wanyu/IteraTeR_v2 huggingface dataset:
Original:  In particular, one potential vulnerability of the financial networks is the "financial contagion" process in which insolvencies of individual entities propagate through the "web of dependencies" to affect the entire system.
Revised:  In particular, a potential vulnerability of the financial networks is the "financial contagion" process in which insolvencies of individual entities propagate through the "web of dependencies" to affect the entire system.
Edit intent: clarity
Original:  Based on such comprehensive evaluations, we discuss some interesting implications of our evaluations of this stability measure, and derive topological properties and parameters combinations that may be used to flag the network as a possible fragile network.
Revised:  Based on our evaluations, we discuss some interesting implications of our evaluations of this stability measure, and derive topological properties and parameters combinations that may be used to flag the network as a possible fragile network.
Edit intent: clarity
Original:  However, when they range over the integers, whether for single-path or multipath loops, the decidability of the Linear Ranking problem has not yet been determined.
Revised:  However, when they range over the integers, whether for single-path or multipath loops, the complexity of the Linear Ranking problem has not yet been determined.
Edit intent: clarity
Original:  We show that it is decidable, but harder than the former case: it is coNP-complete.
Revised:  We show that it is coNP-complete.
Edit intent: coherence
Original: In this paper we study the complexity of the Linear Ranking problem : given a loop, described by linear constraints over a finite set of integer variables, is there a linear  ranking function for this loop?
Revised: In this paper we study the complexity of the problems : given a loop, described by linear constraints over a finite set of integer variables, is there a linear ranking function for this loop?
Edit intent: clarity
Original: In this paper we study the complexity of the Linear Ranking problem : given a loop, described by linear constraints over a finite set of integer variables, is there a linear  ranking function for this loop?
Revised: In this paper we study the complexity of the Linear Ranking problem : given a loop, described by linear constraints over a finite set of variables, is there a linear ranking function for this loop?
Edit intent: clarity
Original:  While existence of such a function implies termination, this problem is not equivalent to termination.
Revised:  While existence of such functions implies termination, this problem is not equivalent to termination.
Edit intent: fluency
Original:  While existence of such a function implies termination, this problem is not equivalent to termination.
Revised:  While existence of such a function implies termination, these problems are not equivalent to termination.
Edit intent: fluency
Original:  However, when they range over the integers, whether for single-path or multipath loops, the complexity of the Linear Ranking problem has not yet been determined.
Revised:  However, when they range over the integers, whether for single-path or multipath loops, the complexity has not yet been determined.
Edit intent: clarity
Original:  We show that it is coNP-complete.
Revised:  We show that both problems are coNP-complete.
Edit intent: clarity
Original: In this paper, we present a new algorithm for reverse-engineering gene interaction networks (GINs) from expression data, by viewing the expression levels of various genes as coupled random variables.
Revised: Constructing gene interaction networks (GINs) from expression data, by viewing the expression levels of various genes as coupled random variables.
Edit intent: clarity
Original:  our proof is an extension of Joyal's proof for Cayley's formula.
Revised:  the proof is an extension of Joyal's proof for Cayley's formula.
Edit intent: fluency
Original:  we determine the statistical significance of the overlap between randomly generated sets of genes and genes annotated to Gene Ontology categories using Fisher's Exact Test (FET), a measure commonly employed in functional enrichment analysis, and show that the significance level of the association between a gene set and a functional category is positively correlated with the both the number of annotations made by genes in that gene set and the number of annotations to that functional category.
Revised:  we determine the statistical significance of the overlap between randomly generated sets of genes and genes annotated to Gene Ontology categories using Fisher's Exact Test (FET), are often employed to assess these associations, but don't account for non-uniformity in the number of genes annotated to individual functions or the number of annotations to that functional category.
Edit intent: clarity
Original:  To correct for this annotation number bias , we develop Annotation Enrichment Analysis (AEA) and use it to evaluate the functional significance of published gene signatures .
Revised:  To correct for these biases , we develop Annotation Enrichment Analysis (AEA) and use it to evaluate the functional significance of published gene signatures .
Edit intent: clarity
Original:  We show that AEA is able to predict biologically meaningful results that are obscured by the many false-positive enrichment scores that occur in FETdue to annotation number bias.
Revised:  We show that AEA is able to identify biologically meaningful functional enrichments that are obscured by the many false-positive enrichment scores that occur in FETdue to annotation number bias.
Edit intent: clarity
Original:  We show that AEA is able to predict biologically meaningful results that are obscured by the many false-positive enrichment scores that occur in FETdue to annotation number bias.
