wanyu/IteraTeR_v2 huggingface dataset:
Original:  Our model generically predicts striking cusps in the distribution of  fitness effects of fixed mutations and predicts that a single element of the chemotype should comprise all mutations at the high fitness end of that distribution . Using extreme value theory, we show that the most fit pair of these cusps are typically well-separated, even when the chemotype consists of thousands of elements , implying that the effects we predict should be observable in practical experiments .
Revised:  Our model generically predicts striking cusps in the distribution of fitness effects of fixed mutations and predicts that a single element of the chemotype should comprise all mutations at the high fitness end of that distribution . Using extreme value theory, we show that the two cusps with the highest fitnesses are typically well-separated, even when the chemotype consists of thousands of elements , implying that the effects we predict should be observable in practical experiments .
Edit intent: clarity
Original:  Our model generically predicts striking cusps in the distribution of  fitness effects of fixed mutations and predicts that a single element of the chemotype should comprise all mutations at the high fitness end of that distribution . Using extreme value theory, we show that the most fit pair of these cusps are typically well-separated, even when the chemotype consists of thousands of elements , implying that the effects we predict should be observable in practical experiments .
Revised:  Our model generically predicts striking cusps in the distribution of fitness effects of fixed mutations and predicts that a single element of the chemotype should comprise all mutations at the high fitness end of that distribution . Using extreme value theory, we show that the most fit pair of these cusps are typically well-separated, even when the chemotype possesses thousands of elements , implying that the effects we predict should be observable in practical experiments .
Edit intent: clarity
Original:  Our model generically predicts striking cusps in the distribution of  fitness effects of fixed mutations and predicts that a single element of the chemotype should comprise all mutations at the high fitness end of that distribution . Using extreme value theory, we show that the most fit pair of these cusps are typically well-separated, even when the chemotype consists of thousands of elements , implying that the effects we predict should be observable in practical experiments .
Revised:  Our model generically predicts striking cusps in the distribution of fitness effects of fixed mutations and predicts that a single element of the chemotype should comprise all mutations at the high fitness end of that distribution . Using extreme value theory, we show that the most fit pair of these cusps are typically well-separated, even when the chemotype consists of thousands of elements ; this suggests a means to observe these cusps experimentally .
Edit intent: clarity
Original:  More broadly, our work demonstrates that new insight can be gain by viewing evolution through the chemotype , the level intermediate between the genotype and the phenotype.
Revised:  More broadly, our work demonstrates that new insights into evolution can arise from the chemotype perspective, a perspective between the genotype and the phenotype.
Edit intent: clarity
Original:  These results strongly disagree with the "frozen accident" hypothesis and imply that the genetic code evolved from a communal state of life prior to the root of the modern ribosomal tree of life.
Revised:  These results strongly support the idea that the genetic code evolved from a communal state of life prior to the root of the modern ribosomal tree of life.
Edit intent: clarity
Original: Using Malliavin calculus techniques, we derive an analytical formula for the price of European options, for any model including local volatility and jump Poisson process.
Revised: Using Malliavin calculus techniques, we derive an analytical formula for the price of European options, for any model including local volatility and Poisson jump process.
Edit intent: fluency
Original:  We show that the accuracy of the formula depends on the smoothness of the payoff  .
Revised:  We show that the accuracy of the formula depends on the smoothness of the payoff function .
Edit intent: clarity
Original: We propose a model which can be jointly calibrated to the bonds and equity options of the same company.
Revised: We propose a model which can be jointly calibrated to the corporate bond term structure and equity option volatility surface of the same company.
Edit intent: clarity
Original:  This is striking since without calibrating any parameter to the CDS spread data, it is matched by the CDS spread  our model generates using the available information from the equity options and corporate bond markets.
Revised:  This is observation is worth noticing since without calibrating any parameter to the CDS spread data, it is matched by the CDS spread our model generates using the available information from the equity options and corporate bond markets.
Edit intent: clarity
Original:  This is striking since without calibrating any parameter to the CDS spread data, it is matched by the CDS spread  our model generates using the available information from the equity options and corporate bond markets.
Revised:  This is striking since without calibrating any parameter to the CDS spread data, it is matched by the CDS spread that our model generates using the available information from the equity options and corporate bond markets.
Edit intent: clarity
Original:  We demonstrate the importance of accounting for the default risk and stochastic interest rate in equity option pricing by comparing our results to Fouque et. al. (2003), which proposed a similar modeling framework in the context of stochastic volatilitymodels .
Revised:  We demonstrate the importance of accounting for the default risk and stochastic interest rate in equity option pricing by comparing our results to Fouque et. al. (2003), which only accounts for stochastic volatility .
