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arXiv 2023年

作者： Maisuradze, Luka King, Megan C. Surovtsev, Ivan V. Mochrie, Simon G.J. Shattuck, Mark D. O’Hern, Corey S. Department of Molecular Biophysics and Biochemistry Yale University New HavenCT United States Department of Cell Biology Yale School of Medicine New HavenCT United States Department of Physics Yale University New HavenCT United States Benjamin Levich Institute Physics Department The City College of New York New YorkNY United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT United States

Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture techniques generate Hi-C maps that can provide insight into the 3D structure of chromatin. Hi-C maps can be represented as a symmetric matrix Aij, where each element represents the average contact probability or number of contacts between chromatin loci i and j. Previous studies have detected topologically associating domains (TADs), or self-interacting regions in Aij within which the contact probability is greater than that outside the region. Many algorithms have been developed to identify TADs within Hi-C maps. However, most TAD identification algorithms are unable to identify nested or overlapping TADs and for a given Hi-C map there is significant variation in the location and number of TADs identified by different methods. We develop a novel method to identify TADs, KerTAD, using a kernel-based technique from computer vision and image processing that is able to accurately identify nested and overlapping TADs. We benchmark this method against state-of-the-art TAD identification methods on both synthetic and experimental data sets. We find that the new method consistently has higher true positive rates (TPR) and lower false discovery rates (FDR) than all tested methods for both synthetic and manually annotated experimental Hi-C maps. The TPR for KerTAD is also largely insensitive to increasing noise and sparsity, in contrast to the other methods. We also find that KerTAD is consistent in the number and size of TADs identified across replicate experimental Hi-C maps for several organisms. Thus, KerTAD will improve automated TAD identification and enable researchers to better correlate changes in TADs to biological phenomena, such as enhancer-promoter interactions and disease states. © 2023, CC BY.

关键词： Topology

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KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection

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science (New York, N.Y.) 2025年第6735期387卷 eadn2337页

作者： Fagerberg, Eric Attanasio, John Dien, Christine Singh, Jaiveer Kessler, Emily A. Abdullah, Leena Shen, Jian Hunt, Brian G. Connolly, Kelli A. De Brouwer, Edward He, Jiaming Iyer, Nivedita R. Buck, Jessica Borr, Emily R. Damo, Martina Foster, Gena G. Giles, Josephine R. Huang, Yina H. Tsang, John S. Krishnaswamy, Smita Cui, Weiguo Joshi, Nikhil S. Department of Immunobiology Yale University School of Medicine New Haven CT United States Program in Computational Biology & Bioinformatics Yale University New Haven CT United States Department of Microbiology and Immunology Geisel School of Medicine at Dartmouth NH United States Department of Pathology Feinberg School of Medicine at Northwestern University Chicago IL United States Department of Genetics and Computer Science Yale University School of Medicine New Haven CT United States Department of Medicine University of Chicago Chicago IL United States Section of Hematology Department of Internal Medicine Yale University School of Medicine New Haven CT United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania Philadelphia PA United States Institute for Immunology Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Parker Institute for Cancer Immunotherapy Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Yale Center for Systems and Engineering Immunology Yale University School of Medicine New Haven CT United States New Haven CT United States Department of Biomedical Engineering Yale University New Haven CT United States Computational Biology and Bioinformatics Program Yale University CT USA New Haven United States Applied Math Program Yale University New Haven CT United States

Naïve CD8 T cells have the potential to differentiate into a spectrum of functional states during an immune response. How these developmental decisions are made and what mechanisms exist to suppress differentiation toward alternative fates remains unclear. We employed in vivo CRISPR-Cas9-based perturbation sequencing to assess the role of ~40 transcription factors (TFs) and epigenetic modulators in T cell fate decisions. Unexpectedly, we found that knockout of the TF Klf2 resulted in aberrant differentiation to exhausted-like CD8 T cells during acute infection. KLF2 was required to suppress the exhaustion-promoting TF TOX and to enable the TF TBET to drive effector differentiation. KLF2 was also necessary to maintain a polyfunctional tumor-specific progenitor state. Thus, KLF2 provides effector CD8 T cell lineage fidelity and suppresses the exhaustion program.

