wanyu/IteraTeR_v2 huggingface dataset:
Original:  Based on this observation, in this paper, (1) we propose generalized tree pattern queries (GTPQs) over graph-structured data, which fully support propositional logic on structural constraints and allow a portion of query nodes as output nodes . (2) We make a thorough study of fundamental problems of satisfiability, containment and minimization, and give computational complexities and decision procedures of these problems.
Revised:  Based on this observation, in this paper, (1) we propose generalized tree pattern queries (GTPQs) over graph-structured data, which fully support propositional logic on structural constraints and allow a portion of query nodes as output nodes . (2) We make a thorough study of fundamental problems of satisfiability, containment and minimization, and analyze the computational complexity and the decision procedures of these problems.
Edit intent: clarity
Original:  (5) Empirical results on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm,  several times to orders of magnitudes more faster than state-of-art methods in terms of evaluation time  even for traditional tree pattern queries with only conjunctive operations.
Revised:  (5) Experiments on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm, several times to orders of magnitudes more faster than state-of-art methods in terms of evaluation time even for traditional tree pattern queries with only conjunctive operations.
Edit intent: clarity
Original:  (5) Empirical results on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm,  several times to orders of magnitudes more faster than state-of-art methods in terms of evaluation time  even for traditional tree pattern queries with only conjunctive operations.
Revised:  (5) Empirical results on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm, several times to orders of magnitude faster than state-of-art methods in terms of evaluation time even for traditional tree pattern queries with only conjunctive operations.
Edit intent: clarity
Original:  (5) Empirical results on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm,  several times to orders of magnitudes more faster than state-of-art methods in terms of evaluation time  even for traditional tree pattern queries with only conjunctive operations.
Revised:  (5) Empirical results on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm, several times to orders of magnitudes more faster than state-of-art algorithms in terms of evaluation time even for traditional tree pattern queries with only conjunctive operations.
Edit intent: clarity
Original:  (5) Empirical results on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm,  several times to orders of magnitudes more faster than state-of-art methods in terms of evaluation time  even for traditional tree pattern queries with only conjunctive operations.
Revised:  (5) Empirical results on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm, several times to orders of magnitudes more faster than state-of-art methods in terms of evaluation time , even for traditional tree pattern queries with only conjunctive operations.
Edit intent: fluency
Original: As data are increasingly modeled as graphs for expressing complex relationships, the tree pattern query on graph-structured data becomes an important query in practical applications.
Revised: As data are increasingly modeled as graphs for expressing complex relationships, the tree pattern query on graph-structured data becomes an important type of queries in real-world applications.
Edit intent: clarity
Original:  Most practical query languages  such as XQuery and SPARQL  support logical expressions using logical-AND/OR/NOT operators to define complex structural constraints of tree patterns.
Revised:  Most practical query languages , such as XQuery and SPARQL support logical expressions using logical-AND/OR/NOT operators to define complex structural constraints of tree patterns.
Edit intent: fluency
Original:  Most practical query languages  such as XQuery and SPARQL  support logical expressions using logical-AND/OR/NOT operators to define complex structural constraints of tree patterns.
Revised:  Most practical query languages such as XQuery and SPARQL , support logical expressions using logical-AND/OR/NOT operators to define complex structural constraints of tree patterns.
Edit intent: fluency
Original:  Most practical query languages  such as XQuery and SPARQL  support logical expressions using logical-AND/OR/NOT operators to define complex structural constraints of tree patterns.
Revised:  Most practical query languages such as XQuery and SPARQL support logical expressions using logical-AND/OR/NOT operators to define structural constraints of tree patterns.
Edit intent: clarity
Original:  In this paper, (1) we propose generalized tree pattern queries (GTPQs) over graph-structured data, which fully support propositional logic on structural constraints.
Revised:  In this paper, (1) we propose generalized tree pattern queries (GTPQs) over graph-structured data, which fully support propositional logic of structural constraints.
Edit intent: clarity
Original:  (2) We make a thorough study of fundamental problems of satisfiability, containment and minimization, and analyze the computational complexity and the decision procedures of these problems.
Revised:  (2) We make a thorough study of fundamental problems including satisfiability, containment and minimization, and analyze the computational complexity and the decision procedures of these problems.
Edit intent: clarity
Original:  (5) Experiments on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm, from several times to orders of magnitude faster than state-of-art algorithms in terms of evaluation time, even for traditional tree pattern queries with only conjunctive operations.
Revised:  (5) Experiments on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our algorithm, from several times to orders of magnitude faster than state-of-the-art algorithms in terms of evaluation time, even for traditional tree pattern queries with only conjunctive operations.
