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This article walks the reader through the author's journey into the establishment of a high-voltage research laboratory in his university with almost nothing. The author introduces the challenges faced and the activities that revived research on natural esters. [ABSTRACT FROM AUTHOR]

Metal-organic networks (MONs) is a family of chemical compounds consisting of clusters or metal ions and organic ligands. These are studied as one, two or three dimensional structures of porous materials and subclasses of coordination polymers. MONs are mostly used in catalysis for the separation & purification of gases and as conducting solids or super-capacitors. In some situations, these networks are found to be stable in the process of removal or solvent of the guest molecules and could be restored with some other chemical compounds. The physical stability and mechanical properties of these networks have become a topic of great interest due to the aforesaid characteristics. Topological indices (TIs) are numeric quantities that are used to forecast the natural relationships among the physico-chemical characteristics of the chemical compounds in their fundamental network. During the studies of the MONs, TIs show an essential role in the theoretical & environmental chemistry and pharmacology. In this paper, we compute various latest developed degree-based TIs for two different metal-organic networks with increasing number of layers consisting on both metal and organic ligands vertices as well. A comparison among the computed different versions of the TIs with the help of the numerical values and their graphs is also included.

Graph-structured data arise ubiquitously in many application domains. A fundamental problem is to quantify their similarities. Graph kernels are often used for this purpose, which decompose graphs into substructures and compare these substructures. However, most of the existing graph kernels do not have the property of scale-adaptivity, i.e., they cannot compare graphs at multiple levels of granularities. Many real-world graphs such as molecules exhibit structure at varying levels of granularities. To tackle this problem, we propose a new graph kernel called Tree++ in this paper. At the heart of Tree++ is a graph kernel called the path-pattern graph kernel. The path-pattern graph kernel first builds a truncated BFS tree rooted at each vertex and then uses paths from the root to every vertex in the truncated BFS tree as features to represent graphs. The path-pattern graph kernel can only capture graph similarity at fine granularities. In order to capture graph similarity at coarse granularities, we incorporate a new concept called super path into it. The super path contains truncated BFS trees rooted at the vertices in a path. Our evaluation on a variety of real-world graphs demonstrates that Tree++ achieves the best classification accuracy compared with previous graph kernels. [ABSTRACT FROM AUTHOR]

In an age of information overload, we are faced with seemingly endless options from which a small number of choices must be made. For applications such as search engines and online stores, Recommender Systems have long become the key tool for assisting users in their choices. Interestingly, the use of Recommender Systems for recommending scientific items remains a rarity. One difficulty is that the development of such systems depends on the availability of adequate datasets of users' feedback. While there are several datasets available with the ratings of the users for books, music, or films, there is a lack of similar datasets for scientific fields, such as Astronomy and Life and Health Sciences. To address this issue, we propose a methodology that explores scientific literature for generating utility matrices of implicit feedback. The proposed methodology consists in identifying a list of items, finding research articles related to them, extracting the authors from each article, and finally creating a dataset where users are unique authors from the collected articles, and the rating values are the number of articles a unique author wrote about an item. Considering that literature is available for every scientific field, the methodology is in principle applicable to Recommender Systems in any scientific field. The methodology, which we call LIBRETTI (LIterature Based RecommEndaTion of scienTific Items), was assessed in two distinct study cases, Astronomy and Chemistry. Several evaluation metrics for the datasets generated with LIBRETTI were compared to those derived from other available datasets using the same set of recommender algorithms. The results were found to be similar, which provides a solid indication that LIBRETTI is a promising approach for generating datasets of implicit feedback for recommending scientific items.

