wanyu/IteraTeR_v2 huggingface dataset:
Original:  Recombination, reassortment , horizontal gene transfer , and species hybridization constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations.
Revised:  Recombination, reassortment , horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations.
Edit intent: clarity
Original:  Starting from tens or hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data.
Revised:  Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data.
Edit intent: clarity
Original:  Ancestral recombination graphs (ARGs) represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes.
Revised:  Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes.
Edit intent: clarity
Original:  However, ARGs are computationally costly to reconstruct and usually become infeasible for more than few tens of genomes.
Revised:  However, they are computationally costly to reconstruct and usually become infeasible for more than few tens of genomes.
Edit intent: clarity
Original:  However, ARGs are computationally costly to reconstruct and usually become infeasible for more than few tens of genomes.
Revised:  However, ARGs are computationally costly to reconstruct , usually being infeasible for more than few tens of genomes.
Edit intent: clarity
Original:  We build on previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations.
Revised:  We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations.
Edit intent: fluency
Original:  For that aim, we extend the notion of barcodes in persistent homology, largely increasing their sensitivity to recombination, and present a new type of summary graph (topological ARG, or tARG), analogous to ARGs, that capture ensembles of minimal recombination histories.
Edit intent: coherence
Original: Divergence dates estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests for the molecular clock.
Revised: Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests for the molecular clock.
Edit intent: fluency
Original:  Here we propose a method for testing the molecular clock in phylogenies that is built upon the assumption of Poisson stochastic process that accommodates rate heterogeneity and is based on ensembles of trees inferred by the Bayesian method .
Revised:  Here we propose a framework for non-parametric test of the (strict) molecular clock in phylogenies that is built upon the assumption of Poisson stochastic process that accommodates rate heterogeneity and is based on ensembles of trees inferred by the Bayesian method .
Edit intent: clarity
Original:  The parameter \lambda  of the expected Poisson distribution is given by the average branch length of this ensemble .
Revised:  The parameter \lambda of the expected Poisson distribution is calculated as the average branch length of this ensemble .
Edit intent: clarity
Original: Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests for the molecular clock .
Revised: Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks .
Edit intent: fluency
Original:  Here we propose a framework for non-parametric test of the (strict ) molecular clock in phylogenies that is built upon the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of trees inferred by the Bayesian method together with a non-parametric  goodness-of-fit test.
Revised:  Here we propose two non-parametric test of the (strict ) molecular clock in phylogenies that is built upon the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of trees inferred by the Bayesian method together with a non-parametric goodness-of-fit test.
Edit intent: clarity
Original:  Here we propose a framework for non-parametric test of the (strict ) molecular clock in phylogenies that is built upon the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of trees inferred by the Bayesian method together with a non-parametric  goodness-of-fit test.
Revised:  Here we propose a framework for non-parametric tests of strict and relaxed molecular clocks built upon a framework that uses the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of trees inferred by the Bayesian method together with a non-parametric goodness-of-fit test.
Edit intent: clarity
Original:  Here we propose a framework for non-parametric test of the (strict ) molecular clock in phylogenies that is built upon the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of trees inferred by the Bayesian method together with a non-parametric  goodness-of-fit test.
Revised:  Here we propose a framework for non-parametric test of the (strict ) molecular clock in phylogenies that is built upon the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of Bayesian trees and well known non-parametric goodness-of-fit test.
Edit intent: clarity
Original:  The ECD is computed from the discretized branch lengths and the parameter \lambda of the expected Poisson distribution is calculated as the average branch length over the ensemble of trees.
Revised:  The ECD is computed from the discretized branch lengths and the parameter \lambda of the expected Poisson distribution is calculated as the average branch length over the ensemble of trees.
Edit intent: fluency
Original:  In order to compensate for the auto-correlation in the ensemble of trees  we take advantage of  two features provided by MCMC samplers used for Bayesian inference methods (thinning and effective sample size) .
Revised:  In order to compensate for the auto-correlation in the ensemble of trees we take advantage of thinning and effective sample size, two features provided by MCMC samplers used for Bayesian inference methods (thinning and effective sample size) .
Edit intent: coherence
Original:  In order to compensate for the auto-correlation in the ensemble of trees  we take advantage of  two features provided by MCMC samplers used for Bayesian inference methods (thinning and effective sample size) .
Revised:  In order to compensate for the auto-correlation in the ensemble of trees we take advantage of two features provided by Bayesian inference MCMC samplers .
