@article{12543, abstract = {Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts.}, author = {Stock, Miriam and Milutinovic, Barbara and Hönigsberger, Michaela and Grasse, Anna V and Wiesenhofer, Florian and Kampleitner, Niklas and Narasimhan, Madhumitha and Schmitt, Thomas and Cremer, Sylvia}, issn = {2397-334X}, journal = {Nature Ecology and Evolution}, pages = {450--460}, publisher = {Springer Nature}, title = {{Pathogen evasion of social immunity}}, doi = {10.1038/s41559-023-01981-6}, volume = {7}, year = {2023}, } @article{12521, abstract = {Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.}, author = {Mrnjavac, Andrea and Khudiakova, Kseniia and Barton, Nicholas H and Vicoso, Beatriz}, issn = {2056-3744}, journal = {Evolution Letters}, keywords = {Genetics, Ecology, Evolution, Behavior and Systematics}, number = {1}, publisher = {Oxford University Press}, title = {{Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution}}, doi = {10.1093/evlett/qrac004}, volume = {7}, year = {2023}, } @article{12679, abstract = {How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression.}, author = {Hippenmeyer, Simon}, issn = {0959-4388}, journal = {Current Opinion in Neurobiology}, keywords = {General Neuroscience}, number = {4}, publisher = {Elsevier}, title = {{Principles of neural stem cell lineage progression: Insights from developing cerebral cortex}}, doi = {10.1016/j.conb.2023.102695}, volume = {79}, year = {2023}, } @article{12429, abstract = {In this paper, we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement is that we can allow general interpolation couples. The abstract results are applied to regularity problems for fractional evolution equations and stochastic evolution equations, where uniform trace estimates on the half-line are shown.}, author = {Agresti, Antonio and Lindemulder, Nick and Veraar, Mark}, issn = {1522-2616}, journal = {Mathematische Nachrichten}, number = {4}, pages = {1319--1350}, publisher = {Wiley}, title = {{On the trace embedding and its applications to evolution equations}}, doi = {10.1002/mana.202100192}, volume = {296}, year = {2023}, } @article{12430, abstract = {We study the time evolution of the Nelson model in a mean-field limit in which N nonrelativistic bosons weakly couple (with respect to the particle number) to a positive or zero mass quantized scalar field. Our main result is the derivation of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove the convergence of the approximate wave function to the many-body wave function in norm, with a convergence rate proportional to the number of corrections taken into account in the approximation. We prove an analogous result for the unitary propagator. As an application, we derive a simple system of partial differential equations describing the time evolution of the first- and second-order approximations to the one-particle reduced density matrices of the particles and the quantum field, respectively.}, author = {Falconi, Marco and Leopold, Nikolai K and Mitrouskas, David Johannes and Petrat, Sören P}, issn = {0129-055X}, journal = {Reviews in Mathematical Physics}, number = {4}, publisher = {World Scientific Publishing}, title = {{Bogoliubov dynamics and higher-order corrections for the regularized Nelson model}}, doi = {10.1142/S0129055X2350006X}, volume = {35}, year = {2023}, } @article{12762, abstract = {Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.}, author = {Lombardi, Fabrizio and Pepic, Selver and Shriki, Oren and Tkačik, Gašper and De Martino, Daniele}, issn = {2662-8457}, journal = {Nature Computational Science}, pages = {254--263}, publisher = {Springer Nature}, title = {{Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain}}, doi = {10.1038/s43588-023-00410-9}, volume = {3}, year = {2023}, } @phdthesis{12891, abstract = {The tight spatiotemporal coordination of signaling activity determining embryo patterning and the physical processes driving embryo morphogenesis renders embryonic development robust, such that key developmental processes can unfold relatively normally even outside of the full embryonic context. For instance, embryonic stem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry leading to germ layer formation and morphogenesis, in a very reduced environment. This leads to questions on specific contributions of embryo-specific features, such as the presence of extraembryonic tissues, which are inherently involved in gastrulation in the full embryonic context. To address this, we established zebrafish embryonic explants without the extraembryonic yolk cell, an important player as a signaling source and for morphogenesis during gastrulation, as a model of ex vivo development. We found that dorsal-marginal determinants are required and sufficient in these explants to form and pattern all three germ layers. However, formation of tissues, which require the highest Nodal-signaling levels, is variable, demonstrating a contribution of extraembryonic tissues for reaching peak Nodal signaling levels. Blastoderm explants also undergo gastrulation-like axis elongation. We found that this elongation movement shows hallmarks of oriented mesendoderm cell intercalations typically associated with dorsal tissues in the intact embryo. These are disrupted by uniform upregulation of BMP signaling activity and concomitant explant ventralization, suggesting that tight spatial control of BMP signaling is a prerequisite for explant morphogenesis. This control is achieved by Nodal signaling, which is critical for effectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal signaling is not only directly required for mesendoderm cell fate specification and morphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side. Collectively, we provide insights into the capacity and organization of signaling and morphogenetic domains to recapitulate features of zebrafish gastrulation outside of the full embryonic context.}, author = {Schauer, Alexandra}, issn = {2663 - 337X}, pages = {190}, publisher = {Institute of Science and Technology Austria}, title = {{Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues}}, doi = {10.15479/at:ista:12891}, year = {2023}, } @inproceedings{14085, abstract = {We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed, unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm in general sparse graphs with arbitrarily good approximation guarantee.}, author = {Goranci, Gramoz and Henzinger, Monika H}, booktitle = {50th International Colloquium on Automata, Languages, and Programming}, isbn = {9783959772785}, issn = {1868-8969}, location = {Paderborn, Germany}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Efficient data structures for incremental exact and approximate maximum flow}}, doi = {10.4230/LIPIcs.ICALP.2023.69}, volume = {261}, year = {2023}, } @inproceedings{14084, abstract = {A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We will consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n]. The partition function is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log Z(β_max))/Z(β_min) We develop a number of algorithms to estimate the counts c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²) samples for integer-valued distributions (ignoring some second-order terms and parameters), We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs and perfect matchings in a graph.}, author = {Harris, David G. and Kolmogorov, Vladimir}, booktitle = {50th International Colloquium on Automata, Languages, and Programming}, isbn = {9783959772785}, issn = {1868-8969}, location = {Paderborn, Germany}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Parameter estimation for Gibbs distributions}}, doi = {10.4230/LIPIcs.ICALP.2023.72}, volume = {261}, year = {2023}, } @inproceedings{14086, abstract = {The maximization of submodular functions have found widespread application in areas such as machine learning, combinatorial optimization, and economics, where practitioners often wish to enforce various constraints; the matroid constraint has been investigated extensively due to its algorithmic properties and expressive power. Though tight approximation algorithms for general matroid constraints exist in theory, the running times of such algorithms typically scale quadratically, and are not practical for truly large scale settings. Recent progress has focused on fast algorithms for important classes of matroids given in explicit form. Currently, nearly-linear time algorithms only exist for graphic and partition matroids [Alina Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone submodular maximization constrained by graphic, transversal matroids, or laminar matroids in time near-linear in the size of their representation. Our algorithms achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the running time of our algorithm cannot be improved within the fast continuous greedy framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák, 2014]. To achieve near-linear running time, we make use of dynamic data structures that maintain bases with approximate maximum cardinality and weight under certain element updates. These data structures need to support a weight decrease operation and a novel Freeze operation that allows the algorithm to freeze elements (i.e. force to be contained) in its basis regardless of future data structure operations. For the laminar matroid, we present a new dynamic data structure using the top tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et al., 2005] that maintains the maximum weight basis under insertions and deletions of elements in O(log n) time. This data structure needs to support certain subtree query and path update operations that are performed every insertion and deletion that are non-trivial to handle in conjunction. For the transversal matroid the Freeze operation corresponds to requiring the data structure to keep a certain set S of vertices matched, a property that we call S-stability. While there is a large body of work on dynamic matching algorithms, none are S-stable and maintain an approximate maximum weight matching under vertex updates. We give the first such algorithm for bipartite graphs with total running time linear (up to log factors) in the number of edges.}, author = {Henzinger, Monika H and Liu, Paul and Vondrák, Jan and Zheng, Da Wei}, booktitle = {50th International Colloquium on Automata, Languages, and Programming}, isbn = {9783959772785}, issn = {18688969}, location = {Paderborn, Germany}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Faster submodular maximization for several classes of matroids}}, doi = {10.4230/LIPIcs.ICALP.2023.74}, volume = {261}, year = {2023}, } @inproceedings{14083, abstract = {In this work we consider the list-decodability and list-recoverability of arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable if every radius pn Hamming ball contains less than L codewords; (p,𝓁,L)_q-list-recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length 𝓁 and again stipulate that there be less than L codewords. Our main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate (p,𝓁,L)_q-list-recoverable codes, the quantity we call the zero-rate threshold. Denoting this value by p_*, we in fact show that codes correcting a p_*+ε fraction of errors must have size O_ε(1), i.e., independent of n. Such a result is typically referred to as a "Plotkin bound." To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p_*-ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery. Technically, proving the Plotkin bound boils down to demonstrating the Schur convexity of a certain function defined on the q-simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q-ary list-decoding; however, we point out that this earlier proof is flawed.}, author = {Resch, Nicolas and Yuan, Chen and Zhang, Yihan}, booktitle = {50th International Colloquium on Automata, Languages, and Programming}, isbn = {9783959772785}, issn = {1868-8969}, location = {Paderborn, Germany}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery}}, doi = {10.4230/LIPIcs.ICALP.2023.99}, volume = {261}, year = {2023}, } @article{12922, abstract = {The influence of structural modifications on the catalytic activity of carbon materials is poorly understood. A collection of carbonaceous materials with different pore networks and high nitrogen content was characterized and used to catalyze four reactions to deduce structure–activity relationships. The CO2 cycloaddition and Knoevenagel reaction depend on Lewis basic sites (electron-rich nitrogen species). The absence of large conjugated carbon domains resulting from the introduction of large amounts of nitrogen in the carbon network is responsible for poor redox activity, as observed through the catalytic reduction of nitrobenzene with hydrazine and the catalytic oxidation of 3,3′,5,5′-tetramethylbenzidine using hydroperoxide. The material with the highest activity towards Lewis acid catalysis (in the hydrolysis of (dimethoxymethyl)benzene to benzaldehyde) is the most effective for small molecule activation and presents the highest concentration of electron-poor nitrogen species.