Revised:  We show that AEA is able to predict biologically meaningful results that are obscured by numerous false-positive enrichment scores that occur in FETdue to annotation number bias.
Edit intent: fluency
Original:  We suggest that AEA should be used alongside or in lieu of traditionally-used statistics when evaluating the functional enrichment of GO categories in gene sets so as to more accurately capture the biological functions represented in those gene sets.
Revised:  We suggest that AEA should be used alongside or in lieu of traditionally-used statistics when evaluating the functional enrichment of GO categories in gene sets so as to more accurately assess the biological properties of gene sets.
Edit intent: clarity
Original: Summary: We introduce cmine, a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets .
Revised: We introduce a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets .
Edit intent: coherence
Original:  Results on microarray and RNA-seq transcriptomics datasets are described .
Revised:  Results on microarray and RNA-seq transcriptomics datasets .
Edit intent: clarity
Original:  Availability and Implementation: Source code implemented in ANSI C (cmine) with wrappers in R (minerva) and Python (minepy) are freely available for download under GPL3 licence URL The R package minerva is also available through the CRAN repository URL The Python library minepy is also in SourceForge URL All software is multiplatform (MS Windows, Unix/Linux and Mac OS X).
Revised:  Availability and Implementation: Source code and binaries are freely available for download under GPL3 licence URL The R package minerva is also available through the CRAN repository URL The Python library minepy is also in SourceForge URL All software is multiplatform (MS Windows, Unix/Linux and Mac OS X).
Edit intent: clarity
Original:  Availability and Implementation: Source code implemented in ANSI C (cmine) with wrappers in R (minerva) and Python (minepy) are freely available for download under GPL3 licence URL The R package minerva is also available through the CRAN repository URL The Python library minepy is also in SourceForge URL All software is multiplatform (MS Windows, Unix/Linux and Mac OS X).
Revised:  Availability and Implementation: Source code implemented in ANSI C (cmine) with wrappers in R (minerva) and Python (minepy) are freely available for download under GPL3 licence URL The R package minerva is also available through the CRAN repository URL for the R package minerva. All software is multiplatform (MS Windows, Unix/Linux and Mac OS X).
Edit intent: coherence
Original: A point-to-point wireless communication system in the presence of an energy harvesting device and a rechargeable battery at the transmitter is considered .
Revised: A point-to-point wireless communication system in which the transmitter is equipped with an energy harvesting device and a rechargeable battery at the transmitter is considered .
Edit intent: clarity
Original: A point-to-point wireless communication system in the presence of an energy harvesting device and a rechargeable battery at the transmitter is considered .
Revised: A point-to-point wireless communication system in the presence of an energy harvesting device and a rechargeable battery , is studied .
Edit intent: clarity
Original:  Delay-limited communication is considered assuming that the underlying channel is block fading with memory and the channel state information is available at the transmitter.
Revised:  Delay-limited communication is considered assuming that the underlying channel is block fading with memory , and the instantaneous channel state information is available at the transmitter.
Edit intent: clarity
Original:  The problem of maximizing the expected total data transmitted during the transmitter's lifetime is studied under three different sets of assumptions regarding the information  about the underlying stochastic processes , available at the transmitter . A learning theoretic approach is introduced, which does not consider any a priori information on the Markov processes governing the communication system.
Revised:  The problem of maximizing the expected total data transmitted during the transmitter's lifetime is studied under three different sets of assumptions regarding the information available at the transmitter about the underlying stochastic processes , available at the transmitter . A learning theoretic approach is introduced, which does not consider any a priori information on the Markov processes governing the communication system.
Edit intent: fluency
Original:  The problem of maximizing the expected total data transmitted during the transmitter's lifetime is studied under three different sets of assumptions regarding the information  about the underlying stochastic processes , available at the transmitter . A learning theoretic approach is introduced, which does not consider any a priori information on the Markov processes governing the communication system.
Revised:  The problem of maximizing the expected total data transmitted during the transmitter's lifetime is studied under three different sets of assumptions regarding the information about the underlying stochastic processes . A learning theoretic approach is introduced, which does not consider any a priori information on the Markov processes governing the communication system.
Edit intent: clarity
Original:  The problem of maximizing the expected total data transmitted during the transmitter's lifetime is studied under three different sets of assumptions regarding the information  about the underlying stochastic processes , available at the transmitter . A learning theoretic approach is introduced, which does not consider any a priori information on the Markov processes governing the communication system.
