TY - CONF
AB - We define and study a discrete process that generalizes the convex-layer decomposition of a planar point set. Our process, which we call homotopic curve shortening (HCS), starts with a closed curve (which might self-intersect) in the presence of a set P⊂ ℝ² of point obstacles, and evolves in discrete steps, where each step consists of (1) taking shortcuts around the obstacles, and (2) reducing the curve to its shortest homotopic equivalent. We find experimentally that, if the initial curve is held fixed and P is chosen to be either a very fine regular grid or a uniformly random point set, then HCS behaves at the limit like the affine curve-shortening flow (ACSF). This connection between HCS and ACSF generalizes the link between "grid peeling" and the ACSF observed by Eppstein et al. (2017), which applied only to convex curves, and which was studied only for regular grids. We prove that HCS satisfies some properties analogous to those of ACSF: HCS is invariant under affine transformations, preserves convexity, and does not increase the total absolute curvature. Furthermore, the number of self-intersections of a curve, or intersections between two curves (appropriately defined), does not increase. Finally, if the initial curve is simple, then the number of inflection points (appropriately defined) does not increase.
AU - Avvakumov, Sergey
AU - Nivasch, Gabriel
ID - 7991
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Homotopic curve shortening and the affine curve-shortening flow
VL - 164
ER -
TY - CONF
AB - We prove general topological Radon-type theorems for sets in ℝ^d, smooth real manifolds or finite dimensional simplicial complexes. Combined with a recent result of Holmsen and Lee, it gives fractional Helly theorem, and consequently the existence of weak ε-nets as well as a (p,q)-theorem. More precisely: Let X be either ℝ^d, smooth real d-manifold, or a finite d-dimensional simplicial complex. Then if F is a finite, intersection-closed family of sets in X such that the ith reduced Betti number (with ℤ₂ coefficients) of any set in F is at most b for every non-negative integer i less or equal to k, then the Radon number of F is bounded in terms of b and X. Here k is the smallest integer larger or equal to d/2 - 1 if X = ℝ^d; k=d-1 if X is a smooth real d-manifold and not a surface, k=0 if X is a surface and k=d if X is a d-dimensional simplicial complex. Using the recent result of the author and Kalai, we manage to prove the following optimal bound on fractional Helly number for families of open sets in a surface: Let F be a finite family of open sets in a surface S such that the intersection of any subfamily of F is either empty, or path-connected. Then the fractional Helly number of F is at most three. This also settles a conjecture of Holmsen, Kim, and Lee about an existence of a (p,q)-theorem for open subsets of a surface.
AU - Patakova, Zuzana
ID - 7989
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Bounding radon number via Betti numbers
VL - 164
ER -
TY - CONF
AB - Let K be a convex body in ℝⁿ (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K ∩ h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p₀ is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n ≥ 2, there are always at least three distinct barycentric cuts through the point p₀ ∈ K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p₀ are guaranteed if n ≥ 3.
AU - Patakova, Zuzana
AU - Tancer, Martin
AU - Wagner, Uli
ID - 7992
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Barycentric cuts through a convex body
VL - 164
ER -
TY - CONF
AB - In the recent study of crossing numbers, drawings of graphs that can be extended to an arrangement of pseudolines (pseudolinear drawings) have played an important role as they are a natural combinatorial extension of rectilinear (or straight-line) drawings. A characterization of the pseudolinear drawings of K_n was found recently. We extend this characterization to all graphs, by describing the set of minimal forbidden subdrawings for pseudolinear drawings. Our characterization also leads to a polynomial-time algorithm to recognize pseudolinear drawings and construct the pseudolines when it is possible.
AU - Arroyo Guevara, Alan M
AU - Bensmail, Julien
AU - Bruce Richter, R.
ID - 7994
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Extending drawings of graphs to arrangements of pseudolines
VL - 164
ER -
TY - JOUR
AB - Relaxation to a thermal state is the inevitable fate of nonequilibrium interacting quantum systems without special conservation laws. While thermalization in one-dimensional systems can often be suppressed by integrability mechanisms, in two spatial dimensions thermalization is expected to be far more effective due to the increased phase space. In this work we propose a general framework for escaping or delaying the emergence of the thermal state in two-dimensional arrays of Rydberg atoms via the mechanism of quantum scars, i.e., initial states that fail to thermalize. The suppression of thermalization is achieved in two complementary ways: by adding local perturbations or by adjusting the driving Rabi frequency according to the local connectivity of the lattice. We demonstrate that these mechanisms allow us to realize robust quantum scars in various two-dimensional lattices, including decorated lattices with nonconstant connectivity. In particular, we show that a small decrease of the Rabi frequency at the corners of the lattice is crucial for mitigating the strong boundary effects in two-dimensional systems. Our results identify synchronization as an important tool for future experiments on two-dimensional quantum scars.
AU - Michailidis, Alexios
AU - Turner, C. J.
AU - Papić, Z.
AU - Abanin, D. A.
AU - Serbyn, Maksym
ID - 8011
IS - 2
JF - Physical Review Research
SN - 2643-1564
TI - Stabilizing two-dimensional quantum scars by deformation and synchronization
VL - 2
ER -
TY - GEN
AB - We present a generative model of images that explicitly reasons over the set
of objects they show. Our model learns a structured latent representation that
separates objects from each other and from the background; unlike prior works,
it explicitly represents the 2D position and depth of each object, as well as
an embedding of its segmentation mask and appearance. The model can be trained
from images alone in a purely unsupervised fashion without the need for object
masks or depth information. Moreover, it always generates complete objects,
even though a significant fraction of training images contain occlusions.
Finally, we show that our model can infer decompositions of novel images into
their constituent objects, including accurate prediction of depth ordering and
segmentation of occluded parts.
AU - Anciukevicius, Titas
AU - Lampert, Christoph
AU - Henderson, Paul M
ID - 8063
T2 - arXiv
TI - Object-centric image generation with factored depths, locations, and appearances
ER -
TY - GEN
AB - Here, we employ micro- and nanosized cellulose particles, namely paper fines and cellulose
nanocrystals, to induce hierarchical organization over a wide length scale. After processing
them into carbonaceous materials, we demonstrate that these hierarchically organized materials
outperform the best materials for supercapacitors operating with organic electrolytes reported
in literature in terms of specific energy/power (Ragone plot) while showing hardly any capacity
fade over 4,000 cycles. The highly porous materials feature a specific surface area as high as
2500 m2ˑg-1 and exhibit pore sizes in the range of 0.5 to 200 nm as proven by scanning electron
microscopy and N2 physisorption. The carbonaceous materials have been further investigated
by X-ray photoelectron spectroscopy and RAMAN spectroscopy. Since paper fines are an
underutilized side stream in any paper production process, they are a cheap and highly available
feedstock to prepare carbonaceous materials with outstanding performance in electrochemical
applications.
AU - Hobisch, Mathias A.
AU - Mourad, Eléonore
AU - Fischer, Wolfgang J.
AU - Prehal, Christian
AU - Eyley, Samuel
AU - Childress, Anthony
AU - Zankel, Armin
AU - Mautner, Andreas
AU - Breitenbach, Stefan
AU - Rao, Apparao M.
AU - Thielemans, Wim
AU - Freunberger, Stefan Alexander
AU - Eckhart, Rene
AU - Bauer, Wolfgang
AU - Spirk, Stefan
ID - 8081
TI - High specific capacitance supercapacitors from hierarchically organized all-cellulose composites
ER -
TY - JOUR
AB - Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality.
AU - Lombardi, Fabrizio
AU - Wang, Jilin W.J.L.
AU - Zhang, Xiyun
AU - Ivanov, Plamen Ch
ID - 8105
JF - EPJ Web of Conferences
SN - 2100-014X
TI - Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality
VL - 230
ER -
TY - CONF
AB - Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics.
AU - Edelsbrunner, Herbert
AU - Nikitenko, Anton
AU - Ölsböck, Katharina
AU - Synak, Peter
ID - 8135
SN - 21932808
T2 - Topological Data Analysis
TI - Radius functions on Poisson–Delaunay mosaics and related complexes experimentally
VL - 15
ER -
TY - COMP
AU - Hauschild, Robert
ID - 8181
TI - Amplified centrosomes in dendritic cells promote immune cell effector functions
ER -
TY - COMP
AB - Automated root growth analysis and tracking of root tips.
AU - Hauschild, Robert
ID - 8294
TI - RGtracker
ER -
TY - CONF
AB - Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz, as a method for protecting cryptographic protocols against attacks on the devices of the honest parties. In a nutshell: a reverse firewall is placed outside of a device and its goal is to “sanitize” the messages sent by it, in such a way that a malicious device cannot leak its secrets to the outside world. It is typically assumed that the cryptographic devices are attacked in a “functionality-preserving way” (i.e. informally speaking, the functionality of the protocol remains unchanged under this attacks). In their paper, Mironov and Stephens-Davidowitz construct a protocol for passively-secure two-party computations with firewalls, leaving extension of this result to stronger models as an open question.
In this paper, we address this problem by constructing a protocol for secure computation with firewalls that has two main advantages over the original protocol from Eurocrypt 2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary number n of the parties, and not just for 2). Secondly, it is secure in much stronger corruption settings, namely in the active corruption model. More precisely: we consider an adversary that can fully corrupt up to 𝑛−1 parties, while the remaining parties are corrupt in a functionality-preserving way.