Edit intent: clarity
Original:  Finally, it is observed that tree topologies with very long or very short branches lead to Poisson mixtures and in this case we propose the use of the two-sample Kolmogorov-Smirnov with samples coming from two continuous branch length distributions, one obtained from an ensemble of clock-constrained trees and the other from an ensemble of unconstrained trees.
Revised:  Finally, it is observed that tree topologies with very long or very short branches lead to Poisson mixtures and in this case we propose the use of the two-sample KS test with samples from two continuous branch length distributions, one obtained from an ensemble of clock-constrained trees and the other from an ensemble of unconstrained trees.
Edit intent: clarity
Original:  Moreover, in this second form the test may be also applied to test for relaxed clock models  .
Revised:  Moreover, in this second form the test can also be applied to test for relaxed clock models .
Edit intent: clarity
Original:  There are many multiagent systems applications, and even real-world elections, where this assumption is not warranted, and this in turn raises the question "How hard is it to manipulate elections if the agents reveal only partial preference orderings?" . It is this question that we study in this paper.
Revised:  There are many multiagent systems applications, and even real-world elections, where this assumption is not warranted, and this in turn raises the question "How hard is it to manipulate elections if the agents reveal only partial preference orderings?" It is this question that we study in this paper.
Edit intent: fluency
Original:  There are many multiagent systems applications, and even real-world elections, where this assumption is not warranted, and this in turn raises the question "How hard is it to manipulate elections if the agents reveal only partial preference orderings?" . It is this question that we study in this paper.
Revised:  There are many multiagent systems applications, and even real-world elections, where this assumption is not warranted, and this in turn raises the question "How hard is it to manipulate elections if the agents reveal only partial preference orderings?" . It is this question we try to address in this paper.
Edit intent: clarity
Original:  In particular, we look at the weighted manipulation problem -- both constructive and destructive manipulation -- when such partial voting is allowed and when there are only a bounded number of candidates.
Revised:  In particular, we look at the weighted manipulation problem -- both constructive and destructive manipulation -- when the voters are allowed to specify any top-truncated ordering over the set of candidates.
Edit intent: clarity
Original:  We study the exact number of candidates that are required to make manipulation hard for all scoring rules, for elimination versions of all scoring rules, for the plurality with runoff rule, for a family of election systems known as Copeland^{\alpha}, and for the maximin protocol  .
Revised:  We provide general results for all scoring rules, for elimination versions of all scoring rules, for the plurality with runoff rule, for a family of election systems known as Copeland^{\alpha}, and for the maximin protocol .
Edit intent: clarity
Original: In this paper, we propose a novel indoor localization scheme , Lightitude, by exploiting ubiquitous visible lights, which are necessarily and densely deployed in almost all indoor environments.
Revised: In this paper, we propose a novel indoor localization scheme that exploits ubiquitous visible lights, which are necessarily and densely deployed in almost all indoor environments.
Edit intent: coherence
Original:  Experiment results show that Lightitude achieves mean accuracy 1.93m and 1.98m in office (720m^2) and library scenario (960m^2) respectively.
Revised:  Experiment results show that our scheme achieves mean accuracy 1.93m and 1.98m in office (720m^2) and library scenario (960m^2) respectively.
Edit intent: clarity
Original: Pairwise ordered tree alignment are combinatorial objects that appear in important applications, such as RNA secondary structure comparison.
Revised: Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison.
Edit intent: clarity
Original:  This ambiguity is uninforma-tive , and detrimental to any probabilistic analysis.
Revised:  This ambiguity is uninformative , and detrimental to any probabilistic analysis.
Edit intent: fluency
Original:  In particular, the largest eigenvalue and its associated principal eigenvector are crucial in the understanding of node's centrality and the unfolding of dynamical processes.
Revised:  In particular, the largest eigenvalue and its associated principal eigenvector are crucial in the understanding of nodes centrality and the unfolding of dynamical processes.
Edit intent: clarity
Original:  for \gamma<5/2 a new type of localization arises on a mesoscopic subgraph associated to the shell with the largest index in the K-core decomposition.
Revised:  for \gamma<5/2 a new type of localization arises on a mesoscopic subgraph associated with the shell with the largest index in the K-core decomposition.
Edit intent: fluency
Original: We propose an improved pure source transfer domain decomposition method ( pSTDDM ) for solving the truncated perfectly matched layer (PML) approximation in bounded domain of Helmholtz scattering problem.
