wanyu/IteraTeR_v2 huggingface dataset:
Original:  Functional annotation of proteins encoded in newly sequenced genomes is expected to meet the conflicting requirements of providing as much comprehensive information as possible while avoiding erroneous functional assignments and over-predictions .
Revised:  Automatic functional annotation of proteins encoded in newly sequenced genomes is expected to meet the conflicting requirements of providing as much comprehensive information as possible while avoiding erroneous functional assignments and over-predictions .
Edit intent: fluency
Original:  Functional annotation of proteins encoded in newly sequenced genomes is expected to meet the conflicting requirements of providing as much comprehensive information as possible while avoiding erroneous functional assignments and over-predictions .
Revised:  Functional annotation of proteins is expected to meet the conflicting requirements of providing as much comprehensive information as possible while avoiding erroneous functional assignments and over-predictions .
Edit intent: clarity
Original:  Functional annotation of proteins encoded in newly sequenced genomes is expected to meet the conflicting requirements of providing as much comprehensive information as possible while avoiding erroneous functional assignments and over-predictions .
Revised:  Functional annotation of proteins encoded in newly sequenced genomes is expected to meet the conflicting requirements of maximizing annotation coverage, while minimizing erroneous functional assignments and over-predictions .
Edit intent: clarity
Original:  Functional annotation of proteins encoded in newly sequenced genomes is expected to meet the conflicting requirements of providing as much comprehensive information as possible while avoiding erroneous functional assignments and over-predictions .
Revised:  Functional annotation of proteins encoded in newly sequenced genomes is expected to meet the conflicting requirements of providing as much comprehensive information as possible while avoiding erroneous functional assignments .
Edit intent: clarity
Original:  The resulting knowledge represents predictive models explaining pathway involvement of UniProtKB entries.
Revised:  The resulting knowledge represents predictive models that assign pathway involvement to UniProtKB entries.
Edit intent: clarity
Original:  We carried out an evaluation study of our system performance using semantic similarity and cross-validation technique.
Revised:  We carried out an evaluation study of our system performance using cross-validation technique.
Edit intent: clarity
Original:  We found that it achieved a very high accuracy of pathway identification with an F1-measure of 0.987 and AUC of 0.99.
Revised:  We found that it achieved very promising results in pathway identification with an F1-measure of 0.987 and AUC of 0.99.
Edit intent: clarity
Original: If a given behavior of a multi-agent system corresponds to restrict the phase variable to a invariant manifold, then we define a phase transition as change of physical characteristics such as speed, coordination  and structure.
Revised: If a given behavior of a multi-agent system restricts the phase variable to a invariant manifold, then we define a phase transition as change of physical characteristics such as speed, coordination and structure.
Edit intent: clarity
Original: If a given behavior of a multi-agent system corresponds to restrict the phase variable to a invariant manifold, then we define a phase transition as change of physical characteristics such as speed, coordination  and structure.
Revised: If a given behavior of a multi-agent system corresponds to restrict the phase variable to a invariant manifold, then we define a phase transition as change of physical characteristics such as speed, coordination , and structure.
Edit intent: fluency
Original:  We define such a phase transition as splitting an underlying manifold into two sub-manifolds with distinct dimensionalities around the singularity where the transition is physically represented on . Here, we propose a method of detecting phase transitions and splitting the manifold into  transitions free sub-manifolds.
Revised:  We define such a phase transition as splitting an underlying manifold into two sub-manifolds with distinct dimensionalities around the singularity where the phase transition physically exists . Here, we propose a method of detecting phase transitions and splitting the manifold into transitions free sub-manifolds.
Edit intent: clarity
Original:  We define such a phase transition as splitting an underlying manifold into two sub-manifolds with distinct dimensionalities around the singularity where the transition is physically represented on . Here, we propose a method of detecting phase transitions and splitting the manifold into  transitions free sub-manifolds.
Revised:  We define such a phase transition as splitting an underlying manifold into two sub-manifolds with distinct dimensionalities around the singularity where the transition is physically represented on . Here, we propose a method of detecting phase transitions and splitting the manifold into phase transitions free sub-manifolds.