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Mass Transport in a Highly Immiscible Alloy on Extended Shear Deformation

SSRN

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SSRN 2022年

作者： Song, Miao Liu, Jia Ma, Xiaolong Pang, Qin Olszta, Matthew J. Silverstein, Joshua Pallaka, Madhusudhan R. Sushko, Peter V. Mathaudhu, Suveen N. Powell, Cynthia Devaraj, Arun Gwalani, Bharat Physical and Computational Sciences Directorate Pacific Northwest National Laboratory 902 Battelle Boulevard RichlandWA99354 United States Energy and Environmental Directorate Pacific Northwest National Laboratory 902 Battelle Boulevard RichlandWA99354 United States Material Science and Engineering Program University of California Riverside RiversideCA92521 United States Colorado School of Mines 1500 Illinois St. GoldenCO8040 United States

Forced mixing to a single-phase or supersaturated solid solution (SSS) and its prerequisite microstructure evolution in immiscible systems has been a focus of research for fundamental science and practical applications. Controlling the formation of SSS by shear deformation could enable a material design beyond conventional equilibrium microstructure in immiscible systems. Here, a highly immiscible Cu-50 at. % Cr binary alloy (mixing enthalpy of ~ 20 kJ·mol-1) was employed to investigate the microstructure evolution and localized tendencies of SSS during severe shear deformation. Our results demonstrate the dislocation mediated microstructural refinement process in each phase of the binary alloy and the mechanisms associated with localized solute supersaturation as a function of shear strain. Pronounced grain refinement in the softer Cu phase occurs owing to the strain localization driving the preferential dynamic recrystallization. The grain refinement of the Cr phase, however, is enabled by the progressive evolution of grain lamination, splitting, and fragmentation as a function of shear strain. The solute supersaturation is found to be strongly dependent on the local environments that affect the dislocation activity, including the level of microstructure refinement, the interfacial orientation relationship, the mechanical incompatibility, and the localized preferential phase oxidation. Ab initio simulations confirm that it is more favorable to oxidize Cr than Cu at incoherent Cu/Cr interfaces, limiting the mass transport on an incoherent boundary. Our results unveil the mechanism underpinning the non-equilibrium mass transport in immiscible systems upon severe deformation that can be applied to produce immiscible alloys with superior mechanical properties. © 2022, The Authors. All rights reserved.

关键词： Tribology

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An optimal algorithm for strict circular seriation

arXiv

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arXiv 2021年

作者： Armstrong, Santiago Guzmán, Cristóbal Long, Carlos A. Sing Institute for Mathematical and Computational Engineering Pontificia Universidad Católica de Chile Santiago Chile Anid - Millennium Science Initiative Program Millennium Nucleus Center for the Discovery of Structures in Complex Data Santiago Chile Department of Applied Mathematics University of Twente Netherlands Institute for Biological and Medical Engineering Pontificia Universidad Católica de Chile Santiago Chile

We study the problem of circular seriation, where we are given a matrix of pairwise dissimilarities between n objects, and the goal is to find a circular order of the objects in a manner that is consistent with their dissimilarity. This problem is a generalization of the classical linear seriation problem where the goal is to find a linear order, and for which optimal O(n2) algorithms are known. Our contributions can be summarized as follows. First, we introduce circular Robinson matrices as the natural class of dissimilarity matrices for the circular seriation problem. Second, for the case of strict circular Robinson dissimilarity matrices we provide an optimal O(n2) algorithm for the circular seriation problem. Finally, we propose a statistical model to analyze the well-posedness of the circular seriation problem for large n. In particular, we establish O(log(n)/n) rates on the distance between any circular ordering found by solving the circular seriation problem to the underlying order of the model, in the Kendall-tau *** Codes 68R01, 05C85, 05C50, 05C25, 65C20 Copyright © 2021, The Authors. All rights reserved.

关键词： Trees (mathematics)

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Position: Bayesian deep learning is needed in the age of large-scale AI 24

Position: Bayesian deep learning is needed in the age of lar...

