Applied Randomized Algorithms for Efficient Genomic Analysis

The scope and scale of biological data continues to grow at an exponential clip, driven by advances in genetic sequencing, annotation and widespread adoption of surveillance efforts. For instance, the Sequence Read Archive (SRA) now contains more than 25 petabases of public data, while RefSeq, a collection of reference genomes, recently surpassed 100,000 complete genomes. In the process, it has outgrown the practical reach of many traditional algorithmic approaches in both time and space. Motivated by this extreme scale, this thesis details efficient methods for clustering and summarizing large collections of sequence data. While our primary area of interest is biological sequences, these approaches largely apply to sequence collections of any type, including natural language, software source code, and graph structured data. We applied recent advances in randomized algorithms to practical problems. We used MinHash and HyperLogLog, both examples of Locality- Sensitive Hashing, as well as coresets, which are approximate representations for finite sum problems, to build methods capable of scaling to billions of items. Ultimately, these are all derived from variations on sampling. We combined these advances with hardware-based optimizations and incorporated into free and open-source software libraries (sketch, frp, lib- simdsampling) and practical software tools built on these libraries (Dashing, Minicore, Dashing 2), empowering users to interact practically with colossal datasets on commodity hardware

Temporal graph mining and distributed processing

Cotutela Universitat Politècnica de Catalunya i Université Libre de BruxellesWith the recent growth of social media platforms and the human desire to interact with the digital world a lot of human-human and human-device interaction data is getting generated every second. With the boom of the Internet of Things (IoT) devices, a lot of device-device interactions are also now on the rise. All these interactions are nothing but a representation of how the underlying network is connecting different entities over time. These interactions when modeled as an interaction network presents a lot of unique opportunities to uncover interesting patterns and to understand the dynamics of the network. Understanding the dynamics of the network is very important because it encapsulates the way we communicate, socialize, consume information and get influenced. To this end, in this PhD thesis, we focus on analyzing an interaction network to understand how the underlying network is being used. We define interaction network as a sequence of time-stamped interactions E over edges of a static graph G=(V, E). Interaction networks can be used to model many real-world networks for example, in a social network or a communication network, each interaction over an edge represents an interaction between two users, e.g., emailing, making a call, re-tweeting, or in case of the financial network an interaction between two accounts to represent a transaction. We analyze interaction network under two settings. In the first setting, we study interaction network under a sliding window model. We assume a node could pass information to other nodes if they are connected to them using edges present in a time window. In this model, we study how the importance or centrality of a node evolves over time. In the second setting, we put additional constraints on how information flows between nodes. We assume a node could pass information to other nodes only if there is a temporal path between them. To restrict the length of the temporal paths we consider a time window in this approach as well. We apply this model to solve the time-constrained influence maximization problem. By analyzing the interaction network data under our model we find the top-k most influential nodes. We test our model both on human-human interaction using social network data as well as on location-location interaction using location-based social network(LBSNs) data. In the same setting, we also mine temporal cyclic paths to understand the communication patterns in a network. Temporal cycles have many applications and appear naturally in communication networks where one person posts a message and after a while reacts to a thread of reactions from peers on the post. In financial networks, on the other hand, the presence of a temporal cycle could be indicative of certain types of fraud. We provide efficient algorithms for all our analysis and test their efficiency and effectiveness on real-world