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In this work, we present the first efficient and practical algorithm for estimating the number of triangles in a graph stream using predictions. Our algorithm combines waiting room sampling and reservoir sampling with a predictor for the heaviness of edges, that is, the number of triangles in which an edge is involved. As a result, our algorithm is fast, provides guarantees on the amount of memory used, and exploits the additional information provided by the predictor to produce highly accurate estimates. We also propose a simple and domain-independent predictor, based on the degree of nodes, that can be easily computed with one pass on a stream of edges when the stream is available beforehand. Our analytical results show that, when the predictor provides useful information on the heaviness of edges, it leads to estimates with reduced variance compared to the state-of-the-art, even when the predictions are far from perfect. Our experimental results show that, when analyzing a single graph stream, our algorithm is faster than the state-of-the-art for a given memory budget, while providing significantly more accurate estimates. Even more interestingly, when sequences of hundreds of graph streams are analyzed, our algorithm significantly outperforms the state-of-the-art using our simple degree-based predictor built by analyzing only the first graph of the sequence., Comment: Accepted to ICDM2024

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. We present a novel and scalable approach to learn nearly optimal rule lists from large datasets. Our algorithm uses sampling to efficiently obtain an approximation of the optimal rule list with rigorous guarantees on the quality of the approximation. In particular, our algorithm guarantees to find a rule list with accuracy very close to the optimal rule list when a rule list with high accuracy exists. Our algorithm builds on the VC-dimension of rule lists, for which we prove novel upper and lower bounds. Our experimental evaluation on large datasets shows that our algorithm identifies nearly optimal rule lists with a speed-up up to two orders of magnitude over state-of-the-art exact approaches. Moreover, our algorithm is as fast as, and sometimes faster than, recent heuristic approaches, while reporting higher quality rule lists. In addition, the rules reported by our algorithm are more similar to the rules in the optimal rule list than the rules from heuristic approaches., Comment: Accepted to KDD 2024

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., Comment: Accepted to VLDB 2024

Finding dense subnetworks, with density based on edges or more complex structures, such as subgraphs or $k$-cliques, is a fundamental algorithmic problem with many applications. While the problem has been studied extensively in static networks, much remains to be explored for temporal networks. In this work we introduce the novel problem of identifying the temporal motif densest subnetwork, i.e., the densest subnetwork with respect to temporal motifs, which are high-order patterns characterizing temporal networks. This problem significantly differs from analogous formulations for dense temporal (or static) subnetworks as these do not account for temporal motifs. Identifying temporal motifs is an extremely challenging task, and thus, efficient methods are required. To this end, we design two novel randomized approximation algorithms with rigorous probabilistic guarantees that provide high-quality solutions. We perform extensive experiments showing that our methods outperform baselines. Furthermore, our algorithms scale on networks with up to billions of temporal edges, while baselines cannot handle such large networks. We use our techniques to analyze a financial network and show that our formulation reveals important network structures, such as bursty temporal events and communities of users with similar interests., Comment: Extended version of the accepted KDD'24 paper

In the past few years, graph neural networks (GNNs) have become the de facto model of choice for graph classification. While, from the theoretical viewpoint, most GNNs can operate on graphs of any size, it is empirically observed that their classification performance degrades when they are applied on graphs with sizes that differ from those in the training data. Previous works have tried to tackle this issue in graph classification by providing the model with inductive biases derived from assumptions on the generative process of the graphs, or by requiring access to graphs from the test domain. The first strategy is tied to the quality of the assumptions made for the generative process, and requires the use of specific models designed after the explicit definition of the generative process of the data, leaving open the question of how to improve the performance of generic GNN models in general settings. On the other hand, the second strategy can be applied to any GNN, but requires access to information that is not always easy to obtain. In this work we consider the scenario in which we only have access to the training data, and we propose a regularization strategy that can be applied to any GNN to improve its generalization capabilities from smaller to larger graphs without requiring access to the test data. Our regularization is based on the idea of simulating a shift in the size of the training graphs using coarsening techniques, and enforcing the model to be robust to such a shift. Experimental results on standard datasets show that popular GNN models, trained on the 50% smallest graphs in the dataset and tested on the 10% largest graphs, obtain performance improvements of up to 30% when trained with our regularization strategy., Comment: Accepted at NeurIPS 2022