Our core techniques are: malleable commitments and malleable non-interactive zero-knowledge, which in particular allow us to create a novel protocol for multiparty augmented coin-tossing into the well with reverse firewalls (that is based on a protocol of Lindell from Crypto 2001).
AU - Chakraborty, Suvradip
AU - Dziembowski, Stefan
AU - Nielsen, Jesper Buus
ID - 8322
SN - 03029743
T2 - Advances in Cryptology – CRYPTO 2020
TI - Reverse firewalls for actively secure MPCs
VL - 12171
ER -
TY - CONF
AB - Discrete Gaussian distributions over lattices are central to lattice-based cryptography, and to the computational and mathematical aspects of lattices more broadly. The literature contains a wealth of useful theorems about the behavior of discrete Gaussians under convolutions and related operations. Yet despite their structural similarities, most of these theorems are formally incomparable, and their proofs tend to be monolithic and written nearly “from scratch,” making them unnecessarily hard to verify, understand, and extend.
In this work we present a modular framework for analyzing linear operations on discrete Gaussian distributions. The framework abstracts away the particulars of Gaussians, and usually reduces proofs to the choice of appropriate linear transformations and elementary linear algebra. To showcase the approach, we establish several general properties of discrete Gaussians, and show how to obtain all prior convolution theorems (along with some new ones) as straightforward corollaries. As another application, we describe a self-reduction for Learning With Errors (LWE) that uses a fixed number of samples to generate an unlimited number of additional ones (having somewhat larger error). The distinguishing features of our reduction are its simple analysis in our framework, and its exclusive use of discrete Gaussians without any loss in parameters relative to a prior mixed discrete-and-continuous approach.
As a contribution of independent interest, for subgaussian random matrices we prove a singular value concentration bound with explicitly stated constants, and we give tighter heuristics for specific distributions that are commonly used for generating lattice trapdoors. These bounds yield improvements in the concrete bit-security estimates for trapdoor lattice cryptosystems.
AU - Genise, Nicholas
AU - Micciancio, Daniele
AU - Peikert, Chris
AU - Walter, Michael
ID - 8339
SN - 03029743
T2 - 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography
TI - Improved discrete Gaussian and subgaussian analysis for lattice cryptography
VL - 12110
ER -
TY - CONF
AB - We present the results of the ARCH 2020 friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. In its fourth edition, eight tools have been applied to solve eight different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, C2E2, HyDRA, Hylaa, Hylaa-Continuous, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.
AU - Althoff, Matthias
AU - Bak, Stanley
AU - Bao, Zongnan
AU - Forets, Marcelo
AU - Frehse, Goran
AU - Freire, Daniel
AU - Kochdumper, Niklas
AU - Li, Yangge
AU - Mitra, Sayan
AU - Ray, Rajarshi
AU - Schilling, Christian
AU - Schupp, Stefan
AU - Wetzlinger, Mark
ID - 8572
T2 - EPiC Series in Computing
TI - ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics
VL - 74
ER -
TY - CONF
AB - We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These tools are applied to solve reachability analysis problems on six benchmark problems, two of them featuring hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.
AU - Geretti, Luca
AU - Alexandre Dit Sandretto, Julien
AU - Althoff, Matthias
AU - Benet, Luis
AU - Chapoutot, Alexandre
AU - Chen, Xin
AU - Collins, Pieter
AU - Forets, Marcelo
AU - Freire, Daniel
AU - Immler, Fabian
AU - Kochdumper, Niklas
AU - Sanders, David
AU - Schilling, Christian
ID - 8571
T2 - EPiC Series in Computing
TI - ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics
VL - 74
ER -
TY - CONF
AB - A vector addition system with states (VASS) consists of a finite set of states and counters. A transition changes the current state to the next state, and every counter is either incremented, or decremented, or left unchanged. A state and value for each counter is a configuration; and a computation is an infinite sequence of configurations with transitions between successive configurations. A probabilistic VASS consists of a VASS along with a probability distribution over the transitions for each state. Qualitative properties such as state and configuration reachability have been widely studied for VASS. In this work we consider multi-dimensional long-run average objectives for VASS and probabilistic VASS. For a counter, the cost of a configuration is the value of the counter; and the long-run average value of a computation for the counter is the long-run average of the costs of the configurations in the computation. The multi-dimensional long-run average problem given a VASS and a threshold value for each counter, asks whether there is a computation such that for each counter the long-run average value for the counter does not exceed the respective threshold. For probabilistic VASS, instead of the existence of a computation, we consider whether the expected long-run average value for each counter does not exceed the respective threshold. Our main results are as follows: we show that the multi-dimensional long-run average problem (a) is NP-complete for integer-valued VASS; (b) is undecidable for natural-valued VASS (i.e., nonnegative counters); and (c) can be solved in polynomial time for probabilistic integer-valued VASS, and probabilistic natural-valued VASS when all computations are non-terminating.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Otop, Jan
ID - 8600
SN - 18688969
T2 - 31st International Conference on Concurrency Theory
TI - Multi-dimensional long-run average problems for vector addition systems with states
VL - 171
ER -
TY - CONF
AB - A graph game is a two-player zero-sum game in which the players move a token throughout a graph to produce an infinite path, which determines the winner or payoff of the game. In bidding games, both players have budgets, and in each turn, we hold an "auction" (bidding) to determine which player moves the token. In this survey, we consider several bidding mechanisms and study their effect on the properties of the game. Specifically, bidding games, and in particular bidding games of infinite duration, have an intriguing equivalence with random-turn games in which in each turn, the player who moves is chosen randomly. We show how minor changes in the bidding mechanism lead to unexpected differences in the equivalence with random-turn games.
AU - Avni, Guy
AU - Henzinger, Thomas A
ID - 8599
SN - 18688969
T2 - 31st International Conference on Concurrency Theory
TI - A survey of bidding games on graphs
VL - 171
ER -
TY - CONF
AB - The design and implementation of efficient concurrent data structures have
seen significant attention. However, most of this work has focused on
concurrent data structures providing good \emph{worst-case} guarantees. In real
workloads, objects are often accessed at different rates, since access
distributions may be non-uniform. Efficient distribution-adaptive data
structures are known in the sequential case, e.g. the splay-trees; however,
they often are hard to translate efficiently in the concurrent case.
In this paper, we investigate distribution-adaptive concurrent data
structures and propose a new design called the splay-list. At a high level, the
splay-list is similar to a standard skip-list, with the key distinction that
the height of each element adapts dynamically to its access rate: popular
elements ``move up,'' whereas rarely-accessed elements decrease in height. We
show that the splay-list provides order-optimal amortized complexity bounds for
a subset of operations while being amenable to efficient concurrent
implementation. Experimental results show that the splay-list can leverage
distribution-adaptivity to improve on the performance of classic concurrent
designs, and can outperform the only previously-known distribution-adaptive
design in certain settings.
AU - Aksenov, Vitaly
AU - Alistarh, Dan-Adrian
AU - Drozdova, Alexandra
AU - Mohtashami, Amirkeivan
ID - 8725
SN - 1868-8969
T2 - 34th International Symposium on Distributed Computing
TI - The splay-list: A distribution-adaptive concurrent skip-list
VL - 179
ER -
TY - JOUR
AB - Several realistic spin-orbital models for transition metal oxides go beyond the classical expectations and could be understood only by employing the quantum entanglement. Experiments on these materials confirm that spin-orbital entanglement has measurable consequences. Here, we capture the essential features of spin-orbital entanglement in complex quantum matter utilizing 1D spin-orbital model which accommodates SU(2)⊗SU(2) symmetric Kugel-Khomskii superexchange as well as the Ising on-site spin-orbit coupling. Building on the results obtained for full and effective models in the regime of strong spin-orbit coupling, we address the question whether the entanglement found on superexchange bonds always increases when the Ising spin-orbit coupling is added. We show that (i) quantum entanglement is amplified by strong spin-orbit coupling and, surprisingly, (ii) almost classical disentangled states are possible. We complete the latter case by analyzing how the entanglement existing for intermediate values of spin-orbit coupling can disappear for higher values of this coupling.
AU - Gotfryd, Dorota
AU - Paerschke, Ekaterina
AU - Wohlfeld, Krzysztof
AU - Oleś, Andrzej M.
ID - 8726
IS - 3
JF - Condensed Matter
SN - 2410-3896
TI - Evolution of spin-orbital entanglement with increasing ising spin-orbit coupling
VL - 5
ER -
TY - CONF
AB - Machine learning and formal methods have complimentary benefits and drawbacks. In this work, we address the controller-design problem with a combination of techniques from both fields. The use of black-box neural networks in deep reinforcement learning (deep RL) poses a challenge for such a combination. Instead of reasoning formally about the output of deep RL, which we call the wizard, we extract from it a decision-tree based model, which we refer to as the magic book. Using the extracted model as an intermediary, we are able to handle problems that are infeasible for either deep RL or formal methods by themselves. First, we suggest, for the first time, a synthesis procedure that is based on a magic book. We synthesize a stand-alone correct-by-design controller that enjoys the favorable performance of RL. Second, we incorporate a magic book in a bounded model checking (BMC) procedure. BMC allows us to find numerous traces of the plant under the control of the wizard, which a user can use to increase the trustworthiness of the wizard and direct further training.
