On Euler Tours in Streaming Models and some Games on Graphs

In this thesis, we take a look at several graph theoretical problems. We present two streaming algorithms for finding an Euler tour in a graph, prove a tight bound on the capture time in the Bridge-Burning Cops and Robbers Game and solve an open problem for the Extreme Vertex Destruction Model. In Chapter 2, we consider the classical Euler tour problem and take a modern look at this problem in the context of the graph streaming model. Here, RAM is of size O(n polylog(n)), where n is the number of nodes, and the graph is given as a stream of its edges. With this restricted memory space, we give a one-pass algorithm for finding Euler tours in the graph streaming model. In Chapter 3, we regard a lesser-known streaming model, the so-called StrSort model, to tackle a downside of our algorithm mentioned above. The algorithm stores an Euler tour on an output tape in form of a successor function. The order of the edges is given, but the edges are not actually sorted in the order of the Euler tour. Therefore, further processing the tour with another streaming algorithm might become difficult. We give an algorithm for sorting the edges of a graph according to a found Euler tour, that has a preparation step in the graph streaming model and a processing step in the StrSort model. The so-called Bridge-Burning Cops and Robbers Game is the topic of Chapter 4. Here, every time the robber traverses an edge, this edge is deleted afterwards. We study winning strategies of a single cop and make statements on the maximum number of turns of such strategies. In Chapter 5, we study networks formed by selfish agents. When a node is ‘destroyed’, i.e. the adjacent edges are deleted, the network is damaged and some players lose the connection to each other. In the Extreme Vertex Destruction Model, we observe the impact of such a deletion on swap equilibrium graphs and make statements on the maximum amount of damage that can cause here

Data-Oblivious Graph Algorithms in Outsourced External Memory

Motivated by privacy preservation for outsourced data, data-oblivious external memory is a computational framework where a client performs computations on data stored at a semi-trusted server in a way that does not reveal her data to the server. This approach facilitates collaboration and reliability over traditional frameworks, and it provides privacy protection, even though the server has full access to the data and he can monitor how it is accessed by the client. The challenge is that even if data is encrypted, the server can learn information based on the client data access pattern; hence, access patterns must also be obfuscated. We investigate privacy-preserving algorithms for outsourced external memory that are based on the use of data-oblivious algorithms, that is, algorithms where each possible sequence of data accesses is independent of the data values. We give new efficient data-oblivious algorithms in the outsourced external memory model for a number of fundamental graph problems. Our results include new data-oblivious external-memory methods for constructing minimum spanning trees, performing various traversals on rooted trees, answering least common ancestor queries on trees, computing biconnected components, and forming open ear decompositions. None of our algorithms make use of constant-time random oracles.Comment: 20 page

Streaming and Massively Parallel Algorithms for Edge Coloring

A valid edge-coloring of a graph is an assignment of "colors" to its edges such that no two incident edges receive the same color. The goal is to find a proper coloring that uses few colors. (Note that the maximum degree, Delta, is a trivial lower bound.) In this paper, we revisit this fundamental problem in two models of computation specific to massive graphs, the Massively Parallel Computations (MPC) model and the Graph Streaming model: - Massively Parallel Computation: We give a randomized MPC algorithm that with high probability returns a Delta+O~(Delta^(3/4)) edge coloring in O(1) rounds using O(n) space per machine and O(m) total space. The space per machine can also be further improved to n^(1-Omega(1)) if Delta = n^Omega(1). Our algorithm improves upon a previous result of Harvey et al. [SPAA 2018]. - Graph Streaming: Since the output of edge-coloring is as large as its input, we consider a standard variant of the streaming model where the output is also reported in a streaming fashion. The main challenge is that the algorithm cannot "remember" all the reported edge colors, yet has to output a proper edge coloring using few colors. We give a one-pass O~(n)-space streaming algorithm that always returns a valid coloring and uses 5.44 Delta colors with high probability if the edges arrive in a random order. For adversarial order streams, we give another one-pass O~(n)-space algorithm that requires O(Delta^2) colors