}, author = {Lepre, Enrico and Rat, Sylvain and Cavedon, Cristian and Seeberger, Peter H. and Pieber, Bartholomäus and Antonietti, Markus and López‐Salas, Nieves}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {2}, publisher = {Wiley}, title = {{Catalytic properties of high nitrogen content carbonaceous materials}}, doi = {10.1002/anie.202211663}, volume = {62}, year = {2023}, } @article{13450, abstract = {In previous work, we identified a population of 38 cool and luminous variable stars in the Magellanic Clouds and examined 11 in detail in order to classify them as either Thorne–Żytkow objects (TŻOs; red supergiants with a neutron star cores) or super-asymptotic giant branch (sAGB) stars (the most massive stars that will not undergo core collapse). This population includes HV 2112, a peculiar star previously considered in other works to be either a TŻO or high-mass asymptotic giant branch (AGB) star. Here we continue this investigation, using the kinematic and radio environments and local star formation history of these stars to place constraints on the age of the progenitor systems and the presence of past supernovae. These stars are not associated with regions of recent star formation, and we find no evidence of past supernovae at their locations. Finally, we also assess the presence of heavy elements and lithium in their spectra compared to red supergiants. We find strong absorption in Li and s-process elements compared to RSGs in most of the sample, consistent with sAGB nucleosynthesis, while HV 2112 shows additional strong lines associated with TŻO nucleosynthesis. Coupled with our previous mass estimates, the results are consistent with the stars being massive (∼4–6.5 M⊙) or sAGB (∼6.5–12 M⊙) stars in the thermally pulsing phase, providing crucial observations of the transition between low- and high-mass stellar populations. HV 2112 is more ambiguous; it could either be a maximally massive sAGB star, or a TŻO if the minimum mass for stability extends down to ≲13 M⊙.}, author = {O‘Grady, Anna J. G. and Drout, Maria R. and Gaensler, B. M. and Kochanek, C. S. and Neugent, Kathryn F. and Doherty, Carolyn L. and Speagle, Joshua S. and Shappee, B. J. and Rauch, Michael and Götberg, Ylva Louise Linsdotter and Ludwig, Bethany and Thompson, Todd A.}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {1}, publisher = {American Astronomical Society}, title = {{Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates}}, doi = {10.3847/1538-4357/aca655}, volume = {943}, year = {2023}, } @article{13449, abstract = {Stars strongly impact their environment, and shape structures on all scales throughout the universe, in a process known as "feedback." Due to the complexity of both stellar evolution and the physics of larger astrophysical structures, there remain many unanswered questions about how feedback operates and what we can learn about stars by studying their imprint on the wider universe. In this white paper, we summarize discussions from the Lorentz Center meeting "Bringing Stellar Evolution and Feedback Together" in 2022 April and identify key areas where further dialog can bring about radical changes in how we view the relationship between stars and the universe they live in.}, author = {Geen, Sam and Agrawal, Poojan and Crowther, Paul A. and Keller, B. W. and de Koter, Alex and Keszthelyi, Zsolt and van de Voort, Freeke and Ali, Ahmad A. and Backs, Frank and Bonne, Lars and Brugaletta, Vittoria and Derkink, Annelotte and Ekström, Sylvia and Fichtner, Yvonne A. and Grassitelli, Luca and Götberg, Ylva Louise Linsdotter and Higgins, Erin R. and Laplace, Eva and You Liow, Kong and Lorenzo, Marta and McLeod, Anna F. and Meynet, Georges and Newsome, Megan and André Oliva, G. and Ramachandran, Varsha and Rey, Martin P. and Rieder, Steven and Romano-Díaz, Emilio and Sabhahit, Gautham and Sander, Andreas A. C. and Sarwar, Rafia and Stinshoff, Hanno and Stoop, Mitchel and Szécsi, Dorottya and Trebitsch, Maxime and Vink, Jorick S. and Winch, Ethan}, issn = {1538-3873}, journal = {Publications of the Astronomical Society of the Pacific}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {1044}, publisher = {IOP Publishing}, title = {{Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop}}, doi = {10.1088/1538-3873/acb6b5}, volume = {135}, year = {2023}, } @article{14104, abstract = {Thorne–Żytkow objects (TŻO) are potential end products of the merger of a neutron star with a non-degenerate star. In this work, we have computed the first grid of evolutionary models of TŻOs with the MESA stellar evolution code. With these models, we predict several observational properties of TŻOs, including their surface temperatures and luminosities, pulsation periods, and nucleosynthetic products. We expand the range of possible TŻO solutions to cover 3.45≲log(Teff/K)≲3.65 and 4.85≲log(L/L⊙)≲5.5⁠. Due to the much higher densities our TŻOs reach compared to previous models, if TŻOs form we expect them to be stable over a larger mass range than previously predicted, without exhibiting a gap in their mass distribution. Using the GYRE stellar pulsation code we show that TŻOs should have fundamental pulsation periods of 1000–2000 d, and period ratios of ≈0.2–0.3. Models computed with a large 399 isotope fully coupled nuclear network show a nucleosynthetic signal that is different to previously predicted. We propose a new nucleosynthetic signal to determine a star’s status as a TŻO: the isotopologues 44TiO2 and 44TiO⁠, which will have a shift in their spectral features as compared to stable titanium-containing molecules. We find that in the local Universe (∼SMC metallicities and above) TŻOs show little heavy metal enrichment, potentially explaining the difficulty in finding TŻOs to-date.}, author = {Farmer, R and Renzo, M and Götberg, Ylva Louise Linsdotter and Bellinger, E and Justham, S and de Mink, S E}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {2}, pages = {1692--1709}, publisher = {Oxford University Press}, title = {{Observational predictions for Thorne–Żytkow objects}}, doi = {10.1093/mnras/stad1977}, volume = {524}, year = {2023}, } @article{13989, abstract = {Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements.}, author = {Hales, Jordyn and Bajpai, Utkarsh and Liu, Tongtong and Baykusheva, Denitsa Rangelova and Li, Mingda and Mitrano, Matteo and Wang, Yao}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering}}, doi = {10.1038/s41467-023-38540-3}, volume = {14}, year = {2023}, } @article{13990, abstract = {Many-body entanglement in condensed matter systems can be diagnosed from equilibrium response functions through the use of entanglement witnesses and operator-specific quantum bounds. Here, we investigate the applicability of this approach for detecting entangled states in quantum systems driven out of equilibrium. We use a multipartite entanglement witness, the quantum Fisher information, to study the dynamics of a paradigmatic fermion chain undergoing a time-dependent change of the Coulomb interaction. Our results show that the quantum Fisher information is able to witness distinct signatures of multipartite entanglement both near and far from equilibrium that are robust against decoherence. We discuss implications of these findings for probing entanglement in light-driven quantum materials with time-resolved optical and x-ray scattering methods.}, author = {Baykusheva, Denitsa Rangelova and Kalthoff, Mona H. and Hofmann, Damian and Claassen, Martin and Kennes, Dante M. and Sentef, Michael A. and Mitrano, Matteo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {10}, publisher = {American Physical Society}, title = {{Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain}}, doi = {10.1103/physrevlett.130.106902}, volume = {130}, year = {2023}, } @article{12697, abstract = {Models for same-material contact electrification in granular media often rely on a local charge-driving parameter whose spatial variations lead to a stochastic origin for charge exchange. Measuring the charge transfer from individual granular spheres after contacts with substrates of the same material, we find instead a “global” charging behavior, coherent over the sample’s whole surface. Cleaning and baking samples fully resets charging magnitude and direction, which indicates the underlying global parameter is not intrinsic to the material, but acquired from its history. Charging behavior is randomly and irreversibly affected by changes in relative humidity, hinting at a mechanism where adsorbates, in particular, water, are fundamental to the charge-transfer process.}, author = {Grosjean, Galien M and Waitukaitis, Scott R}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics, Electrostatics, Triboelectricity, Soft Matter, Acoustic Levitation, Granular Materials}, number = {9}, publisher = {American Physical Society}, title = {{Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media}}, doi = {10.1103/physrevlett.130.098202}, volume = {130}, year = {2023}, } @article{14103, abstract = {Observations of individual massive stars, super-luminous supernovae, gamma-ray bursts, and gravitational wave events involving spectacular black hole mergers indicate that the low-metallicity Universe is fundamentally different from our own Galaxy. Many transient phenomena will remain enigmatic until we achieve a firm understanding of the physics and evolution of massive stars at low metallicity (Z). The Hubble Space Telescope has devoted 500 orbits to observing ∼250 massive stars at low Z in the ultraviolet (UV) with the COS and STIS spectrographs under the ULLYSES programme. The complementary X-Shooting ULLYSES (XShootU) project provides an enhanced legacy value with high-quality optical and near-infrared spectra obtained with the wide-wavelength coverage X-shooter spectrograph at ESO’s Very Large Telescope. We present an overview of the XShootU project, showing that combining ULLYSES UV and XShootU optical spectra is critical for the uniform determination of stellar parameters such as effective temperature, surface gravity, luminosity, and abundances, as well as wind properties such as mass-loss rates as a function of Z. As uncertainties in stellar and wind parameters percolate into many adjacent areas of astrophysics, the data and modelling of the XShootU project is expected to be a game changer for our physical understanding of massive stars at low Z. To be able to confidently interpret James Webb Space Telescope spectra of the first stellar generations, the individual spectra of low-Z stars need to be understood, which is exactly where XShootU can deliver.}, author = {Vink, Jorick S. and Mehner, A. and Crowther, P. A. and Fullerton, A. and Garcia, M. and Martins, F. and Morrell, N. and Oskinova, L. M. and St-Louis, N. and ud-Doula, A. and Sander, A. A. C. and Sana, H. and Bouret, J.-C. and Kubátová, B. and Marchant, P. and Martins, L. P. and Wofford, A. and van Loon, J. Th. and Grace Telford, O. and Götberg, Ylva Louise Linsdotter and Bowman, D. M. and Erba, C. and Kalari, V. M. and Abdul-Masih, M. and Alkousa, T. and Backs, F. and Barbosa, C. L. and Berlanas, S. R. and Bernini-Peron, M. and Bestenlehner, J. M. and Blomme, R. and Bodensteiner, J. and Brands, S. A. and Evans, C. J. and David-Uraz, A. and Driessen, F. A. and Dsilva, K. and Geen, S. and Gómez-González, V. M. A. and Grassitelli, L. and Hamann, W.-R. and Hawcroft, C. and Herrero, A. and Higgins, E. R. and John Hillier, D. and Ignace, R. and Istrate, A. G. and Kaper, L. and Kee, N. D. and Kehrig, C. and Keszthelyi, Z. and Klencki, J. and de Koter, A. and Kuiper, R. and Laplace, E. and Larkin, C. J. K. and Lefever, R. R. and Leitherer, C. and Lennon, D. J. and Mahy, L. and Maíz Apellániz, J. and Maravelias, G. and Marcolino, W. and McLeod, A. F. and de Mink, S. E. and Najarro, F. and Oey, M. S. and Parsons, T. N. and Pauli, D. and Pedersen, M. G. and Prinja, R. K. and Ramachandran, V. and Ramírez-Tannus, M. C. and Sabhahit, G. N. and Schootemeijer, A. and Reyero Serantes, S. and Shenar, T. and Stringfellow, G. S. and Sudnik, N. and Tramper, F. and Wang, L.