AU - Alamdari, Par Alizadeh
AU - Avni, Guy
AU - Henzinger, Thomas A
AU - Lukina, Anna
ID - 9040
SN - 9783854480426
T2 - Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design
TI - Formal methods with a touch of magic
ER -
TY - JOUR
AB - Rhombic dodecahedron is a space filling polyhedron which represents the close packing of spheres in 3D space and the Voronoi structures of the face centered cubic (FCC) lattice. In this paper, we describe a new coordinate system where every 3-integer coordinates grid point corresponds to a rhombic dodecahedron centroid. In order to illustrate the interest of the new coordinate system, we propose the characterization of 3D digital plane with its topological features, such as the interrelation between the thickness of the digital plane and the separability constraint we aim to obtain. We also present the characterization of 3D digital lines and study it as the intersection of multiple digital planes. Characterization of 3D digital sphere with relevant topological features is proposed as well along with the 48-symmetry appearing in the new coordinate system.
AU - Biswas, Ranita
AU - Largeteau-Skapin, Gaëlle
AU - Zrour, Rita
AU - Andres, Eric
ID - 9249
IS - 1
JF - Mathematical Morphology - Theory and Applications
SN - 2353-3390
TI - Digital objects in rhombic dodecahedron grid
VL - 4
ER -
TY - CONF
AB - We call a multigraph non-homotopic if it can be drawn in the plane in such a way that no two edges connecting the same pair of vertices can be continuously transformed into each other without passing through a vertex, and no loop can be shrunk to its end-vertex in the same way. It is easy to see that a non-homotopic multigraph on n>1 vertices can have arbitrarily many edges. We prove that the number of crossings between the edges of a non-homotopic multigraph with n vertices and m>4n edges is larger than cm2n for some constant c>0 , and that this bound is tight up to a polylogarithmic factor. We also show that the lower bound is not asymptotically sharp as n is fixed and m⟶∞ .
AU - Pach, János
AU - Tardos, Gábor
AU - Tóth, Géza
ID - 9299
SN - 0302-9743
T2 - 28th International Symposium on Graph Drawing and Network Visualization
TI - Crossings between non-homotopic edges
VL - 12590
ER -
TY - CONF
AB - Second-order information, in the form of Hessian- or Inverse-Hessian-vector products, is a fundamental tool for solving optimization problems. Recently, there has been significant interest in utilizing this information in the context of deep
neural networks; however, relatively little is known about the quality of existing approximations in this context. Our work examines this question, identifies issues with existing approaches, and proposes a method called WoodFisher to compute a faithful and efficient estimate of the inverse Hessian. Our main application is to neural network compression, where we build on the classic Optimal Brain Damage/Surgeon framework. We demonstrate that WoodFisher significantly outperforms popular state-of-the-art methods for oneshot pruning. Further, even when iterative, gradual pruning is allowed, our method results in a gain in test accuracy over the state-of-the-art approaches, for standard image classification datasets such as ImageNet ILSVRC. We examine how our method can be extended to take into account first-order information, as well as
illustrate its ability to automatically set layer-wise pruning thresholds and perform compression in the limited-data regime. The code is available at the following link, https://github.com/IST-DASLab/WoodFisher.
AU - Singh, Sidak Pal
AU - Alistarh, Dan-Adrian
ID - 9632
SN - 10495258
T2 - Advances in Neural Information Processing Systems
TI - WoodFisher: Efficient second-order approximation for neural network compression
VL - 33
ER -
TY - JOUR
AB - Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.
AU - Edelsbrunner, Herbert
AU - Virk, Ziga
AU - Wagner, Hubert
ID - 9630
IS - 2
JF - Journal of Computational Geometry
TI - Topological data analysis in information space
VL - 11
ER -
TY - CONF
AB - The ability to leverage large-scale hardware parallelism has been one of the key enablers of the accelerated recent progress in machine learning. Consequently, there has been considerable effort invested into developing efficient parallel variants of classic machine learning algorithms. However, despite the wealth of knowledge on parallelization, some classic machine learning algorithms often prove hard to parallelize efficiently while maintaining convergence. In this paper, we focus on efficient parallel algorithms for the key machine learning task of inference on graphical models, in particular on the fundamental belief propagation algorithm. We address the challenge of efficiently parallelizing this classic paradigm by showing how to leverage scalable relaxed schedulers in this context. We present an extensive empirical study, showing that our approach outperforms previous parallel belief propagation implementations both in terms of scalability and in terms of wall-clock convergence time, on a range of practical applications.
AU - Aksenov, Vitaly
AU - Alistarh, Dan-Adrian
AU - Korhonen, Janne
ID - 9631
SN - 10495258
T2 - Advances in Neural Information Processing Systems
TI - Scalable belief propagation via relaxed scheduling
VL - 33
ER -
TY - CONF
AB - Game of Life is a simple and elegant model to study dynamical system over networks. The model consists of a graph where every vertex has one of two types, namely, dead or alive. A configuration is a mapping of the vertices to the types. An update rule describes how the type of a vertex is updated given the types of its neighbors. In every round, all vertices are updated synchronously, which leads to a configuration update. While in general, Game of Life allows a broad range of update rules, we focus on two simple families of update rules, namely, underpopulation and overpopulation, that model several interesting dynamics studied in the literature. In both settings, a dead vertex requires at least a desired number of live neighbors to become alive. For underpopulation (resp., overpopulation), a live vertex requires at least (resp. at most) a desired number of live neighbors to remain alive. We study the basic computation problems, e.g., configuration reachability, for these two families of rules. For underpopulation rules, we show that these problems can be solved in polynomial time, whereas for overpopulation rules they are PSPACE-complete.
AU - Chatterjee, Krishnendu
AU - Ibsen-Jensen, Rasmus
AU - Jecker, Ismael R
AU - Svoboda, Jakub
ID - 8533
SN - 18688969
T2 - 45th International Symposium on Mathematical Foundations of Computer Science
TI - Simplified game of life: Algorithms and complexity
VL - 170
ER -
TY - CONF
AB - A regular language L of finite words is composite if there are regular languages L₁,L₂,…,L_t such that L = ⋂_{i = 1}^t L_i and the index (number of states in a minimal DFA) of every language L_i is strictly smaller than the index of L. Otherwise, L is prime. Primality of regular languages was introduced and studied in [O. Kupferman and J. Mosheiff, 2015], where the complexity of deciding the primality of the language of a given DFA was left open, with a doubly-exponential gap between the upper and lower bounds. We study primality for unary regular languages, namely regular languages with a singleton alphabet. A unary language corresponds to a subset of ℕ, making the study of unary prime languages closer to that of primality in number theory. We show that the setting of languages is richer. In particular, while every composite number is the product of two smaller numbers, the number t of languages necessary to decompose a composite unary language induces a strict hierarchy. In addition, a primality witness for a unary language L, namely a word that is not in L but is in all products of languages that contain L and have an index smaller than L’s, may be of exponential length. Still, we are able to characterize compositionality by structural properties of a DFA for L, leading to a LogSpace algorithm for primality checking of unary DFAs.
AU - Jecker, Ismael R
AU - Kupferman, Orna
AU - Mazzocchi, Nicolas
ID - 8534
SN - 18688969
T2 - 45th International Symposium on Mathematical Foundations of Computer Science
TI - Unary prime languages
VL - 170
ER -
TY - JOUR
AB - We prove some recent experimental observations of Dan Reznik concerning periodic billiard orbits in ellipses. For example, the sum of cosines of the angles of a periodic billiard polygon remains constant in the 1-parameter family of such polygons (that exist due to the Poncelet porism). In our proofs, we use geometric and complex analytic methods.
AU - Akopyan, Arseniy
AU - Schwartz, Richard
AU - Tabachnikov, Serge
ID - 8538
JF - European Journal of Mathematics
SN - 2199-675X
TI - Billiards in ellipses revisited
ER -
TY - GEN
AB - The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we reported that a substantial proportion of blood vessels in the adult brain sporadically occluded and regressed. Their regression proceeded through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels were found to be widespread in mouse, monkey and human brains. Both brief occlusions of the middle cerebral artery and lipopolysaccharide-mediated inflammation induced an increase of vessel regression. Blockage of leukocyte adhesion to endothelial cells alleviated LPS-induced vessel regression. We further revealed that blood vessel regression caused a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain.
AU - Gao, Xiaofei
AU - Li, Jun-Liszt
AU - Chen, Xingjun
AU - Ci, Bo
AU - Chen, Fei
AU - Lu, Nannan
AU - Shen, Bo
AU - Zheng, Lijun
AU - Jia, Jie-Min
AU - Yi, Yating
AU - Zhang, Shiwen
AU - Shi, Ying-Chao
AU - Shi, Kaibin
AU - Propson, Nicholas E
AU - Huang, Yubin
AU - Poinsatte, Katherine
AU - Zhang, Zhaohuan
AU - Yue, Yuanlei
AU - Bosco, Dale B
AU - Lu, Ying-mei
AU - Yang, Shi-bing
AU - Adams, Ralf H.