Graph Neural Networks (GNNs) have become the state-of-the-art method for many applications on graph structured data. GNNs are a model for graph representation learning, which aims at learning to generate low dimensional node embeddings that encapsulate structural and feature-related information. GNNs are usually trained in an end-to-end fashion, leading to highly specialized node embeddings. While this approach achieves great results in the single-task setting, the generation of node embeddings that can be used to perform multiple tasks (with performance comparable to single-task models) is still an open problem. We propose the use of meta-learning to allow the training of a GNN model capable of producing multi-task node embeddings. In particular, we exploit the properties of optimization-based meta-learning to learn GNNs that can produce general node representations by learning parameters that can quickly (i.e. with a few steps of gradient descent) adapt to multiple tasks. Our experiments show that the embeddings produced by a model trained with our purposely designed meta-learning procedure can be used to perform multiple tasks with comparable or, surprisingly, even higher performance than both single-task and multi-task end-to-end models., Comment: Accepted as Oral at IJCNN 2022. arXiv admin note: substantial text overlap with arXiv:2012.06755

Counting the number of occurrences of small connected subgraphs, called temporal motifs, has become a fundamental primitive for the analysis of temporal networks, whose edges are annotated with the time of the event they represent. One of the main complications in studying temporal motifs is the large number of motifs that can be built even with a limited number of vertices or edges. As a consequence, since in many applications motifs are employed for exploratory analyses, the user needs to iteratively select and analyze several motifs that represent different aspects of the network, resulting in an inefficient, time-consuming process. This problem is exacerbated in large networks, where the analysis of even a single motif is computationally demanding. As a solution, in this work we propose and study the problem of simultaneously counting the number of occurrences of multiple temporal motifs, all corresponding to the same (static) topology (e.g., a triangle). Given that for large temporal networks computing the exact counts is unfeasible, we propose odeN, a sampling-based algorithm that provides an accurate approximation of all the counts of the motifs. We provide analytical bounds on the number of samples required by odeN to compute rigorous, probabilistic, relative approximations. Our extensive experimental evaluation shows that odeN enables the approximation of the counts of motifs in temporal networks in a fraction of the time needed by state-of-the-art methods, and that it also reports more accurate approximations than such methods., Comment: 14 pages, 8 figures, accepted at CIKM 2021

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 and counting of small graph patterns, called network motifs, is a fundamental primitive in the analysis of networks, with application in various domains, from social networks to neuroscience. Several techniques have been designed to count the occurrences of motifs in static networks, with recent work focusing on the computational challenges provided by large networks. Modern networked datasets contain rich information, such as the time at which the events modeled by the networks edges happened, which can provide useful insights into the process modeled by the network. The analysis of motifs in temporal networks, called temporal motifs, is becoming an important component in the analysis of modern networked datasets. Several methods have been recently designed to count the number of instances of temporal motifs in temporal networks, which is even more challenging than its counterpart for static networks. Such methods are either exact, and not applicable to large networks, or approximate, but provide only weak guarantees on the estimates they produce and do not scale to very large networks. In this work we present an efficient and scalable algorithm to obtain rigorous approximations of the count of temporal motifs. Our algorithm is based on a simple but effective sampling approach, which renders our algorithm practical for very large datasets. Our extensive experimental evaluation shows that our algorithm provides estimates of temporal motif counts which are more accurate than the state-of-the-art sampling algorithms, with significantly lower running time than exact approaches, enabling the study of temporal motifs, of size larger than the ones considered in previous works, on billion edges networks., Comment: 19 pages, 5 figures, to appear in SDM 2021

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. In this work we present SPRISS, a new efficient algorithm to approximate frequent $k$-mers and their frequencies in next-generation sequencing data. SPRISS employs 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 and the identification of discriminative $k$-mers, to extract insights in a fraction of the time required by the analysis of the whole dataset., Comment: Accepted to RECOMB 2021

Graph Neural Networks (GNNs) are a framework for graph representation learning, where a model learns to generate low dimensional node embeddings that encapsulate structural and feature-related information. GNNs are usually trained in an end-to-end fashion, leading to highly specialized node embeddings. However, generating node embeddings that can be used to perform multiple tasks (with performance comparable to single-task models) is an open problem. We propose a novel meta-learning strategy capable of producing multi-task node embeddings. Our method avoids the difficulties arising when learning to perform multiple tasks concurrently by, instead, learning to quickly (i.e. with a few steps of gradient descent) adapt to multiple tasks singularly. We show that the embeddings produced by our method can be used to perform multiple tasks with comparable or higher performance than classically trained models. Our method is model-agnostic and task-agnostic, thus applicable to a wide variety of multi-task domains., Comment: Accepted at the NeurIPS Workshop on Meta-Learning (MetaLearn) 2020

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.

