@inproceedings{9210, abstract = {Modern neural networks can easily fit their training set perfectly. Surprisingly, despite being “overfit” in this way, they tend to generalize well to future data, thereby defying the classic bias–variance trade-off of machine learning theory. Of the many possible explanations, a prevalent one is that training by stochastic gradient descent (SGD) imposes an implicit bias that leads it to learn simple functions, and these simple functions generalize well. However, the specifics of this implicit bias are not well understood. In this work, we explore the smoothness conjecture which states that SGD is implicitly biased towards learning functions that are smooth. We propose several measures to formalize the intuitive notion of smoothness, and we conduct experiments to determine whether SGD indeed implicitly optimizes for these measures. Our findings rule out the possibility that smoothness measures based on first-order derivatives are being implicitly enforced. They are supportive, though, of the smoothness conjecture for measures based on second-order derivatives.}, author = {Volhejn, Vaclav and Lampert, Christoph}, booktitle = {42nd German Conference on Pattern Recognition}, isbn = {9783030712778}, issn = {1611-3349}, location = {Tübingen, Germany}, pages = {246--259}, publisher = {Springer}, title = {{Does SGD implicitly optimize for smoothness?}}, doi = {10.1007/978-3-030-71278-5_18}, volume = {12544}, year = {2021}, } @article{9212, abstract = {Plant fitness is largely dependent on the root, the underground organ, which, besides its anchoring function, supplies the plant body with water and all nutrients necessary for growth and development. To exploit the soil effectively, roots must constantly integrate environmental signals and react through adjustment of growth and development. Important components of the root management strategy involve a rapid modulation of the root growth kinetics and growth direction, as well as an increase of the root system radius through formation of lateral roots (LRs). At the molecular level, such a fascinating growth and developmental flexibility of root organ requires regulatory networks that guarantee stability of the developmental program but also allows integration of various environmental inputs. The plant hormone auxin is one of the principal endogenous regulators of root system architecture by controlling primary root growth and formation of LR. In this review, we discuss recent progress in understanding molecular networks where auxin is one of the main players shaping the root system and acting as mediator between endogenous cues and environmental factors.}, author = {Cavallari, Nicola and Artner, Christina and Benková, Eva}, issn = {1943-0264}, journal = {Cold Spring Harbor Perspectives in Biology}, number = {7}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Auxin-regulated lateral root organogenesis}}, doi = {10.1101/cshperspect.a039941}, volume = {13}, year = {2021}, } @article{9224, abstract = {We re-examine attempts to study the many-body localization transition using measures that are physically natural on the ergodic/quantum chaotic regime of the phase diagram. Using simple scaling arguments and an analysis of various models for which rigorous results are available, we find that these measures can be particularly adversely affected by the strong finite-size effects observed in nearly all numerical studies of many-body localization. This severely impacts their utility in probing the transition and the localized phase. In light of this analysis, we discuss a recent study (Šuntajs et al., 2020) of the behaviour of the Thouless energy and level repulsion in disordered spin chains, and its implications for the question of whether MBL is a true phase of matter.}, author = {Abanin, D. A. and Bardarson, J. H. and De Tomasi, G. and Gopalakrishnan, S. and Khemani, V. and Parameswaran, S. A. and Pollmann, F. and Potter, A. C. and Serbyn, Maksym and Vasseur, R.}, issn = {1096035X}, journal = {Annals of Physics}, number = {4}, publisher = {Elsevier}, title = {{Distinguishing localization from chaos: Challenges in finite-size systems}}, doi = {10.1016/j.aop.2021.168415}, volume = {427}, year = {2021}, } @article{9225, abstract = {The Landau–Pekar equations describe the dynamics of a strongly coupled polaron. Here, we provide a class of initial data for which the associated effective Hamiltonian has a uniform spectral gap for all times. For such initial data, this allows us to extend the results on the adiabatic theorem for the Landau–Pekar equations and their derivation from the Fröhlich model obtained in previous works to larger times.