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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.

Mesh-based Graph Neural Networks (GNNs) have recently shown capabilities to simulate complex multiphysics problems with accelerated performance times. However, mesh-based GNNs require a large number of message-passing (MP) steps and suffer from over-smoothing for problems involving very fine mesh. In this work, we develop a multiscale mesh-based GNN framework mimicking a conventional iterative multigrid solver, coupled with adaptive mesh refinement (AMR), to mitigate challenges with conventional mesh-based GNNs. We use the framework to accelerate phase field (PF) fracture problems involving coupled partial differential equations with a near-singular operator due to near-zero modulus inside the crack. We define the initial graph representation using all mesh resolution levels. We perform a series of downsampling steps using Transformer MP GNNs to reach the coarsest graph followed by upsampling steps to reach the original graph. We use skip connectors from the generated embedding during coarsening to prevent over-smoothing. We use Transfer Learning (TL) to significantly reduce the size of training datasets needed to simulate different crack configurations and loading conditions. The trained framework showed accelerated simulation times, while maintaining high accuracy for all cases compared to physics-based PF fracture model. Finally, this work provides a new approach to accelerate a variety of mesh-based engineering multiphysics problems

We introduce a higher-dimensional "cubical" chain complex and apply it to the design of quantum locally testable codes. Our cubical chain complex can be constructed for any dimension $t$, and in a precise sense generalizes the Sipser-Spielman construction of expander codes (case $t=1$) and the constructions by Dinur et. al and Panteleev and Kalachev of a square complex (case $t$=2), which have been applied to the design of classical locally testable and quantum low-density parity check codes respectively. For $t=4$ our construction gives a family of quantum locally testable codes conditional on a conjecture about robustness of four-tuples of random linear maps. These codes have linear dimension, inverse poly-logarithmic relative distance and soundness, and polylogarithmic-size parity checks. Our complex can be built in a modular way from two ingredients. Firstly, the geometry (edges, faces, cubes, etc.) is provided by a set $G$ of size $N$, together with pairwise commuting sets of actions $A_1,\ldots,A_t$ on it. Secondly, the chain complex itself is obtained by associating local coefficient spaces based on codes, with each geometric object, and introducing local maps on those coefficient spaces. We bound the cycle and co-cycle expansion of the chain complex. The assumptions we need are two-fold: firstly, each Cayley graph $Cay(G,A_j)$ needs to be a good (spectral) expander, and secondly, the families of codes and their duals both need to satisfy a form of robustness (that generalizes the condition of agreement testability for pairs of codes). While the first assumption is easy to satisfy, it is currently not known if the second can be achieved.

We develop new multilevel Monte Carlo (MLMC) methods to estimate the expectation of the smallest eigenvalue of a stochastic convection-diffusion operator with random coefficients. The MLMC method is based on a sequence of finite element (FE) discretizations of the eigenvalue problem on a hierarchy of increasingly finer meshes. For the discretized, algebraic eigenproblems we use both the Rayleigh quotient (RQ) iteration and implicitly restarted Arnoldi (IRA), providing an analysis of the cost in each case. By studying the variance on each level and adapting classical FE error bounds to the stochastic setting, we are able to bound the total error of our MLMC estimator and provide a complexity analysis. As expected, the complexity bound for our MLMC estimator is superior to plain Monte Carlo. To improve the efficiency of the MLMC further, we exploit the hierarchy of meshes and use coarser approximations as starting values for the eigensolvers on finer ones. To improve the stability of the MLMC method for convection-dominated problems, we employ two additional strategies. First, we consider the streamline upwind Petrov--Galerkin formulation of the discrete eigenvalue problem, which allows us to start the MLMC method on coarser meshes than is possible with standard FEs. Second, we apply a homotopy method to add stability to the eigensolver for each sample. Finally, we present a multilevel quasi-Monte Carlo method that replaces Monte Carlo with a quasi-Monte Carlo (QMC) rule on each level. Due to the faster convergence of QMC, this improves the overall complexity. We provide detailed numerical results comparing our different strategies to demonstrate the practical feasibility of the MLMC method in different use cases. The results support our complexity analysis and further demonstrate the superiority over plain Monte Carlo in all cases.

The evaluation of text-generative vision-language models is a challenging yet crucial endeavor. By addressing the limitations of existing Visual Question Answering (VQA) benchmarks and proposing innovative evaluation methodologies, our research seeks to advance our understanding of these models' capabilities. We propose a novel VQA benchmark based on well-known visual classification datasets which allows a granular evaluation of text-generative vision-language models and their comparison with discriminative vision-language models. To improve the assessment of coarse answers on fine-grained classification tasks, we suggest using the semantic hierarchy of the label space to ask automatically generated follow-up questions about the ground-truth category. Finally, we compare traditional NLP and LLM-based metrics for the problem of evaluating model predictions given ground-truth answers. We perform a human evaluation study upon which we base our decision on the final metric. We apply our benchmark to a suite of vision-language models and show a detailed comparison of their abilities on object, action, and attribute classification. Our contributions aim to lay the foundation for more precise and meaningful assessments, facilitating targeted progress in the exciting field of vision-language modeling.