AU - Lindner, Volkhard
AU - Huang, Fen
AU - Wu, Long-Jun
AU - Zheng, Hui
AU - Han, Feng
AU - Hippenmeyer, Simon
AU - Stowe, Ann M.
AU - Peng, Bo
AU - Margeta, Marta
AU - Wang, Xiaoqun
AU - Liu, Qiang
AU - Körbelin, Jakob
AU - Trepel, Martin
AU - Lu, Hui
AU - Zhou, Bo O.
AU - Zhao, Hu
AU - Su, Wenzhi
AU - Bachoo, Robert M.
AU - Ge, Woo-ping
ID - 8616
T2 - bioRxiv
TI - Reduction of neuronal activity mediated by blood-vessel regression in the brain
ER -
TY - GEN
AB - A look at international activities on Open Science reveals a broad spectrum from individual institutional policies to national action plans. The present Recommendations for a National Open Science Strategy in Austria are based on these international initiatives and present practical considerations for their coordinated implementation with regard to strategic developments in research, technology and innovation (RTI) in Austria until 2030. They are addressed to all relevant actors in the RTI system, in particular to Research Performing Organisations, Research Funding Organisations, Research Policy, memory institutions such as Libraries and Researchers. The recommendation paper was developed from 2018 to 2020 by the OANA working group "Open Science Strategy" and published for the first time in spring 2020 for a public consultation. The now available final version of the recommendation document, which contains feedback and comments from the consultation, is intended to provide an impetus for further discussion and implementation of Open Science in Austria and serves as a contribution and basis for a potential national Open Science Strategy in Austria. The document builds on the diverse expertise of the authors (academia, administration, library and archive, information technology, science policy, funding system, etc.) and reflects their personal experiences and opinions.
AU - Mayer, Katja
AU - Rieck, Katharina
AU - Reichmann, Stefan
AU - Danowski, Patrick
AU - Graschopf, Anton
AU - König, Thomas
AU - Kraker, Peter
AU - Lehner, Patrick
AU - Reckling, Falk
AU - Ross-Hellauer, Tony
AU - Spichtinger, Daniel
AU - Tzatzanis, Michalis
AU - Schürz, Stefanie
ID - 8695
TI - Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria
ER -
TY - JOUR
AB - As part of the Austrian Transition to Open Access (AT2OA) project, subproject TP1-B is working on designing a monitoring solution for the output of Open Access publications in Austria. This report on a potential Open Access monitoring approach in Austria is one of the results of these efforts and can serve as a basis for discussion on an international level.
AU - Danowski, Patrick
AU - Ferus, Andreas
AU - Hikl, Anna-Laetitia
AU - McNeill, Gerda
AU - Miniberger, Clemens
AU - Reding, Steve
AU - Zarka, Tobias
AU - Zojer, Michael
ID - 8706
IS - 2
JF - Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
TI - „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B
VL - 73
ER -
TY - JOUR
AB - Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments.
For complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b).
AU - Laukoter, Susanne
AU - Amberg, Nicole
AU - Pauler, Florian
AU - Hippenmeyer, Simon
ID - 8978
IS - 3
JF - STAR Protocols
SN - 2666-1667
TI - Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy
VL - 1
ER -
TY - CONF
AB - We introduce LRT-NG, a set of techniques and an associated toolset that computes a reachtube (an over-approximation of the set of reachable states over a given time horizon) of a nonlinear dynamical system. LRT-NG significantly advances the state-of-the-art Langrangian Reachability and its associated tool LRT. From a theoretical perspective, LRT-NG is superior to LRT in three ways. First, it uses for the first time an analytically computed metric for the propagated ball which is proven to minimize the ball’s volume. We emphasize that the metric computation is the centerpiece of all bloating-based techniques. Secondly, it computes the next reachset as the intersection of two balls: one based on the Cartesian metric and the other on the new metric. While the two metrics were previously considered opposing approaches, their joint use considerably tightens the reachtubes. Thirdly, it avoids the "wrapping effect" associated with the validated integration of the center of the reachset, by optimally absorbing the interval approximation in the radius of the next ball. From a tool-development perspective, LRT-NG is superior to LRT in two ways. First, it is a standalone tool that no longer relies on CAPD. This required the implementation of the Lohner method and a Runge-Kutta time-propagation method. Secondly, it has an improved interface, allowing the input model and initial conditions to be provided as external input files. Our experiments on a comprehensive set of benchmarks, including two Neural ODEs, demonstrates LRT-NG’s superior performance compared to LRT, CAPD, and Flow*.
AU - Gruenbacher, Sophie
AU - Cyranka, Jacek
AU - Lechner, Mathias
AU - Islam, Md Ariful
AU - Smolka, Scott A.
AU - Grosu, Radu
ID - 9103
SN - 07431546
T2 - Proceedings of the 59th IEEE Conference on Decision and Control
TI - Lagrangian reachtubes: The next generation
VL - 2020
ER -
TY - CONF
AB - Recent works have shown that gradient descent can find a global minimum for over-parameterized neural networks where the widths of all the hidden layers scale polynomially with N (N being the number of training samples). In this paper, we prove that, for deep networks, a single layer of width N following the input layer suffices to ensure a similar guarantee. In particular, all the remaining layers are allowed to have constant widths, and form a pyramidal topology. We show an application of our result to the widely used LeCun’s initialization and obtain an over-parameterization requirement for the single wide layer of order N2.
AU - Nguyen, Quynh
AU - Mondelli, Marco
ID - 9221
T2 - 34th Conference on Neural Information Processing Systems
TI - Global convergence of deep networks with one wide layer followed by pyramidal topology
VL - 33
ER -
TY - CONF
AB - Optimizing convolutional neural networks for fast inference has recently become an extremely active area of research. One of the go-to solutions in this context is weight pruning, which aims to reduce computational and memory footprint by removing large subsets of the connections in a neural network. Surprisingly, much less attention has been given to exploiting sparsity in the activation maps, which tend to be naturally sparse in many settings thanks to the structure of rectified linear (ReLU) activation functions. In this paper, we present an in-depth analysis of methods for maximizing the sparsity of the activations in a trained neural network, and show that, when coupled with an efficient sparse-input convolution algorithm, we can leverage this sparsity for significant performance gains. To induce highly sparse activation maps without accuracy loss, we introduce a new regularization technique, coupled with a new threshold-based sparsification method based on a parameterized activation function called Forced-Activation-Threshold Rectified Linear Unit (FATReLU). We examine the impact of our methods on popular image classification models, showing that most architectures can adapt to significantly sparser activation maps without any accuracy loss. Our second contribution is showing that these these compression gains can be translated into inference speedups: we provide a new algorithm to enable fast convolution operations over networks with sparse activations, and show that it can enable significant speedups for end-to-end inference on a range of popular models on the large-scale ImageNet image classification task on modern Intel CPUs, with little or no retraining cost.
AU - Kurtz, Mark
AU - Kopinsky, Justin
AU - Gelashvili, Rati
AU - Matveev, Alexander
AU - Carr, John
AU - Goin, Michael
AU - Leiserson, William
AU - Moore, Sage
AU - Nell, Bill
AU - Shavit, Nir
AU - Alistarh, Dan-Adrian
ID - 9415
SN - 2640-3498
T2 - 37th International Conference on Machine Learning, ICML 2020
TI - Inducing and exploiting activation sparsity for fast neural network inference
VL - 119
ER -
TY - CONF
AB - The family of feedback alignment (FA) algorithms aims to provide a more biologically motivated alternative to backpropagation (BP), by substituting the computations that are unrealistic to be implemented in physical brains. While FA algorithms have been shown to work well in practice, there is a lack of rigorous theory proofing their learning capabilities. Here we introduce the first feedback alignment algorithm with provable learning guarantees. In contrast to existing work, we do not require any assumption about the size or depth of the network except that it has a single output neuron, i.e., such as for binary classification tasks. We show that our FA algorithm can deliver its theoretical promises in practice, surpassing the learning performance of existing FA methods and matching backpropagation in binary classification tasks. Finally, we demonstrate the limits of our FA variant when the number of output neurons grows beyond a certain quantity.
AU - Lechner, Mathias
ID - 10672
T2 - 8th International Conference on Learning Representations
TI - Learning representations for binary-classification without backpropagation
ER -
TY - CONF
AB - A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that
gives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to
generate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on
depth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking.
AU - Henderson, Paul M
AU - Lampert, Christoph
ID - 8188
SN - 9781713829546
T2 - 34th Conference on Neural Information Processing Systems
TI - Unsupervised object-centric video generation and decomposition in 3D
VL - 33
ER -
TY - BOOK
AB - This booklet is a collection of abstracts presented at the AHPC conference.