Revised: We propose an improved pure source transfer domain decomposition method ( PSTDDM ) for solving the truncated perfectly matched layer (PML) approximation in bounded domain of Helmholtz scattering problem.
Edit intent: fluency
Original:  The two steps of the pSTDDM can run in parallel and the errors of discrete solutions of our pSTDDM aren't larger than those of the STDDM. Besides, we could divide the domain into non-overlapping squares and only need to solve the PML problem defined locally outside the union of four squares, which further reduce the computational complexity.
Revised:  The two steps of the pSTDDM can run in parallel and the errors of discrete solutions of our pSTDDM aren't larger than those of the STDDM. Besides, we could divide the domain into non-overlapping blocks and solve the solution in each block by using a PML method defined locally outside the union of four squares, which further reduce the computational complexity.
Edit intent: clarity
Original: We propose an improved pure source transfer domain decomposition method (PSTDDM) for solving the truncated perfectly matched layer (PML) approximation in bounded domain of Helmholtz scattering problem.
Revised: We propose a pure source transfer domain decomposition method (PSTDDM) for solving the truncated perfectly matched layer (PML) approximation in bounded domain of Helmholtz scattering problem.
Edit intent: clarity
Original:  The idea is ] decomposing the domain into  non-overlapping layers and transferring the sources equivalently layer by layer so that the solution in each layer can be solved using a PML method defined locally outside its two adjacent layers .
Revised:  The idea is ]. After decomposing the domain into non-overlapping layers and transferring the sources equivalently layer by layer so that the solution in each layer can be solved using a PML method defined locally outside its two adjacent layers .
Edit intent: coherence
Original:  First, COUNT , a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome.
Revised:  First, Count , a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome.
Edit intent: fluency
Original:  We compare their merits and their ability to quantify the role of transfers, and  the impact of taxonomic sampling  .
Revised:  We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling .
Edit intent: clarity
Original: The Luria-Delbr{\"u}ck experiment is a cornerstone of evolutionary theory, demonstrating the ran-domness of mutations before selection.
Revised: The Luria-Delbr{\"u}ck experiment is a cornerstone of evolutionary theory, demonstrating the randomness of mutations before selection.
Edit intent: fluency
Original:  Low rank matrix approximation can greatly reduce the computational cost in this situation, for which Cross Approximation (CA) and pivoted Cholesky decomposition (PCD) are two efficient techniques .
Revised:  Pivoted Cholesky decomposition (PCD) are two efficient techniques .
Edit intent: coherence
Original:  The integral terms of these evolution equations have a weighted kernel describing synaptic interactions between neurons at different locations of the network.
Revised:  The integral terms of these evolution equations have a weight kernel describing synaptic interactions between neurons at different locations of the network.
Edit intent: fluency
Original:   As the threshold is increased, these a stable and unstable branch of bump solutions annihilate in a saddle node bifurcation.
Revised:  As the threshold is increased, the stable and unstable branch of bump solutions annihilate in a saddle node bifurcation.
Edit intent: fluency
Original:  Many methods have been developed to reconstruct network models that attempt to capture those interactions.
Revised:  Many methods have been developed to reconstruct network models of those interactions.
Edit intent: clarity
Original:  These methods often draw on large numbers of measured expression samples to tease out subtle signals and infer connections between genes (or gene products).
Revised:  These methods often draw on large numbers of samples with measured gene expression profiles to infer connections between genes (or gene products).
Edit intent: clarity
Original:  The result is an aggregate network model representing a single estimate for edge likelihoods .
Revised:  The result is an aggregate network model representing a single estimate for the likelihood of each interaction, or "edge," in the network .
Edit intent: clarity
Original:  While informative, aggregate models fail to capture the heterogeneity that is often represented in a population.
Revised:  While informative, aggregate models fail to capture the heterogeneity that is represented in any population.
Edit intent: clarity
Original:  We demonstrate the accuracy and applicability of our approach in several datasets , including simulated data, microarray expression data from synchronized yeast cells, and RNA-seq data collected from human subjects .
Revised:  We demonstrate the accuracy and applicability of our approach in several data sets , including simulated data, microarray expression data from synchronized yeast cells, and RNA-seq data collected from human subjects .
Edit intent: clarity
Original:  We show that these sample-specific networks can be used to study the evolution of network topology across time and to characterize shifts in gene regulation that may not be apparent in the expression data.
