@article{12291,
  abstract     = {The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.},
  author       = {Friml, Jiří and Gallei, Michelle C and Gelová, Zuzana and Johnson, Alexander J and Mazur, Ewa and Monzer, Aline and Rodriguez Solovey, Lesia and Roosjen, Mark and Verstraeten, Inge and Živanović, Branka D. and Zou, Minxia and Fiedler, Lukas and Giannini, Caterina and Grones, Peter and Hrtyan, Mónika and Kaufmann, Walter and Kuhn, Andre and Narasimhan, Madhumitha and Randuch, Marek and Rýdza, Nikola and Takahashi, Koji and Tan, Shutang and Teplova, Anastasiia and Kinoshita, Toshinori and Weijers, Dolf and Rakusová, Hana},
  issn         = {1476-4687},
  journal      = {Nature},
  number       = {7927},
  pages        = {575--581},
  publisher    = {Springer Nature},
  title        = {{ABP1–TMK auxin perception for global phosphorylation and auxin canalization}},
  doi          = {10.1038/s41586-022-05187-x},
  volume       = {609},
  year         = {2022},
}

@article{12307,
  abstract     = {Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences.},
  author       = {Shipman, Barbara A. and Stephenson, Elizabeth R},
  issn         = {1935-4053},
  journal      = {PRIMUS},
  keywords     = {Education, General Mathematics},
  number       = {5},
  pages        = {593--609},
  publisher    = {Taylor & Francis},
  title        = {{Tangible topology through the lens of limits}},
  doi          = {10.1080/10511970.2021.1872750},
  volume       = {32},
  year         = {2022},
}

@phdthesis{12358,
  abstract     = {The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and
visual complexity. The small-scale interactions of yarns colliding with and pulling on each
other result in drastically different large-scale stretching and bending behavior, introducing
anisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this
complexity and match the quality of real fabric, it may be too computationally expensive for
large fabrics. On the other hand, continuum-based approaches do not need to discretize the
cloth at a stitch-level, but it is non-trivial to find a material model that would replicate the
large-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,
we discuss three methods to try and bridge the gap between small-scale and large-scale yarn
mechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively
fitting yarn parameters to physical measurements of real fabric.
To start, we present a method for animating yarn-level cloth effects using a thin-shell solver.
We first use a large number of periodic yarn-level simulations to build a model of the potential
energy density of the cloth, and then use it to compute forces in a thin-shell simulator. The
resulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics
and the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of
full yarn-level simulation.
While our thin-shell simulations are able to capture large-scale yarn mechanics, they lack
the rich visual detail of yarn-level simulations. Therefore, we propose a method to animate
yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware
fashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are
able to reproduce effects such as knit loops tightening under stretching at negligible cost.
Finally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,
based on the mechanical response of fabrics in the real world. We compile a database from
physical tests of several knitted fabrics used in the textile industry spanning diverse physical
properties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized
shell models to speed up computation and adding some small-but-necessary extensions to
yarn-level models used in computer graphics.
},
  author       = {Sperl, Georg},
  isbn         = {978-3-99078-020-6},
  issn         = {2663-337X},
  pages        = {138},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting}},
  doi          = {10.15479/at:ista:12103},
  year         = {2022},
}

@phdthesis{12368,
  abstract     = {Metazoan development relies on the formation and remodeling of cell-cell contacts. The 
binding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell 
interaction sites have been implicated in cell-cell contact formation. Yet, how these two 
processes functionally interact to drive cell-cell contact expansion and strengthening 
remains unclear. Here, we study how primary germ layer progenitor cells from zebrafish 
bind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an 
assay system for monitoring cell-cell contact formation at high spatiotemporal resolution. 
We show that cell-cell contact formation represents a two-tiered process: E-cadherinmediated downregulation of the small GTPase RhoA at the forming contact leads to both 
depletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin 
network flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the 
contact zone, with Myosin-2 displaying higher cortical localization outside than inside of 
the contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin 
network at the contact disc, but also lead to an accumulation of both F-actin and Ecadherin at the contact rim. Eventually, this combination of actomyosin downregulation 
and flows at the contact contribute to the characteristic molecular organization implicated 
in contact formation and maintenance: depletion of cortical actomyosin at the contact disc, 
driving contact expansion by lowering interfacial tension at the contact, and accumulation 
of both E-cadherin and F-actin at the contact rim, mechanically linking the contractile 
cortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how 
adhesion signaling and cell mechanics function together to modulate the spatial 
organization of cell-cell contacts.},
  author       = {Arslan, Feyza N},
  isbn         = {978-3-99078-025-1 },
  issn         = {2663-337X},
  pages        = {113},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Remodeling of E-cadherin-mediated contacts via cortical  flows}},
  doi          = {10.15479/at:ista:12153},
  year         = {2022},
}