ED - Schlögl, Alois
ED - Kiss, Janos
ED - Elefante, Stefano
ID - 7474
SN - 978-3-99078-004-6
TI - Austrian High-Performance-Computing meeting (AHPC2020)
ER -
TY - CONF
AB - Quantization converts neural networks into low-bit fixed-point computations which can be carried out by efficient integer-only hardware, and is standard practice for the deployment of neural networks on real-time embedded devices. However, like their real-numbered counterpart, quantized networks are not immune to malicious misclassification caused by adversarial attacks. We investigate how quantization affects a network’s robustness to adversarial attacks, which is a formal verification question. We show that neither robustness nor non-robustness are monotonic with changing the number of bits for the representation and, also, neither are preserved by quantization from a real-numbered network. For this reason, we introduce a verification method for quantized neural networks which, using SMT solving over bit-vectors, accounts for their exact, bit-precise semantics. We built a tool and analyzed the effect of quantization on a classifier for the MNIST dataset. We demonstrate that, compared to our method, existing methods for the analysis of real-numbered networks often derive false conclusions about their quantizations, both when determining robustness and when detecting attacks, and that existing methods for quantized networks often miss attacks. Furthermore, we applied our method beyond robustness, showing how the number of bits in quantization enlarges the gender bias of a predictor for students’ grades.
AU - Giacobbe, Mirco
AU - Henzinger, Thomas A
AU - Lechner, Mathias
ID - 7808
SN - 03029743
T2 - International Conference on Tools and Algorithms for the Construction and Analysis of Systems
TI - How many bits does it take to quantize your neural network?
VL - 12079
ER -
TY - CONF
AB - Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f: ℝ^d → ℝ^(d-n). A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently fine triangulation 𝒯. This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary.
AU - Boissonnat, Jean-Daniel
AU - Wintraecken, Mathijs
ID - 7952
SN - 1868-8969
T2 - 36th International Symposium on Computational Geometry
TI - The topological correctness of PL-approximations of isomanifolds
VL - 164
ER -
TY - CONF
AB - Given a finite point set P in general position in the plane, a full triangulation is a maximal straight-line embedded plane graph on P. A partial triangulation on P is a full triangulation of some subset P' of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge, removes a non-extreme point of degree 3, or adds a point in P ⧵ P' as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The goal of this paper is to investigate the structure of this graph, with emphasis on its connectivity. For sets P of n points in general position, we show that the bistellar flip graph is (n-3)-connected, thereby answering, for sets in general position, an open questions raised in a book (by De Loera, Rambau, and Santos) and a survey (by Lee and Santos) on triangulations. This matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points and projecting the lower convex hull), where (n-3)-connectivity has been known since the late 1980s through the secondary polytope (Gelfand, Kapranov, Zelevinsky) and Balinski’s Theorem. Our methods also yield the following results (see the full version [Wagner and Welzl, 2020]): (i) The bistellar flip graph can be covered by graphs of polytopes of dimension n-3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n-3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations are regular iff the trivial subdivision has height n-3 in the partial order of partial subdivisions. (iv) There are arbitrarily large sets P with non-regular partial triangulations, while every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular partial triangulations (answering a question by F. Santos in the unexpected direction).
AU - Wagner, Uli
AU - Welzl, Emo
ID - 7990
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)
VL - 164
ER -
TY - CONF
AB - In a straight-line embedded triangulation of a point set P in the plane, removing an inner edge and—provided the resulting quadrilateral is convex—adding the other diagonal is called an edge flip. The (edge) flip graph has all triangulations as vertices, and a pair of triangulations is adjacent if they can be obtained from each other by an edge flip. The goal of this paper is to contribute to a better understanding of the flip graph, with an emphasis on its connectivity.
For sets in general position, it is known that every triangulation allows at least edge flips (a tight bound) which gives the minimum degree of any flip graph for n points. We show that for every point set P in general position, the flip graph is at least -vertex connected. Somewhat more strongly, we show that the vertex connectivity equals the minimum degree occurring in the flip graph, i.e. the minimum number of flippable edges in any triangulation of P, provided P is large enough. Finally, we exhibit some of the geometry of the flip graph by showing that the flip graph can be covered by 1-skeletons of polytopes of dimension (products of associahedra).
A corresponding result ((n – 3)-vertex connectedness) can be shown for the bistellar flip graph of partial triangulations, i.e. the set of all triangulations of subsets of P which contain all extreme points of P. This will be treated separately in a second part.
AU - Wagner, Uli
AU - Welzl, Emo
ID - 7807
SN - 9781611975994
T2 - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
TI - Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)
VL - 2020-January
ER -
TY - GEN
AB - The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.
AU - Simon, Alexis
AU - Fraisse, Christelle
AU - El Ayari, Tahani
AU - Liautard-Haag, Cathy
AU - Strelkov, Petr
AU - Welch, John
AU - Bierne, Nicolas
ID - 13073
TI - How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels
ER -
TY - GEN
AB - Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.
AU - Arnoux, Stephanie
AU - Fraisse, Christelle
AU - Sauvage, Christopher
ID - 13065
TI - VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species
ER -
TY - CONF
AB - This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N 1−1/µ ), where N is the block length and µ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 and 1.
AU - Mondelli, Marco
AU - Hashemi, Seyyed Ali
AU - Cioffi, John
AU - Goldsmith, Andrea
ID - 8536
SN - 21578095
T2 - IEEE International Symposium on Information Theory - Proceedings
TI - Simplified successive cancellation decoding of polar codes has sublinear latency
VL - 2020-June
ER -
TY - JOUR
AU - Avvakumov, Sergey
AU - Wagner, Uli
AU - Mabillard, Isaac
AU - Skopenkov, A. B.
ID - 9308
IS - 6
JF - Russian Mathematical Surveys
SN - 0036-0279
TI - Eliminating higher-multiplicity intersections, III. Codimension 2
VL - 75
ER -
TY - JOUR
AB - We study dynamical optimal transport metrics between density matricesassociated to symmetric Dirichlet forms on finite-dimensional C∗-algebras. Our settingcovers arbitrary skew-derivations and it provides a unified framework that simultaneously generalizes recently constructed transport metrics for Markov chains, Lindblad equations, and the Fermi Ornstein–Uhlenbeck semigroup. We develop a non-nommutative differential calculus that allows us to obtain non-commutative Ricci curvature bounds, logarithmic Sobolev inequalities, transport-entropy inequalities, andspectral gap estimates.
AU - Carlen, Eric A.
AU - Maas, Jan
ID - 6358
IS - 2
JF - Journal of Statistical Physics
SN - 00224715
TI - Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems
VL - 178
ER -
TY - CHAP
AB - We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean space, motivated by the famous theorem of Gromov about the waist of radially symmetric Gaussian measures. In particular, it turns our possible to extend Gromov’s original result to the case of not necessarily radially symmetric Gaussian measure. We also provide examples of measures having no t-neighborhood waist property, including a rather wide class
of compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2.
We use a simpler form of Gromov’s pancake argument to produce some estimates of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for reader’s convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian
measures.
AU - Akopyan, Arseniy
AU - Karasev, Roman
ED - Klartag, Bo'az
ED - Milman, Emanuel
ID - 74
SN - 00758434
T2 - Geometric Aspects of Functional Analysis
TI - Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures
VL - 2256
ER -
TY - JOUR
AB - We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree.
AU - Browning, Timothy D
AU - Sawin, Will
ID - 177
IS - 3
JF - Annals of Mathematics
TI - A geometric version of the circle method
VL - 191
ER -
TY - JOUR
AB - While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.
AU - Benedikter, Niels P
AU - Nam, Phan Thành
AU - Porta, Marcello
AU - Schlein, Benjamin
AU - Seiringer, Robert
ID - 6649
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime
VL - 374
ER -
TY - JOUR
AB - Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses.
AU - Stella, Federico
AU - Urdapilleta, Eugenio
AU - Luo, Yifan
AU - Treves, Alessandro
ID - 6796
IS - 4
JF - Hippocampus
SN - 10509631
TI - Partial coherence and frustration in self-organizing spherical grids
VL - 30
ER -
TY - JOUR
AB - In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability.
AU - Avni, Guy
AU - Henzinger, Thomas A
AU - Kupferman, Orna
ID - 6761
JF - Theoretical Computer Science
SN - 03043975
TI - Dynamic resource allocation games
VL - 807
ER -
TY - JOUR
AB - We consider the monotone variational inequality problem in a Hilbert space and describe a projection-type method with inertial terms under the following properties: (a) The method generates a strongly convergent iteration sequence; (b) The method requires, at each iteration, only one projection onto the feasible set and two evaluations of the operator; (c) The method is designed for variational inequality for which the underline operator is monotone and uniformly continuous; (d) The method includes an inertial term. The latter is also shown to speed up the convergence in our numerical results. A comparison with some related methods is given and indicates that the new method is promising.
AU - Shehu, Yekini
AU - Li, Xiao-Huan
AU - Dong, Qiao-Li
ID - 6593
JF - Numerical Algorithms
SN - 1017-1398
TI - An efficient projection-type method for monotone variational inequalities in Hilbert spaces
VL - 84
ER -
TY - JOUR
AB - Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions.
AU - Jahr, Wiebke
AU - Velicky, Philipp
AU - Danzl, Johann G
ID - 6808
IS - 3
JF - Methods
SN - 1046-2023
TI - Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens
VL - 174
ER -
TY - JOUR
AB - This paper presents two algorithms. The first decides the existence of a pointed homotopy between given simplicial maps 𝑓,𝑔:𝑋→𝑌, and the second computes the group [𝛴𝑋,𝑌]∗ of pointed homotopy classes of maps from a suspension; in both cases, the target Y is assumed simply connected. More generally, these algorithms work relative to 𝐴⊆𝑋.
