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Graph Neural Networks (GNNs) have been widely employed for feature representation learning in molecular graphs. Therefore, it is crucial to enhance the expressiveness of feature representation to ensure the effectiveness of GNNs. However, a significant portion of current research primarily focuses on the structural features within individual molecules, often overlooking the structural similarity between molecules, which is a crucial aspect encapsulating rich information on the relationship between molecular properties and structural characteristics. Thus, these approaches fail to capture the rich semantic information at the molecular structure level. To bridge this gap, we introduce the \textbf{Molecular Structural Similarity Motif GNN (MSSM-GNN)}, a novel molecular graph representation learning method that can capture structural similarity information among molecules from a global perspective. In particular, we propose a specially designed graph that leverages graph kernel algorithms to represent the similarity between molecules quantitatively. Subsequently, we employ GNNs to learn feature representations from molecular graphs, aiming to enhance the accuracy of property prediction by incorporating additional molecular representation information. Finally, through a series of experiments conducted on both small-scale and large-scale molecular datasets, we demonstrate that our model consistently outperforms eleven state-of-the-art baselines. The codes are available at https://github.com/yaoyao-yaoyao-cell/MSSM-GNN.

The role of the delta isobar degrees of freedom in nucleon-nucleon scattering is revisited. We attempt to understand why the dimensionally regularized two-pion exchanges with the explicit delta isobar is much stronger than the ones with spectral function regularization. When the cutoff value of spectral function regularization is varied, the isoscalar central component exhibits a rather large cutoff variation. This reveals a surprisingly large numerical factor of the deltaful two-pion exchange potentials. The power counting is adjusted accordingly and we discuss the results and how to improve upon this finding., Comment: 16 pages, 6 figures

Extended regular expressions with counting and interleaving are widely used in practice. However the related theoretical studies for this kind of expressions currently cannot meet the need of practical work. This paper develops syntax definitions for extended deterministic expressions and their subclasses, hope to completely solve the long-standing problem that there are no syntax definitions for this kind of expressions, which has become an important reason for restricting the use of extended expressions., Comment: in Chinese language

Since regular expressions (abbrev. regexes) are difficult to understand and compose, automatically generating regexes has been an important research problem. This paper introduces TransRegex, for automatically constructing regexes from both natural language descriptions and examples. To the best of our knowledge, TransRegex is the first to treat the NLP-and-example-based regex synthesis problem as the problem of NLP-based synthesis with regex repair. For this purpose, we present novel algorithms for both NLP-based synthesis and regex repair. We evaluate TransRegex with ten relevant state-of-the-art tools on three publicly available datasets. The evaluation results demonstrate that the accuracy of our TransRegex is 17.4%, 35.8% and 38.9% higher than that of NLP-based approaches on the three datasets, respectively. Furthermore, TransRegex can achieve higher accuracy than the state-of-the-art multi-modal techniques with 10% to 30% higher accuracy on all three datasets. The evaluation results also indicate TransRegex utilizing natural language and examples in a more effective way., Comment: accepted by ICSE 2021

The advantages offered by the presence of a schema are numerous. However, many XML documents in practice are not accompanied by a (valid) schema, making schema inference an attractive research problem. The fundamental task in XML schema learning is inferring restricted subclasses of regular expressions. Most previous work either lacks support for interleaving or only has limited support for interleaving. In this paper, we first propose a new subclass Single Occurrence Regular Expressions with Interleaving (SOIRE), which has unrestricted support for interleaving. Then, based on single occurrence automaton and maximum independent set, we propose an algorithm iSOIRE to infer SOIREs. Finally, we further conduct a series of experiments on real datasets to evaluate the effectiveness of our work, comparing with both ongoing learning algorithms in academia and industrial tools in real-world. The results reveal the practicability of SOIRE and the effectiveness of iSOIRE, showing the high preciseness and conciseness of our work.

The advantages for the presence of an XML schema for XML documents are numerous. However, many XML documents in practice are not accompanied by a schema or by a valid schema. Relax NG is a popular and powerful schema language, which supports the unconstrained interleaving operator. Focusing on the inference of Relax NG, we propose a new subclass of regular expressions with interleaving and design a polynomial inference algorithm. Then we conducted a series of experiments based on large-scale real data and on three XML data corpora, and experimental results show that our subclass has a better practicality than previous ones, and the regular expressions inferred by our algorithm are more precise.

