TY - GEN
AB - We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems.
AU - Portinale, Lorenzo
AU - Stefanelli, U
ID - 7550
TI - Penalization via global functionals of optimal-control problems for dissipative evolution
ER -
TY - GEN
AB - There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests.
AU - Bialek, William
AU - Gregor, Thomas
AU - Tkačik, Gašper
ID - 7552
T2 - arXiv:1912.08579
TI - Action at a distance in transcriptional regulation
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 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with 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 - Immler, Fabian
AU - Althoff, Matthias
AU - Benet, Luis
AU - Chapoutot, Alexandre
AU - Chen, Xin
AU - Forets, Marcelo
AU - Geretti, Luca
AU - Kochdumper, Niklas
AU - Sanders, David P.
AU - Schilling, Christian
ID - 7576
T2 - EPiC Series in Computing
TI - ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics
VL - 61
ER -
TY - CONF
AB - We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bound is in terms of the joint distribution of the signals and maximum a posteriori decodes (most probable signals given channel output). As part of our derivation, we describe the key properties of the distribution of signals, channel outputs and decodes, that minimizes equivocation and maximizes mutual information. This work addresses a problem in data analysis, where mutual information between signals and decodes is sometimes used to lower bound the mutual information between signals and channel outputs. Our result provides a corresponding upper bound.
AU - Hledik, Michal
AU - Sokolowski, Thomas R
AU - Tkačik, Gašper
ID - 7606
SN - 9781538669006
T2 - IEEE Information Theory Workshop, ITW 2019
TI - A tight upper bound on mutual information
ER -
TY - GEN
AB - Electrodepositing insulating and insoluble Li2O2 is the key process during discharge of aprotic Li-O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and solvated LiO2 governs whether Li2O2 grows as surface film, leading to low capacity even at low rates, or in solution, leading to particles and high capacities. Here we show that Li2O2 forms to the widest extent as particles via solution mediated LiO2 disproportionation. We describe a unified Li2O2 growth model that conclusively explains capacity limitations across the whole range of electrolytes. Deciding for particle morphology, achievable rate and capacities are species mobilities, electrode specific surface area (determining true areal rate) and the concentration distribution of associated LiO2 in solution. Provided that species mobilities and surface are high, high, capacities are possible even with low-donor-number electrolytes, previously considered prototypical for low capacity via surface growth. The tools for these insights are microscopy, hydrodynamic voltammetry, a numerical reaction model, and in situ small/wide angle X-ray scattering (SAXS/WAXS). Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative information from complex multi-phase systems. On a wider perspective, this SAXS method is a powerful in situ metrology with atomic to sub-micron resolution to study mechanisms in complex electrochemical systems and beyond.
AU - Prehal, Christian
AU - Samojlov, Aleksej
AU - Nachtnebel, Manfred
AU - Kriechbaum, Manfred
AU - Amenitsch, Heinz
AU - Freunberger, Stefan Alexander
ID - 7627
TI - A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering
ER -
TY - CONF
AB - Deep neural networks (DNNs) have become increasingly important due to their excellent empirical performance on a wide range of problems. However, regularization is generally achieved by indirect means, largely due to the complex set of functions defined by a network and the difficulty in measuring function complexity. There exists no method in the literature for additive regularization based on a norm of the function, as is classically considered in statistical learning theory. In this work, we study the tractability of function norms for deep neural networks with ReLU activations. We provide, to the best of our knowledge, the first proof in the literature of the NP-hardness of computing function norms of DNNs of 3 or more layers. We also highlight a fundamental difference between shallow and deep networks. In the light on these results, we propose a new regularization strategy based on approximate function norms, and show its efficiency on a segmentation task with a DNN.
AU - Rannen-Triki, Amal
AU - Berman, Maxim
AU - Kolmogorov, Vladimir
AU - Blaschko, Matthew B.
ID - 7639
SN - 9781728150239
T2 - Proceedings of the 2019 International Conference on Computer Vision Workshop
TI - Function norms for neural networks
ER -
TY - CONF
AB - We propose a new model for detecting visual relationships, such as "person riding motorcycle" or "bottle on table". This task is an important step towards comprehensive structured mage understanding, going beyond detecting individual objects. Our main novelty is a Box Attention mechanism that allows to model pairwise interactions between objects using standard object detection pipelines. The resulting model is conceptually clean, expressive and relies on well-justified training and prediction procedures. Moreover, unlike previously proposed approaches, our model does not introduce any additional complex components or hyperparameters on top of those already required by the underlying detection model. We conduct an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating strong quantitative and qualitative results.
AU - Kolesnikov, Alexander
AU - Kuznetsova, Alina
AU - Lampert, Christoph
AU - Ferrari, Vittorio
ID - 7640
SN - 9781728150239
T2 - Proceedings of the 2019 International Conference on Computer Vision Workshop
TI - Detecting visual relationships using box attention
ER -
TY - JOUR
AB - The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.
