIs could be identified with 83% classification accuracy, 87% positive predictive value, and 84% negative predictive value by multidisciplinary classifiers combining demographics data, ApoE ε4-genotype, and a multimodal MRI-based Aβ score.InterpretationMultimodal-MRI can be used to predict the amyloid status of early-MCI individuals. MRI is a very attractive candidate for the identification of inexpensive and non-invasive surrogate biomarkers of Aβ deposition. Our approach is expected to have value for the identification of individuals likely to be Aβ+ in circumstances where cost or logistical problems prevent Aβ detection using cerebrospinal fluid analysis or Aβ-PET. This can also be used in clinical settings and clinical trials, aiding subject recruitment and evaluation of treatment efficacy. Imputation of the Aβ-positivity status could also complement Aβ-PET by identifying individuals who would benefit the most from this assessment

Efficient Asymmetric Co-Tracking using Uncertainty Sampling

Adaptive tracking-by-detection approaches are popular for tracking arbitrary objects. They treat the tracking problem as a classification task and use online learning techniques to update the object model. However, these approaches are heavily invested in the efficiency and effectiveness of their detectors. Evaluating a massive number of samples for each frame (e.g., obtained by a sliding window) forces the detector to trade the accuracy in favor of speed. Furthermore, misclassification of borderline samples in the detector introduce accumulating errors in tracking. In this study, we propose a co-tracking based on the efficient cooperation of two detectors: a rapid adaptive exemplar-based detector and another more sophisticated but slower detector with a long-term memory. The sampling labeling and co-learning of the detectors are conducted by an uncertainty sampling unit, which improves the speed and accuracy of the system. We also introduce a budgeting mechanism which prevents the unbounded growth in the number of examples in the first detector to maintain its rapid response. Experiments demonstrate the efficiency and effectiveness of the proposed tracker against its baselines and its superior performance against state-of-the-art trackers on various benchmark videos.Comment: Submitted to IEEE ICSIPA'201

Proceedings of the second "international Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST'14)

The implicit objective of the biennial "international - Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST) is to foster collaboration between international scientific teams by disseminating ideas through both specific oral/poster presentations and free discussions. For its second edition, the iTWIST workshop took place in the medieval and picturesque town of Namur in Belgium, from Wednesday August 27th till Friday August 29th, 2014. The workshop was conveniently located in "The Arsenal" building within walking distance of both hotels and town center. iTWIST'14 has gathered about 70 international participants and has featured 9 invited talks, 10 oral presentations, and 14 posters on the following themes, all related to the theory, application and generalization of the "sparsity paradigm": Sparsity-driven data sensing and processing; Union of low dimensional subspaces; Beyond linear and convex inverse problem; Matrix/manifold/graph sensing/processing; Blind inverse problems and dictionary learning; Sparsity and computational neuroscience; Information theory, geometry and randomness; Complexity/accuracy tradeoffs in numerical methods; Sparsity? What's next?; Sparse machine learning and inference.Comment: 69 pages, 24 extended abstracts, iTWIST'14 website: http://sites.google.com/site/itwist1