Graph Neural Networks (GNNs) rely on the graph structure to define an aggregation strategy where each node updates its representation by combining information from its neighbours. A known limitation of GNNs is that, as the number of layers increases, information gets smoothed and squashed and node embeddings become indistinguishable, negatively affecting performance. Therefore, practical GNN models employ few layers and only leverage the graph structure in terms of limited, small neighbourhoods around each node. Inevitably, practical GNNs do not capture information depending on the global structure of the graph. While there have been several works studying the limitations and expressivity of GNNs, the question of whether practical applications on graph structured data require global structural knowledge or not, remains unanswered. In this work, we empirically address this question by giving access to global information to several GNN models, and observing the impact it has on downstream performance. Our results show that global information can in fact provide significant benefits for common graph-related tasks. We further identify a novel regularization strategy that leads to an average accuracy improvement of more than 5% on all considered tasks.

Sensor-based human activity recognition (HAR) requires to predict the action of a person based on sensor-generated time series data. HAR has attracted major interest in the past few years, thanks to the large number of applications enabled by modern ubiquitous computing devices. While several techniques based on hand-crafted feature engineering have been proposed, the current state-of-the-art is represented by deep learning architectures that automatically obtain high level representations and that use recurrent neural networks (RNNs) to extract temporal dependencies in the input. RNNs have several limitations, in particular in dealing with long-term dependencies. We propose a novel deep learning framework, \algname, based on a purely attention-based mechanism, that overcomes the limitations of the state-of-the-art. We show that our proposed attention-based architecture is considerably more powerful than previous approaches, with an average increment, of more than $7\%$ on the F1 score over the previous best performing model. Furthermore, we consider the problem of personalizing HAR deep learning models, which is of great importance in several applications. We propose a simple and effective transfer-learning based strategy to adapt a model to a specific user, providing an average increment of $6\%$ on the F1 score on the predictions for that user. Our extensive experimental evaluation proves the significantly superior capabilities of our proposed framework over the current state-of-the-art and the effectiveness of our user adaptation technique., Comment: Accepted for publication on the IEEE Sensors Journal

The most widely used internal measure for clustering evaluation is the silhouette coefficient, whose naive computation requires a quadratic number of distance calculations, which is clearly unfeasible for massive datasets. Surprisingly, there are no known general methods to efficiently approximate the silhouette coefficient of a clustering with rigorously provable high accuracy. In this paper, we present the first scalable algorithm to compute such a rigorous approximation for the evaluation of clusterings based on any metric distances. Our algorithm hinges on a Probability Proportional to Size (PPS) sampling scheme, and, for any fixed $\varepsilon, \delta \in (0,1)$, it approximates the silhouette coefficient within a mere additive error $O(\varepsilon)$ with probability $1-\delta$, using a very small number of distance calculations. We also prove that the algorithm can be adapted to obtain rigorous approximations of other internal measures of clustering quality, such as cohesion and separation. Importantly, we provide a distributed implementation of the algorithm using the MapReduce model, which runs in constant rounds and requires only sublinear local space at each worker, which makes our estimation approach applicable to big data scenarios. We perform an extensive experimental evaluation of our silhouette approximation algorithm, comparing its performance to a number of baseline heuristics on real and synthetic datasets. The experiments provide evidence that, unlike other heuristics, our estimation strategy not only provides tight theoretical guarantees but is also able to return highly accurate estimations while running in a fraction of the time required by the exact computation, and that its distributed implementation is highly scalable, thus enabling the computation of internal measures for very large datasets for which the exact computation is prohibitive., Comment: 16 pages, 4 tables, 1 figure