AU - Delaneau, Olivier
AU - Zagury, Jean-François
AU - Robinson, Matthew Richard
AU - Marchini, Jonathan L.
AU - Dermitzakis, Emmanouil T.
ID - 7710
JF - Nature Communications
SN - 2041-1723
TI - Accurate, scalable and integrative haplotype estimation
VL - 10
ER -
TY - JOUR
AB - The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies.
AU - Bevers, Roel P. J.
AU - Litovchenko, Maria
AU - Kapopoulou, Adamandia
AU - Braman, Virginie S.
AU - Robinson, Matthew Richard
AU - Auwerx, Johan
AU - Hollis, Brian
AU - Deplancke, Bart
ID - 7711
IS - 12
JF - Nature Metabolism
SN - 2522-5812
TI - Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel
VL - 1
ER -
TY - GEN
AB - As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance Embedded Image is significantly (P < 10−56) larger than it would be expected for a similarly correlated variable Embedded Image. We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures.
AU - Sulc, Jonathan
AU - Mounier, Ninon
AU - Günther, Felix
AU - Winkler, Thomas
AU - Wood, Andrew R.
AU - Frayling, Timothy M.
AU - Heid, Iris M.
AU - Robinson, Matthew Richard
AU - Kutalik, Zoltán
ID - 7782
T2 - bioRxiv
TI - Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank
ER -
TY - GEN
AB - The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results:
1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan.
2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2.
3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.
AU - Biniaz, Ahmad
AU - Jain, Kshitij
AU - Lubiw, Anna
AU - Masárová, Zuzana
AU - Miltzow, Tillmann
AU - Mondal, Debajyoti
AU - Naredla, Anurag Murty
AU - Tkadlec, Josef
AU - Turcotte, Alexi
ID - 7950
T2 - arXiv:1903.06981
TI - Token swapping on trees
ER -
TY - JOUR
AB - We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently.
AU - Virosztek, Daniel
ID - 405
JF - Linear Algebra and Its Applications
TI - Jointly convex quantum Jensen divergences
VL - 576
ER -
TY - JOUR
AB - We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent.
AU - Ajanki, Oskari H
AU - Erdös, László
AU - Krüger, Torben H
ID - 429
IS - 1-2
JF - Probability Theory and Related Fields
SN - 01788051
TI - Stability of the matrix Dyson equation and random matrices with correlations
VL - 173
ER -
TY - JOUR
AB - We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the
possibility of a P = W conjecture for a suitable wild Hitchin system.
AU - Hausel, Tamas
AU - Mereb, Martin
AU - Wong, Michael
ID - 439
IS - 10
JF - Journal of the European Mathematical Society
TI - Arithmetic and representation theory of wild character varieties
VL - 21
ER -
TY - JOUR
AU - Kalinin, Nikita
AU - Shkolnikov, Mikhail
ID - 441
IS - 3
JF - European Journal of Mathematics
SN - 2199-675X
TI - Tropical formulae for summation over a part of SL(2,Z)
VL - 5
ER -
TY - JOUR
AB - In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2.
AU - Ganev, Iordan V
ID - 5
IS - 3
JF - Journal of the London Mathematical Society
TI - The wonderful compactification for quantum groups
VL - 99
ER -
TY - JOUR
AB - The order-k Voronoi tessellation of a locally finite set 𝑋⊆ℝ𝑛 decomposes ℝ𝑛 into convex domains whose points have the same k nearest neighbors in X. Assuming X is a stationary Poisson point process, we give explicit formulas for the expected number and total area of faces of a given dimension per unit volume of space. We also develop a relaxed version of discrete Morse theory and generalize by counting only faces, for which the k nearest points in X are within a given distance threshold.
AU - Edelsbrunner, Herbert
AU - Nikitenko, Anton
ID - 5678
IS - 4
JF - Discrete and Computational Geometry
SN - 01795376
TI - Poisson–Delaunay Mosaics of Order k
VL - 62
ER -
TY - JOUR
AB - Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones.
AU - Andalo, Christophe
AU - Burrus, Monique
AU - Paute, Sandrine
AU - Lauzeral, Christine
AU - Field, David
ID - 5680
IS - 1
JF - Botany Letters
SN - 23818107
TI - Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone
VL - 166
ER -
TY - JOUR
AB - The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest.
AU - Chaplick, Steven
AU - Fulek, Radoslav
AU - Klavík, Pavel
ID - 5790
IS - 4
JF - Journal of Graph Theory
SN - 03649024
TI - Extending partial representations of circle graphs
VL - 91
ER -
TY - CHAP
AB - The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis.
AU - Asaoka, Yoichi
AU - Morita, Hitoshi
AU - Furumoto, Hiroko
AU - Heisenberg, Carl-Philipp J
AU - Furutani-Seiki, Makoto
ED - Hergovich, Alexander
ID - 5793
SN - 978-1-4939-8909-6
T2 - The hippo pathway
TI - Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids
VL - 1893
ER -