Regular expressions are a fundamental concept in computer science and widely used in various applications. In this paper we focused on deterministic regular expressions (DREs). Considering that researchers didn't have large datasets as evidence before, we first harvested a large corpus of real data from the Web then conducted a practical study to investigate the usage of DREs. One feature of our work is that the data set is sufficiently large compared with previous work, which is obtained using several data collection strategies we proposed. The results show more than 98\% of expressions in Relax NG are DRE, and more than 56\% of expressions from RegExLib are DRE, while both Relax NG and RegExLib do not have the determinism constraint. These observations indicate that DREs are commonly used in practice. The results also show further study of subclasses of DREs is necessary. As far as we know, we are the first to analyze the determinism and the subclasses of DREs of Relax NG and RegExLib, and give these results. Furthermore, we give some discussions and applications of the data set. We obtain a DRE data set from the original data, which will be useful in practice and it has value in its own right. We find current research in new subclasses of DREs is insufficient, therefore it is necessary to do further study. We also analyze the referencing relationships among XSDs and define SchemaRank, which can be used in XML Schema design., Comment: 9 pages,5 figures

The ring opening polymerization of cyclic butylene terephthalate into poly (butylene terephthalate) (pCBT) in the presence of reduced graphene oxide (RGO) is an effective method for the preparation of polymer nanocomposites. The inclusion of RGO nanoflakes dramatically affects the crystallization of pCBT, shifting crystallization peak temperature to higher temperatures and, overall, increasing the crystallization rate. This was due to a super nucleating effect caused by RGO, which is maximized by highly reduced graphene oxide. Furthermore, combined analyses by differential scanning calorimetry (DSC) experiments and wide angle X-ray diffraction (WAXS) showed the formation of a thick {\alpha}-crystalline form pCBT lamellae with a melting point of ~250 {\deg}C, close to the equilibrium melting temperature of pCBT. WAXS also demonstrated the pair orientation of pCBT crystals with RGO nanoflakes, indicating a strong interfacial interaction between the aromatic rings of pCBT and RGO planes, especially with highly reduced graphene oxide. Such surface self-organization of the polymer onto the RGO nanoflakes may be exploited for the enhancement of interfacial properties in their polymer nanocomposites.

The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology, providing data-guided frameworks that allow us to develop better predictions about and methods for control over specific biological processes and system-wide cell behavior. In this paper we describe an approach to optimizing the use of transcription factors in the context of cellular reprogramming. We construct an approximate model for the natural evolution of a synchronized population of fibroblasts, based on data obtained by sampling the expression of some 22,083 genes at several times along the cell cycle. (These data are based on a colony of cells that have been cell cycle synchronized) In order to arrive at a model of moderate complexity, we cluster gene expression based on the division of the genome into topologically associating domains (TADs) and then model the dynamics of the expression levels of the TADs. Based on this dynamical model and known bioinformatics, we develop a methodology for identifying the transcription factors that are the most likely to be effective toward a specific cellular reprogramming task. The approach used is based on a device commonly used in optimal control. From this data-guided methodology, we identify a number of validated transcription factors used in reprogramming and/or natural differentiation. Our findings highlight the immense potential of dynamical models models, mathematics, and data guided methodologies for improving methods for control over biological processes.

Discovering a concise schema from given XML documents is an important problem in XML applications. In this paper, we focus on the problem of learning an unordered schema from a given set of XML examples, which is actually a problem of learning a restricted regular expression with interleaving using positive example strings. Schemas with interleaving could present meaningful knowledge that cannot be disclosed by previous inference techniques. Moreover, inference of the minimal schema with interleaving is challenging. The problem of finding a minimal schema with interleaving is shown to be NP-hard. Therefore, we develop an approximation algorithm and a heuristic solution to tackle the problem using techniques different from known inference algorithms. We do experiments on real-world data sets to demonstrate the effectiveness of our approaches. Our heuristic algorithm is shown to produce results that are very close to optimal., Comment: 12 pages