Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments

Towards an Efficient Discovery of the Topological Representative Subgraphs

With the emergence of graph databases, the task of frequent subgraph discovery has been extensively addressed. Although the proposed approaches in the literature have made this task feasible, the number of discovered frequent subgraphs is still very high to be efficiently used in any further exploration. Feature selection for graph data is a way to reduce the high number of frequent subgraphs based on exact or approximate structural similarity. However, current structural similarity strategies are not efficient enough in many real-world applications, besides, the combinatorial nature of graphs makes it computationally very costly. In order to select a smaller yet structurally irredundant set of subgraphs, we propose a novel approach that mines the top-k topological representative subgraphs among the frequent ones. Our approach allows detecting hidden structural similarities that existing approaches are unable to detect such as the density or the diameter of the subgraph. In addition, it can be easily extended using any user defined structural or topological attributes depending on the sought properties. Empirical studies on real and synthetic graph datasets show that our approach is fast and scalable

Mining Representative Unsubstituted Graph Patterns Using Prior Similarity Matrix

One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists in parsing proteins three-dimensional (3D) structures into graphs of amino acids. Hence, the search of recurrent spatial motifs is formulated as a process of frequent subgraph discovery where each subgraph represents a spatial motif. In this scope, several efficient approaches for frequent subgraph discovery have been proposed in the literature. However, the set of discovered frequent subgraphs is too large to be efficiently analyzed and explored in any further process. In this paper, we propose a novel pattern selection approach that shrinks the large number of discovered frequent subgraphs by selecting the representative ones. Existing pattern selection approaches do not exploit the domain knowledge. Yet, in our approach we incorporate the evolutionary information of amino acids defined in the substitution matrices in order to select the representative subgraphs. We show the effectiveness of our approach on a number of real datasets. The results issued from our experiments show that our approach is able to considerably decrease the number of motifs while enhancing their interestingness

FS^3: A Sampling based method for top-k Frequent Subgraph Mining

Mining labeled subgraph is a popular research task in data mining because of its potential application in many different scientific domains. All the existing methods for this task explicitly or implicitly solve the subgraph isomorphism task which is computationally expensive, so they suffer from the lack of scalability problem when the graphs in the input database are large. In this work, we propose FS^3, which is a sampling based method. It mines a small collection of subgraphs that are most frequent in the probabilistic sense. FS^3 performs a Markov Chain Monte Carlo (MCMC) sampling over the space of a fixed-size subgraphs such that the potentially frequent subgraphs are sampled more often. Besides, FS^3 is equipped with an innovative queue manager. It stores the sampled subgraph in a finite queue over the course of mining in such a manner that the top-k positions in the queue contain the most frequent subgraphs. Our experiments on database of large graphs show that FS^3 is efficient, and it obtains subgraphs that are the most frequent amongst the subgraphs of a given size

Sparse Learning over Infinite Subgraph Features

We present a supervised-learning algorithm from graph data (a set of graphs) for arbitrary twice-differentiable loss functions and sparse linear models over all possible subgraph features. To date, it has been shown that under all possible subgraph features, several types of sparse learning, such as Adaboost, LPBoost, LARS/LASSO, and sparse PLS regression, can be performed. Particularly emphasis is placed on simultaneous learning of relevant features from an infinite set of candidates. We first generalize techniques used in all these preceding studies to derive an unifying bounding technique for arbitrary separable functions. We then carefully use this bounding to make block coordinate gradient descent feasible over infinite subgraph features, resulting in a fast converging algorithm that can solve a wider class of sparse learning problems over graph data. We also empirically study the differences from the existing approaches in convergence property, selected subgraph features, and search-space sizes. We further discuss several unnoticed issues in sparse learning over all possible subgraph features.Comment: 42 pages, 24 figures, 4 table

Mining Frequent Graph Patterns with Differential Privacy

Discovering frequent graph patterns in a graph database offers valuable information in a variety of applications. However, if the graph dataset contains sensitive data of individuals such as mobile phone-call graphs and web-click graphs, releasing discovered frequent patterns may present a threat to the privacy of individuals. {\em Differential privacy} has recently emerged as the {\em de facto} standard for private data analysis due to its provable privacy guarantee. In this paper we propose the first differentially private algorithm for mining frequent graph patterns. We first show that previous techniques on differentially private discovery of frequent {\em itemsets} cannot apply in mining frequent graph patterns due to the inherent complexity of handling structural information in graphs. We then address this challenge by proposing a Markov Chain Monte Carlo (MCMC) sampling based algorithm. Unlike previous work on frequent itemset mining, our techniques do not rely on the output of a non-private mining algorithm. Instead, we observe that both frequent graph pattern mining and the guarantee of differential privacy can be unified into an MCMC sampling framework. In addition, we establish the privacy and utility guarantee of our algorithm and propose an efficient neighboring pattern counting technique as well. Experimental results show that the proposed algorithm is able to output frequent patterns with good precision