netSmooth: Network-smoothing based imputation for single cell RNA-seq [version 3; referees: 2 approved]

Single cell RNA-seq (scRNA-seq) experiments suffer from a range of characteristic technical biases, such as dropouts (zero or near zero counts) and high variance. Current analysis methods rely on imputing missing values by various means of local averaging or regression, often amplifying biases inherent in the data. We present netSmooth, a network-diffusion based method that uses priors for the covariance structure of gene expression profiles on scRNA-seq experiments in order to smooth expression values. We demonstrate that netSmooth improves clustering results of scRNA-seq experiments from distinct cell populations, time-course experiments, and cancer genomics. We provide an R package for our method, available at: https://github.com/BIMSBbioinfo/netSmooth

Entanglement and replica symmetry breaking in a driven-dissipative quantum spin glass

We describe simulations of the quantum dynamics of a confocal cavity QED system that realizes an intrinsically driven-dissipative spin glass. A close connection between open quantum dynamics and replica symmetry breaking is established, in which individual quantum trajectories are the replicas. We observe that entanglement plays an important role in the emergence of replica symmetry breaking in a fully connected, frustrated spin network of up to fifteen spin-1/2 particles. Quantum trajectories of entangled spins reach steady-state spin configurations of lower energy than that of semiclassical trajectories. Cavity emission allows monitoring of the continuous stochastic evolution of spin configurations, while backaction from this projects entangled states into states of broken Ising and replica symmetry. The emergence of spin glass order manifests itself through the simultaneous absence of magnetization and the presence of nontrivial spin overlap density distributions among replicas. Moreover, these overlaps reveal incipient ultrametric order, in line with the Parisi RSB solution ansatz for the Sherrington-Kirkpatrick model. A nonthermal Parisi order parameter distribution, however, highlights the driven-dissipative nature of this quantum optical spin glass. This practicable system could serve as a testbed for exploring how quantum effects enrich the physics of spin glasses.Comment: 23 pages including 11 figures and 8 appendices; section V and appendix F are ne

Tunable-range, photon-mediated atomic interactions in multimode cavity QED

Funding: EPSRC program TOPNES (EP/I031014/1) (KEB, JK), Leverhulme Trust (IAF-2014-025) (JK).Optical cavity QED provides a platform with which to explore quantum many-body physics in driven-dissipative systems. Single-mode cavities provide strong, infinite-range photon-mediated interactions among intracavity atoms. However, these global all-to-all couplings are limiting from the perspective of exploring quantum many-body physics beyond the mean-field approximation. The present work demonstrates that local couplings can be created using multimode cavity QED. This is established through measurements of the threshold of a superradiant, self-organization phase transition versus atomic position. Specifically, we experimentally show that the interference of near-degenerate cavity modes leads to both a strong and {tunable-range} interaction between Bose-Einstein condensates (BECs) trapped within the cavity. We exploit the symmetry of a confocal cavity to measure the interaction between real BECs and their virtual images without unwanted contributions arising from the merger of real BECs. Atom-atom coupling may be tuned from short range to long range. This capability paves the way toward future explorations of exotic, strongly correlated systems such as quantum liquid crystals and driven-dissipative spin glasses.Publisher PDFPeer reviewe

An optical lattice with sound

Funding: We acknowledge funding support from the Army Research Office. Y.G. and B.M. acknowledge funding from the Stanford Q-FARM Graduate Student Fellowship and the NSF Graduate Research Fellowship, respectively. S.G. acknowledges support from NSF Grant No. DMR-1653271.Quantized sound waves—phonons—govern the elastic response of crystalline materials, and also play an integral part in determining their thermodynamic properties and electrical response (for example, by binding electrons into superconducting Cooper pairs). The physics of lattice phonons and elasticity is absent in simulators of quantum solids constructed of neutral atoms in periodic light potentials: unlike real solids, traditional optical lattices are silent because they are infinitely stiff. Optical-lattice realizations of crystals therefore lack some of the central dynamical degrees of freedom that determine the low-temperature properties of real materials. Here, we create an optical lattice with phonon modes using a Bose–Einstein condensate (BEC) coupled to a confocal optical resonator. Playing the role of an active quantum gas microscope, the multimode cavity QED system both images the phonons and induces the crystallization that supports phonons via short-range, photon-mediated atom–atom interactions. Dynamical susceptibility measurements reveal the phonon dispersion relation, showing that these collective excitations exhibit a sound speed dependent on the BEC–photon coupling strength. Our results pave the way for exploring the rich physics of elasticity in quantum solids, ranging from quantum melting transitions to exotic ‘fractonic’ topological defects in the quantum regime.PostprintPeer reviewe

Entanglement and replica symmetry breaking in a driven-dissipative quantum spin glass

Funding: We are grateful for funding support from the Army Research Office, NTT Research, and the Q-NEXT DOE National Quantum Information Science Research Center. Surya Ganguli acknowledges funding from NSF CAREER award #1845166. B.M. acknowledges funding from the Stanford QFARM Initiative and the NSF Graduate Research Fellowship.We describe simulations of the quantum dynamics of a confocal cavity QED system that realizes an intrinsically driven-dissipative spin glass. A close connection between open quantum dynamics and replica symmetry breaking is established, in which individual quantum trajectories are the replicas. We observe that entanglement plays an important role in the emergence of replica symmetry breaking in a fully connected, frustrated spin network of up to 15 spin-1/2 particles. Quantum trajectories of entangled spins reach steady-state spin configurations of lower energy than that of semiclassical trajectories. Cavity emission allows monitoring of the continuous stochastic evolution of spin configurations, while backaction from this projects entangled states into states of broken Ising and replica symmetry. The emergence of spin glass order manifests itself through the simultaneous absence of magnetization and the presence of nontrivial spin overlap density distributions among replicas. Moreover, these overlaps reveal incipient ultrametric order, in line with the Parisi replica symmetry breaking solution for the Sherrington-Kirkpatrick model. A nonthermal Parisi order parameter distribution, however, highlights the driven-dissipative nature of this quantum optical spin glass. This practicable system could serve as a test bed for exploring how quantum effects enrich the physics of spin glasses.Peer reviewe

