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Bursting cells lead to ambient RNA that contaminates sequencing data. This process is especially problematic in perturbation experiments where transcription factors are implanted into cells to determine their effects. The presence of contaminants makes it difficult to determine whether a factor is truly expressed in the cell. This paper studies the properties of contaminant noise from an analytical perspective, showing that the cell bursting process constrains the form of the noise distribution across factors. These constraints can be leveraged to improve decontamination by removing counts that are more likely the result of noise than expression. In two biological replicates of a perturbation experiment, run across two sequencing protocols, decontaminated counts agree with bulk genomic measurements of the transduction rate and are automatically corrected for differences in sequencing.

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The expressivity of Graph Neural Networks (GNNs) can be entirely characterized by appropriate fragments of the first-order logic. Namely, any query of the two variable fragment of graded modal logic (GC2) interpreted over labeled graphs can be expressed using a GNN whose size depends only on the depth of the query. As pointed out by [Barcelo & Al., 2020, Grohe, 2021], this description holds for a family of activation functions, leaving the possibility for a hierarchy of logics expressible by GNNs depending on the chosen activation function. In this article, we show that such hierarchy indeed exists by proving that GC2 queries cannot be expressed by GNNs with polynomial activation functions. This implies a separation between polynomial and popular non-polynomial activations (such as ReLUs, sigmoid and hyperbolic tan and others) and answers an open question formulated by [Grohe, 2021].

Quantum computing has recently emerged as a transformative technology. Yet, its promised advantages rely on efficiently translating quantum operations into viable physical realizations. In this work, we use generative machine learning models, specifically denoising diffusion models (DMs), to facilitate this transformation. Leveraging text-conditioning, we steer the model to produce desired quantum operations within gate-based quantum circuits. Notably, DMs allow to sidestep during training the exponential overhead inherent in the classical simulation of quantum dynamics -- a consistent bottleneck in preceding ML techniques. We demonstrate the model's capabilities across two tasks: entanglement generation and unitary compilation. The model excels at generating new circuits and supports typical DM extensions such as masking and editing to, for instance, align the circuit generation to the constraints of the targeted quantum device. Given their flexibility and generalization abilities, we envision DMs as pivotal in quantum circuit synthesis, enhancing both practical applications but also insights into theoretical quantum computation.

Remotely sensed data are dominated by mixed Land Use and Land Cover (LULC) types. Spectral unmixing is a technique to extract information from mixed pixels into their constituent LULC types and corresponding abundance fractions. Traditionally, solving this task has relied on either classical methods that require prior knowledge of endmembers or machine learning methods that avoid explicit endmembers calculation, also known as blind spectral unmixing (BSU). Most BSU studies based on Deep Learning (DL) focus on one time-step hyperspectral or multispectral data. To our knowledge, here we provide the first study on BSU of LULC classes using MODIS multispectral time series, in presence of missing data, with end-to-end DL models. We further boost the performance of a Long-Short Term Memory (LSTM)-based model by incorporating geographic plus topographic (geo-topographic) and climatic ancillary information. Our experiments show that combining spectral-temporal input data together with geo-topographic and climatic information substantially improves the abundance estimation of LULC classes in mixed pixels. To carry out this study, we built a new labeled dataset of the region of Andalusia (Spain) with monthly multispectral time series of pixels for the year 2013 from MODIS at 460m resolution, for two hierarchical levels of LULC classes, named Andalusia MultiSpectral MultiTemporal Unmixing (Andalusia-MSMTU). This dataset provides, at the pixel level, a multispectral time series plus ancillary information annotated with the abundance of each LULC class inside each pixel. The dataset (//zenodo.org/record/7752348##.ZBmkkezMLdo) and code (//github.com/jrodriguezortega/MSMTU) are available to the public.

We determine the minimum possible column multiplicity of even, doubly-, and triply-even codes given their length. This refines a classification result for the possible lengths of $q^r$-divisible codes over $\mathbb{F}_q$. We also give a few computational results for field sizes $q>2$. Non-existence results of divisible codes with restricted column multiplicities for a given length have applications e.g. in Galois geometry and can be used for upper bounds on the maximum cardinality of subspace codes.

The flexoelectric effect, coupling polarization and strain gradient as well as strain and electric field gradients, is universal to dielectrics, but, as compared to piezoelectricity, it is more difficult to harness as it requires field gradients and it is a small-scale effect. These drawbacks can be overcome by suitably designing metamaterials made of a non-piezoelectric base material but exhibiting apparent piezoelectricity. We develop a theoretical and computational framework to perform topology optimization of the representative volume element of such metamaterials by accurately modeling the governing equations of flexoelectricity using a Cartesian B-spline method, describing geometry with a level set, and resorting to genetic algorithms for optimization. We consider a multi-objective optimization problem where area fraction competes with four fundamental piezoelectric functionalities (stress/strain sensor/ actuator). We computationally obtain Pareto fronts, and discuss the different geometries depending on the apparent piezoelectric coefficient being optimized. In general, we find competitive estimations of apparent piezoelectricity as compared to reference materials such as quartz and PZT ceramics. This opens the possibility to design devices for sensing, actuation and energy harvesting from a much wider, cheaper and effective class of materials.

