TY - CHAP A1 - Diakonikolas, Jelena A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - Locally Accelerated Conditional Gradients T2 - Proceedings of AISTATS Y1 - 2020 N1 - URL of the Code: https://colab.research.google.com/drive/1ejjfCan7xnEhWWJXCIzb03CwQRG9iW_O N1 - URL of the PDF: http://proceedings.mlr.press/v108/diakonikolas20a/diakonikolas20a.pdf N1 - URL of the Slides: https://app.box.com/s/gphkhapso7d1vrfnzqykkb3vx0agxh8w N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/07/04/LaCG-abstract.html N1 - https://slideslive.com/38930107/locally-accelerated-conditional-gradients?ref=account-folder-52123-folders ER - TY - JOUR A1 - Faenza, Yuri A1 - Muñoz, Gonzalo A1 - Pokutta, Sebastian T1 - New Limits of Treewidth-based tractability in Optimization JF - Mathematical Programming Y1 - 2020 U6 - https://doi.org/10.1007/s10107-020-01563-5 N1 - URL of the PDF: http://link.springer.com/article/10.1007/s10107-020-01563-5 N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2018/09/22/treewidth-abstract.html VL - 191 SP - 559 EP - 594 ER - TY - JOUR A1 - Anari, N. A1 - Haghtalab, N. A1 - Naor, S. A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - Structured Robust Submodular Maximization: Offline and Online Algorithms JF - INFORMS Journal on Computing Y1 - 2020 ER - TY - CHAP A1 - Combettes, Cyrille W. A1 - Pokutta, Sebastian T1 - Boosting Frank-Wolfe by Chasing Gradients T2 - Proceedings of ICML Y1 - 2020 N1 - Additional Note: github code: https://github.com/cyrillewcombettes/boostfw N1 - URL of the Code: https://colab.research.google.com/drive/1TSOVjDFF1X2ADBo_adHLsUVrblSutRKw N1 - URL of the Slides: https://app.box.com/s/wwj247r5d456q0778p9b9y1jm6txuifb N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2020/03/16/boostFW.html N1 - https://www.youtube.com/watch?v=BfyV0C5FRbE ER - TY - CHAP A1 - Pokutta, Sebastian T1 - Restarting Algorithms: Sometimes there is Free Lunch T2 - Proceedings of CPAIOR Y1 - 2020 N1 - URL of the Slides: https://app.box.com/s/8ps8bhjv2phhy182xn55iurk9t3o1xc3 N1 - https://www.youtube.com/watch?v=v3Xzoda2_gQ ER - TY - JOUR A1 - Laydon, Daniel J. A1 - Sunkara, Vikram A1 - Boelen, Lies A1 - Bangham, Charles R. M. A1 - Asquith, Becca T1 - The relative contributions of infectious and mitotic spread to HTLV-1 persistence JF - PLOS Computational Biology Y1 - 2020 U6 - https://doi.org/10.1371/journal.pcbi.1007470 ER - TY - JOUR A1 - Kossen, Tabea A1 - Hirzel, Manuel A. A1 - Madai, Vince I. A1 - Boenisch, Franziska A1 - Hennemuth, Anja A1 - Hildebrand, Kristian A1 - Pokutta, Sebastian A1 - Sharma, Kartikey A1 - Hilbert, Adam A1 - Sobesky, Jan A1 - Galinovic, Ivana A1 - Khalil, Ahmed A. A1 - Fiebach, Jochen B. A1 - Frey, Dietmar T1 - Towards Sharing Brain Images: Differentially Private TOF-MRA Images with Segmentation Labels Using Generative Adversarial Networks JF - Frontiers in Artificial Intelligence N2 - Sharing labeled data is crucial to acquire large datasets for various Deep Learning applications. In medical imaging, this is often not feasible due to privacy regulations. Whereas anonymization would be a solution, standard techniques have been shown to be partially reversible. Here, synthetic data using a Generative Adversarial Network (GAN) with differential privacy guarantees could be a solution to ensure the patient's privacy while maintaining the predictive properties of the data. In this study, we implemented a Wasserstein GAN (WGAN) with and without differential privacy guarantees to generate privacy-preserving labeled Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) image patches for brain vessel segmentation. The synthesized image-label pairs were used to train a U-net which was evaluated in terms of the segmentation performance on real patient images from two different datasets. Additionally, the Fréchet Inception Distance (FID) was calculated between the generated images and the real images to assess their similarity. During the evaluation using the U-Net and the FID, we explored the effect of different levels of privacy which was represented by the parameter ϵ. With stricter privacy guarantees, the segmentation performance and the similarity to the real patient images in terms of FID decreased. Our best segmentation model, trained on synthetic and private data, achieved a Dice Similarity Coefficient (DSC) of 0.75 for ϵ = 7.4 compared to 0.84 for ϵ = ∞ in a brain vessel segmentation paradigm (DSC of 0.69 and 0.88 on the second test set, respectively). We identified a threshold of ϵ <5 for which the performance (DSC <0.61) became unstable and not usable. Our synthesized labeled TOF-MRA images with strict privacy guarantees retained predictive properties necessary for segmenting the brain vessels. Although further research is warranted regarding generalizability to other imaging modalities and performance improvement, our results mark an encouraging first step for privacy-preserving data sharing in medical imaging. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.3389/frai.2022.813842 ER - TY - JOUR A1 - Raharinirina, N. Alexia A1 - Acevedo-Trejos, Esteban A1 - Merico, Agostino T1 - Modelling the acclimation capacity of coral reefs to a warming ocean JF - PLOS COMPUTATIONAL BIOLOGY N2 - The symbiotic relationship between corals and photosynthetic algae is the foundation of coral reef ecosystems. This relationship breaks down, leading to coral death, when sea temperature exceeds the thermal tolerance of the coral-algae complex. While acclimation via phenotypic plasticity at the organismal level is an important mechanism for corals to cope with global warming, community-based shifts in response to acclimating capacities may give valuable indications about the future of corals at a regional scale. Reliable regional-scale predictions, however, are hampered by uncertainties on the speed with which coral communities will be able to acclimate. Here we present a trait-based, acclimation dynamics model, which we use in combination with observational data, to provide a first, crude estimate of the speed of coral acclimation at the community level and to investigate the effects of different global warming scenarios on three iconic reef ecosystems of the tropics: Great Barrier Reef, South East Asia, and Caribbean. The model predicts that coral acclimation may confer some level of protection by delaying the decline of some reefs such as the Great Barrier Reef. However, the current rates of acclimation will not be sufficient to rescue corals from global warming. Based on our estimates of coral acclimation capacities, the model results suggest substantial declines in coral abundances in all three regions, ranging from 12% to 55%, depending on the region and on the climate change scenario considered. Our results highlight the importance and urgency of precise assessments and quantitative estimates, for example through laboratory experiments, of the natural acclimation capacity of corals and of the speed with which corals may be able to acclimate to global warming. Y1 - 2022 U6 - https://doi.org/10.1371/journal.pcbi.1010099 ER - TY - JOUR A1 - Becker, Kaitlyn P A1 - Teeple, Clark A1 - Charles, Nicholas A1 - Jung, Yeonsu A1 - Baum, Daniel A1 - Weaver, James C A1 - Mahadevan, L. A1 - Wood, Robert J T1 - Active entanglement enables stochastic, topological grasping JF - PNAS N2 - Grasping, in both biological and engineered mechanisms, can be highly sensitive to the gripper and object morphology, as well as perception and motion planning. Here we circumvent the need for feedback or precise planning by using an array of fluidically-actuated slender hollow elastomeric filaments to actively entangle with objects that vary in geometric and topological complexity. The resulting stochastic interactions enable a unique soft and conformable grasping strategy across a range of target objects that vary in size, weight, and shape. We experimentally evaluate the grasping performance of our strategy, and use a computational framework for the collective mechanics of flexible filaments in contact with complex objects to explain our findings. Overall, our study highlights how active collective entanglement of a filament array via an uncontrolled, spatially distributed scheme provides new options for soft, adaptable grasping. Y1 - 2022 U6 - https://doi.org/10.1073/pnas.2209819119 VL - 119 IS - 42 SP - e2209819119 ER - TY - CHAP A1 - Berner, Julius A1 - Richter, Lorenz A1 - Ullrich, Karen T1 - An optimal control perspective on diffusion-based generative modeling T2 - Transactions on Machine Learning Research N2 - We establish a connection between stochastic optimal control and generative models based on stochastic differential equations (SDEs) such as recently developed diffusion probabilistic models. In particular, we derive a Hamilton-Jacobi-Bellman equation that governs the evolution of the log-densities of the underlying SDE marginals. This perspective allows to transfer methods from optimal control theory to generative modeling. First, we show that the evidence lower bound is a direct consequence of the well-known verification theorem from control theory. Further, we develop a novel diffusion-based method for sampling from unnormalized densities -- a problem frequently occurring in statistics and computational sciences. Y1 - 2024 UR - https://openreview.net/forum?id=oYIjw37pTP ER - TY - JOUR A1 - Nüsken, Nikolas A1 - Richter, Lorenz T1 - Interpolating between BSDEs and PINNs: deep learning for elliptic and parabolic boundary value problems JF - Journal of Machine Learning N2 - Solving high-dimensional partial differential equations is a recurrent challenge in economics, science and engineering. In recent years, a great number of computational approaches have been developed, most of them relying on a combination of Monte Carlo sampling and deep learning based approximation. For elliptic and parabolic problems, existing methods can broadly be classified into those resting on reformulations in terms of backward stochastic differential equations (BSDEs) and those aiming to minimize a regression-type L2-error (physics-informed neural networks, PINNs). In this paper, we review the literature and suggest a methodology based on the novel diffusion loss that interpolates between BSDEs and PINNs. Our contribution opens the door towards a unified understanding of numerical approaches for high-dimensional PDEs, as well as for implementations that combine the strengths of BSDEs and PINNs. The diffusion loss furthermore bears close similarities to (least squares) temporal difference objectives found in reinforcement learning. We also discuss eigenvalue problems and perform extensive numerical studies, including calculations of the ground state for nonlinear Schr ¨odinger operators and committor functions relevant in molecular dynamics. Y1 - 2023 U6 - https://doi.org/0.4208/jml.220416 VL - 2 IS - 1 SP - 31 EP - 64 ER -