@article{15037,
  abstract     = {Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.},
  author       = {Moulinier-Anzola, Jeanette and Schwihla, Maximilian and De-Araújo, Lucinda and Artner, Christina and Jörg, Lisa and Konstantinova, Nataliia and Luschnig, Christian and Korbei, Barbara},
  issn         = {1674-2052},
  journal      = {Molecular Plant},
  keywords     = {Plant Science, Molecular Biology},
  number       = {5},
  pages        = {717--731},
  publisher    = {Elsevier},
  title        = {{TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants}},
  doi          = {10.1016/j.molp.2020.02.012},
  volume       = {13},
  year         = {2020},
}

@article{15055,
  abstract     = {<jats:p>Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states.</jats:p>},
  author       = {Brázdil, Tomáš and Chatterjee, Krishnendu and Novotný, Petr and Vahala, Jiří},
  issn         = {2374-3468},
  journal      = {Proceedings of the 34th AAAI Conference on Artificial Intelligence},
  keywords     = {General Medicine},
  location     = {New York, NY, United States},
  number       = {06},
  pages        = {9794--9801},
  publisher    = {Association for the Advancement of Artificial Intelligence},
  title        = {{Reinforcement learning of risk-constrained policies in Markov decision processes}},
  doi          = {10.1609/aaai.v34i06.6531},
  volume       = {34},
  year         = {2020},
}

@article{15057,
  abstract     = {Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans.},
  author       = {Park, Sangsoon and Artan, Murat and Han, Seung Hyun and Park, Hae-Eun H. and Jung, Yoonji and Hwang, Ara B. and Shin, Won Sik and Kim, Kyong-Tai and Lee, Seung-Jae V.},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {27},
  publisher    = {American Association for the Advancement of Science},
  title        = {{VRK-1 extends life span by activation of AMPK via phosphorylation}},
  doi          = {10.1126/sciadv.aaw7824},
  volume       = {6},
  year         = {2020},
}

@inproceedings{15059,
  abstract     = {In this paper we present a room temperature radiometer that can eliminate the need of using cryostats in satellite payload reducing its weight and improving reliability. The proposed radiometer is based on an electro-optic upconverter that boosts up microwave photons energy by upconverting them into an optical domain what makes them immune to thermal noise even if operating at room temperature. The converter uses a high-quality factor whispering gallery
mode (WGM) resonator providing naturally narrow bandwidth and therefore might be useful for applications like microwave hyperspectral sensing. The upconversion process is explained by
providing essential information about photon conversion efficiency and sensitivity. To prove the concept, we describe an experiment which shows state-of-the-art photon conversion efficiency n=10-5 per mW of pump power at the frequency of 80 GHz.},
  author       = {Wasiak, Michal and Botello, Gabriel Santamaria and Abdalmalak, Kerlos Atia and Sedlmeir, Florian and Rueda Sanchez, Alfredo R and Segovia-Vargas, Daniel and Schwefel, Harald G. L. and Munoz, Luis Enrique Garcia},
  booktitle    = {14th European Conference on Antennas and Propagation},
  location     = {Copenhagen, Denmark},
  publisher    = {IEEE},
  title        = {{Compact millimeter and submillimeter-wave photonic radiometer for cubesats}},
  doi          = {10.23919/eucap48036.2020.9135962},
  year         = {2020},
}

@article{15061,
  abstract     = {The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.},
  author       = {Pinotsis, Nikos and Zielinska, Karolina and Babuta, Mrigya and Arolas, Joan L. and Kostan, Julius and Khan, Muhammad Bashir and Schreiner, Claudia and Testa Salmazo, Anita P and Ciccarelli, Luciano and Puchinger, Martin and Gkougkoulia, Eirini A. and Ribeiro, Euripedes de Almeida and Marlovits, Thomas C. and Bhattacharya, Alok and Djinovic-Carugo, Kristina},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences},
  number       = {36},
  pages        = {22101--22112},
  publisher    = {Proceedings of the National Academy of Sciences},
  title        = {{Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin}},
  doi          = {10.1073/pnas.1917269117},
  volume       = {117},
  year         = {2020},
}