Augmented Reality (AR) has emerged as a significant advancement in surgical procedures, offering a solution to the challenges posed by traditional neuronavigation methods. These conventional techniques often necessitate surgeons to split their focus between the surgical site and a separate monitor that displays guiding images. Over the years, many systems have been developed to register and track the hologram at the targeted locations, each employed its own evaluation technique. On the other hand, hologram displacement measurement is not a straightforward task because of various factors such as occlusion, Vengence-Accomodation Conflict, and unstable holograms in space. In this study, we explore and classify different techniques for assessing an AR-assisted neurosurgery system and propose a new technique to systematize the assessment procedure. Moreover, we conduct a deeper investigation to assess surgeon error in the pre- and intra-operative phases of the surgery based on the respective feedback given. We found that although the system can undergo registration and tracking errors, physical feedback can significantly reduce the error caused by hologram displacement. However, the lack of visual feedback on the hologram does not have a significant effect on the user 3D perception.

We establish conditions under which latent causal graphs are nonparametrically identifiable and can be reconstructed from unknown interventions in the latent space. Our primary focus is the identification of the latent structure in measurement models without parametric assumptions such as linearity or Gaussianity. Moreover, we do not assume the number of hidden variables is known, and we show that at most one unknown intervention per hidden variable is needed. This extends a recent line of work on learning causal representations from observations and interventions. The proofs are constructive and introduce two new graphical concepts -- imaginary subsets and isolated edges -- that may be useful in their own right. As a matter of independent interest, the proofs also involve a novel characterization of the limits of edge orientations within the equivalence class of DAGs induced by unknown interventions. These are the first results to characterize the conditions under which causal representations are identifiable without making any parametric assumptions in a general setting with unknown interventions and without faithfulness.

In prediction settings where data are collected over time, it is often of interest to understand both the importance of variables for predicting the response at each time point and the importance summarized over the time series. Building on recent advances in estimation and inference for variable importance measures, we define summaries of variable importance trajectories. These measures can be estimated and the same approaches for inference can be applied regardless of the choice of the algorithm(s) used to estimate the prediction function. We propose a nonparametric efficient estimation and inference procedure as well as a null hypothesis testing procedure that are valid even when complex machine learning tools are used for prediction. Through simulations, we demonstrate that our proposed procedures have good operating characteristics, and we illustrate their use by investigating the longitudinal importance of risk factors for suicide attempt.

Quantum error correction is crucial for scalable quantum information processing applications. Traditional discrete-variable quantum codes that use multiple two-level systems to encode logical information can be hardware-intensive. An alternative approach is provided by bosonic codes, which use the infinite-dimensional Hilbert space of harmonic oscillators to encode quantum information. Two promising features of bosonic codes are that syndrome measurements are natively analog and that they can be concatenated with discrete-variable codes. In this work, we propose novel decoding methods that explicitly exploit the analog syndrome information obtained from the bosonic qubit readout in a concatenated architecture. Our methods are versatile and can be generally applied to any bosonic code concatenated with a quantum low-density parity-check (QLDPC) code. Furthermore, we introduce the concept of quasi-single-shot protocols as a novel approach that significantly reduces the number of repeated syndrome measurements required when decoding under phenomenological noise. To realize the protocol, we present a first implementation of time-domain decoding with the overlapping window method for general QLDPC codes, and a novel analog single-shot decoding method. Our results lay the foundation for general decoding algorithms using analog information and demonstrate promising results in the direction of fault-tolerant quantum computation with concatenated bosonic-QLDPC codes.

Graph-centric artificial intelligence (graph AI) has achieved remarkable success in modeling interacting systems prevalent in nature, from dynamical systems in biology to particle physics. The increasing heterogeneity of data calls for graph neural architectures that can combine multiple inductive biases. However, combining data from various sources is challenging because appropriate inductive bias may vary by data modality. Multimodal learning methods fuse multiple data modalities while leveraging cross-modal dependencies to address this challenge. Here, we survey 140 studies in graph-centric AI and realize that diverse data types are increasingly brought together using graphs and fed into sophisticated multimodal models. These models stratify into image-, language-, and knowledge-grounded multimodal learning. We put forward an algorithmic blueprint for multimodal graph learning based on this categorization. The blueprint serves as a way to group state-of-the-art architectures that treat multimodal data by choosing appropriately four different components. This effort can pave the way for standardizing the design of sophisticated multimodal architectures for highly complex real-world problems.

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