Enhancing associative memory recall and storage capacity using confocal cavity QED

Funding: Y.G. and B.M. acknowledgefunding from the Stanford Q-FARM Graduate Student Fellowship and the NSF Graduate Research Fellowship, respectively. J.K. acknowledges support from the Leverhulme Trust (IAF-2014-025), and S.G. acknowledges funding from the James S. McDonnell and Simons Foundations and an NSF Career Award.We introduce a near-term experimental platform for realizing an associative memory. It can simultaneously store many memories by using spinful bosons coupled to a degenerate multimode optical cavity. The associative memory is realized by a confocal cavity QED neural network, with the modes serving as the synapses, connecting a network of superradiant atomic spin ensembles,which serve as the neurons. Memories are encoded in the connectivity matrix between the spins and can be accessed through the input and output of patterns of light. Each aspect of the scheme is based on recently demonstrated technology using a confocal cavity and Bose-condensed atoms. Our scheme has two conceptually novel elements. First, it introduces a new form of random spin system that interpolates between a ferromagnetic and a spin glass regime as a physical parameter is tuned—the positions of ensembles within the cavity. Second, and more importantly, the spins relax via deterministic steepest-descent dynamics rather than Glauber dynamics. We show that this nonequilibrium quantum-optical scheme has significant advantages for associative memory over Glauber dynamics: These dynamics can enhance the network’s ability to store and recall memories beyond that of the standard Hopfield model. Surprisingly, the cavity QED dynamics can retrieve memories even when the system is in the spin glass phase. Thus, the experimental platform provides a novel physical instantiation of associative memories and spin glasses as well as provides an unusual form of relaxational dynamics that is conducive to memory recall even in regimes where it was thought to be impossible.Publisher PDFPeer reviewe

We don’t do Google, we do massive attacks: Notes on creative R&D collaborations

The article presents findings from an exploratory study investigating the nature of collaborative research and development in creative industries. Participants in the study are two creative SMEs with extensive experience of participating in collaborative projects. A collective case study approach is adopted with data collected on the factors impinging on the effectiveness of such collaborations. Findings are presented at the macro and micro levels of such collaborations. The paper concludes with a summary of some of the challenges faced by small creative SMEs when collaborating with other organizations during the research and development process

Andreev reflection in the fractional quantum Hall state

We construct high-quality graphene-based van der Waals devices with narrow superconducting niobium nitride (NbN) electrodes, in which superconductivity and robust fqH coexist. We find crossed Andreev reflection (CAR) across the superconductor separating two fqH edges. Our observed CAR probabilities in the particle-like fractional fillings are markedly higher than those in the integer and hole-conjugate fractional fillings and depend strongly on temperature and magnetic field unlike the other fillings. Further, we find a filling-independent CAR probability in integer fillings, which we attribute to spin-orbit coupling in NbN allowing for Andreev reflection between spin-polarized edges. These results provide a route to realize novel topological superconducting phases in fqH-superconductor hybrid devices based on graphene and NbN.Comment: Revised text, additional main and appendix figure

Spinor self-ordering of a quantum gas in a cavity

Funding: J. K. acknowledges support from SU2P.We observe the joint spin-spatial (spinor) self-organization of a two-component BEC strongly coupled to an optical cavity. This unusual nonequilibrium Hepp-Lieb-Dicke phase transition is driven by an off-resonant two-photon Raman transition formed from a classical pump field and the emergent quantum dynamical cavity field. This mediates a spinor-spinor interaction that, above a critical strength, simultaneously organizes opposite spinor states of the BEC on opposite checkerboard configurations of an emergent 2D lattice. The resulting spinor density-wave polariton condensate is observed by directly detecting the atomic spin and momentum state and by holographically reconstructing the phase of the emitted cavity field. The latter provides a direct measure of the spin state, and a spin-spatial domain wall is observed. The photon-mediated spin interactions demonstrated here may be engineered to create dynamical gauge fields and quantum spin glasses.PostprintPostprintPeer reviewe

PiGx: reproducible genomics analysis pipelines with GNU Guix

In bioinformatics, as well as other computationally intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations and for the wider dissemination of workflows. However, providing this type of reproducibility and traceability is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which generally comes in various versions. Moreover, in many fields (bioinformatics being a prime example), these versions are subject to continual change due to rapidly evolving technologies, further complicating problems related to reproducibility. Here, we propose a principled approach for building analysis pipelines and managing their dependencies with GNU Guix. As a case study to demonstrate the utility of our approach, we present a set of highly reproducible pipelines called PiGx for the analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. Users may install these highly reproducible packages and apply them to their own datasets without any special computational expertise beyond the use of the command line. We hope such a toolkit will provide immediate benefit to laboratory workers wishing to process their own datasets or bioinformaticians seeking to automate all, or parts of, their analyses. In the long term, we hope our approach to reproducibility will serve as a blueprint for reproducible workflows in other areas. Our pipelines, along with their corresponding documentation and sample reports, are available at http://bioinformatics.mdc-berlin.de/pigx Document type: Articl