arXiv subjects

Alessio Conte

Publications and source records attributed to Alessio Conte.

At least 19 recordsLinked to original sources

arXiv2026

Efficient Enumeration of Enclosed Vector Spaces

In this paper, we address several problems concerning vector spaces enclosed in a given set. Let V be a vector space over a finite field of cardinality c, and let $S \subseteq V$ be a set of vectors. A space enclosed in S is a vector subspace W of V that is also contained in S: $W \subseteq S$. We focus on enumeration problems, where the task is to list all solutions, and we first provide an algorithm to enumerate all spaces that are enclosed in S. Our algorithm is further adapted to solve two more problems: the enumeration of (inclusion-)maximal enclosed spaces, and the problem of finding an enclosed space of maximum dimension. The latter problem arises in the context of Boolean functions' regularity detection. It can also be seen as a dual version of the well-known linear span: indeed, the span is the minimum-dimension vector space that contains a given set of vectors S, and it is a fundamental concept in linear algebra. Our proposed algorithms are based on the binary partition paradigm, and have total time complexity $e^{\frac{1}{2\ln c}\ln^2 n - \Theta(\log n \log \log n)}$, where $n= |\inputset|$. The first version, for enumerating all enclosed spaces, also achieves a delay (time between consecutive outputs) of O(n). Our algorithms provide a quadratic speed-up with respect to a brute-force approach, although the speed-up appears even greater in our experimental evaluation on boolean vector spaces.

cs.DS↗

arXiv2026

Compact Path Representation in DAGs via Colored Edge Pebbling

Compactly representing a variation graph is a core problem in computational pangenomics that is usually attacked with techniques that have been originated on texts and adapted to graphs. In this paper we propose a new framework that takes a topology-centric perspective instead. A variation graph is modeled as a directed acyclic graph (DAG) together with a set of distinguished paths, where each path is assigned a distinct color. Our compact representation is centered on pebbling the graph, i.e. placing colored pebbles on edges so that every predefined path can be univocally reconstructed from the pebbled edges. In particular, a saturated pebbling marks each chosen edge with every path (color) traversing it. We first propose a data structure to represent and query a variation graph with storage space depending on the size of the pebbling. The supported queries are: (i) path query, which recovers a path given its color, and (ii) edge query, which reports the colors of paths traversing a given edge. We then prove that the problem of finding a pebbling of minimum size is solvable in polynomial time. On the contrary, we prove that finding a saturated pebbling of minimum size is NP-hard, but can be reduced to the minimum-weight set cover problem, allowing us to leverage integer linear programming (ILP) solvers. We show how to exploit saturated pebblings to achieve faster queries times than minimum size pebbling. Our framework opens a new algorithmic viewpoint on developing more efficient variation graph representations rooted on the study of the topology of those graphs.

cs.DS↗

arXiv2025

Are Depth-2 Regular Expressions Hard to Intersect?

We study the basic regular expression intersection testing problem, which asks to determine whether the intersection of the languages of two regular expressions is nonempty. A textbook solution to this problem is to construct the nondeterministic finite automaton that accepts the language of both expressions. This procedure results in a $\Theta(mn)$ running time, where $m$ and $n$ are the sizes of the two expressions, respectively. Following the approach of Backurs and Indyk [FOCS'16] and Bringmann, Gr{\o}nlund, and Larsen [FOCS'17] on regular expression matching and membership testing, we study the complexity of intersection testing for homogeneous regular expressions of bounded depth involving concatenation, OR, Kleene star, and Kleene plus. Specifically, we consider all combinations of types of depth-2 regular expressions and classify the time complexity of intersection testing as either linear or quadratic, assuming SETH. The most interesting result is a quadratic conditional lower bound for testing the intersection of a ''concatenation of +s'' expression with a ''concatenation of ORs'' expression: this is the only hard case that does not involve the Kleene star operator and is not implied by existing lower bounds for the simpler membership testing problem.