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{X-shooting ULLYSES: Massive stars at low metallicity. I. Project description}}, doi = {10.1051/0004-6361/202245650}, volume = {675}, year = {2023}, } @phdthesis{13175, abstract = {About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. Quantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. Till date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. After decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. Optical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. In this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. With this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. }, author = {Sahu, Rishabh}, isbn = {978-3-99078-030-5}, issn = {2663 - 337X}, keywords = {quantum optics, electrooptics, quantum networks, quantum communication, transduction}, pages = {202}, publisher = {Institute of Science and Technology Austria}, title = {{Cavity quantum electrooptics}}, doi = {10.15479/at:ista:13175}, year = {2023}, } @phdthesis{12900, abstract = {About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. Quantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. Till date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. After decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. Optical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. In this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. With this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. }, author = {Sahu, Rishabh}, isbn = {978-3-99078-030-5}, issn = {2663 - 337X}, keywords = {quantum optics, electrooptics, quantum networks, quantum communication, transduction}, pages = {190}, publisher = {Institute of Science and Technology Austria}, title = {{Cavity quantum electrooptics}}, doi = {10.15479/at:ista:12900}, year = {2023}, } @inproceedings{14242, abstract = {We study the problem of training and certifying adversarially robust quantized neural networks (QNNs). Quantization is a technique for making neural networks more efficient by running them using low-bit integer arithmetic and is therefore commonly adopted in industry. Recent work has shown that floating-point neural networks that have been verified to be robust can become vulnerable to adversarial attacks after quantization, and certification of the quantized representation is necessary to guarantee robustness. In this work, we present quantization-aware interval bound propagation (QA-IBP), a novel method for training robust QNNs. Inspired by advances in robust learning of non-quantized networks, our training algorithm computes the gradient of an abstract representation of the actual network. Unlike existing approaches, our method can handle the discrete semantics of QNNs. Based on QA-IBP, we also develop a complete verification procedure for verifying the adversarial robustness of QNNs, which is guaranteed to terminate and produce a correct answer. Compared to existing approaches, the key advantage of our verification procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate experimentally that our approach significantly outperforms existing methods and establish the new state-of-the-art for training and certifying the robustness of QNNs.}, author = {Lechner, Mathias and Zikelic, Dorde and Chatterjee, Krishnendu and Henzinger, Thomas A and Rus, Daniela}, booktitle = {Proceedings of the 37th AAAI Conference on Artificial Intelligence}, isbn = {9781577358800}, location = {Washington, DC, United States}, number = {12}, pages = {14964--14973}, publisher = {Association for the Advancement of Artificial Intelligence}, title = {{Quantization-aware interval bound propagation for training certifiably robust quantized neural networks}}, doi = {10.1609/aaai.v37i12.26747}, volume = {37}, year = {2023}, } @inproceedings{14243, abstract = {Two-player zero-sum "graph games" are central in logic, verification, and multi-agent systems. The game proceeds by placing a token on a vertex of a graph, and allowing the players to move it to produce an infinite path, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In "bidding games", however, the players have budgets and in each turn, an auction (bidding) determines which player moves the token. So far, bidding games have only been studied as full-information games. In this work we initiate the study of partial-information bidding games: we study bidding games in which a player's initial budget is drawn from a known probability distribution. We show that while for some bidding mechanisms and objectives, it is straightforward to adapt the results from the full-information setting to the partial-information setting, for others, the analysis is significantly more challenging, requires new techniques, and gives rise to interesting results. Specifically, we study games with "mean-payoff" objectives in combination with "poorman" bidding. We construct optimal strategies for a partially-informed player who plays against a fully-informed adversary. We show that, somewhat surprisingly, the "value" under pure strategies does not necessarily exist in such games.}, author = {Avni, Guy and Jecker, Ismael R and Zikelic, Dorde}, booktitle = {Proceedings of the 37th AAAI Conference on Artificial Intelligence}, isbn = {9781577358800}, location = {Washington, DC, United States}, number = {5}, pages = {5464--5471}, title = {{Bidding graph games with partially-observable budgets}}, doi = {10.1609/aaai.v37i5.25679}, volume = {37}, year = {2023}, } @inproceedings{14241, abstract = {We present a technique to optimize the reflectivity of a surface while preserving its overall shape. The naïve optimization of the mesh vertices using the gradients of reflectivity simulations results in undesirable distortion. In contrast, our robust formulation optimizes the surface normal as an independent variable that bridges the reflectivity term with differential rendering, and the regularization term with as-rigid-as-possible elastic energy. We further adaptively subdivide the input mesh to improve the convergence. Consequently, our method can minimize the retroreflectivity of a wide range of input shapes, resulting in sharply creased shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by changing the reward for the direction of the outgoing light directions, our method can be applied to other reflectivity design tasks, such as the optimization of architectural walls to concentrate light in a specific region. We have tested the proposed method using light-transport simulations and real-world 3D-printed objects.}, author = {Tojo, Kenji and Shamir, Ariel and Bickel, Bernd and Umetani, Nobuyuki}, booktitle = {SIGGRAPH 2023 Conference Proceedings}, isbn = {9798400701597}, location = {Los Angeles, CA, United States}, publisher = {Association for Computing Machinery}, title = {{Stealth shaper: Reflectivity optimization as surface stylization}}, doi = {10.1145/3588432.3591542}, year = {2023}, } @article{12562, abstract = {Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons.}, author = {Ladle, David R. and Hippenmeyer, Simon}, issn = {1522-1598}, journal = {Journal of Neurophysiology}, keywords = {Physiology, General Neuroscience}, number = {3}, pages = {501--512}, publisher = {American Physiological Society}, title = {{Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons}}, doi = {10.1152/jn.00172.2022}, volume = {129}, year = {2023}, } @inproceedings{13310, abstract = {Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation.}, author = {Henzinger, Thomas A and Karimi, Mahyar and Kueffner, Konstantin and Mallik, Kaushik}, booktitle = {Computer Aided Verification}, isbn = {9783031377020}, issn = {1611-3349}, location = {Paris, France}, pages = {358–382}, publisher = {Springer Nature}, title = {{Monitoring algorithmic fairness}}, doi = {10.1007/978-3-031-37703-7_17}, volume = {13965}, year = {2023}, } @article{12205, abstract = {Background: This study seeks to evaluate the impact of breast cancer (BRCA) gene status on tumor dissemination pattern, surgical outcome and survival in a multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian cancer (rOC). Patients and Methods: Medical records and follow-up data from 190 patients were gathered retrospectively. All patients had surgery at pOC and at least one further rOC surgery at four European high-volume centers. Patients were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut) and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor presentation, surgical outcome and survival data were analyzed between the two groups. Results: Patients with BRCAmut disease were on average 4 years younger and had significantly more tumor involvement upon diagnosis. Patients with BRCAmut disease showed higher debulking rates at all stages. Multivariate analysis showed that only patient age had significant predictive value for complete tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated with optimal debulking. Patients with BRCAmut disease showed significantly prolonged overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged in the BRCAmut group at all stages as well, reaching statistical significance during recurrence. Conclusions: Patients with BRCAmut disease showed a more aggressive course of disease with earlier onset and more extensive tumor dissemination at pOC. However, surgical outcome and OS were significantly better in patients with BRCAmut disease compared with patients with BRCAwt disease. We therefore propose to consider BRCAmut status in regard to patient selection for cytoreductive surgery, especially in rOC.}, author = {Glajzer, Jacek and Castillo-Tong, Dan Cacsire and Richter, Rolf and Vergote, Ignace and Kulbe, Hagen and Vanderstichele, Adriaan and Ruscito, Ilary and Trillsch, Fabian and Mustea, Alexander and Kreuzinger, Caroline and Gourley, Charlie and Gabra, Hani and Taube, Eliane T. and Dorigo, Oliver and Horst, David and Keunecke, Carlotta and Baum, Joanna and Angelotti, Timothy and Sehouli, Jalid and Braicu, Elena Ioana}, issn = {1534-4681}, journal = {Annals of Surgical Oncology}, keywords = {Oncology, Surgery}, pages = {35--45}, publisher = {Springer Nature}, title = {{Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium}}, doi = {10.1245/s10434-022-12459-3}, volume = {30}, year = {2023}, } @article{12115, author = {Glajzer, Jacek and Castillo-Tong, Dan Cacsire and Richter, Rolf and Vergote, Ignace and Kulbe, Hagen and Vanderstichele, Adriaan and Ruscito, Ilary and Trillsch, Fabian and Mustea, Alexander and Kreuzinger, Caroline and Gourley, Charlie and Gabra, Hani and Taube, Eliane T. and Dorigo, Oliver and Horst, David and Keunecke, Carlotta and Baum, Joanna and Angelotti, Timothy and Sehouli, Jalid and Braicu, Elena Ioana}, issn = {1534-4681}, journal = {Annals of Surgical Oncology}, keywords = {Oncology, Surgery}, pages = {46--47}, publisher = {Springer Nature}, title = {{ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium}}, doi = {10.1245/s10434-022-12681-z}, volume = {30}, year = {2023}, } @article{14253, abstract = {Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell.}, author = {Vierra, Nicholas C. and Ribeiro-Silva, Luisa and Kirmiz, Michael and Van Der List, Deborah and Bhandari, Pradeep and Mack, Olivia A. and Carroll, James and Le Monnier, Elodie and Aicher, Sue A. and Shigemoto, Ryuichi and Trimmer, James S.}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling}}, doi = {10.1038/s41467-023-40930-6}, volume = {14}, year = {2023}, } @inproceedings{14259, abstract = {We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions. In contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning.}, author = {Kretinsky, Jan and Meggendorfer, Tobias and Prokop, Maximilian and Rieder, Sabine}, booktitle = {35th International Conference on Computer Aided Verification }, isbn = {9783031377051}, issn = {1611-3349}, location = {Paris, France}, pages = {390--414}, publisher = {Springer Nature}, title = {{Guessing winning policies in LTL synthesis by semantic learning}}, doi = {10.1007/978-3-031-37706-8_20}, volume = {13964}, year = {2023}, } @inproceedings{14105, abstract = {Despite their recent success, deep neural networks continue to perform poorly when they encounter distribution shifts at test time. Many recently proposed approaches try to counter this by aligning the model to the new distribution prior to inference. With no labels available this requires unsupervised objectives to adapt the model on the observed test data. In this paper, we propose Test-Time SelfTraining (TeST): a technique that takes as input a model trained on some source data and a novel data distribution at test time, and learns invariant and robust representations using a student-teacher framework. We find that models adapted using TeST significantly improve over baseline testtime adaptation algorithms. TeST achieves competitive performance to modern domain adaptation algorithms [4, 43], while having access to 5-10x less data at time of adaption. We thoroughly evaluate a variety of baselines on two tasks: object detection and image segmentation and find that models adapted with TeST. We find that TeST sets the new stateof-the art for test-time domain adaptation algorithms. }, author = {Sinha, Samarth and Gehler, Peter and Locatello, Francesco and Schiele, Bernt}, booktitle = {2023 IEEE/CVF Winter Conference on Applications of Computer Vision}, isbn = {9781665493475}, issn = {2642-9381}, location = {Waikoloa, HI, United States}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{TeST: Test-time Self-Training under distribution shift}}, doi = {10.1109/wacv56688.2023.00278}, year = {2023}, } @article{14256, abstract = {Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes. Aims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields. Methods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies. Results. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies. Conclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries.}, author = {Mathis, S. and Bugnet, Lisa Annabelle}, issn = {1432-0746}, journal = {Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields}}, doi = {10.1051/0004-6361/202346832}, volume = {676}, year = {2023}, } @article{14261, abstract = {In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing.}, author = {Gamper, Jakob and Kluibenschedl, Florian and Weiss, Alexander K.H. and Hofer, Thomas S.}, issn = {1948-7185}, journal = {Journal of Physical Chemistry Letters}, number = {33}, pages = {7395--7403}, publisher = {American Chemical Society}, title = {{Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems}}, doi = {10.1021/acs.jpclett.3c01707}, volume = {14}, year = {2023}, } @inproceedings{14208, abstract = {This paper focuses on over-parameterized deep neural networks (DNNs) with ReLU activation functions and proves that when the data distribution is well-separated, DNNs can achieve Bayes-optimal test error for classification while obtaining (nearly) zero-training error under the lazy training regime. For this purpose, we unify three interrelated concepts of overparameterization, benign overfitting, and the Lipschitz constant of DNNs. Our results indicate that interpolating with smoother functions leads to better generalization. Furthermore, we investigate the special case where interpolating smooth ground-truth functions is performed by DNNs under the Neural Tangent Kernel (NTK) regime for generalization. Our result demonstrates that the generalization error converges to a constant order that only depends on label noise and initialization noise, which theoretically verifies benign overfitting. Our analysis provides a tight lower bound on the normalized margin under non-smooth activation functions, as well as the minimum eigenvalue of NTK under high-dimensional settings, which has its own interest in learning theory.}, author = {Zhu, Zhenyu and Liu, Fanghui and Chrysos, Grigorios G and Locatello, Francesco and Cevher, Volkan}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, location = {Honolulu, Hawaii, United States}, pages = {43105--43128}, publisher = {ML Research Press}, title = {{Benign overfitting in deep neural networks under lazy training}}, volume = {202}, year = {2023}, } @unpublished{14209, abstract = {Diffusion models excel at generating photorealistic images from text-queries. Naturally, many approaches have been proposed to use these generative abilities to augment training datasets for downstream tasks, such as classification. However, diffusion models are themselves trained on large noisily supervised, but nonetheless, annotated datasets. It is an open question whether the generalization capabilities of diffusion models beyond using the additional data of the pre-training process for augmentation lead to improved downstream performance. We perform a systematic evaluation of existing methods to generate images from diffusion models and study new extensions to assess their benefit for data augmentation. While we find that personalizing diffusion models towards the target data outperforms simpler prompting strategies, we also show that using the training data of the diffusion model alone, via a simple nearest neighbor retrieval procedure, leads to even stronger downstream performance. Overall, our study probes the limitations of diffusion models for data augmentation but also highlights its potential in generating new training data to improve performance on simple downstream vision tasks.}, author = {Burg, Max F. and Wenzel, Florian and Zietlow, Dominik and Horn, Max and Makansi, Osama and Locatello, Francesco and Russell, Chris}, booktitle = {arXiv}, title = {{A data augmentation perspective on diffusion models and retrieval}}, doi = {10.48550/arXiv.2304.10253}, year = {2023}, } @inproceedings{14211, abstract = {Causal discovery methods are intrinsically constrained by the set of assumptions needed to ensure structure identifiability. Moreover additional restrictions are often imposed in order to simplify the inference task: this is the case for the Gaussian noise assumption on additive non-linear models, which is common to many causal discovery approaches. In this paper we show the shortcomings of inference under this hypothesis, analyzing the risk of edge inversion under violation of Gaussianity of the noise terms. Then, we propose a novel method for inferring the topological ordering of the variables in the causal graph, from data generated according to an additive non-linear model with a generic noise distribution. This leads to NoGAM (Not only Gaussian Additive noise Models), a causal discovery algorithm with a minimal set of assumptions and state of the art performance, experimentally benchmarked on synthetic data.}, author = {Montagna, Francesco and Noceti, Nicoletta and Rosasco, Lorenzo and Zhang, Kun and Locatello, Francesco}, booktitle = {2nd Conference on Causal Learning and Reasoning}, location = {Tübingen, Germany}, title = {{Causal discovery with score matching on additive models with arbitrary noise}}, year = {2023}, } @inproceedings{14212, abstract = {This paper demonstrates how to discover the whole causal graph from the second derivative of the log-likelihood in observational non-linear additive Gaussian noise models. Leveraging scalable machine learning approaches to approximate the score function ∇logp(X), we extend the work of Rolland et al. (2022) that only recovers the topological order from the score and requires an expensive pruning step removing spurious edges among those admitted by the ordering. Our analysis leads to DAS (acronym for Discovery At Scale), a practical algorithm that reduces the complexity of the pruning by a factor proportional to the graph size. In practice, DAS achieves competitive accuracy with current state-of-the-art while being over an order of magnitude faster. Overall, our approach enables principled and scalable causal discovery, significantly lowering the compute bar.}, author = {Montagna, Francesco and Noceti, Nicoletta and Rosasco, Lorenzo and Zhang, Kun and Locatello, Francesco}, booktitle = {2nd Conference on Causal Learning and Reasoning}, location = {Tübingen, Germany}, title = {{Scalable causal discovery with score matching}}, year = {2023}, } @inproceedings{14214, abstract = {Recent years have seen a surge of interest in learning high-level causal representations from low-level image pairs under interventions. Yet, existing efforts are largely limited to simple synthetic settings that are far away from real-world problems. In this paper, we present Causal Triplet, a causal representation learning benchmark featuring not only visually more complex scenes, but also two crucial desiderata commonly overlooked in previous works: (i) an actionable counterfactual setting, where only certain object-level variables allow for counterfactual observations whereas others do not; (ii) an interventional downstream task with an emphasis on out-of-distribution robustness from the independent causal mechanisms principle. Through extensive experiments, we find that models built with the knowledge of disentangled or object-centric representations significantly outperform their distributed counterparts. However, recent causal representation learning methods still struggle to identify such latent structures, indicating substantial challenges and opportunities for future work.}, author = {Liu, Yuejiang and Alahi, Alexandre and Russell, Chris and Horn, Max and Zietlow, Dominik and Schölkopf, Bernhard and Locatello, Francesco}, booktitle = {2nd Conference on Causal Learning and Reasoning}, location = {Tübingen, Germany}, title = {{Causal triplet: An open challenge for intervention-centric causal representation learning}}, year = {2023}, } @inproceedings{14217, abstract = {Neural networks embed the geometric structure of a data manifold lying in a high-dimensional space into latent representations. Ideally, the distribution of the data points in the latent space should depend only on the task, the data, the loss, and other architecture-specific constraints. However, factors such as the random weights initialization, training hyperparameters, or other sources of randomness in the training phase may induce incoherent latent spaces that hinder any form of reuse. Nevertheless, we empirically observe that, under the same data and modeling choices, the angles between the encodings within distinct latent spaces do not change. In this work, we propose the latent similarity between each sample and a fixed set of anchors as an alternative data representation, demonstrating that it can enforce the desired invariances without any additional training. We show how neural architectures can leverage these relative representations to guarantee, in practice, invariance to latent isometries and rescalings, effectively enabling latent space communication: from zero-shot model stitching to latent space comparison between diverse settings. We extensively validate the generalization capability of our approach on different datasets, spanning various modalities (images, text, graphs), tasks (e.g., classification, reconstruction) and architectures (e.g., CNNs, GCNs, transformers).}, author = {Moschella, Luca and Maiorca, Valentino and Fumero, Marco and Norelli, Antonio and Locatello, Francesco and Rodolà, Emanuele}, booktitle = {The 11th International Conference on Learning Representations}, location = {Kigali, Rwanda}, title = {{Relative representations enable zero-shot latent space communication}}, year = {2023}, } @inproceedings{14222, abstract = {Learning generative object models from unlabelled videos is a long standing problem and required for causal scene modeling. We decompose this problem into three easier subtasks, and provide candidate solutions for each of them. Inspired by the Common Fate Principle of Gestalt Psychology, we first extract (noisy) masks of moving objects via unsupervised motion segmentation. Second, generative models are trained on the masks of the background and the moving objects, respectively. Third, background and foreground models are combined in a conditional "dead leaves" scene model to sample novel scene configurations where occlusions and depth layering arise naturally. To evaluate the individual stages, we introduce the Fishbowl dataset positioned between complex real-world scenes and common object-centric benchmarks of simplistic objects. We show that our approach allows learning generative models that generalize beyond the occlusions present in the input videos, and represent scenes in a modular fashion that allows sampling plausible scenes outside the training distribution by permitting, for instance, object numbers or densities not observed in the training set.