Dense peelable random uniform hypergraphs

We describe a new family of k-uniform hypergraphs with independent random edges. The hypergraphs have a high probability of being peelable, i.e. to admit no sub-hypergraph of minimum degree 2, even when the edge density (number of edges over vertices) is close to 1. In our construction, the vertex set is partitioned into linearly arranged segments and each edge is incident to random vertices of k consecutive segments. Quite surprisingly, the linear geometry allows our graphs to be peeled "from the outside in". The density thresholds f_k for peelability of our hypergraphs (f_3 ~ 0.918, f_4 ~ 0.977, f_5 ~ 0.992, ...) are well beyond the corresponding thresholds (c_3 ~ 0.818, c_4 ~ 0.772, c_5 ~ 0.702, ...) of standard k-uniform random hypergraphs. To get a grip on f_k, we analyse an idealised peeling process on the random weak limit of our hypergraph family. The process can be described in terms of an operator on [0,1]^Z and f_k can be linked to thresholds relating to the operator. These thresholds are then tractable with numerical methods. Random hypergraphs underlie the construction of various data structures based on hashing, for instance invertible Bloom filters, perfect hash functions, retrieval data structures, error correcting codes and cuckoo hash tables, where inputs are mapped to edges using hash functions. Frequently, the data structures rely on peelability of the hypergraph or peelability allows for simple linear time algorithms. Memory efficiency is closely tied to edge density while worst and average case query times are tied to maximum and average edge size. To demonstrate the usefulness of our construction, we used our 3-uniform hypergraphs as a drop-in replacement for the standard 3-uniform hypergraphs in a retrieval data structure by Botelho et al. [Fabiano Cupertino Botelho et al., 2013]. This reduces memory usage from 1.23m bits to 1.12m bits (m being the input size) with almost no change in running time. Using k > 3 attains, at small sacrifices in running time, further improvements to memory usage