}, author = {Feliciangeli, Dario and Rademacher, Simone Anna Elvira and Seiringer, Robert}, issn = {15730530}, journal = {Letters in Mathematical Physics}, publisher = {Springer Nature}, title = {{Persistence of the spectral gap for the Landau–Pekar equations}}, doi = {10.1007/s11005-020-01350-5}, volume = {111}, year = {2021}, } @article{9226, abstract = {Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?}, author = {Tkačik, Gašper and Gregor, Thomas}, issn = {1477-9129}, journal = {Development}, number = {2}, publisher = {The Company of Biologists}, title = {{The many bits of positional information}}, doi = {10.1242/dev.176065}, volume = {148}, year = {2021}, } @inproceedings{9227, abstract = {In the multiway cut problem we are given a weighted undirected graph G=(V,E) and a set T⊆V of k terminals. The goal is to find a minimum weight set of edges E′⊆E with the property that by removing E′ from G all the terminals become disconnected. In this paper we present a simple local search approximation algorithm for the multiway cut problem with approximation ratio 2−2k . We present an experimental evaluation of the performance of our local search algorithm and show that it greatly outperforms the isolation heuristic of Dalhaus et al. and it has similar performance as the much more complex algorithms of Calinescu et al., Sharma and Vondrak, and Buchbinder et al. which have the currently best known approximation ratios for this problem.}, author = {Bloch-Hansen, Andrew and Samei, Nasim and Solis-Oba, Roberto}, booktitle = {Conference on Algorithms and Discrete Applied Mathematics}, isbn = {9783030678982}, issn = {1611-3349}, location = {Rupnagar, India}, pages = {346--358}, publisher = {Springer Nature}, title = {{Experimental evaluation of a local search approximation algorithm for the multiway cut problem}}, doi = {10.1007/978-3-030-67899-9_28}, volume = {12601}, year = {2021}, } @article{9228, abstract = {Legacy conferences are costly and time consuming, and exclude scientists lacking various resources or abilities. During the 2020 pandemic, we created an online conference platform, Neuromatch Conferences (NMC), aimed at developing technological and cultural changes to make conferences more democratic, scalable, and accessible. We discuss the lessons we learned.}, author = {Achakulvisut, Titipat and Ruangrong, Tulakan and Mineault, Patrick and Vogels, Tim P and Peters, Megan A.K. and Poirazi, Panayiota and Rozell, Christopher and Wyble, Brad and Goodman, Dan F.M. and Kording, Konrad Paul}, issn = {1879-307X}, journal = {Trends in Cognitive Sciences}, number = {4}, pages = {265--268}, publisher = {Elsevier}, title = {{Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences}}, doi = {10.1016/j.tics.2021.01.007}, volume = {25}, year = {2021}, } @unpublished{9230, abstract = {We consider a model of the Riemann zeta function on the critical axis and study its maximum over intervals of length (log T)θ, where θ is either fixed or tends to zero at a suitable rate. It is shown that the deterministic level of the maximum interpolates smoothly between the ones of log-correlated variables and of i.i.d. random variables, exhibiting a smooth transition ‘from 3/4 to 1/4’ in the second order. This provides a natural context where extreme value statistics of log-correlated variables with time-dependent variance and rate occur. A key ingredient of the proof is a precise upper tail tightness estimate for the maximum of the model on intervals of size one, that includes a Gaussian correction. This correction is expected to be present for the Riemann zeta function and pertains to the question of the correct order of the maximum of the zeta function in large intervals.