Edit intent: fluency
Original:  To achieve both aims simultaneously, we start from an established reduction semantics for JavaScript and systematically derive its intensional abstract interpretation.
Revised:  To achieve both aims simultaneously, we start from an established reduction semantics for JavaScript and systematically deriving its intensional abstract interpretation.
Edit intent: fluency
Original:  The precise model of stack structure in turn confers precise control-flow analysis over control effects, such as exceptions , finally blocks, and of course, calls and returns.
Revised:  The precise model of stack structure in turn confers precise control-flow analysis even in the presence of control effects, such as exceptions , finally blocks, and of course, calls and returns.
Edit intent: clarity
Original:  Both the finite-state and pushdown frameworks for abstract interpretation are sound and computable.
Revised:  Both the finite-state and pushdown frameworks for abstract interpretation is sound and computable.
Edit intent: fluency
Original:  No general formulation exists for forcing an arbitrary large kinetic model in a manner that is still consistent with the existence of a non-equilibrium steady state.
Revised:  We provide a general formulation to force an arbitrary large kinetic model in a manner that is still consistent with the existence of a non-equilibrium steady state.
Edit intent: clarity
Original:  We prove a theorem that guarantees the existence of a non-equilibrium steady state for chemical kinetic models, assuming two conditions;
Revised:  We can guarantee the existence of a non-equilibrium steady state for chemical kinetic models, assuming two conditions;
Edit intent: clarity
Original:  We prove a theorem that guarantees the existence of a non-equilibrium steady state for chemical kinetic models, assuming two conditions;
Revised:  We prove a theorem that guarantees the existence of a non-equilibrium steady state assuming only two conditions;
Edit intent: clarity
Original:  that every reaction is mass balanced , and that reaction kinetic rate laws never lead to a negative molecule concentration.
Revised:  that every reaction is mass balanced and that continuous kinetic reaction rate laws never lead to a negative molecule concentration.
Edit intent: clarity
Original:  These conditions can be verified in polynomial time and , flexible enough to permit a novel method of forcing a system away from equilibrium.
Revised:  These conditions can be verified in polynomial time and are flexible enough to permit a novel method of forcing a system away from equilibrium.
Edit intent: fluency
Original:  These conditions can be verified in polynomial time and , flexible enough to permit a novel method of forcing a system away from equilibrium.
Revised:  These conditions can be verified in polynomial time and , flexible enough to permit one to force a system away from equilibrium.
Edit intent: clarity
Original:  Our definition of easily testable existence conditions is foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.
Revised:  Easily testable existence conditions is foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.
Edit intent: clarity
Original:  Our definition of easily testable existence conditions is foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.
Revised:  Our definition of easily testable existence conditions are foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.
Edit intent: fluency
Original: In knowledge bases expressed in default logic, outliers are sets of literals , or observations, that feature unexpected properties.
Revised: In default theories, outliers denote sets of literals , or observations, that feature unexpected properties.
Edit intent: clarity
Original: In knowledge bases expressed in default logic, outliers are sets of literals , or observations, that feature unexpected properties.
Revised: In knowledge bases expressed in default logic, outliers are sets of literals featuring unexpected properties.
Edit intent: clarity
Original:  Based on these ]  results, we have designed a polynomial time algorithm for enumerating all strong outliers of bounded size in an acyclic normal unary default theory.
Revised:  Based on these ] results, we present a polynomial time algorithm for enumerating all strong outliers of bounded size in an acyclic normal unary default theory.
Edit intent: clarity
Original:  These tractability results rely on the Incremental Lemma , an interesting result on its own, that provides conditions under which a mixed unary default theory displays a monotonic reasoning behavior .
Revised:  Some of our tractability results rely on the Incremental Lemma , an interesting result on its own, that provides conditions under which a mixed unary default theory displays a monotonic reasoning behavior .
Edit intent: clarity
Original:  These tractability results rely on the Incremental Lemma , an interesting result on its own, that provides conditions under which a mixed unary default theory displays a monotonic reasoning behavior .
Revised:  These tractability results rely on the Incremental Lemma that provides conditions under which a mixed unary default theory displays a monotonic reasoning behavior .
Edit intent: coherence
Original: We present an efficient phylogenetic reconstruction algorithm , allowing insertions and deletions , which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa.
Revised: We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions , which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa.
Edit intent: fluency
Original: We present an efficient phylogenetic reconstruction algorithm , allowing insertions and deletions , which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa.
Revised: We present an efficient phylogenetic reconstruction algorithm , allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa.
Edit intent: fluency
Original: We present a linear-time algorithm for deciding first-order logic (FOL ) properties in classes of graphs with bounded expansion, a notion recently introduced by Nesetril and Ossona de Mendez.