@article{15063,
  abstract     = {We consider the least singular value of a large random matrix with real or complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal lower tail estimate on this singular value in the critical regime where z is around the spectral edge, thus improving the classical bound of Sankar, Spielman and Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395).},
  author       = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J},
  issn         = {2690-1005},
  journal      = {Probability and Mathematical Physics},
  keywords     = {General Medicine},
  number       = {1},
  pages        = {101--146},
  publisher    = {Mathematical Sciences Publishers},
  title        = {{Optimal lower bound on the least singular value of the shifted Ginibre ensemble}},
  doi          = {10.2140/pmp.2020.1.101},
  volume       = {1},
  year         = {2020},
}

@article{15064,
  abstract     = {We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspaces of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for Čech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive Čech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems.},
  author       = {Bauer, U. and Edelsbrunner, Herbert and Jablonski, Grzegorz and Mrozek, M.},
  issn         = {2367-1734},
  journal      = {Journal of Applied and Computational Topology},
  number       = {4},
  pages        = {455--480},
  publisher    = {Springer Nature},
  title        = {{Čech-Delaunay gradient flow and homology inference for self-maps}},
  doi          = {10.1007/s41468-020-00058-8},
  volume       = {4},
  year         = {2020},
}

@inproceedings{15074,
  abstract     = {We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds.},
  author       = {Brandt, Sebastian and Keller, Barbara and Rybicki, Joel and Suomela, Jukka and Uitto, Jara},
  booktitle    = {34th International Symposium on Distributed Computing},
  location     = {Virtual},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Brief announcement: Efficient load-balancing through distributed token dropping}},
  doi          = {10.4230/LIPIcs.DISC.2020.40},
  volume       = {179},
  year         = {2020},
}

@inproceedings{15077,
  abstract     = {We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a "gap covering" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor.},
  author       = {Alistarh, Dan-Adrian and Nadiradze, Giorgi and Sabour, Amirmojtaba},
  booktitle    = {47th International Colloquium on Automata, Languages, and Programming},
  location     = {Saarbrücken, Germany, Virtual},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Dynamic averaging load balancing on cycles}},
  doi          = {10.4230/LIPIcs.ICALP.2020.7},
  volume       = {168},
  year         = {2020},
}

@inproceedings{15082,
  abstract     = {Two plane drawings of geometric graphs on the same set of points are called disjoint compatible if their union is plane and they do not have an edge in common. For a given set S of 2n points two plane drawings of perfect matchings M1 and M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible if there exists a plane drawing of a spanning tree T on S which is disjoint compatible to both M1 and M2.
We show that the graph of all disjoint tree-compatible perfect geometric matchings on 2n points in convex position is connected if and only if 2n ≥ 10. Moreover, in that case the diameter
of this graph is either 4 or 5, independent of n.},
  author       = {Aichholzer, Oswin and Obmann, Julia and Patak, Pavel and Perz, Daniel and Tkadlec, Josef},
  booktitle    = {36th European Workshop on Computational Geometry},
  location     = {Würzburg, Germany, Virtual},
  title        = {{Disjoint tree-compatible plane perfect matchings}},
  year         = {2020},
}

@misc{13056,
  abstract     = {This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request.},
  author       = {Arnold, Georg M and Wulf, Matthias and Barzanjeh, Shabir and Redchenko, Elena and Rueda Sanchez, Alfredo R and Hease, William J and Hassani, Farid and Fink, Johannes M},
  publisher    = {Zenodo},
  title        = {{Converting microwave and telecom photons with a silicon photonic nanomechanical interface}},
  doi          = {10.5281/ZENODO.3961561},
  year         = {2020},
}

@misc{13060,
  abstract     = {Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity ­– influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level.},
  author       = {Milutinovic, Barbara and Stock, Miriam and Grasse, Anna V and Naderlinger, Elisabeth and Hilbe, Christian and Cremer, Sylvia},
  publisher    = {Dryad},
  title        = {{Social immunity modulates competition between coinfecting pathogens}},
  doi          = {10.5061/DRYAD.CRJDFN318},
  year         = {2020},
}

@misc{13065,
  abstract     = {Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.},
  author       = {Arnoux, Stephanie and Fraisse, Christelle and Sauvage, Christopher},
  publisher    = {Dryad},
  title        = {{VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species}},
  doi          = {10.5061/DRYAD.Q2BVQ83HD},
  year         = {2020},
}

@misc{13070,
  abstract     = {This dataset comprises all data shown in the figures of the submitted article "Surpassing the resistance quantum with a geometric superinductor". Additional raw data are available from the corresponding author on reasonable request.},
  author       = {Peruzzo, Matilda and Trioni, Andrea and Hassani, Farid and Zemlicka, Martin and Fink, Johannes M},
  publisher    = {Zenodo},
  title        = {{Surpassing the resistance quantum with a geometric superinductor}},
  doi          = {10.5281/ZENODO.4052882},
  year         = {2020},
}

