@inproceedings{18255,
  abstract     = {Learning an object detection or retrieval system requires a large data set with manual annotations. Such data sets are expensive and time consuming to create and therefore difficult to obtain on a large scale. In this work, we propose to exploit the natural correlation in narrations and the visual presence of objects in video, to learn an object detector and retrieval without any manual labeling involved. We pose the problem as weakly supervised learning with noisy labels, and propose a novel object detection paradigm under these constraints. We handle the background rejection by using contrastive samples and confront the high level of label noise with a new clustering score. Our evaluation is based on a set of 11 manually annotated objects in over 5000 frames. We show comparison to a weakly-supervised approach as baseline and provide a strongly labeled upper bound.},
  author       = {Amrani, Elad and Ben-Ari, Rami and Hakim, Tal and Bronstein, Alexander},
  booktitle    = {2019 IEEE/CVF International Conference on Computer Vision Workshop (ICCVW)},
  isbn         = {9781728150246},
  issn         = {2473-9944},
  location     = {Seoul, Korea (South)},
  publisher    = {IEEE},
  title        = {{Learning to detect and retrieve objects from unlabeled videos}},
  doi          = {10.1109/iccvw.2019.00567},
  year         = {2020},
}

@inproceedings{18258,
  abstract     = {Distance metric learning (DML) has been successfully applied to object classification, both in the standard regime of rich training data and in the few-shot scenario, where each category is represented by only a few examples. In this work, we propose a new method for DML that simultaneously learns the backbone network parameters, the embedding space, and the multi-modal distribution of each of the training categories in that space, in a single end-to-end training process. Our approach outperforms state-of-the-art methods for DML-based object classification on a variety of standard fine-grained datasets. Furthermore, we demonstrate the effectiveness of our approach on the problem of few-shot object detection, by incorporating the proposed DML architecture as a classification head into a standard object detection model. We achieve the best results on the ImageNet-LOC dataset compared to strong baselines, when only a few training examples are available. We also offer the community a new episodic benchmark based on the ImageNet dataset for the few-shot object detection task.},
  author       = {Karlinsky, Leonid and Shtok, Joseph and Harary, Sivan and Schwartz, Eli and Aides, Amit and Feris, Rogerio and Giryes, Raja and Bronstein, Alexander},
  booktitle    = {2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  isbn         = {9781728132945},
  issn         = {2575-7075},
  location     = {Long Beach, CA, United States},
  publisher    = {IEEE},
  title        = {{Repmet: Representative-based metric learning for classification and few-shot object detection}},
  doi          = {10.1109/cvpr.2019.00534},
  year         = {2020},
}

@inproceedings{18259,
  abstract     = {Example synthesis is one of the leading methods to tackle the problem of few-shot learning, where only a small number of samples per class are available. However, current synthesis approaches only address the scenario of a single category label per image. In this work, we propose a novel technique for synthesizing samples with multiple labels for the (yet unhandled) multi-label few-shot classification scenario. We propose to combine pairs of given examples in feature space, so that the resulting synthesized feature vectors will correspond to examples whose label sets are obtained through certain set operations on the label sets of the corresponding input pairs. Thus, our method is capable of producing a sample containing the intersection, union or set-difference of labels present in two input samples. As we show, these set operations generalize to labels unseen during training. This enables performing augmentation on examples of novel categories, thus, facilitating multi-label few-shot classifier learning. We conduct numerous experiments showing promising results for the label-set manipulation capabilities of the proposed approach, both directly (using the classification and retrieval metrics), and in the context of performing data augmentation for multi-label few-shot learning. We propose a benchmark for this new and challenging task and show that our method compares favorably to all the common baselines.},
  author       = {Alfassy, Amit and Karlinsky, Leonid and Aides, Amit and Shtok, Joseph and Harary, Sivan and Feris, Rogerio and Giryes, Raja and Bronstein, Alexander},
  booktitle    = {2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  isbn         = {9781728132945},
  issn         = {2575-7075},
  location     = {Long Beach, CA, United States},
  publisher    = {IEEE},
  title        = {{Laso: Label-set operations networks for multi-label few-shot learning}},
  doi          = {10.1109/cvpr.2019.00671},
  year         = {2020},
}