Edit intent: fluency
Original:  Therein, we utilize a relationship between curvature and singular value ratio of points sampled in a curve, and then extend the assertion to higher dimensions using the shape operator.
Revised:  Therein, we utilize a relationship between curvature and singular value ratio of points sampled in a curve, and then extend the assertion into higher-dimensions using the shape operator.
Edit intent: fluency
Original:  The center region, far from the overlap ends, has a constant motor density as one would na\"ively expect.
Revised:  The center region, far from the overlap ends, has a constant motor density as one would naively expect.
Edit intent: fluency
Original:  The antiparallel microtubule overlap geometry may offer a novel mechanism for biological regulation of protein concentration and consequent activity.
Revised:  The antiparallel microtubule overlap geometry may offer a previously unrecognized mechanism for biological regulation of protein concentration and consequent activity.
Edit intent: clarity
Original:  The technology relatedness network's structure can reveal properties of technologies and of human behavior, if it can be mapped accurately.
Revised:  The technology network's structure can reveal properties of technologies and of human behavior, if it can be mapped accurately.
Edit intent: fluency
Original:  Technology networks have been made from patent data, using several measures of relatedness .
Revised:  Technology networks have been made from patent data, using several measures of proximity .
Edit intent: clarity
Original:  Different measures of technology relatedness became more correlated with each other after normalization , approaching a single dimension of technology relatedness .
Revised:  Different measures of technology relatedness became more correlated with each other , approaching a single dimension of technology relatedness .
Edit intent: clarity
Original:  firms' portfolios combined ~50\% of pairs of technology domains at rates greater than chance .
Revised:  firms' portfolios combined ~50\% of pairs of technology domains about twice as often as inventors .
Edit intent: clarity
Original:  These results suggest that controlling for impinging factors brings us closer to uncovering a true technology space, and that this space has explanatory power for human invention .
Revised:  These results suggest that controlling for impinging factors brings us closer to uncovering a true technology space, and that this map can be used to aid in technology innovation planning and management .
Edit intent: clarity
Original:  This work represents the first implementation of a generative RBM on a neuromorphic VLSI substrate.
Revised:  This work represents the first implementation of generative RBM inference on a neuromorphic VLSI substrate.
Edit intent: clarity
Original:  Availability: TRONCO is released under the GPL license, and it is hosted at (Software section ) URL and archived also at bioconductor.org.
Revised:  Availability: TRONCO is released under the GPL license, is hosted in the Software section at URL and archived also at bioconductor.org.
Edit intent: coherence
Original:  Availability: TRONCO is released under the GPL license,  is hosted in the Software section at URL and archived also at bioconductor.org.
Revised:  Availability: TRONCO is released under the GPL license, it is hosted in the Software section at URL and archived also at bioconductor.org.
Edit intent: clarity
Original:  We make progress on both problems: we introduce a class of gameswe call anchored, and prove exponential-decay parallel repetition theorems for anchored games in the multiplayer and entangled-player settings.
Revised:  We make progress on both problems: we introduce a class of gameswe call anchored, and prove exponential-decay parallel repetition theorem for all anchored games in the multiplayer and entangled-player settings.
Edit intent: clarity
Original:  The smallest number of edges in a rectifier network that computes M is a classic complexity measure on matrices, which has been studied for more than half a century.
Revised:  The smallest number of edges in a rectifier network computing M is a classic complexity measure on matrices, which has been studied for more than half a century.
Edit intent: clarity
Original:  Both of them build upon a basic fact that depth-2 rectifier networks are essentially weighted coverings of Boolean matrices with rectangles.
Revised:  Both of them build on a basic fact that depth-2 rectifier networks are essentially weighted coverings of Boolean matrices with rectangles.
Edit intent: fluency
Original:  Our second and third results constitute progress on open problems 7.3 and  7.5 from a recent book by Jukna and Sergeev (in Foundations and Trends in Theoretical Computer Science (2013)).