Edit intent: clarity
Original:  In this paper  the security of the scheme is studied and the following problems are found: (1) a differential chosen-plaintext attack can break the scheme with only three chosen plain-images;
Revised:  In this paper , the security of the scheme is studied and the following problems are found: (1) a differential chosen-plaintext attack can break the scheme with only three chosen plain-images;
Edit intent: fluency
Original:  We investigate Neural Networks (NNs) and Support Vector Machines (SVM) for the learning based pattern recognition functionality of our distributed intelligence.
Revised:  We investigate Neural Networks and Support Vector Machines (SVM) for the learning based pattern recognition functionality of our distributed intelligence.
Edit intent: clarity
Original:  We investigate Neural Networks (NNs) and Support Vector Machines (SVM) for the learning based pattern recognition functionality of our distributed intelligence.
Revised:  We investigate Neural Networks (NNs) and Support Vector Machine for the learning based pattern recognition functionality of our distributed intelligence.
Edit intent: clarity
Original: A novel optimisation technique inspired by natural ecosystems is presented, where the optimisation works at two levels: a first optimisation, migration of services which are distributed in a decentralised peer-to-peer network, operating continuously in time;
Revised: A novel optimisation technique where the optimisation works at two levels: a first optimisation, migration of services which are distributed in a decentralised peer-to-peer network, operating continuously in time;
Edit intent: clarity
Original: A novel optimisation technique inspired by natural ecosystems is presented, where the optimisation works at two levels: a first optimisation, migration of services which are distributed in a decentralised peer-to-peer network, operating continuously in time;
Revised: A novel optimisation technique inspired by natural ecosystems is presented, where the optimisation works at two levels: a first optimisation, migration of agents (representing services) which are distributed in a decentralised peer-to-peer network, operating continuously in time;
Edit intent: clarity
Original: A primary motivation for research in digital ecosystems is the desire to exploit the self-organising properties of natural ecosystems.
Revised: A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of natural ecosystems.
Edit intent: fluency
Original: A primary motivation for research in digital ecosystems is the desire to exploit the self-organising properties of natural ecosystems.
Revised: A primary motivation for research in digital ecosystems is the desire to exploit the self-organising properties of biological ecosystems.
Edit intent: clarity
Original:  However, the biological processes that contribute to these properties have not been made explicit in digital ecosystem research.
Revised:  However, the biological processes that contribute to these properties have not been made explicit in Digital Ecosystems research.
Edit intent: fluency
Original:  These properties include populations of evolving agents, a complex dynamic environment, and spatial distributions which generate local interactions.
Revised:  These properties include populations of evolving agents, a complex dynamic environment, and spatial distributions for generating local interactions.
Edit intent: clarity
Original:   An example architecture, the Digital Business Ecosystem(DBE) , is considered in detail.
Revised:  An example architecture, the Digital Ecosystem , is considered in detail.
Edit intent: clarity
Original: We start with a discussion of the relevant literature, including Nature Inspired Comuting as a framework in which to understand this work, and the process of biomimicry to be used in mimicking the necessary biological processes to create Digital Ecosystems.
Revised: We start with a discussion of the relevant literature, including Nature Inspired Computing as a framework in which to understand this work, and the process of biomimicry to be used in mimicking the necessary biological processes to create Digital Ecosystems.
Edit intent: fluency
Original:  The collective movement of the kinesins on a microtubule is, therefore, analogous to vehicular traffic on multi-lane highways where each protofilament is the analogue of a single lane.
Revised:  The collective movement of the kinesins on a MT is, therefore, analogous to vehicular traffic on multi-lane highways where each protofilament is the analogue of a single lane.
Edit intent: clarity
Original:  On the basis of analytical treatment of our model, we predict the effects of lane changing on the flux of the KIF1A motors .
Revised:  On the basis of analytical treatment of our model, we predict that the flux per lane can increase or decrease with the increasing rate of lane changing on the flux of the KIF1A motors .
Edit intent: clarity
Original: Relations between a contact matrix and a contact energy matrix in proteins are analyzed under an assumption that the total conformational energy of a protein can be approximated by a sum of pairwise interaction energies represented as a product of corresponding elements of these matrices each of which corresponds to a conformation-dependent function and an sequence-dependent energy parameter.
Revised: Relations between a contact matrix and a contact energy matrix (E-matrix) under an assumption that the total conformational energy of a protein can be approximated by a sum of pairwise interaction energies represented as a product of corresponding elements of these matrices each of which corresponds to a conformation-dependent function and an sequence-dependent energy parameter.
Edit intent: clarity
Original: Relations between a contact matrix and a contact energy matrix in proteins are analyzed under an assumption that the total conformational energy of a protein can be approximated by a sum of pairwise interaction energies represented as a product of corresponding elements of these matrices each of which corresponds to a conformation-dependent function and an sequence-dependent energy parameter.
