{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

Protective effects of the thioredoxin and glutaredoxin systems in dopamine-induced cell death

Although the etiology of sporadic Parkinson disease (PD) is unknown, it is well established that oxidative stress plays an important role in the pathogenic mechanism. The thioredoxin (Trx) and glutaredoxin (Grx) systems are two central systems upholding the sulfhydryl homeostasis by reducing disulfides and mixed disulfides within the cell and thereby protecting against oxidative stress. By examining the expression of redox proteins in human postmortem PD brains, we found the levels of Trx1 and thioredoxin reductase 1 (TrxR1) to be significantly decreased. The human neuroblastoma cell line SH-SY5Y and the nematode Caenorhabditis elegans were used as model systems to explore the potential protective effects of the redox proteins against 6-hydroxydopamine (6-OHDA)-induced cytotoxicity. 6-OHDA is highly prone to oxidation, resulting in the formation of the quinone of 6-OHDA, a highly reactive species and powerful neurotoxin. Treatment of human cells with 6-OHDA resulted in an increased expression of Trx1, TrxR1, Grx1, and Grx2, and small interfering RNA for these genes significantly increased the cytotoxic effects exerted by the 6-OHDA neurotoxin. Evaluation of the dopaminergic neurons in C. elegans revealed that nematodes lacking trxr-1 were significantly more sensitive to 6-OHDA, with significantly increased neuronal degradation. Importantly, both the Trx and the Grx systems were also found to directly mediate reduction of the 6-OHDA-quinone in vitro and thus render its cytotoxic effects. In conclusion, our results suggest that the two redox systems are important for neuronal survival in dopamine-induced cell death. © 2014 Elsevier Inc.A.P.F. was supported by Stiftelsen Lars Hiertas Minne and Karolinska Institutet research grants. Research in the Swoboda laboratory was supported by the Swedish Research Council (VR) and the NordForsk Nordic network for C. elegans research. A.M.-V. was supported by the Instituto de Salud Carlos III (Projects PI050065 and PI080557, cofinanced by the Fondo Social Europeo, FEDER) and Junta de Andalucía (Projects P07-CVI-02697 and P08-CVI-03629), Spain. Some C. elegans strains were provided by the CGC, which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440).Peer Reviewe

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

Componentes de la tasa de crecimiento poblacional en el negrón especulado de Saskatchewan, Canadá

Breeding range and abundance of White–winged Scoters (Melanitta fusca deglandi) have declined in northwestern North America. Hypotheses proposed to account for this trend are that survival and/or recruitment of females had declined. Thus, we used a reverse–time capture–recapture approach to directly estimate survival, seniority and capture probabilities for females of breeding age at Redberry Lake, Saskatchewan, Canada for 1975–1980 and 2000–2003. We also estimated population size of breeding females for 1975–1985 and 2000–2003 using capture–recapture data. Initially, this local population was in serious decline [95% CL ( ) = 0.89 ± 0.09], but has since stabilized and may be slowly increasing [95% CL ( ) = 1.07 ± 0.11]. This reversal in trajectory apparently resulted from increased recruitment rather than increased apparent survival. Importantly, recent recruitment of adult females appeared to be driven solely by immigration of adult females with no detectable in situ recruitment, suggesting a hypothesis that the local population is being rescued by females produced elsewhere.El rango reproductivo y la abundancia del negrón especulado (Melanitta fusca deglandi) han disminuido en la zona noroeste de América del Norte. La hipótesis propuesta para explicar esta tendencia es que se ha producido una disminución en la supervivencia y/o el reclutamiento de hembras. Por consiguiente, utilizamos un enfoque de captura–recaptura con el tiempo invertido para estimar directamente la supervivencia, la jerarquía y las probabilidades de captura de las hembras en edad reproductora del lago Redberry, Saskatchewan, Canadá, durante los periodos 1975–1980 y 2000– 2003. También estimamos el tamaño poblacional de las hembras reproductoras durante los periodos 1975–1985 y 2000–2003, mediante el empleo de datos de captura–recaptura. En un principio, esta población local experimentó una importante disminución [95% CL ( ) = 0,89 ± 0,09], pero posteriormente se estabilizó, y es posible que poco a poco vaya aumentando [95% CL ( ) = 1,07 ± 0,11]. Por lo visto, la inversión de esta trayectoria se produjo como consecuencia de un mayor reclutamiento, en lugar de una mayor supervivencia aparente. Es importante destacar que el reclutamiento reciente de hembras adultas parece haber obedecido exclusivamente a la migración de hembras adultas sin un reclutamiento detectable in situ, lo que sugiere la hipótesis de que la población local está siendo rescatada por hembras procedentes de otros lugares