Revised:  Our second and third results constitute progress on open problem 7.3 and 7.5 from a recent book by Jukna and Sergeev (in Foundations and Trends in Theoretical Computer Science (2013)).
Edit intent: fluency
Original: A dedicated algorithm for sparse spectral modeling of music sound is presented.
Revised: A dedicated algorithm for sparse spectral representation of music sound is presented.
Edit intent: clarity
Original:  Here we generalize this result by taking into account the influence of connexions between positive and negative cycles.
Revised:  Here we generalize this result by taking into account the influence of connections between positive and negative cycles.
Edit intent: fluency
Original:  Beside , Aracena proved that if G is strongly connected and have no negative cycle , then f has two fixed points with Hamming distance n, and we prove that the same conclusion can be obtain under the following condition: G is strongly connected, has a unique negative cycle C, has at least one positive cycle, and f canalizes no arc of C.
Revised:  Besides , Aracena proved that if G is strongly connected and have no negative cycle , then f has two fixed points with Hamming distance n, and we prove that the same conclusion can be obtain under the following condition: G is strongly connected, has a unique negative cycle C, has at least one positive cycle, and f canalizes no arc of C.
Edit intent: coherence
Original:  Beside , Aracena proved that if G is strongly connected and have no negative cycle , then f has two fixed points with Hamming distance n, and we prove that the same conclusion can be obtain under the following condition: G is strongly connected, has a unique negative cycle C, has at least one positive cycle, and f canalizes no arc of C.
Revised:  Beside , Aracena proved that if G is strongly connected and has no negative cycles , then f has two fixed points with Hamming distance n, and we prove that the same conclusion can be obtain under the following condition: G is strongly connected, has a unique negative cycle C, has at least one positive cycle, and f canalizes no arc of C.
Edit intent: fluency
Original:  Beside , Aracena proved that if G is strongly connected and have no negative cycle , then f has two fixed points with Hamming distance n, and we prove that the same conclusion can be obtain under the following condition: G is strongly connected, has a unique negative cycle C, has at least one positive cycle, and f canalizes no arc of C.
Revised:  Beside , Aracena proved that if G is strongly connected and have no negative cycle , then f has two fixed points with Hamming distance n, and we prove that the same conclusion can be obtained under the following condition: G is strongly connected, has a unique negative cycle C, has at least one positive cycle, and f canalizes no arc of C.
Edit intent: fluency
Original: We are interested in the relationships between the number of fixed points in a Boolean network f:\{0,1\} ^ n \to\{0,1\}^n and its interaction graph G , which is the signed digraph on \{1,\dots,n\} that describes the positive and negative influences between the components of the network.
Revised: We are interested in the relationships between the number fixed points in a Boolean network f:\{0,1\} ^ n \to\{0,1\}^n and its interaction graph G , which is the signed digraph on \{1,\dots,n\} that describes the positive and negative influences between the components of the network.
Edit intent: clarity
Original: We are interested in the relationships between the number of fixed points in a Boolean network f:\{0,1\} ^ n \to\{0,1\}^n and its interaction graph G , which is the signed digraph on \{1,\dots,n\} that describes the positive and negative influences between the components of the network.
Revised: We are interested in the relationships between the number of fixed points in a Boolean network f:\{0,1\} ^n \to\{0,1\}^n and its interaction graph G , which is the signed digraph on \{1,\dots,n\} that describes the positive and negative influences between the components of the network.
Edit intent: fluency
Original: We are interested in the relationships between the number of fixed points in a Boolean network f:\{0,1\} ^ n \to\{0,1\}^n and its interaction graph G , which is the signed digraph on \{1,\dots,n\} that describes the positive and negative influences between the components of the network.
Revised: We are interested in the relationships between the number of fixed points in a Boolean network f:\{0,1\} ^ n \to\{0,1\}^n and its interaction graph , which is the signed digraph on \{1,\dots,n\} that describes the positive and negative influences between the components of the network.