}, author = {Tangemann, Matthias and Schneider, Steffen and Kügelgen, Julius von and Locatello, Francesco and Gehler, Peter and Brox, Thomas and Kümmerer, Matthias and Bethge, Matthias and Schölkopf, Bernhard}, booktitle = {2nd Conference on Causal Learning and Reasoning}, location = {Tübingen, Germany}, title = {{Unsupervised object learning via common fate}}, year = {2023}, } @inproceedings{14218, abstract = {Humans naturally decompose their environment into entities at the appropriate level of abstraction to act in the world. Allowing machine learning algorithms to derive this decomposition in an unsupervised way has become an important line of research. However, current methods are restricted to simulated data or require additional information in the form of motion or depth in order to successfully discover objects. In this work, we overcome this limitation by showing that reconstructing features from models trained in a self-supervised manner is a sufficient training signal for object-centric representations to arise in a fully unsupervised way. Our approach, DINOSAUR, significantly out-performs existing image-based object-centric learning models on simulated data and is the first unsupervised object-centric model that scales to real-world datasets such as COCO and PASCAL VOC. DINOSAUR is conceptually simple and shows competitive performance compared to more involved pipelines from the computer vision literature.}, author = {Seitzer, Maximilian and Horn, Max and Zadaianchuk, Andrii and Zietlow, Dominik and Xiao, Tianjun and Carl-Johann Simon-Gabriel, Carl-Johann Simon-Gabriel and He, Tong and Zhang, Zheng and Schölkopf, Bernhard and Brox, Thomas and Locatello, Francesco}, booktitle = {The 11th International Conference on Learning Representations}, location = {Kigali, Rwanda}, title = {{Bridging the gap to real-world object-centric learning}}, year = {2023}, } @inproceedings{14219, abstract = {In this paper, we show that recent advances in self-supervised feature learning enable unsupervised object discovery and semantic segmentation with a performance that matches the state of the field on supervised semantic segmentation 10 years ago. We propose a methodology based on unsupervised saliency masks and self-supervised feature clustering to kickstart object discovery followed by training a semantic segmentation network on pseudo-labels to bootstrap the system on images with multiple objects. We present results on PASCAL VOC that go far beyond the current state of the art (50.0 mIoU), and we report for the first time results on MS COCO for the whole set of 81 classes: our method discovers 34 categories with more than $20\%$ IoU, while obtaining an average IoU of 19.6 for all 81 categories.}, author = {Zadaianchuk, Andrii and Kleindessner, Matthaeus and Zhu, Yi and Locatello, Francesco and Brox, Thomas}, booktitle = {The 11th International Conference on Learning Representations}, location = {Kigali, Rwanda}, title = {{Unsupervised semantic segmentation with self-supervised object-centric representations}}, year = {2023}, } @unpublished{14333, abstract = {As causal ground truth is incredibly rare, causal discovery algorithms are commonly only evaluated on simulated data. This is concerning, given that simulations reflect common preconceptions about generating processes regarding noise distributions, model classes, and more. In this work, we propose a novel method for falsifying the output of a causal discovery algorithm in the absence of ground truth. Our key insight is that while statistical learning seeks stability across subsets of data points, causal learning should seek stability across subsets of variables. Motivated by this insight, our method relies on a notion of compatibility between causal graphs learned on different subsets of variables. We prove that detecting incompatibilities can falsify wrongly inferred causal relations due to violation of assumptions or errors from finite sample effects. Although passing such compatibility tests is only a necessary criterion for good performance, we argue that it provides strong evidence for the causal models whenever compatibility entails strong implications for the joint distribution. We also demonstrate experimentally that detection of incompatibilities can aid in causal model selection.}, author = {Faller, Philipp M. and Vankadara, Leena Chennuru and Mastakouri, Atalanti A. and Locatello, Francesco and Janzing, Dominik}, booktitle = {arXiv}, title = {{Self-compatibility: Evaluating causal discovery without ground truth}}, doi = {10.48550/arXiv.2307.09552}, year = {2023}, } @article{14277, abstract = {Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels.}, author = {Boocock, Daniel R and Hirashima, Tsuyoshi and Hannezo, Edouard B}, issn = {2835-8279}, journal = {PRX Life}, number = {1}, publisher = {American Physical Society}, title = {{Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers}}, doi = {10.1103/prxlife.1.013001}, volume = {1}, year = {2023}, } @article{14314, abstract = {The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations.}, author = {Nardin, Michele and Käfer, Karola and Stella, Federico and Csicsvari, Jozsef L}, issn = {2211-1247}, journal = {Cell Reports}, number = {9}, publisher = {Elsevier}, title = {{Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions}}, doi = {10.1016/j.celrep.2023.113015}, volume = {42}, year = {2023}, } @article{14315, abstract = {During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.}, author = {Cho, Ukrae H. and Hetzer, Martin W}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress}}, doi = {10.7554/eLife.89066}, volume = {12}, year = {2023}, } @article{14319, abstract = {We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We also make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour multiplicities.}, author = {Anastos, Michael and Fabian, David and Müyesser, Alp and Szabó, Tibor}, issn = {1077-8926}, journal = {Electronic Journal of Combinatorics}, number = {3}, publisher = {Electronic Journal of Combinatorics}, title = {{Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets}}, doi = {10.37236/11714}, volume = {30}, year = {2023}, } @inproceedings{14318, abstract = {Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis. In this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice.}, author = {Sun, Yican and Fu, Hongfei and Chatterjee, Krishnendu and Goharshady, Amir Kafshdar}, booktitle = {Computer Aided Verification}, isbn = {9783031377082}, issn = {1611-3349}, location = {Paris, France}, pages = {16--39}, publisher = {Springer Nature}, title = {{Automated tail bound analysis for probabilistic recurrence relations}}, doi = {10.1007/978-3-031-37709-9_2}, volume = {13966}, year = {2023}, } @inproceedings{14317, abstract = {Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization. In light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples.}, author = {Akshay, S. and Chatterjee, Krishnendu and Meggendorfer, Tobias and Zikelic, Dorde}, booktitle = {International Conference on Computer Aided Verification}, isbn = {9783031377082}, issn = {1611-3349}, location = {Paris, France}, pages = {86--112}, publisher = {Springer Nature}, title = {{MDPs as distribution transformers: Affine invariant synthesis for safety objectives}}, doi = {10.1007/978-3-031-37709-9_5}, volume = {13966}, year = {2023}, } @article{14316, abstract = {Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway.}, author = {Nagano, Makoto and Aoshima, Kaito and Shimamura, Hiroki and Siekhaus, Daria E and Toshima, Junko Y. and Toshima, Jiro}, issn = {1477-9137}, journal = {Journal of Cell Science}, number = {17}, publisher = {The Company of Biologists}, title = {{Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway}}, doi = {10.1242/jcs.261448}, volume = {136}, year = {2023}, } @article{14320, abstract = {The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance.}, author = {Henderson, Paul M and Ghazaryan, Areg and Zibrov, Alexander A. and Young, Andrea F. and Serbyn, Maksym}, issn = {2469-9969}, journal = {Physical Review B}, number = {12}, publisher = {American Physical Society}, title = {{Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene}}, doi = {10.1103/physrevb.108.125411}, volume = {108}, year = {2023}, } @phdthesis{12732, abstract = {Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices. Going beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium. In this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models. In particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models. Using tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods. In this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges. Inspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect. In the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model. The system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping. We show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon. We further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes. The study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times. This work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies. Next, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density. This feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies. The time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities. Our results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument. To support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied. In the last Chapter of this Thesis, we address the topic of many-body localization proximity effect. We study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons. The interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques. Our simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong. We furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory. Finally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.}, author = {Brighi, Pietro}, issn = {2663-337X}, pages = {158}, publisher = {Institute of Science and Technology Austria}, title = {{Ergodicity breaking in disordered and kinetically constrained quantum many-body systems}}, doi = {10.15479/at:ista:12732}, year = {2023}, } @article{14334, abstract = {Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies.}, author = {Brighi, Pietro and Ljubotina, Marko and Serbyn, Maksym}, issn = {2542-4653}, journal = {SciPost Physics}, keywords = {General Physics and Astronomy}, number = {3}, publisher = {SciPost Foundation}, title = {{Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models}}, doi = {10.21468/scipostphys.15.3.093}, volume = {15}, year = {2023}, } @article{14321, abstract = {We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.}, author = {Al Hyder, Ragheed and Cappellaro, Alberto and Lemeshko, Mikhail and Volosniev, Artem}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {10}, publisher = {AIP Publishing}, title = {{Achiral dipoles on a ferromagnet can affect its magnetization direction}}, doi = {10.1063/5.0165806}, volume = {159}, year = {2023}, } @article{14342, abstract = {We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared frequency range that avoids using sophisticated infrared detectors. Our approach is based on using a near-infrared probe beam which interacts with a mid-IR beam via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring XPM-induced spectral modifications in the probe beam and comparing the experimental data with simulation results, we extract the value for the non-degenerate Kerr index. Finally, in order to obtain the value of degenerate mid-IR Kerr index, we use the well-established two-band formalism of Sheik-Bahae et al., which is shown to become particularly simple in the limit of low frequencies. The proposed technique is complementary to the conventional techniques, such as z-scan, and has the advantage of not requiring any mid-infrared detectors.}, author = {Lorenc, Dusan and Alpichshev, Zhanybek}, issn = {0003-6951}, journal = {Applied Physics Letters}, number = {9}, publisher = {AIP Publishing}, title = {{Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam}}, doi = {10.1063/5.0161713}, volume = {123}, year = {2023}, } @article{14341, abstract = {Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines.}, author = {Scarselli, Davide and Lopez Alonso, Jose M and Varshney, Atul and Hof, Björn}, issn = {1476-4687}, journal = {Nature}, number = {7977}, pages = {71--74}, publisher = {Springer Nature}, title = {{Turbulence suppression by cardiac-cycle-inspired driving of pipe flow}}, doi = {10.1038/s41586-023-06399-5}, volume = {621}, year = {2023}, } @article{14368, abstract = {Purpose: Biallelic variants in TARS2, encoding the mitochondrial threonyl-tRNA-synthetase, have been reported in a small group of individuals displaying a neurodevelopmental phenotype but with limited neuroradiological data and insufficient evidence for causality of the variants. Methods: Exome or genome sequencing was carried out in 15 families. Clinical and neuroradiological evaluation was performed for all affected individuals, including review of 10 previously reported individuals. The pathogenicity of TARS2 variants was evaluated using in vitro assays and a zebrafish model. Results: We report 18 new individuals harboring biallelic TARS2 variants. Phenotypically, these individuals show developmental delay/intellectual disability, regression, cerebellar and cerebral atrophy, basal ganglia signal alterations, hypotonia, cerebellar signs, and increased blood lactate. In vitro studies showed that variants within the TARS2301-381 region had decreased binding to Rag GTPases, likely impairing mTORC1 activity. The zebrafish model recapitulated key features of the human phenotype and unraveled dysregulation of downstream targets of mTORC1 signaling. Functional testing of the variants confirmed the pathogenicity in a zebrafish model. Conclusion: We define the clinico-radiological spectrum of TARS2-related mitochondrial disease, unveil the likely involvement of the mTORC1 signaling pathway as a distinct molecular mechanism, and establish a TARS2 zebrafish model as an important tool to study variant pathogenicity.}, author = {Accogli, Andrea and Lin, Sheng-Jia and Severino, Mariasavina and Kim, Sung-Hoon and Huang, Kevin and Rocca, Clarissa and Landsverk, Megan and Zaki, Maha S. and Al-Maawali, Almundher and Srinivasan, Varunvenkat M. and Al-Thihli, Khalid and Schaefer, G. Bradly and Davis, Monica and Tonduti, Davide and Doneda, Chiara and Marten, Lara M. and Mühlhausen, Chris and Gomez, Maria and Lamantea, Eleonora and Mena, Rafael and Nizon, Mathilde and Procaccio, Vincent and Begtrup, Amber and Telegrafi, Aida and Cui, Hong and Schulz, Heidi L. and Mohr, Julia and Biskup, Saskia and Loos, Mariana Amina and Aráoz, Hilda Verónica and Salpietro, Vincenzo and Keppen, Laura Davis and Chitre, Manali and Petree, Cassidy and Raymond, Lucy and Vogt, Julie and Sawyer, Lindsey B. and Basinger, Alice A. and Pedersen, Signe Vandal and Pearson, Toni S. and Grange, Dorothy K. and Lingappa, Lokesh and McDunnah, Paige and Horvath, Rita and Cognè, Benjamin and Isidor, Bertrand and Hahn, Andreas and Gripp, Karen W. and Jafarnejad, Seyed Mehdi and Østergaard, Elsebet and Prada, Carlos E. and Ghezzi, Daniele and Gowda, Vykuntaraju K. and Taylor, Robert W. and Sonenberg, Nahum and Houlden, Henry and Sissler, Marie and Varshney, Gaurav K. and Maroofian, Reza}, issn = {1098-3600}, journal = {Genetics in Medicine}, keywords = {Genetics (clinical)}, number = {11}, publisher = {Elsevier}, title = {{Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder}}, doi = {10.1016/j.gim.2023.100938}, volume = {25}, year = {2023}, } @inproceedings{13120, abstract = {We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction.}, author = {Dvorak, Martin and Blanchette, Jasmin}, booktitle = {14th International Conference on Interactive Theorem Proving}, isbn = {9783959772846}, issn = {1868-8969}, location = {Bialystok, Poland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Closure properties of general grammars - formally verified}}, doi = {10.4230/LIPIcs.ITP.2023.15}, volume = {268}, year = {2023}, } @article{13969, abstract = {Bundling crossings is a strategy which can enhance the readability of graph drawings. In this paper we consider good drawings, i.e., we require that any two edges have at most one common point which can be a common vertex or a crossing. Our main result is that there is a polynomial-time algorithm to compute an 8-approximation of the bundled crossing number of a good drawing with no toothed hole. In general the number of toothed holes has to be added to the 8-approximation. In the special case of circular drawings the approximation factor is 8, this improves upon the 10-approximation of Fink et al. [14]. Our approach also works with the same approximation factor for families of pseudosegments, i.e., curves intersecting at most once. We also show how to compute a 9/2-approximation when the intersection graph of the pseudosegments is bipartite and has no toothed hole.}, author = {Arroyo Guevara, Alan M and Felsner, Stefan}, issn = {1526-1719}, journal = {Journal of Graph Algorithms and Applications}, number = {6}, pages = {433--457}, publisher = {Brown University}, title = {{Approximating the bundled crossing number}}, doi = {10.7155/jgaa.00629}, volume = {27}, year = {2023}, } @inproceedings{14344, abstract = {We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in two different settings. In the first one, G is given to us in the form of randomly ordered adjacency lists while in the second one, we are given the adjacency matrix of G. In each of the two settings we derive a deterministic algorithm that w.h.p. either finds a Hamilton cycle or returns a certificate that such a cycle does not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and respectively, each being best possible in its own setting.}, author = {Anastos, Michael}, booktitle = {Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms}, isbn = {9781611977554}, location = {Florence, Italy}, pages = {2286--2323}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Fast algorithms for solving the Hamilton cycle problem with high probability}}, doi = {10.1137/1.9781611977554.ch88}, volume = {2023}, year = {2023}, } @article{12710, abstract = {Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes.}, author = {Schamberger, Barbara and Ziege, Ricardo and Anselme, Karine and Ben Amar, Martine and Bykowski, Michał and Castro, André P.G. and Cipitria, Amaia and Coles, Rhoslyn A. and Dimova, Rumiana and Eder, Michaela and Ehrig, Sebastian and Escudero, Luis M. and Evans, Myfanwy E. and Fernandes, Paulo R. and Fratzl, Peter and Geris, Liesbet and Gierlinger, Notburga and Hannezo, Edouard B and Iglič, Aleš and Kirkensgaard, Jacob J.K. and Kollmannsberger, Philip and Kowalewska, Łucja and Kurniawan, Nicholas A. and Papantoniou, Ioannis and Pieuchot, Laurent and Pires, Tiago H.V. and Renner, Lars D. and Sageman-Furnas, Andrew O. and Schröder-Turk, Gerd E. and Sengupta, Anupam and Sharma, Vikas R. and Tagua, Antonio and Tomba, Caterina and Trepat, Xavier and Waters, Sarah L. and Yeo, Edwina F. and Roschger, Andreas and Bidan, Cécile M. and Dunlop, John W.C.}, issn = {1521-4095}, journal = {Advanced Materials}, number = {13}, publisher = {Wiley}, title = {{Curvature in biological systems: Its quantification, emergence, and implications across the scales}}, doi = {10.1002/adma.202206110}, volume = {35}, year = {2023}, } @article{14377, abstract = {Coherent flows of self-propelled particles are characterized by vortices and jets that sustain chaotic flows, referred to as active turbulence. Here, we reveal a crossover between defect-free active turbulence and active turbulence laden with topological defects. Interestingly, we show that concurrent to the crossover from defect-free to defect-laden active turbulence is the restoration of the previously broken SO(2) symmetry signaled by the fast decay of the two-point correlations. By stability analyses of the topological charge density field, we provide theoretical insights on the criterion for the crossover to the defect-laden active turbulent state. Despite the distinct symmetry features between these two active turbulence regimes, the flow fluctuations exhibit universal statistical scaling behaviors at large scales, while the spectrum of polarity fluctuations decays exponentially at small length scales compared to the active energy injection length. These findings reveal a dynamical crossover between distinct spatiotemporal organization patterns in polar active matter.}, author = {Andersen, Benjamin H. and Renaud, Julian B and Rønning, Jonas and Angheluta, Luiza and Doostmohammadi, Amin}, issn = {2469-990X}, journal = {Physical Review Fluids}, keywords = {Fluid Flow and Transfer Processes, Modeling and Simulation, Computational Mechanics}, number = {6}, publisher = {American Physical Society}, title = {{Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter}}, doi = {10.1103/physrevfluids.8.063101}, volume = {8}, year = {2023}, } @article{13340, abstract = {Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation.}, author = {Gemen, Julius and Church, Jonathan R. and Ruoko, Tero-Petri and Durandin, Nikita and Białek, Michał J. and Weissenfels, Maren and Feller, Moran and Kazes, Miri and Borin, Veniamin A. and Odaybat, Magdalena and Kalepu, Rishir and Diskin-Posner, Yael and Oron, Dan and Fuchter, Matthew J. and Priimagi, Arri and Schapiro, Igor and Klajn, Rafal}, issn = {1095-9203}, journal = {Science}, number = {6664}, pages = {1357--1363}, publisher = {American Association for the Advancement of Science}, title = {{Disequilibrating azoarenes by visible-light sensitization under confinement}}, doi = {10.1126/science.adh9059}, volume = {381}, year = {2023}, } @article{12705, abstract = {The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.}, author = {Sorichetti, Valerio and Ninarello, Andrea and Ruiz-Franco, José and Hugouvieux, Virginie and Zaccarelli, Emanuela and Micheletti, Cristian and Kob, Walter and Rovigatti, Lorenzo}, issn = {1089-7690}, journal = {Journal of Chemical Physics}, number = {7}, publisher = {American Institute of Physics}, title = {{Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks}}, doi = {10.1063/5.0134271}, volume = {158}, year = {2023}, } @article{12738, abstract = {We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies.}, author = {Chatterjee, Krishnendu and Katoen, Joost P and Mohr, Stefanie and Weininger, Maximilian and Winkler, Tobias}, issn = {1572-8102}, journal = {Formal Methods in System Design}, publisher = {Springer Nature}, title = {{Stochastic games with lexicographic objectives}}, doi = {10.1007/s10703-023-00411-4}, year = {2023}, } @misc{14279, abstract = {The zip file includes source data used in the manuscript "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript. A sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.}, author = {Ucar, Mehmet C}, publisher = {Zenodo}, title = {{Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration"}}, doi = {10.5281/ZENODO.8133960}, year = {2023}, } @article{10405, abstract = {We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32]. }, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J}, issn = {1097-0312}, journal = {Communications on Pure and Applied Mathematics}, number = {5}, pages = {946--1034}, publisher = {Wiley}, title = {{Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices}}, doi = {10.1002/cpa.22028}, volume = {76}, year = {2023}, } @article{10770, abstract = {Mathematical models often aim to describe a complicated mechanism in a cohesive and simple manner. However, reaching perfect balance between being simple enough or overly simplistic is a challenging task. Frequently, game-theoretic models have an underlying assumption that players, whenever they choose to execute a specific action, do so perfectly. In fact, it is rare that action execution perfectly coincides with intentions of individuals, giving rise to behavioural mistakes. The concept of incompetence of players was suggested to address this issue in game-theoretic settings. Under the assumption of incompetence, players have non-zero probabilities of executing a different strategy from the one they chose, leading to stochastic outcomes of the interactions. In this article, we survey results related to the concept of incompetence in classic as well as evolutionary game theory and provide several new results. We also suggest future extensions of the model and argue why it is important to take into account behavioural mistakes when analysing interactions among players in both economic and biological settings.}, author = {Graham, Thomas and Kleshnina, Maria and Filar, Jerzy A.}, issn = {2153-0793}, journal = {Dynamic Games and Applications}, pages = {231--264}, publisher = {Springer Nature}, title = {{Where do mistakes lead? A survey of games with incompetent players}}, doi = {10.1007/s13235-022-00425-3}, volume = {13}, year = {2023}, } @article{10145, abstract = {We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique.}, author = {Dello Schiavo, Lorenzo}, issn = {1572-929X}, journal = {Potential Analysis}, pages = {573--615}, publisher = {Springer Nature}, title = {{Ergodic decomposition of Dirichlet forms via direct integrals and applications}}, doi = {10.1007/s11118-021-09951-y}, volume = {58}, year = {2023}, } @article{12669, abstract = {The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.