data. Finally, given that many of the algorithms we study have huge computational demands, we also studied distributed graph processing algorithms. An important aspect of distributed graph processing is to correctly partition the graph data between different machine. A lot of research has been done on efficient graph partitioning strategies but there is no one good partitioning strategy for all kind of graphs and algorithms. Choosing the best partitioning strategy is nontrivial and is mostly a trial and error exercise. To address this problem we provide a cost model based approach to give a better understanding of how a given partitioning strategy is performing for a given graph and algorithm.Con el reciente crecimiento de las redes sociales y el deseo humano de interactuar con el mundo digital, una gran cantidad de datos de interacción humano-a-humano o humano-a-dispositivo se generan cada segundo. Con el auge de los dispositivos IoT, las interacciones dispositivo-a-dispositivo también están en alza. Todas estas interacciones no son más que una representación de como la red subyacente conecta distintas entidades en el tiempo. Modelar estas interacciones en forma de red de interacciones presenta una gran cantidad de oportunidades únicas para descubrir patrones interesantes y entender la dinamicidad de la red. Entender la dinamicidad de la red es clave ya que encapsula la forma en la que nos comunicamos, socializamos, consumimos información y somos influenciados. Para ello, en esta tesis doctoral, nos centramos en analizar una red de interacciones para entender como la red subyacente es usada. Definimos una red de interacciones como una sequencia de interacciones grabadas en el tiempo E sobre aristas de un grafo estático G=(V, E). Las redes de interacción se pueden usar para modelar gran cantidad de aplicaciones reales, por ejemplo en una red social o de comunicaciones cada interacción sobre una arista representa una interacción entre dos usuarios (correo electrónico, llamada, retweet), o en el caso de una red financiera una interacción entre dos cuentas para representar una transacción. Analizamos las redes de interacción bajo múltiples escenarios. En el primero, estudiamos las redes de interacción bajo un modelo de ventana deslizante. Asumimos que un nodo puede mandar información a otros nodos si estan conectados utilizando aristas presentes en una ventana temporal. En este modelo, estudiamos como la importancia o centralidad de un nodo evoluciona en el tiempo. En el segundo escenario añadimos restricciones adicionales respecto como la información fluye entre nodos. Asumimos que un nodo puede mandar información a otros nodos solo si existe un camino temporal entre ellos. Para restringir la longitud de los caminos temporales también asumimos una ventana temporal. Aplicamos este modelo para resolver este problema de maximización de influencia restringido temporalmente. Analizando los datos de la red de interacción bajo nuestro modelo intentamos descubrir los k nodos más influyentes. Examinamos nuestro modelo en interacciones humano-a-humano, usando datos de redes sociales, como en ubicación-a-ubicación usando datos de redes sociales basades en localización (LBSNs). En el mismo escenario también minamos camínos cíclicos temporales para entender los patrones de comunicación en una red. Existen múltiples aplicaciones para cíclos temporales y aparecen naturalmente en redes de comunicación donde una persona envía un mensaje y después de un tiempo reacciona a una cadena de reacciones de compañeros en el mensaje. En redes financieras, por otro lado, la presencia de un ciclo temporal puede indicar ciertos tipos de fraude. Proponemos algoritmos eficientes para todos nuestros análisis y evaluamos su eficiencia y efectividad en datos reales. Finalmente, dado que muchos de los algoritmos estudiados tienen una gran demanda computacional, también estudiamos los algoritmos de procesado distribuido de grafos. Un aspecto importante de procesado distribuido de grafos es el de correctamente particionar los datos del grafo entre distintas máquinas. Gran cantidad de investigación se ha realizado en estrategias para particionar eficientemente un grafo, pero no existe un particionamento bueno para todos los tipos de grafos y algoritmos. Escoger la mejor estrategia de partición no es trivial y es mayoritariamente un ejercicio de prueba y error. Con tal de abordar este problema, proporcionamos un modelo de costes para dar un mejor entendimiento en como una estrategia de particionamiento actúa dado un grafo y un algoritmo.Postprint (published version