Searching similar graphs in graph databases for a query graph has attracted extensive attention recently. Existing works on graph similarity queries are threshold based approaches which return graphs with distances to the query smaller than a given threshold. However, in many applications the number of answer graphs for the same threshold can vary significantly for different queries. In this paper, we study the problem of finding top- $k$ k most similar graphs for a query under the distance measure based on maximum common subgraph (MCS). Since computing MCS is NP-hard, we devise a novel framework to prune unqualified graphs based on the lower bounds of graph distance, and accordingly derive four lower bounds with different tightness and computational cost for pruning. To further reduce the number of MCS computations, we also propose an improved framework based on both lower and upper bounds, and derive three new upper bounds. To support efficient pruning, we design three indexes with different tradeoffs between pruning power and construction cost. To accelerate the index construction, we explore bound relaxation techniques, based on which approximate indexes can be efficiently built. We conducted extensive performance studies on real-life graph datasets to validate the effectiveness and efficiency of our approaches. [ABSTRACT FROM AUTHOR]

Enumerating chemical compounds with given structural properties plays an important role in structure elucidation, with applications such as drug design. We focus on the problem of enumerating tree-like chemical graphs specified by upper and lower bounds on feature vectors, where chemical graphs represent compounds, and a feature vector characterizes frequencies of finite paths in a graph. Building on the branch-and-bound algorithm proposed in earlier work, we propose a new bounding procedure, called Resource Cut, to speed up the enumeration process. Tree-like chemical graphs are modeled as vertex-colored trees, colors representing chemical elements. The algorithm is based on a scheme of generating each unique colored tree with a specified number $n$ of vertices. A colored tree is constructed by repeatedly appending vertices. Given a set $\mathcal {R}$ of $n$ colored vertices, we found that the algorithm often constructs trees that cannot be extended to a unique representation of a colored tree no matter how the remaining unused colored vertices in the set $\mathcal {R}$ are appended. We derive a mathematical condition to detect and discard such trees. Experimental results show that Resource Cut significantly reduces the search space. We have been able to obtain exact numbers of chemical graphs with up to 17 vertices excluding hydrogen atoms. [ABSTRACT FROM AUTHOR]

Existing graph classification usually relies on an exhaustive enumeration of substructure patterns, where the number of substructures expands exponentially w.r.t. with the size of the graph set. Recently, the Weisfeiler-Lehman (WL) graph kernel has achieved the best performance in terms of both accuracy and efficiency among state-of-the-art methods. However, it is still time-consuming, especially for large-scale graph classification tasks. In this paper, we present a -Ary Tree based Hashing (KATH) algorithm, which is able to obtain competitive accuracy with a very fast runtime. The main idea of KATH is to construct a traversal table to quickly approximate the subtree patterns in WL using $K$-ary trees. Based on the traversal table, KATH employs a recursive indexing process that performs only $r$ times of matrix indexing to generate all $(r-1)$ -depth $K$ -ary trees, where the leaf node labels of a tree can uniquely specify the pattern. After that, the MinHash scheme is used to fingerprint the acquired subtree patterns for a graph. Our experimental results on both real world and synthetic data sets show that KATH runs significantly faster than state-of-the-art methods while achieving competitive or better accuracy. [ABSTRACT FROM AUTHOR]

Enumeration of chemical structures is useful for drug design, which is one of the main targets of computational biology and bioinformatics. A chemical graph $G$ with no other cycles than benzene rings is called tree-like, and becomes a tree $T$ possibly with multiple edges if we contract each benzene ring into a single virtual atom of valence 6. All tree-like chemical graphs with a given tree representation $T$ are called the substituted benzene isomers of $T$ . When we replace each virtual atom in $T$ with a benzene ring to obtain a substituted benzene isomer, distinct isomers of $T$ are caused by the difference in arrangements of atom groups around a benzene ring. In this paper, we propose an efficient algorithm that enumerates all substituted benzene isomers of a given tree representation $T$ . Our algorithm first counts the number $f$ of all the isomers of the tree representation by a dynamic programming method. To enumerate all the isomers, for each $k=1,2,\ldots, f$ , our algorithm then generates the $k$ th isomer by backtracking the counting phase of the dynamic programming. We also implemented our algorithm for computational experiments. [ABSTRACT FROM PUBLISHER]