@inproceedings{18260,
  abstract     = {We introduce the first completely unsupervised correspondence learning approach for deformable 3D shapes. Key to our model is the understanding that natural deformations (such as changes in pose) approximately preserve the metric structure of the surface, yielding a natural criterion to drive the learning process toward distortion-minimizing predictions. On this basis, we overcome the need for annotated data and replace it by a purely geometric criterion. The resulting learning model is class-agnostic, and is able to leverage any type of deformable geometric data for the training phase. In contrast to existing supervised approaches which specialize on the class seen at training time, we demonstrate stronger generalization as well as applicability to a variety of challenging settings. We showcase our method on a wide selection of correspondence benchmarks, where we outperform other methods in terms of accuracy, generalization, and efficiency.},
  author       = {Halimi, Oshri and Litany, Or and Rodola, Emanuele Rodola and Bronstein, Alexander and Kimmel, Ron},
  booktitle    = {2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  isbn         = {9781728132945},
  issn         = {2575-7075},
  location     = {Long Beach, CA, United States},
  publisher    = {IEEE},
  title        = {{Unsupervised learning of dense shape correspondence}},
  doi          = {10.1109/cvpr.2019.00450},
  year         = {2020},
}

@article{22054,
  abstract     = {We consider the Korteweg–de Vries equation with white noise initial data, posed on the whole real line, and prove the almost sure existence of solutions. Moreover, we show that the solutions obey the group property and follow a white noise law at all times, past or future. As an offshoot of our methods, we also obtain a new proof of the existence of solutions and the invariance of white noise measure in the torus setting.},
  author       = {Killip, Rowan and Murphy, Jason and Visan, Monica},
  issn         = {1432-1297},
  journal      = {Inventiones mathematicae},
  number       = {1},
  pages        = {203--282},
  publisher    = {Springer Nature},
  title        = {{Invariance of white noise for KdV on the line}},
  doi          = {10.1007/s00222-020-00964-9},
  volume       = {222},
  year         = {2020},
}

@article{22080,
  abstract     = {We consider discrete analogues of two well-known open problems regarding invariant measures for dispersive PDE, namely, the invariance of the Gibbs measure for the continuum (classical) Heisenberg model and the invariance of white noise under focusing cubic nonlinear Schrödinger equation. These continuum models are completely integrable and connected by the Hasimoto transform; correspondingly, we focus our attention on discretizations that are also completely integrable and also connected by a discrete Hasimoto transform. We consider these models on the infinite lattice ℤ. Concretely, for a completely integrable variant of the classical Heisenberg spin chain model (introduced independently by Haldane, Ishimori, and Sklyanin) we prove the existence and uniqueness of solutions for initial data following a Gibbs law (which we show is unique) and show that the Gibbs measure is preserved under these dynamics. In the setting of the focusing Ablowitz--Ladik system, we prove invariance of a measure that we will show is the appropriate discrete analogue of white noise. We also include a thorough discussion of the Poisson geometry associated to the discrete Hasimoto transform introduced by Ishimori that connects the two models studied in this article.},
  author       = {Angelopoulos, Yannis and Killip, Rowan and Visan, Monica},
  issn         = {1095-7154},
  journal      = {SIAM Journal on Mathematical Analysis},
  number       = {1},
  pages        = {135--163},
  publisher    = {Society for Industrial & Applied Mathematics},
  title        = {{Invariant measures for integrable spin chains and an integrable discrete nonlinear Schrödinger equation}},
  doi          = {10.1137/19m1265314},
  volume       = {52},
  year         = {2020},
}

@article{15079,
  abstract     = {Large complex systems tend to develop universal patterns that often represent their essential characteristics. For example, the cumulative effects of independent or weakly dependent random variables often yield the Gaussian universality class via the central limit theorem. For non-commutative random variables, e.g. matrices, the Gaussian behavior is often replaced by another universality class, commonly called random matrix statistics. Nearby eigenvalues are strongly correlated, and, remarkably, their correlation structure is universal, depending only on the symmetry type of the matrix. Even more surprisingly, this feature is not restricted to matrices; in fact Eugene Wigner, the pioneer of the field, discovered in the 1950s that distributions of the gaps between energy levels of complicated quantum systems universally follow the same random matrix statistics. This claim has never been rigorously proved for any realistic physical system but experimental data and extensive numerics leave no doubt as to its correctness. Since then random matrices have proved to be extremely useful phenomenological models in a wide range of applications beyond quantum physics that include number theory, statistics, neuroscience, population dynamics, wireless communication and mathematical finance. The ubiquity of random matrices in natural sciences is still a mystery, but recent years have witnessed a breakthrough in the mathematical description of the statistical structure of their spectrum. Random matrices and closely related areas such as log-gases have become an extremely active research area in probability theory.
This workshop brought together outstanding researchers from a variety of mathematical backgrounds whose areas of research are linked to random matrices. While there are strong links between their motivations, the techniques used by these researchers span a large swath of mathematics, ranging from purely algebraic techniques to stochastic analysis, classical probability theory, operator algebra, supersymmetry, orthogonal polynomials, etc.},
  author       = {Erdös, László and Götze, Friedrich and Guionnet, Alice},
  issn         = {1660-8933},
  journal      = {Oberwolfach Reports},
  number       = {4},
  pages        = {3459--3527},
  publisher    = {EMS Press},
  title        = {{Random matrices}},
  doi          = {10.4171/owr/2019/56},
  volume       = {16},
  year         = {2020},
}