AU - Filakovský, Marek
AU - Vokřínek, Lukas
ID - 6563
JF - Foundations of Computational Mathematics
SN - 16153375
TI - Are two given maps homotopic? An algorithmic viewpoint
VL - 20
ER -
TY - JOUR
AB - We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn.
AU - Henderson, Paul M
AU - Ferrari, Vittorio
ID - 6952
JF - International Journal of Computer Vision
SN - 0920-5691
TI - Learning single-image 3D reconstruction by generative modelling of shape, pose and shading
VL - 128
ER -
TY - JOUR
AB - Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality.
AU - Donahue, RJ
AU - Maes, Margaret E
AU - Grosser, JA
AU - Nickells, RW
ID - 7033
IS - 2
JF - Molecular Neurobiology
SN - 0893-7648
TI - BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage
VL - 57
ER -
TY - JOUR
AU - Zhang, Yuzhou
AU - Friml, Jiří
ID - 6997
IS - 3
JF - New Phytologist
SN - 0028-646x
TI - Auxin guides roots to avoid obstacles during gravitropic growth
VL - 225
ER -
TY - JOUR
AB - We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds.
AU - Rapcak, Miroslav
AU - Soibelman, Yan
AU - Yang, Yaping
AU - Zhao, Gufang
ID - 7004
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Cohomological Hall algebras, vertex algebras and instantons
VL - 376
ER -
TY - JOUR
AB - Plant root architecture dynamically adapts to various environmental conditions, such as salt‐containing soil. The phytohormone abscisic acid (ABA) is involved among others also in these developmental adaptations, but the underlying molecular mechanism remains elusive. Here, a novel branch of the ABA signaling pathway in Arabidopsis involving PYR/PYL/RCAR (abbreviated as PYLs) receptor‐protein phosphatase 2A (PP2A) complex that acts in parallel to the canonical PYLs‐protein phosphatase 2C (PP2C) mechanism is identified. The PYLs‐PP2A signaling modulates root gravitropism and lateral root formation through regulating phytohormone auxin transport. In optimal conditions, PYLs ABA receptor interacts with the catalytic subunits of PP2A, increasing their phosphatase activity and thus counteracting PINOID (PID) kinase‐mediated phosphorylation of PIN‐FORMED (PIN) auxin transporters. By contrast, in salt and osmotic stress conditions, ABA binds to PYLs, inhibiting the PP2A activity, which leads to increased PIN phosphorylation and consequently modulated directional auxin transport leading to adapted root architecture. This work reveals an adaptive mechanism that may flexibly adjust plant root growth to withstand saline and osmotic stresses. It occurs via the cross‐talk between the stress hormone ABA and the versatile developmental regulator auxin.
AU - Li, Yang
AU - Wang, Yaping
AU - Tan, Shutang
AU - Li, Zhen
AU - Yuan, Zhi
AU - Glanc, Matous
AU - Domjan, David
AU - Wang, Kai
AU - Xuan, Wei
AU - Guo, Yan
AU - Gong, Zhizhong
AU - Friml, Jiří
AU - Zhang, Jing
ID - 7204
IS - 3
JF - Advanced Science
TI - Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex
VL - 7
ER -
TY - JOUR
AB - In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors.
AU - Ucar, Mehmet C
AU - Lipowsky, Reinhard
ID - 7166
IS - 1
JF - Nano Letters
SN - 1530-6984
TI - Collective force generation by molecular motors is determined by strain-induced unbinding
VL - 20
ER -
TY - JOUR
AB - T lymphocytes utilize amoeboid migration to navigate effectively within complex microenvironments. The precise rearrangement of the actin cytoskeleton required for cellular forward propulsion is mediated by actin regulators, including the actin‐related protein 2/3 (Arp2/3) complex, a macromolecular machine that nucleates branched actin filaments at the leading edge. The consequences of modulating Arp2/3 activity on the biophysical properties of the actomyosin cortex and downstream T cell function are incompletely understood. We report that even a moderate decrease of Arp3 levels in T cells profoundly affects actin cortex integrity. Reduction in total F‐actin content leads to reduced cortical tension and disrupted lamellipodia formation. Instead, in Arp3‐knockdown cells, the motility mode is dominated by blebbing migration characterized by transient, balloon‐like protrusions at the leading edge. Although this migration mode seems to be compatible with interstitial migration in three‐dimensional environments, diminished locomotion kinetics and impaired cytotoxicity interfere with optimal T cell function. These findings define the importance of finely tuned, Arp2/3‐dependent mechanophysical membrane integrity in cytotoxic effector T lymphocyte activities.
AU - Obeidy, Peyman
AU - Ju, Lining A.
AU - Oehlers, Stefan H.
AU - Zulkhernain, Nursafwana S.
AU - Lee, Quintin
AU - Galeano Niño, Jorge L.
AU - Kwan, Rain Y.Q.
AU - Tikoo, Shweta
AU - Cavanagh, Lois L.
AU - Mrass, Paulus
AU - Cook, Adam J.L.
AU - Jackson, Shaun P.
AU - Biro, Maté
AU - Roediger, Ben
AU - Sixt, Michael K
AU - Weninger, Wolfgang
ID - 7234
IS - 2
JF - Immunology and Cell Biology
SN - 08189641
TI - Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes
VL - 98
ER -
TY - JOUR
AB - The cyclin-dependent kinase inhibitor p57KIP2 is encoded by the imprinted Cdkn1c locus, exhibits maternal expression, and is essential for cerebral cortex development. How Cdkn1c regulates corticogenesis is however not clear. To this end we employ Mosaic Analysis with Double Markers (MADM) technology to genetically dissect Cdkn1c gene function in corticogenesis at single cell resolution. We find that the previously described growth-inhibitory Cdkn1c function is a non-cell-autonomous one, acting on the whole organism. In contrast we reveal a growth-promoting cell-autonomous Cdkn1c function which at the mechanistic level mediates radial glial progenitor cell and nascent projection neuron survival. Strikingly, the growth-promoting function of Cdkn1c is highly dosage sensitive but not subject to genomic imprinting. Collectively, our results suggest that the Cdkn1c locus regulates cortical development through distinct cell-autonomous and non-cell-autonomous mechanisms. More generally, our study highlights the importance to probe the relative contributions of cell intrinsic gene function and tissue-wide mechanisms to the overall phenotype.
AU - Laukoter, Susanne
AU - Beattie, Robert J
AU - Pauler, Florian
AU - Amberg, Nicole
AU - Nakayama, Keiichi I.
AU - Hippenmeyer, Simon
ID - 7253
JF - Nature Communications
SN - 2041-1723
TI - Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development
VL - 11
ER -
TY - JOUR
AB - Cytoskeletal filaments such as microtubules (MTs) and filamentous actin (F-actin) dynamically support cell structure and functions. In central presynaptic terminals, F-actin is expressed along the release edge and reportedly plays diverse functional roles, but whether axonal MTs extend deep into terminals and play any physiological role remains controversial. At the calyx of Held in rats of either sex, confocal and high-resolution microscopy revealed that MTs enter deep into presynaptic terminal swellings and partially colocalize with a subset of synaptic vesicles (SVs). Electrophysiological analysis demonstrated that depolymerization of MTs specifically prolonged the slow-recovery time component of EPSCs from short-term depression induced by a train of high-frequency stimulation, whereas depolymerization of F-actin specifically prolonged the fast-recovery component. In simultaneous presynaptic and postsynaptic action potential recordings, depolymerization of MTs or F-actin significantly impaired the fidelity of high-frequency neurotransmission. We conclude that MTs and F-actin differentially contribute to slow and fast SV replenishment, thereby maintaining high-frequency neurotransmission.
AU - Piriya Ananda Babu, Lashmi
AU - Wang, Han Ying
AU - Eguchi, Kohgaku
AU - Guillaud, Laurent
AU - Takahashi, Tomoyuki
ID - 7339
IS - 1
JF - Journal of neuroscience
TI - Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission
VL - 40
ER -
TY - JOUR
AB - The ability to sense environmental temperature and to coordinate growth and development accordingly, is critical to the reproductive success of plants. Flowering time is regulated at the level of gene expression by a complex network of factors that integrate environmental and developmental cues. One of the main players, involved in modulating flowering time in response to changes in ambient temperature is FLOWERING LOCUS M (FLM). FLM transcripts can undergo extensive alternative splicing producing multiple variants, of which FLM-β and FLM-δ are the most representative. While FLM-β codes for the flowering repressor FLM protein, translation of FLM-δ has the opposite effect on flowering. Here we show that the cyclin-dependent kinase G2 (CDKG2), together with its cognate cyclin, CYCLYN L1 (CYCL1) affects the alternative splicing of FLM, balancing the levels of FLM-β and FLM-δ across the ambient temperature range. In the absence of the CDKG2/CYCL1 complex, FLM-β expression is reduced while FLM-δ is increased in a temperature dependent manner and these changes are associated with an early flowering phenotype in the cdkg2 mutant lines. In addition, we found that transcript variants retaining the full FLM intron 1 are sequestered in the cell nucleus. Strikingly, FLM intron 1 splicing is also regulated by CDKG2/CYCL1. Our results provide evidence that temperature and CDKs regulate the alternative splicing of FLM, contributing to flowering time definition.