@phdthesis{12390,
  abstract     = {The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that
is broken on the level of the corresponding effective theory. In particular we are going to
investigate translation-invariant Bose gases in the mean field limit, effectively described by
the Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively
described by the Pekar functional. The latter is a model describing the interaction between a
charged particle and the optical modes of a polar crystal. Regarding the former, we assume in
addition that the particles in the gas are unconfined, and typically we will consider particles
that are subject to an attractive interaction. In both cases the ground state energy of the
Hamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on
the contrary there exists a whole invariant orbit of minimizers for the corresponding effective
functionals. Both, the absence of proper eigenstates and the broken symmetry of the effective
theory, make the study significantly more involved and it is the content of this thesis to
develop a frameworks which allows for a systematic way to circumvent these issues.
It is a well-established result that the ground state energy of Bose gases in the mean field limit,
as well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is
to leading order given by the minimal energy of the corresponding effective theory. As part
of this thesis we identify the sub-leading term in the expansion of the ground state energy,
which can be interpreted as the quantum correction to the classical energy, since the effective
theories under consideration can be seen as classical counterparts.
We are further going to establish an asymptotic expression for the energy-momentum relation
of the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,
this asymptotic expression agrees with the energy-momentum relation of a free particle having
an effectively increased mass, and we find that this effectively increased mass agrees with the
conjectured value in the physics literature.
In addition we will discuss two unrelated papers written by the author during his stay at ISTA
in the appendix. The first one concerns the realization of anyons, which are quasi-particles
acquiring a non-trivial phase under the exchange of two particles, as molecular impurities.
The second one provides a classification of those vector fields defined on a given manifold
that can be written as the gradient of a given functional with respect to a suitable metric,
provided that some mild smoothness assumptions hold. This classification is subsequently
used to identify those quantum Markov semigroups that can be written as a gradient flow of
the relative entropy.
},
  author       = {Brooks, Morris},
  issn         = {2663-337X},
  pages        = {196},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Translation-invariant quantum systems with effectively broken symmetry}},
  doi          = {10.15479/at:ista:12390},
  year         = {2022},
}

@unpublished{12677,
  abstract     = {In modern sample-driven Prophet Inequality, an adversary chooses a sequence of n items with values v1,v2,…,vn to be presented to a decision maker (DM). The process follows in two phases. In the first phase (sampling phase), some items, possibly selected at random, are revealed to the DM, but she can never accept them. In the second phase, the DM is presented with the other items in a random order and online fashion. For each item, she must make an irrevocable decision to either accept the item and stop the process or reject the item forever and proceed to the next item. The goal of the DM is to maximize the expected value as compared to a Prophet (or offline algorithm) that has access to all information. In this setting, the sampling phase has no cost and is not part of the optimization process. However, in many scenarios, the samples are obtained as part of the decision-making process.
We model this aspect as a two-phase Prophet Inequality where an adversary chooses a sequence of 2n items with values v1,v2,…,v2n and the items are randomly ordered. Finally, there are two phases of the Prophet Inequality problem with the first n-items and the rest of the items, respectively. We show that some basic algorithms achieve a ratio of at most 0.450. We present an algorithm that achieves a ratio of at least 0.495. Finally, we show that for every algorithm the ratio it can achieve is at most 0.502. Hence our algorithm is near-optimal.},
  author       = {Chatterjee, Krishnendu and Mohammadi, Mona and Saona Urmeneta, Raimundo J},
  booktitle    = {arXiv},
  title        = {{Repeated prophet inequality with near-optimal bounds}},
  doi          = {10.48550/ARXIV.2209.14368},
  year         = {2022},
}

@unpublished{12750,
  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 a 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 universality classes of dynamics and invite their further theoretical and experimental studies.},
  author       = {Brighi, Pietro and Ljubotina, Marko and Serbyn, Maksym},
  booktitle    = {arXiv},
  title        = {{Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models}},
  doi          = {10.48550/arXiv.2210.15607},
  year         = {2022},
}