cs.CC↗

arXiv2025

Indexing Strings with Utilities

Applications in domains ranging from bioinformatics to advertising feature strings that come with numerical scores (utilities). The utilities quantify the importance, interest, profit, or risk of the letters occurring at every position of a string. Motivated by the ever-increasing rate of generating such data, as well as by their importance in several domains, we introduce Useful String Indexing (USI), a natural generalization of the classic String Indexing problem. Given a string $S$ (the text) of length $n$, USI asks for preprocessing $S$ into a compact data structure supporting the following queries efficiently: given a shorter string $P$ (the pattern), return the global utility $U(P)$ of $P$ in $S$, where $U$ is a function that maps any string $P$ to a utility score based on the utilities of the letters of every occurrence of $P$ in $S$. Our work also makes the following contributions: (1) We propose a novel and efficient data structure for USI based on finding the top-$K$ frequent substrings of $S$. (2) We propose a linear-space data structure that can be used to mine the top-$K$ frequent substrings of $S$ or to tune the parameters of the USI data structure. (3) We propose a novel space-efficient algorithm for estimating the set of the top-$K$ frequent substrings of $S$, thus improving the construction space of the data structure for USI. (4) We show that popular space-efficient top-$K$ frequent item mining strategies employed by state-of-the-art algorithms do not smoothly translate from items to substrings. (5) Using billion-letter datasets, we experimentally demonstrate that: (i) our top-$K$ frequent substring mining algorithms are accurate and scalable, unlike two state-of-the-art methods; and (ii) our USI data structures are up to $15$ times faster in querying than $4$ nontrivial baselines while occupying the same space with them.

cs.DS↗

arXiv2025

The Complexity of Maximal Common Subsequence Enumeration

Frequent pattern mining is widely used to find ``important'' or ``interesting'' patterns in data. While it is not easy to mathematically define such patterns, maximal frequent patterns are promising candidates, as frequency is a natural indicator of relevance and maximality helps to summarize the output. As such, their mining has been studied on various data types, including itemsets, graphs, and strings. The complexity of mining maximal frequent itemsets and subtrees has been thoroughly investigated (e.g., [Boros et al., 2003], [Uno et al., 2004]) in the literature. On the other hand, while the idea of mining frequent subsequences in sequential data was already introduced in the seminal paper [Agrawal et al., 1995], the complexity of the problem is still open. In this paper, we investigate the complexity of the maximal common subsequence enumeration problem, which is both an important special case of maximal frequent subsequence mining and a generalization of the classic longest common subsequence (LCS) problem. We show the hardness of enumerating maximal common subsequences between multiple strings, ruling out the possibility of an \emph{output-polynomial time} enumeration algorithm under $P \neq NP$, that is, an algorithm that runs in time ${\rm poly}(|\mathcal I| + N)$, where $|\mathcal I|$ and $N$ are the size of the input and number of output solutions, respectively. To circumvent this intractability, we also investigate the parameterized complexity of the problem, and show several results when the alphabet size, the number of strings, and the length of a string are taken into account as parameters.

cs.DS↗

arXiv2024

Enumerating Graphlets with Amortized Time Complexity Independent of Graph Size

Graphlets of order $k$ in a graph $G$ are connected subgraphs induced by $k$ nodes (called $k$-graphlets) or by $k$ edges (called edge $k$-graphlets). They are among the interesting subgraphs in network analysis to get insights on both the local and global structure of a network. While several algorithms exist for discovering and enumerating graphlets, the cost per solution of such algorithms typically depends on the size of the graph $G$, or its maximum degree. In real networks, even the latter can be in the order of millions, whereas $k$ is typically required to be a small value. In this paper we provide the first algorithm to list all graphlets of order $k$ in a graph $G=(V,E)$ with an amortized cost per solution depending \emph{solely} on the order $k$, contrarily to previous approaches where the cost depends \emph{also} on the size of $G$ or its maximum degree. Specifically, we show that it is possible to list $k$-graphlets in $O(k^2)$ time per solution, and to list edge $k$-graphlets in $O(k)$ time per solution. Furthermore we show that, if the input graph has bounded degree, then the cost per solution for listing $k$-graphlets is reduced to $O(k)$. Whenever $k = O(1)$, as it is often the case in practical settings, these algorithms are the first to achieve constant time per solution.

