In this work we present PERCIS, an algorithm based on Importance Sampling to approximate the percolation centrality of all the nodes of a graph. Percolation centrality is a generalization of betweenness centrality to attributed graphs, and is a useful measure to quantify the importance of the vertices in a contagious process or to diffuse information. However, it is impractical to compute it exactly on modern-sized networks. First, we highlight key limitations of state-of-the-art samplingbased approximation methods for the percolation centrality, showing that in most cases they cannot achieve accurate solutions efficiently. Then, we propose and analyze a novel sampling algorithm based on Importance Sampling, proving tight sample size bounds to achieve high-quality approximations. Our extensive experimental evaluation shows that PercIS computes high-quality estimates and scales to large real-world networks, while significantly outperforming, in terms of sample sizes, accuracy and running times, the state-of-the-art.

Learning interpretable models has become a major focus of machine learning research, given the increasing prominence of machine learning in socially important decision-making. Among interpretable models, rule lists are among the best-known and easily interpretable ones. However, finding optimal rule lists is computationally challenging, and current approaches are impractical for large datasets.

Significant pattern mining is a fundamental task in mining transactional data, requiring to identify patterns significantly associated with the value of a given feature, the target. In several applications, such as biomedicine, basket market analysis, and social networks, the goal is to discover patterns whose association with the target is defined with respect to an underlying population, or process, of which the dataset represents only a collection of observations, or samples. A natural way to capture the association of a pattern with the target is to consider its statistical significance , assessing its deviation from the (null) hypothesis of independence between the pattern and the target. While several algorithms have been proposed to find statistically significant patterns, it remains a computationally demanding task, and for complex patterns such as subgroups, no efficient solution exists. We present FSR, an efficient algorithm to identify statistically significant patterns with rigorous guarantees on the probability of false discoveries. FSR builds on a novel general framework for mining significant patterns that captures some of the most commonly considered patterns, including itemsets, sequential patterns, and subgroups. FSR uses a small number of resampled datasets, obtained by assigning i.i.d. labels to each transaction, to rigorously bound the supremum deviation of a quality statistic measuring the significance of patterns. FSR builds on novel tight bounds on the supremum deviation that require to mine a small number of resampled datasets, while providing a high effectiveness in discovering significant patterns. As a test case, we consider significant subgroup mining, and our evaluation on several real datasets shows that FSR is effective in discovering significant subgroups, while requiring a small number of resampled datasets.

“Sim Sala Bim!” —Silvan, https://en.wikipedia.org/wiki/Silvan_(illusionist) Betweenness centrality is a popular centrality measure with applications in several domains and whose exact computation is impractical for modern-sized networks. We present SILVAN , a novel, efficient algorithm to compute, with high probability, accurate estimates of the betweenness centrality of all nodes of a graph and a high-quality approximation of the top- k betweenness centralities. SILVAN follows a progressive sampling approach and builds on novel bounds based on Monte Carlo Empirical Rademacher Averages, a powerful and flexible tool from statistical learning theory. SILVAN relies on a novel estimation scheme providing non-uniform bounds on the deviation of the estimates of the betweenness centrality of all the nodes from their true values and a refined characterisation of the number of samples required to obtain a high-quality approximation. Our extensive experimental evaluation shows that SILVAN extracts high-quality approximations while outperforming, in terms of number of samples and accuracy, the state-of-the-art approximation algorithm with comparable quality guarantees.

The identification of the set of k most central nodes of a graph, or centrality maximization, is a key task in network analysis, with various applications ranging from finding communities in social and biological networks to understanding which seed nodes are important to diffuse information in a graph. As the exact computation of centrality measures does not scale to modern-sized networks, the most practical solution is to resort to rigorous, but efficiently computable, randomized approximations. In this work we present CentRA, the first algorithm based on progressive sampling to compute high-quality approximations of the set of k most central nodes. CentRA is based on a novel approach to efficiently estimate Monte Carlo Rademacher Averages, a powerful tool from statistical learning theory to compute sharp data-dependent approximation bounds. Then, we study the sample complexity of centrality maximization using the VC-dimension, a key concept from statistical learning theory. We show that the number of random samples required to compute high-quality approximations scales with finer characteristics of the graph, such as its vertex diameter, or of the centrality of interest, significantly improving looser bounds derived from standard techniques. We apply CentRA to analyze large real-world networks, showing that it significantly outperforms the state-of-the-art approximation algorithm in terms of number of samples, running times, and accuracy.