@unpublished{12860,
  abstract     = {Memorization of the relation between entities in a dataset can lead to privacy issues when using a trained model for question answering. We introduce Relational Memorization (RM) to understand, quantify and control this phenomenon. While bounding general memorization can have detrimental effects on the performance of a trained model, bounding RM does not prevent effective learning. The difference is most pronounced when the data distribution is long-tailed, with many queries having only few training examples: Impeding general memorization prevents effective learning, while impeding only relational memorization still allows learning general properties of the underlying concepts. We formalize the notion of Relational Privacy (RP) and, inspired by Differential Privacy (DP), we provide a possible definition of Differential Relational Privacy (DrP). These notions can be used to describe and compute bounds on the amount of RM in a trained model. We illustrate Relational Privacy concepts in experiments with large-scale models for Question Answering.},
  author       = {Bombari, Simone and Achille, Alessandro and Wang, Zijian and Wang, Yu-Xiang and Xie, Yusheng and Singh, Kunwar Yashraj and Appalaraju, Srikar and Mahadevan, Vijay and Soatto, Stefano},
  booktitle    = {arXiv},
  title        = {{Towards differential relational privacy and its use in question answering}},
  doi          = {10.48550/arXiv.2203.16701},
  year         = {2022},
}

@article{14355,
  abstract     = {Purpose: The mediator (MED) multisubunit-complex modulates the activity of the transcriptional machinery, and genetic defects in different MED subunits (17, 20, 27) have been implicated in neurologic diseases. In this study, we identified a recurrent homozygous variant in MED11 (c.325C>T; p.Arg109Ter) in 7 affected individuals from 5 unrelated families. Methods: To investigate the genetic cause of the disease, exome or genome sequencing were performed in 5 unrelated families identified via different research networks and Matchmaker Exchange. Deep clinical and brain imaging evaluations were performed by clinical pediatric neurologists and neuroradiologists. The functional effect of the candidate variant on both MED11 RNA and protein was assessed using reverse transcriptase polymerase chain reaction and western blotting using fibroblast cell lines derived from 1 affected individual and controls and through computational approaches. Knockouts in zebrafish were generated using clustered regularly interspaced short palindromic repeats/Cas9. Results: The disease was characterized by microcephaly, profound neurodevelopmental impairment, exaggerated startle response, myoclonic seizures, progressive widespread neurodegeneration, and premature death. Functional studies on patient-derived fibroblasts did not show a loss of protein function but rather disruption of the C-terminal of MED11, likely impairing binding to other MED subunits. A zebrafish knockout model recapitulates key clinical phenotypes. Conclusion: Loss of the C-terminal of MED subunit 11 may affect its binding efficiency to other MED subunits, thus implicating the MED-complex stability in brain development and neurodegeneration. (C) 2022 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics.},
  author       = {Cali, Elisa and Lin, Sheng-Jia and Rocca, Clarissa and Sahin, Yavuz and Al Shamsi, Aisha and El Chehadeh, Salima and Chaabouni, Myriam and Mankad, Kshitij and Galanaki, Evangelia and Efthymiou, Stephanie and Sudhakar, Sniya and Athanasiou-Fragkouli, Alkyoni and Celik, Tamer and Narli, Nejat and Bianca, Sebastiano and Murphy, David and Moreira, Francisco Martins De Carvalho and Accogli, Andrea and Petree, Cassidy and Huang, Kevin and Monastiri, Kamel and Edizadeh, Masoud and Nardello, Rosaria and Ognibene, Marzia and De Marco, Patrizia and Ruggieri, Martino and Zara, Federico and Striano, Pasquale and Sahin, Yavuz and Al-Gazali, Lihadh and Warde, Marie Therese Abi and Gerard, Benedicte and Zifarelli, Giovanni and Beetz, Christian and Fortuna, Sara and Soler, Miguel and Valente, Enza Maria and Varshney, Gaurav and Maroofian, Reza and Salpietro, Vincenzo and Houlden, Henry and Grp, SYNaPS Study},
  issn         = {1098-3600},
  journal      = {Genetics in Medicine},
  keywords     = {Human mediator complex, MED11, MEDopathies},
  number       = {10},
  pages        = {2194--2203},
  publisher    = {Elsevier},
  title        = {{A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease}},
  doi          = {10.1016/j.gim.2022.07.013},
  volume       = {24},
  year         = {2022},
}

