{RAMA}: {A} Rapid Multicut Algorithm on {GPU}

We propose a highly parallel primal-dual algorithm for the multicut (a.k.a. correlation clustering) problem, a classical graph clustering problem widely used in machine learning and computer vision. Our algorithm consists of three steps executed recursively: (1) Finding conflicted cycles that correspond to violated inequalities of the underlying multicut relaxation, (2) Performing message passing between the edges and cycles to optimize the Lagrange relaxation coming from the found violated cycles producing reduced costs and (3) Contracting edges with high reduced costs through matrix-matrix multiplications. Our algorithm produces primal solutions and dual lower bounds that estimate the distance to optimum. We implement our algorithm on GPUs and show resulting one to two order-of-magnitudes improvements in execution speed without sacrificing solution quality compared to traditional serial algorithms that run on CPUs. We can solve very large scale benchmark problems with up to $\mathcal{O}(10^8)$ variables in a few seconds with small primal-dual gaps. We make our code available at https://github.com/pawelswoboda/RAMA

Bottleneck Potentials in {Markov Random Fields}

We consider general discrete Markov Random Fields(MRFs) with additional bottleneck potentials which penalize the maximum (instead of the sum) over local potential value taken by the MRF-assignment. Bottleneck potentials or analogous constructions have been considered in (i) combinatorial optimization (e.g. bottleneck shortest path problem, the minimum bottleneck spanning tree problem, bottleneck function minimization in greedoids), (ii) inverse problems with $L_{\infty}$-norm regularization, and (iii) valued constraint satisfaction on the $(\min,\max)$-pre-semirings. Bottleneck potentials for general discrete MRFs are a natural generalization of the above direction of modeling work to Maximum-A-Posteriori (MAP) inference in MRFs. To this end, we propose MRFs whose objective consists of two parts: terms that factorize according to (i) $(\min,+)$, i.e. potentials as in plain MRFs, and (ii) $(\min,\max)$, i.e. bottleneck potentials. To solve the ensuing inference problem, we propose high-quality relaxations and efficient algorithms for solving them. We empirically show efficacy of our approach on large scale seismic horizon tracking problems

Structured Prediction Problem Archive

Structured prediction problems are one of the fundamental tools in machinelearning. In order to facilitate algorithm development for their numericalsolution, we collect in one place a large number of datasets in easy to readformats for a diverse set of problem classes. We provide archival links todatasets, description of the considered problems and problem formats, and ashort summary of problem characteristics including size, number of instancesetc. For reference we also give a non-exhaustive selection of algorithmsproposed in the literature for their solution. We hope that this centralrepository will make benchmarking and comparison to established works easier.We welcome submission of interesting new datasets and algorithms for inclusionin our archive.<br

Macroscopic effects in attosecond pulse generation

We examine how the generation and propagation of high-order harmonics in a partly ionized gas medium affect their strength and synchronization. The temporal properties of the resulting attosecond pulses generated in long gas targets can be significantly influenced by macroscopic effects, in particular by the intensity in the medium and the degree of ionization. Under some conditions, the use of gas targets longer than the absorption length can lead to the generation of self-compressed attosecond pulses. We show this effect experimentally, using long argon-filled gas cells as generating medium.Comment: 5 pages 4 figure

Probing single-photon ionization on the attosecond time scale

We study photoionization of argon atoms excited by attosecond pulses using an interferometric measurement technique. We measure the difference in time delays between electrons emitted from the $3s^2$ and from the $3p^6$ shell, at different excitation energies ranging from 32 to 42 eV. The determination of single photoemission time delays requires to take into account the measurement process, involving the interaction with a probing infrared field. This contribution can be estimated using an universal formula and is found to account for a substantial fraction of the measured delay.Comment: 4 pages, 4 figures, under consideratio

Molecular differentiation between osteophytic and articular cartilage – clues for a transient and permanent chondrocyte phenotype

SummaryObjectiveTo identify the molecular differences between the transient and permanent chondrocyte phenotype in osteophytic and articular cartilage.MethodsTotal RNA was isolated from the cartilaginous layer of osteophytes and from intact articular cartilage from knee joints of 15 adult human donors and subjected to cDNA microarray analysis. The differential expression of relevant genes between these two cartilaginous tissues was additionally validated by quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and by immunohistochemistry.ResultsAmong 47,000 screened transcripts, 600 transcripts were differentially expressed between osteophytic and articular chondrocytes. Osteophytic chondrocytes were characterized by increased expression of genes involved in the endochondral ossification process [bone gamma-carboxyglutamate protein/osteocalcin (BGLAP), bone morphogenetic protein-8B (BMP8B), collagen type I, alpha 2 (COL1A2), sclerostin (SOST), growth arrest and DNA damage-induced gene 45ß (GADD45ß), runt-related transcription factor 2 (RUNX2)], and genes encoding tissue remodeling enzymes [matrix metallopeptidase (MMP)9, 13, hyaluronan synthase 1 (HAS1)]. Articular chondrocytes expressed increased transcript levels of antagonists and inhibitors of the BMP- and Wnt-signaling pathways [Gremlin-1 (GREM1), frizzled-related protein (FRZB), WNT1 inducible signaling pathway protein-3 (WISP3)], as well as factors that inhibit terminal chondrocyte differentiation and endochondral bone formation [parathyroid hormone-like hormone (PTHLH), sex-determining region Y-box 9 (SOX9), stanniocalcin-2 (STC2), S100 calcium binding protein A1 (S100A1), S100 calcium binding protein B (S100B)].Immunohistochemistry of tissue sections for GREM1 and BGLAP, the two most prominent differentially expressed genes, confirmed selective detection of GREM1 in articular chondrocytes and that of BGLAP in osteophytic chondrocytes and bone.ConclusionsOsteophytic and articular chondrocytes significantly differ in their gene expression pattern. In articular cartilage, a prominent expression of antagonists inhibiting the BMP- and Wnt-pathway may serve to lock and stabilize the permanent chondrocyte phenotype and thus prevent their terminal differentiation. In contrast, osteophytic chondrocytes express genes with roles in the endochondral ossification process, which may account for their transient phenotype

Intensity Dependence of Laser-Assisted Attosecond Photoionization Spectra

We study experimentally the influence of the intensity of the infrared (IR) probe field on attosecond pulse train (APT) phase measurements performed with the RABITT method (Reconstruction of Attosecond Beating by Interference in Two-Photon Transitions). We find that if a strong IR field is applied, the attosecond pulses will appear to have lower-than-actual chirp rates. We also observe the onset of the streaking regime in the breakdown of the weak-field RABITT conditions. We perform a Fourier-analysis of harmonic and sideband continuum states and show that the mutual phase relation of the harmonics can be extracted from higher Fourier components.Comment: preprint to article in Laser Physics Nikolai B. Delone memorial issue 11 pages, 9 figures, published online 15 July 200