}, author = {Manavella, Pablo A and Godoy Herz, Micaela A and Kornblihtt, Alberto R and Sorenson, Reed and Sieburth, Leslie E and Nakaminami, Kentaro and Seki, Motoaki and Ding, Yiliang and Sun, Qianwen and Kang, Hunseung and Ariel, Federico D and Crespi, Martin and Giudicatti, Axel J and Cai, Qiang and Jin, Hailing and Feng, Xiaoqi and Qi, Yijun and Pikaard, Craig S}, issn = {1532-298X}, journal = {The Plant Cell}, keywords = {Cell Biology, Plant Science}, number = {6}, publisher = {Oxford University Press}, title = {{Beyond transcription: compelling open questions in plant RNA biology}}, doi = {10.1093/plcell/koac346}, volume = {35}, year = {2023}, } @article{11706, abstract = {We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. }, author = {Liebenau, Anita and Mattos, Letícia and Mendonca Dos Santos, Walner and Skokan, Jozef}, issn = {1098-2418}, journal = {Random Structures and Algorithms}, number = {4}, pages = {1035--1055}, publisher = {Wiley}, title = {{Asymmetric Ramsey properties of random graphs involving cliques and cycles}}, doi = {10.1002/rsa.21106}, volume = {62}, year = {2023}, } @article{12707, abstract = {We establish precise right-tail small deviation estimates for the largest eigenvalue of real symmetric and complex Hermitian matrices whose entries are independent random variables with uniformly bounded moments. The proof relies on a Green function comparison along a continuous interpolating matrix flow for a long time. Less precise estimates are also obtained in the left tail.}, author = {Erdös, László and Xu, Yuanyuan}, issn = {1350-7265}, journal = {Bernoulli}, number = {2}, pages = {1063--1079}, publisher = {Bernoulli Society for Mathematical Statistics and Probability}, title = {{Small deviation estimates for the largest eigenvalue of Wigner matrices}}, doi = {10.3150/22-BEJ1490}, volume = {29}, year = {2023}, } @article{12837, abstract = {As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues.}, author = {Bocanegra, Laura and Singh, Amrita and Hannezo, Edouard B and Zagórski, Marcin P and Kicheva, Anna}, issn = {1745-2481}, journal = {Nature Physics}, pages = {1050--1058}, publisher = {Springer Nature}, title = {{Cell cycle dynamics control fluidity of the developing mouse neuroepithelium}}, doi = {10.1038/s41567-023-01977-w}, volume = {19}, year = {2023}, } @phdthesis{13081, abstract = {During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.}, author = {Bocanegra, Laura}, issn = {2663 - 337X}, pages = {93}, publisher = {Institute of Science and Technology Austria}, title = {{Epithelial dynamics during mouse neural tube development}}, doi = {10.15479/at:ista:13081}, year = {2023}, } @article{12863, abstract = {In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.}, author = {Filipović Marijić, Vlatka and Krasnici, Nesrete and Valić, Damir and Kapetanović, Damir and Vardić Smrzlić, Irena and Jordanova, Maja and Rebok, Katerina and Ramani, Sheriban and Kostov, Vasil and Nastova, Rodne and Dragun, Zrinka}, issn = {1614-7499}, journal = {Environmental Science and Pollution Research}, pages = {63510--63521}, publisher = {Springer Nature}, title = {{Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish}}, doi = {10.1007/s11356-023-26844-2}, volume = {30}, year = {2023}, } @article{12836, abstract = {Coherent control and manipulation of quantum degrees of freedom such as spins forms the basis of emerging quantum technologies. In this context, the robust valley degree of freedom and the associated valley pseudospin found in two-dimensional transition metal dichalcogenides is a highly attractive platform. Valley polarization and coherent superposition of valley states have been observed in these systems even up to room temperature. Control of valley coherence is an important building block for the implementation of valley qubit. Large magnetic fields or high-power lasers have been used in the past to demonstrate the control (initialization and rotation) of the valley coherent states. Here, the control of layer–valley coherence via strong coupling of valley excitons in bilayer WS2 to microcavity photons is demonstrated by exploiting the pseudomagnetic field arising in optical cavities owing to the transverse electric–transverse magnetic (TE–TM)mode splitting. The use of photonic structures to generate pseudomagnetic fields which can be used to manipulate exciton-polaritons presents an attractive approach to control optical responses without the need for large magnets or high-intensity optical pump powers.}, author = {Khatoniar, Mandeep and Yama, Nicholas and Ghazaryan, Areg and Guddala, Sriram and Ghaemi, Pouyan and Majumdar, Kausik and Menon, Vinod}, issn = {2195-1071}, journal = {Advanced Optical Materials}, number = {13}, publisher = {Wiley}, title = {{Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities}}, doi = {10.1002/adom.202202631}, volume = {11}, year = {2023}, } @article{12959, abstract = {This paper deals with the large-scale behaviour of dynamical optimal transport on Zd -periodic graphs with general lower semicontinuous and convex energy densities. Our main contribution is a homogenisation result that describes the effective behaviour of the discrete problems in terms of a continuous optimal transport problem. The effective energy density can be explicitly expressed in terms of a cell formula, which is a finite-dimensional convex programming problem that depends non-trivially on the local geometry of the discrete graph and the discrete energy density. Our homogenisation result is derived from a Γ -convergence result for action functionals on curves of measures, which we prove under very mild growth conditions on the energy density. We investigate the cell formula in several cases of interest, including finite-volume discretisations of the Wasserstein distance, where non-trivial limiting behaviour occurs.}, author = {Gladbach, Peter and Kopfer, Eva and Maas, Jan and Portinale, Lorenzo}, issn = {1432-0835}, journal = {Calculus of Variations and Partial Differential Equations}, number = {5}, publisher = {Springer Nature}, title = {{Homogenisation of dynamical optimal transport on periodic graphs}}, doi = {10.1007/s00526-023-02472-z}, volume = {62}, year = {2023}, } @article{12915, abstract = {Cu2–xS and Cu2–xSe have recently been reported as promising thermoelectric (TE) materials for medium-temperature applications. In contrast, Cu2–xTe, another member of the copper chalcogenide family, typically exhibits low Seebeck coefficients that limit its potential to achieve a superior thermoelectric figure of merit, zT, particularly in the low-temperature range where this material could be effective. To address this, we investigated the TE performance of Cu1.5–xTe–Cu2Se nanocomposites by consolidating surface-engineered Cu1.5Te nanocrystals. This surface engineering strategy allows for precise adjustment of Cu/Te ratios and results in a reversible phase transition at around 600 K in Cu1.5–xTe–Cu2Se nanocomposites, as systematically confirmed by in situ high-temperature X-ray diffraction combined with differential scanning calorimetry analysis. The phase transition leads to a conversion from metallic-like to semiconducting-like TE properties. Additionally, a layer of Cu2Se generated around Cu1.5–xTe nanoparticles effectively inhibits Cu1.5–xTe grain growth, minimizing thermal conductivity and decreasing hole concentration. These properties indicate that copper telluride based compounds have a promising thermoelectric potential, translated into a high dimensionless zT of 1.3 at 560 K.}, author = {Xing, Congcong and Zhang, Yu and Xiao, Ke and Han, Xu and Liu, Yu and Nan, Bingfei and Ramon, Maria Garcia and Lim, Khak Ho and Li, Junshan and Arbiol, Jordi and Poudel, Bed and Nozariasbmarz, Amin and Li, Wenjie and Ibáñez, Maria and Cabot, Andreu}, issn = {1936-086X}, journal = {ACS Nano}, number = {9}, pages = {8442--8452}, publisher = {American Chemical Society}, title = {{Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites}}, doi = {10.1021/acsnano.3c00495}, volume = {17}, year = {2023}, } @article{12961, abstract = {Two notes separated by a doubling in frequency sound similar to humans. This “octave equivalence” is critical to perception and production of music and speech and occurs early in human development. Because it also occurs cross-culturally, a biological basis of octave equivalence has been hypothesized. Members of our team previousy suggested four human traits are at the root of this phenomenon: (1) vocal learning, (2) clear octave information in vocal harmonics, (3) differing vocal ranges, and (4) vocalizing together. Using cross-species studies, we can test how relevant these respective traits are, while controlling for enculturation effects and addressing questions of phylogeny. Common marmosets possess forms of three of the four traits, lacking differing vocal ranges. We tested 11 common marmosets by adapting an established head-turning paradigm, creating a parallel test to an important infant study. Unlike human infants, marmosets responded similarly to tones shifted by an octave or other intervals. Because previous studies with the same head-turning paradigm produced differential results to discernable acoustic stimuli in common marmosets, our results suggest that marmosets do not perceive octave equivalence. Our work suggests differing vocal ranges between adults and children and men and women and the way they are used in singing together may be critical to the development of octave equivalence.}, author = {Wagner, Bernhard and Šlipogor, Vedrana and Oh, Jinook and Varga, Marion and Hoeschele, Marisa}, issn = {1467-7687}, journal = {Developmental Science}, number = {5}, publisher = {Wiley}, title = {{A comparison between common marmosets (Callithrix jacchus) and human infants sheds light on traits proposed to be at the root of human octave equivalence}}, doi = {10.1111/desc.13395}, volume = {26}, year = {2023}, } @article{12877, abstract = {We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table.}, author = {De Simoi, Jacopo and Kaloshin, Vadim and Leguil, Martin}, issn = {1432-1297}, journal = {Inventiones Mathematicae}, pages = {829--901}, publisher = {Springer Nature}, title = {{Marked Length Spectral determination of analytic chaotic billiards with axial symmetries}}, doi = {10.1007/s00222-023-01191-8}, volume = {233}, year = {2023}, } @article{12349, abstract = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.}, author = {Gupta, Divyansh and Mlynarski, Wiktor F and Sumser, Anton L and Symonova, Olga and Svaton, Jan and Jösch, Maximilian A}, issn = {1546-1726}, journal = {Nature Neuroscience}, pages = {606--614}, publisher = {Springer Nature}, title = {{Panoramic visual statistics shape retina-wide organization of receptive fields}}, doi = {10.1038/s41593-023-01280-0}, volume = {26}, year = {2023}, } @misc{12370, abstract = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. }, author = {Gupta, Divyansh and Sumser, Anton L and Jösch, Maximilian A}, publisher = {Institute of Science and Technology Austria}, title = {{Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields}}, doi = {10.15479/AT:ISTA:12370}, year = {2023}, } @article{12829, abstract = {The deployment of direct formate fuel cells (DFFCs) relies on the development of active and stable catalysts for the formate oxidation reaction (FOR). Palladium, providing effective full oxidation of formate to CO2, has been widely used as FOR catalyst, but it suffers from low stability, moderate activity, and high cost. Herein, we detail a colloidal synthesis route for the incorporation of P on Pd2Sn nanoparticles. These nanoparticles are dispersed on carbon black and the obtained composite is used as electrocatalytic material for the FOR. The Pd2Sn0.8P-based electrodes present outstanding catalytic activities with record mass current densities up to 10.0 A mgPd-1, well above those of Pd1.6Sn/C reference electrode. These high current densities are further enhanced by increasing the temperature from 25 °C to 40 °C. The Pd2Sn0.8P electrode also allows for slowing down the rapid current decay that generally happens during operation and can be rapidly re-activated through potential cycling. The excellent catalytic performance obtained is rationalized using density functional theory (DFT) calculations.