Revised:  The problem of maximizing the expected total data transmitted during the transmitter's lifetime is studied under three different sets of assumptions regarding the information about the underlying stochastic processes , available at the transmitter . A learning theoretic approach is introduced, which does not assume any a priori information on the Markov processes governing the communication system.
Edit intent: clarity
Original:  In addition, online and offline optimization problems are studied for the same setup assuming full statistical knowledge and causal information on the realizations , and non-causal knowledge in the realizations of the stochastic processes, respectively . Comparing the optimal solutions in all three frameworks  the performance loss due to the lack of  transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Revised:  In addition, online and offline optimization problems are studied for the same setting. Full statistical knowledge and causal information on the realizations , and non-causal knowledge in the realizations of the stochastic processes, respectively . Comparing the optimal solutions in all three frameworks the performance loss due to the lack of transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Edit intent: clarity
Original:  In addition, online and offline optimization problems are studied for the same setup assuming full statistical knowledge and causal information on the realizations , and non-causal knowledge in the realizations of the stochastic processes, respectively . Comparing the optimal solutions in all three frameworks  the performance loss due to the lack of  transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Revised:  In addition, online and offline optimization problems are studied for the same setup assuming full statistical knowledge and causal information on the realizations of the underlying stochastic processes are assumed in the online optimization problem, while the offline optimization problem assumes non-causal knowledge in the realizations of the stochastic processes, respectively . Comparing the optimal solutions in all three frameworks the performance loss due to the lack of transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Edit intent: coherence
Original:  In addition, online and offline optimization problems are studied for the same setup assuming full statistical knowledge and causal information on the realizations , and non-causal knowledge in the realizations of the stochastic processes, respectively . Comparing the optimal solutions in all three frameworks  the performance loss due to the lack of  transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Revised:  In addition, online and offline optimization problems are studied for the same setup assuming full statistical knowledge and causal information on the realizations , and non-causal knowledge of the realizations in advance . Comparing the optimal solutions in all three frameworks the performance loss due to the lack of transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Edit intent: clarity
Original:  In addition, online and offline optimization problems are studied for the same setup assuming full statistical knowledge and causal information on the realizations , and non-causal knowledge in the realizations of the stochastic processes, respectively . Comparing the optimal solutions in all three frameworks  the performance loss due to the lack of  transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Revised:  In addition, online and offline optimization problems are studied for the same setup assuming full statistical knowledge and causal information on the realizations , and non-causal knowledge in the realizations of the stochastic processes, respectively . Comparing the optimal solutions in all three frameworks , the performance loss due to the lack of transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Edit intent: fluency
Original:  In addition, online and offline optimization problems are studied for the same setup assuming full statistical knowledge and causal information on the realizations , and non-causal knowledge in the realizations of the stochastic processes, respectively . Comparing the optimal solutions in all three frameworks  the performance loss due to the lack of  transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Revised:  In addition, online and offline optimization problems are studied for the same setup assuming full statistical knowledge and causal information on the realizations , and non-causal knowledge in the realizations of the stochastic processes, respectively . Comparing the optimal solutions in all three frameworks the performance loss due to the lack of the transmitter's information regarding the behaviors of the underlying Markov processes is identified.
Edit intent: fluency
Original: Shape-based regularization has proven to be a useful method for delineating objects from the noisy images encountered in many applications when one has prior knowledge of the shape of the targeted object.
Revised: Shape-based regularization has proven to be a useful method for delineating objects within noisy images where one has prior knowledge of the shape of the targeted object.
Edit intent: clarity
Original:  Here, we show how one may recast the energy minization problem into a form that is minimizable iteratively  using graph cuts.
Revised:  Here, we show how one may recast the energy functional into a form that is minimizable iteratively using graph cuts.
Edit intent: clarity
Original:  Second, in addition to accessing the channel if the PU is idel , the SU possibly accesses the channel if it is declared to be busy with some access probability b_s.
Revised:  Second, in addition to accessing the channel if the PU is idle , the SU possibly accesses the channel if it is declared to be busy with some access probability b_s.
Edit intent: fluency
Original:  In addition, we propose  variable sensing duration schemes where the SU optimizes over the optimal sensing time to achieve the maximum stable throughput of the network.
Revised:  In addition, we propose a variable sensing duration schemes where the SU optimizes over the optimal sensing time to achieve the maximum stable throughput of the network.
Edit intent: fluency
Original: We propose a new analysis tool for signals that is based on complex wavelet signs, called a signature.
Revised: We propose a signal analysis tool based on the sign (or the phase) of complex wavelet coefficients, which we call a signature.
