1967 Publications

Nuclear instance segmentation and tracking for preimplantation mouse embryos

H. Nunley , Binglun Shao, Prateek Grover, A. Watters, S. Shvartsman, L. M. Brown, et al.

For investigations into fate specification and cell rearrangements in live images of preimplantation embryos, automated and accurate 3D instance segmentation of nuclei is invaluable; however, the performance of segmentation methods is limited by the images' low signal-to-noise ratio and high voxel anisotropy and the nuclei's dense packing and variable shapes. Supervised machine learning approaches have the potential to radically improve segmentation accuracy but are hampered by a lack of fully annotated 3D data. In this work, we first establish a novel mouse line expressing near-infrared nuclear reporter H2B-miRFP720. H2B-miRFP720 is the longest wavelength nuclear reporter in mice and can be imaged simultaneously with other reporters with minimal overlap. We then generate a dataset, which we call BlastoSPIM, of 3D microscopy images of H2B-miRFP720-expressing embryos with ground truth for nuclear instance segmentation. Using BlastoSPIM, we benchmark the performance of five convolutional neural networks and identify Stardist-3D as the most accurate instance segmentation method across preimplantation development. Stardist-3D, trained on BlastoSPIM, performs robustly up to the end of preimplantation development (> 100 nuclei) and enables studies of fate patterning in the late blastocyst. We, then, demonstrate BlastoSPIM's usefulness as pre-train data for related problems. BlastoSPIM and its corresponding Stardist-3D models are available at: blastospim.flatironinstitute.org.

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Efficient tensor network simulation of IBM’s Eagle kicked Ising experiment

We report an accurate and efficient classical simulation of a kicked Ising quantum system on the heavy hexagon lattice. A simulation of this system was recently performed on a 127-qubit quantum processor using noise-mitigation techniques to enhance accuracy [Y. Kim et al., Nature, 618, 500–5 (2023)]. Here we show that, by adopting a tensor network approach that reflects the geometry of the lattice and is approximately contracted using belief propagation, we can perform a classical simulation that is significantly more accurate and precise than the results obtained from the quantum processor and many other classical methods. We quantify the treelike correlations of the wave function in order to explain the accuracy of our belief propagation-based approach. We also show how our method allows us to perform simulations of the system to long times in the thermodynamic limit, corresponding to a quantum computer with an infinite number of qubits. Our tensor network approach has broader applications for simulating the dynamics of quantum systems with treelike correlations.

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Nested R̂ : Assessing the convergence of Markov chain Monte Carlo when running many short chains

C. Margossian, Matthew D. Hoffman, Pavel Sountsov, Lionel Riou-Durand, Aki Vehtari, Andrew Gelman

Recent developments in Markov chain Monte Carlo (MCMC) algorithms allow us to run thousands of chains in parallel almost as quickly as a single chain, using hardware accelerators such as GPUs. While each chain still needs to forget its initial point during a warmup phase, the subsequent sampling phase can be shorter than in classical settings, where we run only a few chains. To determine if the resulting short chains are reliable, we need to assess how close the Markov chains are to their stationary distribution after warmup. The potential scale reduction factor Rˆ is a popular convergence diagnostic but unfortunately can require a long sampling phase to work well. We present a nested design to overcome this challenge and a generalization called nested Rˆ. This new diagnostic works under conditions similar to Rˆ and completes the workflow for GPU-friendly samplers. In addition, the proposed nesting provides theoretical insights into the utility of Rˆ, in both classical and short-chains regimes.

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Decomposing imaginary time Feynman diagrams using separable basis functions: Anderson impurity model strong coupling expansion

J. Kaye, H. Strand, D. Golez

We present a deterministic algorithm for the efficient evaluation of imaginary time diagrams based on the recently introduced discrete Lehmann representation (DLR) of imaginary time Green's functions. In addition to the efficient discretization of diagrammatic integrals afforded by its approximation properties, the DLR basis is separable in imaginary time, allowing us to decompose diagrams into linear combinations of nested sequences of one-dimensional products and convolutions. Focusing on the strong coupling bold-line expansion of generalized Anderson impurity models, we show that our strategy reduces the computational complexity of evaluating an $M$th-order diagram at inverse temperature $\beta$ and spectral width $\omega_{\max}$ from $\mathcal{O}((\beta \omega_{\max})^{2M-1})$ for a direct quadrature to $\mathcal{O}(M (\log (\beta \omega_{\max}))^{M+1})$, with controllable high-order accuracy. We benchmark our algorithm using third-order expansions for multi-band impurity problems with off-diagonal hybridization and spin-orbit coupling, presenting comparisons with exact diagonalization and quantum Monte Carlo approaches. In particular, we perform a self-consistent dynamical mean-field theory calculation for a three-band Hubbard model with strong spin-orbit coupling representing a minimal model of Ca$_2$RuO$_4$, demonstrating the promise of the method for modeling realistic strongly correlated multi-band materials. For both strong and weak coupling expansions of low and intermediate order, in which diagrams can be enumerated, our method provides an efficient, straightforward, and robust black-box evaluation procedure. In this sense, it fills a gap between diagrammatic approximations of the lowest order, which are simple and inexpensive but inaccurate, and those based on Monte Carlo sampling of high-order diagrams.