Revised: Relations between a contact matrix and a contact energy matrix in proteins are analyzed under an assumption that the total conformational energy can be approximated by a sum of pairwise interaction energies represented as a product of corresponding elements of these matrices each of which corresponds to a conformation-dependent function and an sequence-dependent energy parameter.
Edit intent: clarity
Original:  Here, the contact matrix is represented in a spectral expansion but unlike their analyses, the contact energy matrix is expanded in a series of eigenspaces with an additional constant  .
Revised:  Here, the contact matrix is represented in a spectral expansion but unlike their analyses, the contact energy matrix is expanded in a series of eigenspaces with an additional constant term .
Edit intent: clarity
Original:  The additional constant  is indicated by the lowest bound of the total energy function , which is equal to the total energy of the native conformation interacting in a Go-like pairwise potential (Annu.
Revised:  The additional constant term is indicated by the lowest bound of the total energy function , which is equal to the total energy of the native conformation interacting in a Go-like pairwise potential (Annu.
Edit intent: clarity
Original:  Bioeng. 12, 183, 1983), to correspond to a threshold of contact energy to approximately separate native contacts from non-naive contacts.
Revised:  Bioeng. 12, 183, 1983), to correspond to a threshold of contact energy that approximately separates native contacts from non-naive contacts.
Edit intent: fluency
Original:  The most efficient way to approach the lowest bound of energy may be to make the principal eigenvector of C-matrix parallel to that of E-matrix .
Revised:  Inner products between the principal eigenvector of C-matrix parallel to that of E-matrix .
Edit intent: clarity
Original:  The most efficient way to approach the lowest bound of energy may be to make the principal eigenvector of C-matrix parallel to that of E-matrix .
Revised:  The most efficient way to approach the lowest bound of energy may be to make the principal eigenvector of C-matrix , that of E-matrix .
Edit intent: clarity
Original: Properties of contact matrices (C-matrices) for native proteins to be the lowest energy conformations are considered in relation with a contact energy matrix (E-matrix) under an assumption that the total conformational energy can be approximated by a sum of pairwise interaction energies represented as a product of corresponding elements of these matrices .
Revised: The total conformational energy can be approximated by a sum of pairwise interaction energies represented as a product of corresponding elements of these matrices .
Edit intent: clarity
Original: Properties of contact matrices (C-matrices) for native proteins to be the lowest energy conformations are considered in relation with a contact energy matrix (E-matrix) under an assumption that the total conformational energy can be approximated by a sum of pairwise interaction energies represented as a product of corresponding elements of these matrices .
Revised: Properties of contact matrices (C-matrices) for native proteins to be the lowest energy conformations are considered in relation with a contact energy matrix (E-matrix) under an assumption that the total conformational energy is assumed to consist of pairwise interaction energies represented as a product of corresponding elements of these matrices .
Edit intent: clarity
Original: Properties of contact matrices (C-matrices) for native proteins to be the lowest energy conformations are considered in relation with a contact energy matrix (E-matrix) under an assumption that the total conformational energy can be approximated by a sum of pairwise interaction energies represented as a product of corresponding elements of these matrices .
Revised: Properties of contact matrices (C-matrices) for native proteins to be the lowest energy conformations are considered in relation with a contact energy matrix (E-matrix) under an assumption that the total conformational energy can be approximated by a sum of pairwise interaction energies between atoms or residues, each of which is expressed as a product of corresponding elements of these matrices .
Edit intent: clarity
Original:  This relationship corresponds to 1 ) a parallel relationship between the eigenvectors of C-matrix and those of E-matrix and a linear relationship between their eigenvalues, 2 ) a parallel relationship between a contact number vector and the principal eigenvectors of C-matrix and of E-matrix , where E-matrix is expanded in a series of eigenspaces with an additional constant term .
Revised:  This relationship corresponds to 1 ) a parallel relationship between the eigenvectors of the C- and E-matrices and a linear relationship between their eigenvalues, 2 ) a parallel relationship between a contact number vector and the principal eigenvectors of C-matrix and of E-matrix , where E-matrix is expanded in a series of eigenspaces with an additional constant term .
Edit intent: clarity
Original:  This relationship corresponds to 1 ) a parallel relationship between the eigenvectors of C-matrix and those of E-matrix and a linear relationship between their eigenvalues, 2 ) a parallel relationship between a contact number vector and the principal eigenvectors of C-matrix and of E-matrix , where E-matrix is expanded in a series of eigenspaces with an additional constant term .
Revised:  This relationship corresponds to 1 ) a parallel relationship between the eigenvectors of C-matrix and those of E-matrix and a linear relationship between their eigenvalues, 2 ) a parallel relationship between a contact number vector and the principal eigenvectors of the C- and E-matrices; the E-matrix , where E-matrix is expanded in a series of eigenspaces with an additional constant term .