Temporal graph mining and distributed processing

With the recent growth of social media platforms and the human desire to interact with the digital world a lot of human-human and human-device interaction data is getting generated every second. With the boom of the Internet of Things (IoT) devices, a lot of device-device interactions are also now on the rise. All these interactions are nothing but a representation of how the underlying network is connecting different entities over time. These interactions when modeled as an interaction network presents a lot of unique opportunities to uncover interesting patterns and to understand the dynamics of the network. Understanding the dynamics of the network is very important because it encapsulates the way we communicate, socialize, consume information and get influenced. To this end, in this PhD thesis, we focus on analyzing an interaction network to understand how the underlying network is being used. We define interaction network as a sequence of time-stamped interactions E over edges of a static graph G=(V, E). Interaction networks can be used to model many real-world networks for example, in a social network or a communication network, each interaction over an edge represents an interaction between two users, e.g., emailing, making a call, re-tweeting, or in case of the financial network an interaction between two accounts to represent a transaction. We analyze interaction network under two settings. In the first setting, we study interaction network under a sliding window model. We assume a node could pass information to other nodes if they are connected to them using edges present in a time window. In this model, we study how the importance or centrality of a node evolves over time. In the second setting, we put additional constraints on how information flows between nodes. We assume a node could pass information to other nodes only if there is a temporal path between them. To restrict the length of the temporal paths we consider a time window in this approach as well. We apply this model to solve the time-constrained influence maximization problem. By analyzing the interaction network data under our model we find the top-k most influential nodes. We test our model both on human-human interaction using social network data as well as on location-location interaction using location-based social network(LBSNs) data. In the same setting, we also mine temporal cyclic paths to understand the communication patterns in a network. Temporal cycles have many applications and appear naturally in communication networks where one person posts a message and after a while reacts to a thread of reactions from peers on the post. In financial networks, on the other hand, the presence of a temporal cycle could be indicative of certain types of fraud. We provide efficient algorithms for all our analysis and test their efficiency and effectiveness on real-world data. Finally, given that many of the algorithms we study have huge computational demands, we also studied distributed graph processing algorithms. An important aspect of distributed graph processing is to correctly partition the graph data between different machine. A lot of research has been done on efficient graph partitioning strategies but there is no one good partitioning strategy for all kind of graphs and algorithms. Choosing the best partitioning strategy is nontrivial and is mostly a trial and error exercise. To address this problem we provide a cost model based approach to give a better understanding of how a given partitioning strategy is performing for a given graph and algorithm.Con el reciente crecimiento de las redes sociales y el deseo humano de interactuar con el mundo digital, una gran cantidad de datos de interacción humano-a-humano o humano-a-dispositivo se generan cada segundo. Con el auge de los dispositivos IoT, las interacciones dispositivo-a-dispositivo también están en alza. Todas estas interacciones no son más que una representación de como la red subyacente conecta distintas entidades en el tiempo. Modelar estas interacciones en forma de red de interacciones presenta una gran cantidad de oportunidades únicas para descubrir patrones interesantes y entender la dinamicidad de la red. Entender la dinamicidad de la red es clave ya que encapsula la forma en la que nos comunicamos, socializamos, consumimos información y somos influenciados. Para ello, en esta tesis doctoral, nos centramos en analizar una red de interacciones para entender como la red subyacente es usada. Definimos una red de interacciones como una sequencia de interacciones grabadas en el tiempo E sobre aristas de un grafo estático G=(V, E). Las redes de interacción se pueden usar para modelar gran cantidad de aplicaciones reales, por ejemplo en una red social o de comunicaciones cada interacción sobre una arista representa una interacción entre dos usuarios (correo electrónico, llamada, retweet), o en el caso de una red financiera una interacción entre dos cuentas para representar una transacción. Analizamos las redes de interacción bajo múltiples escenarios. En el primero, estudiamos las redes de interacción bajo un modelo de ventana deslizante. Asumimos que un nodo puede mandar información a otros nodos si estan conectados utilizando aristas presentes en una ventana temporal. En este modelo, estudiamos como la importancia o centralidad de un nodo evoluciona en el tiempo. En el segundo escenario añadimos restricciones adicionales respecto como la información fluye entre nodos. Asumimos que un nodo puede mandar información a otros nodos solo si existe un camino temporal entre ellos. Para restringir la longitud de los caminos temporales también asumimos una ventana temporal. Aplicamos este modelo para resolver este problema de maximización de influencia restringido temporalmente. Analizando los datos de la red de interacción bajo nuestro modelo intentamos descubrir los k nodos más influyentes. Examinamos nuestro modelo en interacciones humano-a-humano, usando datos de redes sociales, como en ubicación-a-ubicación usando datos de redes sociales basades en localización (LBSNs). En el mismo escenario también minamos camínos cíclicos temporales para entender los patrones de comunicación en una red. Existen múltiples aplicaciones para cíclos temporales y aparecen naturalmente en redes de comunicación donde una persona envía un mensaje y después de un tiempo reacciona a una cadena de reacciones de compañeros en el mensaje. En redes financieras, por otro lado, la presencia de un ciclo temporal puede indicar ciertos tipos de fraude. Proponemos algoritmos eficientes para todos nuestros análisis y evaluamos su eficiencia y efectividad en datos reales. Finalmente, dado que muchos de los algoritmos estudiados tienen una gran demanda computacional, también estudiamos los algoritmos de procesado distribuido de grafos. Un aspecto importante de procesado distribuido de grafos es el de correctamente particionar los datos del grafo entre distintas máquinas. Gran cantidad de investigación se ha realizado en estrategias para particionar eficientemente un grafo, pero no existe un particionamento bueno para todos los tipos de grafos y algoritmos. Escoger la mejor estrategia de partición no es trivial y es mayoritariamente un ejercicio de prueba y error. Con tal de abordar este problema, proporcionamos un modelo de costes para dar un mejor entendimiento en como una estrategia de particionamiento actúa dado un grafo y un algoritmo

