We introduce Scylla, a primal heuristic for mixed-integer optimization problems. It exploits approximate solves of the Linear Programming relaxations through the matrix-free Primal-Dual Hybrid Gradient algorithm with specialized termination criteria, and derives integer-feasible solutions via fix-and-propagate procedures and feasibility-pump-like updates to the objective function. Computational experiments show that the method is particularly suited to instances with hard linear relaxations.
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We show that contrary to appearances, Multimodal Type Theory (MTT) over a 2-category M can be interpreted in any M-shaped diagram of categories having, and functors preserving, M-sized limits, without the need for extra left adjoints. This is achieved by a construction called "co-dextrification" that co-freely adds left adjoints to any such diagram, which can then be used to interpret the "context lock" functors of MTT. Furthermore, if any of the functors in the diagram have right adjoints, these can also be internalized in type theory as negative modalities in the style of FitchTT. We introduce the name Multimodal Adjoint Type Theory (MATT) for the resulting combined general modal type theory. In particular, we can interpret MATT in any finite diagram of toposes and geometric morphisms, with positive modalities for inverse image functors and negative modalities for direct image functors.
The convergence analysis for least-squares finite element methods led to various adaptive mesh-refinement strategies: Collective marking algorithms driven by the built-in a posteriori error estimator or an alternative explicit residual-based error estimator as well as a separate marking strategy based on the alternative error estimator and an optimal data approximation algorithm. This paper reviews and discusses available convergence results. In addition, all three strategies are investigated empirically for a set of benchmarks examples of second-order elliptic partial differential equations in two spatial dimensions. Particular interest is on the choice of the marking and refinement parameters and the approximation of the given data. The numerical experiments are reproducible using the author's software package octAFEM available on the platform Code Ocean.
In this paper, new unfitted mixed finite elements are presented for elliptic interface problems with jump coefficients. Our model is based on a fictitious domain formulation with distributed Lagrange multiplier. The relevance of our investigations is better seen when applied to the framework of fluid structure interaction problems. Two finite elements schemes with piecewise constant Lagrange multiplier are proposed and their stability is proved theoretically. Numerical results compare the performance of those elements, confirming the theoretical proofs and verifying that the schemes converge with optimal rate.
Untargeted metabolomic profiling through liquid chromatography-mass spectrometry (LC-MS) measures a vast array of metabolites within biospecimens, advancing drug development, disease diagnosis, and risk prediction. However, the low throughput of LC-MS poses a major challenge for biomarker discovery, annotation, and experimental comparison, necessitating the merging of multiple datasets. Current data pooling methods encounter practical limitations due to their vulnerability to data variations and hyperparameter dependence. Here we introduce GromovMatcher, a flexible and user-friendly algorithm that automatically combines LC-MS datasets using optimal transport. By capitalizing on feature intensity correlation structures, GromovMatcher delivers superior alignment accuracy and robustness compared to existing approaches. This algorithm scales to thousands of features requiring minimal hyperparameter tuning. Applying our method to experimental patient studies of liver and pancreatic cancer, we discover shared metabolic features related to patient alcohol intake, demonstrating how GromovMatcher facilitates the search for biomarkers associated with lifestyle risk factors linked to several cancer types.
This paper presents a numerical method for the simulation of elastic solid materials coupled to fluid inclusions. The application is motivated by the modeling of vascularized tissues and by problems in medical imaging which target the estimation of effective (i.e., macroscale) material properties, taking into account the influence of microscale dynamics, such as fluid flow in the microvasculature. The method is based on the recently proposed Reduced Lagrange Multipliers framework. In particular, the interface between solid and fluid domains is not resolved within the computational mesh for the elastic material but discretized independently, imposing the coupling condition via non-matching Lagrange multipliers. Exploiting the multiscale properties of the problem, the resulting Lagrange multipliers space is reduced to a lower-dimensional characteristic set. We present the details of the stability analysis of the resulting method considering a non-standard boundary condition that enforces a local deformation on the solid-fluid boundary. The method is validated with several numerical examples.
We introduce a novel methodology that leverages the strength of Physics-Informed Neural Networks (PINNs) to address the counterdiabatic (CD) protocol in the optimization of quantum circuits comprised of systems with $N_{Q}$ qubits. The primary objective is to utilize physics-inspired deep learning techniques to accurately solve the time evolution of the different physical observables within the quantum system. To accomplish this objective, we embed the necessary physical information into an underlying neural network to effectively tackle the problem. In particular, we impose the hermiticity condition on all physical observables and make use of the principle of least action, guaranteeing the acquisition of the most appropriate counterdiabatic terms based on the underlying physics. The proposed approach offers a dependable alternative to address the CD driving problem, free from the constraints typically encountered in previous methodologies relying on classical numerical approximations. Our method provides a general framework to obtain optimal results from the physical observables relevant to the problem, including the external parameterization in time known as scheduling function, the gauge potential or operator involving the non-adiabatic terms, as well as the temporal evolution of the energy levels of the system, among others. The main applications of this methodology have been the $\mathrm{H_{2}}$ and $\mathrm{LiH}$ molecules, represented by a 2-qubit and 4-qubit systems employing the STO-3G basis. The presented results demonstrate the successful derivation of a desirable decomposition for the non-adiabatic terms, achieved through a linear combination utilizing Pauli operators. This attribute confers significant advantages to its practical implementation within quantum computing algorithms.