@article{8042,
  abstract     = {We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.},
  author       = {Boccato, Chiara and Brennecke, Christian and Cenatiempo, Serena and Schlein, Benjamin},
  issn         = {1435-9855},
  journal      = {Journal of the European Mathematical Society},
  number       = {7},
  pages        = {2331--2403},
  publisher    = {EMS Press},
  title        = {{The excitation spectrum of Bose gases interacting through singular potentials}},
  doi          = {10.4171/JEMS/966},
  volume       = {22},
  year         = {2020},
}

@article{9007,
  abstract     = {Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals.},
  author       = {Browning, Timothy D and Sawin, Will},
  issn         = {1420-8946},
  journal      = {Commentarii Mathematici Helvetici},
  number       = {4},
  pages        = {635--659},
  publisher    = {EMS Press},
  title        = {{Free rational points on smooth hypersurfaces}},
  doi          = {10.4171/CMH/499},
  volume       = {95},
  year         = {2020},
}

@article{15070,
  abstract     = {This workshop focused on interactions between the various perspectives on the moduli space of Higgs bundles over a Riemann surface. This subject draws on algebraic geometry, geometric topology, geometric analysis and mathematical physics, and the goal was to promote interactions between these various branches of the subject. The main current directions of research were well represented by the participants, and the talks included many from both senior and junior participants.},
  author       = {Anderson, Lara and Hausel, Tamás and Mazzeo, Rafe and Schaposnik, Laura},
  issn         = {1660-8933},
  journal      = {Oberwolfach Reports},
  keywords     = {Organic Chemistry, Biochemistry},
  number       = {2},
  pages        = {1357--1417},
  publisher    = {EMS Press},
  title        = {{Geometry and physics of Higgs bundles}},
  doi          = {10.4171/owr/2019/23},
  volume       = {16},
  year         = {2020},
}

@article{15072,
  abstract     = {The interaction among fundamental particles in nature leads to many interesting effects in quantum statistical mechanics; examples include superconductivity for charged systems and superfluidity in cold gases. It is a huge challenge for mathematical physics to understand the collective behavior of systems containing a large number of particles, emerging from known microscopic interactions. In this workshop we brought together researchers working on different aspects of many-body quantum mechanics to discuss recent developments, exchange ideas and propose new challenges and research directions.},
  author       = {Hainzl, Christian and Schlein, Benjamin and Seiringer, Robert and Warzel, Simone},
  issn         = {1660-8933},
  journal      = {Oberwolfach Reports},
  number       = {3},
  pages        = {2541--2603},
  publisher    = {EMS Press},
  title        = {{Many-body quantum systems}},
  doi          = {10.4171/owr/2019/41},
  volume       = {16},
  year         = {2020},
}

@article{8973,
  abstract     = {We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity.},
  author       = {Redig, Frank and Saada, Ellen and Sau, Federico},
  issn         = {1083-6489},
  journal      = {Electronic Journal of Probability},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Symmetric simple exclusion process in dynamic environment: Hydrodynamics}},
  doi          = {10.1214/20-EJP536},
  volume       = {25},
  year         = {2020},
}

@article{8040,
  abstract     = {The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form—a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.},
  author       = {Gupta, Chitrak and Khaniya, Umesh and Chan, Chun Kit and Dehez, Francois and Shekhar, Mrinal and Gunner, M. R. and Sazanov, Leonid A and Chipot, Christophe and Singharoy, Abhishek},
  issn         = {1520-5126},
  journal      = {Journal of the American Chemical Society},
  number       = {20},
  pages        = {9220--9230},
  publisher    = {American Chemical Society},
  title        = {{Charge transfer and chemo-mechanical coupling in respiratory complex I}},
  doi          = {10.1021/jacs.9b13450},
  volume       = {142},
  year         = {2020},
}