Stream Sampling for Frequency Cap Statistics

Unaggregated data, in streamed or distributed form, is prevalent and come from diverse application domains which include interactions of users with web services and IP traffic. Data elements have {\em keys} (cookies, users, queries) and elements with different keys interleave. Analytics on such data typically utilizes statistics stated in terms of the frequencies of keys. The two most common statistics are {\em distinct}, which is the number of active keys in a specified segment, and {\em sum}, which is the sum of the frequencies of keys in the segment. Both are special cases of {\em cap} statistics, defined as the sum of frequencies {\em capped} by a parameter $T$, which are popular in online advertising platforms. Aggregation by key, however, is costly, requiring state proportional to the number of distinct keys, and therefore we are interested in estimating these statistics or more generally, sampling the data, without aggregation. We present a sampling framework for unaggregated data that uses a single pass (for streams) or two passes (for distributed data) and state proportional to the desired sample size. Our design provides the first effective solution for general frequency cap statistics. Our $\ell$-capped samples provide estimates with tight statistical guarantees for cap statistics with $T=\Theta(\ell)$ and nonnegative unbiased estimates of {\em any} monotone non-decreasing frequency statistics. An added benefit of our unified design is facilitating {\em multi-objective samples}, which provide estimates with statistical guarantees for a specified set of different statistics, using a single, smaller sample.Comment: 21 pages, 4 figures, preliminary version will appear in KDD 201

Selected problems in cardinality estimation

Cardinality estimation remains a critical task in query processing. Query optimizers rely on the accuracy of cardinality estimates when generating execution plans, and, in approximate query answering, estimated cardinalities affect the quality of query results. In this thesis, we present multiple new cardinality estimation techniques. The techniques differ vastly by the query under consideration. For single relation queries, we use the principle of maximum entropy to combine information extracted from samples and histograms. For join size estimation, we rely on a model that requires one to find estimates for the intersection size of join attributes. For queries with multiple joins, sketches serve as compact representations of join results that are combined via a data structure that approximates the joint frequency distribution of join attributes. In addition, we present a technique to transform selection predicates into a representation that allows estimators based on machine learning to effectively learn query result cardinalities. For each cardinality estimator presented in this thesis, we precisely define its problem scope, the construction process, and how to obtain estimates. Then, we compare to state-of-the-art cardinality estimators and run a thorough evaluation with queries over multiple data sets. Based on our observations, we analyze the strengths and limitations of each of our cardinality estimators and identify its preferred use case

P2KMV: A Privacy-preserving Counting Sketch for Efficient and Accurate Set Intersection Cardinality Estimations

In this paper, we propose P2KMV, a novel privacy-preserving counting sketch, based on the k minimum values algorithm. With P2KMV, we offer a versatile privacy-enhanced technology for obtaining statistics, following the principle of data minimization, and aiming for the sweet spot between privacy, accuracy, and computational efficiency. As our main contribution, we develop methods to perform set operations, which facilitate cardinality estimates under strong privacy requirements. Most notably, we propose an efficient, privacy-preserving algorithm to estimate the set intersection cardinality. P2KMV provides plausible deniability for all data items contained in the sketch. We discuss the algorithm's privacy guarantees as well as the accuracy of the obtained estimates. An experimental evaluation confirms our analytical expectations and provides insights regarding parameter choices

Composition and Homology in the Taxonomic Classification of Escherichia coli

As new techniques have been introduced, specifically the possibility of complete genome sequencing, better methods of defining bacterial species have also been proposed. One of the most recently proposed methods, using bioinformatic techniques, is to calculate the average nucleotide identity (ANI) between the homologous genome segments of different isolates. Another method for species discrimination that has been tested successfully is the similarity of DNA compositional signatures. However, in a recent update, DNA signatures split the available Escherichia coli complete genomes into three groups. To check if this result was consistent with such genomes belonging to different species, we tested methods based on genomic composition and compared them to classic homology methods. The five methods used were ANI, DNA signatures, 16s rRNA, 23s rRNA, and genomic similarity score. All species discrimination methods grouped genomes of E. coli slightly differently. However, the DNA signatures and ANI split the groups similarly, suggesting that methods of delimitation based on genetic composition are just as effective as methods based on homology