@misc{13071,
  abstract     = {This dataset comprises all data shown in the plots of the main part of the submitted article "Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State". Additional raw data are available from the corresponding author on reasonable request.},
  author       = {Hease, William J and Rueda Sanchez, Alfredo R and Sahu, Rishabh and Wulf, Matthias and Arnold, Georg M and Schwefel, Harald and Fink, Johannes M},
  publisher    = {Zenodo},
  title        = {{Bidirectional electro-optic wavelength conversion in the quantum ground state}},
  doi          = {10.5281/ZENODO.4266025},
  year         = {2020},
}

@misc{13073,
  abstract     = {The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.},
  author       = {Simon, Alexis and Fraisse, Christelle and El Ayari, Tahani and Liautard-Haag, Cathy and Strelkov, Petr and Welch, John and Bierne, Nicolas},
  publisher    = {Dryad},
  title        = {{How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels}},
  doi          = {10.5061/DRYAD.R4XGXD29N},
  year         = {2020},
}

@article{14125,
  abstract     = {Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.
Results: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.},
  author       = {Stark, Stefan G and Ficek, Joanna and Locatello, Francesco and Bonilla, Ximena and Chevrier, Stéphane and Singer, Franziska and Aebersold, Rudolf and Al-Quaddoomi, Faisal S and Albinus, Jonas and Alborelli, Ilaria and Andani, Sonali and Attinger, Per-Olof and Bacac, Marina and Baumhoer, Daniel and Beck-Schimmer, Beatrice and Beerenwinkel, Niko and Beisel, Christian and Bernasconi, Lara and Bertolini, Anne and Bodenmiller, Bernd and Bonilla, Ximena and Casanova, Ruben and Chevrier, Stéphane and Chicherova, Natalia and D'Costa, Maya and Danenberg, Esther and Davidson, Natalie and gan, Monica-Andreea Dră and Dummer, Reinhard and Engler, Stefanie and Erkens, Martin and Eschbach, Katja and Esposito, Cinzia and Fedier, André and Ferreira, Pedro and Ficek, Joanna and Frei, Anja L and Frey, Bruno and Goetze, Sandra and Grob, Linda and Gut, Gabriele and Günther, Detlef and Haberecker, Martina and Haeuptle, Pirmin and Heinzelmann-Schwarz, Viola and Herter, Sylvia and Holtackers, Rene and Huesser, Tamara and Irmisch, Anja and Jacob, Francis and Jacobs, Andrea and Jaeger, Tim M and Jahn, Katharina and James, Alva R and Jermann, Philip M and Kahles, André and Kahraman, Abdullah and Koelzer, Viktor H and Kuebler, Werner and Kuipers, Jack and Kunze, Christian P and Kurzeder, Christian and Lehmann, Kjong-Van and Levesque, Mitchell and Lugert, Sebastian and Maass, Gerd and Manz, Markus and Markolin, Philipp and Mena, Julien and Menzel, Ulrike and Metzler, Julian M and Miglino, Nicola and Milani, Emanuela S and Moch, Holger and Muenst, Simone and Murri, Riccardo and Ng, Charlotte KY and Nicolet, Stefan and Nowak, Marta and Pedrioli, Patrick GA and Pelkmans, Lucas and Piscuoglio, Salvatore and Prummer, Michael and Ritter, Mathilde and Rommel, Christian and Rosano-González, María L and Rätsch, Gunnar and Santacroce, Natascha and Castillo, Jacobo Sarabia del and Schlenker, Ramona and Schwalie, Petra C and Schwan, Severin and Schär, Tobias and Senti, Gabriela and Singer, Franziska and Sivapatham, Sujana and Snijder, Berend and Sobottka, Bettina and Sreedharan, Vipin T and Stark, Stefan and Stekhoven, Daniel J and Theocharides, Alexandre PA and Thomas, Tinu M and Tolnay, Markus and Tosevski, Vinko and Toussaint, Nora C and Tuncel, Mustafa A and Tusup, Marina and Drogen, Audrey Van and Vetter, Marcus and Vlajnic, Tatjana and Weber, Sandra and Weber, Walter P and Wegmann, Rebekka and Weller, Michael and Wendt, Fabian and Wey, Norbert and Wicki, Andreas and Wollscheid, Bernd and Yu, Shuqing and Ziegler, Johanna and Zimmermann, Marc and Zoche, Martin and Zuend, Gregor and Rätsch, Gunnar and Lehmann, Kjong-Van},
  issn         = {1367-4811},
  journal      = {Bioinformatics},
  keywords     = {Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability},
  number       = {Supplement_2},
  pages        = {i919--i927},
  publisher    = {Oxford University Press},
  title        = {{SCIM: Universal single-cell matching with unpaired feature sets}},
  doi          = {10.1093/bioinformatics/btaa843},
  volume       = {36},
  year         = {2020},
}