}, author = {Montaña-Mora, Guillem and Qi, Xueqiang and Wang, Xiang and Chacón-Borrero, Jesus and Martinez-Alanis, Paulina R. and Yu, Xiaoting and Li, Junshan and Xue, Qian and Arbiol, Jordi and Ibáñez, Maria and Cabot, Andreu}, issn = {1572-6657}, journal = {Journal of Electroanalytical Chemistry}, publisher = {Elsevier}, title = {{Phosphorous incorporation into palladium tin nanoparticles for the electrocatalytic formate oxidation reaction}}, doi = {10.1016/j.jelechem.2023.117369}, volume = {936}, year = {2023}, } @article{12764, abstract = {We study a new discretization of the Gaussian curvature for polyhedral surfaces. This discrete Gaussian curvature is defined on each conical singularity of a polyhedral surface as the quotient of the angle defect and the area of the Voronoi cell corresponding to the singularity. We divide polyhedral surfaces into discrete conformal classes using a generalization of discrete conformal equivalence pioneered by Feng Luo. We subsequently show that, in every discrete conformal class, there exists a polyhedral surface with constant discrete Gaussian curvature. We also provide explicit examples to demonstrate that this surface is in general not unique.}, author = {Kourimska, Hana}, issn = {1432-0444}, journal = {Discrete and Computational Geometry}, pages = {123--153}, publisher = {Springer Nature}, title = {{Discrete yamabe problem for polyhedral surfaces}}, doi = {10.1007/s00454-023-00484-2}, volume = {70}, year = {2023}, } @phdthesis{13331, abstract = {The extension of extremal combinatorics to the setting of exterior algebra is a work in progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms. }, author = {Köse, Seyda}, issn = {2791-4585}, pages = {26}, publisher = {Institute of Science and Technology Austria}, title = {{Exterior algebra and combinatorics}}, doi = {10.15479/at:ista:13331}, year = {2023}, } @article{12765, abstract = {Animals exhibit a variety of behavioural defences against socially transmitted parasites. These defences evolved to increase host fitness by avoiding, resisting or tolerating infection. Because they can occur in both infected individuals and their uninfected social partners, these defences often have important consequences for the social group. Here, we discuss the evolution and ecology of anti-parasite behavioural defences across a taxonomically wide social spectrum, considering colonial groups, stable groups, transitional groups and solitary animals. We discuss avoidance, resistance and tolerance behaviours across these social group structures, identifying how social complexity, group composition and interdependent social relationships may contribute to the expression and evolution of behavioural strategies. Finally, we outline avenues for further investigation such as approaches to quantify group-level responses, and the connection of the physiological and behavioural response to parasites in different social contexts.}, author = {Stockmaier, Sebastian and Ulrich, Yuko and Albery, Gregory F. and Cremer, Sylvia and Lopes, Patricia C.}, issn = {1365-2435}, journal = {Functional Ecology}, number = {4}, pages = {809--820}, publisher = {British Ecological Society}, title = {{Behavioural defences against parasites across host social structures}}, doi = {10.1111/1365-2435.14310}, volume = {37}, year = {2023}, } @article{12680, abstract = {The celebrated Erdős–Ko–Rado theorem about the maximal size of an intersecting family of r-element subsets of was extended to the setting of exterior algebra in [5, Theorem 2.3] and in [6, Theorem 1.4]. However, the equality case has not been settled yet. In this short note, we show that the extension of the Erdős–Ko–Rado theorem and the characterization of the equality case therein, as well as those of the Hilton–Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms follow from a folklore puzzle about possible arrangements of an intersecting family of lines.}, author = {Ivanov, Grigory and Köse, Seyda}, issn = {0012-365X}, journal = {Discrete Mathematics}, number = {6}, publisher = {Elsevier}, title = {{Erdős-Ko-Rado and Hilton-Milner theorems for two-forms}}, doi = {10.1016/j.disc.2023.113363}, volume = {346}, year = {2023}, } @article{12792, abstract = {In the physics literature the spectral form factor (SFF), the squared Fourier transform of the empirical eigenvalue density, is the most common tool to test universality for disordered quantum systems, yet previous mathematical results have been restricted only to two exactly solvable models (Forrester in J Stat Phys 183:33, 2021. https://doi.org/10.1007/s10955-021-02767-5, Commun Math Phys 387:215–235, 2021. https://doi.org/10.1007/s00220-021-04193-w). We rigorously prove the physics prediction on SFF up to an intermediate time scale for a large class of random matrices using a robust method, the multi-resolvent local laws. Beyond Wigner matrices we also consider the monoparametric ensemble and prove that universality of SFF can already be triggered by a single random parameter, supplementing the recently proven Wigner–Dyson universality (Cipolloni et al. in Probab Theory Relat Fields, 2021. https://doi.org/10.1007/s00440-022-01156-7) to larger spectral scales. Remarkably, extensive numerics indicates that our formulas correctly predict the SFF in the entire slope-dip-ramp regime, as customarily called in physics.}, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, pages = {1665--1700}, publisher = {Springer Nature}, title = {{On the spectral form factor for random matrices}}, doi = {10.1007/s00220-023-04692-y}, volume = {401}, year = {2023}, } @article{12709, abstract = {Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness.}, author = {Corbet, René and Kerber, Michael and Lesnick, Michael and Osang, Georg F}, issn = {1432-0444}, journal = {Discrete and Computational Geometry}, pages = {376--405}, publisher = {Springer Nature}, title = {{Computing the multicover bifiltration}}, doi = {10.1007/s00454-022-00476-8}, volume = {70}, year = {2023}, } @article{12763, abstract = {Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift 176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann’s and Bangert’s extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality.}, author = {Boissonnat, Jean Daniel and Wintraecken, Mathijs}, issn = {2367-1734}, journal = {Journal of Applied and Computational Topology}, pages = {619--641}, publisher = {Springer Nature}, title = {{The reach of subsets of manifolds}}, doi = {10.1007/s41468-023-00116-x}, volume = {7}, year = {2023}, } @inproceedings{13221, abstract = {The safety-liveness dichotomy is a fundamental concept in formal languages which plays a key role in verification. Recently, this dichotomy has been lifted to quantitative properties, which are arbitrary functions from infinite words to partially-ordered domains. We look into harnessing the dichotomy for the specific classes of quantitative properties expressed by quantitative automata. These automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totallyordered domain of real numbers. In this automata-theoretic setting, we establish a connection between quantitative safety and topological continuity and provide an alternative characterization of quantitative safety and liveness in terms of their boolean counterparts. For all common value functions, we show how the safety closure of a quantitative automaton can be constructed in PTime, and we provide PSpace-complete checks of whether a given quantitative automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata, for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf, and LimSup automata, we give PTime decompositions into safe and live automata. These decompositions enable the separation of techniques for safety and liveness verification for quantitative specifications.}, author = {Boker, Udi and Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, booktitle = {34th International Conference on Concurrency Theory}, isbn = {9783959772990}, issn = {1868-8969}, location = {Antwerp, Belgium}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Safety and liveness of quantitative automata}}, doi = {10.4230/LIPIcs.CONCUR.2023.17}, volume = {279}, year = {2023}, } @article{14406, abstract = {Recently, a concept of generalized multifractality, which characterizes fluctuations and correlations of critical eigenstates, was introduced and explored for all 10 symmetry classes of disordered systems. Here, by using the nonlinear sigma-model ( NL σ M ) field theory, we extend the theory of generalized multifractality to boundaries of systems at criticality. Our numerical simulations on two-dimensional systems of symmetry classes A, C, and AII fully confirm the analytical predictions of pure-scaling observables and Weyl symmetry relations between critical exponents of surface generalized multifractality. This demonstrates the validity of the NL σ M for the description of Anderson-localization critical phenomena, not only in the bulk but also on the boundary. The critical exponents strongly violate generalized parabolicity, in analogy with earlier results for the bulk, corroborating the conclusion that the considered Anderson-localization critical points are not described by conformal field theories. We further derive relations between generalized surface multifractal spectra and linear combinations of Lyapunov exponents of a strip in quasi-one-dimensional geometry, which hold under the assumption of invariance with respect to a logarithmic conformal map. Our numerics demonstrate that these relations hold with an excellent accuracy. Taken together, our results indicate an intriguing situation: the conformal invariance is broken but holds partially at critical points of Anderson localization.}, author = {Babkin, Serafim and Karcher, Jonas F. and Burmistrov, Igor S. and Mirlin, Alexander D.}, issn = {2469-9969}, journal = {Physical Review B}, number = {10}, publisher = {American Physical Society}, title = {{Generalized surface multifractality in two-dimensional disordered systems}}, doi = {10.1103/PhysRevB.108.104205}, volume = {108}, year = {2023}, } @inproceedings{14410, abstract = {This paper focuses on the implementation details of the baseline methods and a recent lightweight conditional model extrapolation algorithm LIMES [5] for streaming data under class-prior shift. LIMES achieves superior performance over the baseline methods, especially concerning the minimum-across-day accuracy, which is important for the users of the system. In this work, the key measures to facilitate reproducibility and enhance the credibility of the results are described.}, author = {Tomaszewska, Paulina and Lampert, Christoph}, booktitle = {International Workshop on Reproducible Research in Pattern Recognition}, isbn = {9783031407727}, issn = {1611-3349}, location = {Montreal, Canada}, pages = {67--73}, publisher = {Springer Nature}, title = {{On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift}}, doi = {10.1007/978-3-031-40773-4_6}, volume = {14068}, year = {2023}, } @inproceedings{14405, abstract = {We introduce hypernode automata as a new specification formalism for hyperproperties of concurrent systems. They are finite automata with nodes labeled with hypernode logic formulas and transitions labeled with actions. A hypernode logic formula specifies relations between sequences of variable values in different system executions. Unlike HyperLTL, hypernode logic takes an asynchronous view on execution traces by constraining the values and the order of value changes of each variable without correlating the timing of the changes. Different execution traces are synchronized solely through the transitions of hypernode automata. Hypernode automata naturally combine asynchronicity at the node level with synchronicity at the transition level. We show that the model-checking problem for hypernode automata is decidable over action-labeled Kripke structures, whose actions induce transitions of the specification automata. For this reason, hypernode automaton is a suitable formalism for specifying and verifying asynchronous hyperproperties, such as declassifying observational determinism in multi-threaded programs.}, author = {Bartocci, Ezio and Henzinger, Thomas A and Nickovic, Dejan and Oliveira da Costa, Ana}, booktitle = {34th International Conference on Concurrency Theory}, isbn = {9783959772990}, issn = {18688969}, location = {Antwerp, Belgium}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Hypernode automata}}, doi = {10.4230/LIPIcs.CONCUR.2023.21}, volume = {279}, year = {2023}, } @article{14408, abstract = {We prove that the mesoscopic linear statistics ∑if(na(σi−z0)) of the eigenvalues {σi}i of large n×n non-Hermitian random matrices with complex centred i.i.d. entries are asymptotically Gaussian for any H20-functions f around any point z0 in the bulk of the spectrum on any mesoscopic scale 0