The human colorectal carcinoma cell line (Caco-2) is a commonly used in-vitro test that predicts the absorption potential of orally administered drugs. In-silico prediction methods, based on the Caco-2 assay data, may increase the effectiveness of the high-throughput screening of new drug candidates. However, previously developed in-silico models that predict the Caco-2 cellular permeability of chemical compounds use handcrafted features that may be dataset-specific and induce over-fitting problems. Deep Neural Network (DNN) generates high-level features based on non-linear transformations for raw features, which provides high discriminant power and, therefore, creates a good generalized model. We present a DNN-based binary Caco-2 permeability classifier. Our model was constructed based on 663 chemical compounds with in-vitro Caco-2 apparent permeability data. Two hundred nine molecular descriptors are used for generating the high-level features during DNN model generation. Dropout regularization is applied to solve the over-fitting problem and the non-linear activation. The Rectified Linear Unit (ReLU) is adopted to reduce the vanishing gradient problem. The results demonstrate that the high-level features generated by the DNN are more robust than handcrafted features for predicting the cellular permeability of structurally diverse chemical compounds in Caco-2 cell lines. [ABSTRACT FROM PUBLISHER]

In this paper, we propose an approach to determine the time constants and the amplitudes of the mass loading effect and of the viscoelastic contribution of SAW sensor’s frequency shift. This approach consists in optimizing a function of these parameters, which is independent of the concentration profile. We experimentally establish in laboratory conditions ( $T$ = 22 °C), on a data set composed of seven different gases, that these features are suitable for chemical compounds identification. In particular, we obtain a higher classification rate than the traditional amplitudes of the signals during the steady state, and we show that the classification success rate can be increased by using both of them in conjunction with a feature subset selection heuristic. We also propose a method based on deconvolution and kernel regression to estimate the temporal concentration profile. [ABSTRACT FROM PUBLISHER]

Graph classification aims to learn models to classify structure data. To date, all existing graph classification methods are designed to target one single learning task and require a large number of labeled samples for learning good classification models. In reality, each real-world task may only have a limited number of labeled samples, yet multiple similar learning tasks can provide useful knowledge to benefit all tasks as a whole. In this paper, we formulate a new multi-task graph classification (MTG) problem, where multiple graph classification tasks are jointly regularized to find discriminative subgraphs shared by all tasks for learning. The niche of MTG stems from the fact that with a limited number of training samples, subgraph features selected for one single graph classification task tend to overfit the training data. By using additional tasks as evaluation sets, MTG can jointly regularize multiple tasks to explore high quality subgraph features for graph classification. To achieve this goal, we formulate an objective function which combines multiple graph classification tasks to evaluate the informativeness score of a subgraph feature. An iterative subgraph feature exploration and multi-task learning process is further proposed to incrementally select subgraph features for graph classification. Experiments on real-world multi-task graph classification datasets demonstrate significant performance gain. [ABSTRACT FROM PUBLISHER]

Answering why-not questions in databases is promised to have wide application prospect in many areas and thereby, has attracted recent attention in the database research community. This paper addresses the problem of answering these so-called why-not questions in similar graph matching for graph databases. Given a set of answer graphs of an initial query graph $q$ and a set of missing ( why-not) graphs, we aim to modify $q$ into a new query graph $q^*$ such that the missing graphs are included in the new answer set of $q^*$ . We present an approximate solution to address the above as the optimal solution is NP-hard to compute. In our approach, we first compute the bounded search space and the distance to be minimized for $q^*$ . Then, we present a two-phase algorithm to find the new query $q^*$ . In the first phase, we generate a set of candidate edges to be added/deleted into/from the initial query $q$ within the bounded search space and in the second phase, we select a subset of candidate edges generated in the first phase to minimize the distance for $q^*$ . We also demonstrate the effectiveness and efficiency of our approach by conducting extensive experiments on two real datasets. [ABSTRACT FROM PUBLISHER]