Edit intent: clarity
Original:  This relationship corresponds to 1 ) a parallel relationship between the eigenvectors of C-matrix and those of E-matrix and a linear relationship between their eigenvalues, 2 ) a parallel relationship between a contact number vector and the principal eigenvectors of C-matrix and of E-matrix , where E-matrix is expanded in a series of eigenspaces with an additional constant term .
Revised:  This relationship corresponds to 1 ) a parallel relationship between the eigenvectors of C-matrix and those of E-matrix and a linear relationship between their eigenvalues, 2 ) a parallel relationship between a contact number vector and the principal eigenvectors of C-matrix and of E-matrix is expanded in a series of eigenspaces with an additional constant term .
Edit intent: coherence
Original:  Inner products between the principal eigenvector of  C-matrix, that of  E-matrix  , and a contact number vector have been examined for 182 proteins each of which is a representative from each family of the SCOP database, and the results indicate the parallel tendencies between those vectors.
Revised:  Inner products between the principal eigenvector of the C-matrix, that of E-matrix , and a contact number vector have been examined for 182 proteins each of which is a representative from each family of the SCOP database, and the results indicate the parallel tendencies between those vectors.
Edit intent: fluency
Original:  Inner products between the principal eigenvector of  C-matrix, that of  E-matrix  , and a contact number vector have been examined for 182 proteins each of which is a representative from each family of the SCOP database, and the results indicate the parallel tendencies between those vectors.
Revised:  Inner products between the principal eigenvector of C-matrix, that of the E-matrix , and a contact number vector have been examined for 182 proteins each of which is a representative from each family of the SCOP database, and the results indicate the parallel tendencies between those vectors.
Edit intent: fluency
Original: We show that the graph isomorphism problem is determined in a polynomial time.
Revised: We relate the graph isomorphism problem is determined in a polynomial time.
Edit intent: coherence
Original:  This version replaces the previous version of this paper named "Graph isomorphism is polynomial" .
Revised:  This version replaces the previous version of this paper .
Edit intent: coherence
Original:  Then we propose an algorithm for finding this graph, given the degree sequence of the input graph G 
Revised:  Then we propose an algorithm for finding this graph, given the degree sequence of the input graph G .
Edit intent: fluency
Original:  The first step suffices to show CBV termination of a single, stand-alone lambda-expression .
Revised:  The first step suffices to show CBV termination of a single, stand-alone lambda;-expression .
Edit intent: fluency
Original:  A mean-field description can be solved analytically via a mapping to a restricted random-graph ensemble  .
Revised:  A mean-field approximation can be described analytically via a mapping to a restricted random-graph ensemble .
Edit intent: clarity
Original: In this paper we study a new class of words that are 'rich' in palindromes  .
Revised: In this paper , we develop the theory of new class of words that are 'rich' in palindromes .
Edit intent: clarity
Original:  A characteristic property of so-called "rich words" is that the 'complete returns ' to any palindromic factor are themselves palindromes.
Revised:  A characteristic property of so-called "rich words" is that all complete returns to any palindromic factor are themselves palindromes.
Edit intent: clarity
Original:   Amongst our main results, we give an explicit characterization of the periodic rich infinite words  .
Revised:  Amongst our main results, we give an explicit description of the periodic rich infinite words .
Edit intent: clarity
Original:  hence they satisfy Fraenkel's conjecture , as does a certain class of "almost rich " words .
Revised:  hence they satisfy Fraenkel's conjecture . Likewise, we prove that a certain class of "almost rich " words .
Edit intent: clarity
Original:  Other examples of rich words have appeared in many different contexts , but until now, no-one has taken a unified approach to the study of this intriguing class of words.
Revised:  Other examples of rich words have appeared in many different contexts . Here we present the first unified approach to the study of this intriguing class of words.
Edit intent: clarity
Original:  Other examples of rich words have appeared in many different contexts , but until now, no-one has taken a unified approach to the study of this intriguing class of words.
Revised:  Other examples of rich words have appeared in many different contexts , but until now, no-one has taken a unified approach to the study of this intriguing family of words.
Edit intent: clarity
Original: Computational modelling of multi-agent systems is becoming an important technique in studying language evolution.
Revised: Computational modelling with multi-agent systems is becoming an important technique in studying language evolution.
Edit intent: fluency
Original: Computational modelling of multi-agent systems is becoming an important technique in studying language evolution.
Revised: Computational modelling of multi-agent systems is becoming an important technique of studying language evolution.
Edit intent: clarity
Original:  In our opinion, this model shows that linguistic and biological processes have a strong influence on each other and this influence certainly has contributed to an explosive development of our species.
Revised:  In our opinion, this model shows that linguistic and biological processes have a strong influence on each other and this effect certainly has contributed to an explosive development of our species.
Edit intent: clarity