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Ancestral state reconstruction is one of the most important tasks in evolutionary biology. Conditions under which we can reliably reconstruct the ancestral state have been studied for both discrete and continuous traits. However, the connection between these results is unclear, and it seems that each model needs different conditions. In this work, we provide a unifying theory on the consistency of ancestral state reconstruction for various types of trait evolution models. Notably, we show that for a sequence of nested trees with bounded heights, the necessary and sufficient conditions for the existence of a consistent ancestral state reconstruction method under discrete models, the Brownian motion model, and the threshold model are equivalent. When tree heights are unbounded, we provide a simple counter-example to show that this equivalence is no longer valid.

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Recently, self-supervised vision transformers have attracted unprecedented attention for their impressive representation learning ability. However, the dominant method, contrastive learning, mainly relies on an instance discrimination pretext task, which learns a global understanding of the image. This paper incorporates local feature learning into self-supervised vision transformers via Reconstructive Pre-training (RePre). Our RePre extends contrastive frameworks by adding a branch for reconstructing raw image pixels in parallel with the existing contrastive objective. RePre is equipped with a lightweight convolution-based decoder that fuses the multi-hierarchy features from the transformer encoder. The multi-hierarchy features provide rich supervisions from low to high semantic information, which are crucial for our RePre. Our RePre brings decent improvements on various contrastive frameworks with different vision transformer architectures. Transfer performance in downstream tasks outperforms supervised pre-training and state-of-the-art (SOTA) self-supervised counterparts.

Image reconstruction based on indirect, noisy, or incomplete data remains an important yet challenging task. While methods such as compressive sensing have demonstrated high-resolution image recovery in various settings, there remain issues of robustness due to parameter tuning. Moreover, since the recovery is limited to a point estimate, it is impossible to quantify the uncertainty, which is often desirable. Due to these inherent limitations, a sparse Bayesian learning approach is sometimes adopted to recover a posterior distribution of the unknown. Sparse Bayesian learning assumes that some linear transformation of the unknown is sparse. However, most of the methods developed are tailored to specific problems, with particular forward models and priors. Here, we present a generalized approach to sparse Bayesian learning. It has the advantage that it can be used for various types of data acquisitions and prior information. Some preliminary results on image reconstruction/recovery indicate its potential use for denoising, deblurring, and magnetic resonance imaging.

We improve the bound on K\"uhnel's problem to determine the smallest $n$ such that the $k$-skeleton of an $n$-simplex $\Delta_n^{(k)}$ does not embed into a compact PL $2k$-manifold $M$ by showing that if $\Delta_n^{(k)}$ embeds into $M$, then $n\leq (2k+1)+(k+1)\beta_k(M;\mathbb Z_2)$. As a consequence we obtain improved Radon and Helly type results for set systems in such manifolds. Our main tool is a new description of an obstruction for embeddability of a $k$-complex $K$ into a compact PL $2k$-manifold $M$ via the intersection form on $M$. In our approach we need that for every map $f\colon K\to M$ the restriction to the $(k-1)$-skeleton of $K$ is nullhomotopic. In particular, this condition is satisfied in interesting cases if $K$ is $(k-1)$-connected, for example a $k$-skeleton of $n$-simplex, or if $M$ is $(k-1)$-connected. In addition, if $M$ is $(k-1)$-connected and $k\geq 3$, the obstruction is complete, meaning that a $k$-complex $K$ embeds into $M$ if and only if the obstruction vanishes. For trivial intersection forms, our obstruction coincides with the standard van Kampen obstruction. However, if the form is non-trivial, the obstruction is not linear but rather 'quadratic' in a sense that it vanishes if and only if certain system of quadratic diophantine equations is solvable. This may potentially be useful in attacking algorithmic decidability of embeddability of $k$-complexes into PL $2k$-manifolds.

The Granular Instrumental Variables (GIV) methodology exploits panels with factor error structures to construct instruments to estimate structural time series models with endogeneity even after controlling for latent factors. We extend the GIV methodology in several dimensions. First, we extend the identification procedure to a large $N$ and large $T$ framework, which depends on the asymptotic Herfindahl index of the size distribution of $N$ cross-sectional units. Second, we treat both the factors and loadings as unknown and show that the sampling error in the estimated instrument and factors is negligible when considering the limiting distribution of the structural parameters. Third, we show that the sampling error in the high-dimensional precision matrix is negligible in our estimation algorithm. Fourth, we overidentify the structural parameters with additional constructed instruments, which leads to efficiency gains. Monte Carlo evidence is presented to support our asymptotic theory and application to the global crude oil market leads to new results.

Lattice Boltzmann schemes rely on the enlargement of the size of the target problem in order to solve PDEs in a highly parallelizable and efficient kinetic-like fashion, split into a collision and a stream phase. This structure, despite the well-known advantages from a computational standpoint, is not suitable to construct a rigorous notion of consistency with respect to the target equations and to provide a precise notion of stability. In order to alleviate these shortages and introduce a rigorous framework, we demonstrate that any lattice Boltzmann scheme can be rewritten as a corresponding multi-step Finite Difference scheme on the conserved variables. This is achieved by devising a suitable formalism based on operators, commutative algebra and polynomials. Therefore, the notion of consistency of the corresponding Finite Difference scheme allows to invoke the Lax-Richtmyer theorem in the case of linear lattice Boltzmann schemes. Moreover, we show that the frequently-used von Neumann-like stability analysis for lattice Boltzmann schemes entirely corresponds to the von Neumann stability analysis of their Finite Difference counterpart. More generally, the usual tools for the analysis of Finite Difference schemes are now readily available to study lattice Boltzmann schemes. Their relevance is verified by means of numerical illustrations.