Edit intent: clarity
Original:  A fundamental theorem of Aracena , suggested by the biologist Thomas, says that if G has no positive (resp. negative) cycles , then f has at most (resp. at least) one fixed point;
Revised:  A fundamental theorem of Aracena says that if G has no positive (resp. negative) cycles , then f has at most (resp. at least) one fixed point;
Edit intent: coherence
Original:  A fundamental theorem of Aracena , suggested by the biologist Thomas, says that if G has no positive (resp. negative) cycles , then f has at most (resp. at least) one fixed point;
Revised:  A fundamental theorem of Aracena , suggested by the biologist Thomas, says that if G has no positive (resp. negative) cycle , then f has at most (resp. at least) one fixed point;
Edit intent: fluency
Original:  Here we generalize this result by taking into account the influence of connections between positive and negative cycles.
Revised:  In this note, we generalize this result by taking into account the influence of connections between positive and negative cycles.
Edit intent: clarity
Original:  In particular, we prove that if every positive (resp. negative) cycle of G has an arc a such that G\setminus a has a non-trivial initial strongly connected component containing the final vertex of a and only negative (resp. positive) cycles, then f has at most (resp. at least) one fixed point.
Revised:  In particular, we prove that if every positive (resp. negative) cycle of G has an arc a such that G\setminus a has a non-trivial initial strongly connected component containing the terminal vertex of a and only negative (resp. positive) cycles, then f has at most (resp. at least) one fixed point.
Edit intent: clarity
Original: In the present communication, effort is given for the development of a common platform that helps to address several  growth processes found in literature.
Revised: Effort has been given for the development of a common platform that helps to address several growth processes found in literature.
Edit intent: clarity
Original:  Based on first principle approach, the role of rate of specific growth rate in different growth processes has been considered in an unified manner.
Revised:  In the proposed approach, the role of rate of specific growth rate in different growth processes has been considered in an unified manner.
Edit intent: clarity
Original:  Based on first principle approach, the role of rate of specific growth rate in different growth processes has been considered in an unified manner.
Revised:  Based on first principle approach, the role of specific growth rate in different growth processes has been considered in an unified manner.
Edit intent: fluency
Original:  It is found that  different growth equations can be derived from the same  rate equation of specific growth rate.
Revised:  It is found that the different growth equations can be derived from the same rate equation of specific growth rate.
Edit intent: coherence
Original:  It is found that  competitive environment may increase the saturation level of population size .
Revised:  It is found that the competitive environment may increase the saturation level of population size .
Edit intent: fluency
Original:  We prove that the for the set of all possible values of the parameters, the equilibrium locus is a smooth manifold with boundaries, while for a given value of the parameters, it is an embedded smooth and connected curve.
Revised:  We prove that when considering the set of all possible values of the parameters, the equilibrium locus is a smooth manifold with boundaries, while for a given value of the parameters, it is an embedded smooth and connected curve.
Edit intent: clarity
Original: A broad range of quantum optimisation problems can be phrased as the question whether a specific system has a ground state at zero energy, i.e.  whether its Hamiltonian is frustration free.
Revised: A broad range of quantum optimisation problems can be phrased as the question whether a specific system has a ground state at zero energy, i.e. \ whether its Hamiltonian is frustration free.
Edit intent: fluency
Original:  Here we prove a general criterion -- a sufficient condition -- under which a local Hamiltonian is guaranteed to be frustration free by lifting Shearer's theorem from classical probability theory to the quantum world.
Revised:  Here we prove a general criterion - a sufficient condition -- under which a local Hamiltonian is guaranteed to be frustration free by lifting Shearer's theorem from classical probability theory to the quantum world.
Edit intent: fluency
Original:  Here we prove a general criterion -- a sufficient condition -- under which a local Hamiltonian is guaranteed to be frustration free by lifting Shearer's theorem from classical probability theory to the quantum world.
Revised:  Here we prove a general criterion -- a sufficient condition - under which a local Hamiltonian is guaranteed to be frustration free by lifting Shearer's theorem from classical probability theory to the quantum world.
