@article{392, abstract = {We used femtosecond optical pump-probe spectroscopy to study the photoinduced change in reflectivity of thin films of the electron-doped cuprate La2-xCexCuO4 (LCCO) with dopings of x=0.08 (underdoped) and x=0.11 (optimally doped). Above Tc, we observe fluence-dependent relaxation rates that begin at a temperature similar to the one where transport measurements first show signatures of antiferromagnetic correlations. Upon suppressing superconductivity with a magnetic field, it is found that the fluence and temperature dependence of relaxation rates are consistent with bimolecular recombination of electrons and holes across a gap (2ΔAF) originating from antiferromagnetic correlations which comprise the pseudogap in electron-doped cuprates. This can be used to learn about coupling between electrons and high-energy (ω>2ΔAF) excitations in these compounds and set limits on the time scales on which antiferromagnetic correlations are static.}, author = {Vishik, Inna and Mahmood, Fahad and Alpichshev, Zhanybek and Gedik, Nuh and Higgins, Joshu and Greene, Richard}, journal = {Physical Review B}, number = {11}, publisher = {American Physical Society}, title = {{Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ}}, doi = {10.1103/PhysRevB.95.115125}, volume = {95}, year = {2017}, } @article{393, abstract = {We use a three-pulse ultrafast optical spectroscopy to study the relaxation processes in a frustrated Mott insulator Na2IrO3. By being able to independently produce the out-of-equilibrium bound states (excitons) of doublons and holons with the first pulse and suppress the underlying antiferromagnetic order with the second one, we were able to elucidate the relaxation mechanism of quasiparticles in this system. By observing the difference in the exciton dynamics in the magnetically ordered and disordered phases we found that the mass of this quasiparticle is mostly determined by its interaction with the surrounding spins. }, author = {Alpichshev, Zhanybek and Sie, Edbert and Mahmood, Fahad and Cao, Gang and Gedik, Nuh}, journal = {Physical Review B}, number = {23}, publisher = {American Physical Society}, title = {{Origin of the exciton mass in the frustrated Mott insulator Na2IrO3}}, doi = {10.1103/PhysRevB.96.235141}, volume = {96}, year = {2017}, } @inbook{424, abstract = {We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b, d) such that the following holds. If F is a finite family of subsets of Rd such that βi(∩G)≤b for any G⊊F and every 0 ≤ i ≤ [d/2]-1 then F has Helly number at most h(b, d). Here βi denotes the reduced Z2-Betti numbers (with singular homology). These topological conditions are sharp: not controlling any of these [d/2] first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map C*(K)→C*(Rd).}, author = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, booktitle = {A Journey through Discrete Mathematics: A Tribute to Jiri Matousek}, editor = {Loebl, Martin and Nešetřil, Jaroslav and Thomas, Robin}, isbn = {978-331944479-6}, pages = {407 -- 447}, publisher = {Springer}, title = {{Bounding helly numbers via betti numbers}}, doi = {10.1007/978-3-319-44479-6_17}, year = {2017}, } @inproceedings{431, abstract = {Parallel implementations of stochastic gradient descent (SGD) have received significant research attention, thanks to its excellent scalability properties. A fundamental barrier when parallelizing SGD is the high bandwidth cost of communicating gradient updates between nodes; consequently, several lossy compresion heuristics have been proposed, by which nodes only communicate quantized gradients. Although effective in practice, these heuristics do not always converge. In this paper, we propose Quantized SGD (QSGD), a family of compression schemes with convergence guarantees and good practical performance. QSGD allows the user to smoothly trade off communication bandwidth and convergence time: nodes can adjust the number of bits sent per iteration, at the cost of possibly higher variance. We show that this trade-off is inherent, in the sense that improving it past some threshold would violate information-theoretic lower bounds. QSGD guarantees convergence for convex and non-convex objectives, under asynchrony, and can be extended to stochastic variance-reduced techniques. When applied to training deep neural networks for image classification and automated speech recognition, QSGD leads to significant reductions in end-to-end training time. For instance, on 16GPUs, we can train the ResNet-152 network to full accuracy on ImageNet 1.8 × faster than the full-precision variant. }, author = {Alistarh, Dan-Adrian and Grubic, Demjan and Li, Jerry and Tomioka, Ryota and Vojnović, Milan}, issn = {10495258}, location = {Long Beach, CA, United States}, pages = {1710--1721}, publisher = {Neural Information Processing Systems Foundation}, title = {{QSGD: Communication-efficient SGD via gradient quantization and encoding}}, volume = {2017}, year = {2017}, } @inproceedings{432, abstract = {Recently there has been significant interest in training machine-learning models at low precision: by reducing precision, one can reduce computation and communication by one order of magnitude. We examine training at reduced precision, both from a theoretical and practical perspective, and ask: is it possible to train models at end-to-end low precision with provable guarantees? Can this lead to consistent order-of-magnitude speedups? We mainly focus on linear models, and the answer is yes for linear models. We develop a simple framework called ZipML based on one simple but novel strategy called double sampling. Our ZipML framework is able to execute training at low precision with no bias, guaranteeing convergence, whereas naive quanti- zation would introduce significant bias. We val- idate our framework across a range of applica- tions, and show that it enables an FPGA proto- type that is up to 6.5 × faster than an implemen- tation using full 32-bit precision. We further de- velop a variance-optimal stochastic quantization strategy and show that it can make a significant difference in a variety of settings. When applied to linear models together with double sampling, we save up to another 1.7 × in data movement compared with uniform quantization. When training deep networks with quantized models, we achieve higher accuracy than the state-of-the- art XNOR-Net. }, author = {Zhang, Hantian and Li, Jerry and Kara, Kaan and Alistarh, Dan-Adrian and Liu, Ji and Zhang, Ce}, booktitle = {Proceedings of Machine Learning Research}, isbn = {978-151085514-4}, location = {Sydney, Australia}, pages = {4035 -- 4043}, publisher = {ML Research Press}, title = {{ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning}}, volume = { 70}, year = {2017}, } @article{443, abstract = {Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited.}, author = {Hardie, Rae and Van Dam, Ellen and Cowley, Mark and Han, Ting and Balaban, Seher and Pajic, Marina and Pinese, Mark and Iconomou, Mary and Shearer, Robert and Mckenna, Jessie and Miller, David and Waddell, Nicola and Pearson, John and Grimmond, Sean and Sazanov, Leonid A and Biankin, Andrew and Villas Boas, Silas and Hoy, Andrew and Turner, Nigel and Saunders, Darren}, journal = {Cancer & Metabolism}, number = {2}, publisher = {BioMed Central}, title = {{Mitochondrial mutations and metabolic adaptation in pancreatic cancer}}, doi = {10.1186/s40170-017-0164-1}, volume = {5}, year = {2017}, } @inbook{444, abstract = {Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations.}, author = {Sazanov, Leonid A}, booktitle = {Mechanisms of primary energy transduction in biology }, editor = {Wikström, Mårten}, isbn = {978-1-78262-865-1}, pages = {25 -- 59}, publisher = {Royal Society of Chemistry}, title = {{Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions}}, doi = {10.1039/9781788010405-00025}, year = {2017}, } @article{445, abstract = {The Loschmidt echo, defined as the overlap between quantum wave function evolved with different Hamiltonians, quantifies the sensitivity of quantum dynamics to perturbations and is often used as a probe of quantum chaos. In this work we consider the behavior of the Loschmidt echo in the many-body localized phase, which is characterized by emergent local integrals of motion and provides a generic example of nonergodic dynamics. We demonstrate that the fluctuations of the Loschmidt echo decay as a power law in time in the many-body localized phase, in contrast to the exponential decay in few-body ergodic systems. We consider the spin-echo generalization of the Loschmidt echo and argue that the corresponding correlation function saturates to a finite value in localized systems. Slow, power-law decay of fluctuations of such spin-echo-type overlap is related to the operator spreading and is present only in the many-body localized phase, but not in a noninteracting Anderson insulator. While most of the previously considered probes of dephasing dynamics could be understood by approximating physical spin operators with local integrals of motion, the Loschmidt echo and its generalizations crucially depend on the full expansion of the physical operators via local integrals of motion operators, as well as operators which flip local integrals of motion. Hence these probes allow one to get insights into the relation between physical operators and local integrals of motion and access the operator spreading in the many-body localized phase.}, author = {Maksym Serbyn and Abanin, Dimitry A}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {1}, publisher = {American Physical Society}, title = {{Loschmidt echo in many body localized phases}}, doi = {10.1103/PhysRevB.96.014202}, volume = {96}, year = {2017}, } @article{447, abstract = {We consider last passage percolation (LPP) models with exponentially distributed random variables, which are linked to the totally asymmetric simple exclusion process (TASEP). The competition interface for LPP was introduced and studied in Ferrari and Pimentel (2005a) for cases where the corresponding exclusion process had a rarefaction fan. Here we consider situations with a shock and determine the law of the fluctuations of the competition interface around its deter- ministic law of large number position. We also study the multipoint distribution of the LPP around the shock, extending our one-point result of Ferrari and Nejjar (2015).}, author = {Ferrari, Patrik and Nejjar, Peter}, journal = {Revista Latino-Americana de Probabilidade e Estatística}, pages = {299 -- 325}, publisher = {Instituto Nacional de Matematica Pura e Aplicada}, title = {{Fluctuations of the competition interface in presence of shocks}}, doi = {10.30757/ALEA.v14-17}, volume = {9}, year = {2017}, } @article{452, abstract = {Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. Yet, due to the exceeding difficulty of creating stably spinning objects of asymmetric shape in a manual trial-and-error process, there has been little departure from rotationally symmetric designs. With modern 3D printing technologies, however, we can manufacture shapes of almost unbounded complexity at the press of a button, shifting this design complexity toward computation. In this article, we describe an algorithm to generate designs for spinning objects by optimizing their mass distribution: as input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the interior mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. To create voids inside the model, we represent its volume with an adaptive multiresolution voxelization and optimize the discrete voxel fill values using a continuous, nonlinear formulation. We further optimize for rotational stability by maximizing the dominant principal moment. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance.}, author = {Bächer, Moritz and Bickel, Bernd and Whiting, Emily and Sorkine Hornung, Olga}, journal = {Communications of the ACM}, number = {8}, pages = {92 -- 99}, publisher = {ACM}, title = {{Spin it: Optimizing moment of inertia for spinnable objects}}, doi = {10.1145/3068766}, volume = {60}, year = {2017}, } @article{453, abstract = {Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.}, author = {Fallesen, Todd and Roostalu, Johanna and Düllberg, Christian F and Pruessner, Gunnar and Surrey, Thomas}, journal = {Biophysical Journal}, number = {9}, pages = {2055 -- 2067}, publisher = {Biophysical Society}, title = {{Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement}}, doi = {10.1016/j.bpj.2017.09.006}, volume = {113}, year = {2017}, }