The rapid recent progress in machine learning (ML) has raised a number of scientific questions that challenge the longstanding dogma of the field. One of the most important riddles is the good empirical generalization of overparameterized models. Overparameterized models are excessively complex with respect to the size of the training dataset, which results in them perfectly fitting (i.e., interpolating) the training data, which is usually noisy. Such interpolation of noisy data is traditionally associated with detrimental overfitting, and yet a wide range of interpolating models -- from simple linear models to deep neural networks -- have recently been observed to generalize extremely well on fresh test data. Indeed, the recently discovered double descent phenomenon has revealed that highly overparameterized models often improve over the best underparameterized model in test performance. Understanding learning in this overparameterized regime requires new theory and foundational empirical studies, even for the simplest case of the linear model. The underpinnings of this understanding have been laid in very recent analyses of overparameterized linear regression and related statistical learning tasks, which resulted in precise analytic characterizations of double descent. This paper provides a succinct overview of this emerging theory of overparameterized ML (henceforth abbreviated as TOPML) that explains these recent findings through a statistical signal processing perspective. We emphasize the unique aspects that define the TOPML research area as a subfield of modern ML theory and outline interesting open questions that remain.

It is not until recently that graph neural networks (GNNs) are adopted to perform graph representation learning, among which, those based on the aggregation of features within the neighborhood of a node achieved great success. However, despite such achievements, GNNs illustrate defects in identifying some common structural patterns which, unfortunately, play significant roles in various network phenomena. In this paper, we propose GraLSP, a GNN framework which explicitly incorporates local structural patterns into the neighborhood aggregation through random anonymous walks. Specifically, we capture local graph structures via random anonymous walks, powerful and flexible tools that represent structural patterns. The walks are then fed into the feature aggregation, where we design various mechanisms to address the impact of structural features, including adaptive receptive radius, attention and amplification. In addition, we design objectives that capture similarities between structures and are optimized jointly with node proximity objectives. With the adequate leverage of structural patterns, our model is able to outperform competitive counterparts in various prediction tasks in multiple datasets.

Solving complex, temporally-extended tasks is a long-standing problem in reinforcement learning (RL). We hypothesize that one critical element of solving such problems is the notion of compositionality. With the ability to learn concepts and sub-skills that can be composed to solve longer tasks, i.e. hierarchical RL, we can acquire temporally-extended behaviors. However, acquiring effective yet general abstractions for hierarchical RL is remarkably challenging. In this paper, we propose to use language as the abstraction, as it provides unique compositional structure, enabling fast learning and combinatorial generalization, while retaining tremendous flexibility, making it suitable for a variety of problems. Our approach learns an instruction-following low-level policy and a high-level policy that can reuse abstractions across tasks, in essence, permitting agents to reason using structured language. To study compositional task learning, we introduce an open-source object interaction environment built using the MuJoCo physics engine and the CLEVR engine. We find that, using our approach, agents can learn to solve to diverse, temporally-extended tasks such as object sorting and multi-object rearrangement, including from raw pixel observations. Our analysis find that the compositional nature of language is critical for learning diverse sub-skills and systematically generalizing to new sub-skills in comparison to non-compositional abstractions that use the same supervision.

Machine learning methods are powerful in distinguishing different phases of matter in an automated way and provide a new perspective on the study of physical phenomena. We train a Restricted Boltzmann Machine (RBM) on data constructed with spin configurations sampled from the Ising Hamiltonian at different values of temperature and external magnetic field using Monte Carlo methods. From the trained machine we obtain the flow of iterative reconstruction of spin state configurations to faithfully reproduce the observables of the physical system. We find that the flow of the trained RBM approaches the spin configurations of the maximal possible specific heat which resemble the near criticality region of the Ising model. In the special case of the vanishing magnetic field the trained RBM converges to the critical point of the Renormalization Group (RG) flow of the lattice model. Our results suggest an alternative explanation of how the machine identifies the physical phase transitions, by recognizing certain properties of the configuration like the maximization of the specific heat, instead of associating directly the recognition procedure with the RG flow and its fixed points. Then from the reconstructed data we deduce the critical exponent associated to the magnetization to find satisfactory agreement with the actual physical value. We assume no prior knowledge about the criticality of the system and its Hamiltonian.

Machine Learning models become increasingly proficient in complex tasks. However, even for experts in the field, it can be difficult to understand what the model learned. This hampers trust and acceptance, and it obstructs the possibility to correct the model. There is therefore a need for transparency of machine learning models. The development of transparent classification models has received much attention, but there are few developments for achieving transparent Reinforcement Learning (RL) models. In this study we propose a method that enables a RL agent to explain its behavior in terms of the expected consequences of state transitions and outcomes. First, we define a translation of states and actions to a description that is easier to understand for human users. Second, we developed a procedure that enables the agent to obtain the consequences of a single action, as well as its entire policy. The method calculates contrasts between the consequences of a policy derived from a user query, and of the learned policy of the agent. Third, a format for generating explanations was constructed. A pilot survey study was conducted to explore preferences of users for different explanation properties. Results indicate that human users tend to favor explanations about policy rather than about single actions.

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