@unpublished{17157,
  abstract     = {An action of a complex reductive group G on a smooth projective variety X is regular when all regular unipotent elements in G act with finitely many fixed points. Then the complex G-equivariant cohomology ring of X is isomorphic to the coordinate ring of a certain regular fixed point scheme. Examples include partial flag varieties, smooth Schubert varieties and Bott-Samelson varieties. We also show that a more general version of the fixed point scheme allows a generalisation to GKM spaces, such as toric varieties.},
  author       = {Hausel, Tamás and Rychlewicz, Kamil P},
  booktitle    = {arXiv},
  title        = {{Spectrum of equivariant cohomology as a fixed point scheme}},
  doi          = {10.48550/arXiv.2212.11836},
  year         = {2022},
}

@article{10600,
  abstract     = {We show that recent results on adiabatic theory for interacting gapped many-body systems on finite lattices remain valid in the thermodynamic limit. More precisely, we prove a generalized super-adiabatic theorem for the automorphism group describing the infinite volume dynamics on the quasi-local algebra of observables. The key assumption is the existence of a sequence of gapped finite volume Hamiltonians, which generates the same infinite volume dynamics in the thermodynamic limit. Our adiabatic theorem also holds for certain perturbations of gapped ground states that close the spectral gap (so it is also an adiabatic theorem for resonances and, in this sense, “generalized”), and it provides an adiabatic approximation to all orders in the adiabatic parameter (a property often called “super-adiabatic”). In addition to the existing results for finite lattices, we also perform a resummation of the adiabatic expansion and allow for observables that are not strictly local. Finally, as an application, we prove the validity of linear and higher order response theory for our class of perturbations for infinite systems. While we consider the result and its proof as new and interesting in itself, we also lay the foundation for the proof of an adiabatic theorem for systems with a gap only in the bulk, which will be presented in a follow-up article.},
  author       = {Henheik, Sven Joscha and Teufel, Stefan},
  issn         = {1089-7658},
  journal      = {Journal of Mathematical Physics},
  keywords     = {mathematical physics, statistical and nonlinear physics},
  number       = {1},
  publisher    = {AIP Publishing},
  title        = {{Adiabatic theorem in the thermodynamic limit: Systems with a uniform gap}},
  doi          = {10.1063/5.0051632},
  volume       = {63},
  year         = {2022},
}

@article{10623,
  abstract     = {We investigate the BCS critical temperature Tc in the high-density limit and derive an asymptotic formula, which strongly depends on the behavior of the interaction potential V on the Fermi-surface. Our results include a rigorous confirmation for the behavior of Tc at high densities proposed by Langmann et al. (Phys Rev Lett 122:157001, 2019) and identify precise conditions under which superconducting domes arise in BCS theory.},
  author       = {Henheik, Sven Joscha},
  issn         = {1572-9656},
  journal      = {Mathematical Physics, Analysis and Geometry},
  keywords     = {geometry and topology, mathematical physics},
  number       = {1},
  publisher    = {Springer Nature},
  title        = {{The BCS critical temperature at high density}},
  doi          = {10.1007/s11040-021-09415-0},
  volume       = {25},
  year         = {2022},
}

@article{10642,
  abstract     = {Based on a result by Yarotsky (J Stat Phys 118, 2005), we prove that localized but otherwise arbitrary perturbations of weakly interacting quantum spin systems with uniformly gapped on-site terms change the ground state of such a system only locally, even if they close the spectral gap. We call this a strong version of the local perturbations perturb locally (LPPL) principle which is known to hold for much more general gapped systems, but only for perturbations that do not close the spectral gap of the Hamiltonian. We also extend this strong LPPL-principle to Hamiltonians that have the appropriate structure of gapped on-site terms and weak interactions only locally in some region of space. While our results are technically corollaries to a theorem of Yarotsky, we expect that the paradigm of systems with a locally gapped ground state that is completely insensitive to the form of the Hamiltonian elsewhere extends to other situations and has important physical consequences.},
  author       = {Henheik, Sven Joscha and Teufel, Stefan and Wessel, Tom},
  issn         = {1573-0530},
  journal      = {Letters in Mathematical Physics},
  keywords     = {mathematical physics, statistical and nonlinear physics},
  number       = {1},
  publisher    = {Springer Nature},
  title        = {{Local stability of ground states in locally gapped and weakly interacting quantum spin systems}},
  doi          = {10.1007/s11005-021-01494-y},
  volume       = {112},
  year         = {2022},
}