Revised: We present a linear-time algorithm for deciding first-order (FO ) properties in classes of graphs with bounded expansion, a notion recently introduced by Nesetril and Ossona de Mendez.
Edit intent: clarity
Original:  We deduce that there is an almost linear-time algorithm for deciding FOL properties in classes of graphs with locally bounded expansion.
Revised:  We deduce that there is an almost linear-time algorithm for deciding FO properties in classes of graphs with locally bounded expansion.
Edit intent: fluency
Original:  After a linear-time initialization the data structure allows us to test an FOL property in constant time, and the data structure can be updated in constant time after addition/deletion of an edge, provided the list of possible edges to be added is known in advance and their simultaneous addition results in a graph in the class.
Revised:  After a linear-time initialization the data structure allows us to test an FO property in constant time, and the data structure can be updated in constant time after addition/deletion of an edge, provided the list of possible edges to be added is known in advance and their simultaneous addition results in a graph in the class.
Edit intent: fluency
Original: In this work we extend the characterization of injectivity via the Jacobian criterion first developed by Craciun and Feinberg for chemical reaction networks with outflow reactions to arbitrary chemical reaction networks taken with mass action kinetics .
Revised: We provide a Jacobian criterion that applies to chemical reaction networks taken with mass action kinetics .
Edit intent: clarity
Original:  It is shown that a network is injective if and only if the determinant of the Jacobian of the system of ordinary differential equations associated to the network never vanishes .
Revised:  We show that a network is injective if and only if the determinant of the Jacobian of the system of ordinary differential equations associated to the network never vanishes .
Edit intent: clarity
Original:  The determinant  is a polynomial on the species concentrations and the rate constants , and its coefficients are fully determined.
Revised:  The determinant is a polynomial in the species concentrations and the rate constants , and its coefficients are fully determined.
Edit intent: clarity
Original: The free energy of random heteropolymers which can form hierarchical cloverleaf--like secondary structure, typical for RNA molecules, is analyzed.
Revised: The free energy of random heteropolymers which can form hierarchical cactus-like secondary structure, typical for RNA molecules, is analyzed.
Edit intent: clarity
Original:  In particular, the fraction  of nucleotides involved in the formation of the secondary structure f as a function of the number c of different monomer species in the cloverleaf--forming heteropolymers is investigated.
Revised:  In particular, the fraction f of nucleotides involved in the formation of the secondary structure f as a function of the number c of different monomer species in the cloverleaf--forming heteropolymers is investigated.
Edit intent: fluency
Original:  In particular, the fraction  of nucleotides involved in the formation of the secondary structure f as a function of the number c of different monomer species in the cloverleaf--forming heteropolymers is investigated.
Revised:  In particular, the fraction of nucleotides involved in the formation of the secondary structure as a function of the number c of different monomer species in the cloverleaf--forming heteropolymers is investigated.
Edit intent: fluency
Original:  In particular, the fraction  of nucleotides involved in the formation of the secondary structure f as a function of the number c of different monomer species in the cloverleaf--forming heteropolymers is investigated.
Revised:  In particular, the fraction of nucleotides involved in the formation of the secondary structure f as a function of the number c of different monomer species is investigated.
Edit intent: clarity
Original:  It is shown, that with changing c the secondary structures of random heteropolymers undergo a morphological transition.
Revised:  It is shown, that with changing c the secondary structures of random heteropolymers undergo a phase transition.
Edit intent: clarity
Original:  Namely, for c \le c_{ \rm cr} = 4 the fraction of "active" nucleotides f tends to 1 as the length of the chain goes to infinity, signaling the formation of a virtually "perfect" secondary structure without gaps .
Revised:  Namely, for c \le c_{ \rm cr} = 4 the fraction of "active" nucleotides f tends to 1 as the chain length n goes to infinity, signaling the formation of a virtually "perfect" secondary structure without gaps .
Edit intent: clarity
Original:  Namely, for c \le c_{ \rm cr} = 4 the fraction of "active" nucleotides f tends to 1 as the length of the chain goes to infinity, signaling the formation of a virtually "perfect" secondary structure without gaps .
Revised:  Namely, for c \le c_{ \rm cr} = 4 the fraction of "active" nucleotides f tends to 1 as the length of the chain goes to infinity, signaling the formation of a virtually "perfect" gapless secondary structure .
Edit intent: clarity
Original:  The value c_{cr}=4 is critical: f approaches 1 logarithmically as chain length tends to infinity\to .
Revised:  The value c_{cr}=4 is critical: f approaches 1 logarithmically for n\to .
Edit intent: clarity
Original:  Such a critical behavior allows one to speculate about exclusivity of a four--letter alphabet used in natural RNAs  .