MOTIVATION: Tumors are the result of a somatic evolutionary process leading to substantial intra-tumor heterogeneity. Single-cell and multi-region sequencing enable the detailed characterization of the clonal architecture of tumors and have highlighted its extensive diversity across tumors. While several computational methods have been developed to characterize the clonal composition and the evolutionary history of tumors, the identification of significantly conserved evolutionary trajectories across tumors is still a major challenge. RESULTS: We present a new algorithm, MAximal tumor treeS TRajectOries (MASTRO), to discover significantly conserved evolutionary trajectories in cancer. MASTRO discovers all conserved trajectories in a collection of phylogenetic trees describing the evolution of a cohort of tumors, allowing the discovery of conserved complex relations between alterations. MASTRO assesses the significance of the trajectories using a conditional statistical test that captures the coherence in the order in which alterations are observed in different tumors. We apply MASTRO to data from nonsmall-cell lung cancer bulk sequencing and to acute myeloid leukemia data from single-cell panel sequencing, and find significant evolutionary trajectories recapitulating and extending the results reported in the original studies. AVAILABILITY AND IMPLEMENTATION: MASTRO is available at https://github.com/VandinLab/MASTRO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: The extraction of k-mers is a fundamental component in many complex analyses of large next-generation sequencing datasets, including reads classification in genomics and the characterization of RNA-seq datasets. The extraction of all k-mers and their frequencies is extremely demanding in terms of running time and memory, owing to the size of the data and to the exponential number of k-mers to be considered. However, in several applications, only frequent k-mers, which are k-mers appearing in a relatively high proportion of the data, are required by the analysis. RESULTS: In this work, we present SPRISS, a new efficient algorithm to approximate frequent k-mers and their frequencies in next-generation sequencing data. SPRISS uses a simple yet powerful reads sampling scheme, which allows to extract a representative subset of the dataset that can be used, in combination with any k-mer counting algorithm, to perform downstream analyses in a fraction of the time required by the analysis of the whole data, while obtaining comparable answers. Our extensive experimental evaluation demonstrates the efficiency and accuracy of SPRISS in approximating frequent k-mers, and shows that it can be used in various scenarios, such as the comparison of metagenomic datasets, the identification of discriminative k-mers, and SNP (single nucleotide polymorphism) genotyping, to extract insights in a fraction of the time required by the analysis of the whole dataset. AVAILABILITY AND IMPLEMENTATION: SPRISS [a preliminary version (Santoro et al., 2021) of this work was presented at RECOMB 2021] is available at https://github.com/VandinLab/SPRISS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

“I’m an MC still as honest” – Eminem, Rap God We present MCRapper , an algorithm for efficient computation of Monte-Carlo Empirical Rademacher Averages (MCERA) for families of functions exhibiting poset (e.g., lattice) structure, such as those that arise in many pattern mining tasks. The MCERA allows us to compute upper bounds to the maximum deviation of sample means from their expectations, thus it can be used to find both (1) statistically-significant functions (i.e., patterns) when the available data is seen as a sample from an unknown distribution, and (2) approximations of collections of high-expectation functions (e.g., frequent patterns) when the available data is a small sample from a large dataset. This flexibility offered by MCRapper is a big advantage over previously proposed solutions, which could only achieve one of the two. MCRapper uses upper bounds to the discrepancy of the functions to efficiently explore and prune the search space, a technique borrowed from pattern mining itself. To show the practical use of MCRapper , we employ it to develop an algorithm TFP-R for the task of True Frequent Pattern (TFP) mining, by appropriately computing approximations of the negative and positive borders of the collection of patterns of interest, which allow an effective pruning of the pattern space and the computation of strong bounds to the supremum deviation. TFP-R gives guarantees on the probability of including any false positives (precision) and exhibits higher statistical power (recall) than existing methods offering the same guarantees. We evaluate MCRapper and TFP-R and show that they outperform the state-of-the-art for their respective tasks.