AU - Nibau, Candida
AU - Gallemi, Marçal
AU - Dadarou, Despoina
AU - Doonan, John H.
AU - Cavallari, Nicola
ID - 7350
JF - Frontiers in Plant Science
SN - 1664-462X
TI - Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2
VL - 10
ER -
TY - JOUR
AB - Neuronal responses to complex stimuli and tasks can encompass a wide range of time scales. Understanding these responses requires measures that characterize how the information on these response patterns are represented across multiple temporal resolutions. In this paper we propose a metric – which we call multiscale relevance (MSR) – to capture the dynamical variability of the activity of single neurons across different time scales. The MSR is a non-parametric, fully featureless indicator in that it uses only the time stamps of the firing activity without resorting to any a priori covariate or invoking any specific structure in the tuning curve for neural activity. When applied to neural data from the mEC and from the ADn and PoS regions of freely-behaving rodents, we found that neurons having low MSR tend to have low mutual information and low firing sparsity across the correlates that are believed to be encoded by the region of the brain where the recordings were made. In addition, neurons with high MSR contain significant information on spatial navigation and allow to decode spatial position or head direction as efficiently as those neurons whose firing activity has high mutual information with the covariate to be decoded and significantly better than the set of neurons with high local variations in their interspike intervals. Given these results, we propose that the MSR can be used as a measure to rank and select neurons for their information content without the need to appeal to any a priori covariate.
AU - Cubero, Ryan J
AU - Marsili, Matteo
AU - Roudi, Yasser
ID - 7369
JF - Journal of Computational Neuroscience
KW - Time series analysis
KW - Multiple time scale analysis
KW - Spike train data
KW - Information theory
KW - Bayesian decoding
SN - 0929-5313
TI - Multiscale relevance and informative encoding in neuronal spike trains
VL - 48
ER -
TY - JOUR
AB - We present nsCouette, a highly scalable software tool to solve the Navier–Stokes equations for incompressible fluid flow between differentially heated and independently rotating, concentric cylinders. It is based on a pseudospectral spatial discretization and dynamic time-stepping. It is implemented in modern Fortran with a hybrid MPI-OpenMP parallelization scheme and thus designed to compute turbulent flows at high Reynolds and Rayleigh numbers. An additional GPU implementation (C-CUDA) for intermediate problem sizes and a version for pipe flow (nsPipe) are also provided.
AU - Lopez Alonso, Jose M
AU - Feldmann, Daniel
AU - Rampp, Markus
AU - Vela-Martín, Alberto
AU - Shi, Liang
AU - Avila, Marc
ID - 7364
JF - SoftwareX
TI - nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow
VL - 11
ER -
TY - JOUR
AB - In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.
AU - Kolchinsky, Artemy
AU - Corominas-Murtra, Bernat
ID - 7431
IS - 162
JF - Journal of the Royal Society Interface
TI - Decomposing information into copying versus transformation
VL - 17
ER -
TY - JOUR
AB - Recently Kloeckner described the structure of the isometry group of the quadratic Wasserstein space W_2(R^n). It turned out that the case of the real line is exceptional in the sense that there exists an exotic isometry flow. Following this line of investigation, we compute Isom(W_p(R)), the isometry group of the Wasserstein space
W_p(R) for all p \in [1,\infty) \setminus {2}. We show that W_2(R) is also exceptional regarding the
parameter p: W_p(R) is isometrically rigid if and only if p is not equal to 2. Regarding the underlying
space, we prove that the exceptionality of p = 2 disappears if we replace R by the compact
interval [0,1]. Surprisingly, in that case, W_p([0,1]) is isometrically rigid if and only if
p is not equal to 1. Moreover, W_1([0,1]) admits isometries that split mass, and Isom(W_1([0,1]))
cannot be embedded into Isom(W_1(R)).
AU - Geher, Gyorgy Pal
AU - Titkos, Tamas
AU - Virosztek, Daniel
ID - 7389
IS - 8
JF - Transactions of the American Mathematical Society
KW - Wasserstein space
KW - isometric embeddings
KW - isometric rigidity
KW - exotic isometry flow
SN - 00029947
TI - Isometric study of Wasserstein spaces - the real line
VL - 373
ER -
TY - JOUR
AB - Nanomaterials produced from the bottom-up assembly of nanocrystals may incorporate ∼1020–1021 cm–3 not fully coordinated surface atoms, i.e., ∼1020–1021 cm–3 potential donor or acceptor states that can strongly affect transport properties. Therefore, to exploit the full potential of nanocrystal building blocks to produce functional nanomaterials and thin films, a proper control of their surface chemistry is required. Here, we analyze how the ligand stripping procedure influences the charge and heat transport properties of sintered PbSe nanomaterials produced from the bottom-up assembly of colloidal PbSe nanocrystals. First, we show that the removal of the native organic ligands by thermal decomposition in an inert atmosphere leaves relatively large amounts of carbon at the crystal interfaces. This carbon blocks crystal growth during consolidation and at the same time hampers charge and heat transport through the final nanomaterial. Second, we demonstrate that, by stripping ligands from the nanocrystal surface before consolidation, nanomaterials with larger crystal domains, lower porosity, and higher charge carrier concentrations are obtained, thus resulting in nanomaterials with higher electrical and thermal conductivities. In addition, the ligand displacement leaves the nanocrystal surface unprotected, facilitating oxidation and chalcogen evaporation. The influence of the ligand displacement on the nanomaterial charge transport properties is rationalized here using a two-band model based on the standard Boltzmann transport equation with the relaxation time approximation. Finally, we present an application of the produced functional nanomaterials by modeling, fabricating, and testing a simple PbSe-based thermoelectric device with a ring geometry.
AU - Cadavid, Doris
AU - Ortega, Silvia
AU - Illera, Sergio
AU - Liu, Yu
AU - Ibáñez, Maria
AU - Shavel, Alexey
AU - Zhang, Yu
AU - Li, Mengyao
AU - López, Antonio M.
AU - Noriega, Germán
AU - Durá, Oscar Juan
AU - López De La Torre, M. A.
AU - Prades, Joan Daniel
AU - Cabot, Andreu
ID - 7467
IS - 3
JF - ACS Applied Energy Materials
TI - Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials
VL - 3
ER -
TY - JOUR
AB - The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization.
AU - Mazur, Ewa
AU - Gallei, Michelle C
AU - Adamowski, Maciek
AU - Han, Huibin
AU - Robert, Hélène S.
AU - Friml, Jiří
ID - 7465
IS - 4
JF - Plant Science
SN - 01689452
TI - Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis
VL - 293
ER -
TY - JOUR
AB - Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis.
AU - Kierdorf, Katrin
AU - Hersperger, Fabian
AU - Sharrock, Jessica
AU - Vincent, Crystal M.
AU - Ustaoglu, Pinar
AU - Dou, Jiawen
AU - György, Attila
AU - Groß, Olaf
AU - Siekhaus, Daria E
AU - Dionne, Marc S.
ID - 7466
JF - eLife
TI - Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila
VL - 9
ER -
TY - JOUR
AB - Temporally organized reactivation of experiences during awake immobility periods is thought to underlie cognitive processes like planning and evaluation. While replay of trajectories is well established for the hippocampus, it is unclear whether the medial prefrontal cortex (mPFC) can reactivate sequential behavioral experiences in the awake state to support task execution. We simultaneously recorded from hippocampal and mPFC principal neurons in rats performing a mPFC-dependent rule-switching task on a plus maze. We found that mPFC neuronal activity encoded relative positions between the start and goal. During awake immobility periods, the mPFC replayed temporally organized sequences of these generalized positions, resembling entire spatial trajectories. The occurrence of mPFC trajectory replay positively correlated with rule-switching performance. However, hippocampal and mPFC trajectory replay occurred independently, indicating different functions. These results demonstrate that the mPFC can replay ordered activity patterns representing generalized locations and suggest that mPFC replay might have a role in flexible behavior.
AU - Käfer, Karola
AU - Nardin, Michele
AU - Blahna, Karel
AU - Csicsvari, Jozsef L
ID - 7472
IS - 1
JF - Neuron
SN - 0896-6273
TI - Replay of behavioral sequences in the medial prefrontal cortex during rule switching
VL - 106
ER -
TY - JOUR
AB - We give a Wong-Zakai type characterisation of the solutions of quasilinear heat equations driven by space-time white noise in 1 + 1 dimensions. In order to show that the renormalisation counterterms are local in the solution, a careful arrangement of a few hundred terms is required. The main tool in this computation is a general ‘integration by parts’ formula that provides a number of linear identities for the renormalisation constants.