@article{7166,
  abstract     = {In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors.},
  author       = {Ucar, Mehmet C and Lipowsky, Reinhard},
  issn         = {1530-6992},
  journal      = {Nano Letters},
  number       = {1},
  pages        = {669--676},
  publisher    = {American Chemical Society},
  title        = {{Collective force generation by molecular motors is determined by strain-induced unbinding}},
  doi          = {10.1021/acs.nanolett.9b04445},
  volume       = {20},
  year         = {2020},
}

@misc{9713,
  abstract     = {Additional analyses of the trajectories},
  author       = {Gupta, Chitrak and Khaniya, Umesh and Chan, Chun Kit and Dehez, Francois and Shekhar, Mrinal and Gunner, M.R. and Sazanov, Leonid A and Chipot, Christophe and Singharoy, Abhishek},
  publisher    = {American Chemical Society},
  title        = {{Supporting information}},
  doi          = {10.1021/jacs.9b13450.s001},
  year         = {2020},
}

@misc{9885,
  abstract     = {Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)},
  author       = {Ucar, Mehmet C and Lipowsky, Reinhard},
  publisher    = {American Chemical Society},
  title        = {{MURL_Dataz}},
  doi          = {10.1021/acs.nanolett.9b04445.s002},
  year         = {2020},
}

@phdthesis{8155,
  abstract     = {In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as
transcriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal
non-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.
In the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are
hard to evolve or maintain. },
  author       = {Grah, Rok},
  issn         = {2663-337X},
  pages        = {310},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Gene regulation across scales – how biophysical constraints shape evolution}},
  doi          = {10.15479/AT:ISTA:8155},
  year         = {2020},
}

@unpublished{7675,
  abstract     = {In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.},
  author       = {Grah, Rok and Zoller, Benjamin and Tkačik, Gašper},
  booktitle    = {bioRxiv},
  title        = {{Normative models of enhancer function}},
  doi          = {10.1101/2020.04.08.029405},
  year         = {2020},
}

@unpublished{8813,
  abstract     = {In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.},
  author       = {Santini, Laura and Halbritter, Florian and Titz-Teixeira, Fabian and Suzuki, Toru and Asami, Maki and Ramesmayer, Julia and Ma, Xiaoyan and Lackner, Andreas and Warr, Nick and Pauler, Florian and Hippenmeyer, Simon and Laue, Ernest and Farlik, Matthias and Bock, Christoph and Beyer, Andreas and Perry, Anthony C. F. and Leeb, Martin},
  booktitle    = {bioRxiv},
  title        = {{Novel imprints in mouse blastocysts are predominantly DNA methylation independent}},
  doi          = {10.1101/2020.11.03.366948},
  year         = {2020},
}

@unpublished{7601,
  abstract     = {Plasmodesmata (PD) are crucial structures for intercellular communication in multicellular plants with remorins being their crucial plant-specific structural and functional constituents. The PD biogenesis is an intriguing but poorly understood process. By expressing an Arabidopsis remorin protein in mammalian cells, we have reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting neighboring cells physically and physiologically. Notably, RFs are capable of transporting macromolecules intercellularly, in a way similar to plant PD. With further super-resolution microscopic analysis and biochemical characterization, we found that RFs are also composed of actin filaments, forming the core skeleton structure, aligned with the remorin protein. This unique heterologous filamentous structure might explain the molecular mechanism for remorin function as well as PD construction. Furthermore, remorin protein exhibits a specific distribution manner in the plasma membrane in mammalian cells, representing a lipid nanodomain, depending on its lipid modification status. Our studies not only provide crucial insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental mechanistic and evolutionary links between intercellular communication systems of plants and animals.},
  author       = {Wei, Zhuang and Tan, Shutang and Liu, Tao and Wu, Yuan and Lei, Ji-Gang and Chen, ZhengJun and Friml, Jiří and Xue, Hong-Wei and Liao, Kan},
  booktitle    = {bioRxiv},
  pages        = {22},
  title        = {{Plasmodesmata-like intercellular connections by plant remorin in animal cells}},
  doi          = {10.1101/791137},
  year         = {2020},
}