Magnetic resonance imaging (MRI) plays an important role in modern medical diagnostic but suffers from prolonged scan time. Current deep learning methods for undersampled MRI reconstruction exhibit good performance in image de-aliasing which can be tailored to the specific kspace undersampling scenario. But it is very troublesome to configure different deep networks when the sampling setting changes. In this work, we propose a deep plug-and-play method for undersampled MRI reconstruction, which effectively adapts to different sampling settings. Specifically, the image de-aliasing prior is first learned by a deep denoiser trained to remove general white Gaussian noise from synthetic data. Then the learned deep denoiser is plugged into an iterative algorithm for image reconstruction. Results on in vivo data demonstrate that the proposed method provides nice and robust accelerated image reconstruction performance under different undersampling patterns and sampling rates, both visually and quantitatively.
This study focuses on the use of model and data fusion for improving the Spalart-Allmaras (SA) closure model for Reynolds-averaged Navier-Stokes solutions of separated flows. In particular, our goal is to develop of models that not-only assimilate sparse experimental data to improve performance in computational models, but also generalize to unseen cases by recovering classical SA behavior. We achieve our goals using data assimilation, namely the Ensemble Kalman Filtering approach (EnKF), to calibrate the coefficients of the SA model for separated flows. A holistic calibration strategy is implemented via a parameterization of the production, diffusion, and destruction terms. This calibration relies on the assimilation of experimental data collected velocity profiles, skin friction, and pressure coefficients for separated flows. Despite using of observational data from a single flow condition around a backward-facing step (BFS), the recalibrated SA model demonstrates generalization to other separated flows, including cases such as the 2D-bump and modified BFS. Significant improvement is observed in the quantities of interest, i.e., skin friction coefficient ($C_f$) and pressure coefficient ($C_p$) for each flow tested. Finally, it is also demonstrated that the newly proposed model recovers SA proficiency for external, unseparated flows, such as flow around a NACA-0012 airfoil without any danger of extrapolation, and that the individually calibrated terms in the SA model are targeted towards specific flow-physics wherein the calibrated production term improves the re-circulation zone while destruction improves the recovery zone.
We introduce a novel ridge detection algorithm for time-frequency (TF) analysis, particularly tailored for intricate nonstationary time series encompassing multiple non-sinusoidal oscillatory components. The algorithm is rooted in the distinctive geometric patterns that emerge in the TF domain due to such non-sinusoidal oscillations. We term this method \textit{shape-adaptive mode decomposition-based multiple harmonic ridge detection} (\textsf{SAMD-MHRD}). A swift implementation is available when supplementary information is at hand. We demonstrate the practical utility of \textsf{SAMD-MHRD} through its application to a real-world challenge. We employ it to devise a cutting-edge walking activity detection algorithm, leveraging accelerometer signals from an inertial measurement unit across diverse body locations of a moving subject.
Graph Neural Networks (GNNs) have emerged as one of the leading approaches for machine learning on graph-structured data. Despite their great success, critical computational challenges such as over-smoothing, over-squashing, and limited expressive power continue to impact the performance of GNNs. In this study, inspired from the time-reversal principle commonly utilized in classical and quantum physics, we reverse the time direction of the graph heat equation. The resulted reversing process yields a class of high pass filtering functions that enhance the sharpness of graph node features. Leveraging this concept, we introduce the Multi-Scaled Heat Kernel based GNN (MHKG) by amalgamating diverse filtering functions' effects on node features. To explore more flexible filtering conditions, we further generalize MHKG into a model termed G-MHKG and thoroughly show the roles of each element in controlling over-smoothing, over-squashing and expressive power. Notably, we illustrate that all aforementioned issues can be characterized and analyzed via the properties of the filtering functions, and uncover a trade-off between over-smoothing and over-squashing: enhancing node feature sharpness will make model suffer more from over-squashing, and vice versa. Furthermore, we manipulate the time again to show how G-MHKG can handle both two issues under mild conditions. Our conclusive experiments highlight the effectiveness of proposed models. It surpasses several GNN baseline models in performance across graph datasets characterized by both homophily and heterophily.
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