@inproceedings{14186,
  abstract     = {The goal of the unsupervised learning of disentangled representations is to
separate the independent explanatory factors of variation in the data without
access to supervision. In this paper, we summarize the results of Locatello et
al., 2019, and focus on their implications for practitioners. We discuss the
theoretical result showing that the unsupervised learning of disentangled
representations is fundamentally impossible without inductive biases and the
practical challenges it entails. Finally, we comment on our experimental
findings, highlighting the limitations of state-of-the-art approaches and
directions for future research.},
  author       = {Locatello, Francesco and Bauer, Stefan and Lucic, Mario and Rätsch, Gunnar and Gelly, Sylvain and Schölkopf, Bernhard and Bachem, Olivier},
  booktitle    = {The 34th AAAI Conference on Artificial Intelligence},
  isbn         = {9781577358350},
  issn         = {2374-3468},
  location     = {New York, NY, United States},
  number       = {9},
  pages        = {13681--13684},
  publisher    = {Association for the Advancement of Artificial Intelligence},
  title        = {{A commentary on the unsupervised learning of disentangled representations}},
  doi          = {10.1609/aaai.v34i09.7120},
  volume       = {34},
  year         = {2020},
}

@inproceedings{14187,
  abstract     = {We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient)
algorithm for constrained smooth finite-sum minimization with a generalized
linear prediction/structure. This class of problems includes empirical risk
minimization with sparse, low-rank, or other structured constraints. The
proposed method is simple to implement, does not require step-size tuning, and
has a constant per-iteration cost that is independent of the dataset size.
Furthermore, as a byproduct of the method we obtain a stochastic estimator of
the Frank-Wolfe gap that can be used as a stopping criterion. Depending on the
setting, the proposed method matches or improves on the best computational
guarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several
datasets highlight different regimes in which the proposed method exhibits a
faster empirical convergence than related methods. Finally, we provide an
implementation of all considered methods in an open-source package.},
  author       = {Négiar, Geoffrey and Dresdner, Gideon and Tsai, Alicia and Ghaoui, Laurent El and Locatello, Francesco and Freund, Robert M. and Pedregosa, Fabian},
  booktitle    = {Proceedings of the 37th International Conference on Machine Learning},
  location     = {Virtual},
  pages        = {7253--7262},
  title        = {{Stochastic Frank-Wolfe for constrained finite-sum minimization}},
  volume       = {119},
  year         = {2020},
}

@inproceedings{14188,
  abstract     = {Intelligent agents should be able to learn useful representations by
observing changes in their environment. We model such observations as pairs of
non-i.i.d. images sharing at least one of the underlying factors of variation.
First, we theoretically show that only knowing how many factors have changed,
but not which ones, is sufficient to learn disentangled representations.
Second, we provide practical algorithms that learn disentangled representations
from pairs of images without requiring annotation of groups, individual
factors, or the number of factors that have changed. Third, we perform a
large-scale empirical study and show that such pairs of observations are
sufficient to reliably learn disentangled representations on several benchmark
data sets. Finally, we evaluate our learned representations and find that they
are simultaneously useful on a diverse suite of tasks, including generalization
under covariate shifts, fairness, and abstract reasoning. Overall, our results
demonstrate that weak supervision enables learning of useful disentangled
representations in realistic scenarios.},
  author       = {Locatello, Francesco and Poole, Ben and Rätsch, Gunnar and Schölkopf, Bernhard and Bachem, Olivier and Tschannen, Michael},
  booktitle    = {Proceedings of the 37th International Conference on Machine Learning},
  location     = {Virtual},
  pages        = {6348–6359},
  title        = {{Weakly-supervised disentanglement without compromises}},
  volume       = {119},
  year         = {2020},
}