Revised:  We show that these sample-specific networks can be used to study changes in network topology across time and to characterize shifts in gene regulation that may not be apparent in the expression data.
Edit intent: clarity
Original:  We show that these sample-specific networks can be used to study the evolution of network topology across time and to characterize shifts in gene regulation that may not be apparent in the expression data.
Revised:  We show that these sample-specific networks can be used to study the evolution of network topology across time and to characterize shifts in gene regulation that may not be apparent in expression data.
Edit intent: fluency
Original:  We believe the ability to generate sample-specific networks will revolutionize the field of network biology and has the potential to usher in an era of precision network medicine.
Revised:  We believe the ability to generate sample-specific networks will greatly facilitate the application of network methods to the increasingly large, complex, and heterogeneous multi-omic data sets that are currently being generated, and ultimately support the emerging field of precision network medicine.
Edit intent: clarity
Original: The applications of wireless power transfer technology to wireless communications can help build a wireless powered communication network (WPCN) with larger throughput, higher robustness, and increased flexibility compared to the conventional battery-powered network.
Revised: The applications of wireless power transfer technology to wireless communications can help build a wireless powered communication network (WPCN) with more reliable and sustainable power supply compared to the conventional battery-powered network.
Edit intent: clarity
Original:  Based on the obtained results, we further study the placement optimization when each pair of EN and AP are co-located and integrated as a hybrid access point, and propose an efficient algorithm to solve this problem.
Revised:  Then, we study the placement optimization when each pair of EN and AP are co-located and integrated as a hybrid access point, and propose an efficient algorithm to solve this problem.
Edit intent: coherence
Original: Caching popular contents at the base station (BS ) can reduce the backhaul cost and improve the network throughput.
Revised: Caching popular contents at base stations (BSs ) can reduce the backhaul cost and improve the network throughput.
Edit intent: clarity
Original:  Yet whether locally caching at the BSs can improve the energy efficiency (EE), a major goal for 5th-generation cellular networks, remains unclear.
Revised:  Yet whether locally caching at the BSs can improve the energy efficiency (EE), a major goal for 5th generation cellular networks, remains unclear.
Edit intent: fluency
Original:  By deriving the closed-form expression of the  EE, we provide the condition when the EE can benefit from caching, find the optimal cache capacity that maximizes the network EE, and analyze the maximal EE gain brought by caching.
Revised:  By deriving closed-form expression of the EE, we provide the condition when the EE can benefit from caching, find the optimal cache capacity that maximizes the network EE, and analyze the maximal EE gain brought by caching.
Edit intent: fluency
Original:  When local caching has EE gain over not caching, caching more files at the BSs may not provide higher EE.
Revised:  When local caching has EE gain over not caching, caching more contents at the BSs may not provide higher EE.
Edit intent: clarity
Original:  Numerical and simulation results validate our analysis and show that the caching EE gain is large when the backhaul capacity is stringent, interference level is low, cached files are popular , and when caching at pico BSs instead of macro BSs.
Revised:  Numerical and simulation results show that the caching EE gain is large when the backhaul capacity is stringent, interference level is low, cached files are popular , and when caching at pico BSs instead of macro BSs.
Edit intent: clarity
Original:  Numerical and simulation results validate our analysis and show that the caching EE gain is large when the backhaul capacity is stringent, interference level is low, cached files are popular , and when caching at pico BSs instead of macro BSs.
Revised:  Numerical and simulation results validate our analysis and show that the caching EE gain is large when the backhaul capacity is stringent, interference level is low, content popularity is skewed , and when caching at pico BSs instead of macro BSs.
Edit intent: clarity
Original: Mating strategies of many biological species are  season-dependent.
Revised: Mating strategies of many biological species are not constant but season-dependent.
Edit intent: clarity
Original:  In evolutionary game theory this can be modelled with two finite opposite-sex populations whose members are playing against each other following rules which are modulated in time.
Revised:  In evolutionary game theory this can be modeled with two finite opposite-sex populations whose members are playing against each other following rules which are modulated in time.
Edit intent: fluency
Original:  By combining Floquet theory and the concept of quasi-stationary distributions, we show the existence of metastable time-periodic states in the stochastic evolution of the populations.
Revised:  By combining Floquet theory and the concept of quasi-stationary distributions, we show the existence of seasonally periodic states in the stochastic evolution of the populations.
Edit intent: clarity