Edit intent: clarity
Original:  The complex-valued signature of a signal at some spatial location is defined as the fine-scale limit of the signs of its complex wavelet coefficients.
Revised:  The signature is defined as the fine-scale limit of the signs of its complex wavelet coefficients.
Edit intent: clarity
Original:  The complex-valued signature of a signal at some spatial location is defined as the fine-scale limit of the signs of its complex wavelet coefficients.
Revised:  The complex-valued signature of a signal at some spatial location is defined as the fine-scale limit of the signs of a signal's complex wavelet coefficients.
Edit intent: fluency
Original:  We establish that signature is invariant under fractional differentiation and rotates in the complex plane under fractional Hilbert transforms.
Revised:  We establish that the signature rotates in the complex plane under fractional Hilbert transforms.
Edit intent: clarity
Original:  We argue that this model is a natural starting point to describe more complex situations, most notably competition in marine environments where individuals are transported by fluid flows .
Revised:  We argue that this model is a natural choice to describe competition in marine environments where individuals are transported by fluid flows .
Edit intent: clarity
Original:  We argue that this model is a natural starting point to describe more complex situations, most notably competition in marine environments where individuals are transported by fluid flows .
Revised:  We argue that this model is a natural starting point to describe more complex situations, most notably competition in marine environments .
Edit intent: clarity
Original: Algorithms for persistent homology and zigzag persistent homology are well studied for homology modules where homomorphisms are induced by inclusion maps.
Revised: Algorithms for persistent homology and zigzag persistent homology are well-studied for homology modules where homomorphisms are induced by inclusion maps.
Edit intent: fluency
Original:  However, the same is not true for homomorphisms induced by other continuous maps such as simplicial ones.
Edit intent: coherence
Original:  In this paper, we propose a practical algorithm for computing persistence and zigzag persistence with homology under Z_2 coefficients for a sequence of general simplicial maps.
Revised:  In this paper, we propose a practical algorithm for computing persistence under Z_2 coefficients for a sequence of general simplicial maps.
Edit intent: coherence
Original:  We leverage the fact that every simplicial map can be simulated by inclusion maps , but not necessarily in  monotone direction.
Revised:  First, we observe that it is not hard to simulate simplicial maps by inclusion maps , but not necessarily in monotone direction.
Edit intent: clarity
Original:  We leverage the fact that every simplicial map can be simulated by inclusion maps , but not necessarily in  monotone direction.
Revised:  We leverage the fact that every simplicial map can be simulated by inclusion maps but not necessarily in monotone direction.
Edit intent: fluency
Original:  We leverage the fact that every simplicial map can be simulated by inclusion maps , but not necessarily in  monotone direction.
Revised:  We leverage the fact that every simplicial map can be simulated by inclusion maps , but not necessarily in a monotone direction.
Edit intent: fluency
Original:  With this new tool , we also provide an alternative way to approximate the persistence diagram of a filtration of Rips complexes where vertex collapses are used to tame the blow-up in size.
Revised:  With this new tool in which we approximate the persistence diagram of a filtration of Rips complexes where vertex collapses are used to tame the blow-up in size.
Edit intent: clarity
Original: Algorithms for persistent homology and zigzag persistent homology are well-studied for homology modules where homomorphisms are induced by inclusion maps.
Revised: Algorithms for persistent homology and zigzag persistent homology are well-studied for persistence modules where homomorphisms are induced by inclusion maps.
Edit intent: clarity
Original:  A consistent annotation through  atomic operations implies the maintenance of a consistent cohomology basis, hence a homology basis by duality.
Revised:  A consistent annotation through these atomic operations implies the maintenance of a consistent cohomology basis, hence a homology basis by duality.
Edit intent: clarity
Original:  Here, we demonstrate that without changing the physiological condition, a DNA may be brought to a new dynamic state from the zipped or unzipped state by varying the frequency of the applied force.
Revised:  Here, we demonstrate that without changing the physiological condition, it is possible to bring DNA from the zipped or unzipped state by varying the frequency of the applied force.
Edit intent: clarity
Original:  both algorithms generate the next minimal edge dominating set with incremental-polynomial delay O(m ^4 |L| ^2 ) and O(m^4 |L|) respectively, when L is the set of already generated minimal edge dominating sets.
Revised:  both algorithms generate the next minimal edge dominating set with incremental-polynomial delay O(m ^4 |L| ) and O(m^4 |L|) respectively, when L is the set of already generated minimal edge dominating sets.
Edit intent: clarity