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Proceedings of the 41st International Conference on Machine Learning

作者： Theodore Papamarkou Maria Skoularidou Konstantina Palla Laurence Aitchison Julyan Arbel David Dunson Maurizio Filippone Vincent Fortuin Philipp Hennig José Miguel Hernández-Lobato Aliaksandr Hubin Alexander Immer Theofanis Karaletsos Mohammad Emtiyaz Khan Agustinus Kristiadi Yingzhen Li Stephan Mandt Christopher Nemeth Michael A. Osborne Tim G. J. Rudner David Rügamer Yee Whye Teh Max Welling Andrew Gordon Wilson Ruqi Zhang Department of Mathematics The University of Manchester Manchester UK Eric and Wendy Schmidt Center Broad Institute of MIT and Harvard Cambridge Spotify London UK Computational Neuroscience Unit University of Bristol Bristol UK Centre Inria de l'Université Grenoble Alpes Grenoble France Department of Statistical Science Duke University Statistics Program KAUST Saudi Arabia Helmholtz AI Munich Germany and Department of Computer Science Technical University of Munich Munich Germany and Munich Center for Machine Learning Munich Germany Tübingen AI Center University of Tübingen Tübingen Germany Department of Engineering University of Cambridge Cambridge UK Department of Mathematics University of Oslo Oslo Norway and Bioinformatics and Applied Statistics Norwegian University of Life Sciences Ås Norway Department of Computer Science ETH Zurich Switzerland Chan Zuckerberg Initiative California Center for Advanced Intelligence Project RIKEN Tokyo Japan Vector Institute Toronto Canada Department of Computing Imperial College London London UK Department of Computer Science UC Irvine Irvine Department of Mathematics and Statistics Lancaster University Lancaster UK Department of Engineering Science University of Oxford Oxford UK Center for Data Science New York University New York Munich Center for Machine Learning Munich Germany and Department of Statistics LMU Munich Munich Germany DeepMind London UK and Department of Statistics University of Oxford Oxford UK Informatics Institute University of Amsterdam Amsterdam Netherlands Courant Institute of Mathematical Sciences and Center for Data Science Computer Science Department New York University New York Department of Computer Science Purdue University West Lafayette

In the current landscape of deep learning research, there is a predominant emphasis on achieving high predictive accuracy in supervised tasks involving large image and language datasets. However, a broader perspective reveals a multitude of overlooked metrics, tasks, and data types, such as uncertainty, active and continual learning, and scientific data, that demand attention. Bayesian deep learning (BDL) constitutes a promising avenue, offering advantages across these diverse settings. This paper posits that BDL can elevate the capabilities of deep learning. It revisits the strengths of BDL, acknowledges existing challenges, and highlights some exciting research avenues aimed at addressing these obstacles. Looking ahead, the discussion focuses on possible ways to combine large-scale foundation models with BDL to unlock their full potential.

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Layer-dependent optically-induced spin polarization in InSe

arXiv

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arXiv 2022年

作者： Nelson, Jovan Stanev, Teodor K. Lebedev, Dmitry LaMountain, Trevor Tyler Gish, J. Zeng, Hongfei Shin, Hyeondeok Heinonen, Olle Watanabe, Kenji Taniguchi, Takashi Hersam, Mark C. Stern, Nathaniel P. Applied Physics Program Northwestern University EvanstonIL60208 United States Department of Physics and Astronomy Northwestern University EvanstonIL60208 United States Department of Material Science & Engineering Northwestern University EvanstonIL60208 United States Computational Science Division Argonne National Laboratory LemontIL60439 United States Material Science Division Argonne National Laboratory LemontIL60439 United States Research Center for Functional Materials National Institute for Materials Science 1-1 Namiki Tsukuba305-0044 Japan International Center for Materials Nanoarchitectonics National Institute for Materials Science 1-1 Namiki Tsukuba305-0044 Japan Department of Chemistry Northwestern University EvanstonIL60208 United States Department of Electrical Engineering and Computer Science Northwestern University EvanstonIL60208 United States

