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Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot be explained via a gene tree that both contains the depicted orthologs/paralogs, and that is consistent with a species tree $S$. This idea of detecting errors through inconsistency with a species tree has mostly been studied in the presence of speciation and duplication events only. In this work, we ask: could the given set of relations be consistent if we allow lateral gene transfers in the evolutionary model? We formalize this question and provide a variety of algorithmic results regarding the underlying problems. Namely, we show that deciding if a relation graph $R$ is consistent with a given species network $N$ is NP-hard, and that it is W[1]-hard under the parameter "minimum number of transfers". However, we present an FPT algorithm based on the degree of the $DS$-tree associated with $R$. We also study analogous problems in the case that the transfer highways on a species tree are unknown.

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Since 2010, the output of a risk assessment tool that predicts how likely an individual is to commit severe violence against their partner has been integrated within the Basque country courtrooms. The EPV-R, the tool developed to assist police officers during the assessment of gender-based violence cases, was also incorporated to assist the decision-making of judges. With insufficient training, judges are exposed to an algorithmic output that influences the human decision of adopting measures in cases of gender-based violence. In this paper, we examine the risks, harms and limits of algorithmic governance within the context of gender-based violence. Through the lens of an Spanish judge exposed to this tool, we analyse how the EPV-R is impacting on the justice system. Moving beyond the risks of unfair and biased algorithmic outputs, we examine legal, social and technical pitfalls such as opaque implementation, efficiency's paradox and feedback loop, that could led to unintended consequences on women who suffer gender-based violence. Our interdisciplinary framework highlights the importance of understanding the impact and influence of risk assessment tools within judicial decision-making and increase awareness about its implementation in this context.

The basic goal of survivable network design is to build cheap networks that guarantee the connectivity of certain pairs of nodes despite the failure of a few edges or nodes. A celebrated result by Jain [Combinatorica'01] provides a 2-approximation for a wide class of these problems. However nothing better is known even for very basic special cases, raising the natural question whether any improved approximation factor is possible at all. In this paper we address one of the most basic problems in this family for which 2 is still the best-known approximation factor, the Forest Augmentation Problem (FAP): given an undirected unweighted graph (that w.l.o.g. is a forest) and a collection of extra edges (links), compute a minimum cardinality subset of links whose addition to the graph makes it 2-edge-connected. Several better-than-2 approximation algorithms are known for the special case where the input graph is a tree, a.k.a. the Tree Augmentation Problem (TAP). Recently this was achieved also for the weighted version of TAP, and for the k-edge-connectivity generalization of TAP. These results heavily exploit the fact that the input graph is connected, a condition that does not hold in FAP. In this paper we breach the 2-approximation barrier for FAP. Our result is based on two main ingredients. First, we describe a reduction to the Path Augmentation Problem (PAP), the special case of FAP where the input graph is a collection of disjoint paths. Our reduction is not approximation preserving, however it is sufficiently accurate to improve on a factor 2 approximation. Second, we present a better-than-2 approximation algorithm for PAP, an open problem on its own. Here we exploit a novel notion of implicit credits which might turn out to be helpful in future related work.

We study the problem of testing whether a function $f: \mathbb{R}^n \to \mathbb{R}$ is a polynomial of degree at most $d$ in the \emph{distribution-free} testing model. Here, the distance between functions is measured with respect to an unknown distribution $\mathcal{D}$ over $\mathbb{R}^n$ from which we can draw samples. In contrast to previous work, we do not assume that $\mathcal{D}$ has finite support. We design a tester that given query access to $f$, and sample access to $\mathcal{D}$, makes $(d/\varepsilon)^{O(1)}$ many queries to $f$, accepts with probability $1$ if $f$ is a polynomial of degree $d$, and rejects with probability at least $2/3$ if every degree-$d$ polynomial $P$ disagrees with $f$ on a set of mass at least $\varepsilon$ with respect to $\mathcal{D}$. Our result also holds under mild assumptions when we receive only a polynomial number of bits of precision for each query to $f$, or when $f$ can only be queried on rational points representable using a logarithmic number of bits. Along the way, we prove a new stability theorem for multivariate polynomials that may be of independent interest.

A natural way of increasing our understanding of NP-complete graph problems is to restrict the input to a special graph class. Classes of $H$-free graphs, that is, graphs that do not contain some graph $H$ as an induced subgraph, have proven to be an ideal testbed for such a complexity study. However, if the forbidden graph $H$ contains a cycle or claw, then these problems often stay NP-complete. A recent complexity study on the $k$-Colouring problem shows that we may still obtain tractable results if we also bound the diameter of the $H$-free input graph. We continue this line of research by initiating a complexity study on the impact of bounding the diameter for a variety of classical vertex partitioning problems restricted to $H$-free graphs. We prove that bounding the diameter does not help for Independent Set, but leads to new tractable cases for problems closely related to 3-Colouring. That is, we show that Near-Bipartiteness, Independent Feedback Vertex Set, Independent Odd Cycle Transversal, Acyclic 3-Colouring and Star 3-Colouring are all polynomial-time solvable for chair-free graphs of bounded diameter. To obtain these results we exploit a new structural property of 3-colourable chair-free graphs.