Edit intent: fluency
Original:  Remarkably, evaluating this condition proceeds via a fully classical analysis of a hard-core lattice gas at negative fugacity on the Hamiltonian's interaction graph which  as a statistical mechanics problem  is of interest in their own right.
Revised:  Remarkably, evaluating this condition proceeds via a fully classical analysis of a hard-core lattice gas at negative fugacity on the Hamiltonian's interaction graph which , as a statistical mechanics problem is of interest in their own right.
Edit intent: fluency
Original:  Remarkably, evaluating this condition proceeds via a fully classical analysis of a hard-core lattice gas at negative fugacity on the Hamiltonian's interaction graph which  as a statistical mechanics problem  is of interest in their own right.
Revised:  Remarkably, evaluating this condition proceeds via a fully classical analysis of a hard-core lattice gas at negative fugacity on the Hamiltonian's interaction graph which as a statistical mechanics problem , is of interest in their own right.
Edit intent: fluency
Original:  Remarkably, evaluating this condition proceeds via a fully classical analysis of a hard-core lattice gas at negative fugacity on the Hamiltonian's interaction graph which  as a statistical mechanics problem  is of interest in their own right.
Revised:  Remarkably, evaluating this condition proceeds via a fully classical analysis of a hard-core lattice gas at negative fugacity on the Hamiltonian's interaction graph which as a statistical mechanics problem is of interest in its own right.
Edit intent: fluency
Original:  We concretely apply this criterion to local Hamiltonians on various regular lattices, while bringing to bear the tools of spin glass theory which permit us to obtain new bounds on the SAT/UNSAT transition in random quantum satisfiability.
Revised:  We concretely apply this criterion to local Hamiltonians on various regular lattices, while bringing to bear the tools of spin glass physics which permit us to obtain new bounds on the SAT/UNSAT transition in random quantum satisfiability.
Edit intent: clarity
Original:  These also lead us to natural conjectures for when such bounds will be exact (tight) , as well as to a novel notion of universality for these computer science problems.
Revised:  These also lead us to natural conjectures for when such bounds will be tight , as well as to a novel notion of universality for these computer science problems.
Edit intent: clarity
Original:  We prove that for any fixed \varepsilon and m, a Sherali-Adams / Lasserre lift of the time-index LP with a slightly super poly-logarithmic number of r = (\log(n))^{\Theta(\log \log n)} rounds provides a (1 + \varepsilon)-approximation  .
Revised:  We prove that for any fixed \varepsilon and m, a Sherali-Adams / Lasserre lift of the time-indexed LP with a slightly super poly-logarithmic number of r = (\log(n))^{\Theta(\log \log n)} rounds provides a (1 + \varepsilon)-approximation .
Edit intent: fluency
Original:  An \ell_2-penalized maximum-likelihood approach is employed.
Revised:  An \ell_2-penalized maximum likelihood approach is employed.
Edit intent: fluency
Original:  In addition, the approach allows for the specification of target matrices through which prior knowledge may be incorporated and which can stabilize the estimation procedure in high-dimensional settings.
Revised:  In addition, the approach allows specification of target matrices through which prior knowledge may be incorporated and which can stabilize the estimation procedure in high-dimensional settings.
Edit intent: fluency
Original:  Situations are considered in which the classes are defined by data sets and /or (subtypes of ) diseases.
Revised:  Situations are considered in which the classes are defined by data sets and subtypes of diseases.
Edit intent: fluency
Original:  Its practical usability is illustrated by the differential network modeling of 11 large-scale diffuse large B-cell lymphoma gene expression data sets  .
Revised:  Its practical usability is illustrated by the differential network modeling of 11 large-scale gene expression data sets .
Edit intent: clarity
Original: Efficiency of a Peer-to-Peer increases with increase in resources by its members . Members being rational share as minimum as possible because they have to pay for upload bandwidth.
Revised: P2P system rely on voluntary allocation of resources by its members . Members being rational share as minimum as possible because they have to pay for upload bandwidth.
Edit intent: clarity