@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}, } @article{261, abstract = {Let G = SL(2, R) ⋉R2 and Γ = SL(2, Z) ⋉Z2. Building on recent work of Strömbergsson, we prove a rate of equidistribution for the orbits of a certain one-dimensional unipotent flow of Γ\G, which projects to a closed horocycle in the unit tangent bundle to the modular surface. We use this to answer a question of Elkies and McMullen by making effective the convergence of the gap distribution of √n mod 1.}, author = {Timothy Browning and Vinogradov, Ilya}, journal = {Journal of the London Mathematical Society}, number = {1}, pages = {61 -- 84}, publisher = {John Wiley and Sons Ltd}, title = {{Effective ratner theorem for SL (2, R) ⋉R2 and gaps in √n modulo 1}}, doi = {10.1112/jlms/jdw025}, volume = {94}, year = {2016}, } @article{262, abstract = {For any number field we calculate the exact proportion of rational numbers which are everywhere locally a norm but not globally a norm from the number field.}, author = {Timothy Browning and Newton, Rachel}, journal = {Mathematika}, number = {2}, pages = {337 -- 347}, publisher = {Cambridge University Press}, title = {{The proportion of failures of the Hasse norm principle}}, doi = {10.1112/S0025579315000261}, volume = {62}, year = {2016}, } @article{263, abstract = {We count rational points of bounded height on the Cayley ruled cubic surface and interpret the result in the context of general conjectures due to Batyrev and Tschinkel.}, author = {de la Bretèche, Régis and Timothy Browning and Salberger, Per}, journal = {European Journal of Mathematics}, number = {1}, pages = {55 -- 72}, publisher = {Springer Nature}, title = {{Counting rational points on the Cayley ruled cubic}}, doi = {10.1007/s40879-015-0049-1}, volume = {2}, year = {2016}, } @article{264, abstract = {Given a family of varieties over a number field, we determine conditions under which there is a Brauer-Manin obstruction to weak approximation for 100% of the fibres which are everywhere locally soluble.}, author = {Bright, Maritn J and Timothy Browning and Loughran, Daniel}, journal = {Compositio Mathematica}, number = {7}, pages = {1435 -- 1475}, publisher = {Cambridge University Press}, title = {{Failures of weak approximation in families}}, doi = {10.1112/S0010437X16007405}, volume = {152}, year = {2016}, } @inproceedings{1068, abstract = {Games on graphs provide the appropriate framework to study several central problems in computer science, such as verification and synthesis of reactive systems. One of the most basic objectives for games on graphs is the liveness (or Büchi) objective that given a target set of vertices requires that some vertex in the target set is visited infinitely often. We study generalized Büchi objectives (i.e., conjunction of liveness objectives), and implications between two generalized Büchi objectives (known as GR(1) objectives), that arise in numerous applications in computer-aided verification. We present improved algorithms and conditional super-linear lower bounds based on widely believed assumptions about the complexity of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider graph games with n vertices, m edges, and generalized Büchi objectives with k conjunctions. First, we present an algorithm with running time O(k*n^2), improving the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm is optimal for dense graphs under (A1). Second, we show that the basic algorithm for the problem is optimal for sparse graphs when the target sets have constant size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1 k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time algorithm for m > n^{1.5}. }, author = {Chatterjee, Krishnendu and Dvorák, Wolfgang and Henzinger, Monika H and Loitzenbauer, Veronika}, location = {Krakow, Poland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Conditionally optimal algorithms for generalized Büchi Games}}, doi = {10.4230/LIPIcs.MFCS.2016.25}, volume = {58}, year = {2016}, } @inproceedings{1069, abstract = {The Continuous Skolem Problem asks whether a real-valued function satisfying a linear differen- tial equation has a zero in a given interval of real numbers. This is a fundamental reachability problem for continuous linear dynamical systems, such as linear hybrid automata and continuous- time Markov chains. Decidability of the problem is currently open – indeed decidability is open even for the sub-problem in which a zero is sought in a bounded interval. In this paper we show decidability of the bounded problem subject to Schanuel’s Conjecture, a unifying conjecture in transcendental number theory. We furthermore analyse the unbounded problem in terms of the frequencies of the differential equation, that is, the imaginary parts of the characteristic roots. We show that the unbounded problem can be reduced to the bounded problem if there is at most one rationally linearly independent frequency, or if there are two rationally linearly independent frequencies and all characteristic roots are simple. We complete the picture by showing that de- cidability of the unbounded problem in the case of two (or more) rationally linearly independent frequencies would entail a major new effectiveness result in Diophantine approximation, namely computability of the Diophantine-approximation types of all real algebraic numbers.