Traversing large graphs in realistic settings

The notion of graph traversal is of fundamental importance to solving many computational problems. In many modern applications involving graph traversal such as those arising in the domain of social networks, Internet based services, fraud detection in telephone calls etc., the underlying graph is very large and dynamically evolving. This thesis deals with the design and engineering of First Search (BFS) algorithms for massive sparse undirected graphs. Our pipelined implementations with low constant factors, together with some heuristics preserving the worst-case guarantees makes BFS viable on massive graphs. We perform an extensive set of experiments to study the effect of various graph properties such as diameter, inititraversal algorithms for such graphs. We engineer various I/O-efficient Breadth al disk layouts, tuning parameters, disk parallelism, cache-obliviousness etc. on the relative performance of these algorithms. We characterize the performance of NAND flash based storage devices, including many solid state disks. We show that despite the similarities between flash memory and RAM (fast random reads) and between flash disk and hard disk (both are block based devices), the algorithms designed in the RAM model or the external memory model do not realize the full potential of the flash memory devices. We also analyze the effect of misalignments, aging, past I/O patterns, etc. on the performance obtained on these devices. We also consider I/O-efficient BFS algorithms for the case when a hard disk and a solid state disk are used together. We present a simple algorithm which maintains the topological order of a directed acyclic graph with n nodes under an online edge insertion sequence in O(n2.75)time, independent of the number m of edges inserted. For dense DAGs, this is an improvement over the previous best result of O (min{m3/2 logn,m3/2 +n2 logn}). While our analysis holds only for the incremental setting, our algorithm itself is fully dynamic. We also present the first average-case analysis of online topological ordering algorithms. We prove an expected runtime of O (n2 polylog(n)) under insertion of the edges of a complete DAG in a random order for various incremental topological ordering algorithms.Die Traversierung von Graphen ist von fundamentaler Bedeutung für das Lösen vieler Berechnungsprobleme. Moderne Anwendungen, die auf Graphtraversierung beruhen, findet man unter anderem in sozialen Netzwerken, internetbasierten Dienstleistungen, Betrugserkennung bei Telefonanrufen. In vielen dieser lAnwendungen ist der zugrunde iegende Graph sehr gross und ändert sich kontinuierlich. Wir entwickelnmehrere I/O-effiziente Breitensuch-Algorithmen für massive, dünnbesiedelte, ungerichtete Graphen. Im Zusammenspiel mit Heuristiken zur Einhaltung von Worst-Case-Garantien, ermöglichen unsere pipeline-basierten Implementierungen die Praktikabilität von Breitensuche auf massiven Graphen. Wir führen eine Vielfalt an Experimente durch, um die Wirkung unterschiedlicher Grapheigenschaften zu untersuchen, wie z.B. Graph-Durchmesser, anfängliche Belegung der Festplatte, Tuning-Parameter, Plattenparallelismus. Wir charakterisieren die Leistung von NAND-Flash basierten Speichermedien, einschliesslich vieler solid-state Disks. Wir zeigen, dass trotz der Ähnlichkeiten von Flash-Speicher und RAM (schnelle wahlfreie Lese-Zugriffe) und von Flash-Platten und Festplatten (beide sind blockbasiert) Algorithmen, die für das RAMModell oder das Externspeicher-Modell entworfenen wurden, nicht das volle Potential der Flash-Speicher-Medien ausschöpfen. Zusätzlich analysieren wir die Wirkung von Ausrichtungsfehlern, Alterung, vorausgehenden I/O-Mustern, usw., auf die Leistung dieser Medien. Wir berücksichtigen auch I/O-effiziente Breitensuch-Algorithmen für die gleichzeitige Nutzung von Festplatten und solid-state Disks. Wir stellen einen einfachen Algorithmus vor, der beim Online-Einfügen von Kanten die topologische Ordnung von einem gerichteten, azyklischen Graphen (DAG) mit n Knoten beibehält. Dieser Algorithmus hat eine Laufzeitkomplexität von O(n2.75) unabhängig von der Anzahl m der eingefügten Kanten. Für dichte DAGs ist dies eine Verbesserung des besten, vorherigen Ergebnisses von O(min{m3/2 logn,m3/2 +n2 logn}). Während die Analyse nur im inkrementellen Szenario gütlig ist, ist unser Algorithmus vollständig dynamisch. Ferner stellen wir die erste Average-Case-Analyse von Online-Algorithmen zur Unterhaltung einer topologischen Ordnung vor. Für mehrere inkrementelle Algorithmen, welche die Kanten eines kompletten DAGs in zufälliger Reihenfolge einfügen, beweisen wir eine erwartete Laufzeit von O(n2 polylog(n))

LIPIcs, Volume 274, ESA 2023, Complete Volume

LIPIcs, Volume 274, ESA 2023, Complete Volum

Genome assembly from sequence reads

Assembling genomes can be roughly described as finding Eulerian tours in de Bruijn graphs. We present the theory behind (de Bruijn) graph data structures and describe some of the implementations. A directed graph G(V,E) can be represented as a set of its edges in the form of ordered pairs vi → vj ∈ E. De Bruijn graphs are defined in a way that allows all possible neighbors of a node to be calculated from the given node’s label, which means that, given the adjacency set, we can navigate the graph by testing set membership. The edge set can be stored as a dictionary. The dictionary can be either a deterministic data structure, like a tree or an FM-index, or a probabilistic data structure, like a Bloom filter. In this thesis we present kBWT, a new space efficient deterministic data structure for storing a de Bruijn graph, which uses near-optimal n · σ + o(n) bits of memory, where n is the number of k-grams in the graph and σ is the size of the alphabet. It can retrieve neighborhood information for a given node in Θ(σ · k) time. We also compare it to an existing data structure found in the GATB framework, which is based on Bloom filters and therefore probabilistic. Benchmarks of the deterministic kBWT show it is slower in practice, compared to GATB’s data structure. Testing showed kBWT had better cache efficiency, which did not make up for the number of processor cycles used for executing the algorithm