Optical control of spin in semiconductors has been pioneered using nanostructures of III-V and II-VI semiconductors, but the emergence of two-dimensional van der Waals materials offers an alternative low-dimensional platform for spintronic phenomena. Indium selenide (InSe), a group-III monochalcogenide van der Waals material, has shown promise for opto-electronics due to its high electron mobility, tunable direct bandgap, and quantum transport. In addition to these confirmed properties, there are predictions of spin-dependent optical selection rules suggesting potential for all-optical excitation and control of spin in a two-dimensional layered material. Despite these predictions, layer-dependent optical spin phenomena in InSe have yet to be explored. Here, we present measurements of layer-dependent optical spin dynamics in few-layer and bulk InSe. Polarized photo-luminescence reveals layer-dependent optical orientation of spin, thereby demonstrating the optical selection rules in few-layer InSe. Spin dynamics are also studied in many-layer InSe using time-resolved Kerr rotation spectroscopy. By applying out-of-plane and in-plane static magnetic fields for polarized emission measurements and Kerr measurements, respectively, the g-factor for InSe was extracted. Further investigations are done by calculating precession values using a k·p model, which is supported by ab-initio density functional theory. Comparison of predicted precession rates with experimental measurements highlights the importance of excitonic effects in InSe for understanding spin dynamics. Optical orientation of spin is an important prerequisite for opto-spintronic phenomena and devices, and these first demonstrations of layer-dependent optical excitation of spins in InSe lay the foundation for combining layer-dependent spin properties with advantageous electronic properties found in this material. Copyright © 2022, The Authors. All rights reserved.

关键词： Spin dynamics

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Stability of stochastic gradient descent on nonsmooth convex losses 20

Stability of stochastic gradient descent on nonsmooth convex...

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Proceedings of the 34th International Conference on Neural Information Processing Systems

作者： Raef Bassily Vitaly Feldman Cristóbal Guzmán Kunal Talwar Department of Computer Science & Engineering The Ohio State University Apple Pontificia Universidad Católica de Chile Institute for Mathematical and Computational Engineering ANID – Millennium Science Initiative Program Millennium Nucleus Center for the Discovery of Structures in Complex Data

ISBN: (纸本)9781713829546

Uniform stability is a notion of algorithmic stability that bounds the worst case change in the model output by the algorithm when a single data point in the dataset is replaced. An influential work of Hardt et al. [20] provides strong upper bounds on the uniform stability of the stochastic gradient descent (SGD) algorithm on sufficiently smooth convex losses. These results led to important progress in understanding of the generalization properties of SGD and several applications to differentially private convex optimization for smooth *** work is the first to address uniform stability of SGD on nonsmooth convex losses. Specifically, we provide sharp upper and lower bounds for several forms of SGD and full-batch GD on arbitrary Lipschitz nonsmooth convex losses. Our lower bounds show that, in the nonsmooth case, (S)GD can be inherently less stable than in the smooth case. On the other hand, our upper bounds show that (S)GD is sufficiently stable for deriving new and useful bounds on generalization error. Most notably, we obtain the first dimension-independent generalization bounds for multi-pass SGD in the nonsmooth case. In addition, our bounds allow us to derive a new algorithm for differentially private nonsmooth stochastic convex optimization with optimal excess population risk. Our algorithm is simpler and more efficient than the best known algorithm for the nonsmooth case [16].

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Seebeck Coefficient in a Cuprate Superconductor: Particle-Hole Asymmetry in the Strange Metal Phase and Fermi Surface Transformation in the Pseudogap Phase

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Physical Review X 2022年第1期12卷 011037-011037页

作者： A. Gourgout G. Grissonnanche F. Laliberté A. Ataei L. Chen S. Verret J.-S. Zhou J. Mravlje A. Georges N. Doiron-Leyraud Louis Taillefer Institut Quantique Département de physique and RQMP Université de Sherbrooke Sherbrooke Québec Canada Laboratory of Atomic and Solid State Physics Cornell University Ithaca New York USA Kavli Institute at Cornell for Nanoscale Science Ithaca New York USA Materials Science and Engineering Program/Mechanical Engineering University of Texas-Austin Austin Texas USA Department of Theoretical Physics Institute Jožef Stefan Ljubljana Slovenia Collège de France 11 place Marcelin Berthelot Paris France Center for Computational Quantum Physics Flatiron Institute New York New York USA CPHT CNRS Ecole Polytechnique IP Paris Palaiseau France DQMP Université de Genève Geneva Switzerland Canadian Institute for Advanced Research Toronto Ontario Canada