Estimating the abundances of all $k$-mers in a set of biological sequences is a fundamental and challenging problem with many applications in biological analysis. While several methods have been designed for the exact or approximate solution of this problem, they all require to process the entire dataset, that can be extremely expensive for high-throughput sequencing datasets. While in some applications it is crucial to estimate all $k$-mers and their abundances, in other situations reporting only frequent $k$-mers, that appear with relatively high frequency in a dataset, may suffice. This is the case, for example, in the computation of $k$-mers' abundance-based distances among datasets of reads, commonly used in metagenomic analyses. In this work, we develop, analyze, and test, a sampling-based approach, called SAKEIMA, to approximate the frequent $k$-mers and their frequencies in a high-throughput sequencing dataset while providing rigorous guarantees on the quality of the approximation. SAKEIMA employs an advanced sampling scheme and we show how the characterization of the VC dimension, a core concept from statistical learning theory, of a properly defined set of functions leads to practical bounds on the sample size required for a rigorous approximation. Our experimental evaluation shows that SAKEIMA allows to rigorously approximate frequent $k$-mers by processing only a fraction of a dataset and that the frequencies estimated by SAKEIMA lead to accurate estimates of $k$-mer based distances between high-throughput sequencing datasets. Overall, SAKEIMA is an efficient and rigorous tool to estimate $k$-mers abundances providing significant speed-ups in the analysis of large sequencing datasets., Comment: Accepted for RECOMB 2019

Recent large cancer studies have measured somatic alterations in an unprecedented number of tumours. These large datasets allow the identification of cancer-related sets of genetic alterations by identifying relevant combinatorial patterns. Among such patterns, mutual exclusivity has been employed by several recent methods that have shown its effectivenes in characterizing gene sets associated to cancer. Mutual exclusivity arises because of the complementarity, at the functional level, of alterations in genes which are part of a group (e.g., a pathway) performing a given function. The availability of quantitative target profiles, from genetic perturbations or from clinical phenotypes, provides additional information that can be leveraged to improve the identification of cancer related gene sets by discovering groups with complementary functional associations with such targets. In this work we study the problem of finding groups of mutually exclusive alterations associated with a quantitative (functional) target. We propose a combinatorial formulation for the problem, and prove that the associated computation problem is computationally hard. We design two algorithms to solve the problem and implement them in our tool UNCOVER. We provide analytic evidence of the effectiveness of UNCOVER in finding high-quality solutions and show experimentally that UNCOVER finds sets of alterations significantly associated with functional targets in a variety of scenarios. In addition, our algorithms are much faster than the state-of-the-art, allowing the analysis of large datasets of thousands of target profiles from cancer cell lines. We show that on one such dataset from project Achilles our methods identify several significant gene sets with complementary functional associations with targets., Comment: Accepted at RECOMB 2018

An uncertain graph $\mathcal{G} = (V, E, p : E \rightarrow (0,1])$ can be viewed as a probability space whose outcomes (referred to as \emph{possible worlds}) are subgraphs of $\mathcal{G}$ where any edge $e\in E$ occurs with probability $p(e)$, independently of the other edges. These graphs naturally arise in many application domains where data management systems are required to cope with uncertainty in interrelated data, such as computational biology, social network analysis, network reliability, and privacy enforcement, among the others. For this reason, it is important to devise fundamental querying and mining primitives for uncertain graphs. This paper contributes to this endeavor with the development of novel strategies for clustering uncertain graphs. Specifically, given an uncertain graph $\mathcal{G}$ and an integer $k$, we aim at partitioning its nodes into $k$ clusters, each featuring a distinguished center node, so to maximize the minimum/average connection probability of any node to its cluster's center, in a random possible world. We assess the NP-hardness of maximizing the minimum connection probability, even in the presence of an oracle for the connection probabilities, and develop efficient approximation algorithms for both problems and some useful variants. Unlike previous works in the literature, our algorithms feature provable approximation guarantees and are capable to keep the granularity of the returned clustering under control. Our theoretical findings are complemented with several experiments that compare our algorithms against some relevant competitors, with respect to both running-time and quality of the returned clusterings.