}, author = {Arguin, Louis-Pierre and Dubach, Guillaume and Hartung, Lisa}, booktitle = {arXiv}, title = {{Maxima of a random model of the Riemann zeta function over intervals of varying length}}, doi = {10.48550/arXiv.2103.04817}, year = {2021}, } @article{9234, abstract = {In this paper, we present two new inertial projection-type methods for solving multivalued variational inequality problems in finite-dimensional spaces. We establish the convergence of the sequence generated by these methods when the multivalued mapping associated with the problem is only required to be locally bounded without any monotonicity assumption. Furthermore, the inertial techniques that we employ in this paper are quite different from the ones used in most papers. Moreover, based on the weaker assumptions on the inertial factor in our methods, we derive several special cases of our methods. Finally, we present some experimental results to illustrate the profits that we gain by introducing the inertial extrapolation steps.}, author = {Izuchukwu, Chinedu and Shehu, Yekini}, issn = {1572-9427}, journal = {Networks and Spatial Economics}, keywords = {Computer Networks and Communications, Software, Artificial Intelligence}, number = {2}, pages = {291--323}, publisher = {Springer Nature}, title = {{New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity}}, doi = {10.1007/s11067-021-09517-w}, volume = {21}, year = {2021}, } @article{9235, abstract = {Cu2–xS has become one of the most promising thermoelectric materials for application in the middle-high temperature range. Its advantages include the abundance, low cost, and safety of its elements and a high performance at relatively elevated temperatures. However, stability issues limit its operation current and temperature, thus calling for the optimization of the material performance in the middle temperature range. Here, we present a synthetic protocol for large scale production of covellite CuS nanoparticles at ambient temperature and atmosphere, and using water as a solvent. The crystal phase and stoichiometry of the particles are afterward tuned through an annealing process at a moderate temperature under inert or reducing atmosphere. While annealing under argon results in Cu1.8S nanopowder with a rhombohedral crystal phase, annealing in an atmosphere containing hydrogen leads to tetragonal Cu1.96S. High temperature X-ray diffraction analysis shows the material annealed in argon to transform to the cubic phase at ca. 400 K, while the material annealed in the presence of hydrogen undergoes two phase transitions, first to hexagonal and then to the cubic structure. The annealing atmosphere, temperature, and time allow adjustment of the density of copper vacancies and thus tuning of the charge carrier concentration and material transport properties. In this direction, the material annealed under Ar is characterized by higher electrical conductivities but lower Seebeck coefficients than the material annealed in the presence of hydrogen. By optimizing the charge carrier concentration through the annealing time, Cu2–xS with record figures of merit in the middle temperature range, up to 1.41 at 710 K, is obtained. We finally demonstrate that this strategy, based on a low-cost and scalable solution synthesis process, is also suitable for the production of high performance Cu2–xS layers using high throughput and cost-effective printing technologies.}, author = {Li, Mengyao and Liu, Yu and Zhang, Yu and Han, Xu and Zhang, Ting and Zuo, Yong and Xie, Chenyang and Xiao, Ke and Arbiol, Jordi and Llorca, Jordi and Ibáñez, Maria and Liu, Junfeng and Cabot, Andreu}, issn = {1936-086X}, journal = {ACS Nano}, keywords = {General Engineering, General Physics and Astronomy, General Materials Science}, number = {3}, pages = {4967–4978}, publisher = {American Chemical Society }, title = {{Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide}}, doi = {10.1021/acsnano.0c09866}, volume = {15}, year = {2021}, } @article{9239, abstract = {A graph game proceeds as follows: two players move a token through a graph to produce a finite or infinite path, which determines the payoff of the game. We study bidding games in which in each turn, an auction determines which player moves the token. Bidding games were largely studied in combination with two variants of first-price auctions called “Richman” and “poorman” bidding. We study taxman bidding, which span the spectrum between the two. The game is parameterized by a constant : portion τ of the winning bid is paid to the other player, and portion to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games: we unify, generalize, and simplify previous equivalences between bidding games and a class of stochastic games called random-turn games.