Random hypergraphs for hashing-based data structures

This thesis concerns dictionaries and related data structures that rely on providing several random possibilities for storing each key. Imagine information on a set S of m = |S| keys should be stored in n memory locations, indexed by [n] = {1,…,n}. Each object x [ELEMENT OF] S is assigned a small set e(x) [SUBSET OF OR EQUAL TO] [n] of locations by a random hash function, independent of other objects. Information on x must then be stored in the locations from e(x) only. It is possible that too many objects compete for the same locations, in particular if the load c = m/n is high. Successfully storing all information may then be impossible. For most distributions of e(x), however, success or failure can be predicted very reliably, since the success probability is close to 1 for loads c less than a certain load threshold c^* and close to 0 for loads greater than this load threshold. We mainly consider two types of data structures: • A cuckoo hash table is a dictionary data structure where each key x [ELEMENT OF] S is stored together with an associated value f(x) in one of the memory locations with an index from e(x). The distribution of e(x) is controlled by the hashing scheme. We analyse three known hashing schemes, and determine their exact load thresholds. The schemes are unaligned blocks, double hashing and a scheme for dynamically growing key sets. • A retrieval data structure also stores a value f(x) for each x [ELEMENT OF] S. This time, the values stored in the memory locations from e(x) must satisfy a linear equation that characterises the value f(x). The resulting data structure is extremely compact, but unusual. It cannot answer questions of the form “is y [ELEMENT OF] S?”. Given a key y it returns a value z. If y [ELEMENT OF] S, then z = f(y) is guaranteed, otherwise z may be an arbitrary value. We consider two new hashing schemes, where the elements of e(x) are contained in one or two contiguous blocks. This yields good access times on a word RAM and high cache efficiency. An important question is whether these types of data structures can be constructed in linear time. The success probability of a natural linear time greedy algorithm exhibits, once again, threshold behaviour with respect to the load c. We identify a hashing scheme that leads to a particularly high threshold value in this regard. In the mathematical model, the memory locations [n] correspond to vertices, and the sets e(x) for x [ELEMENT OF] S correspond to hyperedges. Three properties of the resulting hypergraphs turn out to be important: peelability, solvability and orientability. Therefore, large parts of this thesis examine how hyperedge distribution and load affects the probabilities with which these properties hold and derive corresponding thresholds. Translated back into the world of data structures, we achieve low access times, high memory efficiency and low construction times. We complement and support the theoretical results by experiments.Diese Arbeit behandelt Wörterbücher und verwandte Datenstrukturen, die darauf aufbauen, mehrere zufällige Möglichkeiten zur Speicherung jedes Schlüssels vorzusehen. Man stelle sich vor, Information über eine Menge S von m = |S| Schlüsseln soll in n Speicherplätzen abgelegt werden, die durch [n] = {1,…,n} indiziert sind. Jeder Schlüssel x [ELEMENT OF] S bekommt eine kleine Menge e(x) [SUBSET OF OR EQUAL TO] [n] von Speicherplätzen durch eine zufällige Hashfunktion unabhängig von anderen Schlüsseln zugewiesen. Die Information über x darf nun ausschließlich in den Plätzen aus e(x) untergebracht werden. Es kann hierbei passieren, dass zu viele Schlüssel um dieselben Speicherplätze konkurrieren, insbesondere bei hoher Auslastung c = m/n. Eine erfolgreiche Speicherung der Gesamtinformation ist dann eventuell unmöglich. Für die meisten Verteilungen von e(x) lässt sich Erfolg oder Misserfolg allerdings sehr zuverlässig vorhersagen, da für Auslastung c unterhalb eines gewissen Auslastungsschwellwertes c* die Erfolgswahrscheinlichkeit nahezu 1 ist und für c jenseits dieses Auslastungsschwellwertes nahezu 0 ist. Hauptsächlich werden wir zwei Arten von Datenstrukturen betrachten: • Eine Kuckucks-Hashtabelle ist eine Wörterbuchdatenstruktur, bei der jeder Schlüssel x [ELEMENT OF] S zusammen mit einem assoziierten Wert f(x) in einem der Speicherplätze mit Index aus e(x) gespeichert wird. Die Verteilung von e(x) wird hierbei vom Hashing-Schema festgelegt. Wir analysieren drei bekannte Hashing-Schemata und bestimmen erstmals deren exakte Auslastungsschwellwerte im obigen Sinne. Die Schemata sind unausgerichtete Blöcke, Doppel-Hashing sowie ein Schema für dynamisch wachsenden Schlüsselmengen. • Auch eine Retrieval-Datenstruktur speichert einen Wert f(x) für alle x [ELEMENT OF] S. Diesmal sollen die Werte in den Speicherplätzen aus e(x) eine lineare Gleichung erfüllen, die den Wert f(x) charakterisiert. Die entstehende Datenstruktur ist extrem platzsparend, aber ungewöhnlich: Sie ist ungeeignet um Fragen der Form „ist y [ELEMENT OF] S?“ zu beantworten. Bei Anfrage eines Schlüssels y wird ein Ergebnis z zurückgegeben. Falls y [ELEMENT OF] S ist, so ist z = f(y) garantiert, andernfalls darf z ein beliebiger Wert sein. Wir betrachten zwei neue Hashing-Schemata, bei denen die Elemente von e(x) in einem oder in zwei zusammenhängenden Blöcken liegen. So werden gute Zugriffszeiten auf Word-RAMs und eine hohe Cache-Effizienz erzielt. Eine wichtige Frage ist, ob Datenstrukturen obiger Art in Linearzeit konstruiert werden können. Die Erfolgswahrscheinlichkeit eines naheliegenden Greedy-Algorithmus weist abermals ein Schwellwertverhalten in Bezug auf die Auslastung c auf. Wir identifizieren ein Hashing-Schema, das diesbezüglich einen besonders hohen Schwellwert mit sich bringt. In der mathematischen Modellierung werden die Speicherpositionen [n] als Knoten und die Mengen e(x) für x [ELEMENT OF] S als Hyperkanten aufgefasst. Drei Eigenschaften der entstehenden Hypergraphen stellen sich dann als zentral heraus: Schälbarkeit, Lösbarkeit und Orientierbarkeit. Weite Teile dieser Arbeit beschäftigen sich daher mit den Wahrscheinlichkeiten für das Vorliegen dieser Eigenschaften abhängig von Hashing Schema und Auslastung, sowie mit entsprechenden Schwellwerten. Eine Rückübersetzung der Ergebnisse liefert dann Datenstrukturen mit geringen Anfragezeiten, hoher Speichereffizienz und geringen Konstruktionszeiten. Die theoretischen Überlegungen werden dabei durch experimentelle Ergebnisse ergänzt und gestützt

Irregular Invertible Bloom Look-Up Tables

We consider invertible Bloom lookup tables (IBLTs) which are probabilistic data structures that allow to store keyvalue pairs. An IBLT supports insertion and deletion of key-value pairs, as well as the recovery of all key-value pairs that have been inserted, as long as the number of key-value pairs stored in the IBLT does not exceed a certain number. The recovery operation on an IBLT can be represented as a peeling process on a bipartite graph. We present a density evolution analysis of IBLTs which allows to predict the maximum number of key-value pairs that can be inserted in the table so that recovery is still successful with high probability. This analysis holds for arbitrary irregular degree distributions and generalizes results in the literature. We complement our analysis by numerical simulations of our own IBLT design which allows to recover a larger number of key-value pairs as state-of-the-art IBLTs of same size.Comment: Accepted for presentation at ISTC 202