cs.DS↗

arXiv2024

Output-Sensitive Enumeration of Potential Maximal Cliques in Polynomial Space

A set of vertices in a graph forms a potential maximal clique if there exists a minimal chordal completion in which it is a maximal clique. Potential maximal cliques were first introduced as a key tool to obtain an efficient, though exponential-time algorithm to compute the treewidth of a graph. As a byproduct, this allowed to compute the treewidth of various graph classes in polynomial time. In recent years, the concept of potential maximal cliques regained interest as it proved to be useful for a handful of graph algorithmic problems. In particular, it turned out to be a key tool to obtain a polynomial time algorithm for computing maximum weight independent sets in $P_5$-free and $P_6$-free graphs (Lokshtanov et al., SODA `14 and Grzeskik et al., SODA `19. In most of their applications, obtaining all the potential maximal cliques constitutes an algorithmic bottleneck, thus motivating the question of how to efficiently enumerate all the potential maximal cliques in a graph $G$. The state-of-the-art algorithm by Bouchitt\'e \& Todinca can enumerate potential maximal cliques in output-polynomial time by using exponential space, a significant limitation for the size of feasible instances. In this paper, we revisit this algorithm and design an enumeration algorithm that preserves an output-polynomial time complexity while only requiring polynomial space.

cs.DS↗

arXiv2023

A Compact DAG for Storing and Searching Maximal Common Subsequences

Maximal Common Subsequences (MCSs) between two strings X and Y are subsequences of both X and Y that are maximal under inclusion. MCSs relax and generalize the well known and widely used concept of Longest Common Subsequences (LCSs), which can be seen as MCSs of maximum length. While the number both LCSs and MCSs can be exponential in the length of the strings, LCSs have been long exploited for string and text analysis, as simple compact representations of all LCSs between two strings, built via dynamic programming or automata, have been known since the '70s. MCSs appear to have a more challenging structure: even listing them efficiently was an open problem open until recently, thus narrowing the complexity difference between the two problems, but the gap remained significant. In this paper we close the complexity gap: we show how to build DAG of polynomial size-in polynomial time-which allows for efficient operations on the set of all MCSs such as enumeration in Constant Amortized Time per solution (CAT), counting, and random access to the i-th element (i.e., rank and select operations). Other than improving known algorithmic results, this work paves the way for new sequence analysis methods based on MCSs.

cs.DS↗

arXiv2023

Computing matching statistics on Wheeler DFAs

Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for computing matching statistics which relies on some components of a compressed suffix tree - notably, the longest common prefix (LCP) array. In this paper, we show how their algorithm can be generalized from strings to Wheeler deterministic finite automata. Most importantly, we introduce a notion of LCP array for Wheeler automata, thus establishing a first clear step towards extending (compressed) suffix tree functionalities to labeled graphs.

cs.DS↗

arXiv2022

Generalizing Downsampling from Regular Data to Graphs

Downsampling produces coarsened, multi-resolution representations of data and it is used, for example, to produce lossy compression and visualization of large images, reduce computational costs, and boost deep neural representation learning. Unfortunately, due to their lack of a regular structure, there is still no consensus on how downsampling should apply to graphs and linked data. Indeed reductions in graph data are still needed for the goals described above, but reduction mechanisms do not have the same focus on preserving topological structures and properties, while allowing for resolution-tuning, as is the case in regular data downsampling. In this paper, we take a step in this direction, introducing a unifying interpretation of downsampling in regular and graph data. In particular, we define a graph coarsening mechanism which is a graph-structured counterpart of controllable equispaced coarsening mechanisms in regular data. We prove theoretical guarantees for distortion bounds on path lengths, as well as the ability to preserve key topological properties in the coarsened graphs. We leverage these concepts to define a graph pooling mechanism that we empirically assess in graph classification tasks, providing a greedy algorithm that allows efficient parallel implementation on GPUs, and showing that it compares favorably against pooling methods in literature.