Self-ordered arrays of Ni, Ni(50)Pd(50), and Ni(78)Pd(22) nanowires were synthesized by simultaneous electrochemical deposition of Ni and Pd components into porous templates of anodic aluminum oxide using alternating current. This paper is focused on the interplay of structure and chemical composition of Ni and Ni–Pd bicomponent nanowires arrays and the peculiarities of its magnetic anisotropy. [ABSTRACT FROM AUTHOR]

Computational techniques that build models to correctly assign chemical compounds to various classes of interest have many applications in pharmaceutical research and are used extensively at various phases during the drug development process. These techniques are used to solve a number of classification problems such as predicting whether or not a chemical compound has the desired biological activity, is toxic or nontoxic, and filtering out drug-like compounds from large compound libraries. This paper presents a substructure-based classification algorithm that decouples the substructure discovery process from the classification model construction and uses frequent subgraph discovery algorithms to find all topological and geometric substructures present in the data set. The advantage of this approach is that during classification model construction, all relevant substructures are available allowing the classifier to intelligently select the most discriminating ones. The computational scalability is ensured by the use of highly efficient frequent subgraph discovery algorithms coupled with aggressive feature selection. Experimental evaluation on eight different classification problems shows that our approach is computationally scalable and, on average, outperforms existing schemes by 7 percent to 35 percent. [ABSTRACT FROM AUTHOR]

The graph structure is a very important means to model schemaless data with complicated structures, such as protein-protein interaction networks, chemical compounds, knowledge query inferring systems, and road networks. This paper focuses on the index structure for similarity search on a set of large sparse graphs and proposes an efficient indexing mechanism by introducing the Q-Gram idea. By decomposing graphs to small grams (organized by κ-Adjacent Tree patterns) and pairing-up on those κ-Adjacent Tree patterns, the lower bound estimation of their edit distance can be calculated for candidate filtering. Furthermore, we have developed a series of techniques for inverted index construction and online query processing. By building the candidate set for the query graph before the exact edit distance calculation, the number of graphs need to proceed into exact matching can be greatly reduced. Extensive experiments on real and synthetic data sets have been conducted to show the effectiveness and efficiency of the proposed indexing mechanism. [ABSTRACT FROM AUTHOR]

Metabolic pathways show the complex interactions among enzymes that transform chemical compounds. The state of a metabolic pathway can be expressed as a vector, which denotes the yield of the compounds or the flux in that pathway at a given time. The steady state is a state that remains unchanged over time. Altering the state of the metabolism is very important for many applications such as biomedicine, biofuels, food industry, and cosmetics. The goal of the enzymatic target identification problem is to identify the set of enzymes whose knockouts lead the metabolism to a state that is close to a given goal state. Given that the size of the search space is exponential in the number of enzymes, the target identification problem is very computationally intensive. We develop efficient algorithms to solve the enzymatic target identification problem in this paper. Unlike existing algorithms, our method works for a broad set of metabolic network models. We measure the effect of the knockouts of a set of enzymes as a function of the deviation of the steady state of the pathway after their knockouts from the goal state. We develop two algorithms to find the enzyme set with minimal deviation from the goal state. The first one is a traversal approach that explores possible solutions in a systematic way using a branch and bound method. The second one uses genetic algorithms to derive good solutions from a set of alternative solutions iteratively. Unlike the former one, this one can run for very large pathways. Our experiments show that our algorithms' results follow those obtained in vitro in the literature from a number of applications. They also show that the traversal method is a good approximation of the exhaustive search algorithm and it is up to 11 times faster than the exhaustive one. This algorithm runs efficiently for pathways with up to 30 enzymes. For large pathways, our genetic algorithm can find good solutions in less than 10 minutes. [ABSTRACT FROM PUBLISHER]