The quest to understand consciousness, once the purview of philosophers and theologians, is now actively pursued by scientists of many stripes. We examine consciousness from the perspective of theoretical computer science (TCS), a branch of mathematics concerned with understanding the underlying principles of computation and complexity, including the implications and surprising consequences of resource limitations. In the spirit of Alan Turing's simple yet powerful definition of a computer, the Turing Machine (TM), and perspective of computational complexity theory, we formalize a modified version of the Global Workspace Theory (GWT) of consciousness originated by cognitive neuroscientist Bernard Baars and further developed by him, Stanislas Dehaene, Jean-Pierre Changeaux and others. We are not looking for a complex model of the brain nor of cognition, but for a simple computational model of (the admittedly complex concept of) consciousness. We do this by defining the Conscious Turing Machine (CTM), also called a conscious AI, and then we define consciousness and related notions in the CTM. While these are only mathematical (TCS) definitions, we suggest why the CTM has the feeling of consciousness. The TCS perspective provides a simple formal framework to employ tools from computational complexity theory and machine learning to help us understand consciousness and related concepts. Previously we explored high level explanations for the feelings of pain and pleasure in the CTM. Here we consider three examples related to vision (blindsight, inattentional blindness, and change blindness), followed by discussions of dreams, free will, and altered states of consciousness.

A digital twin contains up-to-date data-driven models of the physical world being studied and can use simulation to optimise the physical world. However, the analysis made by the digital twin is valid and reliable only when the model is equivalent to the physical world. Maintaining such an equivalent model is challenging, especially when the physical systems being modelled are intelligent and autonomous. The paper focuses in particular on digital twin models of intelligent systems where the systems are knowledge-aware but with limited capability. The digital twin improves the acting of the physical system at a meta-level by accumulating more knowledge in the simulated environment. The modelling of such an intelligent physical system requires replicating the knowledge-awareness capability in the virtual space. Novel equivalence maintaining techniques are needed, especially in synchronising the knowledge between the model and the physical system. This paper proposes the notion of knowledge equivalence and an equivalence maintaining approach by knowledge comparison and updates. A quantitative analysis of the proposed approach confirms that compared to state equivalence, knowledge equivalence maintenance can tolerate deviation thus reducing unnecessary updates and achieve more Pareto efficient solutions for the trade-off between update overhead and simulation reliability.

The minimum energy path (MEP) describes the mechanism of reaction, and the energy barrier along the path can be used to calculate the reaction rate in thermal systems. The nudged elastic band (NEB) method is one of the most commonly used schemes to compute MEPs numerically. It approximates an MEP by a discrete set of configuration images, where the discretization size determines both computational cost and accuracy of the simulations. In this paper, we consider a discrete MEP to be a stationary state of the NEB method and prove an optimal convergence rate of the discrete MEP with respect to the number of images. Numerical simulations for the transitions of some several proto-typical model systems are performed to support the theory.

Recently, stemming from the rapid development of artificial intelligence, which has gained expansive success in pattern recognition, robotics, and bioinformatics, neuroscience is also gaining tremendous progress. A kind of spiking neural network with biological interpretability is gradually receiving wide attention, and this kind of neural network is also regarded as one of the directions toward general artificial intelligence. This review introduces the following sections, the biological background of spiking neurons and the theoretical basis, different neuronal models, the connectivity of neural circuits, the mainstream neural network learning mechanisms and network architectures, etc. This review hopes to attract different researchers and advance the development of brain-inspired intelligence and artificial intelligence.

Graph Convolutional Network (GCN) has achieved extraordinary success in learning effective task-specific representations of nodes in graphs. However, regarding Heterogeneous Information Network (HIN), existing HIN-oriented GCN methods still suffer from two deficiencies: (1) they cannot flexibly explore all possible meta-paths and extract the most useful ones for a target object, which hinders both effectiveness and interpretability; (2) they often need to generate intermediate meta-path based dense graphs, which leads to high computational complexity. To address the above issues, we propose an interpretable and efficient Heterogeneous Graph Convolutional Network (ie-HGCN) to learn the representations of objects in HINs. It is designed as a hierarchical aggregation architecture, i.e., object-level aggregation first, followed by type-level aggregation. The novel architecture can automatically extract useful meta-paths for each object from all possible meta-paths (within a length limit), which brings good model interpretability. It can also reduce the computational cost by avoiding intermediate HIN transformation and neighborhood attention. We provide theoretical analysis about the proposed ie-HGCN in terms of evaluating the usefulness of all possible meta-paths, its connection to the spectral graph convolution on HINs, and its quasi-linear time complexity. Extensive experiments on three real network datasets demonstrate the superiority of ie-HGCN over the state-of-the-art methods.

Meta-learning, or learning to learn, has gained renewed interest in recent years within the artificial intelligence community. However, meta-learning is incredibly prevalent within nature, has deep roots in cognitive science and psychology, and is currently studied in various forms within neuroscience. The aim of this review is to recast previous lines of research in the study of biological intelligence within the lens of meta-learning, placing these works into a common framework. More recent points of interaction between AI and neuroscience will be discussed, as well as interesting new directions that arise under this perspective.

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