cs.LG↗

arXiv2020

Efficient Estimation of Graph Trussness

A $k$-truss is an edge-induced subgraph $H$ such that each of its edges belongs to at least $k-2$ triangles of $H$. This notion has been introduced around ten years ago in social network analysis and security, as a form of cohesive subgraph that is rich of triangles and less stringent than the clique. The \emph{trussness} of a graph is the maximum $k$ such that a $k$-truss exists. The problem of computing $k$-trusses has been largely investigated from the practical and engineering point of view. On the other hand, the theoretical side of the problem has received much less attention, despite presenting interesting challenges. The existing methods share a common design, based on iteratively removing the edge with smallest support, where the support of an edge is the number of triangles containing it. The aim of this paper is studying algorithmic aspects of graph trussness. While it is possible to show that the time complexity of computing exactly the graph trussness and that of counting/listing all triangles is inherently the same, we provide efficient algorithms for estimating its value, under suitable conditions, with significantly lower complexity than the exact approach. In particular, we provide a $(1 \pm \epsilon)$-approximation algorithm that is asymptotically faster than the exact approach, on graphs which contain $\omega(m \, polylog(n))$ triangles, and has the same running time on graphs that do not. For the latter case, we also show that it is impossible to obtain an approximation algorithm with faster running time than the one of the exact approach when the number of triangles is $O(m)$, unless well known conjectures on triangle-freeness and Boolean matrix multiplication are false.

cs.DS↗

arXiv2020

Zuckerli: A New Compressed Representation for Graphs

Zuckerli is a scalable compression system meant for large real-world graphs. Graphs are notoriously challenging structures to store efficiently due to their linked nature, which makes it hard to separate them into smaller, compact components. Therefore, effective compression is crucial when dealing with large graphs, which can have billions of nodes and edges. Furthermore, a good compression system should give the user fast and reasonably flexible access to parts of the compressed data without requiring full decompression, which may be unfeasible on their system. Zuckerli improves multiple aspects of WebGraph, the current state-of-the-art in compressing real-world graphs, by using advanced compression techniques and novel heuristic graph algorithms. It can produce both a compressed representation for storage and one which allows fast direct access to the adjacency lists of the compressed graph without decompressing the entire graph. We validate the effectiveness of Zuckerli on real-world graphs with up to a billion nodes and 90 billion edges, conducting an extensive experimental evaluation of both compression density and decompression performance. We show that Zuckerli-compressed graphs are 10% to 29% smaller, and more than 20% in most cases, with a resource usage for decompression comparable to that of WebGraph.

cs.DS↗

arXiv2020

Radiomics and artificial intelligence analysis of CT data for the identification of prognostic features in multiple myeloma

Multiple Myeloma (MM) is a blood cancer implying bone marrow involvement, renal damages and osteolytic lesions. The skeleton involvement of MM is at the core of the present paper, exploiting radiomics and artificial intelligence to identify image-based biomarkers for MM. Preliminary results show that MM is associated to an extension of the intrabone volume for the whole body and that machine learning can identify CT image features mostly correlating with the disease evolution. This computational approach allows an automatic stratification of MM patients relying of these biomarkers and the formulation of a prognostic procedure for determining the disease follow-up.

q-bio.TO↗

arXiv2019

Proximity Search For Maximal Subgraph Enumeration

This paper proposes a new general technique for maximal subgraph enumeration which we call proximity search, whose aim is to design efficient enumeration algorithms for problems that could not be solved by existing frameworks. To support this claim and illustrate the technique we include output-polynomial algorithms for several problems for which output-polynomial algorithms were not known, including the enumeration of Maximal Bipartite Subgraphs, Maximal k-Degenerate Subgraphs (for bounded k), Maximal Induced Chordal Subgraphs, and Maximal Induced Trees. Using known techniques, such as reverse search, the space of all maximal solutions induces an implicit directed graph called "solution graph" or "supergraph", and solutions are enumerated by traversing it; however, nodes in this graph can have exponential out-degree, thus requiring exponential time to be spent on each solution. The novelty of proximity search is a formalization that allows us to define a better solution graph, and a technique, which we call canonical reconstruction, by which we can exploit the properties of given problems to build such graphs. This results in solution graphs whose nodes have significantly smaller (i.e., polynomial) out-degree with respect to existing approaches, but that remain strongly connected, so that all solutions can be enumerated in polynomial delay by a traversal. A drawback of this approach is the space required to keep track of visited solutions, which can be exponential: we further propose a technique to induce a parent-child relationship among solutions and achieve polynomial space when suitable conditions are met.