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Finite Temperature Minimal Entangled Typical Thermal States Impurity Solver

We present a minimally entangled typical thermal state (METTS) quantum impurity solver for general multi-orbital systems at finite temperatures. We introduce an improved estimator for the single-particle Green's function that strongly reduces the large fluctuations at long imaginary time and low temperature, which were a severe limitation of the original algorithm. In combination with the fork tensor product states ansatz, we obtain a dynamical mean field theory (DMFT) quantum impurity solver, which we benchmark for single and three-band models down to low temperatures, including the effect of spin-orbit coupling in a realistic DMFT computation for the Hund's metal Sr2RuO4 down to low temperatures.

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Interpretable neural architecture search and transfer learning for understanding CRISPR–Cas9 off-target enzymatic reactions

Finely-tuned enzymatic pathways control cellular processes, and their dysregulation can lead to disease. Creating predictive and interpretable models for these pathways is challenging because of the complexity of the pathways and of the cellular and genomic contexts. Here we introduce Elektrum, a deep learning framework which addresses these challenges with data-driven and biophysically interpretable models for determining the kinetics of biochemical systems. First, it uses in vitro kinetic assays to rapidly hypothesize an ensemble of high-quality Kinetically Interpretable Neural Networks (KINNs) that predict reaction rates. It then employs a novel transfer learning step, where the KINNs are inserted as intermediary layers into deeper convolutional neural networks, fine-tuning the predictions for reaction-dependent in vivo outcomes. Elektrum makes effective use of the limited, but clean in vitro data and the complex, yet plentiful in vivo data that captures cellular context. We apply Elektrum to predict CRISPR-Cas9 off-target editing probabilities and demonstrate that Elektrum achieves state-of-the-art performance, regularizes neural network architectures, and maintains physical interpretability

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Explainable Equivariant Neural Networks for Particle Physics: PELICAN

A. Bogatskii, Timothy Hoffman, David W. Miller, Jan T. Offermann, Xiaoyang Liu

PELICAN is a novel permutation equivariant and Lorentz invariant or covariant aggregator network designed to overcome common limitations found in architectures applied to particle physics problems. Compared to many approaches that use non-specialized architectures that neglect underlying physics principles and require very large numbers of parameters, PELICAN employs a fundamentally symmetry group-based architecture that demonstrates benefits in terms of reduced complexity, increased interpretability, and raw performance. We present a comprehensive study of the PELICAN algorithm architecture in the context of both tagging (classification) and reconstructing (regression) Lorentz-boosted top quarks, including the difficult task of specifically identifying and measuring the $W$-boson inside the dense environment of the Lorentz-boosted top-quark hadronic final state. We also extend the application of PELICAN to the tasks of identifying quark-initiated vs.~gluon-initiated jets, and a multi-class identification across five separate target categories of jets. When tested on the standard task of Lorentz-boosted top-quark tagging, PELICAN outperforms existing competitors with much lower model complexity and high sample efficiency. On the less common and more complex task of 4-momentum regression, PELICAN also outperforms hand-crafted, non-machine learning algorithms. We discuss the implications of symmetry-restricted architectures for the wider field of machine learning for physics.

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Dynamical correlation functions from complex time evolution

We present an approach to tame the growth of entanglement during time evolution by tensor network methods. It combines time evolution in the complex plane with a perturbative and controlled reconstruction of correlation functions on the real-time axis. We benchmark our approach on the single impurity Anderson model. Compared to purely real-time evolution, the complex time evolution significantly reduces the required bond dimension to obtain the spectral function. Notably, our approach yields self-energy results with high precision at low frequencies, comparable to numerical renormalization group (NRG) results, and it successfully captures the exponentially small Kondo energy scale.

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Confirmations, correlatons and instabilities of a flexible fiber in an active fluid

S. Weady, D. Stein, Alexandra Zidovska, M. Shelley

Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the chromatin fiber over micron lengths. Motivated by this system, we develop a multiscale model of a long flexible polymer immersed in a suspension of active force dipoles as an analog to a chromatin fiber in an active fluid – the nucleoplasm. Linear analysis identifies an orientational instability driven by hydrodynamic and alignment interactions between the fiber and the suspension, and numerical simulations show activity can drive coherent motions and structured conformations. These results demonstrate how active and passive components, connected through fluid-structure interactions, can generate coherent structures and self-organize on large scales.

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December 6, 2023

Uniqueness and characteristic flow for a non strictly convex singular variational problem

Jean-FrançoisBabadjian, G. Francfort

This work addresses the question of uniqueness of the minimizers of a convex but not strictly convex integral functional with linear growth in a two-dimensional setting. The integrand -- whose precise form derives directly from the theory of perfect plasticity -- behaves quadratically close to the origin and grows linearly once a specific threshold is reached. Thus, in contrast with the only existing literature on uniqueness for functionals with linear growth, that is that which pertains to the generalized least gradient, the integrand is not a norm. We make use of hyperbolic conservation laws hidden in the structure of the problem to tackle uniqueness. Our argument strongly relies on the regularity of a vector field -- the Cauchy stress in the terminology of perfect plasticity -- which allows us to define characteristic lines, and then to employ the method of characteristics. Using the detailed structure of the characteristic landscape evidenced in our preliminary study \cite{BF}, we show that this vector field is actually continuous, save for possibly two points. The different behaviors of the energy density at zero and at infinity imply an inequality constraint on the Cauchy stress. Under a barrier type convexity assumption on the set where the inequality constraint is saturated, we show that uniqueness holds for pure Dirichlet boundary data, a stronger result than that of uniqueness for a given trace on the whole boundary since our minimizers can fail to attain the boundary data.

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2023
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