Revised:  Such a critical behavior allows one to speculate about exclusivity of a four-letter alphabet used in natural RNAs .
Edit intent: fluency
Original:  It is shown , that with changing c  the secondary structures of random heteropolymers undergo a phase transition.
Revised:  It is shown , that with changing c , the secondary structures of random heteropolymers undergo a phase transition.
Edit intent: fluency
Original:  Namely,\to  for c \le c_{\rm cr} = 4 the fraction of "active" nucleotides f tends to 1 as the chain length n goes to infinity, signaling the formation of a virtually "perfect" gapless secondary structure .
Revised:  Namely,\to 1 for c \le c_{\rm cr} = 4 the fraction of "active" nucleotides f tends to 1 as the chain length n goes to infinity, signaling the formation of a virtually "perfect" gapless secondary structure .
Edit intent: fluency
Original:  The value c\le  _{ \rm cr} = \le 4 is critical: f approaches 1 logarithmically for n%DIFDELCMD < \to%%% \infty.
Revised:  The value c\le _{ \rm cr} \le 4 is critical: f approaches 1 logarithmically for n%DIFDELCMD < \to%%% \infty.
Edit intent: clarity
Original:  The value c\le  _{ \rm cr} = \le 4 is critical: f approaches 1 logarithmically for n%DIFDELCMD < \to%%% \infty.
Revised:  The value c\le _{ \rm cr} = \le 4 %DIFDELCMD < \to%%% \infty.
Edit intent: coherence
Original:  Preferred degree networks with adaptive \kappa provide a natural platform to study adaptive contact processes.
Edit intent: clarity
Original:  A simple mean field analysis is shown to capture the qualitative and some of the quantitative features of the infection phase diagram.
Revised:  A simple mean field theory is presented for the selective adaptations which capture the qualitative and some of the quantitative features of the infection phase diagram.
Edit intent: clarity
Original: We investigate  distributed sensors' failure detection in networks with a small number of defective sensors .
Revised: We investigate the problem of distributed sensors' failure detection in networks with a small number of defective sensors .
Edit intent: clarity
Original:  We consider that the defective sensors are well represented by binary sparse signals.
Revised:  Defective sensors are represented by non-zero values in binary sparse signals.
Edit intent: clarity
Original:  Given a network setup, we provide parameter selection rules that improve the detection accuracy . Simulations demonstrate that in terms of detection performance the proposed method outperforms methods based on random walk measurements collection .
Revised:  Given a network setup, we provide parameter selection rules that improve the detection accuracy . Simulations demonstrate that the proposed method outperforms methods based on random walk measurements collection .
Edit intent: clarity
Original:  Availability and Implementation: We provide  freely available and open source R code that can be used to analyze mapped reads in SAM format at URL  Contact: lpachter@math.berkeley.edu
Revised:  Availability and Implementation: We provide a freely available and open source R code that can be used to analyze mapped reads in SAM format at URL Contact: lpachter@math.berkeley.edu
Edit intent: fluency
Original:  Availability and Implementation: We provide  freely available and open source R code that can be used to analyze mapped reads in SAM format at URL  Contact: lpachter@math.berkeley.edu
Revised:  Availability and Implementation: We provide freely available and open source R code that can be used to analyze mapped reads in SAM format at URL . Contact: lpachter@math.berkeley.edu
Edit intent: fluency
Original: Nivat's conjecture is about the link between the pure periodicity of a subset M of%DIFDELCMD < \ZZ%%% ^2, i.e., invariance under translation by a fixed vector, and some upper bound on the function counting the number of different rectangular blocks occurring in M. Attempts to solve this conjecture have been considered during the last fifteen years.
Revised: %DIFDELCMD < \ZZ%%% ^2, i.e., invariance under translation by a fixed vector, and some upper bound on the function counting the number of different rectangular blocks occurring in M. Attempts to solve this conjecture have been considered during the last fifteen years.
Edit intent: coherence
Original:  The solver computes the unique  min-length solution to x \in \mathbb{R^n} \|A x - b\|_2, where A \in R^{m \times n} can be either full rank or rank-deficient, and where m \gg n or m \ll n . Since A is only involved in matrix-matrix and matrix-vector multiplications, A can be a dense matrix, a sparse matrix , or a linear operator ;
Revised:  The solver computes the unique computes the min-length solution to x \in \mathbb{R^n} \|A x - b\|_2, where A \in R^{m \times n} can be either full rank or rank-deficient, and where m \gg n or m \ll n . Since A is only involved in matrix-matrix and matrix-vector multiplications, A can be a dense matrix, a sparse matrix , or a linear operator ;
Edit intent: fluency