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

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

Frequent Subgraph Mining via Sampling with Rigorous Guarantees

Frequent subgraph mining is a fundamental task in the analysis of collections of graphs that aims at finding all the subgraphs that appear with more than a user-specified frequency in the dataset. While several exact approaches have been proposed to solve the task, it remains computationally challenging on large graph datasets due to the complexity of the subgraph isomorphism problem inherent in the task and the huge number of candidate patterns even for fairly small subgraphs. In this thesis, we study two statistical learning measures of complexity, VC-dimension and Rademacher averages, for subgraphs, and derive efficiently computable bounds for both. We then show how such bounds can be applied to devise efficient sampling-based approaches for rigorously approximating the solutions of the frequent subgraph mining problem, providing sample sizes which are much tighter than what would be obtained by a straightforward application of Chernoff and union bounds. We also show that our bounds can be used for true frequent subgraph mining, which requires to identify subgraphs generated with probability above a given threshold using samples from an unknown generative process. Moreover, we carried out an extensive experimental evaluation of our methods on real datasets, which shows that our bounds lead to efficiently computable and high-quality approximations for both applications.Frequent subgraph mining is a fundamental task in the analysis of collections of graphs that aims at finding all the subgraphs that appear with more than a user-specified frequency in the dataset. While several exact approaches have been proposed to solve the task, it remains computationally challenging on large graph datasets due to the complexity of the subgraph isomorphism problem inherent in the task and the huge number of candidate patterns even for fairly small subgraphs. In this thesis, we study two statistical learning measures of complexity, VC-dimension and Rademacher averages, for subgraphs, and derive efficiently computable bounds for both. We then show how such bounds can be applied to devise efficient sampling-based approaches for rigorously approximating the solutions of the frequent subgraph mining problem, providing sample sizes which are much tighter than what would be obtained by a straightforward application of Chernoff and union bounds. We also show that our bounds can be used for true frequent subgraph mining, which requires to identify subgraphs generated with probability above a given threshold using samples from an unknown generative process. Moreover, we carried out an extensive experimental evaluation of our methods on real datasets, which shows that our bounds lead to efficiently computable and high-quality approximations for both applications

Peregrine: A Pattern-Aware Graph Mining System

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.Comment: This is the full version of the paper appearing in the European Conference on Computer Systems (EuroSys), 202

Private Graph Data Release: A Survey

The application of graph analytics to various domains have yielded tremendous societal and economical benefits in recent years. However, the increasingly widespread adoption of graph analytics comes with a commensurate increase in the need to protect private information in graph databases, especially in light of the many privacy breaches in real-world graph data that was supposed to preserve sensitive information. This paper provides a comprehensive survey of private graph data release algorithms that seek to achieve the fine balance between privacy and utility, with a specific focus on provably private mechanisms. Many of these mechanisms fall under natural extensions of the Differential Privacy framework to graph data, but we also investigate more general privacy formulations like Pufferfish Privacy that can deal with the limitations of Differential Privacy. A wide-ranging survey of the applications of private graph data release mechanisms to social networks, finance, supply chain, health and energy is also provided. This survey paper and the taxonomy it provides should benefit practitioners and researchers alike in the increasingly important area of private graph data release and analysis

A Survey on Graph Kernels

Graph kernels have become an established and widely-used technique for solving classification tasks on graphs. This survey gives a comprehensive overview of techniques for kernel-based graph classification developed in the past 15 years. We describe and categorize graph kernels based on properties inherent to their design, such as the nature of their extracted graph features, their method of computation and their applicability to problems in practice. In an extensive experimental evaluation, we study the classification accuracy of a large suite of graph kernels on established benchmarks as well as new datasets. We compare the performance of popular kernels with several baseline methods and study the effect of applying a Gaussian RBF kernel to the metric induced by a graph kernel. In doing so, we find that simple baselines become competitive after this transformation on some datasets. Moreover, we study the extent to which existing graph kernels agree in their predictions (and prediction errors) and obtain a data-driven categorization of kernels as result. Finally, based on our experimental results, we derive a practitioner's guide to kernel-based graph classification

Labeled Subgraph Entropy Kernel

In recent years, kernel methods are widespread in tasks of similarity measuring. Specifically, graph kernels are widely used in fields of bioinformatics, chemistry and financial data analysis. However, existing methods, especially entropy based graph kernels are subject to large computational complexity and the negligence of node-level information. In this paper, we propose a novel labeled subgraph entropy graph kernel, which performs well in structural similarity assessment. We design a dynamic programming subgraph enumeration algorithm, which effectively reduces the time complexity. Specially, we propose labeled subgraph, which enriches substructure topology with semantic information. Analogizing the cluster expansion process of gas cluster in statistical mechanics, we re-derive the partition function and calculate the global graph entropy to characterize the network. In order to test our method, we apply several real-world datasets and assess the effects in different tasks. To capture more experiment details, we quantitatively and qualitatively analyze the contribution of different topology structures. Experimental results successfully demonstrate the effectiveness of our method which outperforms several state-of-the-art methods.Comment: 9 pages,5 figure