Next-generation sequencing technologies allow the measurement of somatic mutations in a large number of patients from the same cancer type. One of the main goals in analyzing these mutations is the identification of mutations associated with clinical parameters, such as survival time. This goal is hindered by the genetic heterogeneity of mutations in cancer, due to the fact that genes and mutations act in the context of pathways. To identify mutations associated with survival time it is therefore crucial to study mutations in the context of interaction networks. In this work we study the problem of identifying subnetworks of a large gene-gene interaction network that have mutations associated with survival. We formally define the associated computational problem by using a score for subnetworks based on the test statistic of the log-rank test, a widely used statistical test for comparing the survival of two populations. We show that the computational problem is NP-hard and we propose a novel algorithm, called Network of Mutations Associated with Survival (NoMAS), to solve it. NoMAS is based on the color-coding technique, that has been previously used in other applications to find the highest scoring subnetwork with high probability when the subnetwork score is additive. In our case the score is not additive; nonetheless, we prove that under a reasonable model for mutations in cancer NoMAS does identify the optimal solution with high probability. We test NoMAS on simulated and cancer data, comparing it to approaches based on single gene tests and to various greedy approaches. We show that our method does indeed find the optimal solution and performs better than the other approaches. Moreover, on two cancer datasets our method identifies subnetworks with significant association to survival when none of the genes has significant association with survival when considered in isolation., Comment: This paper was selected for oral presentation at RECOMB 2016 and an abstract is published in the conference proceedings

Cancer is a heterogeneous disease with different combinations of genetic and epigenetic alterations driving the development of cancer in different individuals. While these alterations are believed to converge on genes in key cellular signaling and regulatory pathways, our knowledge of these pathways remains incomplete, making it difficult to identify driver alterations by their recurrence across genes or known pathways. We introduce Combinations of Mutually Exclusive Alterations (CoMEt), an algorithm to identify combinations of alterations de novo, without any prior biological knowledge (e.g. pathways or protein interactions). CoMEt searches for combinations of mutations that exhibit mutual exclusivity, a pattern expected for mutations in pathways. CoMEt has several important feature that distinguish it from existing approaches to analyze mutual exclusivity among alterations. These include: an exact statistical test for mutual exclusivity that is more sensitive in detecting combinations containing rare alterations; simultaneous identification of collections of one or more combinations of mutually exclusive alterations; simultaneous analysis of subtype-specific mutations; and summarization over an ensemble of collections of mutually exclusive alterations. These features enable CoMEt to robustly identify alterations affecting multiple pathways, or hallmarks of cancer. We show that CoMEt outperforms existing approaches on simulated and real data. Application of CoMEt to hundreds of samples from four different cancer types from TCGA reveals multiple mutually exclusive sets within each cancer type. Many of these overlap known pathways, but others reveal novel putative cancer genes. *Equal contribution., Comment: Accepted to RECOMB 2015

A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in many genomics applications. This is because: the two populations determined by a genetic variant may have very different sizes; and the evaluation of many possible variants demands highly accurate computation of very small p-values. We demonstrate this problem for cancer genomics data where the standard log-rank test leads to many false positive associations between somatic mutations and survival time. We develop and analyze a novel algorithm, Exact Log-rank Test (ExaLT), that accurately computes the p-value of the log-rank statistic under an exact distribution that is appropriate for any size populations. We demonstrate the advantages of ExaLT on data from published cancer genomics studies, finding significant differences from the reported p-values. We analyze somatic mutations in six cancer types from The Cancer Genome Atlas (TCGA), finding mutations with known association to survival as well as several novel associations. In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations., Comment: Full version of RECOMB 2013 paper

We present space-efficient parallel strategies for two fundamental combinatorial search problems, namely, backtrack search and branch-and-bound, both involving the visit of an $n$-node tree of height $h$ under the assumption that a node can be accessed only through its father or its children. For both problems we propose efficient algorithms that run on a $p$-processor distributed-memory machine. For backtrack search, we give a deterministic algorithm running in $O(n/p+h\log p)$ time, and a Las Vegas algorithm requiring optimal $O(n/p+h)$ time, with high probability. Building on the backtrack search algorithm, we also derive a Las Vegas algorithm for branch-and-bound which runs in $O((n/p+h\log p \log n)h\log^2 n)$ time, with high probability. A remarkable feature of our algorithms is the use of only constant space per processor, which constitutes a significant improvement upon previous algorithms whose space requirements per processor depend on the (possibly huge) tree to be explored., Comment: Extended version of the paper in the Proc. of 38th International Symposium on Mathematical Foundations of Computer Science (MFCS)