We report measurements of the Seebeck effect in both the ab plane (Sa) and along the c axis (Sc) of the cuprate superconductor La1.6−xNd0.4SrxCuO4 (Nd-LSCO), performed in magnetic fields large enough to suppress superconductivity down to low temperature. We use the Seebeck coefficient as a probe of the particle-hole asymmetry of the electronic structure across the pseudogap critical doping p⋆=0.23. Outside the pseudogap phase, at p=0.24>p⋆, we observe a positive and essentially isotropic Seebeck coefficient as T→0. That S>0 at p=0.24 is at odds with expectations given the electronic band structure of Nd-LSCO above p⋆ and its known electronlike Fermi surface. We can reconcile this observation by invoking an energy-dependent scattering rate with a particle-hole asymmetry, possibly rooted in the non-Fermi-liquid nature of cuprates just above p⋆. Inside the pseudogap phase, for p

关键词： Superconductivity Strongly correlated systems

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Finding shortest and nearly shortest path nodes in large substantially incomplete networks

arXiv

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arXiv 2022年

作者： Kitsak, Maksim Ganin, Alexander Elmokashfi, Ahmed Cui, Hongzhu Eisenberg, Daniel A. Alderson, David L. Korkin, Dmitry Linkov, Igor Faculty of Electrical Engineering Mathematics and Computer Science Delft University of Technology Delft Netherlands Network Science Institute Northeastern University BostonMA02115 United States Department of Systems and Information Engineering University of Virginia CharlottesvilleVA22904 United States U.S. Army Engineer Research and Development Center Contractor Concord MA01742 United States Simula Metropolitan Center for Digital Engineering Oslo Norway Bioinformatics and Computational Biology Program Worcester Polytechnic Institute WorcesterMA01609 United States Institute for Genomic Medicine Columbia University Medical Center New YorkNY United States Operations Research Department Naval Postgraduate School MontereyCA93943 United States Data Science Program Worcester Polytechnic Institute WorcesterMA01609 United States Computer Science Department Worcester Polytechnic Institute WorcesterMA01609 United States U.S. Army Engineer Research and Development Center Environmental Laboratory Concord MA01742 United States

Dynamic processes on networks, be it information transfer in the Internet, contagious spreading in a social network, or neural signaling, take place along shortest or nearly shortest paths. Unfortunately, our maps of most large networks are substantially incomplete due to either the highly dynamic nature of networks, or high cost of network measurements, or both, rendering traditional path finding methods inefficient. We find that shortest paths in large real networks, such as the network of protein-protein interactions (PPI) and the Internet at the autonomous system (AS) level, are not random but are organized according to latent-geometric rules. If nodes of these networks are mapped to points in latent hyperbolic spaces, shortest paths in them align along geodesic curves connecting endpoint nodes. We find that this alignment is sufficiently strong to allow for the identification of shortest path nodes even in the case of substantially incomplete networks. We demonstrate the utility of latent-geometric path finding in problems of cellular pathway reconstruction and communication security. Copyright © 2022, The Authors. All rights reserved.

关键词： Proteins

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Augment Reality-Based Teaching Practice

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Biomedical engineering education 2021年第1期1卷 237-241页

作者： You Wu Mingzhen Zhang Xiaosi Li Yu Gan Chao Zhao Department of Chemical and Biological Engineering The University of Alabama P. O. Box870203 Tuscaloosa AL 35401 USA. Computational Structural Biology Section Basic Science Program Frederick National Laboratory for Cancer Research Frederick MD 21702 USA. Department of Electrical and Computer Engineering The University of Alabama P. O. Box870286 Tuscaloosa AL 35401 USA.

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