}, author = {Avni, Guy and Henzinger, Thomas A and Žikelić, Đorđe}, issn = {1090-2724}, journal = {Journal of Computer and System Sciences}, number = {8}, pages = {133--144}, publisher = {Elsevier}, title = {{Bidding mechanisms in graph games}}, doi = {10.1016/j.jcss.2021.02.008}, volume = {119}, year = {2021}, } @article{9240, abstract = {A stochastic PDE, describing mesoscopic fluctuations in systems of weakly interacting inertial particles of finite volume, is proposed and analysed in any finite dimension . It is a regularised and inertial version of the Dean–Kawasaki model. A high-probability well-posedness theory for this model is developed. This theory improves significantly on the spatial scaling restrictions imposed in an earlier work of the same authors, which applied only to significantly larger particles in one dimension. The well-posedness theory now applies in d-dimensions when the particle-width ϵ is proportional to for and N is the number of particles. This scaling is optimal in a certain Sobolev norm. Key tools of the analysis are fractional Sobolev spaces, sharp bounds on Bessel functions, separability of the regularisation in the d-spatial dimensions, and use of the Faà di Bruno's formula.}, author = {Cornalba, Federico and Shardlow, Tony and Zimmer, Johannes}, issn = {1090-2732}, journal = {Journal of Differential Equations}, number = {5}, pages = {253--283}, publisher = {Elsevier}, title = {{Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions}}, doi = {10.1016/j.jde.2021.02.048}, volume = {284}, year = {2021}, } @article{9241, abstract = {Volumetric light transport is a pervasive physical phenomenon, and therefore its accurate simulation is important for a broad array of disciplines. While suitable mathematical models for computing the transport are now available, obtaining the necessary material parameters needed to drive such simulations is a challenging task: direct measurements of these parameters from material samples are seldom possible. Building on the inverse scattering paradigm, we present a novel measurement approach which indirectly infers the transport parameters from extrinsic observations of multiple-scattered radiance. The novelty of the proposed approach lies in replacing structured illumination with a structured reflector bonded to the sample, and a robust fitting procedure that largely compensates for potential systematic errors in the calibration of the setup. We show the feasibility of our approach by validating simulations of complex 3D compositions of the measured materials against physical prints, using photo-polymer resins. As presented in this paper, our technique yields colorspace data suitable for accurate appearance reproduction in the area of 3D printing. Beyond that, and without fundamental changes to the basic measurement methodology, it could equally well be used to obtain spectral measurements that are useful for other application areas.}, author = {Elek, Oskar and Zhang, Ran and Sumin, Denis and Myszkowski, Karol and Bickel, Bernd and Wilkie, Alexander and Křivánek, Jaroslav and Weyrich, Tim}, issn = {1094-4087}, journal = {Optics Express}, number = {5}, pages = {7568--7588}, publisher = {The Optical Society}, title = {{Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing}}, doi = {10.1364/OE.406095}, volume = {29}, year = {2021}, } @article{9242, abstract = {In the recent years important experimental advances in resonant electro-optic modulators as high-efficiency sources for coherent frequency combs and as devices for quantum information transfer have been realized, where strong optical and microwave mode coupling were achieved. These features suggest electro-optic-based devices as candidates for entangled optical frequency comb sources. In the present work, I study the generation of entangled optical frequency combs in millimeter-sized resonant electro-optic modulators. These devices profit from the experimentally proven advantages such as nearly constant optical free spectral ranges over several gigahertz, and high optical and microwave quality factors. The generation of frequency multiplexed quantum channels with spectral bandwidth in the MHz range for conservative parameter values paves the way towards novel uses in long-distance hybrid quantum networks, quantum key distribution, enhanced optical metrology, and quantum computing.