We present MCRapper, an algorithm for efficient computation of Monte-Carlo Empirical Rademacher Averages (MCERA) for families of functions exhibiting poset (e.g., lattice) structure, such as those that arise in many pattern mining tasks. The MCERA allows us to compute upper bounds to the maximum deviation of sample means from their expectations, thus it can be used to find both statistically-significant functions (i.e., patterns) when the available data is seen as a sample from an unknown distribution, and approximations of collections of high-expectation functions (e.g., frequent patterns) when the available data is a small sample from a large dataset. This feature is a strong improvement over previously proposed solutions that could only achieve one of the two. MCRapper uses upper bounds to the discrepancy of the functions to efficiently explore and prune the search space, a technique borrowed from pattern mining itself. To show the practical use of MCRapper, we employ it to develop an algorithm TFP-R for the task of True Frequent Pattern (TFP) mining. TFP-R gives guarantees on the probability of including any false positives (precision) and exhibits higher statistical power (recall) than existing methods offering the same guarantees. We evaluate MCRapper and TFP-R and show that they outperform the state-of-the-art for their respective tasks.

We present SPuManTE, an efficient algorithm for mining significant patterns from a transactional dataset. SPuManTE controls the Family-wise Error Rate: it ensures that the probability of reporting one or more false discoveries is less than an user-specified threshold. A key ingredient of SPuManTE is UT, our novel unconditional statistical test for evaluating the significance of a pattern, that requires fewer assumptions on the data generation process and is more appropriate for a knowledge discovery setting than classical conditional tests, such as the widely used Fisher's exact test. Computational requirements have limited the use of unconditional tests in significant pattern discovery, but UT overcomes this issue by obtaining the required probabilities in a novel efficient way. SPuManTE combines UT with recent results on the supremum of the deviations of pattern frequencies from their expectations, founded in statistical learning theory. This combination allows SPuManTE to be very efficient, while also enjoying high statistical power. The results of our experimental evaluation show that SPuManTE allows the discovery of statistically significant patterns while properly accounting for uncertainties in patterns' frequencies due to the data generation process.

The availability of massive datasets has highlighted the need of computationally efficient and statistically-sound methods to extracts patterns while providing rigorous guarantees on the quality of the results, in particular with respect to false discoveries. In this tutorial we survey recent methods that properly combine computational and statistical considerations to efficiently mine statistically reliable patterns from large datasets. We start by introducing the fundamental concepts in statistical hypothesis testing, including conditional and unconditional tests, which may not be familiar to everyone in the data mining community. We then explain how the computational and statistical challenges in pattern mining have been tackled in different ways. Finally, we describe the application of these methods in areas such as market basket analysis, subgraph mining, social networks analysis, and cancer genomics.

The extraction of patterns displaying significant association with a class label is a key data mining task with wide application in many domains. We study a variant of the problem that requires to mine the top-k statistically significant patterns, thus providing tight control on the number of patterns reported in output. We develop TopKWY, the first algorithm to mine the top-k significant patterns while rigorously controlling the family-wise error rate of the output and provide theoretical evidence of its effectiveness. TopKWY crucially relies on a novel strategy to explore statistically significant patterns and on several key implementation choices, which may be of independent interest. Our extensive experimental evaluation shows that TopKWY enables the extraction of the most significant patterns from large datasets which could not be analyzed by the state-of-the-art. In addition, TopKWY improves over the state-of-the-art even for the extraction of all significant patterns.