Sparsity Invariant CNNs

In this paper, we consider convolutional neural networks operating on sparse inputs with an application to depth upsampling from sparse laser scan data. First, we show that traditional convolutional networks perform poorly when applied to sparse data even when the location of missing data is provided to the network. To overcome this problem, we propose a simple yet effective sparse convolution layer which explicitly considers the location of missing data during the convolution operation. We demonstrate the benefits of the proposed network architecture in synthetic and real experiments with respect to various baseline approaches. Compared to dense baselines, the proposed sparse convolution network generalizes well to novel datasets and is invariant to the level of sparsity in the data. For our evaluation, we derive a novel dataset from the KITTI benchmark, comprising 93k depth annotated RGB images. Our dataset allows for training and evaluating depth upsampling and depth prediction techniques in challenging real-world settings and will be made available upon publication

DeMoN: Depth and Motion Network for Learning Monocular Stereo

In this paper we formulate structure from motion as a learning problem. We train a convolutional network end-to-end to compute depth and camera motion from successive, unconstrained image pairs. The architecture is composed of multiple stacked encoder-decoder networks, the core part being an iterative network that is able to improve its own predictions. The network estimates not only depth and motion, but additionally surface normals, optical flow between the images and confidence of the matching. A crucial component of the approach is a training loss based on spatial relative differences. Compared to traditional two-frame structure from motion methods, results are more accurate and more robust. In contrast to the popular depth-from-single-image networks, DeMoN learns the concept of matching and, thus, better generalizes to structures not seen during training.Comment: Camera ready version for CVPR 2017. Supplementary material included. Project page: http://lmb.informatik.uni-freiburg.de/people/ummenhof/depthmotionnet

Partially gapped fermions in 2D

We compute mean field phase diagrams of two closely related interacting fermion models in two spatial dimensions (2D). The first is the so-called 2D t-t'-V model describing spinless fermions on a square lattice with local hopping and density-density interactions. The second is the so-called 2D Luttinger model that provides an effective description of the 2D t-t'-V model and in which parts of the fermion degrees of freedom are treated exactly by bosonization. In mean field theory, both models have a charge-density-wave (CDW) instability making them gapped at half-filling. The 2D t-t'-V model has a significant parameter regime away from half-filling where neither the CDW nor the normal state are thermodynamically stable. We show that the 2D Luttinger model allows to obtain more detailed information about this mixed region. In particular, we find in the 2D Luttinger model a partially gapped phase that, as we argue, can be described by an exactly solvable model.Comment: v1: 36 pages, 10 figures, v2: minor corrections; equation references to arXiv:0903.0055 updated

O DESAFIO DO LICENCIAMENTO AMBIENTAL NO MUNICÍPIO DE ROCA SALES, RIO GRANDE DO SUL, BRASIL

The public administrations are increasingly concerned with preserving the environment.From the Resolution No. 237/97 of the National Council for the Environment, the assessment of local environmental impacts, caused by enterprises, became to be the competence of the municipalities. This study presents the main demands of environmental licensing of local impact in the period of January 2010 to July 2012, in the municipality of Roca Sales / RS. From the analysis of the environmental licensing procedures applied by the municipal Department of Environment technical criteria were established for the licensing activities of environmental of local impact, thereby promoting the sustainability of local properties and making aware entrepreneurs about the importance of using sustainable practices aimed at streamlining the overuse of natural resources. The data were obtained from 522 licenses issued by the municipality. The results show a significant demand for the Operating License and Single License. The data express the interests of the entrepreneurs to regularize the enterprises and the municipal government in acting by inspecting,  licensing and acting in order to educate the population about the  importance of environmental licensing.As administrações públicas estão cada vez mais preocupadas com a preservação do ambiente. A partir da Resolução nº 237/97 do Conselho Nacional do Meio Ambiente, a avaliação dos impactos ambientais locais, causados pelos empreendimentos, passaram a ser de competência dos municípios. Assim, este estudo apresenta as principais demandas de licenciamento ambiental de impacto local realizadas no período de janeiro de 2010 a julho de 2012, no município de Roca Sales/RS. A partir da análise dos procedimentos de licenciamento ambiental aplicados pelo Departamento de Meio Ambiente municipal, foram estabelecidos critérios técnicos para as atividades de licenciamento ambiental de impacto local, promovendo assim a sustentabilidade das propriedades locais e conscientizando os empreendedores da importância de uso de práticas sustentáveis que visam à racionalização do uso excessivo de recursos naturais. Obtiveram-se os dados de 522 licenças emitidas pelo município. Os resultados mostram uma procura significativa pela Licença de Operação de Regularização e pela Licença Única. Os dados expressam o interesse dos empreendedores em regularizar os empreendimentos e do poder público municipal em atuar fiscalizando, licenciando e atuando no sentido de conscientizar a população sobre a importância do licenciamento ambiental