AU - Gerencser, Mate
ID - 7388
IS - 3
JF - Annales de l'Institut Henri Poincaré C, Analyse non linéaire
SN - 0294-1449
TI - Nondivergence form quasilinear heat equations driven by space-time white noise
VL - 37
ER -
TY - JOUR
AB - Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis playing a key role in cancer metabolic reprogramming. Humans express two types of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2 is repressed in many tumor cells and a better understanding of its function in tumorigenesis may further the development of new therapeutic approaches. We analyzed GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7 cells. We studied GLS2 expression after induction of differentiation with phorbol ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we investigated cell cycle progression and levels of p53, p21 and c-Myc proteins. Using the baculovirus system, human GLS2 protein was overexpressed, purified and analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform. We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry and subcellular fractionation gave consistent results demonstrating nuclear and mitochondrial locations, with the latter being predominant. Nuclear targeting was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins. We assessed the subnuclear location finding a widespread distribution of GLS2 in the nucleoplasm without clear overlapping with specific nuclear substructures. GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore, human GLS2 was identified as being hypusinated by MS analysis, a posttranslational modification which may be relevant for its nuclear targeting and/or function. Our studies provide evidence for a tumor suppressor role of GLS2 in certain types of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in cancer cells induced an antiproliferative response with cell cycle arrest at the G2/M phase.
AU - López De La Oliva, Amada R.
AU - Campos-Sandoval, José A.
AU - Gómez-García, María C.
AU - Cardona, Carolina
AU - Martín-Rufián, Mercedes
AU - Sialana, Fernando J.
AU - Castilla, Laura
AU - Bae, Narkhyun
AU - Lobo, Carolina
AU - Peñalver, Ana
AU - García-Frutos, Marina
AU - Carro, David
AU - Enrique, Victoria
AU - Paz, José C.
AU - Mirmira, Raghavendra G.
AU - Gutiérrez, Antonia
AU - Alonso, Francisco J.
AU - Segura, Juan A.
AU - Matés, José M.
AU - Lubec, Gert
AU - Márquez, Javier
ID - 7487
IS - 1
JF - Scientific reports
TI - Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation
VL - 10
ER -
TY - JOUR
AB - In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.
AU - Narasimhan, Madhumitha
AU - Johnson, Alexander J
AU - Prizak, Roshan
AU - Kaufmann, Walter
AU - Tan, Shutang
AU - Casillas Perez, Barbara E
AU - Friml, Jiří
ID - 7490
JF - eLife
TI - Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants
VL - 9
ER -
TY - JOUR
AB - Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS.
AU - Latorre-Pellicer, Ana
AU - Ascaso, Ángela
AU - Trujillano, Laura
AU - Gil-Salvador, Marta
AU - Arnedo, Maria
AU - Lucia-Campos, Cristina
AU - Antoñanzas-Pérez, Rebeca
AU - Marcos-Alcalde, Iñigo
AU - Parenti, Ilaria
AU - Bueno-Lozano, Gloria
AU - Musio, Antonio
AU - Puisac, Beatriz
AU - Kaiser, Frank J.
AU - Ramos, Feliciano J.
AU - Gómez-Puertas, Paulino
AU - Pié, Juan
ID - 7488
IS - 3
JF - International Journal of Molecular Sciences
SN - 16616596
TI - Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes
VL - 21
ER -
TY - CONF
AB - Neural networks have demonstrated unmatched performance in a range of classification tasks. Despite numerous efforts of the research community, novelty detection remains one of the significant limitations of neural networks. The ability to identify previously unseen inputs as novel is crucial for our understanding of the decisions made by neural networks. At runtime, inputs not falling into any of the categories learned during training cannot be classified correctly by the neural network. Existing approaches treat the neural network as a black box and try to detect novel inputs based on the confidence of the output predictions. However, neural networks are not trained to reduce their confidence for novel inputs, which limits the effectiveness of these approaches. We propose a framework to monitor a neural network by observing the hidden layers. We employ a common abstraction from program analysis - boxes - to identify novel behaviors in the monitored layers, i.e., inputs that cause behaviors outside the box. For each neuron, the boxes range over the values seen in training. The framework is efficient and flexible to achieve a desired trade-off between raising false warnings and detecting novel inputs. We illustrate the performance and the robustness to variability in the unknown classes on popular image-classification benchmarks.
AU - Henzinger, Thomas A
AU - Lukina, Anna
AU - Schilling, Christian
ID - 7505
T2 - 24th European Conference on Artificial Intelligence
TI - Outside the box: Abstraction-based monitoring of neural networks
VL - 325
ER -
TY - JOUR
AB - In this paper, we introduce a novel method for deriving higher order corrections to the mean-field description of the dynamics of interacting bosons. More precisely, we consider the dynamics of N d-dimensional bosons for large N. The bosons initially form a Bose–Einstein condensate and interact with each other via a pair potential of the form (N−1)−1Ndβv(Nβ·)forβ∈[0,14d). We derive a sequence of N-body functions which approximate the true many-body dynamics in L2(RdN)-norm to arbitrary precision in powers of N−1. The approximating functions are constructed as Duhamel expansions of finite order in terms of the first quantised analogue of a Bogoliubov time evolution.
AU - Bossmann, Lea
AU - Pavlović, Nataša
AU - Pickl, Peter
AU - Soffer, Avy
ID - 7508
JF - Journal of Statistical Physics
SN - 0022-4715
TI - Higher order corrections to the mean-field description of the dynamics of interacting bosons
VL - 178
ER -
TY - JOUR
AB - Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.
AU - Turoňová, Beata
AU - Hagen, Wim J.H.
AU - Obr, Martin
AU - Mosalaganti, Shyamal
AU - Beugelink, J. Wouter
AU - Zimmerli, Christian E.
AU - Kräusslich, Hans Georg
AU - Beck, Martin
ID - 7511
JF - Nature Communications
TI - Benchmarking tomographic acquisition schemes for high-resolution structural biology
VL - 11
ER -
TY - JOUR
AB - Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover, the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross‐talk between JA signalling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants.
AU - Han, L
AU - Zhou, X
AU - Zhao, Y
AU - Zhu, S
AU - Wu, L
AU - He, Y
AU - Ping, X
AU - Lu, X
AU - Huang, W
AU - Qian, J
AU - Zhang, L
AU - Jiang, X
AU - Zhu, D
AU - Luo, C
AU - Li, S
AU - Dong, Q
AU - Fu, Q
AU - Deng, K
AU - Wang, X
AU - Wang, L
AU - Peng, S
AU - Wu, J
AU - Li, W
AU - Friml, Jiří
AU - Zhu, Y
AU - He, X
AU - Du, Y
ID - 7497
IS - 9
JF - Journal of Integrative Plant Biology
SN - 1672-9072
TI - Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid
VL - 62
ER -
TY - JOUR
AB - In the past two decades, our understanding of the transition to turbulence in shear flows with linearly stable laminar solutions has greatly improved. Regarding the susceptibility of the laminar flow, two concepts have been particularly useful: the edge states and the minimal seeds. In this nonlinear picture of the transition, the basin boundary of turbulence is set by the edge state's stable manifold and this manifold comes closest in energy to the laminar equilibrium at the minimal seed. We begin this paper by presenting numerical experiments in which three-dimensional perturbations are too energetic to trigger turbulence in pipe flow but they do lead to turbulence when their amplitude is reduced. We show that this seemingly counterintuitive observation is in fact consistent with the fully nonlinear description of the transition mediated by the edge state. In order to understand the physical mechanisms behind this process, we measure the turbulent kinetic energy production and dissipation rates as a function of the radial coordinate. Our main observation is that the transition to turbulence relies on the energy amplification away from the wall, as opposed to the turbulence itself, whose energy is predominantly produced near the wall. This observation is further supported by the similar analyses on the minimal seeds and the edge states. Furthermore, we show that the time evolution of production-over-dissipation curves provides a clear distinction between the different initial amplification stages of the transition to turbulence from the minimal seed.
AU - Budanur, Nazmi B
AU - Marensi, Elena
AU - Willis, Ashley P.
AU - Hof, Björn
ID - 7534
IS - 2
JF - Physical Review Fluids
SN - 2469-990X
TI - Upper edge of chaos and the energetics of transition in pipe flow
VL - 5
ER -
TY - JOUR
AB - We consider general self-adjoint polynomials in several independent random matrices whose entries are centered and have the same variance. We show that under certain conditions the local law holds up to the optimal scale, i.e., the eigenvalue density on scales just above the eigenvalue spacing follows the global density of states which is determined by free probability theory. We prove that these conditions hold for general homogeneous polynomials of degree two and for symmetrized products of independent matrices with i.i.d. entries, thus establishing the optimal bulk local law for these classes of ensembles. In particular, we generalize a similar result of Anderson for anticommutator. For more general polynomials our conditions are effectively checkable numerically.
AU - Erdös, László
AU - Krüger, Torben H
AU - Nemish, Yuriy
ID - 7512
IS - 12
JF - Journal of Functional Analysis
SN - 00221236
TI - Local laws for polynomials of Wigner matrices
VL - 278
ER -
TY - JOUR
AB - In this paper we study the joint convexity/concavity of the trace functions Ψp,q,s(A,B)=Tr(Bq2K∗ApKBq2)s, p,q,s∈R,
where A and B are positive definite matrices and K is any fixed invertible matrix. We will give full range of (p,q,s)∈R3 for Ψp,q,s to be jointly convex/concave for all K. As a consequence, we confirm a conjecture of Carlen, Frank and Lieb. In particular, we confirm a weaker conjecture of Audenaert and Datta and obtain the full range of (α,z) for α-z Rényi relative entropies to be monotone under completely positive trace preserving maps. We also give simpler proofs of many known results, including the concavity of Ψp,0,1/p for 0