}, author = {Chonev, Ventsislav K and Ouaknine, Joël and Worrell, James}, location = {Rome, Italy}, publisher = {Schloss Dagstuhl- Leibniz-Zentrum fur Informatik}, title = {{On the skolem problem for continuous linear dynamical systems}}, doi = {10.4230/LIPIcs.ICALP.2016.100}, volume = {55}, year = {2016}, } @inproceedings{1070, abstract = {We present a logic that extends CTL (Computation Tree Logic) with operators that express synchronization properties. A property is synchronized in a system if it holds in all paths of a certain length. The new logic is obtained by using the same path quantifiers and temporal operators as in CTL, but allowing a different order of the quantifiers. This small syntactic variation induces a logic that can express non-regular properties for which known extensions of MSO with equality of path length are undecidable. We show that our variant of CTL is decidable and that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We analogously consider quantifier exchange in extensions of CTL, and we present operators defined using basic operators of CTL* that express the occurrence of infinitely many synchronization points. We show that the model-checking problem remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide if the Next operator is allowed in the logics, thus the classical bisimulation quotient can be used for state-space reduction before model checking. }, author = {Chatterjee, Krishnendu and Doyen, Laurent}, location = {Rome, Italy}, publisher = {Schloss Dagstuhl- Leibniz-Zentrum fur Informatik}, title = {{Computation tree logic for synchronization properties}}, doi = {10.4230/LIPIcs.ICALP.2016.98}, volume = {55}, year = {2016}, } @inproceedings{1071, abstract = {We consider data-structures for answering reachability and distance queries on constant-treewidth graphs with n nodes, on the standard RAM computational model with wordsize W=Theta(log n). Our first contribution is a data-structure that after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time; and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries. The data-structure uses at all times O(n) space. Our second contribution is a space-time tradeoff data-structure for distance queries. For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing time that allows pair queries in O(n^{1-\epsilon} alpha(n)) time, where alpha is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space. The input graph G is not considered in the space complexity. }, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas}, location = {Aarhus, Denmark}, publisher = {Schloss Dagstuhl- Leibniz-Zentrum fur Informatik}, title = {{Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs}}, doi = {10.4230/LIPIcs.ESA.2016.28}, volume = {57}, year = {2016}, } @inproceedings{10746, abstract = {Vortex states in superconducting (SC) structures, their dynamics and ways to manipulate them are topics of great interest. We report a new method of magnetic force microscopy (MFM) that allows the study of vortex states in mesoscopic SC samples. For the case of a SC ring, which is biased to a half-integer flux quantum, the flux modulation through the ring caused by the motion of the magnetic tip drives the ring between two consecutive fluxoid states. The corresponding current switching in the ring produces strong position-dependent forces on the cantilever. In the regime where the frequency of the thermally activated jumps between fluxoid states is close to the frequency of the cantilever, large changes in the cantilever frequency and dissipation are observed. This effect may be understood as a stochastic resonance (SR) process. These changes in the cantilever’s mechanical properties are used to “image” the barrier energies between fluxoid states. Additionally, SR imaging of the barrier energies are used to study the effect of the locally applied magnetic field from the MFM tip on the barrier heights. We report the results of measurements for Al rings. Further, the same imaging technique can be applied to more sophisticated SC structures such as arrays of Josephson junctions.}, author = {Polshyn, Hryhoriy and Naibert, Tyler and Chua, Victor and Budakian, Raffi}, booktitle = {APS March Meeting 2016}, issn = {0003-0503}, location = {Baltimore, MD, United States}, number = {2}, publisher = {American Physical Society}, title = {{Study of vortex states and dynamics in mesoscopic superconducting samples with MFM}}, volume = {61}, year = {2016}, } @inproceedings{10747, abstract = {Vortex interactions are key to explaining the behavior of many two dimensional superconducting systems. We report on the development of a technique to locally probe vortex interactions in a 2D array of Josephson junctions. Scanning a magnetic tip attached to an ultra-soft cantilever over the array produces changes in the frequency of the cantilever along certain lines, forming geometric patterns in the scans. Different tip-surface separations and external magnetic fields produce a number of different patterns. These patterns correspond to tip locations in which two configurations of vortices in the lattice have degenerate energies. By imaging the locations of these degeneracies, information on the local vortex interactions may be obtained.}, author = {Naibert, Tyler and Polshyn, Hryhoriy and Wolin, Brian and Durkin, Malcolm and Garrido Menacho, Rita and Shem, Ian Mondragon and Chua, Victor and Hughes, Taylor and Mason, Nadya and Budakian, Raffi}, booktitle = {APS March Meeting 2016}, issn = {0003-0503}, location = {Baltimore, MD, United States}, number = {2}, publisher = {American Physical Society}, title = {{Stochastic resonance magnetic force microscopy imaging of Josephson arrays}}, volume = {61}, year = {2016}, } @article{1081, abstract = {The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.}, author = {Łangowski, Łukasz and Wabnik, Krzysztof T and Li, Hongjiang and Vanneste, Steffen and Naramoto, Satoshi and Tanaka, Hirokazu and Friml, Jirí}, journal = {Cell Discovery}, publisher = {Nature Publishing Group}, title = {{Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells}}, doi = {10.1038/celldisc.2016.18}, volume = {2}, year = {2016}, } @inproceedings{10810, abstract = {The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements and annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. }, author = {Rubel, Paul and Pani, Danilo and Schlögl, Alois and Fayn, Jocelyne and Badilini, Fabio and Macfarlane, Peter and Varri, Alpo}, booktitle = {2016 Computing in Cardiology Conference}, issn = {2325-887X}, location = {Vancouver, Canada}, pages = {309--312}, publisher = {Computing in Cardiology}, title = {{SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography}}, doi = {10.22489/cinc.2016.090-500}, volume = {43}, year = {2016}, } @inproceedings{1082, abstract = {In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y.}, author = {Chalk, Matthew J and Marre, Olivier and Tkacik, Gasper}, location = {Barcelona, Spain}, pages = {1965--1973}, publisher = {Neural Information Processing Systems}, title = {{Relevant sparse codes with variational information bottleneck}}, volume = {29}, year = {2016}, }