cs.DS↗

arXiv2019

Combinatorial Algorithms for String Sanitization

String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge. In this paper, we consider the problem of sanitizing a string by concealing the occurrences of sensitive patterns, while maintaining data utility, in two settings that are relevant to many common string processing tasks. In the first setting, we aim to generate the minimal-length string that preserves the order of appearance and frequency of all non-sensitive patterns. Such a string allows accurately performing tasks based on the sequential nature and pattern frequencies of the string. To construct such a string, we propose a time-optimal algorithm, TFS-ALGO. We also propose another time-optimal algorithm, PFS-ALGO, which preserves a partial order of appearance of non-sensitive patterns but produces a much shorter string that can be analyzed more efficiently. The strings produced by either of these algorithms are constructed by concatenating non-sensitive parts of the input string. However, it is possible to detect the sensitive patterns by ``reversing'' the concatenation operations. In response, we propose a heuristic, MCSR-ALGO, which replaces letters in the strings output by the algorithms with carefully selected letters, so that sensitive patterns are not reinstated, implausible patterns are not introduced, and occurrences of spurious patterns are prevented. In the second setting, we aim to generate a string that is at minimal edit distance from the original string, in addition to preserving the order of appearance and frequency of all non-sensitive patterns. To construct such a string, we propose an algorithm, ETFS-ALGO, based on solving specific instances of approximate regular expression matching.

cs.DS↗

arXiv2018

Efficient Enumeration of Subgraphs and Induced Subgraphs with Bounded Girth

The girth of a graph is the length of its shortest cycle. Due to its relevance in graph theory, network analysis and practical fields such as distributed computing, girth-related problems have been object of attention in both past and recent literature. In this paper, we consider the problem of listing connected subgraphs with bounded girth. As a large girth is index of sparsity, this allows to extract sparse structures from the input graph. We propose two algorithms, for enumerating respectively vertex induced subgraphs and edge induced subgraphs with bounded girth, both running in $O(n)$ amortized time per solution and using $O(n^3)$ space. Furthermore, the algorithms can be easily adapted to relax the connectivity requirement and to deal with weighted graphs. As a byproduct, the second algorithm can be used to answer the well known question of finding the densest $n$-vertex graph(s) of girth $k$.

cs.DS↗

arXiv2018

Listing Maximal Subgraphs in Strongly Accessible Set Systems

Algorithms for listing the subgraphs satisfying a given property (e.g.,being a clique, a cut, a cycle, etc.) fall within the general framework of set systems. A set system (U, F) uses a ground set U (e.g., the network nodes) and an indicator F, subset of 2^U, of which subsets of U have the required property. For the problem of listing all sets in F maximal under inclusion, the ambitious goal is to cover a large class of set systems, preserving at the same time the efficiency of the enumeration. Among the existing algorithms, the best-known ones list the maximal subsets in time proportional to their number but may require exponential space. In this paper we improve the state of the art in two directions by introducing an algorithmic framework that, under standard suitable conditions, simultaneously (i) extends the class of problems that can be solved efficiently to strongly accessible set systems, and (ii) reduces the additional space usage from exponential in |U| to stateless, thus accounting for just O(q) space, where q <= |U| is the largest size of a maximal set in F

cs.DM↗

arXiv2017

Efficiently Clustering Very Large Attributed Graphs

Attributed graphs model real networks by enriching their nodes with attributes accounting for properties. Several techniques have been proposed for partitioning these graphs into clusters that are homogeneous with respect to both semantic attributes and to the structure of the graph. However, time and space complexities of state of the art algorithms limit their scalability to medium-sized graphs. We propose SToC (for Semantic-Topological Clustering), a fast and scalable algorithm for partitioning large attributed graphs. The approach is robust, being compatible both with categorical and with quantitative attributes, and it is tailorable, allowing the user to weight the semantic and topological components. Further, the approach does not require the user to guess in advance the number of clusters. SToC relies on well known approximation techniques such as bottom-k sketches, traditional graph-theoretic concepts, and a new perspective on the composition of heterogeneous distance measures. Experimental results demonstrate its ability to efficiently compute high-quality partitions of large scale attributed graphs.

cs.SI↗