}, author = {Rueda Sanchez, Alfredo R}, issn = {2469-9934}, journal = {Physical Review A}, number = {2}, publisher = {American Physical Society}, title = {{Frequency-multiplexed hybrid optical entangled source based on the Pockels effect}}, doi = {10.1103/PhysRevA.103.023708}, volume = {103}, year = {2021}, } @article{9243, abstract = {Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.}, author = {Hernández-Rocamora, Víctor M. and Baranova, Natalia S. and Peters, Katharina and Breukink, Eefjan and Loose, Martin and Vollmer, Waldemar}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins}}, doi = {10.7554/eLife.61525}, volume = {10}, year = {2021}, } @article{9244, abstract = {Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models.}, author = {Hankeova, Simona and Salplachta, Jakub and Zikmund, Tomas and Kavkova, Michaela and Van Hul, Noémi and Brinek, Adam and Smekalova, Veronika and Laznovsky, Jakub and Dawit, Feven and Jaros, Josef and Bryja, Vítězslav and Lendahl, Urban and Ellis, Ewa and Nemeth, Antal and Fischler, Björn and Hannezo, Edouard B and Kaiser, Jozef and Andersson, Emma Rachel}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome}}, doi = {10.7554/eLife.60916}, volume = {10}, year = {2021}, } @inbook{9245, abstract = {Tissue morphogenesis is driven by mechanical forces triggering cell movements and shape changes. Quantitatively measuring tension within tissues is of great importance for understanding the role of mechanical signals acting on the cell and tissue level during morphogenesis. Here we introduce laser ablation as a useful tool to probe tissue tension within the granulosa layer, an epithelial monolayer of somatic cells that surround the zebrafish female gamete during folliculogenesis. We describe in detail how to isolate follicles, mount samples, perform laser surgery, and analyze the data.}, author = {Xia, Peng and Heisenberg, Carl-Philipp J}, booktitle = {Germline Development in the Zebrafish}, editor = {Dosch, Roland}, isbn = {978-1-0716-0969-9}, issn = {1940-6029}, keywords = {Tissue tension, Morphogenesis, Laser ablation, Zebrafish folliculogenesis, Granulosa cells}, pages = {117--128}, publisher = {Humana}, title = {{Quantifying tissue tension in the granulosa layer after laser surgery}}, doi = {10.1007/978-1-0716-0970-5_10}, volume = {2218}, year = {2021}, } @article{9246, abstract = {We consider the Fröhlich Hamiltonian in a mean-field limit where many bosonic particles weakly couple to the quantized phonon field. For large particle numbers and a suitably small coupling, we show that the dynamics of the system is approximately described by the Landau–Pekar equations. These describe a Bose–Einstein condensate interacting with a classical polarization field, whose dynamics is effected by the condensate, i.e., the back-reaction of the phonons that are created by the particles during the time evolution is of leading order.}, author = {Leopold, Nikolai K and Mitrouskas, David Johannes and Seiringer, Robert}, issn = {14320673}, journal = {Archive for Rational Mechanics and Analysis}, pages = {383--417}, publisher = {Springer Nature}, title = {{Derivation of the Landau–Pekar equations in a many-body mean-field limit}}, doi = {10.1007/s00205-021-01616-9}, volume = {240}, year = {2021}, } @article{9250, abstract = {Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate.}, author = {Petit, Yann K. and Mourad, Eléonore and Prehal, Christian and Leypold, Christian and Windischbacher, Andreas and Mijailovic, Daniel and Slugovc, Christian and Borisov, Sergey M. and Zojer, Egbert and Brutti, Sergio and Fontaine, Olivier and Freunberger, Stefan Alexander}, issn = {1755-4349}, journal = {Nature Chemistry}, keywords = {General Chemistry, General Chemical Engineering}, number = {5}, pages = {465--471}, publisher = {Springer Nature}, title = {{Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation}}, doi = {10.1038/s41557-021-00643-z}, volume = {13}, year = {2021}, } @article{9252, abstract = {This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.}, author = {Szep, Eniko and Sachdeva, Himani and Barton, Nicholas H}, issn = {1558-5646}, journal = {Evolution}, keywords = {Genetics, Ecology, Evolution, Behavior and Systematics, General Agricultural and Biological Sciences}, number = {5}, pages = {1030--1045}, publisher = {Wiley}, title = {{Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model}}, doi = {10.1111/evo.14210}, volume = {75}, year = {2021}, }