Frequent Itemsets (FIs) mining is a fundamental primitive in data mining. It requires to identify all itemsets appearing in at least a fraction $\theta$ of a transactional dataset $\mathcal{D}$. Often though, the ultimate goal of mining $\mathcal{D}$ is not an analysis of the dataset \emph{per se}, but the understanding of the underlying process that generated it. Specifically, in many applications $\mathcal{D}$ is a collection of samples obtained from an unknown probability distribution $\pi$ on transactions, and by extracting the FIs in $\mathcal{D}$ one attempts to infer itemsets that are frequently (i.e., with probability at least $\theta$) generated by $\pi$, which we call the True Frequent Itemsets (TFIs). Due to the inherently stochastic nature of the generative process, the set of FIs is only a rough approximation of the set of TFIs, as it often contains a huge number of \emph{false positives}, i.e., spurious itemsets that are not among the TFIs. In this work we design and analyze an algorithm to identify a threshold $\hat{\theta}$ such that the collection of itemsets with frequency at least $\hat{\theta}$ in $\mathcal{D}$ contains only TFIs with probability at least $1-\delta$, for some user-specified $\delta$. Our method uses results from statistical learning theory involving the (empirical) VC-dimension of the problem at hand. This allows us to identify almost all the TFIs without including any false positive. We also experimentally compare our method with the direct mining of $\mathcal{D}$ at frequency $\theta$ and with techniques based on widely-used standard bounds (i.e., the Chernoff bounds) of the binomial distribution, and show that our algorithm outperforms these methods and achieves even better results than what is guaranteed by the theoretical analysis., Comment: 13 pages, Extended version of work appeared in SIAM International Conference on Data Mining, 2014

We study the use of sampling for efficiently mining the top-K frequent itemsets of cardinality at most w. To this purpose, we define an approximation to the top-K frequent itemsets to be a family of itemsets which includes (resp., excludes) all very frequent (resp., very infrequent) itemsets, together with an estimate of these itemsets' frequencies with a bounded error. Our first result is an upper bound on the sample size which guarantees that the top-K frequent itemsets mined from a random sample of that size approximate the actual top-K frequent itemsets, with probability larger than a specified value. We show that the upper bound is asymptotically tight when w is constant. Our main algorithmic contribution is a progressive sampling approach, combined with suitable stopping conditions, which on appropriate inputs is able to extract approximate top-K frequent itemsets from samples whose sizes are smaller than the general upper bound. In order to test the stopping conditions, this approach maintains the frequency of all itemsets encountered, which is practical only for small w. However, we show how this problem can be mitigated by using a variation of Bloom filters. A number of experiments conducted on both synthetic and real bench- mark datasets show that using samples substantially smaller than the original dataset (i.e., of size defined by the upper bound or reached through the progressive sampling approach) enable to approximate the actual top-K frequent itemsets with accuracy much higher than what analytically proved., Comment: 16 pages, 2 figures, accepted for presentation at ECML PKDD 2010 and publication in the ECML PKDD 2010 special issue of the Data Mining and Knowledge Discovery journal

As advances in technology allow for the collection, storage, and analysis of vast amounts of data, the task of screening and assessing the significance of discovered patterns is becoming a major challenge in data mining applications. In this work, we address significance in the context of frequent itemset mining. Specifically, we develop a novel methodology to identify a meaningful support threshold s* for a dataset, such that the number of itemsets with support at least s* represents a substantial deviation from what would be expected in a random dataset with the same number of transactions and the same individual item frequencies. These itemsets can then be flagged as statistically significant with a small false discovery rate. We present extensive experimental results to substantiate the effectiveness of our methodology., Comment: A preliminary version of this work was presented in ACM PODS 2009. 20 pages, 0 figures

We develop, analyze and experiment with a new tool, called MADMX, which extracts frequent motifs, possibly including don't care characters, from biological sequences. We introduce density, a simple and flexible measure for bounding the number of don't cares in a motif, defined as the ratio of solid (i.e., different from don't care) characters to the total length of the motif. By extracting only maximal dense motifs, MADMX reduces the output size and improves performance, while enhancing the quality of the discoveries. The efficiency of our approach relies on a newly defined combining operation, dubbed fusion, which allows for the construction of maximal dense motifs in a bottom-up fashion, while avoiding the generation of nonmaximal ones. We provide experimental evidence of the efficiency and the quality of the motifs returned by MADMX, Comment: A preliminary version of this work was presented in WABI 2009. 10 pages, 0 figures