Dynamical decoupling and noise spectroscopy with a superconducting flux qubit

The characterization and mitigation of decoherence in natural and artificial two-level systems (qubits) is fundamental to quantum information science and its applications. Decoherence of a quantum superposition state arises from the interaction between the constituent system and the uncontrolled degrees of freedom in its environment. Within the standard Bloch-Redfield picture of two-level system dynamics, qubit decoherence is characterized by two rates: a longitudinal relaxation rate Gamma1 due to the exchange of energy with the environment, and a transverse relaxation rate Gamma2 = Gamma1/2 + Gamma_phi which contains the pure dephasing rate Gamma_phi. Irreversible energy relaxation can only be mitigated by reducing the amount of environmental noise, reducing the qubit's internal sensitivity to that noise, or through multi-qubit encoding and error correction protocols (which already presume ultra-low error rates). In contrast, dephasing is in principle reversible and can be refocused dynamically through the application of coherent control pulse methods. In this work we demonstrate how dynamical-decoupling techniques can moderate the dephasing effects of low-frequency noise on a superconducting qubit with energy-relaxation time T1 = 1/Gamma1 = 12 us. Using the CPMG sequence with up to 200 pi-pulses, we demonstrate a 50-fold improvement in the transverse relaxation time T2 over its baseline value. We observe relaxation-limited times T2(CPMG) = 23 us = 2 T1 resulting from CPMG-mediated Gaussian pure-dephasing times in apparent excess of 100 us. We leverage the filtering property of this sequence in conjunction with Rabi and energy relaxation measurements to facilitate the spectroscopy and reconstruction of the environmental noise power spectral density.Comment: 21 pages (incl. 11-page appendix); 4 (+7) figure

Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome

Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein level. Here, we report a high‐resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 hr light:12 hr dark diurnal cycle and the phosphoproteome immediately before and after the light‐to‐dark and dark‐to‐light transitions. We quantified nearly 5,000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light–dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin‐dependent kinases among the primary light–dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.ISSN:0140-7791ISSN:1365-304

Deconvolution of sarcoma methylomes reveals varying degrees of immune cell infiltrates with association to genomic aberrations

Background!#!Soft-tissue sarcomas (STS) are a heterogeneous group of mesenchymal tumors for which response to immunotherapies is not well established. Therefore, it is important to risk-stratify and identify STS patients who will most likely benefit from these treatments.!##!Results!#!To reveal shared and distinct methylation signatures present in STS, we performed unsupervised deconvolution of DNA methylation data from the TCGA sarcoma and an independent validation cohort. We showed that leiomyosarcoma can be subclassified into three distinct methylation groups. More importantly, we identified a component associated with tumor-infiltrating leukocytes, which suggests varying degrees of immune cell infiltration in STS subtypes and an association with prognosis. We further investigated the genomic alterations that may influence tumor infiltration by leukocytes including RB1 loss in undifferentiated pleomorphic sarcomas and ELK3 amplification in dedifferentiated liposarcomas.!##!Conclusions!#!In summary, we have leveraged unsupervised methylation-based deconvolution to characterize the immune compartment and molecularly stratify subtypes in STS, which may benefit precision medicine in the future

Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag

The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates. SNAP-tag labeling rate constants, however, are less affected by the structure of the label than those of HaloTag7, which vary over 6 orders of magnitude for commonly employed substrates. Determining the crystal structures of HaloTag7 and SNAP-tag labeled with fluorescent substrates allowed us to rationalize their substrate preferences. We also demonstrate how these insights can be exploited to design substrates with improved labeling kinetics.ISSN:0006-2960ISSN:1520-499