Exploiting Latent Features of Text and Graphs

As the size and scope of online data continues to grow, new machine learning techniques become necessary to best capitalize on the wealth of available information. However, the models that help convert data into knowledge require nontrivial processes to make sense of large collections of text and massive online graphs. In both scenarios, modern machine learning pipelines produce embeddings --- semantically rich vectors of latent features --- to convert human constructs for machine understanding. In this dissertation we focus on information available within biomedical science, including human-written abstracts of scientific papers, as well as machine-generated graphs of biomedical entity relationships. We present the Moliere system, and our method for identifying new discoveries through the use of natural language processing and graph mining algorithms. We propose heuristically-based ranking criteria to augment Moliere, and leverage this ranking to identify a new gene-treatment target for HIV-associated Neurodegenerative Disorders. We additionally focus on the latent features of graphs, and propose a new bipartite graph embedding technique. Using our graph embedding, we advance the state-of-the-art in hypergraph partitioning quality. Having newfound intuition of graph embeddings, we present Agatha, a deep-learning approach to hypothesis generation. This system learns a data-driven ranking criteria derived from the embeddings of our large proposed biomedical semantic graph. To produce human-readable results, we additionally propose CBAG, a technique for conditional biomedical abstract generation

LIPIcs, Volume 244, ESA 2022, Complete Volume

LIPIcs, Volume 244, ESA 2022, Complete Volum

Multidimensional Network analysis

This thesis is focused on the study of multidimensional networks. A multidimensional network is a network in which among the nodes there may be multiple different qualitative and quantitative relations. Traditionally, complex network analysis has focused on networks with only one kind of relation. Even with this constraint, monodimensional networks posed many analytic challenges, being representations of ubiquitous complex systems in nature. However, it is a matter of common experience that the constraint of considering only one single relation at a time limits the set of real world phenomena that can be represented with complex networks. When multiple different relations act at the same time, traditional complex network analysis cannot provide suitable analytic tools. To provide the suitable tools for this scenario is exactly the aim of this thesis: the creation and study of a Multidimensional Network Analysis, to extend the toolbox of complex network analysis and grasp the complexity of real world phenomena. The urgency and need for a multidimensional network analysis is here presented, along with an empirical proof of the ubiquity of this multifaceted reality in different complex networks, and some related works that in the last two years were proposed in this novel setting, yet to be systematically defined. Then, we tackle the foundations of the multidimensional setting at different levels, both by looking at the basic extensions of the known model and by developing novel algorithms and frameworks for well-understood and useful problems, such as community discovery (our main case study), temporal analysis, link prediction and more. We conclude this thesis with two real world scenarios: a monodimensional study of international trade, that may be improved with our proposed multidimensional analysis; and the analysis of literature and bibliography in the field of classical archaeology, used to show how natural and useful the choice of a multidimensional network analysis strategy is in a problem traditionally tackled with different techniques

Graph-based Methods for Visualization and Clustering

The amount of data that we produce and consume is larger than it has been at any point in the history of mankind, and it keeps growing exponentially. All this information, gathered in overwhelming volumes, often comes with two problematic characteristics: it is complex and deprived of semantical context. A common step to address those issues is to embed raw data in lower dimensions, by finding a mapping which preserves the similarity between data points from their original space to a new one. Measuring similarity between large sets of high-dimensional objects is, however, problematic for two main reasons: first, high-dimensional points are subject to the curse of dimensionality and second, the number of pairwise distances between points is quadratic with respect to the amount of data points. Both problems can be addressed by using nearest neighbours graphs to understand the structure in data. As a matter of fact, most dimensionality reduction methods use similarity matrices that can be interpreted as graph adjacency matrices. Yet, despite recent progresses, dimensionality reduction is still very challenging when applied to very large datasets. Indeed, although recent methods specifically address the problem of scaleability, processing datasets of millions of elements remain a very lengthy process. In this thesis, we propose new contributions which address the problem of scaleability using the framework of Graph Signal Processing, which extends traditional signal processing to graphs. We do so motivated by the premise that graphs are well suited to represent the structure of the data. In the first part of this thesis, we look at quantitative measures for the evaluation of dimensionality reduction methods. Using tools from graph theory and Graph Signal Processing, we show that specific characteristics related to quality can be assessed by taking measures on the graph, which indirectly validates the hypothesis relating graph to structure. The second contribution is a new method for a fast eigenspace approximation of the graph Laplacian. Using principles of GSP and random matrices, we show that an approximated eigensubpace can be recovered very efficiently, which be used for fast spectral clustering or visualization. Next, we propose a compressive scheme to accelerate any dimensionality reduction technique. The idea is based on compressive sampling and transductive learning on graphs: after computing the embedding for a small subset of data points, we propagate the information everywhere using transductive inference. The key components of this technique are a good sampling strategy to select the subset and the application of transductive learning on graphs. Finally, we address the problem of over-discriminative feature spaces by proposing a hierarchical clustering structure combined with multi-resolution graphs. Using efficient coarsening and refinement procedures on this structure, we show that dimensionality reduction algorithms can be run on intermediate levels and up-sampled to all points leading to a very fast dimensionality reduction method. For all contributions, we provide extensive experiments on both synthetic and natural datasets, including large-scale problems. This allows us to show the pertinence of our models and the validity of our proposed algorithms. Following reproducible principles, we provide everything needed to repeat the examples and the experiments presented in this work