@article{10643,
  abstract     = {We prove a generalised super-adiabatic theorem for extended fermionic systems assuming a spectral gap only in the bulk. More precisely, we assume that the infinite system has a unique ground state and that the corresponding Gelfand–Naimark–Segal Hamiltonian has a spectral gap above its eigenvalue zero. Moreover, we show that a similar adiabatic theorem also holds in the bulk of finite systems up to errors that vanish faster than any inverse power of the system size, although the corresponding finite-volume Hamiltonians need not have a spectral gap.

},
  author       = {Henheik, Sven Joscha and Teufel, Stefan},
  issn         = {2050-5094},
  journal      = {Forum of Mathematics, Sigma},
  keywords     = {computational mathematics, discrete mathematics and combinatorics, geometry and topology, mathematical physics, statistics and probability, algebra and number theory, theoretical computer science, analysis},
  publisher    = {Cambridge University Press},
  title        = {{Adiabatic theorem in the thermodynamic limit: Systems with a gap in the bulk}},
  doi          = {10.1017/fms.2021.80},
  volume       = {10},
  year         = {2022},
}

@article{10658,
  abstract     = {We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.},
  author       = {Sachdeva, Himani and Olusanya, Oluwafunmilola O and Barton, Nicholas H},
  issn         = {1471-2970},
  journal      = {Philosophical Transactions of the Royal Society B},
  number       = {1846},
  publisher    = {The Royal Society},
  title        = {{Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity}},
  doi          = {10.1098/rstb.2021.0010},
  volume       = {377},
  year         = {2022},
}

@phdthesis{10759,
  abstract     = {In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data.},
  author       = {Rzadkowski, Wojciech},
  issn         = {2663-337X},
  pages        = {120},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Analytic and machine learning approaches to composite quantum impurities}},
  doi          = {10.15479/at:ista:10759},
  year         = {2022},
}

@article{10787,
  abstract     = {A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.
This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.},
  author       = {Barton, Nicholas H and Olusanya, Oluwafunmilola O},
  issn         = {1471-2970},
  journal      = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  keywords     = {General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology},
  number       = {1848},
  publisher    = {The Royal Society},
  title        = {{The response of a metapopulation to a changing environment}},
  doi          = {10.1098/rstb.2021.0009},
  volume       = {377},
  year         = {2022},
}

@phdthesis{10799,
  abstract     = {Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the
sake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range
of training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the
data they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting.},
  author       = {Konstantinov, Nikola H},
  isbn         = {978-3-99078-015-2},
  issn         = {2663-337X},
  keywords     = {robustness, fairness, machine learning, PAC learning, adversarial learning},
  pages        = {176},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Robustness and fairness in machine learning}},
  doi          = {10.15479/at:ista:10799},
  year         = {2022},
}

@article{9311,
  abstract     = {Partially observable Markov decision processes (POMDPs) are standard models for dynamic systems with probabilistic and nondeterministic behaviour in uncertain environments. We prove that in POMDPs with long-run average objective, the decision maker has approximately optimal strategies with finite memory. This implies notably that approximating the long-run value is recursively enumerable, as well as a weak continuity property of the value with respect to the transition function. },
  author       = {Chatterjee, Krishnendu and Saona Urmeneta, Raimundo J and Ziliotto, Bruno},
  issn         = {1526-5471},
  journal      = {Mathematics of Operations Research},
  keywords     = {Management Science and Operations Research, General Mathematics, Computer Science Applications},
  number       = {1},
  pages        = {100--119},
  publisher    = {Institute for Operations Research and the Management Sciences},
  title        = {{Finite-memory strategies in POMDPs with long-run average objectives}},
  doi          = {10.1287/moor.2020.1116},
  volume       = {47},
  year         = {2022},
}

@phdthesis{11196,
  abstract     = {One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). 
	In addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.
},
  author       = {Kim, Olena},
  issn         = {2663-337X},
  pages        = {132},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses}},
  doi          = {10.15479/at:ista:11196},
  year         = {2022},
}