We propose a hybrid iterative method based on MIONet for PDEs, which combines the traditional numerical iterative solver and the recent powerful machine learning method of neural operator, and further systematically analyze its theoretical properties, including the convergence condition, the spectral behavior, as well as the convergence rate, in terms of the errors of the discretization and the model inference. We show the theoretical results for the frequently-used smoothers, i.e. Richardson (damped Jacobi) and Gauss-Seidel. We give an upper bound of the convergence rate of the hybrid method w.r.t. the model correction period, which indicates a minimum point to make the hybrid iteration converge fastest. Several numerical examples including the hybrid Richardson (Gauss-Seidel) iteration for the 1-d (2-d) Poisson equation are presented to verify our theoretical results, and also reflect an excellent acceleration effect. As a meshless acceleration method, it is provided with enormous potentials for practice applications.

The availability of data is limited in some fields, especially for object detection tasks, where it is necessary to have correctly labeled bounding boxes around each object. A notable example of such data scarcity is found in the domain of marine biology, where it is useful to develop methods to automatically detect submarine species for environmental monitoring. To address this data limitation, the state-of-the-art machine learning strategies employ two main approaches. The first involves pretraining models on existing datasets before generalizing to the specific domain of interest. The second strategy is to create synthetic datasets specifically tailored to the target domain using methods like copy-paste techniques or ad-hoc simulators. The first strategy often faces a significant domain shift, while the second demands custom solutions crafted for the specific task. In response to these challenges, here we propose a transfer learning framework that is valid for a generic scenario. In this framework, generated images help to improve the performances of an object detector in a few-real data regime. This is achieved through a diffusion-based generative model that was pretrained on large generic datasets, and is not trained on the task-specific domain. We validate our approach on object detection tasks, specifically focusing on fishes in an underwater environment, and on the more common domain of cars in an urban setting. Our method achieves detection performance comparable to models trained on thousands of images, using only a few hundreds of input data. Our results pave the way for new generative AI-based protocols for machine learning applications in various domains, for instance ranging from geophysics to biology and medicine.

The stochastic simulation algorithm (SSA) and the corresponding Monte Carlo (MC) method are among the most common approaches for studying stochastic processes. They rely on knowledge of interevent probability density functions (PDFs) and on information about dependencies between all possible events. Analytical representations of a PDF are difficult to specify in advance, in many real life applications. Knowing the shapes of PDFs, and using experimental data, different optimization schemes can be applied in order to evaluate probability density functions and, therefore, the properties of the studied system. Such methods, however, are computationally demanding, and often not feasible. We show that, in the case where experimentally accessed properties are directly related to the frequencies of events involved, it may be possible to replace the heavy Monte Carlo core of optimization schemes with an analytical solution. Such a replacement not only provides a more accurate estimation of the properties of the process, but also reduces the simulation time by a factor of order of the sample size (at least $\approx 10^4$). The proposed analytical approach is valid for any choice of PDF. The accuracy, computational efficiency, and advantages of the method over MC procedures are demonstrated in the exactly solvable case and in the evaluation of branching fractions in controlled radical polymerization (CRP) of acrylic monomers. This polymerization can be modeled by a constrained stochastic process. Constrained systems are quite common, and this makes the method useful for various applications.

This study proposes a Network to recognize displacement of a RC frame structure from a video by a monocular camera. The proposed Network consists of two modules which is FlowNet2 and POFRN-Net. FlowNet2 is used to generate dense optical flow as well as POFRN-Net is to extract pose parameter H. FlowNet2 convert two video frames into dense optical flow. POFRN-Net is inputted dense optical flow from FlowNet2 to output the pose parameter H. The displacement of any points of structure can be calculated from parameter H. The Fast Fourier Transform (FFT) is applied to obtain frequency domain signal from corresponding displacement signal. Furthermore, the comparison of the truth displacement on the First floor of the First video is shown in this study. Finally, the predicted displacements on four floors of RC frame structure of given three videos are exhibited in the last of this study.

In recent years, object detection has experienced impressive progress. Despite these improvements, there is still a significant gap in the performance between the detection of small and large objects. We analyze the current state-of-the-art model, Mask-RCNN, on a challenging dataset, MS COCO. We show that the overlap between small ground-truth objects and the predicted anchors is much lower than the expected IoU threshold. We conjecture this is due to two factors; (1) only a few images are containing small objects, and (2) small objects do not appear enough even within each image containing them. We thus propose to oversample those images with small objects and augment each of those images by copy-pasting small objects many times. It allows us to trade off the quality of the detector on large objects with that on small objects. We evaluate different pasting augmentation strategies, and ultimately, we achieve 9.7\% relative improvement on the instance segmentation and 7.1\% on the object detection of small objects, compared to the current state of the art method on MS COCO.