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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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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 introduce a new constrained optimization method for policy gradient reinforcement learning, which uses two trust regions to regulate each policy update. In addition to using the proximity of one single old policy as the first trust region as done by prior works, we propose to form a second trust region through the construction of another virtual policy that represents a wide range of past policies. We then enforce the new policy to stay closer to the virtual policy, which is beneficial in case the old policy performs badly. More importantly, we propose a mechanism to automatically build the virtual policy from a memory buffer of past policies, providing a new capability for dynamically selecting appropriate trust regions during the optimization process. Our proposed method, dubbed as Memory-Constrained Policy Optimization (MCPO), is examined on a diverse suite of environments including robotic locomotion control, navigation with sparse rewards and Atari games, consistently demonstrating competitive performance against recent on-policy constrained policy gradient methods.

Applications of Reinforcement Learning (RL), in which agents learn to make a sequence of decisions despite lacking complete information about the latent states of the controlled system, that is, they act under partial observability of the states, are ubiquitous. Partially observable RL can be notoriously difficult -- well-known information-theoretic results show that learning partially observable Markov decision processes (POMDPs) requires an exponential number of samples in the worst case. Yet, this does not rule out the existence of large subclasses of POMDPs over which learning is tractable. In this paper we identify such a subclass, which we call weakly revealing POMDPs. This family rules out the pathological instances of POMDPs where observations are uninformative to a degree that makes learning hard. We prove that for weakly revealing POMDPs, a simple algorithm combining optimism and Maximum Likelihood Estimation (MLE) is sufficient to guarantee polynomial sample complexity. To the best of our knowledge, this is the first provably sample-efficient result for learning from interactions in overcomplete POMDPs, where the number of latent states can be larger than the number of observations.

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.

In this paper we study the finite sample and asymptotic properties of various weighting estimators of the local average treatment effect (LATE), several of which are based on Abadie (2003)'s kappa theorem. Our framework presumes a binary endogenous explanatory variable ("treatment") and a binary instrumental variable, which may only be valid after conditioning on additional covariates. We argue that one of the Abadie estimators, which we show is weight normalized, is likely to dominate the others in many contexts. A notable exception is in settings with one-sided noncompliance, where certain unnormalized estimators have the advantage of being based on a denominator that is bounded away from zero. We use a simulation study and three empirical applications to illustrate our findings. In applications to causal effects of college education using the college proximity instrument (Card, 1995) and causal effects of childbearing using the sibling sex composition instrument (Angrist and Evans, 1998), the unnormalized estimates are clearly unreasonable, with "incorrect" signs, magnitudes, or both. Overall, our results suggest that (i) the relative performance of different kappa weighting estimators varies with features of the data-generating process; and that (ii) the normalized version of Tan (2006)'s estimator may be an attractive alternative in many contexts. Applied researchers with access to a binary instrumental variable should also consider covariate balancing or doubly robust estimators of the LATE.

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.

Vector Perturbation Precoding (VPP) can speed up downlink data transmissions in Large and Massive Multi-User MIMO systems but is known to be NP-hard. While there are several algorithms in the literature for VPP under total power constraint, they are not applicable for VPP under per-antenna power constraint. This paper proposes a novel, parallel tree search algorithm for VPP under per-antenna power constraint, called \emph{\textbf{TreeStep}}, to find good quality solutions to the VPP problem with practical computational complexity. We show that our method can provide huge performance gain over simple linear precoding like Regularised Zero Forcing. We evaluate TreeStep for several large MIMO~($16\times16$ and $24\times24$) and massive MIMO~($16\times32$ and $24\times 48$) and demonstrate that TreeStep outperforms the popular polynomial-time VPP algorithm, the Fixed Complexity Sphere Encoder, by achieving the extremely low BER of $10^{-6}$ at a much lower SNR.

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.

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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